Query psy2476
Match_columns 151
No_of_seqs 112 out of 184
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 17:14:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2476.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2476hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3380|consensus 100.0 3.1E-65 6.7E-70 397.7 13.5 150 1-151 1-151 (152)
2 PF04699 P16-Arc: ARP2/3 compl 100.0 1.1E-65 2.4E-70 402.2 7.7 143 8-151 1-151 (152)
3 PF08625 Utp13: Utp13 specific 96.6 0.0047 1E-07 48.0 5.1 97 40-145 1-111 (141)
4 PF04003 Utp12: Dip2/Utp12 Fam 95.8 0.034 7.4E-07 39.8 6.0 61 78-138 4-64 (110)
5 KOG0291|consensus 94.8 0.089 1.9E-06 51.0 7.0 86 40-139 725-810 (893)
6 PF09384 UTP15_C: UTP15 C term 94.5 0.37 8.1E-06 37.3 8.6 91 36-138 18-108 (148)
7 KOG0319|consensus 81.0 3.2 7E-05 40.3 5.4 67 39-114 637-704 (775)
8 KOG2964|consensus 75.2 4.6 9.9E-05 36.0 4.3 69 10-87 281-355 (361)
9 PF13838 Clathrin_H_link: Clat 67.9 6.2 0.00014 27.2 2.8 24 40-63 10-33 (66)
10 PF14337 DUF4393: Domain of un 67.2 17 0.00037 28.3 5.5 59 59-118 22-84 (186)
11 KOG3420|consensus 57.0 7.3 0.00016 31.7 1.8 32 54-85 113-144 (185)
12 PF04675 DNA_ligase_A_N: DNA l 56.8 21 0.00046 27.3 4.3 80 48-130 86-176 (177)
13 PF12931 Sec16_C: Sec23-bindin 54.6 11 0.00024 31.8 2.6 24 42-65 1-24 (284)
14 PF14691 Fer4_20: Dihydroprymi 52.9 16 0.00036 27.1 3.0 31 36-66 38-68 (111)
15 CHL00133 psbV photosystem II c 49.9 24 0.00051 28.3 3.7 70 36-114 78-148 (163)
16 cd07298 PX_RICS The phosphoino 48.1 5.8 0.00013 30.3 -0.1 28 104-131 86-114 (115)
17 PF10607 CLTH: CTLH/CRA C-term 44.0 43 0.00092 24.6 4.1 55 41-96 6-60 (145)
18 PF09068 EF-hand_2: EF hand; 43.8 41 0.00088 25.5 4.0 62 79-142 42-114 (127)
19 PF13442 Cytochrome_CBB3: Cyto 42.7 17 0.00037 23.4 1.5 33 78-111 35-67 (67)
20 TIGR02568 LcrE type III secret 40.9 88 0.0019 25.9 5.9 102 38-146 76-193 (240)
21 cd06171 Sigma70_r4 Sigma70, re 40.8 53 0.0011 18.8 3.5 45 91-135 3-52 (55)
22 PRK13773 formimidoylglutamase; 39.1 24 0.00052 30.4 2.3 73 10-89 244-321 (324)
23 PF08281 Sigma70_r4_2: Sigma-7 38.2 27 0.00058 21.6 1.9 28 91-118 3-30 (54)
24 PF03195 DUF260: Protein of un 37.8 67 0.0014 23.6 4.2 44 63-112 19-62 (101)
25 PRK02868 hypothetical protein; 36.4 43 0.00093 28.5 3.4 52 54-110 27-78 (245)
26 smart00668 CTLH C-terminal to 36.4 44 0.00096 20.5 2.7 27 40-66 5-31 (58)
27 COG0091 RplV Ribosomal protein 35.3 23 0.00049 27.1 1.4 69 38-118 23-101 (120)
28 PF14127 DUF4294: Domain of un 34.9 90 0.002 25.0 4.8 56 55-118 52-107 (157)
29 PRK06771 hypothetical protein; 34.5 38 0.00082 25.0 2.4 26 38-63 54-79 (93)
30 PF10346 Con-6: Conidiation pr 33.9 50 0.0011 20.3 2.5 26 50-78 4-29 (36)
31 PRK01722 formimidoylglutamase; 32.9 32 0.0007 29.4 2.1 72 10-87 241-316 (320)
32 PRK13776 formimidoylglutamase; 32.5 30 0.00064 29.8 1.8 67 10-84 243-315 (318)
33 PRK13620 psbV cytochrome c-550 32.1 54 0.0012 27.6 3.2 70 35-113 129-199 (215)
34 PF04545 Sigma70_r4: Sigma-70, 32.1 31 0.00068 21.1 1.5 24 95-118 1-24 (50)
35 PF13867 SAP30_Sin3_bdg: Sin3 31.4 38 0.00082 21.9 1.8 31 71-113 21-51 (53)
36 PF04505 Dispanin: Interferon- 31.3 43 0.00093 23.5 2.2 21 39-59 40-60 (82)
37 cd07278 PX_RICS_like The phosp 31.3 16 0.00036 27.8 0.1 28 104-131 85-113 (114)
38 TIGR03045 PS_II_C550 cytochrom 30.9 66 0.0014 25.6 3.4 70 36-114 77-147 (159)
39 TIGR00574 dnl1 DNA ligase I, A 30.3 3.3E+02 0.0072 24.9 8.4 82 44-130 26-119 (514)
40 PF04659 Arch_fla_DE: Archaeal 29.6 17 0.00037 26.8 -0.1 25 122-146 17-41 (99)
41 PRK13774 formimidoylglutamase; 29.5 34 0.00075 29.3 1.8 68 10-84 238-310 (311)
42 COG3334 Uncharacterized conser 28.9 79 0.0017 26.1 3.7 35 79-113 147-181 (192)
43 cd07299 PX_TCGAP The phosphoin 28.8 17 0.00037 27.7 -0.2 28 104-131 84-112 (113)
44 PF06790 UPF0259: Uncharacteri 28.6 72 0.0016 27.1 3.5 34 79-112 50-83 (248)
45 PF03542 Tuberin: Tuberin; In 27.0 4E+02 0.0087 23.7 8.0 42 73-119 210-251 (356)
46 PF06528 Phage_P2_GpE: Phage P 26.9 60 0.0013 20.3 2.0 19 123-141 20-38 (39)
47 cd02577 PSTD1 PSTD1: Pseudouri 26.7 3.7E+02 0.0081 23.4 7.7 31 38-68 151-181 (319)
48 PF11880 DUF3400: Domain of un 26.7 60 0.0013 21.0 2.1 19 128-146 26-44 (45)
49 TIGR02937 sigma70-ECF RNA poly 26.1 81 0.0018 21.8 2.9 47 89-135 101-152 (158)
50 PRK13772 formimidoylglutamase; 25.8 40 0.00087 28.9 1.5 68 10-83 242-313 (314)
51 TIGR02952 Sig70_famx2 RNA poly 25.8 87 0.0019 23.0 3.2 29 90-118 114-142 (170)
52 COG2263 Predicted RNA methylas 25.5 13 0.00027 30.9 -1.6 16 53-68 106-121 (198)
53 PF13925 Katanin_con80: con80 25.3 2.3E+02 0.0051 22.0 5.6 84 40-138 18-101 (164)
54 COG0010 SpeB Arginase/agmatina 24.9 44 0.00095 28.5 1.6 71 10-87 226-301 (305)
55 KOG0310|consensus 24.7 3.8E+02 0.0082 25.3 7.6 91 37-139 351-441 (487)
56 KOG2538|consensus 24.4 81 0.0018 30.1 3.3 32 39-70 452-483 (578)
57 PF04192 Utp21: Utp21 specific 24.3 1.4E+02 0.0031 24.9 4.5 63 75-137 124-197 (237)
58 PF10475 DUF2450: Protein of u 24.2 75 0.0016 26.8 2.8 24 38-61 129-152 (291)
59 TIGR01229 rocF_arginase argina 24.0 32 0.0007 29.1 0.6 70 10-85 221-296 (300)
60 PF06711 DUF1198: Protein of u 23.8 31 0.00067 27.5 0.4 60 81-141 31-105 (148)
61 PF07721 TPR_4: Tetratricopept 23.7 91 0.002 16.7 2.2 18 42-59 7-24 (26)
62 PRK09047 RNA polymerase factor 23.4 1.1E+02 0.0024 22.3 3.4 29 90-118 98-126 (161)
63 PF03395 Pox_P4A: Poxvirus P4A 22.8 32 0.0007 34.3 0.4 11 12-22 649-659 (888)
64 PRK12528 RNA polymerase sigma 22.6 81 0.0017 23.3 2.5 28 91-118 106-133 (161)
65 smart00421 HTH_LUXR helix_turn 21.9 1.4E+02 0.003 17.4 3.0 43 98-141 3-50 (58)
66 COG0632 RuvA Holliday junction 21.7 33 0.00072 28.3 0.2 15 127-141 69-83 (201)
67 COG1610 Uncharacterized conser 21.5 1.6E+02 0.0035 23.4 4.0 51 52-112 7-59 (148)
68 PF08349 DUF1722: Protein of u 21.3 3.3E+02 0.0072 19.8 5.7 42 40-88 12-63 (117)
69 PF05778 Apo-CIII: Apolipoprot 21.2 1.3E+02 0.0028 21.1 3.1 37 74-110 16-52 (70)
70 PF01170 UPF0020: Putative RNA 20.7 62 0.0013 25.3 1.5 15 55-69 106-120 (179)
71 PRK12547 RNA polymerase sigma 20.6 96 0.0021 23.1 2.5 28 91-118 105-132 (164)
72 PRK09706 transcriptional repre 20.4 1.8E+02 0.0039 21.4 4.0 34 90-135 90-123 (135)
No 1
>KOG3380|consensus
Probab=100.00 E-value=3.1e-65 Score=397.66 Aligned_cols=150 Identities=53% Similarity=0.838 Sum_probs=142.9
Q ss_pred CCCccCCCCCccccccCCCCCCCCccccCCCCCCCCCCCHHHHHHHHhcCCHHHHHHHHhcCCCCCCCChHHHHHHHHHH
Q psy2476 1 MAKNTSSSAFRKIDVDQYNEDNYKEEEQGEVPQLGAGVDESEILSLLNQGKHQDALKTVLKNAPLGSKNQHVKDSALNLT 80 (151)
Q Consensus 1 msknt~~~~~RkIDVD~~d~d~f~~~~~~~~~~~~~~~~~~qvr~ll~~gd~~~ALk~aL~npP~g~~~~~~K~~~~~~V 80 (151)
|||||++++|||||||+|||+.|.++++. ...++++|+++|||+||++|+..+||++||.||||++|+|++|++++.+|
T Consensus 1 Ms~nt~~t~~rk~dvd~fd~~~f~~~~~e-~~~a~~gp~~~ev~sll~qg~~~~AL~~aL~~~P~~t~~q~vK~~a~~~v 79 (152)
T KOG3380|consen 1 MSKNTLSTSFRKIDVDEFDEAKFVEEDEE-VESAALGPDEREVRSLLTQGKSLEALQTALLNPPYGTKDQEVKDRALNVV 79 (152)
T ss_pred CCccchhhccccccccccChhhhcCchhh-hhhhccCCChHHHHHHHHcccHHHHHHHHHhCCCCCCccHHHHHHHHHHH
Confidence 99999999999999999999999998875 34677999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhccHHHHHhccChhhhHHHHHHHHhhcCCCCCc-chhhHHHHHHHHHHhhCCCceEEEeccCCC
Q psy2476 81 LKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGFEIPSEK-SSSHLLTWHEKVFAIGGLGSIVRVLTDSKR 151 (151)
Q Consensus 81 l~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkgm~~~~~~-~~~~LL~WheKl~~~~G~G~IvRvltdRkt 151 (151)
++||++||++||+++|++||.++.|+|||||||||+.|++. +|..||.||||+++++|+||||||||||+|
T Consensus 80 ~~vL~~ik~adI~~~v~~Ls~e~~DiLmKYiYkGm~~p~d~~s~~~LL~WHEk~~~~~GvG~IvRvLs~r~~ 151 (152)
T KOG3380|consen 80 LKVLTSIKQADIEAAVKKLSTEEIDILMKYIYKGMEIPSDNSSCVSLLQWHEKLVAKSGVGCIVRVLSDRQR 151 (152)
T ss_pred HHHHHHHHHHhHHHHHHHhhHHHHHHHHHHHHHHhcCccccchHHHHHHHHHHHHHhcCCceEEEeecCCcC
Confidence 99999999999999999999999999999999999999765 455599999999999999999999999986
No 2
>PF04699 P16-Arc: ARP2/3 complex 16 kDa subunit (p16-Arc); InterPro: IPR006789 The Arp2/3 protein complex has been implicated in the control of actin polymerisation. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices [, ].; GO: 0030833 regulation of actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_G 1TYQ_G 1U2V_G 2P9U_G 2P9L_G 1K8K_G 3DXM_G 2P9N_G 3DXK_G 2P9I_G ....
Probab=100.00 E-value=1.1e-65 Score=402.23 Aligned_cols=143 Identities=50% Similarity=0.820 Sum_probs=113.7
Q ss_pred CCCccccccCCCCCCCCccccCC--C-----CCCCCCCCHHHHHHHHhcCCHHHHHHHHhcCCCCCCCChHHHHHHHHHH
Q psy2476 8 SAFRKIDVDQYNEDNYKEEEQGE--V-----PQLGAGVDESEILSLLNQGKHQDALKTVLKNAPLGSKNQHVKDSALNLT 80 (151)
Q Consensus 8 ~~~RkIDVD~~d~d~f~~~~~~~--~-----~~~~~~~~~~qvr~ll~~gd~~~ALk~aL~npP~g~~~~~~K~~~~~~V 80 (151)
++|||||||+||||+|.+++... | ..+.++++++|||++|++||+.+||++||+|||||+++ ++|++++++|
T Consensus 1 ~~fRkiDID~~ded~~~~~~~~~~~p~~~~~~~~~~~~~~~qvr~ll~~g~~~~ALk~aL~npP~~~k~-~~K~~~~~~V 79 (152)
T PF04699_consen 1 EDFRKIDIDAYDEDSFVDEEEEDLDPESPPVSSAEVQPKEQQVRQLLSSGDNEEALKAALENPPYGSKD-AVKDRALQLV 79 (152)
T ss_dssp -GGGCS-GGGG-TTS-------------------GGGGTHHHHHHHHHCT-HHHHHHHHTSS--TT-S--HHHHHHHHHH
T ss_pred CCCeeCccccCCCcccccccccccCCCCcccchhhhchhHHHHHHHHhCCCHHHHHHHhccCCCcCCCc-chHHHHHHHH
Confidence 48999999999999997776442 1 25667899999999999999999999999999999999 9999999999
Q ss_pred HHHHHhhhhccHHHHHhccChhhhHHHHHHHHhhcCCCCCcc-hhhHHHHHHHHHHhhCCCceEEEeccCCC
Q psy2476 81 LKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGFEIPSEKS-SSHLLTWHEKVFAIGGLGSIVRVLTDSKR 151 (151)
Q Consensus 81 l~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkgm~~~~~~~-~~~LL~WheKl~~~~G~G~IvRvltdRkt 151 (151)
++||++||++||+++|++|+++|+|+|||||||||+.|++++ |++||+||||+++++|+||||||||||||
T Consensus 80 l~vL~s~k~sdI~~~v~~L~~~~~D~LMKYiYkg~~~~~~~s~~~~LL~WheK~~~~~G~G~IvRvltdRkt 151 (152)
T PF04699_consen 80 LEVLTSIKSSDIENAVKSLDSDQQDILMKYIYKGMESPSENSSGGVLLSWHEKLVEVAGVGSIVRVLTDRKT 151 (152)
T ss_dssp HHHHHCS-GGGHHHHHCCS-HHHHHHHHHHHHHHTTS--TTHH-CHHHHHHHHHHHCCHCHHHHHHCC-SS-
T ss_pred HHHHHHccHHHHHHHHHhCCHHHHhHHHHHHHHhccCccCccHHHHHHHHHHHHHHHcCCCcEEEEeecCcC
Confidence 999999999999999999999999999999999999998765 49999999999999999999999999997
No 3
>PF08625 Utp13: Utp13 specific WD40 associated domain; InterPro: IPR013934 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp13 is a nucleolar protein and component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA []. Upt13 is also a component of the Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome []. Components of the Pwp2 complex are: Utp1 (Pwp2), Utp6, Utp12 (Dip2), Utp13, Utp18, and Utp21. The relationship between the Pwp2 complex and the t-Utps complex [] that also associates with the 5' end of nascent pre-18S rRNA is unclear. ; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=96.56 E-value=0.0047 Score=47.96 Aligned_cols=97 Identities=28% Similarity=0.456 Sum_probs=61.3
Q ss_pred HHHHHHHHhcCCHHHHHHHHhc-CCCCCCCChHHHHHHHHHHHHHHH------hhhhccHHHHHhccChhhhHHHHHHHH
Q psy2476 40 ESEILSLLNQGKHQDALKTVLK-NAPLGSKNQHVKDSALNLTLKVLL------AIKSSQMDETVSNLDQDLLDTLMKYIY 112 (151)
Q Consensus 40 ~~qvr~ll~~gd~~~ALk~aL~-npP~g~~~~~~K~~~~~~Vl~vL~------s~K~sdI~~~v~~L~~e~~D~LMKYiY 112 (151)
+++..++++.||+.+||+.||+ |=|+. .+.++-+++. ++-..+|+++|++|+.++...|++|+=
T Consensus 1 eQ~L~N~l~~~~y~~Al~LAl~L~~P~~---------ll~i~~~~~~~~~~~~~~g~~~l~~~i~~L~~~~l~~LL~~ir 71 (141)
T PF08625_consen 1 EQELSNLLRQKDYKEALRLALKLDHPFR---------LLKILKDLLETEEDEDSIGSEELDEVIKKLDDEQLEKLLRFIR 71 (141)
T ss_pred CchHHHHHHhhhHHHHHHHHHhcCCcHH---------HHHHHHHHHhcccccccchHHHHHHHHHhcCHHHHHHHHHHHH
Confidence 4678999999999999999997 33542 2233333331 222356999999999999999999986
Q ss_pred hhcCCCC-----Ccc-hhhHHHHH-HHHHHhhCCCceEEE
Q psy2476 113 KGFEIPS-----EKS-SSHLLTWH-EKVFAIGGLGSIVRV 145 (151)
Q Consensus 113 kgm~~~~-----~~~-~~~LL~Wh-eKl~~~~G~G~IvRv 145 (151)
.=-..+- +.- ..+|-.|. +++.++.|...++..
T Consensus 72 ~WNTNsr~~~vAQ~vL~~il~~~~~~~L~~~~~~~~~le~ 111 (141)
T PF08625_consen 72 DWNTNSRTSHVAQRVLNAILKSHPPEELLKIPGLKEILEA 111 (141)
T ss_pred HhhcccccHHHHHHHHHHHHHhCCHHHHHccccHHHHHHH
Confidence 4422221 000 12222332 456677777666543
No 4
>PF04003 Utp12: Dip2/Utp12 Family; InterPro: IPR007148 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. This domain is found at the C terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein. In yeast, these proteins are called Utp5, Utp1 or Pwp2, Utp12 or DIP2 Q12220 from SWISSPROT. They interact with snoRNA U3 and with MPP10 []. Pwp2 is an essential Saccharomyces cerevisiae (Baker's yeast) protein involved in cell separation.
Probab=95.79 E-value=0.034 Score=39.82 Aligned_cols=61 Identities=23% Similarity=0.433 Sum_probs=51.7
Q ss_pred HHHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHhhcCCCCCcchhhHHHHHHHHHHhhC
Q psy2476 78 NLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGFEIPSEKSSSHLLTWHEKVFAIGG 138 (151)
Q Consensus 78 ~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkgm~~~~~~~~~~LL~WheKl~~~~G 138 (151)
..+.+||.++..++|+.+|..|+......|++||-.+|+.........++.|-.-++..-|
T Consensus 4 ~ll~~vl~~~~~~~I~~tv~~Lp~~~~~~LL~~l~~~l~~~~~~~~e~~l~Wl~~ll~~H~ 64 (110)
T PF04003_consen 4 ELLLEVLERIPPSDIENTVRSLPFSYAERLLQFLSERLQTRKSPHVEFLLRWLKALLKTHG 64 (110)
T ss_pred HHHHHHHhhCCHHHHHHHHHhCCHHHHHHHHHHHHHHhcccCCCchhHHHHHHHHHHHHHH
Confidence 4789999999999999999999999999999999999884333346888999888776644
No 5
>KOG0291|consensus
Probab=94.84 E-value=0.089 Score=51.02 Aligned_cols=86 Identities=19% Similarity=0.266 Sum_probs=71.0
Q ss_pred HHHHHHHHhcCCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHhhcCCCC
Q psy2476 40 ESEILSLLNQGKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGFEIPS 119 (151)
Q Consensus 40 ~~qvr~ll~~gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkgm~~~~ 119 (151)
..-|+..|+.+++..||-.+|.= ..-++|-+||-++-..||+-++++|+..-.+.|||||-+-|+...
T Consensus 725 Pe~v~~al~~qey~~AlvmslRL------------Ne~~lI~evlesvp~~~Ie~V~~~Lp~~y~erll~~l~~~l~~s~ 792 (893)
T KOG0291|consen 725 PESVREALREQEYLKALVMSLRL------------NEYKLIKEVLESVPIKDIELVASSLPTAYLERLLKALSRFLENSP 792 (893)
T ss_pred HHHHHHHHhcchHHHHHHHHHhc------------CHHHHHHHHHHhCChhhhhhhhhcCcHHHHHHHHHHHHHHHhcCc
Confidence 34599999999999999998852 223578899999999999999999999999999999999776532
Q ss_pred CcchhhHHHHHHHHHHhhCC
Q psy2476 120 EKSSSHLLTWHEKVFAIGGL 139 (151)
Q Consensus 120 ~~~~~~LL~WheKl~~~~G~ 139 (151)
---..|.|-..++...|.
T Consensus 793 --HieF~l~W~~~il~~hG~ 810 (893)
T KOG0291|consen 793 --HIEFYLRWLRAILTYHGS 810 (893)
T ss_pred --hHHHHHHHHHHHHHHhhh
Confidence 125568899998888774
No 6
>PF09384 UTP15_C: UTP15 C terminal; InterPro: IPR018983 This entry represents the C-terminal domain of the U3 small nucleolar RNA-associated protein 15 (UTP15). This protein is involved in nucleolar processing of pre-18S ribosomal RNA, and is required for optimal pre-ribosomal RNA transcription by RNA polymerase I together with a subset of U3 proteins required for transcription (t-UTPs). UTP15 is a component of the ribosomal small subunit (SSU) processome, which is a large ribonucleoprotein (RNP) required for processing of precursors to the small subunit RNA, the 18S, of the ribosome [, ]. This domain is found C-terminal to the WD40 repeat (IPR001680 from INTERPRO). UTP15 associates with U3 snoRNA, which is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA []. ; GO: 0006364 rRNA processing, 0005730 nucleolus
Probab=94.46 E-value=0.37 Score=37.28 Aligned_cols=91 Identities=18% Similarity=0.250 Sum_probs=67.9
Q ss_pred CCCCHHHHHHHHhcCCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHhhc
Q psy2476 36 AGVDESEILSLLNQGKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGF 115 (151)
Q Consensus 36 ~~~~~~qvr~ll~~gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkgm 115 (151)
..++-+....+|++.++.+||..|| ...++ ....-+|++.|..= .-+..++.+.|.+.+--|++||.|-+
T Consensus 18 ~~~kl~~~D~~Lr~F~y~~ALD~aL----~~~~~----p~~~vavl~EL~~R--~~L~~AL~~Rde~~L~piL~Fl~k~i 87 (148)
T PF09384_consen 18 KKKKLSKYDKLLRKFRYKKALDAAL----VKNKS----PEVVVAVLEELIRR--GALRAALAGRDEESLEPILKFLIKNI 87 (148)
T ss_pred ccccchHHHHHHHcCCHHHHHHHHH----hcCCC----hHHHHHHHHHHHHc--cHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence 5667889999999999999999999 11111 22233344444332 46889999999999999999999999
Q ss_pred CCCCCcchhhHHHHHHHHHHhhC
Q psy2476 116 EIPSEKSSSHLLTWHEKVFAIGG 138 (151)
Q Consensus 116 ~~~~~~~~~~LL~WheKl~~~~G 138 (151)
..|-- +.+|..+-+.++++-+
T Consensus 88 ~~pr~--~~~l~~v~~~ildiY~ 108 (148)
T PF09384_consen 88 TDPRY--TRILVDVANIILDIYS 108 (148)
T ss_pred CCccc--HHHHHHHHHHHHHHHH
Confidence 88743 5788888887777654
No 7
>KOG0319|consensus
Probab=81.03 E-value=3.2 Score=40.32 Aligned_cols=67 Identities=21% Similarity=0.318 Sum_probs=51.2
Q ss_pred CHHHHHHHHhcCCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhhhh-ccHHHHHhccChhhhHHHHHHHHhh
Q psy2476 39 DESEILSLLNQGKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVLLAIKS-SQMDETVSNLDQDLLDTLMKYIYKG 114 (151)
Q Consensus 39 ~~~qvr~ll~~gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K~-sdI~~~v~~L~~e~~D~LMKYiYkg 114 (151)
.++++.++|+.+++..|+-+|+..- |-..+-.|++.+..=++ .++...|.+|+.||.-.||+|+-+=
T Consensus 637 q~QeL~n~l~~~~~~~A~~LA~tLd---------~P~~~f~vi~~~~r~r~~e~l~~av~~L~~dq~~~Ll~~~~~W 704 (775)
T KOG0319|consen 637 QEQELENLLSQKRYTKAFVLALTLD---------KPHLVFTVINALYRERDPEELGQAVFRLNEDQPEALLQFVVKW 704 (775)
T ss_pred HHHHHHHHHhhhhhHHHHHhHhhcc---------CchhHHHHHHHHHhcCCcHHHHHHHHHhhhhhHHHHHHHHHHh
Confidence 5788999999999999999999742 22223344444444443 4688999999999999999999875
No 8
>KOG2964|consensus
Probab=75.23 E-value=4.6 Score=35.97 Aligned_cols=69 Identities=20% Similarity=0.302 Sum_probs=47.3
Q ss_pred CccccccCCCCCCCCccccCCC--CCCCC-CCCHHHHHHHHhc--C-CHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHH
Q psy2476 10 FRKIDVDQYNEDNYKEEEQGEV--PQLGA-GVDESEILSLLNQ--G-KHQDALKTVLKNAPLGSKNQHVKDSALNLTLKV 83 (151)
Q Consensus 10 ~RkIDVD~~d~d~f~~~~~~~~--~~~~~-~~~~~qvr~ll~~--g-d~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~v 83 (151)
|=.||||.+||.. .| ..|++ +-..+|+++.|++ | |+.+| -.+==+|||-.. +.+--.+.++++|+
T Consensus 281 YiSiDID~LDPaf-------APgtgtpE~gGlt~re~l~ILrglqGl~lVGa-DvVEvsP~yD~a-e~Tal~AA~llfEi 351 (361)
T KOG2964|consen 281 YISIDIDVLDPAF-------APGTGTPETGGLTTREMLNILRGLQGLNLVGA-DVVEVSPPYDVA-EMTALAAADLLFEI 351 (361)
T ss_pred EEEEeecccCccc-------CCCCCCCCCCCcCHHHHHHHHhhCcccccccc-ceEEecCccchh-hhHHHHHHHHHHHH
Confidence 5579999999932 12 13333 4478899999984 5 55554 234458999854 47777888899999
Q ss_pred HHhh
Q psy2476 84 LLAI 87 (151)
Q Consensus 84 L~s~ 87 (151)
|+..
T Consensus 352 ~s~m 355 (361)
T KOG2964|consen 352 LSKM 355 (361)
T ss_pred HHhc
Confidence 8865
No 9
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=67.90 E-value=6.2 Score=27.24 Aligned_cols=24 Identities=21% Similarity=0.326 Sum_probs=20.6
Q ss_pred HHHHHHHHhcCCHHHHHHHHhcCC
Q psy2476 40 ESEILSLLNQGKHQDALKTVLKNA 63 (151)
Q Consensus 40 ~~qvr~ll~~gd~~~ALk~aL~np 63 (151)
.++-.+++++|++.+|-+.|...|
T Consensus 10 ~~~F~~l~~~g~y~eAA~~AA~sP 33 (66)
T PF13838_consen 10 VQQFNELFSQGQYEEAAKVAANSP 33 (66)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHSG
T ss_pred HHHHHHHHHcCCHHHHHHHHHhCc
Confidence 467889999999999999999877
No 10
>PF14337 DUF4393: Domain of unknown function (DUF4393)
Probab=67.21 E-value=17 Score=28.34 Aligned_cols=59 Identities=22% Similarity=0.379 Sum_probs=47.2
Q ss_pred HhcCCCCCCCChHHHHHHHHHHHHHHHhhhhcc----HHHHHhccChhhhHHHHHHHHhhcCCC
Q psy2476 59 VLKNAPLGSKNQHVKDSALNLTLKVLLAIKSSQ----MDETVSNLDQDLLDTLMKYIYKGFEIP 118 (151)
Q Consensus 59 aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K~sd----I~~~v~~L~~e~~D~LMKYiYkgm~~~ 118 (151)
||++.-|...++.+++....++-..+..-+.++ ...++++|++++.- ++||||++-..|
T Consensus 22 ~le~~~~~~~~e~Lremfa~LLass~d~~~~~~~hp~fv~Ii~qLsp~EA~-iL~~l~~~~~~p 84 (186)
T PF14337_consen 22 ALEAASYEIDDEELREMFANLLASSMDKRKNDDVHPSFVEIIKQLSPDEAR-ILKYLYDNNQIP 84 (186)
T ss_pred HHHhccCcCCcHHHHHHHHHHHHHHhCcCccccccHHHHHHHHhCCHHHHH-HHHHHHhcCCCc
Confidence 677777876778999999999999998887755 56788999999865 559999665555
No 11
>KOG3420|consensus
Probab=56.96 E-value=7.3 Score=31.71 Aligned_cols=32 Identities=25% Similarity=0.365 Sum_probs=23.0
Q ss_pred HHHHHHhcCCCCCCCChHHHHHHHHHHHHHHH
Q psy2476 54 DALKTVLKNAPLGSKNQHVKDSALNLTLKVLL 85 (151)
Q Consensus 54 ~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~ 85 (151)
+-.-.|+-|||||++...+-.+..+..|++-+
T Consensus 113 g~fDtaviNppFGTk~~~aDm~fv~~al~~~~ 144 (185)
T KOG3420|consen 113 GIFDTAVINPPFGTKKKGADMEFVSAALKVAS 144 (185)
T ss_pred CeEeeEEecCCCCcccccccHHHHHHHHHHHH
Confidence 34457889999999986666666666666554
No 12
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=56.76 E-value=21 Score=27.31 Aligned_cols=80 Identities=11% Similarity=0.115 Sum_probs=47.5
Q ss_pred hcCCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhhh-----------hccHHHHHhccChhhhHHHHHHHHhhcC
Q psy2476 48 NQGKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVLLAIK-----------SSQMDETVSNLDQDLLDTLMKYIYKGFE 116 (151)
Q Consensus 48 ~~gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K-----------~sdI~~~v~~L~~e~~D~LMKYiYkgm~ 116 (151)
..||+.+++..++...+-.... -......-|.+.|..+- ..-+..++..++++|.-+|++-|=|.|-
T Consensus 86 ~~GD~g~~~~~~~~~~~~~~~~--~~~lTi~~V~~~L~~la~~~g~~s~~~k~~~l~~ll~~~s~~E~k~i~Riil~~lr 163 (177)
T PF04675_consen 86 KVGDLGEVAEEVLQKRKSETSK--PSPLTISEVNETLDELAAASGKGSQDEKIDILKELLRRCSPEEAKWIVRIILKDLR 163 (177)
T ss_dssp HHS-HHHHHHHHHHHHTTTS----SS--BHHHHHHHHHHHHH--STTHHHHHHHHHHHHHTTS-HHHHHHHHHHHTT--S
T ss_pred hcCcHHHHHHHHHhhccccccC--CCCCCHHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhCCHHHHHHHHHHHhCCCe
Confidence 5899999999999876643210 11223333433333332 2346788889999999999999999887
Q ss_pred CCCCcchhhHHHHH
Q psy2476 117 IPSEKSSSHLLTWH 130 (151)
Q Consensus 117 ~~~~~~~~~LL~Wh 130 (151)
.+-. ...+|-.||
T Consensus 164 iG~~-~~~il~ala 176 (177)
T PF04675_consen 164 IGVS-EKTILDALA 176 (177)
T ss_dssp SS---HHHHHHHHH
T ss_pred eCcc-HHHHHHHhC
Confidence 7622 246777776
No 13
>PF12931 Sec16_C: Sec23-binding domain of Sec16; PDB: 3MZK_C.
Probab=54.64 E-value=11 Score=31.80 Aligned_cols=24 Identities=29% Similarity=0.414 Sum_probs=18.6
Q ss_pred HHHHHHhcCCHHHHHHHHhcCCCC
Q psy2476 42 EILSLLNQGKHQDALKTVLKNAPL 65 (151)
Q Consensus 42 qvr~ll~~gd~~~ALk~aL~npP~ 65 (151)
+|+++|-.|+.++||+.||++==|
T Consensus 1 ~I~~~Ll~G~~~~Av~~al~~~~w 24 (284)
T PF12931_consen 1 KIQQLLLVGNREEAVELALDNGLW 24 (284)
T ss_dssp HHHHHHHTT-HHHHHHHHHHTT-H
T ss_pred CHHHHHhCCCHHHHHHHHHHCCCh
Confidence 578899999999999999986544
No 14
>PF14691 Fer4_20: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster; PDB: 2VDC_G 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B.
Probab=52.95 E-value=16 Score=27.09 Aligned_cols=31 Identities=23% Similarity=0.502 Sum_probs=23.6
Q ss_pred CCCCHHHHHHHHhcCCHHHHHHHHhcCCCCC
Q psy2476 36 AGVDESEILSLLNQGKHQDALKTVLKNAPLG 66 (151)
Q Consensus 36 ~~~~~~qvr~ll~~gd~~~ALk~aL~npP~g 66 (151)
.+-++.+.-.+++.|++.+|+..++++-|+.
T Consensus 38 ~~~dip~~i~~i~~g~~~~A~~~i~~~np~p 68 (111)
T PF14691_consen 38 AHIDIPEYIRLIREGNFKEAYELIREDNPFP 68 (111)
T ss_dssp T---HHHHHHHHHCT-HHHHHHHHHHH-TTH
T ss_pred CCCcHHHHHHHHHCCCHHHHHHHHHHhCCCc
Confidence 5568888899999999999999999998874
No 15
>CHL00133 psbV photosystem II cytochrome c550; Validated
Probab=49.91 E-value=24 Score=28.32 Aligned_cols=70 Identities=17% Similarity=0.174 Sum_probs=47.3
Q ss_pred CCCCHHHHHHHHhcCCHHHHHHHHhcCC-CCCCCChHHHHHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHhh
Q psy2476 36 AGVDESEILSLLNQGKHQDALKTVLKNA-PLGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKG 114 (151)
Q Consensus 36 ~~~~~~qvr~ll~~gd~~~ALk~aL~np-P~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkg 114 (151)
.+++-..+.+.--..+..++|...+.|| .|.+-+ .+.++-.++|..++=+....|+.|+++.+--||..-
T Consensus 78 vgl~l~~L~~A~~~r~~~~~Lv~~iknP~~ydg~~---------~i~~~~~~~K~~~~MPa~~~LsdeEL~aVAaYIl~q 148 (163)
T CHL00133 78 VGLDPEALSLATPPRDNIEALVDYMKNPTTYDGLE---------SIAEIHPSIKSADIFPKMRSLTDEDLYAIAGHILLQ 148 (163)
T ss_pred CCCCHHHHhhcCCCcccHHHHHHHHhCcccccchH---------HHHHhhcccCccccCCCCCCCCHHHHHHHHHHHHhc
Confidence 3444455554333446788888999998 665422 222455677876655555889999999999999963
No 16
>cd07298 PX_RICS The phosphoinositide binding Phox Homology domain of PX-RICS. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. RICS is a Rho GTPase-activating protein for cdc42 and Rac1. It is implicated in the regulation of postsynaptic signaling and neurite outgrowth. An N-terminal splicing variant of RICS containing additional PX and Src Homology 3 (SH3) domains, also called PX-RICS, is the main isoform expressed during neural development. PX-RICS is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and
Probab=48.06 E-value=5.8 Score=30.33 Aligned_cols=28 Identities=32% Similarity=0.501 Sum_probs=22.8
Q ss_pred hHHHHHHHHhhcCCCCCc-chhhHHHHHH
Q psy2476 104 LDTLMKYIYKGFEIPSEK-SSSHLLTWHE 131 (151)
Q Consensus 104 ~D~LMKYiYkgm~~~~~~-~~~~LL~Whe 131 (151)
...||+||-|-=+..+++ +||-.|+|.|
T Consensus 86 ~~~l~~YL~RlS~Ia~~~~nCGPvLtWle 114 (115)
T cd07298 86 TQMLMAYLSRLSAIAGNKINCGPALTWME 114 (115)
T ss_pred HHHHHHHHHHHHHHhhCCccchhcceeee
Confidence 478999999976666554 8999999976
No 17
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=43.99 E-value=43 Score=24.61 Aligned_cols=55 Identities=13% Similarity=0.076 Sum_probs=33.7
Q ss_pred HHHHHHHhcCCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhhhhccHHHHH
Q psy2476 41 SEILSLLNQGKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVLLAIKSSQMDETV 96 (151)
Q Consensus 41 ~qvr~ll~~gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v 96 (151)
.+|++.|..||+..|+..+=++-|.--+. .-.=....-.++.+.-++..++.+++
T Consensus 6 ~~I~~~I~~g~i~~Ai~w~~~~~~~l~~~-~~~L~f~L~~q~fiell~~~~~~~Ai 60 (145)
T PF10607_consen 6 KKIRQAILNGDIDPAIEWLNENFPELLKR-NSSLEFELRCQQFIELLREGDIMEAI 60 (145)
T ss_pred HHHHHHHHcCCHHHHHHHHHHcCHHHHhc-CCchhHHHHHHHHHHHHHHHhHHHHH
Confidence 57889999999999999988877654321 00111222334444455566666666
No 18
>PF09068 EF-hand_2: EF hand; InterPro: IPR015153 Like other EF hand domains, this domain forms a helix-loop-helix motif, though since it does not contain the canonical pattern of calcium binding residues found in many EF hand domains, it does not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (IPR001202 from INTERPRO), enhancing dystroglycan binding []. ; PDB: 1EG3_A 1EG4_A.
Probab=43.78 E-value=41 Score=25.50 Aligned_cols=62 Identities=24% Similarity=0.381 Sum_probs=36.9
Q ss_pred HHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHhhcC--CCC---------CcchhhHHHHHHHHHHhhCCCce
Q psy2476 79 LTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGFE--IPS---------EKSSSHLLTWHEKVFAIGGLGSI 142 (151)
Q Consensus 79 ~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkgm~--~~~---------~~~~~~LL~WheKl~~~~G~G~I 142 (151)
.|++++....-.... =..|+..|.-.+.-=||-... .|. +.....+|+|--.+|...+.|.|
T Consensus 42 ~v~~~f~~~~l~~~~--d~~l~v~~l~~~L~~iy~~l~~~~p~~~~i~~~~v~~a~~L~ln~Ll~vyD~~rtG~I 114 (127)
T PF09068_consen 42 NVIEAFREHGLNQSN--DSSLSVSQLETLLSSIYEFLNKRLPTLHQIPSRPVDLAVDLLLNWLLNVYDSQRTGKI 114 (127)
T ss_dssp HHHHHHHHTT---T---TSEEEHHHHHHHHHHHHHHHHHHSTTS--HH-----HHHHHHHHHHHHHH-TT--SEE
T ss_pred HHHHHHHHcCCCccc--CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCchhHHHHHHHHHHHHHHHhCCCCCCee
Confidence 445555444333320 134888888888999994332 221 13468999999999999999976
No 19
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=42.66 E-value=17 Score=23.39 Aligned_cols=33 Identities=15% Similarity=0.238 Sum_probs=25.4
Q ss_pred HHHHHHHHhhhhccHHHHHhccChhhhHHHHHHH
Q psy2476 78 NLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYI 111 (151)
Q Consensus 78 ~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYi 111 (151)
..+..++...+ ..|+..-..|+++|+.-|+.||
T Consensus 35 ~~l~~~i~~g~-~~Mp~~~~~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 35 EELYNIIRNGR-GGMPPFGGQLSDEEIEALAAYI 67 (67)
T ss_dssp HHHHHHHHHTB-TTBSCTTTTSTHHHHHHHHHHH
T ss_pred HHHHHHHHhCc-CCCCCCCCCCCHHHHHHHHHHC
Confidence 44555555555 4688888899999999999997
No 20
>TIGR02568 LcrE type III secretion regulator YopN/LcrE/InvE/MxiC. This protein is found in type III secretion operons and, in Yersinia is localized to the cell surface and is involved in the Low-Calicium Response (LCR), possibly by sensing the calcium concentration. In Salmonella, the gene is known as InvE and is believed to perform an essential role in the secretion process and interacts with the proteins SipBCD and SicA.//Altered name to reflect regulatory role. Added GO and role IDs. Negative regulation of type III secretion in Y pestis is mediated in part by a multiprotein complex that has been proposed to act as a physical impediment to type III secretion by blocking the entrance to the secretion apparatus prior to contact with mammalian cells. This complex is composed of YopN, its heterodimeric secretion chaperone SycN-YscB, and TyeA. PubMed: 15701523
Probab=40.87 E-value=88 Score=25.88 Aligned_cols=102 Identities=13% Similarity=0.154 Sum_probs=64.0
Q ss_pred CCHHHHHHHHhc-----CCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhhhhccHHHHHhccC-----hhhhH--
Q psy2476 38 VDESEILSLLNQ-----GKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLD-----QDLLD-- 105 (151)
Q Consensus 38 ~~~~qvr~ll~~-----gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~-----~e~~D-- 105 (151)
+...++.+++.+ ++..-||+.++..-+... ..+.....+..+.|..-....|..-++..- ....+
T Consensus 76 ~~~~~ll~~l~~~f~D~s~~~laL~~ll~~~~~~~---~~~~~l~~~~~~ll~~~~~~~i~agin~al~a~~f~~~~~~~ 152 (240)
T TIGR02568 76 AGLEQLLALARGAFPDPSDQALALRAALQRLELDP---AERKALEEAAQALLELEDGPTIRAGINTALAAAAFADQGDLK 152 (240)
T ss_pred CCHHHHHHHHHhhCCChHHHHHHHHHHHHhccCCh---hHHHHHHHHHHHHHHHhhccchhhhhhHHHHHHHHHHhhccc
Confidence 466677777766 567778999999888654 445555555566666444444444333321 11112
Q ss_pred -HHHHHHHhhcCCCCCcchhhHHHHHHHHHHhhCCCc---eEEEe
Q psy2476 106 -TLMKYIYKGFEIPSEKSSSHLLTWHEKVFAIGGLGS---IVRVL 146 (151)
Q Consensus 106 -~LMKYiYkgm~~~~~~~~~~LL~WheKl~~~~G~G~---IvRvl 146 (151)
..++=+|+-+-.... -+-.|++.+.+..|-.. ++|+|
T Consensus 153 ~~~LR~lYr~~v~~~~----~~~~~~~~~~~~~~~~~~~~~l~fL 193 (240)
T TIGR02568 153 AAALRDLYRQAVSDQS----SLVQLLSDLIERYGAQRFDIVLDFL 193 (240)
T ss_pred HHHHHHHHHHHHcCCc----cHHHHHHHHHHHhCchHHHHHHHHH
Confidence 568999998876433 27788888888888764 55443
No 21
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=40.82 E-value=53 Score=18.79 Aligned_cols=45 Identities=11% Similarity=0.197 Sum_probs=29.3
Q ss_pred cHHHHHhccChhhhHHHHHHHHhhcCCCC-----CcchhhHHHHHHHHHH
Q psy2476 91 QMDETVSNLDQDLLDTLMKYIYKGFEIPS-----EKSSSHLLTWHEKVFA 135 (151)
Q Consensus 91 dI~~~v~~L~~e~~D~LMKYiYkgm~~~~-----~~~~~~LL~WheKl~~ 135 (151)
.|..++..|++++..++.-+-..|+.... .-+.+.+-.|+.+..+
T Consensus 3 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 3 RLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred HHHHHHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 57888899998888777665457765331 1244666667666543
No 22
>PRK13773 formimidoylglutamase; Provisional
Probab=39.12 E-value=24 Score=30.39 Aligned_cols=73 Identities=15% Similarity=0.115 Sum_probs=43.7
Q ss_pred CccccccCCCCCCCCccccCCC-CCCC-CCCCHHHHHHHHhc---CCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHH
Q psy2476 10 FRKIDVDQYNEDNYKEEEQGEV-PQLG-AGVDESEILSLLNQ---GKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVL 84 (151)
Q Consensus 10 ~RkIDVD~~d~d~f~~~~~~~~-~~~~-~~~~~~qvr~ll~~---gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL 84 (151)
|=.||||.+||.- .|. ..|+ -|-...|+..+++. +...-++-.+=-||||...+ .+-..+..++.++|
T Consensus 244 ylS~DiD~lDps~------aPGtgtP~pgGlt~~E~~~ll~~l~~~~~vvg~DvvE~~P~~D~~~-~Ta~laa~li~~~l 316 (324)
T PRK13773 244 YLTIDLDVLPAAV------APGVSAPAAYGVPLEVIQAVCDRVAASGKLALVDVAELNPRFDIDN-RTARVAARLIHTIV 316 (324)
T ss_pred EEEEeeCcCCccc------CCCCCCCCCCCCCHHHHHHHHHHHHhcCCEEEEEEEEECCccCCCC-CHHHHHHHHHHHHH
Confidence 3478999999832 111 1222 23456777666652 11222344445689998765 55567788888888
Q ss_pred Hhhhh
Q psy2476 85 LAIKS 89 (151)
Q Consensus 85 ~s~K~ 89 (151)
...+.
T Consensus 317 ~~~~~ 321 (324)
T PRK13773 317 TAHLP 321 (324)
T ss_pred Hhhcc
Confidence 76653
No 23
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=38.23 E-value=27 Score=21.57 Aligned_cols=28 Identities=7% Similarity=0.325 Sum_probs=20.7
Q ss_pred cHHHHHhccChhhhHHHHHHHHhhcCCC
Q psy2476 91 QMDETVSNLDQDLLDTLMKYIYKGFEIP 118 (151)
Q Consensus 91 dI~~~v~~L~~e~~D~LMKYiYkgm~~~ 118 (151)
.|..++.+|++++..++.-+-+.||...
T Consensus 3 ~l~~~l~~L~~~~r~i~~l~~~~g~s~~ 30 (54)
T PF08281_consen 3 ALQQALAQLPERQREIFLLRYFQGMSYA 30 (54)
T ss_dssp HHHHHHHCS-HHHHHHHHHHHTS---HH
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCcCHH
Confidence 4788999999999999999889998754
No 24
>PF03195 DUF260: Protein of unknown function DUF260; InterPro: IPR004883 The lateral organ boundaries (LOB) gene is expressed at the adaxial base of initiating lateral organs and encodes a plant-specific protein of unknown function. The N-terminal one half of the LOB protein contains a conserved approximately 100-amino acid domain (the LOB domain) that is present in 42 other Arabidopsis thaliana proteins and in proteins from a variety of other plant species. Genes encoding LOB domain (LBD) proteins are expressed in a variety of temporal- and tissue-specific patterns, suggesting that they may function in diverse processes [] The LOB domain contains conserved blocks of amino acids that identify the LBD gene family. In particular, a conserved C-x(2)-C-x(6)-C-x(3)-C motif, which is defining feature of the LOB domain, is present in all LBD proteins. It is possible that this motif forms a new zinc finger [].
Probab=37.82 E-value=67 Score=23.64 Aligned_cols=44 Identities=14% Similarity=0.185 Sum_probs=33.9
Q ss_pred CCCCCCChHHHHHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHHHH
Q psy2476 63 APLGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIY 112 (151)
Q Consensus 63 pP~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiY 112 (151)
+||-+.+ +...+..|.+|...- .|.++++.|++++.+..|+=|+
T Consensus 19 aPyFP~~---~~~~F~~vhkvFG~s---ni~k~L~~~~~~~R~~a~~Sl~ 62 (101)
T PF03195_consen 19 APYFPAD---QPQRFANVHKVFGVS---NISKMLQELPPEQREDAMRSLV 62 (101)
T ss_pred CCCCChh---HHHHHHHHHHHHchh---HHHHHHHhCCccchhhHHHHHH
Confidence 5776654 356677888887654 6999999999999988888654
No 25
>PRK02868 hypothetical protein; Provisional
Probab=36.41 E-value=43 Score=28.54 Aligned_cols=52 Identities=23% Similarity=0.245 Sum_probs=32.5
Q ss_pred HHHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHH
Q psy2476 54 DALKTVLKNAPLGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKY 110 (151)
Q Consensus 54 ~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKY 110 (151)
.|+-.++-+-=+.++.++ +...-+-+.....+-+.++|+++++||+-+|+|+
T Consensus 27 ~a~itv~i~~~~~p~~~~-----l~~l~~~~~~~~~~~l~~~v~~ms~eqq~~ll~~ 78 (245)
T PRK02868 27 TAFITVLLGHAFSPSDEQ-----LSILENGIPISGSSGLFELVQNMSPEQQQILLKA 78 (245)
T ss_pred HHHHHHHHHHHhCCCHHH-----HHHHHhhhhccccccHHHHHHhCCHHHHHHHHHH
Confidence 344455555555555433 2222222333444569999999999999999986
No 26
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=36.36 E-value=44 Score=20.54 Aligned_cols=27 Identities=22% Similarity=0.243 Sum_probs=23.5
Q ss_pred HHHHHHHHhcCCHHHHHHHHhcCCCCC
Q psy2476 40 ESEILSLLNQGKHQDALKTVLKNAPLG 66 (151)
Q Consensus 40 ~~qvr~ll~~gd~~~ALk~aL~npP~g 66 (151)
..++++.+..|+...|++.+=++-|..
T Consensus 5 ~~~i~~~i~~g~~~~a~~~~~~~~~~l 31 (58)
T smart00668 5 RKRIRELILKGDWDEALEWLSSLKPPL 31 (58)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHcCHHH
Confidence 467999999999999999998887754
No 27
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=35.32 E-value=23 Score=27.14 Aligned_cols=69 Identities=22% Similarity=0.220 Sum_probs=46.9
Q ss_pred CCHHHHHHHHhcCCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhhhhccHHHHHhccChh----------hhHHH
Q psy2476 38 VDESEILSLLNQGKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLDQD----------LLDTL 107 (151)
Q Consensus 38 ~~~~qvr~ll~~gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e----------~~D~L 107 (151)
.....|-.++++....+|++. |++-|.. +...|.+||.|--++=-.+ ++||.| +.-+|
T Consensus 23 kk~r~Va~~IrG~~v~~A~~~-L~~~pkK---------aa~~v~KvL~sA~aNAe~n--~gLd~d~L~V~~i~v~~gp~l 90 (120)
T COG0091 23 KKARLVADLIRGKKVAEALAI-LEFVPKK---------AAKLVKKVLESAIANAENN--KGLDPDKLVVSHIAVDKGPVL 90 (120)
T ss_pred HHHHHHHHHHcCCcHHHHHHH-HHhChHH---------HHHHHHHHHHHHHhhHHhc--cCCChHHEEEEEEEeCCCcee
Confidence 368899999999999999999 9998753 3447888888775432111 466654 33445
Q ss_pred HHHHHhhcCCC
Q psy2476 108 MKYIYKGFEIP 118 (151)
Q Consensus 108 MKYiYkgm~~~ 118 (151)
=+|..|+++..
T Consensus 91 KR~~pRA~GRa 101 (120)
T COG0091 91 KRFMPRARGRA 101 (120)
T ss_pred eeecccccCcc
Confidence 55555555543
No 28
>PF14127 DUF4294: Domain of unknown function (DUF4294)
Probab=34.87 E-value=90 Score=24.98 Aligned_cols=56 Identities=16% Similarity=0.189 Sum_probs=41.1
Q ss_pred HHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHhhcCCC
Q psy2476 55 ALKTVLKNAPLGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGFEIP 118 (151)
Q Consensus 55 ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkgm~~~ 118 (151)
.+..-|+.-|- ...|.+|+..|-+-|. .+-++-++.|+..|.-+|+|-|||--+..
T Consensus 52 e~~~~l~~l~~----kk~kkky~K~vek~i~----~ef~~~lKkLT~sQGkiLiKLI~Retg~T 107 (157)
T PF14127_consen 52 ELNEYLETLPN----KKAKKKYIKRVEKYIK----EEFTPELKKLTRSQGKILIKLIDRETGST 107 (157)
T ss_pred HHHHHHHhCCC----hHHHHHHHHHHHHHHH----HHHHHHHHHHhHHHHHHHHHHHHHhcCCc
Confidence 34444555443 3667888888877665 35788899999999999999999975544
No 29
>PRK06771 hypothetical protein; Provisional
Probab=34.51 E-value=38 Score=25.00 Aligned_cols=26 Identities=23% Similarity=0.302 Sum_probs=22.0
Q ss_pred CCHHHHHHHHhcCCHHHHHHHHhcCC
Q psy2476 38 VDESEILSLLNQGKHQDALKTVLKNA 63 (151)
Q Consensus 38 ~~~~qvr~ll~~gd~~~ALk~aL~np 63 (151)
+...|+++|++.|+..+|+|.+=+--
T Consensus 54 ~~~~e~~~Li~~Gkki~AIK~~Re~t 79 (93)
T PRK06771 54 PVNKELRQLMEEGQTVTAVKRVREAF 79 (93)
T ss_pred cccHHHHHHHHcCCchHHHHHHHHHc
Confidence 56788999999999999999876543
No 30
>PF10346 Con-6: Conidiation protein 6; InterPro: IPR018824 This entry represents a conserved region found in fungal conidiation-specific protein 6 []. This protein is expressed approximately 6 hours after the induction of development and is induced just prior to major constriction-chain growth [].
Probab=33.87 E-value=50 Score=20.34 Aligned_cols=26 Identities=19% Similarity=0.267 Sum_probs=19.7
Q ss_pred CCHHHHHHHHhcCCCCCCCChHHHHHHHH
Q psy2476 50 GKHQDALKTVLKNAPLGSKNQHVKDSALN 78 (151)
Q Consensus 50 gd~~~ALk~aL~npP~g~~~~~~K~~~~~ 78 (151)
++..+.+|++|.||=.. +++|+.+-.
T Consensus 4 ~~V~~G~KAal~NPnvS---eeaK~~A~~ 29 (36)
T PF10346_consen 4 NNVAGGYKAALHNPNVS---EEAKQHARE 29 (36)
T ss_pred HHHHHHHHHHhcCCCcC---HHHHHHHHH
Confidence 56788999999999663 377776544
No 31
>PRK01722 formimidoylglutamase; Provisional
Probab=32.89 E-value=32 Score=29.37 Aligned_cols=72 Identities=17% Similarity=0.154 Sum_probs=42.0
Q ss_pred CccccccCCCCCCCCccccCCCCCC-CCCCCHHHHHHHHhc---CCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHHH
Q psy2476 10 FRKIDVDQYNEDNYKEEEQGEVPQL-GAGVDESEILSLLNQ---GKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVLL 85 (151)
Q Consensus 10 ~RkIDVD~~d~d~f~~~~~~~~~~~-~~~~~~~qvr~ll~~---gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~ 85 (151)
|=.||||.+||....-- ..| .-+-...|+..+++. ....-++-.+==+|||...+ .+-..+..++.++|.
T Consensus 241 yvS~DiDvlDps~aPgt-----gtp~pgGls~~e~~~il~~l~~~~~vvg~DivE~~P~~D~~~-~Ta~laa~li~~~l~ 314 (320)
T PRK01722 241 YLTIDLDVLPAAEAPGV-----SAPAAGGVPLETLLRAIEPICRSGKLQAADLVEYNPTFDFDD-MTARVAARLIWQIAH 314 (320)
T ss_pred EEEEEecCcChhhCCCC-----CCCcCCCCCHHHHHHHHHHHHhcCCEEEEEEEEECCCCCCCC-cHHHHHHHHHHHHHH
Confidence 44799999998432111 122 234456666666542 12223444555689998765 555677777777775
Q ss_pred hh
Q psy2476 86 AI 87 (151)
Q Consensus 86 s~ 87 (151)
.+
T Consensus 315 ~~ 316 (320)
T PRK01722 315 AW 316 (320)
T ss_pred Hh
Confidence 43
No 32
>PRK13776 formimidoylglutamase; Provisional
Probab=32.49 E-value=30 Score=29.81 Aligned_cols=67 Identities=19% Similarity=0.181 Sum_probs=38.6
Q ss_pred CccccccCCCCCCCCccccCCC-CCCC-CCCCHHHHHHHHhc----CCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHH
Q psy2476 10 FRKIDVDQYNEDNYKEEEQGEV-PQLG-AGVDESEILSLLNQ----GKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKV 83 (151)
Q Consensus 10 ~RkIDVD~~d~d~f~~~~~~~~-~~~~-~~~~~~qvr~ll~~----gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~v 83 (151)
|=.||||.+||.- .|. ..|+ -|-...|+..+++. ++ .-++-.+==||||...+ .+-..+..++.++
T Consensus 243 yvS~DiD~lDps~------aPGtgtP~pgGLt~~e~~~il~~l~~~~~-vvg~DvvEv~P~~D~~~-~Ta~laa~li~~~ 314 (318)
T PRK13776 243 YLTICLDVLPAAV------APGVSAPAARGVSLWVIEPLVKRIIASGK-LRLADIAELNPPLDIDQ-RTARVAARLVAEL 314 (318)
T ss_pred EEEEEeCCcCccc------CCCCCCCCCCCCCHHHHHHHHHHHHccCC-EEEEEEEEECCCCCCCC-cHHHHHHHHHHHH
Confidence 4468999999832 111 1222 23456666666542 22 22344555689998765 4545666666666
Q ss_pred H
Q psy2476 84 L 84 (151)
Q Consensus 84 L 84 (151)
|
T Consensus 315 l 315 (318)
T PRK13776 315 V 315 (318)
T ss_pred H
Confidence 6
No 33
>PRK13620 psbV cytochrome c-550; Provisional
Probab=32.12 E-value=54 Score=27.62 Aligned_cols=70 Identities=17% Similarity=0.185 Sum_probs=48.8
Q ss_pred CCCCCHHHHHHHHhcCCHHHHHHHHhcCCC-CCCCChHHHHHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHh
Q psy2476 35 GAGVDESEILSLLNQGKHQDALKTVLKNAP-LGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYK 113 (151)
Q Consensus 35 ~~~~~~~qvr~ll~~gd~~~ALk~aL~npP-~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYk 113 (151)
..+++-.-+....-.++..++|...|.||= |..-+ . +-|+==|+|+.+|=+-...|+.|+++.|..||--
T Consensus 129 ~vgpdLt~LaaAtppRdn~e~Lv~wLkdP~sydg~~-s--------iae~HPs~~s~d~mP~~r~LtdedL~aIa~~IL~ 199 (215)
T PRK13620 129 NVGLDPEALALATPPRDSVESLVDYLHNPTTYDGER-E--------ISELHPSTKSTDIFPKMRNLTEDDLVAISGHILL 199 (215)
T ss_pred CCCCCHHHHhccCCCCCCHHHHHHHHhCccccCCcc-h--------hhhcCccccccccccccCCCCHHHHHHHHHHHhc
Confidence 345554433333344577899999999984 43322 3 3344458888888888899999999999999965
No 34
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=32.06 E-value=31 Score=21.12 Aligned_cols=24 Identities=8% Similarity=0.247 Sum_probs=18.0
Q ss_pred HHhccChhhhHHHHHHHHhhcCCC
Q psy2476 95 TVSNLDQDLLDTLMKYIYKGFEIP 118 (151)
Q Consensus 95 ~v~~L~~e~~D~LMKYiYkgm~~~ 118 (151)
++.+|+++|..+|.-|.|.|+...
T Consensus 1 Al~~L~~~er~vi~~~y~~~~t~~ 24 (50)
T PF04545_consen 1 ALDQLPPREREVIRLRYFEGLTLE 24 (50)
T ss_dssp HHCTS-HHHHHHHHHHHTST-SHH
T ss_pred ChhhCCHHHHHHHHHHhcCCCCHH
Confidence 468899999999988888887644
No 35
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=31.43 E-value=38 Score=21.95 Aligned_cols=31 Identities=19% Similarity=0.255 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHh
Q psy2476 71 HVKDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYK 113 (151)
Q Consensus 71 ~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYk 113 (151)
..|++....|-+=.. ++..+|.|+++.+||+
T Consensus 21 ~sK~qLa~~V~kHF~------------s~~v~E~evI~~Fly~ 51 (53)
T PF13867_consen 21 SSKEQLANAVRKHFN------------SQPVDENEVIANFLYK 51 (53)
T ss_dssp --HHHHHHHHHHHHT------------T----HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHh------------cCCCCHHHHHHHHHHH
Confidence 456665555554443 3446778999999997
No 36
>PF04505 Dispanin: Interferon-induced transmembrane protein; InterPro: IPR007593 This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression [].; GO: 0009607 response to biotic stimulus, 0016021 integral to membrane
Probab=31.26 E-value=43 Score=23.48 Aligned_cols=21 Identities=19% Similarity=0.167 Sum_probs=18.5
Q ss_pred CHHHHHHHHhcCCHHHHHHHH
Q psy2476 39 DESEILSLLNQGKHQDALKTV 59 (151)
Q Consensus 39 ~~~qvr~ll~~gd~~~ALk~a 59 (151)
.+.+||.+...||.++|.+.+
T Consensus 40 ~s~kv~~~~~~Gd~~~A~~aS 60 (82)
T PF04505_consen 40 YSSKVRSRYAAGDYEGARRAS 60 (82)
T ss_pred echhhHHHHHCCCHHHHHHHH
Confidence 478999999999999998764
No 37
>cd07278 PX_RICS_like The phosphoinositide binding Phox Homology domain of PX-RICS-like proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this family include PX-RICS, TCGAP (Tc10/Cdc42 GTPase-activating protein), and similar proteins. They contain N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal extensions. They act as Rho GTPase-activating proteins. PX-RICS is the main isoform expressed during neural development. It is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. TCGAP is widely expressed in the brain where it is involved in regulating the outgrowth of axons and d
Probab=31.25 E-value=16 Score=27.85 Aligned_cols=28 Identities=21% Similarity=0.386 Sum_probs=22.1
Q ss_pred hHHHHHHHHhhcCCCCCc-chhhHHHHHH
Q psy2476 104 LDTLMKYIYKGFEIPSEK-SSSHLLTWHE 131 (151)
Q Consensus 104 ~D~LMKYiYkgm~~~~~~-~~~~LL~Whe 131 (151)
...|.+|+-|-=+..++. +||-.|+|.|
T Consensus 85 ~~~l~~YL~RlS~Ia~~~inCGPvLtWle 113 (114)
T cd07278 85 HQVLSDYLKRLSSIAGNLLNCGPVLNWLE 113 (114)
T ss_pred HHHHHHHHHHHHHHhcCcccchhcceeee
Confidence 467899998876666554 8999999976
No 38
>TIGR03045 PS_II_C550 cytochrome c-550. Members of this protein family are cytochrome c-550, the PsbV extrinsic protein of photosystem II, from both Cyanobacteria and chloroplasts. A paralog to this protein, PsbV2, is found in some species in addition to PsbV itself.
Probab=30.87 E-value=66 Score=25.59 Aligned_cols=70 Identities=17% Similarity=0.234 Sum_probs=45.2
Q ss_pred CCCCHHHHHHHHhcCCHHHHHHHHhcCC-CCCCCChHHHHHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHhh
Q psy2476 36 AGVDESEILSLLNQGKHQDALKTVLKNA-PLGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKG 114 (151)
Q Consensus 36 ~~~~~~qvr~ll~~gd~~~ALk~aL~np-P~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkg 114 (151)
.++.-..+...-...+..++|..-+.|| ||-..+ .+ .+.--++|..++=+-...|+.+|++.|--||..-
T Consensus 77 vgl~l~~L~~A~~~r~~v~~Lv~~iknP~~~dg~~-~~--------~~~hp~~k~~~~mP~~~~LsdeEL~avAaYIl~q 147 (159)
T TIGR03045 77 VGLDPEALALATPPRDNVEALVDYMKNPTSYDGEE-SI--------AELHPSIRSADIFPKMRNLTDEDLRLIAGHILVQ 147 (159)
T ss_pred CCCChhhHHhcCCCccCHHHHHHHHhCcccccccc-hh--------hhcccccCcccccCCcCCCCHHHHHHHHHHHHHh
Confidence 3344445554444557788899999998 664432 11 1112255665655555789999999999999874
No 39
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1). All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.34 E-value=3.3e+02 Score=24.93 Aligned_cols=82 Identities=9% Similarity=0.073 Sum_probs=52.5
Q ss_pred HHHHhcCCHHHHHHHHhcCCC-CCCCChHHHHHHHHHHHHHHHhhhh-----------ccHHHHHhccChhhhHHHHHHH
Q psy2476 44 LSLLNQGKHQDALKTVLKNAP-LGSKNQHVKDSALNLTLKVLLAIKS-----------SQMDETVSNLDQDLLDTLMKYI 111 (151)
Q Consensus 44 r~ll~~gd~~~ALk~aL~npP-~g~~~~~~K~~~~~~Vl~vL~s~K~-----------sdI~~~v~~L~~e~~D~LMKYi 111 (151)
...+..||..++...++.+.+ ..... +...+.-|.+.|..+.+ .-+..+++.+++.++-.|.+.|
T Consensus 26 ~~~~~~gd~g~~~~~~~~~~~~~~~~~---~~lti~eV~~~L~~ia~~~g~~s~~~k~~~l~~ll~~~~~~e~k~l~r~i 102 (514)
T TIGR00574 26 EKVKEDGDLGEVIEGLFSKQKQTSFFS---APLTVKEVYETLKNIAETSGEGSQDKKIKLLKSLLKRASPLEAKYLIRTI 102 (514)
T ss_pred HHHHhcCCHHHHHHHHhccccccccCC---CCcCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 344678999999999888765 11111 12333444444443322 2378888899999999999999
Q ss_pred HhhcCCCCCcchhhHHHHH
Q psy2476 112 YKGFEIPSEKSSSHLLTWH 130 (151)
Q Consensus 112 Ykgm~~~~~~~~~~LL~Wh 130 (151)
-+.|-.+-. -..+|.+.
T Consensus 103 ~~~lriG~~--~~~il~al 119 (514)
T TIGR00574 103 LGDLRIGIA--EKTILDAL 119 (514)
T ss_pred hhhcccCcc--HHHHHHHH
Confidence 999887532 24444443
No 40
>PF04659 Arch_fla_DE: Archaeal flagella protein ; InterPro: IPR006752 Archaeal flagella are unique motility structures, and the absence of bacterial structural motility genes in the complete genome sequences of flagellated archaeal species has always suggested that archaeal flagellar biogenesis is likely mediated by novel components. FlaD and FlaE, are present in the cell as membrane-associated proteins but are not major components of isolated flagellar filaments. Interestingly, flaD was found to encode two proteins, each translated from a separate ribosome binding site. This group of sequences contain the archaeal flaD and flaE proteins. The conserved region that defines these sequences is found in the N-teminal region of flaE but towards the C-terminal region of flaD [].; GO: 0001539 ciliary or flagellar motility
Probab=29.61 E-value=17 Score=26.85 Aligned_cols=25 Identities=20% Similarity=0.271 Sum_probs=21.6
Q ss_pred chhhHHHHHHHHHHhhCCCceEEEe
Q psy2476 122 SSSHLLTWHEKVFAIGGLGSIVRVL 146 (151)
Q Consensus 122 ~~~~LL~WheKl~~~~G~G~IvRvl 146 (151)
+.-+++.|-|-|++.+|.-..+|+|
T Consensus 17 s~~~~~eWLefLve~~G~~~~~~~L 41 (99)
T PF04659_consen 17 SEIVVFEWLEFLVERVGHNNAADAL 41 (99)
T ss_pred HHHHHHHHHHHHHHHcccccHHHHH
Confidence 4678999999999999998877765
No 41
>PRK13774 formimidoylglutamase; Provisional
Probab=29.55 E-value=34 Score=29.26 Aligned_cols=68 Identities=15% Similarity=0.150 Sum_probs=36.4
Q ss_pred CccccccCCCCCCCCccccCCC-CCCC-CCCCHHHHHHHHhc---CCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHH
Q psy2476 10 FRKIDVDQYNEDNYKEEEQGEV-PQLG-AGVDESEILSLLNQ---GKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVL 84 (151)
Q Consensus 10 ~RkIDVD~~d~d~f~~~~~~~~-~~~~-~~~~~~qvr~ll~~---gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL 84 (151)
|=+||||.|||.. .|. ..|+ -|-...|+..+++. ....-++-.+==||+|...+ .+-..+..++++.|
T Consensus 238 yvS~DiD~lDps~------aPGtgtP~pgGLt~~e~l~il~~l~~~~~v~g~DivE~nP~~D~~~-~Ta~laa~li~~~l 310 (311)
T PRK13774 238 MFTICMDVIDSAF------APGVSAPAVLGLYPHTVLELAKRIIPSDKVSSVSIAEMNPTYDADN-RTAKLVANLVHHFL 310 (311)
T ss_pred EEEEeeCCcChhh------CCCCCCCCCCCCCHHHHHHHHHHHHhcCCEEEEEEEEECCCCCCCC-hHHHHHHHHHHHHh
Confidence 4469999999832 111 1222 23356777766652 11222334444689988765 34445555555543
No 42
>COG3334 Uncharacterized conserved protein [Function unknown]
Probab=28.86 E-value=79 Score=26.11 Aligned_cols=35 Identities=17% Similarity=0.306 Sum_probs=26.2
Q ss_pred HHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHh
Q psy2476 79 LTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYK 113 (151)
Q Consensus 79 ~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYk 113 (151)
.-+.+|..++......|+..++|+..-+||.||-.
T Consensus 147 ~Aa~Il~~L~~r~~~~ILakMdPekAA~lt~~i~~ 181 (192)
T COG3334 147 EAAAILMKLKPRKLGLILAKMDPEKAATLTELIAS 181 (192)
T ss_pred HHHHHHHhCChhHHHHHHHcCCHHHHHHHHHHHhc
Confidence 44567777777777778888888888888888754
No 43
>cd07299 PX_TCGAP The phosphoinositide binding Phox Homology domain of Tc10/Cdc42 GTPase-activating protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. TCGAP (Tc10/Cdc42 GTPase-activating protein) contains N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal proline-rich regions. It is widely expressed in the brain where it is involved in regulating the outgrowth of axons and dendrites and is regulated by the protein tyrosine kinase Fyn. It interacts with cdc42 and TC10beta through its GAP domain and with phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] through its PX domain. It is translocated to the plasma membrane in adipocytes in response to insulin and may be involved in the regulation of insulin-stimulated glucose transport. TCGAP has also been named sorting nexins 26 (SNX26). SNXs
Probab=28.79 E-value=17 Score=27.68 Aligned_cols=28 Identities=25% Similarity=0.404 Sum_probs=22.2
Q ss_pred hHHHHHHHHhhcCCCCCc-chhhHHHHHH
Q psy2476 104 LDTLMKYIYKGFEIPSEK-SSSHLLTWHE 131 (151)
Q Consensus 104 ~D~LMKYiYkgm~~~~~~-~~~~LL~Whe 131 (151)
...|.+|+-|-=+..+++ +||-.|+|.|
T Consensus 84 ~~~l~~YL~RlS~Ia~~~inCGPVLtWme 112 (113)
T cd07299 84 TPLLSEYLNRLTGIVDSNLNCGPVLTWME 112 (113)
T ss_pred HHHHHHHHHHHHHHhcCCccccccceeee
Confidence 478899998876666554 8999999976
No 44
>PF06790 UPF0259: Uncharacterised protein family (UPF0259); InterPro: IPR009627 This is a group of proteins of unknown function.
Probab=28.62 E-value=72 Score=27.07 Aligned_cols=34 Identities=12% Similarity=0.077 Sum_probs=24.6
Q ss_pred HHHHHHHhhhhccHHHHHhccChhhhHHHHHHHH
Q psy2476 79 LTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIY 112 (151)
Q Consensus 79 ~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiY 112 (151)
...+-....++.-+.++|+++++||+-+|+|+--
T Consensus 50 ~l~~~~~~~~~~sl~~~v~~ms~eqq~~ll~~sa 83 (248)
T PF06790_consen 50 ILSNNSDFSSSMSLQDIVQQMSPEQQNVLLKASA 83 (248)
T ss_pred HHHhhhchhccccHHHHHHhCCHHHHHHHHHHHH
Confidence 3344333444455889999999999999999854
No 45
>PF03542 Tuberin: Tuberin; InterPro: IPR018515 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This domain is found in Tuberin proteins. ; GO: 0005096 GTPase activator activity, 0043547 positive regulation of GTPase activity
Probab=26.98 E-value=4e+02 Score=23.74 Aligned_cols=42 Identities=14% Similarity=0.171 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHhhcCCCC
Q psy2476 73 KDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGFEIPS 119 (151)
Q Consensus 73 K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkgm~~~~ 119 (151)
|.-....++.+|+++ -..=.-|+..++|.|++-+..|+....
T Consensus 210 ~~D~~~~~~~~Ls~L-----isYh~~~~k~~qd~iV~~l~~GL~s~~ 251 (356)
T PF03542_consen 210 RADLQVCVFPVLSAL-----ISYHSHFSKQEQDEIVRALESGLGSKT 251 (356)
T ss_pred HHHHHHHHHHHHHHH-----HHHHHhcCHhHHHHHHHHHHHHhccCc
Confidence 555556677777765 334467788999999999999987653
No 46
>PF06528 Phage_P2_GpE: Phage P2 GpE; InterPro: IPR009493 This entry is represented by Burkholderia phage phiE202, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage and bacterial proteins which are closely related to the GpE tail protein from Phage P2.
Probab=26.86 E-value=60 Score=20.28 Aligned_cols=19 Identities=21% Similarity=0.466 Sum_probs=15.7
Q ss_pred hhhHHHHHHHHHHhhCCCc
Q psy2476 123 SSHLLTWHEKVFAIGGLGS 141 (151)
Q Consensus 123 ~~~LL~WheKl~~~~G~G~ 141 (151)
-.-|+.|+||.....|.|.
T Consensus 20 l~El~~Wre~A~~R~~a~~ 38 (39)
T PF06528_consen 20 LDELMDWRERARRRSGAEN 38 (39)
T ss_pred HHHHHHHHHHHHHHhccCC
Confidence 3668999999999988763
No 47
>cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD.
Probab=26.69 E-value=3.7e+02 Score=23.41 Aligned_cols=31 Identities=19% Similarity=0.059 Sum_probs=25.4
Q ss_pred CCHHHHHHHHhcCCHHHHHHHHhcCCCCCCC
Q psy2476 38 VDESEILSLLNQGKHQDALKTVLKNAPLGSK 68 (151)
Q Consensus 38 ~~~~qvr~ll~~gd~~~ALk~aL~npP~g~~ 68 (151)
+..-+|=..|-.||+++|++..|..|+.+.+
T Consensus 151 ~~th~iG~~ll~gd~~~Av~~il~~~~~~~~ 181 (319)
T cd02577 151 PVTHFVGKLILEGDYEEAAKTYLTARYPLEE 181 (319)
T ss_pred CCcHHHHHHHHccCHHHHHHHHhcCCccccc
Confidence 5677888899999999999999998754333
No 48
>PF11880 DUF3400: Domain of unknown function (DUF3400); InterPro: IPR021817 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 50 amino acids in length. This domain is found associated with PF02754 from PFAM, PF02913 from PFAM, PF01565 from PFAM.
Probab=26.67 E-value=60 Score=21.02 Aligned_cols=19 Identities=32% Similarity=0.594 Sum_probs=18.1
Q ss_pred HHHHHHHHhhCCCceEEEe
Q psy2476 128 TWHEKVFAIGGLGSIVRVL 146 (151)
Q Consensus 128 ~WheKl~~~~G~G~IvRvl 146 (151)
.|.+..++.+..|-|=|||
T Consensus 26 ~W~~~~v~~a~~GGIErVL 44 (45)
T PF11880_consen 26 NWQQDYVERANNGGIERVL 44 (45)
T ss_pred hHHHHHHHHHHcCCeeeec
Confidence 6999999999999999997
No 49
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=26.09 E-value=81 Score=21.79 Aligned_cols=47 Identities=11% Similarity=0.118 Sum_probs=30.3
Q ss_pred hccHHHHHhccChhhhHHHHHHHHhhcCCCC-----CcchhhHHHHHHHHHH
Q psy2476 89 SSQMDETVSNLDQDLLDTLMKYIYKGFEIPS-----EKSSSHLLTWHEKVFA 135 (151)
Q Consensus 89 ~sdI~~~v~~L~~e~~D~LMKYiYkgm~~~~-----~~~~~~LL~WheKl~~ 135 (151)
...+..+++.|++.+..++.-+.+.|+.... +-+-+.+-.|..++.+
T Consensus 101 ~~~l~~~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 101 REALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARK 152 (158)
T ss_pred HHHHHHHHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3468889999999999988766668876431 1133445555554443
No 50
>PRK13772 formimidoylglutamase; Provisional
Probab=25.84 E-value=40 Score=28.89 Aligned_cols=68 Identities=12% Similarity=0.098 Sum_probs=36.4
Q ss_pred CccccccCCCCCCCCccccCCCCCCC-CCCCHHHHHHHHhc---CCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHH
Q psy2476 10 FRKIDVDQYNEDNYKEEEQGEVPQLG-AGVDESEILSLLNQ---GKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKV 83 (151)
Q Consensus 10 ~RkIDVD~~d~d~f~~~~~~~~~~~~-~~~~~~qvr~ll~~---gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~v 83 (151)
|=+||||.+||.- -.-. ..|+ -|-...|+..+++. ....-++-.+==||||...+ .+-..+..++.+.
T Consensus 242 ylS~DiD~lDps~-aPGv----gtP~pgGlt~~e~~~il~~l~~~~~v~g~DvvEv~P~~D~~~-~Ta~laa~li~~~ 313 (314)
T PRK13772 242 YLTIDLDVLPAAV-APGV----SAPAAYGVPLPVVEEIVLHVRASGKLRVADLAEYNPQYDRDR-RTARVAARLAYRL 313 (314)
T ss_pred EEEEEecCcCccc-CCCC----CCCCCCCCCHHHHHHHHHHHHhcCCeeEEEEEEECCCCCCCC-CHHHHHHHHHHHh
Confidence 4579999999832 1110 1222 23456677666642 11223444555689998765 3444444455443
No 51
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=25.80 E-value=87 Score=23.01 Aligned_cols=29 Identities=7% Similarity=0.069 Sum_probs=25.1
Q ss_pred ccHHHHHhccChhhhHHHHHHHHhhcCCC
Q psy2476 90 SQMDETVSNLDQDLLDTLMKYIYKGFEIP 118 (151)
Q Consensus 90 sdI~~~v~~L~~e~~D~LMKYiYkgm~~~ 118 (151)
..+..++..|++.+..+|+-+.|.||...
T Consensus 114 ~~l~~~l~~L~~~~r~vl~l~~~~g~s~~ 142 (170)
T TIGR02952 114 EKLLKALKILTPKQQHVIALRFGQNLPIA 142 (170)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhcCCCHH
Confidence 45788899999999999999989998754
No 52
>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=25.47 E-value=13 Score=30.95 Aligned_cols=16 Identities=38% Similarity=0.729 Sum_probs=12.4
Q ss_pred HHHHHHHhcCCCCCCC
Q psy2476 53 QDALKTVLKNAPLGSK 68 (151)
Q Consensus 53 ~~ALk~aL~npP~g~~ 68 (151)
.....+++.|||||+.
T Consensus 106 ~~~~dtvimNPPFG~~ 121 (198)
T COG2263 106 RGKFDTVIMNPPFGSQ 121 (198)
T ss_pred CCccceEEECCCCccc
Confidence 3344499999999994
No 53
>PF13925 Katanin_con80: con80 domain of Katanin
Probab=25.27 E-value=2.3e+02 Score=21.95 Aligned_cols=84 Identities=15% Similarity=0.138 Sum_probs=46.4
Q ss_pred HHHHHHHHhcCCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHhhcCCCC
Q psy2476 40 ESEILSLLNQGKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGFEIPS 119 (151)
Q Consensus 40 ~~qvr~ll~~gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkgm~~~~ 119 (151)
-+.||.+-++||..+|+..+..- .| ..++.++|..+......+. ++-+..-.|+=-|..-+....
T Consensus 18 L~~v~~~W~~~~~k~ai~~~~~~-----~D-------~svlvD~L~vl~~~~~~~~---~tLd~c~~lLP~i~~LL~Sk~ 82 (164)
T PF13925_consen 18 LQVVRTFWRRNDIKGAIEYAVRM-----ND-------PSVLVDVLSVLNQSLKPEK---WTLDLCVDLLPLIEELLQSKY 82 (164)
T ss_pred HHHHHHHHhcCcHHHHHHHHHhc-----CC-------chHHHHHHHHHHHhcCcCc---ccHHHHHHHHHHHHHHHhCCc
Confidence 35688999999999999988765 12 1244555555442222221 444444444444555555554
Q ss_pred CcchhhHHHHHHHHHHhhC
Q psy2476 120 EKSSSHLLTWHEKVFAIGG 138 (151)
Q Consensus 120 ~~~~~~LL~WheKl~~~~G 138 (151)
+..-.+=|.|-.+++..+|
T Consensus 83 E~~i~~aL~~L~~i~~~f~ 101 (164)
T PF13925_consen 83 ESYISVALEMLRSILKKFG 101 (164)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4434444555555555443
No 54
>COG0010 SpeB Arginase/agmatinase/formimionoglutamate hydrolase, arginase family [Amino acid transport and metabolism]
Probab=24.88 E-value=44 Score=28.54 Aligned_cols=71 Identities=23% Similarity=0.262 Sum_probs=39.6
Q ss_pred CccccccCCCCCCCCccccCCCCCCC-CCCCHHHHHHH----HhcCCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHH
Q psy2476 10 FRKIDVDQYNEDNYKEEEQGEVPQLG-AGVDESEILSL----LNQGKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVL 84 (151)
Q Consensus 10 ~RkIDVD~~d~d~f~~~~~~~~~~~~-~~~~~~qvr~l----l~~gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL 84 (151)
|=+||||.||| .|-... .+|+ -+..-.|+..+ +.+++ .-++-.+=-||+|...+ .+=.....++.+.|
T Consensus 226 ylSiDiD~lDP-a~aPgv----gtp~~gGlt~~e~~~~~~~l~~~~~-vvg~DvvEv~P~~D~~~-~Ta~~aa~l~~~ll 298 (305)
T COG0010 226 YLSIDLDVLDP-AFAPGV----GTPEPGGLTFRELLDLLERLLKSGK-VVGFDVVEVNPALDISG-RTARLAARLIAELL 298 (305)
T ss_pred EEEEecCCcCc-ccCCCC----CCCCCCCCCHHHHHHHHHHHhccCC-EEEEEEEEECCCCCCCc-cHHHHHHHHHHHHH
Confidence 55799999999 322211 1222 34455555553 33422 23334445689998544 55566666666666
Q ss_pred Hhh
Q psy2476 85 LAI 87 (151)
Q Consensus 85 ~s~ 87 (151)
...
T Consensus 299 ~~~ 301 (305)
T COG0010 299 GKR 301 (305)
T ss_pred HHh
Confidence 544
No 55
>KOG0310|consensus
Probab=24.72 E-value=3.8e+02 Score=25.26 Aligned_cols=91 Identities=18% Similarity=0.198 Sum_probs=68.3
Q ss_pred CCCHHHHHHHHhcCCHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHHHHhhcC
Q psy2476 37 GVDESEILSLLNQGKHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGFE 116 (151)
Q Consensus 37 ~~~~~qvr~ll~~gd~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkgm~ 116 (151)
+..-.-....|++=+..+||..+|+- +. +.+..-+||..|..- .-+-.++.+.+..++--|..+|-|++.
T Consensus 351 r~~L~~~Dk~Lk~F~~kkALd~vl~~---~~-----~pelvvavl~eL~~R--g~l~~AL~grde~eL~~lLnfl~~~l~ 420 (487)
T KOG0310|consen 351 RLKLTYFDKRLKQFKHKKALDHVLEP---KK-----DPELVVAVLSELVHR--GGLRRALAGRDESELAPLLNFLVKNLT 420 (487)
T ss_pred ccCCchHHHHHhhhhHHHHHHHHhcc---cC-----ChhHHHHHHHHHHHh--hHHHHHhcCccHHHHHHHHHHHHhhcc
Confidence 44556677788888999999999974 22 233444555555443 357888899999999999999999988
Q ss_pred CCCCcchhhHHHHHHHHHHhhCC
Q psy2476 117 IPSEKSSSHLLTWHEKVFAIGGL 139 (151)
Q Consensus 117 ~~~~~~~~~LL~WheKl~~~~G~ 139 (151)
.+.- +++|-.|-+.++++.|.
T Consensus 421 ~~rf--~~~L~~~~~~iLd~Y~~ 441 (487)
T KOG0310|consen 421 VVRF--ASILMEVVSVILDLYAR 441 (487)
T ss_pred chhh--HHHHHHHHHHHHHHHHh
Confidence 8754 58999999999988764
No 56
>KOG2538|consensus
Probab=24.41 E-value=81 Score=30.13 Aligned_cols=32 Identities=22% Similarity=0.296 Sum_probs=29.7
Q ss_pred CHHHHHHHHhcCCHHHHHHHHhcCCCCCCCCh
Q psy2476 39 DESEILSLLNQGKHQDALKTVLKNAPLGSKNQ 70 (151)
Q Consensus 39 ~~~qvr~ll~~gd~~~ALk~aL~npP~g~~~~ 70 (151)
...++|+.|.+|.+-.||.+++-||-|..+++
T Consensus 452 ~~~tl~q~l~s~~~RsalhTa~n~P~yyl~~e 483 (578)
T KOG2538|consen 452 SISTLRQMLKSGANRSALHTALNDPVYYLHPE 483 (578)
T ss_pred chHHHHHHHhcccchhHHHHhhcCceeecccH
Confidence 57899999999999999999999999988775
No 57
>PF04192 Utp21: Utp21 specific WD40 associated putative domain ; InterPro: IPR007319 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp21 is a component of the SSU processome, which is required for pre-18S rRNA processing. It interacts with Utp18 [].; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=24.27 E-value=1.4e+02 Score=24.88 Aligned_cols=63 Identities=16% Similarity=0.216 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHhhhhccHHHHHhccC------hhhhHHHHHHHHhhcCCCC-----CcchhhHHHHHHHHHHhh
Q psy2476 75 SALNLTLKVLLAIKSSQMDETVSNLD------QDLLDTLMKYIYKGFEIPS-----EKSSSHLLTWHEKVFAIG 137 (151)
Q Consensus 75 ~~~~~Vl~vL~s~K~sdI~~~v~~L~------~e~~D~LMKYiYkgm~~~~-----~~~~~~LL~WheKl~~~~ 137 (151)
.....+++.|.+.-.|-|+--|.+|+ .++.-..++++-.++..-. |.-.+++|++|..++-..
T Consensus 124 ~dy~~~~~~LkslsPS~iDlEIRsL~~~~~~~~~~l~~Fl~~l~~~L~~~~dfElvQa~l~vFLk~Hgd~i~~~ 197 (237)
T PF04192_consen 124 EDYSEFLEYLKSLSPSAIDLEIRSLSPESGGSYEELVSFLRFLTYRLKSRRDFELVQAYLSVFLKVHGDVIMES 197 (237)
T ss_pred ccHHHHHHHHHhCChhHHHHHHHhccCccCCcHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHcC
Confidence 34667888898888888888889998 6777788888888888653 334699999998887543
No 58
>PF10475 DUF2450: Protein of unknown function N-terminal domain (DUF2450) ; InterPro: IPR019515 This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known.
Probab=24.21 E-value=75 Score=26.79 Aligned_cols=24 Identities=25% Similarity=0.372 Sum_probs=20.1
Q ss_pred CCHHHHHHHHhcCCHHHHHHHHhc
Q psy2476 38 VDESEILSLLNQGKHQDALKTVLK 61 (151)
Q Consensus 38 ~~~~qvr~ll~~gd~~~ALk~aL~ 61 (151)
.....++.+|+.||+.+||..+.+
T Consensus 129 ~~~~~l~~ll~~~dy~~Al~li~~ 152 (291)
T PF10475_consen 129 QTQSRLQELLEEGDYPGALDLIEE 152 (291)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHH
Confidence 356788999999999999987654
No 59
>TIGR01229 rocF_arginase arginase. This model helps resolve arginases from known and putative agmatinases, formiminoglutamases, and other related proteins of unknown specifity. The pathway from arginine to the polyamine putrescine may procede by hydrolysis to remove urea (arginase) followed by decarboxylation (ornithine decarboxylase), or by decarboxylation first (arginine decarboxylase) followed by removal of urea (agmatinase).
Probab=24.05 E-value=32 Score=29.12 Aligned_cols=70 Identities=21% Similarity=0.217 Sum_probs=38.8
Q ss_pred CccccccCCCCCCCCccccCCCCCCCCCCCHHHHHHHHh----cCCHHHHHHHHhcCCCCC--CCChHHHHHHHHHHHHH
Q psy2476 10 FRKIDVDQYNEDNYKEEEQGEVPQLGAGVDESEILSLLN----QGKHQDALKTVLKNAPLG--SKNQHVKDSALNLTLKV 83 (151)
Q Consensus 10 ~RkIDVD~~d~d~f~~~~~~~~~~~~~~~~~~qvr~ll~----~gd~~~ALk~aL~npP~g--~~~~~~K~~~~~~Vl~v 83 (151)
|=.||||.+||.-+.--. .+..-+-...|+..+++ +++ .-++-.+==|||+. ..+ .+-..+..++.++
T Consensus 221 yvS~DiDvlDps~aPgv~----tp~pgGl~~~e~~~~l~~i~~~~~-v~g~DivE~~P~~D~~~~~-~Ta~laa~li~~~ 294 (300)
T TIGR01229 221 HLSLDVDGLDPSLAPATG----TPVVGGLTFREGLLIMEMLYETGL-LTALDVVEVNPTLDIKHVN-RTIKTAVEIVRSL 294 (300)
T ss_pred EEEEeccccCcccCCCCC----CCCCCCCCHHHHHHHHHHHHhcCC-EEEEEEEEECccccccccc-HHHHHHHHHHHHH
Confidence 668999999983322110 11113445566655543 333 23455555689998 555 4445556666666
Q ss_pred HH
Q psy2476 84 LL 85 (151)
Q Consensus 84 L~ 85 (151)
|.
T Consensus 295 lg 296 (300)
T TIGR01229 295 LG 296 (300)
T ss_pred hc
Confidence 54
No 60
>PF06711 DUF1198: Protein of unknown function (DUF1198); InterPro: IPR009587 This family consists of several bacterial proteins of around 150 residues in length which are specific to Escherichia coli, Salmonella species and Yersinia pestis. The function of this family is unknown.
Probab=23.77 E-value=31 Score=27.45 Aligned_cols=60 Identities=20% Similarity=0.365 Sum_probs=42.6
Q ss_pred HHHHHhhhhccHHHHHhccChhhhHHHHHHHHhhcCCCC---------------CcchhhHHHHHHHHHHhhCCCc
Q psy2476 81 LKVLLAIKSSQMDETVSNLDQDLLDTLMKYIYKGFEIPS---------------EKSSSHLLTWHEKVFAIGGLGS 141 (151)
Q Consensus 81 l~vL~s~K~sdI~~~v~~L~~e~~D~LMKYiYkgm~~~~---------------~~~~~~LL~WheKl~~~~G~G~ 141 (151)
+..+..||.-=|++++.++-..+...+.+||-+|=+.-- +++-.-|..||.-+. ++|..+
T Consensus 31 Ls~rL~I~Pv~iESMl~qMGk~~~~~Firyl~~~~e~hl~nAA~vllIyQ~~Ivd~sd~Nl~~W~~~L~-ka~l~~ 105 (148)
T PF06711_consen 31 LSERLNIKPVYIESMLDQMGKRAGQEFIRYLSRGNEEHLQNAAQVLLIYQTFIVDGSDENLQRWRRILQ-KAGLSP 105 (148)
T ss_pred HHHHhCCCceeHHHHHHHHhHhHHHHHHHHHcCCCHHHHHhhhhhhheeeeeeecCCHHHHHHHHHHHH-HcCCCC
Confidence 445567788889999999999999999999988855331 223456778887664 455443
No 61
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=23.69 E-value=91 Score=16.66 Aligned_cols=18 Identities=28% Similarity=0.337 Sum_probs=14.3
Q ss_pred HHHHHHhcCCHHHHHHHH
Q psy2476 42 EILSLLNQGKHQDALKTV 59 (151)
Q Consensus 42 qvr~ll~~gd~~~ALk~a 59 (151)
..+.++..|++.+|+..+
T Consensus 7 la~~~~~~G~~~eA~~~l 24 (26)
T PF07721_consen 7 LARALLAQGDPDEAERLL 24 (26)
T ss_pred HHHHHHHcCCHHHHHHHH
Confidence 456788899999998764
No 62
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=23.36 E-value=1.1e+02 Score=22.26 Aligned_cols=29 Identities=7% Similarity=0.320 Sum_probs=24.6
Q ss_pred ccHHHHHhccChhhhHHHHHHHHhhcCCC
Q psy2476 90 SQMDETVSNLDQDLLDTLMKYIYKGFEIP 118 (151)
Q Consensus 90 sdI~~~v~~L~~e~~D~LMKYiYkgm~~~ 118 (151)
..+..++..|++.+..+++-+.+.|+...
T Consensus 98 ~~l~~~l~~Lp~~~r~v~~l~~~~g~s~~ 126 (161)
T PRK09047 98 QLIEEAIQKLPARQREAFLLRYWEDMDVA 126 (161)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHhcCCHH
Confidence 34788899999999999988888898754
No 63
>PF03395 Pox_P4A: Poxvirus P4A protein; InterPro: IPR005058 P4A is one of the most abundant structural proteins in the Vaccinia virion.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=22.77 E-value=32 Score=34.26 Aligned_cols=11 Identities=36% Similarity=0.685 Sum_probs=9.4
Q ss_pred cccccCCCCCC
Q psy2476 12 KIDVDQYNEDN 22 (151)
Q Consensus 12 kIDVD~~d~d~ 22 (151)
=+|||+|-||+
T Consensus 649 ~m~vD~F~PEN 659 (888)
T PF03395_consen 649 MMDVDAFMPEN 659 (888)
T ss_pred HhcccccCcch
Confidence 46899999998
No 64
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=22.62 E-value=81 Score=23.29 Aligned_cols=28 Identities=11% Similarity=0.179 Sum_probs=24.8
Q ss_pred cHHHHHhccChhhhHHHHHHHHhhcCCC
Q psy2476 91 QMDETVSNLDQDLLDTLMKYIYKGFEIP 118 (151)
Q Consensus 91 dI~~~v~~L~~e~~D~LMKYiYkgm~~~ 118 (151)
.+..++.+|++++..+++-+.|.||...
T Consensus 106 ~l~~~l~~L~~~~r~v~~L~~~~g~s~~ 133 (161)
T PRK12528 106 ELDQLLDGLPPLVKRAFLLAQVDGLGYG 133 (161)
T ss_pred HHHHHHHHCCHHHHHHHHHHHHcCCCHH
Confidence 5788899999999999999999998754
No 65
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=21.93 E-value=1.4e+02 Score=17.41 Aligned_cols=43 Identities=16% Similarity=0.179 Sum_probs=23.4
Q ss_pred ccChhhhHHHHHHHHhhcCCCC-----CcchhhHHHHHHHHHHhhCCCc
Q psy2476 98 NLDQDLLDTLMKYIYKGFEIPS-----EKSSSHLLTWHEKVFAIGGLGS 141 (151)
Q Consensus 98 ~L~~e~~D~LMKYiYkgm~~~~-----~~~~~~LL~WheKl~~~~G~G~ 141 (151)
.|++++..++ .+++.|+.... .-+-+.+-.|..++.++.|..+
T Consensus 3 ~l~~~e~~i~-~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~~~ 50 (58)
T smart00421 3 SLTPREREVL-RLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRS 50 (58)
T ss_pred CCCHHHHHHH-HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Confidence 4566666644 44566654331 1133556666666777766554
No 66
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=21.74 E-value=33 Score=28.25 Aligned_cols=15 Identities=13% Similarity=0.423 Sum_probs=14.0
Q ss_pred HHHHHHHHHhhCCCc
Q psy2476 127 LTWHEKVFAIGGLGS 141 (151)
Q Consensus 127 L~WheKl~~~~G~G~ 141 (151)
..||++|..+.|+||
T Consensus 69 R~lF~~LisVnGIGp 83 (201)
T COG0632 69 RELFRLLISVNGIGP 83 (201)
T ss_pred HHHHHHHHccCCccH
Confidence 489999999999997
No 67
>COG1610 Uncharacterized conserved protein [Function unknown]
Probab=21.51 E-value=1.6e+02 Score=23.42 Aligned_cols=51 Identities=33% Similarity=0.401 Sum_probs=33.6
Q ss_pred HHHHHHHHhcCCCCCCCChHHHHHHH-HHHHHHHHhhhhccHHHHHhccChhh-hHHHHHHHH
Q psy2476 52 HQDALKTVLKNAPLGSKNQHVKDSAL-NLTLKVLLAIKSSQMDETVSNLDQDL-LDTLMKYIY 112 (151)
Q Consensus 52 ~~~ALk~aL~npP~g~~~~~~K~~~~-~~Vl~vL~s~K~sdI~~~v~~L~~e~-~D~LMKYiY 112 (151)
+.+.|+.|+. +||..- .++--++.+||+-||..-...|+.++ ..+|.|-|-
T Consensus 7 l~~dlK~AMk----------akDk~r~~tiRli~AAik~~ei~~rk~~l~d~~il~vl~k~iK 59 (148)
T COG1610 7 LTEDLKEAMK----------AKDKDRLGTIRLILAAIKQEEIDERKDELDDEEILKVLAKEIK 59 (148)
T ss_pred HHHHHHHHHH----------hhhhhhHHHHHHHHHHHHHHHHHccCCCCChHHHHHHHHHHHH
Confidence 4556666663 345543 44445667899999999877787654 577777654
No 68
>PF08349 DUF1722: Protein of unknown function (DUF1722); InterPro: IPR013560 This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from Escherichia coli.
Probab=21.34 E-value=3.3e+02 Score=19.82 Aligned_cols=42 Identities=19% Similarity=0.249 Sum_probs=28.9
Q ss_pred HHHHHHHHhcC----------CHHHHHHHHhcCCCCCCCChHHHHHHHHHHHHHHHhhh
Q psy2476 40 ESEILSLLNQG----------KHQDALKTVLKNAPLGSKNQHVKDSALNLTLKVLLAIK 88 (151)
Q Consensus 40 ~~qvr~ll~~g----------d~~~ALk~aL~npP~g~~~~~~K~~~~~~Vl~vL~s~K 88 (151)
-.++++++++. .+...|..||..||-. ..+..+.+.+..-||
T Consensus 12 y~~lg~~va~~~~~~~~~~~~~Y~~~l~~al~~~~~~-------~~~~Nvl~Hi~Gyfk 63 (117)
T PF08349_consen 12 YRELGRLVANAGKRPLEEVFEEYEELLMEALSKPPTR-------GSHINVLQHIFGYFK 63 (117)
T ss_pred HHHHHHHHhcCCCCChHHHHHHHHHHHHHHHhcCCCc-------hhHHHHHHHHHHHHH
Confidence 45667777652 4566789999999874 455666777777666
No 69
>PF05778 Apo-CIII: Apolipoprotein CIII (Apo-CIII); InterPro: IPR008403 This family consists of several mammalian apolipoprotein CIII (Apo-CIII) sequences. Apolipoprotein C-III is a 79-residue glycoprotein. It is synthesised in the intestine and liver as part of the very low density lipoprotein (VLDL) and the high density lipoprotein (HDL) particles. Owing to its positive correlation with plasma triglyceride (Tg) levels, Apo-CIII is suggested to play a role in Tg metabolism and is therefore of interest regarding atherosclerosis. However, unlike other apolipoproteins such as Apo-AI, Apo E or CII for which many naturally occurring mutations are known, the structure-function relationships of apo C-III remains a subject of debate. One possibility is that apo C-III inhibits lipoprotein lipase (LPL) activity, as shown by in vitro experiments. Another suggestion, is that elevated levels of Apo-CIII displace other apolipoproteins at the lipoprotein surface, modifying their clearance from plasma [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0042157 lipoprotein metabolic process, 0005576 extracellular region; PDB: 2JQ3_A.
Probab=21.22 E-value=1.3e+02 Score=21.15 Aligned_cols=37 Identities=19% Similarity=0.305 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHhhhhccHHHHHhccChhhhHHHHHH
Q psy2476 74 DSALNLTLKVLLAIKSSQMDETVSNLDQDLLDTLMKY 110 (151)
Q Consensus 74 ~~~~~~Vl~vL~s~K~sdI~~~v~~L~~e~~D~LMKY 110 (151)
.++..++-+.|++++.++|..-++.-=.+-.+.|=-|
T Consensus 16 qqAtktAqdaLtsVqES~vAqqAr~wmt~~~sslk~Y 52 (70)
T PF05778_consen 16 QQATKTAQDALTSVQESQVAQQARDWMTDSFSSLKDY 52 (70)
T ss_dssp HHHGGGHHHHHHGGGGGGGHHHHHHHTTTTTTHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence 4566788999999999999988776666666666555
No 70
>PF01170 UPF0020: Putative RNA methylase family UPF0020; InterPro: IPR000241 This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains [].; PDB: 3LDU_A 3LDG_A 3K0B_A 3V8V_B 3V97_A 3TLJ_A 3TM5_B 3TM4_A 3TMA_A.
Probab=20.71 E-value=62 Score=25.30 Aligned_cols=15 Identities=20% Similarity=0.596 Sum_probs=9.4
Q ss_pred HHHHHhcCCCCCCCC
Q psy2476 55 ALKTVLKNAPLGSKN 69 (151)
Q Consensus 55 ALk~aL~npP~g~~~ 69 (151)
..-.++.|||||-.-
T Consensus 106 ~~d~IvtnPPyG~r~ 120 (179)
T PF01170_consen 106 SVDAIVTNPPYGRRL 120 (179)
T ss_dssp BSCEEEEE--STTSH
T ss_pred CCCEEEECcchhhhc
Confidence 344788999999854
No 71
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.55 E-value=96 Score=23.13 Aligned_cols=28 Identities=14% Similarity=0.258 Sum_probs=25.1
Q ss_pred cHHHHHhccChhhhHHHHHHHHhhcCCC
Q psy2476 91 QMDETVSNLDQDLLDTLMKYIYKGFEIP 118 (151)
Q Consensus 91 dI~~~v~~L~~e~~D~LMKYiYkgm~~~ 118 (151)
.+..++..|++.+..+++.+-|.||+..
T Consensus 105 ~l~~~l~~L~~~~r~v~~l~~~~g~s~~ 132 (164)
T PRK12547 105 DFKKALNLLSADQREAIILIGASGFSYE 132 (164)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCCHH
Confidence 5789999999999999999989999865
No 72
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=20.38 E-value=1.8e+02 Score=21.42 Aligned_cols=34 Identities=15% Similarity=0.182 Sum_probs=23.6
Q ss_pred ccHHHHHhccChhhhHHHHHHHHhhcCCCCCcchhhHHHHHHHHHH
Q psy2476 90 SQMDETVSNLDQDLLDTLMKYIYKGFEIPSEKSSSHLLTWHEKVFA 135 (151)
Q Consensus 90 sdI~~~v~~L~~e~~D~LMKYiYkgm~~~~~~~~~~LL~WheKl~~ 135 (151)
.++-....+|++++++.+++++ ..++.+.+++++
T Consensus 90 ~~ll~~~~~L~~~~~~~~l~~l------------~~~~~~~~~~~~ 123 (135)
T PRK09706 90 KELLELFDALPESEQDAQLSEM------------RARVENFNKLFE 123 (135)
T ss_pred HHHHHHHHHCCHHHHHHHHHHH------------HHHHHHHHHHHH
Confidence 4566777888888888888876 345556666654
Done!