Query psy8743
Match_columns 154
No_of_seqs 97 out of 99
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 18:05:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8743.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8743hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2297|consensus 100.0 4E-57 8.7E-62 381.5 13.0 153 1-154 216-368 (412)
2 KOG1461|consensus 99.7 1.1E-16 2.4E-21 145.2 12.8 118 35-154 505-625 (673)
3 smart00515 eIF5C Domain at the 98.8 5E-09 1.1E-13 72.8 4.8 44 110-154 1-44 (83)
4 PF02020 W2: eIF4-gamma/eIF5/e 98.1 2.8E-06 6.2E-11 59.2 3.4 33 122-154 2-34 (84)
5 KOG2767|consensus 96.2 0.052 1.1E-06 47.6 9.7 56 99-154 290-346 (400)
6 PF09090 MIF4G_like_2: MIF4G l 94.8 0.34 7.4E-06 40.0 9.8 93 42-141 13-110 (253)
7 KOG1104|consensus 85.7 4.1 9E-05 39.0 8.0 92 42-139 502-594 (759)
8 PF02847 MA3: MA3 domain; Int 75.6 25 0.00053 24.6 8.6 48 38-88 1-48 (113)
9 smart00509 TFS2N Domain in the 69.7 31 0.00068 23.3 7.2 70 41-114 3-74 (75)
10 PF08542 Rep_fac_C: Replicatio 65.3 38 0.00083 22.7 7.4 33 55-88 19-51 (89)
11 COG5103 CDC39 Cell division co 57.7 30 0.00065 35.7 6.3 56 34-89 597-652 (2005)
12 PRK07668 hypothetical protein; 56.9 94 0.002 26.1 8.5 76 7-89 3-86 (254)
13 KOG0886|consensus 56.7 13 0.00028 29.1 3.0 61 5-65 90-159 (167)
14 PRK15039 transcriptional repre 51.3 85 0.0019 22.2 6.6 66 44-109 23-88 (90)
15 TIGR01806 CM_mono2 chorismate 50.8 73 0.0016 23.3 6.2 64 22-89 5-72 (114)
16 PF02583 Trns_repr_metal: Meta 50.5 67 0.0014 22.2 5.6 66 44-109 19-85 (85)
17 PF04233 Phage_Mu_F: Phage Mu 49.2 29 0.00064 24.1 3.8 27 41-67 2-28 (112)
18 PRK11352 regulator protein Frm 48.8 94 0.002 22.0 6.6 67 44-110 23-90 (91)
19 PF00286 Flexi_CP: Viral coat 46.0 85 0.0019 24.1 6.1 65 53-118 3-80 (140)
20 KOG1992|consensus 45.8 36 0.00077 33.5 4.7 82 13-95 325-424 (960)
21 smart00544 MA3 Domain in DAP-5 44.6 1.1E+02 0.0023 21.4 8.2 80 39-134 2-81 (113)
22 PF08656 DASH_Dad3: DASH compl 44.2 97 0.0021 21.5 5.6 60 36-95 16-76 (78)
23 PF08102 Antimicrobial_7: Scor 43.5 49 0.0011 20.4 3.5 30 81-110 3-35 (43)
24 KOG0898|consensus 42.5 37 0.0008 26.3 3.5 83 8-94 16-107 (152)
25 COG4709 Predicted membrane pro 40.9 24 0.00052 28.6 2.4 23 2-24 15-39 (195)
26 KOG3709|consensus 40.5 26 0.00055 33.0 2.8 27 126-152 406-443 (778)
27 PF07739 TipAS: TipAS antibiot 40.0 71 0.0015 22.2 4.6 41 101-145 58-98 (118)
28 KOG3831|consensus 39.2 1.3E+02 0.0028 23.9 6.2 73 6-87 28-101 (196)
29 PF04121 Nup84_Nup100: Nuclear 38.0 79 0.0017 29.9 5.7 115 13-146 379-493 (697)
30 PF08542 Rep_fac_C: Replicatio 37.8 1.2E+02 0.0026 20.1 10.5 53 24-80 9-61 (89)
31 PF08651 DASH_Duo1: DASH compl 37.5 1.1E+02 0.0023 21.1 4.9 48 101-149 5-52 (78)
32 PF13324 GCIP: Grap2 and cycli 37.5 41 0.0009 27.9 3.5 87 21-111 45-147 (275)
33 PF07739 TipAS: TipAS antibiot 36.5 1.4E+02 0.0031 20.6 6.1 46 40-85 38-88 (118)
34 PF13625 Helicase_C_3: Helicas 36.0 72 0.0016 23.3 4.2 32 42-74 43-74 (129)
35 PF09832 DUF2059: Uncharacteri 36.0 63 0.0014 20.5 3.5 30 11-40 10-39 (64)
36 cd01046 Rubrerythrin_like rubr 35.5 1.7E+02 0.0037 21.1 9.7 96 12-116 21-122 (123)
37 TIGR03147 cyt_nit_nrfF cytochr 35.4 72 0.0016 24.1 4.1 33 37-69 57-89 (126)
38 PHA03056 putative myristoylate 35.3 1E+02 0.0022 23.9 4.9 42 46-90 70-111 (165)
39 PF08349 DUF1722: Protein of u 35.3 1.7E+02 0.0036 21.1 6.0 52 23-74 55-106 (117)
40 PF06777 DUF1227: Protein of u 34.7 2.1E+02 0.0044 22.2 6.6 95 2-119 50-146 (146)
41 PF08318 COG4: COG4 transport 34.2 2.7E+02 0.0059 23.7 8.0 85 20-139 42-126 (331)
42 PF01320 Colicin_Pyocin: Colic 32.7 54 0.0012 23.1 2.9 20 54-73 62-81 (85)
43 PRK10144 formate-dependent nit 32.5 85 0.0018 23.7 4.1 33 37-69 57-89 (126)
44 PF00816 Histone_HNS: H-NS his 31.9 74 0.0016 21.9 3.5 37 39-77 7-43 (93)
45 COG1528 Ftn Ferritin-like prot 31.6 2.6E+02 0.0057 22.1 7.3 26 13-38 26-51 (167)
46 PRK10304 ferritin; Provisional 30.2 2.6E+02 0.0056 21.6 8.8 30 13-42 26-55 (165)
47 COG4396 Mu-like prophage host- 29.5 35 0.00077 26.6 1.6 29 107-139 50-78 (170)
48 PF11220 DUF3015: Protein of u 29.0 1.2E+02 0.0025 23.5 4.4 49 21-69 84-135 (144)
49 PLN03025 replication factor C 28.8 3.4E+02 0.0075 22.6 7.9 33 54-87 238-270 (319)
50 PRK15022 ferritin-like protein 28.8 2.8E+02 0.0062 21.6 6.7 30 13-42 26-55 (167)
51 TIGR01641 phageSPP1_gp7 phage 28.8 80 0.0017 22.1 3.3 25 43-67 2-26 (108)
52 PF02881 SRP54_N: SRP54-type p 28.5 90 0.002 20.2 3.4 49 36-84 24-74 (75)
53 PF09999 DUF2240: Uncharacteri 28.5 1.9E+02 0.0041 22.3 5.5 31 52-82 98-129 (144)
54 PF09371 Tex_N: Tex-like prote 27.5 1.2E+02 0.0025 24.4 4.4 75 6-87 100-177 (193)
55 PHA03074 late transcription fa 26.9 3.7E+02 0.0079 22.3 8.5 82 54-139 63-146 (225)
56 PF12554 MOZART1: Mitotic-spin 26.5 1.4E+02 0.003 18.9 3.7 29 39-67 20-48 (48)
57 PF01452 Rota_NSP4: Rotavirus 25.9 1.1E+02 0.0023 24.3 3.7 58 76-134 70-133 (173)
58 PF10265 DUF2217: Uncharacteri 25.7 79 0.0017 29.3 3.4 75 8-87 335-426 (514)
59 PF03918 CcmH: Cytochrome C bi 25.6 1.1E+02 0.0024 23.4 3.8 36 37-72 57-92 (148)
60 PF05184 SapB_1: Saposin-like 25.4 1.4E+02 0.0029 16.8 3.7 27 40-66 8-34 (39)
61 PRK09685 DNA-binding transcrip 25.3 2.9E+02 0.0062 22.4 6.5 63 10-78 227-298 (302)
62 KOG2580|consensus 24.4 3E+02 0.0066 25.1 6.7 23 109-138 328-351 (459)
63 PRK09940 transcriptional regul 23.4 4.4E+02 0.0095 22.0 8.1 62 10-80 163-233 (253)
64 TIGR01385 TFSII transcription 23.1 4.5E+02 0.0098 22.5 7.4 67 43-116 8-78 (299)
65 PF04255 DUF433: Protein of un 23.0 2E+02 0.0043 18.0 4.0 31 44-81 22-53 (56)
66 PRK15186 AraC family transcrip 23.0 3.1E+02 0.0067 23.1 6.3 62 10-79 210-280 (291)
67 PRK10328 DNA binding protein, 22.7 3.4E+02 0.0075 20.5 7.5 66 13-80 13-78 (134)
68 PRK08402 replication factor A; 22.5 2.6E+02 0.0056 24.6 5.9 42 38-81 5-46 (355)
69 PF01372 Melittin: Melittin; 22.3 56 0.0012 18.0 1.1 15 20-34 10-24 (26)
70 KOG1900|consensus 22.2 6.8E+02 0.015 26.1 9.2 109 25-137 1071-1210(1311)
71 PF02403 Seryl_tRNA_N: Seryl-t 22.0 2.8E+02 0.0061 19.3 7.1 61 10-70 10-83 (108)
72 PF03271 EB1: EB1-like C-termi 21.9 1.1E+02 0.0023 18.7 2.5 28 127-154 12-43 (43)
73 PF06109 HlyE: Haemolysin E (H 21.7 2.9E+02 0.0064 22.9 5.7 68 57-131 38-116 (299)
74 PF00745 GlutR_dimer: Glutamyl 21.1 92 0.002 21.2 2.4 36 13-48 13-48 (101)
75 PF01402 RHH_1: Ribbon-helix-h 20.2 1.8E+02 0.0039 16.3 3.9 28 56-83 7-34 (39)
No 1
>KOG2297|consensus
Probab=100.00 E-value=4e-57 Score=381.49 Aligned_cols=153 Identities=52% Similarity=0.935 Sum_probs=151.7
Q ss_pred CCCCCCCCCCHHHHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHH
Q psy8743 1 MEFVPPNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVL 80 (154)
Q Consensus 1 ~~ffP~~kRs~~~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~ 80 (154)
|+||||||||.|||.+||+++||.+|++|+++|++++.+||+++.|++++++|.|.++||..||+.++.+|+||++||++
T Consensus 216 meffPpnkrs~E~Fak~Ft~agL~elvey~~~q~~~~a~kElq~~L~~q~s~e~p~~evi~~VKee~k~~nlPe~eVi~i 295 (412)
T KOG2297|consen 216 MEFFPPNKRSVEHFAKYFTDAGLKELVEYHRNQQSEGARKELQKELQEQVSEEDPVKEVILYVKEEMKRNNLPETEVIGI 295 (412)
T ss_pred HHhcCCcchhHHHHHHHHhHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcCCCCceEEee
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhhccchHHHHHHHHHHHHhhHhhHHHHhcCCCcHHHHHHHHHHHHHhHhhhhhhHHHHHHHHhhcC
Q psy8743 81 IWSTVMAQVEWNKKEELVAEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFYK 154 (154)
Q Consensus 81 iw~~lM~~vews~k~~~~~e~a~~~lkk~~pLL~~F~~~~~~~ql~LL~kvQ~~Cye~~~~mk~F~kIl~~LY~ 154 (154)
||+++|++|+||++++++++||+||+|+|+|||++||+++ ++|++||+|||+|||||++|||+||+||++||+
T Consensus 296 vWs~iMsaveWnKkeelva~qalrhlK~yaPLL~af~s~g-~sEL~Ll~KvQe~CYen~~fMKaFqkiV~lfYk 368 (412)
T KOG2297|consen 296 VWSGIMSAVEWNKKEELVAEQALRHLKQYAPLLAAFCSQG-QSELELLLKVQEYCYENIHFMKAFQKIVVLFYK 368 (412)
T ss_pred eHhhhhHHHhhchHHHHHHHHHHHHHHhhhHHHHHHhcCC-hHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999 999999999999999999999999999999995
No 2
>KOG1461|consensus
Probab=99.71 E-value=1.1e-16 Score=145.16 Aligned_cols=118 Identities=19% Similarity=0.390 Sum_probs=109.6
Q ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhhh---ccchHHHHHHHHHHHHhhHhh
Q psy8743 35 SQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQVE---WNKKEELVAEQALKHLKQFTP 111 (154)
Q Consensus 35 ~~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~ve---ws~k~~~~~e~a~~~lkk~~p 111 (154)
...|++|+.++|+|++++++..+.++++||+++.++|++.+||+++++.++|+.+. .|+-.+ ...++++.+++|+|
T Consensus 505 ~~~F~~Ev~~s~~ra~Een~~~D~~vlEINslRla~N~s~~ev~~av~~all~~~~~~~~~~~~~-~~~~~~~~~~~w~~ 583 (673)
T KOG1461|consen 505 TKDFEKEVLGSLQRAFEENSDMDNLVLEINSLRLAYNVSLKEVAGAVFMALLKLILHQDHSSMNE-VKRAALKVFTQWGP 583 (673)
T ss_pred hHHHHHHHHHHHHHHHHhccchHHHHHHHhhhHHhhcCCHHHHHHHHHHHHHHHHhcCCCccchh-HHHHHHHHHHHhhH
Confidence 45799999999999999999999999999999999999999999999999999983 444333 67799999999999
Q ss_pred HHHHhcCCCcHHHHHHHHHHHHHhHhhhhhhHHHHHHHHhhcC
Q psy8743 112 LFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFYK 154 (154)
Q Consensus 112 LL~~F~~~~~~~ql~LL~kvQ~~Cye~~~~mk~F~kIl~~LY~ 154 (154)
|++.+.++. +.|+++|++++++|.|+..+.+.|.+++++||+
T Consensus 584 l~~~y~ks~-deqid~l~~led~~~e~~~~~~~~~~~v~~lY~ 625 (673)
T KOG1461|consen 584 LLGNYIKSE-DEQIDLLLALEDKCVESEELGPKAAKLVHYLYD 625 (673)
T ss_pred HhhhhhhhH-HHHHHHHHHHHHHHHhcccchHHHHHHHHHHHH
Confidence 999999999 999999999999999998889999999999995
No 3
>smart00515 eIF5C Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5.
Probab=98.83 E-value=5e-09 Score=72.82 Aligned_cols=44 Identities=25% Similarity=0.586 Sum_probs=42.1
Q ss_pred hhHHHHhcCCCcHHHHHHHHHHHHHhHhhhhhhHHHHHHHHhhcC
Q psy8743 110 TPLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQKIILLFYK 154 (154)
Q Consensus 110 ~pLL~~F~~~~~~~ql~LL~kvQ~~Cye~~~~mk~F~kIl~~LY~ 154 (154)
+|||++|+++. ++|+++|+.+|.+|+++...++.|++|++.|||
T Consensus 1 ~~ll~~~~~~~-~~q~~~L~ale~~~~~~~~~~~~~~~il~~LYd 44 (83)
T smart00515 1 GPLLKFLAKDE-EEQIDLLYAIEEFCVELEKLIKLLPKILKSLYD 44 (83)
T ss_pred ChHHHHHHCCh-HHHHHHHHHHHHHHHHcchHHHHHHHHHHHHhh
Confidence 58999999999 999999999999999988889999999999996
No 4
>PF02020 W2: eIF4-gamma/eIF5/eIF2-epsilon; InterPro: IPR003307 This entry represents the W2 domain (two invariant tryptophans) and is a region of ~165 amino acids which is found in the C terminus of the following eIFs [, , , ]: Eukaryotic translation initiation factor 2B epsilon (eIF-2B-epsilon) Eukaryotic translation initiation factor 4 gamma (eIF-4-gamma) Eukaryotic translation initiation factor 5 (eIF-5), a GTPase-activating protein (GAP) specific for eIF2 Translation initiation is a sophisticated, well regulated and highly coordinated cellular process in eukaryotes, in which at least 11 eukayrotic initiation factors (eIFs) are included []. The W2 domain has a globular fold and is exclusively composed out of alpha-helices [, , ]. The structure can be divided into a structural C-terminal core onto which the two N-terminal helices are attached. The core contains two aromatic/acidic residue-rich regions (AA boxes), which are important for mediating protein-protein interactions. For example, the W2 domain of H. sapiens eIF5 binds eIF2-beta, eIF3 and eIF1 [], and therefore plays an important role in multifactor complex assembly. The entry covers the entire W2 domain.; GO: 0005488 binding; PDB: 3D3M_A 3L6A_A 1PAQ_A 2FUL_D 2IU1_A 1UG3_B 3JUI_A.
Probab=98.10 E-value=2.8e-06 Score=59.21 Aligned_cols=33 Identities=39% Similarity=0.720 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHhHhhhhhhHHHHHHHHhhcC
Q psy8743 122 RAELALMLKVQEFCYENMNLMRVFQKIILLFYK 154 (154)
Q Consensus 122 ~~ql~LL~kvQ~~Cye~~~~mk~F~kIl~~LY~ 154 (154)
++|+++|..+|.||+++.++++.|+.|++.||+
T Consensus 2 ~~Q~~~L~ale~~~~~~~~~~~~~~~il~~LYd 34 (84)
T PF02020_consen 2 DDQVDLLNALEEFCAENPNLMPLFPKILQQLYD 34 (84)
T ss_dssp HHHHHHHHHHHHHHHHTCGHGGHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCccHHHHHHHHHHHHhh
Confidence 689999999999999999999999999999996
No 5
>KOG2767|consensus
Probab=96.16 E-value=0.052 Score=47.59 Aligned_cols=56 Identities=18% Similarity=0.301 Sum_probs=49.9
Q ss_pred HHHHHHHHhhHhhHHHHhcCCCcHHHHHHHHHHHHHhHhh-hhhhHHHHHHHHhhcC
Q psy8743 99 AEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYEN-MNLMRVFQKIILLFYK 154 (154)
Q Consensus 99 ~e~a~~~lkk~~pLL~~F~~~~~~~ql~LL~kvQ~~Cye~-~~~mk~F~kIl~~LY~ 154 (154)
.+...+.|.++.++|.+||+++.+.|..||.-|+.+|.-. ..+++.-+.||+.|||
T Consensus 290 ~e~ivkei~k~~~~l~k~~~~~~k~qr~LLggiE~~~~~~~~el~~kva~ilk~lYd 346 (400)
T KOG2767|consen 290 DEKIVKEILKHRALLLKFCTNNEKAQRYLLGGIERFVEKHEAELISKVAGILKELYD 346 (400)
T ss_pred hhHHHHHHHHHHHHHHHHHhccHHHHHHHHhHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence 4567799999999999999996699999999999999885 4568999999999996
No 6
>PF09090 MIF4G_like_2: MIF4G like; InterPro: IPR015174 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 2", and is found in nuclear cap-binding proteins and eIF4G. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA.; GO: 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A.
Probab=94.82 E-value=0.34 Score=39.99 Aligned_cols=93 Identities=16% Similarity=0.235 Sum_probs=66.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCC----hHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHhhHhhHHHHh-
Q psy8743 42 LQEQLEEQISEGASIKDIVADIREIANKHCIP----DQELIVLIWSTVMAQVEWNKKEELVAEQALKHLKQFTPLFGAF- 116 (154)
Q Consensus 42 l~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~----~~evi~~iw~~lM~~vews~k~~~~~e~a~~~lkk~~pLL~~F- 116 (154)
+.+.|.+++....|++++...+++.....+-+ +.-++.++++|++... | .... -+...|.+|.+.|..+
T Consensus 13 ~a~~l~~~ir~k~~~eei~~~l~~i~~~~~~~~~~~~~~~i~v~~q~ll~~G--S---kS~S-H~~~~lery~~~Lk~l~ 86 (253)
T PF09090_consen 13 LAQKLLDLIRKKAPPEEISELLEEIEEPAEEHGSDFDKFVIDVFVQCLLHIG--S---KSFS-HVLSALERYKEVLKELE 86 (253)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHTTS------------HHHHHHHHHHHHHHT--T---TSHH-HHHHHHHHTHHHHHHH-
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhccccccccccchhhHHHHHHHHHHHHhc--C---chHH-HHHHHHHHHHHHHHHhc
Confidence 66778899988888888888777666554432 2347888888888765 1 2233 6677899999999999
Q ss_pred cCCCcHHHHHHHHHHHHHhHhhhhh
Q psy8743 117 TDTAPRAELALMLKVQEFCYENMNL 141 (154)
Q Consensus 117 ~~~~~~~ql~LL~kvQ~~Cye~~~~ 141 (154)
+.+. ..|..+|..+-.|.-.++.+
T Consensus 87 ~~~~-~~q~~il~~v~~~W~~~~q~ 110 (253)
T PF09090_consen 87 AESE-EAQFWILDAVFRFWKNNPQM 110 (253)
T ss_dssp TSSH-HHHHHHHHHHHHHHTT-HHH
T ss_pred cCCh-HHHHHHHHHHHHHHhcCCce
Confidence 8888 99999999999998887655
No 7
>KOG1104|consensus
Probab=85.71 E-value=4.1 Score=38.97 Aligned_cols=92 Identities=17% Similarity=0.227 Sum_probs=69.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCh-HHHHHHHHHHHHhhhhccchHHHHHHHHHHHHhhHhhHHHHhcCCC
Q psy8743 42 LQEQLEEQISEGASIKDIVADIREIANKHCIPD-QELIVLIWSTVMAQVEWNKKEELVAEQALKHLKQFTPLFGAFTDTA 120 (154)
Q Consensus 42 l~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~-~evi~~iw~~lM~~vews~k~~~~~e~a~~~lkk~~pLL~~F~~~~ 120 (154)
+..++..++..-.++++++.++|+--.+...+. .=.|+++.+++++.. |+. .. -+...+.+|..+|+++|-+.
T Consensus 502 ~~~~l~~~~~~k~~~e~~~~iLk~~~~~~~~~~n~~~i~lfvq~~l~lG--SKS---fS-H~f~~lek~~~vfk~l~~~~ 575 (759)
T KOG1104|consen 502 VAVQLIVAFREKATAEEIVNILKSEDESEIGSFNRLKIILFVQTLLDLG--SKS---FS-HAFSALEKYHTVFKKLCEDS 575 (759)
T ss_pred HHHHHHHHHhccCCHHHHHHHHhcCccccccCCcceehhhHHHHHHHhc--cch---hh-hHHHHHHHHHHHHHHHhcCC
Confidence 467899999999999999999993222222222 336788888998886 222 11 34778889999999999999
Q ss_pred cHHHHHHHHHHHHHhHhhh
Q psy8743 121 PRAELALMLKVQEFCYENM 139 (154)
Q Consensus 121 ~~~ql~LL~kvQ~~Cye~~ 139 (154)
...|+.+|..|=++.-.|.
T Consensus 576 e~~q~~vl~~vft~Wk~n~ 594 (759)
T KOG1104|consen 576 ETKQIIVLEAVFTFWKANP 594 (759)
T ss_pred chhHHHHHHHHHHHHhcCc
Confidence 3449999999999988764
No 8
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=75.62 E-value=25 Score=24.59 Aligned_cols=48 Identities=17% Similarity=0.294 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhh
Q psy8743 38 AKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQ 88 (154)
Q Consensus 38 ~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~ 88 (154)
+||.+...|.+.+.. .+.+|++..|+++... --.++++..+....|+.
T Consensus 1 ~rk~i~~~l~ey~~~-~d~~ea~~~l~el~~~--~~~~~vv~~~l~~~le~ 48 (113)
T PF02847_consen 1 LRKKIFSILMEYFSS-GDVDEAVECLKELKLP--SQHHEVVKVILECALEE 48 (113)
T ss_dssp HHHHHHHHHHHHHHH-T-HHHHHHHHHHTT-G--GGHHHHHHHHHHHHHTS
T ss_pred ChHHHHHHHHHHhcC-CCHHHHHHHHHHhCCC--ccHHHHHHHHHHHHhhc
Confidence 577888899999977 4789999888886444 55678888888888877
No 9
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=69.69 E-value=31 Score=23.26 Aligned_cols=70 Identities=16% Similarity=0.194 Sum_probs=48.3
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhhh-ccch-HHHHHHHHHHHHhhHhhHHH
Q psy8743 41 ELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQVE-WNKK-EELVAEQALKHLKQFTPLFG 114 (154)
Q Consensus 41 el~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~ve-ws~k-~~~~~e~a~~~lkk~~pLL~ 114 (154)
+....+..+.+++.+.+.++..++.+.. .+++...+... -+...|. ..+. ...+...|...+++|..++.
T Consensus 3 ~~~k~~~k~~~~~~~~~~~l~~L~~L~~-~~~t~~~L~~T---~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 3 RAAKKLDKVANNGKEVSRCLDILKKLKK-LPITVDLLEET---RIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhc-CCCCHHHHHHC---cHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence 3556677777777778889999999885 77777665543 3333332 2222 46677799999999998764
No 10
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=65.34 E-value=38 Score=22.65 Aligned_cols=33 Identities=6% Similarity=0.187 Sum_probs=17.1
Q ss_pred CHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhh
Q psy8743 55 SIKDIVADIREIANKHCIPDQELIVLIWSTVMAQ 88 (154)
Q Consensus 55 ~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~ 88 (154)
+.+++...++++..+ .+|-.|++.-+...++..
T Consensus 19 ~~~~~~~~~~~l~~~-G~s~~~Il~~l~~~l~~~ 51 (89)
T PF08542_consen 19 DFKEARKKLYELLVE-GYSASDILKQLHEVLVES 51 (89)
T ss_dssp CHHHHHHHHHHHHHT-T--HHHHHHHHHHHHHTS
T ss_pred CHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHHh
Confidence 455555555555555 555555555555555554
No 11
>COG5103 CDC39 Cell division control protein, negative regulator of transcription [Cell division and chromosome partitioning / Transcription]
Probab=57.65 E-value=30 Score=35.70 Aligned_cols=56 Identities=13% Similarity=0.265 Sum_probs=51.5
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhh
Q psy8743 34 ASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQV 89 (154)
Q Consensus 34 ~~~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~v 89 (154)
.+-+.++|++.-++.+.+....++.+|..+|+++.+.|--|.|+..+|..|+++--
T Consensus 597 ~~~dIE~E~~sy~q~~y~~~~~I~~~I~~l~~f~~senprd~elfsci~hal~~ey 652 (2005)
T COG5103 597 KEIDIEEEASSYIQQIYNSQRGIESSINQLKEFLRSENPRDKELFSCIFHALLEEY 652 (2005)
T ss_pred cCccHHHHHHHHHHHHHHhcccHHHHHHHHHHHhhcCCcchHHHHHHHHHHHHHHh
Confidence 45578999999999999999999999999999999999999999999999999653
No 12
>PRK07668 hypothetical protein; Validated
Probab=56.91 E-value=94 Score=26.12 Aligned_cols=76 Identities=18% Similarity=0.258 Sum_probs=53.2
Q ss_pred CCCCHH---HHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHH-----HHHHHHhhcCCChHHHH
Q psy8743 7 NKRSDE---YFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVA-----DIREIANKHCIPDQELI 78 (154)
Q Consensus 7 ~kRs~~---~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~-----~ik~~~~~~~~~~~evi 78 (154)
+||+++ ++..+++.+|++ .++.++...|+..++.++=.+|.+.+++.- ..++...+...+..+-.
T Consensus 3 TkeNeefl~~L~~yL~~~gls-------eeeieeiL~Ei~~hLlEgQk~GkTA~~IfG~sPk~yA~EL~~~~~~~~~~~~ 75 (254)
T PRK07668 3 SKEGRKFLDDTRVYLIAKGIK-------EEDIESFLEDAELHLIEGEKDGKTVEDIFGDSPKEYANELVKEMEVDRKENI 75 (254)
T ss_pred CHHHHHHHHHHHHHHHHCCCC-------HHHHHHHHHHHHHHHHHHHHcCCcHHHHhCCCHHHHHHHHhcccCCCcchHH
Confidence 344444 445667777876 456678889999999999999988877765 35566666666666666
Q ss_pred HHHHHHHHhhh
Q psy8743 79 VLIWSTVMAQV 89 (154)
Q Consensus 79 ~~iw~~lM~~v 89 (154)
..+-.++|+.+
T Consensus 76 ~~l~~~ii~~l 86 (254)
T PRK07668 76 KLILFIIIGIL 86 (254)
T ss_pred HHHHHHHHHHH
Confidence 66666666655
No 13
>KOG0886|consensus
Probab=56.74 E-value=13 Score=29.06 Aligned_cols=61 Identities=20% Similarity=0.339 Sum_probs=48.6
Q ss_pred CCCCCCHHHHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHH---------cCCCHHHHHHHHHH
Q psy8743 5 PPNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQIS---------EGASIKDIVADIRE 65 (154)
Q Consensus 5 P~~kRs~~~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~---------~~~~~~~ii~~ik~ 65 (154)
||-.|...-=..|=-.-.++++++-.+..+...+-+|+..++.+.+. +|..+.+|+.+|+.
T Consensus 90 PpRDRKk~knikh~Gni~~deiv~iar~mr~rS~a~~l~gt~keilgt~~svgc~vDgk~Phdi~~~i~~ 159 (167)
T KOG0886|consen 90 PPRDRKKQKNIKHSGNITFDEIVEIARIMRPRSLARELSGTVKEILGTAQSVGCTVDGKHPHDIIDEINA 159 (167)
T ss_pred CcchhhhhccccccCcccHHHHHHHHHHhhhHhhhhhhhhhHHHHhchhhhcccccCCCChHHHHhhhcC
Confidence 66677666555666667789999999999999999999999988763 46778899988864
No 14
>PRK15039 transcriptional repressor RcnR to maintain nickel and cobalt homeostasis; Provisional
Probab=51.32 E-value=85 Score=22.22 Aligned_cols=66 Identities=17% Similarity=0.093 Sum_probs=39.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHhhH
Q psy8743 44 EQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQVEWNKKEELVAEQALKHLKQF 109 (154)
Q Consensus 44 ~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~vews~k~~~~~e~a~~~lkk~ 109 (154)
..+.+++++|.+-.+|+.-+.+.+.+-+--..+++.-=...++....-++..+...+..++.|++|
T Consensus 23 ~gI~~Miee~~~C~dIl~Ql~Avr~Al~~~~~~vl~~hl~~cv~~~~~~~~~~~~i~el~~~i~~~ 88 (90)
T PRK15039 23 VALKKMLDEPHECAAVLQQIAAIRGAVNGLMREVIKGHLTEHIVHQGDELKREEDLDVVLKVLDSY 88 (90)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHH
Confidence 467899999999999999999888876654444444433333322211122233344555555555
No 15
>TIGR01806 CM_mono2 chorismate mutase, putative. This model represents a clade of probable chorismate mutases from alpha, beta and gamma proteobacteria as well as Mycobacterium tuberculosis and a clade of nematodes. Although the most likely function for the enzymes represented by this model is as a chorismate mutase, in no species are these enzymes the sole chorismate mutase in the genome. Also, in no case are these enzymes located in a region of the genome proximal to any other enzymes involved in chorismate pathways. Although the Pantoea enzyme has been shown to complement a CM-free mutant of E. coli, this was also shown to be the case with isochorismate-pyruvate lyase which only has a secondary (non-physiologically relevant) chorismate mutase activity. This enzyme is believed to be a homodimer and be localized to the periplasm.
Probab=50.82 E-value=73 Score=23.27 Aligned_cols=64 Identities=8% Similarity=0.181 Sum_probs=38.7
Q ss_pred CchhHHHHHHHhhHHHHHHHHHHHHHH----HHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhh
Q psy8743 22 GLADIVKLHMAQASQEAKKELQEQLEE----QISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQV 89 (154)
Q Consensus 22 gL~~l~~~~~~~~~~~~~kel~~~l~~----~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~v 89 (154)
++.+|+++..++..-..+ + +.+.. .|.+-.-.++|+..+.+...++++++ +.+..||..+|+..
T Consensus 5 ~~~eLv~Ll~eR~~la~e--V-a~~K~~~~~pI~Dp~RE~~Vl~~~~~~a~~~gL~~-~~i~~if~~Ii~~S 72 (114)
T TIGR01806 5 QLGQLVDAANERLQLADD--V-AGYKARNNLPIEDSPREEQVLDSLRAQAQSAGLDP-DYVTRFFQAQINAN 72 (114)
T ss_pred hHHHHHHHHHHHHHHHHH--H-HHHHHHCCCCCCChHHHHHHHHHHHHHhHcCCCCH-HHHHHHHHHHHHHH
Confidence 577889998877542111 1 11111 11111123478888888777766655 66688899999875
No 16
>PF02583 Trns_repr_metal: Metal-sensitive transcriptional repressor; InterPro: IPR003735 This entry describes proteins of unknown function.; PDB: 2HH7_A 3AAI_A 4ADZ_B.
Probab=50.52 E-value=67 Score=22.17 Aligned_cols=66 Identities=14% Similarity=0.197 Sum_probs=44.0
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhh-hccchHHHHHHHHHHHHhhH
Q psy8743 44 EQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQV-EWNKKEELVAEQALKHLKQF 109 (154)
Q Consensus 44 ~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~v-ews~k~~~~~e~a~~~lkk~ 109 (154)
..+.+++++|.+-.+|+.-|...+.+-+--...++.-=...+|... +-.+..+...+..++.|++|
T Consensus 19 ~gI~~Miee~~~C~dIl~Qi~Av~~Al~~~~~~vl~~hl~~c~~~~~~~~~~~~~~i~el~~~i~ky 85 (85)
T PF02583_consen 19 RGIERMIEEDRDCEDILQQIAAVRSALDKVGKLVLEDHLEHCLVEAIQDEEDREEAIEELIKLIDKY 85 (85)
T ss_dssp HHHHHHHHTTE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHCCTCCCHHHHHHHHHHHHHH-
T ss_pred HHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhcCcccHHHHHHHHHHHHhcC
Confidence 4578899999999999999999998887666666655555555543 22233444455777777765
No 17
>PF04233 Phage_Mu_F: Phage Mu protein F like protein; InterPro: IPR006528 This domain is found exclusively in phage-related proteins, internally or toward the C terminus. Some of these proteins have been identified as being involved in phage head morphogenesis [, ].
Probab=49.19 E-value=29 Score=24.08 Aligned_cols=27 Identities=19% Similarity=0.432 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHH
Q psy8743 41 ELQEQLEEQISEGASIKDIVADIREIA 67 (154)
Q Consensus 41 el~~~l~~~i~~~~~~~~ii~~ik~~~ 67 (154)
.+++.|.+++..|.+++++...|++..
T Consensus 2 ~i~~~v~~~i~~G~~~~~~~~~l~~~~ 28 (112)
T PF04233_consen 2 RIRQAVTQGIERGKSPQEIAKRLRDRG 28 (112)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 478899999999999999998888873
No 18
>PRK11352 regulator protein FrmR; Provisional
Probab=48.83 E-value=94 Score=21.96 Aligned_cols=67 Identities=9% Similarity=0.196 Sum_probs=43.1
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhhh-ccchHHHHHHHHHHHHhhHh
Q psy8743 44 EQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQVE-WNKKEELVAEQALKHLKQFT 110 (154)
Q Consensus 44 ~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~ve-ws~k~~~~~e~a~~~lkk~~ 110 (154)
..+.++|.+|.+-.+|+.-+.+.+.+-+--...++.-=...++.... -++..+...+..++.|++|.
T Consensus 23 ~gi~~Mie~~~~C~dil~Ql~Avr~Al~~~~~~ile~hl~~cv~~~~~~~~~~~~~i~el~~~i~~~~ 90 (91)
T PRK11352 23 DALERSLEGDAECRAILQQIAAVRGAANGLMAEVLESHIRETFDRNDCYSREVSQSVDDTIELVRAYL 90 (91)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCccchHHHHHHHHHHHHHHh
Confidence 45789999999999999999999888765554444433333333321 12333455556777777764
No 19
>PF00286 Flexi_CP: Viral coat protein; InterPro: IPR000052 Potexviruses and Carlaviruses are plant-infecting viruses whose genome consist of a single-stranded RNA molecule encapsided in a coat protein. The genome of many Potexviruses is known and their coat protein sequence has been shown to be rather well conserved []. The same observation applies to the coat protein of a variety of Carlaviruses whose sequences are related to those of Potexviruses [, ]. The coat proteins of Potexviruses and of Carlaviruses contain from 190 to 300 amino acid residues. The best conserved region of these coat proteins is located in the central part.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 4DOX_B.
Probab=46.04 E-value=85 Score=24.07 Aligned_cols=65 Identities=12% Similarity=0.195 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhhh--------ccchHH-----HHHHHHHHHHhhHhhHHHHhcC
Q psy8743 53 GASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQVE--------WNKKEE-----LVAEQALKHLKQFTPLFGAFTD 118 (154)
Q Consensus 53 ~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~ve--------ws~k~~-----~~~e~a~~~lkk~~pLL~~F~~ 118 (154)
+.+..+-+..|...-....+|...+..++|+-.+.-.+ +.|..+ ...+.+...++..++ |+.||.
T Consensus 3 ~vAt~e~i~~I~~~~~~lgvp~~~~~~~~~~la~~C~d~gSS~~~~~~G~~~~~~g~~~~~la~aiik~~~t-LRqfC~ 80 (140)
T PF00286_consen 3 NVATPEEIAAISAALQGLGVPTESVAKVAWDLARYCADNGSSRYTDPKGTSPFPGGVIRADLAAAIIKEHCT-LRQFCR 80 (140)
T ss_dssp SS--HHHHHHHHHHHHHTT--GGGHHHHHHHHHHHHHHH---TT----SB--SSTT-BHHHHH-HHHHHTTS-HHHHHH
T ss_pred CCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCcccccCCcccCCCCccHHHHHHHHHHccCC-HHHHHH
Confidence 34455556666676677999999999999998885543 223221 124455577888887 777774
No 20
>KOG1992|consensus
Probab=45.83 E-value=36 Score=33.50 Aligned_cols=82 Identities=15% Similarity=0.255 Sum_probs=61.3
Q ss_pred HHHHHHhhcC-chhHHHH-------HHHhhHHHHHHHHHHHHHHHHHcCCCHH----HHHHHHHHHHhhcCCChHHHHHH
Q psy8743 13 YFRTVFEEKG-LADIVKL-------HMAQASQEAKKELQEQLEEQISEGASIK----DIVADIREIANKHCIPDQELIVL 80 (154)
Q Consensus 13 ~~~~~f~~~g-L~~l~~~-------~~~~~~~~~~kel~~~l~~~i~~~~~~~----~ii~~ik~~~~~~~~~~~evi~~ 80 (154)
|..++|++.| |.++.+- .+..-.+-|+.+-.+-.+|.+ +|.+++ .++..+|++.+.+.-....|++.
T Consensus 325 ~y~~~F~~~~vl~~i~e~VvlpN~~lR~eDeElFED~pleYiRRDl-EGsDvdTRRR~a~dlvrgL~~~fe~~vt~v~~~ 403 (960)
T KOG1992|consen 325 HYAELFEGENVLAQICEKVVLPNLILREEDEELFEDNPLEYIRRDL-EGSDVDTRRRAAIDLVRGLCKNFEGQVTGVFSS 403 (960)
T ss_pred hhHhhhcchHHHHHHHHhhcccccccchhhHHHhccCHHHHHHHhc-ccCCcchhHHHHHHHHHHHHHHhcchhHHHHHH
Confidence 4556676644 3333332 234455667777777777877 566666 89999999999999999999999
Q ss_pred HHHHHHh------hhhccchH
Q psy8743 81 IWSTVMA------QVEWNKKE 95 (154)
Q Consensus 81 iw~~lM~------~vews~k~ 95 (154)
...++|+ |.+|.+|+
T Consensus 404 ~v~~~l~~y~~nPS~nWk~kd 424 (960)
T KOG1992|consen 404 EVQRLLDQYSKNPSGNWKKKD 424 (960)
T ss_pred HHHHHHHHhccCCCccccccc
Confidence 9999999 77899985
No 21
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=44.57 E-value=1.1e+02 Score=21.36 Aligned_cols=80 Identities=11% Similarity=0.171 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhhhccchHHHHHHHHHHHHhhHhhHHHHhcC
Q psy8743 39 KKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQVEWNKKEELVAEQALKHLKQFTPLFGAFTD 118 (154)
Q Consensus 39 ~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~vews~k~~~~~e~a~~~lkk~~pLL~~F~~ 118 (154)
+|.+...+.+..+. .+.+|++.-++++... --.++++..+..+.|+. +. +.-..++.||..+|+
T Consensus 2 ~k~i~~~l~ey~~~-~D~~ea~~~l~~L~~~--~~~~~vv~~~i~~~le~---~~----------~~~~~~~~Ll~~L~~ 65 (113)
T smart00544 2 KKKIFLIIEEYLSS-GDTDEAVHCLLELKLP--EQHHEVVKVLLTCALEE---KR----------TYREMYSVLLSRLCQ 65 (113)
T ss_pred hhHHHHHHHHHHHc-CCHHHHHHHHHHhCCC--cchHHHHHHHHHHHHcC---Cc----------cHHHHHHHHHHHHHH
Confidence 56677788888866 4889999888887655 25788999888888876 11 122336667777775
Q ss_pred CCcHHHHHHHHHHHHH
Q psy8743 119 TAPRAELALMLKVQEF 134 (154)
Q Consensus 119 ~~~~~ql~LL~kvQ~~ 134 (154)
.+..+.-.+...+...
T Consensus 66 ~~~~~~~~~~~~f~~~ 81 (113)
T smart00544 66 ANVISTKQFEKGFWRL 81 (113)
T ss_pred cCCcCHHHHHHHHHHH
Confidence 4434444444444444
No 22
>PF08656 DASH_Dad3: DASH complex subunit Dad3; InterPro: IPR013965 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ].
Probab=44.25 E-value=97 Score=21.52 Aligned_cols=60 Identities=17% Similarity=0.279 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhh-hccchH
Q psy8743 36 QEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQV-EWNKKE 95 (154)
Q Consensus 36 ~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~v-ews~k~ 95 (154)
+.--+.+-+++...-..+.|++.+...++++-++..+=..=+-+.||+-+...= +|..++
T Consensus 16 a~~L~~L~~~l~~L~~~~~~~~~lL~~LR~LE~K~glV~TL~KaSVYslvlq~~~~~e~~~ 76 (78)
T PF08656_consen 16 ADNLKTLSDTLKDLNSSNSPSEELLDGLRELERKIGLVYTLFKASVYSLVLQQEIDNEEEQ 76 (78)
T ss_pred HHHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Confidence 344455777777775567889999999999988888777777788887776553 455543
No 23
>PF08102 Antimicrobial_7: Scorpion antimicrobial peptide ; InterPro: IPR012526 This family consists of antimicrobial peptides secreted by scorpions. Novel antimicrobial peptides have been isolated from scorpions, namely the opistoporin [] and the pandinin []. These peptides form essentially helical structures and demonstrate high antimicrobial activity against Gram-negative and Gram-positive bacteria respectively.; GO: 0005576 extracellular region
Probab=43.55 E-value=49 Score=20.44 Aligned_cols=30 Identities=23% Similarity=0.613 Sum_probs=23.8
Q ss_pred HHHHHHhhhh--ccch-HHHHHHHHHHHHhhHh
Q psy8743 81 IWSTVMAQVE--WNKK-EELVAEQALKHLKQFT 110 (154)
Q Consensus 81 iw~~lM~~ve--ws~k-~~~~~e~a~~~lkk~~ 110 (154)
||+.+=+.+. ||+. -+++..+|+...+.|.
T Consensus 3 vwd~IK~~Akk~wnS~~~~~Lk~kalnAaknfV 35 (43)
T PF08102_consen 3 VWDWIKSTAKKAWNSDPVQQLKNKALNAAKNFV 35 (43)
T ss_pred HHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHH
Confidence 7888877773 9998 5788889998888774
No 24
>KOG0898|consensus
Probab=42.48 E-value=37 Score=26.32 Aligned_cols=83 Identities=12% Similarity=0.241 Sum_probs=55.5
Q ss_pred CCCHHHHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHH-HHHHhhcCCChHHHHH------H
Q psy8743 8 KRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADI-REIANKHCIPDQELIV------L 80 (154)
Q Consensus 8 kRs~~~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~i-k~~~~~~~~~~~evi~------~ 80 (154)
|||-.-| .|++-+|++|.+.-..|.-.-+---+...|.+.+ ...+-.+|.-+ |..+.+......|++. +
T Consensus 16 KRTFrkf--tyrGVdld~Lldms~~~~~~l~~ar~rrR~~RGL--~~k~~~liKklrkAkk~A~~~ekpe~VkTHlR~mI 91 (152)
T KOG0898|consen 16 KRTFRKF--TYRGVDLDQLLDMSTEQLVKLFPARQRRRLNRGL--TRKPHSLIKKLRKAKKEAPPMEKPEVVKTHLRNMI 91 (152)
T ss_pred hhhhhhc--cccCCCHHHHhcCCHHHHHHHHHHHHHHHHHccc--ccchHHHHHHHHHHHhhcCcccCcHHHHHHhhcce
Confidence 4554444 3678889999888876666555544555555555 23445666666 5555555666688875 6
Q ss_pred HHHHHHhhh--hccch
Q psy8743 81 IWSTVMAQV--EWNKK 94 (154)
Q Consensus 81 iw~~lM~~v--ews~k 94 (154)
||+.++.++ -.|+|
T Consensus 92 I~PEMvGs~VGVyNGK 107 (152)
T KOG0898|consen 92 IVPEMVGSMVGVYNGK 107 (152)
T ss_pred eeHhhhcceEEEecCc
Confidence 999999998 48887
No 25
>COG4709 Predicted membrane protein [Function unknown]
Probab=40.93 E-value=24 Score=28.62 Aligned_cols=23 Identities=26% Similarity=0.257 Sum_probs=15.5
Q ss_pred CCCCCCCCC--HHHHHHHHhhcCch
Q psy8743 2 EFVPPNKRS--DEYFRTVFEEKGLA 24 (154)
Q Consensus 2 ~ffP~~kRs--~~~~~~~f~~~gL~ 24 (154)
+-+|+..|. ..++++||.++|.+
T Consensus 15 ~~Lp~~~r~e~m~dyeehF~~a~~~ 39 (195)
T COG4709 15 EGLPREERREIMYDYEEHFREAQEA 39 (195)
T ss_pred HhCCHHHHHHHHHHHHHHHHhhhhc
Confidence 346766663 46788888886654
No 26
>KOG3709|consensus
Probab=40.50 E-value=26 Score=32.96 Aligned_cols=27 Identities=19% Similarity=0.550 Sum_probs=21.2
Q ss_pred HHHHHHHHHhHhhhhh-----------hHHHHHHHHhh
Q psy8743 126 ALMLKVQEFCYENMNL-----------MRVFQKIILLF 152 (154)
Q Consensus 126 ~LL~kvQ~~Cye~~~~-----------mk~F~kIl~~L 152 (154)
++|++||.||..|.+. -++|..+|+.+
T Consensus 406 ~~~~riq~~c~sns~~P~~vkV~~IGgd~l~s~vlR~y 443 (778)
T KOG3709|consen 406 HVINRIQNFCHSNSSNPPLVKVGIIGGDKLFSQVLRAY 443 (778)
T ss_pred HHHHHHHHHhhcCCCCCCceEEEEecchHHHHHHHHHH
Confidence 7999999999998642 17888887753
No 27
>PF07739 TipAS: TipAS antibiotic-recognition domain; InterPro: IPR012925 TipAL is a bacterial transcriptional regulator of the MerR family. The tipA gene can be expressed as a long form, TipAL, and a short form, TipAS, which constitutes the C-terminal part of TipAL. TipAS forms the antibiotic-recognition domain []. This domain, which has an alpha-helical globin-like fold, is also found at the C terminus of other MerR family transcription factors, including Mta, a central regulator of multidrug resistance in Bacillus subtilis [], and SkgA from Caulobacter crescentus []. ; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1NY9_A 3HH0_A 3QAO_A.
Probab=40.02 E-value=71 Score=22.25 Aligned_cols=41 Identities=12% Similarity=0.266 Sum_probs=25.1
Q ss_pred HHHHHHhhHhhHHHHhcCCCcHHHHHHHHHHHHHhHhhhhhhHHH
Q psy8743 101 QALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVF 145 (154)
Q Consensus 101 ~a~~~lkk~~pLL~~F~~~~~~~ql~LL~kvQ~~Cye~~~~mk~F 145 (154)
.|-..+++|..++..|+..+ .+++..+-....+|..|...|
T Consensus 58 evq~l~~~~~~~~~~~~~~~----~~~~~~l~~~y~~~~~~~~~~ 98 (118)
T PF07739_consen 58 EVQELAERWMELINQFTGGD----PELLRGLAQMYVEDPRFAAMY 98 (118)
T ss_dssp HHHHHHHHHHHHHHHSS-------HHHHHHHHHHTTSTHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCCC----HHHHHHHHHHHHcCHHHHhhc
Confidence 45556667888888777755 346667777766666665444
No 28
>KOG3831|consensus
Probab=39.16 E-value=1.3e+02 Score=23.87 Aligned_cols=73 Identities=14% Similarity=0.236 Sum_probs=48.6
Q ss_pred CCCCCHHHHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHhhcCCChHHHHHHHHHH
Q psy8743 6 PNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISE-GASIKDIVADIREIANKHCIPDQELIVLIWST 84 (154)
Q Consensus 6 ~~kRs~~~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~-~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~ 84 (154)
.|.|+++..+.-.++.|.-..-=|.-. +-=-+.+++++ +.||..+..-+|..-++.++.+.-...++|+.
T Consensus 28 ~~~~n~~q~r~dlegrgv~~~~ffdia---------idfiildafedlenppaav~av~kn~~ls~s~k~sal~t~~wsi 98 (196)
T KOG3831|consen 28 LNDENEAQLRLDLEGRGVCCMGFFDIA---------IDFIILDAFEDLENPPAAVLAVLKNRFLSDSFKESALATACWSI 98 (196)
T ss_pred cCcccHHHHHHhhccCceeEechHHHH---------HHHHHHHHHHhccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356666666666666665332211110 01113455544 57888999999999999999999999999987
Q ss_pred HHh
Q psy8743 85 VMA 87 (154)
Q Consensus 85 lM~ 87 (154)
+=+
T Consensus 99 ika 101 (196)
T KOG3831|consen 99 IKA 101 (196)
T ss_pred HHH
Confidence 653
No 29
>PF04121 Nup84_Nup100: Nuclear pore protein 84 / 107 ; InterPro: IPR007252 Nup84p forms a complex with five proteins, including Nup120p, Nup85p, Sec13p, and a Sec13p homolog. This Nup84p complex in conjunction with Sec13-type proteins is required for correct nuclear pore biogenesis [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 3CQC_A 3CQG_A 3I4R_A 3IKO_I 3JRO_C.
Probab=37.99 E-value=79 Score=29.86 Aligned_cols=115 Identities=11% Similarity=0.148 Sum_probs=37.8
Q ss_pred HHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhhhcc
Q psy8743 13 YFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQVEWN 92 (154)
Q Consensus 13 ~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~vews 92 (154)
...+++..+|+.++|++|..+-.....-|+=..+...|.+.......+ +++++++++-..++..++.-+++..+-.
T Consensus 379 ~Yi~~L~~~~~~~LIplY~S~L~~~~~~e~ys~~L~~i~d~~~R~~~L----~la~~~gld~~~i~k~~v~~v~~~~~~~ 454 (697)
T PF04121_consen 379 AYISYLRSAGLYELIPLYASFLPEERAIEVYSRFLISITDPEEREKQL----ELAKKLGLDVSAILKRTVERVFEDTESK 454 (697)
T ss_dssp HHHHHHHHTT-GGGHHHHHTTGGGGGG-----------------------------------------------------
T ss_pred HHHHHHHHCCCcccHHHHHccCCHHHHHHHHHHHHHhcCChHHHHHHH----HHHHHcCCCHHHHHHHHHHHHHhccccc
Confidence 346788999999999999999887777788888888886554444444 5667777776666666666555543111
Q ss_pred chHHHHHHHHHHHHhhHhhHHHHhcCCCcHHHHHHHHHHHHHhHhhhhhhHHHH
Q psy8743 93 KKEELVAEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQ 146 (154)
Q Consensus 93 ~k~~~~~e~a~~~lkk~~pLL~~F~~~~~~~ql~LL~kvQ~~Cye~~~~mk~F~ 146 (154)
..+. ....+ .....+ .....+|..|+.. |++...-.++.
T Consensus 455 ~~~~----~~~~~--------~~~~vs--~~D~~lI~sleWL-~~~~~~~eAl~ 493 (697)
T PF04121_consen 455 YPPE----NDISV--------DDDEVS--EEDERLIRSLEWL-FDPEQYPEALK 493 (697)
T ss_dssp ------------------------------HHHHHHHHHHHH-HSGGGHHHHHH
T ss_pred cccC----ccccc--------cCCCCC--HHHHHHHHHHHHH-cCcccHHHHHH
Confidence 1000 00000 122223 3345688889998 88755444443
No 30
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=37.75 E-value=1.2e+02 Score=20.11 Aligned_cols=53 Identities=26% Similarity=0.384 Sum_probs=37.2
Q ss_pred hhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHH
Q psy8743 24 ADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVL 80 (154)
Q Consensus 24 ~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~ 80 (154)
.++++...+... +++...+.+.+.+|.++.+|+..+.+......+++..-..+
T Consensus 9 ~~i~~~~~~~~~----~~~~~~~~~l~~~G~s~~~Il~~l~~~l~~~~~~~~~k~~i 61 (89)
T PF08542_consen 9 EEILESCLNGDF----KEARKKLYELLVEGYSASDILKQLHEVLVESDIPDSQKAEI 61 (89)
T ss_dssp HHHHHHHHHTCH----HHHHHHHHHHHHTT--HHHHHHHHHHHHHTSTSSHHHHHHH
T ss_pred HHHHHHHHhCCH----HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhhccHHHHHHH
Confidence 445555554433 44777788888999999999999999999998886544443
No 31
>PF08651 DASH_Duo1: DASH complex subunit Duo1; InterPro: IPR013960 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ].
Probab=37.50 E-value=1.1e+02 Score=21.11 Aligned_cols=48 Identities=23% Similarity=0.409 Sum_probs=38.1
Q ss_pred HHHHHHhhHhhHHHHhcCCCcHHHHHHHHHHHHHhHhhhhhhHHHHHHH
Q psy8743 101 QALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYENMNLMRVFQKII 149 (154)
Q Consensus 101 ~a~~~lkk~~pLL~~F~~~~~~~ql~LL~kvQ~~Cye~~~~mk~F~kIl 149 (154)
.-+..|++..++++.+..+- +.=..=|.+|+..|.+...++..+.+|+
T Consensus 5 kEL~~Lr~IN~~ie~~~~~L-~~a~~~~~~v~~~~~~t~~LLd~w~~Il 52 (78)
T PF08651_consen 5 KELEQLRKINPVIEGLIETL-RSAKSNMNRVQETVESTNTLLDKWIRIL 52 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55778888888888888877 5556888899999888777777777776
No 32
>PF13324 GCIP: Grap2 and cyclin-D-interacting; PDB: 3AY5_A.
Probab=37.49 E-value=41 Score=27.87 Aligned_cols=87 Identities=13% Similarity=0.195 Sum_probs=42.7
Q ss_pred cCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHH----HhhcCCChHHHHHHHHHHHHhhh--hccch
Q psy8743 21 KGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREI----ANKHCIPDQELIVLIWSTVMAQV--EWNKK 94 (154)
Q Consensus 21 ~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~----~~~~~~~~~evi~~iw~~lM~~v--ews~k 94 (154)
.||-.++-...+.+.-.+++++.....+.+.. ...++..+... ..+..-.-.-..|.||.++=... ..+++
T Consensus 45 ~~l~~~~~~~~~~~G~tL~~~i~~~v~~lv~~---~~~L~~~~~~~~~s~~~~~~~~~~~~tG~VWeaCd~l~~lp~~n~ 121 (275)
T PF13324_consen 45 LGLLSLYHGLPKGQGPTLRKEIRSAVKSLVDS---SIQLVEELVSAYGSSSQSEKNEVLQSTGRVWEACDQLKKLPKDNK 121 (275)
T ss_dssp HHHHHHHTTS-GGG-HHHHHHHHHHHHHHHHH---HHHHHHHHH-------------------HHHHHHHTTTTS-SSHH
T ss_pred HHHHHHHhhCcHhhHHHHHHHHHHHHHHHHHH---HHHHHHHHHHhccCcccCccchhHHHHhHHHHHHHHHHHhhhhhH
Confidence 34444444445667788899999888888833 34444433331 11112233457899999984332 22222
Q ss_pred ----------HHHHHHHHHHHHhhHhh
Q psy8743 95 ----------EELVAEQALKHLKQFTP 111 (154)
Q Consensus 95 ----------~~~~~e~a~~~lkk~~p 111 (154)
-++ ...|++.++.|.|
T Consensus 122 ~av~~~~~~~~~l-vkDa~~El~E~~~ 147 (275)
T PF13324_consen 122 VAVLRRLKQSRDL-VKDALEELEEWDE 147 (275)
T ss_dssp HHHHHHHHHHHHH-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHh
Confidence 233 3478888888876
No 33
>PF07739 TipAS: TipAS antibiotic-recognition domain; InterPro: IPR012925 TipAL is a bacterial transcriptional regulator of the MerR family. The tipA gene can be expressed as a long form, TipAL, and a short form, TipAS, which constitutes the C-terminal part of TipAL. TipAS forms the antibiotic-recognition domain []. This domain, which has an alpha-helical globin-like fold, is also found at the C terminus of other MerR family transcription factors, including Mta, a central regulator of multidrug resistance in Bacillus subtilis [], and SkgA from Caulobacter crescentus []. ; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1NY9_A 3HH0_A 3QAO_A.
Probab=36.55 E-value=1.4e+02 Score=20.61 Aligned_cols=46 Identities=22% Similarity=0.242 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHcCCCHH-----HHHHHHHHHHhhcCCChHHHHHHHHHHH
Q psy8743 40 KELQEQLEEQISEGASIK-----DIVADIREIANKHCIPDQELIVLIWSTV 85 (154)
Q Consensus 40 kel~~~l~~~i~~~~~~~-----~ii~~ik~~~~~~~~~~~evi~~iw~~l 85 (154)
.+|...|...+..|.+|+ +++....+......-.+.++...++..-
T Consensus 38 ~~l~~~l~~~~~~g~~p~s~evq~l~~~~~~~~~~~~~~~~~~~~~l~~~y 88 (118)
T PF07739_consen 38 DELFAELAALMEEGVDPDSPEVQELAERWMELINQFTGGDPELLRGLAQMY 88 (118)
T ss_dssp HHHHHHHHHHHHHT--TT-HHHHHHHHHHHHHHHHSS---HHHHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 345555666666654433 3333333333333333444444444443
No 34
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=36.02 E-value=72 Score=23.26 Aligned_cols=32 Identities=19% Similarity=0.306 Sum_probs=26.9
Q ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCh
Q psy8743 42 LQEQLEEQISEGASIKDIVADIREIANKHCIPD 74 (154)
Q Consensus 42 l~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~ 74 (154)
-...|.++++.|.+.++|+..++... .+.+|+
T Consensus 43 T~~Sl~~A~~~G~~~e~i~~~L~~~S-~~~lP~ 74 (129)
T PF13625_consen 43 TPASLWRAASAGLTAEEIIEFLERYS-KNPLPQ 74 (129)
T ss_pred CHHHHHHHHHcCCCHHHHHHHHHHHc-CCCCCH
Confidence 35679999999999999999998877 566775
No 35
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=36.02 E-value=63 Score=20.51 Aligned_cols=30 Identities=17% Similarity=0.218 Sum_probs=22.7
Q ss_pred HHHHHHHHhhcCchhHHHHHHHhhHHHHHH
Q psy8743 11 DEYFRTVFEEKGLADIVKLHMAQASQEAKK 40 (154)
Q Consensus 11 ~~~~~~~f~~~gL~~l~~~~~~~~~~~~~k 40 (154)
...+.+||+++.|.+++.|+..-..+.+-+
T Consensus 10 ~~~y~~~ft~~El~~i~~FY~Sp~Gqk~~~ 39 (64)
T PF09832_consen 10 APIYAEHFTEEELDAILAFYESPLGQKIVA 39 (64)
T ss_dssp HHHHHHHS-HHHHHHHHHHHHSHHHHHHHH
T ss_pred HHHHHHHCCHHHHHHHHHHHCCHHhHHHHH
Confidence 457899999999999999999665544433
No 36
>cd01046 Rubrerythrin_like rubrerythrin-like, diiron-binding domain. Rubrerythrin-like domain, similar to rubrerythrin, a nonheme iron binding domain found in many air-sensitive bacteria and archaea, and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Rubrerythrin is thought to reduce hydrogen peroxide as part of an oxidative stress protection system. The rubrerythrin protein has two domains, a binuclear metal center located within a four-helix bundle of the rubrerythrin domain, and a rubredoxin domain. The Rubrerythrin-like domains in this CD are singular domains (no C-terminus rubredoxin domain) and are phylogenetically distinct from rubrerythrin domains of rubrerythrin-rubredoxin proteins.
Probab=35.47 E-value=1.7e+02 Score=21.14 Aligned_cols=96 Identities=14% Similarity=0.085 Sum_probs=53.8
Q ss_pred HHHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhh--
Q psy8743 12 EYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQV-- 89 (154)
Q Consensus 12 ~~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~v-- 89 (154)
-.|..+.+..|++.+.+|.+.+..++...- ..+.+.+ .+.+ .++. +.....---+..+... ...+.+..
T Consensus 21 ~~~a~~a~~eG~~~~A~~f~~~a~eE~~HA--~~~~~~l-~~i~-~~~~----~~le~a~~~E~~~~~~-~~~~~~~A~~ 91 (123)
T cd01046 21 LAMARVAQREGYPEVAEELKRIAMEEAEHA--ARFAELL-GKVS-EDTK----ENLEMMLEGEAGANEG-KKDAATEAKA 91 (123)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHHHH--HHHHHHH-hcCc-ccHH----HHHHHHHHhHHHHHHh-HHHHHHHHHH
Confidence 358889999999999999999877766554 2344444 2222 2222 2222222223333333 23444443
Q ss_pred --hccchH--HHHHHHHHHHHhhHhhHHHHh
Q psy8743 90 --EWNKKE--ELVAEQALKHLKQFTPLFGAF 116 (154)
Q Consensus 90 --ews~k~--~~~~e~a~~~lkk~~pLL~~F 116 (154)
+..... ..+.+.-..|.+.|..+|..|
T Consensus 92 egd~~~~~~~~~~~~~E~~H~~~~~~~l~~~ 122 (123)
T cd01046 92 EGLDEAHDFFHEAAKDEARHGKMLKGLLERY 122 (123)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 122221 334556778888888888776
No 37
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=35.41 E-value=72 Score=24.11 Aligned_cols=33 Identities=15% Similarity=0.216 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhh
Q psy8743 37 EAKKELQEQLEEQISEGASIKDIVADIREIANK 69 (154)
Q Consensus 37 ~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~ 69 (154)
.+-+.|...+.+++.+|.+-++|+.+..+.=-+
T Consensus 57 ~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~ 89 (126)
T TIGR03147 57 PIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGD 89 (126)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCC
Confidence 455778889999999999999999887765433
No 38
>PHA03056 putative myristoylated protein; Provisional
Probab=35.31 E-value=1e+02 Score=23.87 Aligned_cols=42 Identities=21% Similarity=0.225 Sum_probs=33.9
Q ss_pred HHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhhh
Q psy8743 46 LEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQVE 90 (154)
Q Consensus 46 l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~ve 90 (154)
|-+....+.+++..++-||-.-..+++|+.+| ||.-+|+--|
T Consensus 70 LCKd~l~~~~p~T~~~~IK~Il~qy~IP~S~V---vw~Pia~~cD 111 (165)
T PHA03056 70 LCKDHAEKSSPETQQMIIKHIYEQYLIPVSEV---LLKPMMSMGD 111 (165)
T ss_pred HHHHHHHcCCchHHHHHHHHHHHHhcCChhHH---HHHHHHhhCC
Confidence 33444456778888888999999999999998 9999998765
No 39
>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=35.26 E-value=1.7e+02 Score=21.14 Aligned_cols=52 Identities=13% Similarity=0.121 Sum_probs=43.0
Q ss_pred chhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCh
Q psy8743 23 LADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPD 74 (154)
Q Consensus 23 L~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~ 74 (154)
|.-++.|.+++.+..=|+++.+.+.+--.+..|...++..++.....++.+.
T Consensus 55 l~Hi~Gyfk~~ls~~EK~~~~~~i~~yr~g~i~l~~~l~~L~~~~~ry~~~Y 106 (117)
T PF08349_consen 55 LQHIFGYFKKKLSSEEKQHFLDLIEDYREGKIPLSVPLTLLKHLARRYPDEY 106 (117)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHCCCHH
Confidence 3457788888888888888888888877777899999999999999888654
No 40
>PF06777 DUF1227: Protein of unknown function (DUF1227); InterPro: IPR010643 This domain represents a conserved region within a number of eukaryotic DNA repair helicases.; GO: 0005634 nucleus
Probab=34.67 E-value=2.1e+02 Score=22.19 Aligned_cols=95 Identities=18% Similarity=0.276 Sum_probs=55.2
Q ss_pred CCCCCCCCCHHHHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChH--HHHH
Q psy8743 2 EFVPPNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQ--ELIV 79 (154)
Q Consensus 2 ~ffP~~kRs~~~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~--evi~ 79 (154)
+..|-|-|..+||-..+ .-+++|.+.+- .....+ .++|......+++. ..+.-. -+..
T Consensus 50 eaVPGnIR~AeHFv~fl-----kR~veylk~rl----------rv~~v~--~e~P~sFL~~~~~~---~~id~k~LrFc~ 109 (146)
T PF06777_consen 50 EAVPGNIRRAEHFVAFL-----KRFVEYLKTRL----------RVQHVI--SESPLSFLQHLKDE---TFIDRKPLRFCS 109 (146)
T ss_pred hcCCchHHhHHHHHHHH-----HHHHHHHHHHh----------hhccee--ecCHHHHHHHHHHH---hCCCcHHHHHHH
Confidence 35799999999999886 46899998763 122222 23555555444443 222211 1122
Q ss_pred HHHHHHHhhhhccchHHHHHHHHHHHHhhHhhHHHHhcCC
Q psy8743 80 LIWSTVMAQVEWNKKEELVAEQALKHLKQFTPLFGAFTDT 119 (154)
Q Consensus 80 ~iw~~lM~~vews~k~~~~~e~a~~~lkk~~pLL~~F~~~ 119 (154)
-=-.++|...+-. +.-.=.++..|-.|+.|++.|.++
T Consensus 110 eRL~sLl~TLei~---d~~df~~L~~Va~FaTLv~tY~~G 146 (146)
T PF06777_consen 110 ERLSSLLRTLEIT---DIDDFSALQLVADFATLVSTYSKG 146 (146)
T ss_pred HHHHHHHHHHCCC---cHhhhhHHHHHHHHHHHHHHhcCC
Confidence 2234555554433 222335778888899999988764
No 41
>PF08318 COG4: COG4 transport protein; InterPro: IPR013167 This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport [].
Probab=34.17 E-value=2.7e+02 Score=23.70 Aligned_cols=85 Identities=15% Similarity=0.197 Sum_probs=55.0
Q ss_pred hcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhhhccchHHHHH
Q psy8743 20 EKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQVEWNKKEELVA 99 (154)
Q Consensus 20 ~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~vews~k~~~~~ 99 (154)
++||+....|....-....++.+.......- + ...++.+++++.-+ -
T Consensus 42 eeGL~~Y~~ylc~~i~~~~r~~~~~~~~~~~--------------~--~~~~~~~~~~lt~L-----------------F 88 (331)
T PF08318_consen 42 EEGLDLYSKYLCDIIAEQSRKLLDSATSGSS--------------D--SRSPVFYADALTKL-----------------F 88 (331)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccccc--------------c--ccccccHHHHHHHH-----------------H
Confidence 5788888888886655555544332211000 0 23444444444433 3
Q ss_pred HHHHHHHhhHhhHHHHhcCCCcHHHHHHHHHHHHHhHhhh
Q psy8743 100 EQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEFCYENM 139 (154)
Q Consensus 100 e~a~~~lkk~~pLL~~F~~~~~~~ql~LL~kvQ~~Cye~~ 139 (154)
+.+...|..+.|+++.+...+ . =+.+|.++|.-|..-.
T Consensus 89 e~ia~ii~~h~~lI~~~yG~~-~-~~~vi~~Lq~E~D~q~ 126 (331)
T PF08318_consen 89 EHIATIIEQHQPLIEKYYGPG-Y-MVYVIEKLQKECDLQA 126 (331)
T ss_pred HHHHHHHHHccHHHHHHcCCc-H-HHHHHHHHHHHHHHHH
Confidence 466778888999999998876 5 5789999999998753
No 42
>PF01320 Colicin_Pyocin: Colicin immunity protein / pyocin immunity protein; InterPro: IPR023802 Bacterial colicin and pyocin immunity proteins [, ] can bind specifically to the DNase-type colicins and pyocins and inhibit their bactericidal activity. The 1.8-angstrom crystal structure of the ImmE7 protein consists of four antiparallel alpha-helices []. Sequence similarities between colicins E2, A and E1 [] are less striking. The colicin E2 (pyocin) immunity protein does not share similarity with either the colicin E3 or cloacin DF13 [] immunity proteins. Pyocin protects a cell that harbours the plasmid ColE2 encoding colicin E2 against colicin E2; it is thus essential both for autonomous replication and colicin E2 immunity []. This entry represents the structural domain of colicin and pyocin immunity proteins.; GO: 0015643 toxin binding, 0030153 bacteriocin immunity; PDB: 1GXH_A 1GXG_A 1MZ8_C 2ERH_A 1ZNV_C 1AYI_A 1UNK_A 2JBG_A 7CEI_A 1CEI_A ....
Probab=32.70 E-value=54 Score=23.15 Aligned_cols=20 Identities=25% Similarity=0.365 Sum_probs=16.6
Q ss_pred CCHHHHHHHHHHHHhhcCCC
Q psy8743 54 ASIKDIVADIREIANKHCIP 73 (154)
Q Consensus 54 ~~~~~ii~~ik~~~~~~~~~ 73 (154)
.+|+.|+..||+.+.++..|
T Consensus 62 dsPegIv~~vKeWRa~nG~p 81 (85)
T PF01320_consen 62 DSPEGIVKEVKEWRASNGKP 81 (85)
T ss_dssp SSHHHHHHHHHHHHHHTT--
T ss_pred CCHHHHHHHHHHHHHHcCCC
Confidence 57999999999999999877
No 43
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=32.49 E-value=85 Score=23.73 Aligned_cols=33 Identities=18% Similarity=0.229 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhh
Q psy8743 37 EAKKELQEQLEEQISEGASIKDIVADIREIANK 69 (154)
Q Consensus 37 ~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~ 69 (154)
.+-+.+...+.+++.+|.+-++|+.+..+.=-+
T Consensus 57 ~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~ 89 (126)
T PRK10144 57 PVAVSMRHQVYSMVAEGKSEVEIIGWMTERYGD 89 (126)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCC
Confidence 455678889999999999999999887765433
No 44
>PF00816 Histone_HNS: H-NS histone family Partial NMR structure.; InterPro: IPR001801 The histone-like nucleoid-structuring (H-NS) protein belongs to a family of bacterial proteins that play a role in the formation of nucleoid structure and affect gene expression under certain conditions [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2LEV_A 1HNS_A 1LR1_B 1HNR_A 1NI8_A 1OV9_A 2JR1_A 3NR7_A 2L93_A 2L92_A.
Probab=31.90 E-value=74 Score=21.91 Aligned_cols=37 Identities=32% Similarity=0.518 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHH
Q psy8743 39 KKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQEL 77 (154)
Q Consensus 39 ~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~ev 77 (154)
.++++..+.+.-.. ...+++..|++++.++.++-.|+
T Consensus 7 ~~~l~~~~~~~~~~--e~~~~~~~i~~~~~~~Gis~~el 43 (93)
T PF00816_consen 7 IKELEKEIEERRKQ--EREEAIAEIRELMAEYGISPEEL 43 (93)
T ss_dssp HHHHHHHHHHHHHH--CCHHHHHHHHHHHHHTT--HHHC
T ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHhCCCHHHh
Confidence 34455555554433 36789999999999999999998
No 45
>COG1528 Ftn Ferritin-like protein [Inorganic ion transport and metabolism]
Probab=31.62 E-value=2.6e+02 Score=22.12 Aligned_cols=26 Identities=23% Similarity=0.225 Sum_probs=23.2
Q ss_pred HHHHHHhhcCchhHHHHHHHhhHHHH
Q psy8743 13 YFRTVFEEKGLADIVKLHMAQASQEA 38 (154)
Q Consensus 13 ~~~~~f~~~gL~~l~~~~~~~~~~~~ 38 (154)
+++.+|...||+-...|.++|+.++.
T Consensus 26 ~maa~~~~~~l~G~A~f~~~qa~EE~ 51 (167)
T COG1528 26 QMAAWCSSESLPGFAKFLRAQAQEEL 51 (167)
T ss_pred HHHHHHhhcCChhHHHHHHHHHHHHH
Confidence 57889999999999999999987666
No 46
>PRK10304 ferritin; Provisional
Probab=30.23 E-value=2.6e+02 Score=21.56 Aligned_cols=30 Identities=7% Similarity=-0.017 Sum_probs=24.5
Q ss_pred HHHHHHhhcCchhHHHHHHHhhHHHHHHHH
Q psy8743 13 YFRTVFEEKGLADIVKLHMAQASQEAKKEL 42 (154)
Q Consensus 13 ~~~~~f~~~gL~~l~~~~~~~~~~~~~kel 42 (154)
.+..+|...||+-+..|.+++..++...-.
T Consensus 26 ~ma~~~~~~gl~g~A~~f~~qs~EE~~HA~ 55 (165)
T PRK10304 26 QMSAWCSYHTFEGAAAFLRRHAQEEMTHMQ 55 (165)
T ss_pred HHHHHHhhCCChHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999988777665543
No 47
>COG4396 Mu-like prophage host-nuclease inhibitor protein Gam [General function prediction only]
Probab=29.50 E-value=35 Score=26.61 Aligned_cols=29 Identities=21% Similarity=0.507 Sum_probs=22.7
Q ss_pred hhHhhHHHHhcCCCcHHHHHHHHHHHHHhHhhh
Q psy8743 107 KQFTPLFGAFTDTAPRAELALMLKVQEFCYENM 139 (154)
Q Consensus 107 kk~~pLL~~F~~~~~~~ql~LL~kvQ~~Cye~~ 139 (154)
..|+|-+.+.|... ..|--.||.||.-|.
T Consensus 50 e~Yapq~~~lk~EI----~~L~k~vq~yCeanr 78 (170)
T COG4396 50 EEYAPQAAPLKAEI----MSLTKRVQAYCEANR 78 (170)
T ss_pred HHhhhhhHHHHHHH----HHHHHHHHHHHHhCH
Confidence 45899988887665 567778999998764
No 48
>PF11220 DUF3015: Protein of unknown function (DUF3015); InterPro: IPR021383 This bacterial family of proteins has no known function.
Probab=29.01 E-value=1.2e+02 Score=23.46 Aligned_cols=49 Identities=12% Similarity=0.192 Sum_probs=35.4
Q ss_pred cCchhHHHHHHH--hhHHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHHhh
Q psy8743 21 KGLADIVKLHMA--QASQEAKKELQEQLEEQISEGA-SIKDIVADIREIANK 69 (154)
Q Consensus 21 ~gL~~l~~~~~~--~~~~~~~kel~~~l~~~i~~~~-~~~~ii~~ik~~~~~ 69 (154)
+-|+.+.....- .....|.+.+++.+.+.+..+. ++++++..|...+..
T Consensus 84 E~L~ala~llgv~~~d~~~f~~~~q~nF~~if~s~~~t~~~v~~~i~~~~~~ 135 (144)
T PF11220_consen 84 EHLDALAELLGVPAEDRAAFGAVLQENFASIFPSESVTSEEVLDNIVAVMAG 135 (144)
T ss_pred chHHHHHHHhCCCHhhHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHhc
Confidence 446666666655 5667788888888888887764 777888877776654
No 49
>PLN03025 replication factor C subunit; Provisional
Probab=28.85 E-value=3.4e+02 Score=22.60 Aligned_cols=33 Identities=9% Similarity=0.257 Sum_probs=21.2
Q ss_pred CCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHh
Q psy8743 54 ASIKDIVADIREIANKHCIPDQELIVLIWSTVMA 87 (154)
Q Consensus 54 ~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~ 87 (154)
.+.+.+...+.++. ....+..+++..++..++.
T Consensus 238 ~~~~~a~~~l~~ll-~~g~~~~~Il~~l~~~~~~ 270 (319)
T PLN03025 238 GKFDDACDGLKQLY-DLGYSPTDIITTLFRVVKN 270 (319)
T ss_pred CCHHHHHHHHHHHH-HcCCCHHHHHHHHHHHHHh
Confidence 55666666666664 4477777777777655543
No 50
>PRK15022 ferritin-like protein; Provisional
Probab=28.85 E-value=2.8e+02 Score=21.64 Aligned_cols=30 Identities=17% Similarity=0.168 Sum_probs=24.3
Q ss_pred HHHHHHhhcCchhHHHHHHHhhHHHHHHHH
Q psy8743 13 YFRTVFEEKGLADIVKLHMAQASQEAKKEL 42 (154)
Q Consensus 13 ~~~~~f~~~gL~~l~~~~~~~~~~~~~kel 42 (154)
.|..+|...||+-+..|.++|..++...-.
T Consensus 26 sMa~~~~~~~L~GfA~ff~~qa~EEreHA~ 55 (167)
T PRK15022 26 HLSEWCSEQSLNGTATFLRAQAQSNVTQMM 55 (167)
T ss_pred HHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 568899999999999999988776655433
No 51
>TIGR01641 phageSPP1_gp7 phage putative head morphogenesis protein, SPP1 gp7 family. This model describes a region of about 110 amino acids found exclusively in phage-related proteins, internally or toward the C-terminus. One member, gp7 of phage SPP1, appears involved in head morphogenesis.
Probab=28.81 E-value=80 Score=22.06 Aligned_cols=25 Identities=12% Similarity=0.343 Sum_probs=22.1
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH
Q psy8743 43 QEQLEEQISEGASIKDIVADIREIA 67 (154)
Q Consensus 43 ~~~l~~~i~~~~~~~~ii~~ik~~~ 67 (154)
+..|.+++..|.++++|...|++..
T Consensus 2 ~~~l~~gi~~G~~~~~iak~i~~~~ 26 (108)
T TIGR01641 2 EDILADGVQRGLGPNELAKRLRKEL 26 (108)
T ss_pred hHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 5678999999999999999988775
No 52
>PF02881 SRP54_N: SRP54-type protein, helical bundle domain; InterPro: IPR013822 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the N-terminal helical bundle domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 1J8M_F 1J8Y_F 2J37_W 2OG2_A 3B9Q_A 2V3C_C 3NDB_B 1ZU5_B 1ZU4_A 1WGW_A ....
Probab=28.55 E-value=90 Score=20.25 Aligned_cols=49 Identities=22% Similarity=0.248 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHH-HHhhcCCCh-HHHHHHHHHH
Q psy8743 36 QEAKKELQEQLEEQISEGASIKDIVADIRE-IANKHCIPD-QELIVLIWST 84 (154)
Q Consensus 36 ~~~~kel~~~l~~~i~~~~~~~~ii~~ik~-~~~~~~~~~-~evi~~iw~~ 84 (154)
+.+-++++..|..+--.=....+|+..|+. ......++. .++..++...
T Consensus 24 ~~~l~ele~~Li~aDVg~~~a~~i~~~ik~~~~~~~~~~~~~~v~~~l~~~ 74 (75)
T PF02881_consen 24 EEFLEELEEALIEADVGVEVAEKIIENIKKKLIKKKGINPREEVKKALKEE 74 (75)
T ss_dssp HHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHHCTTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhcccCCCcHHHHHHHHHHH
Confidence 555666666665544332334477778877 555556655 4555555543
No 53
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=28.45 E-value=1.9e+02 Score=22.28 Aligned_cols=31 Identities=26% Similarity=0.494 Sum_probs=26.0
Q ss_pred cCCCHHHHHHHHHHHHhhcC-CChHHHHHHHH
Q psy8743 52 EGASIKDIVADIREIANKHC-IPDQELIVLIW 82 (154)
Q Consensus 52 ~~~~~~~ii~~ik~~~~~~~-~~~~evi~~iw 82 (154)
.|.+..+++.+||+.+..+. +=+.+++.++.
T Consensus 98 ~g~~~~evv~~in~~q~~~~~~l~~e~aall~ 129 (144)
T PF09999_consen 98 TGIEKQEVVAEINELQEELGGLLDPEAAALLY 129 (144)
T ss_pred cCCCHHHHHHHHHHHHHHHhccCCHHHHHHHH
Confidence 38999999999999999988 67777777664
No 54
>PF09371 Tex_N: Tex-like protein N-terminal domain; InterPro: IPR018974 This presumed domain is found at the N terminus of Q45388 from SWISSPROT. This protein defines a novel family of prokaryotic transcriptional accessory factors []. ; PDB: 2OCE_A 3BZK_A 3BZC_A.
Probab=27.53 E-value=1.2e+02 Score=24.39 Aligned_cols=75 Identities=17% Similarity=0.295 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcC---CCHHHHHHHHHHHHhhcCCChHHHHHHHH
Q psy8743 6 PNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEG---ASIKDIVADIREIANKHCIPDQELIVLIW 82 (154)
Q Consensus 6 ~~kRs~~~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~---~~~~~ii~~ik~~~~~~~~~~~evi~~iw 82 (154)
|.|||...- =++.||..++++.-.+........ +..-++.+ .++++++.-++....+.--.+.+++..+=
T Consensus 100 ~kr~T~A~~---Are~GLeplA~~il~~~~~~~~~~----a~~~v~~~~gv~s~e~al~Ga~dIiAE~is~d~~~r~~lr 172 (193)
T PF09371_consen 100 PKRKTRATI---AREAGLEPLADKILEQPESDPEVE----AKKFVNEEKGVPSVEEALAGAQDIIAERISEDPELREKLR 172 (193)
T ss_dssp ---S-HHHH---HHHTTTHHHHHHHHH-TTS-HHHH----HHTT-BGGGTB-SHHHHHHHHHHHHHHHHTT-HHHHHHHH
T ss_pred cCcCCHHHH---HHHcCCHHHHHHHHcCCccchHHH----HHHHhCcccCCCCHHHHHHhHHHHHHHHHHcCHHHHHHHH
Confidence 355565444 458999999999998766533333 33333322 45667776666666666666666665554
Q ss_pred HHHHh
Q psy8743 83 STVMA 87 (154)
Q Consensus 83 ~~lM~ 87 (154)
..+..
T Consensus 173 ~~~~~ 177 (193)
T PF09371_consen 173 KLLWK 177 (193)
T ss_dssp HHHHH
T ss_pred HHHHh
Confidence 44443
No 55
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=26.92 E-value=3.7e+02 Score=22.27 Aligned_cols=82 Identities=22% Similarity=0.282 Sum_probs=59.3
Q ss_pred CCHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhhh-ccchHHHHHHHHHHHHhhHhhHHHHhcCCCcHHHHHHHHH-H
Q psy8743 54 ASIKDIVADIREIANKHCIPDQELIVLIWSTVMAQVE-WNKKEELVAEQALKHLKQFTPLFGAFTDTAPRAELALMLK-V 131 (154)
Q Consensus 54 ~~~~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~ve-ws~k~~~~~e~a~~~lkk~~pLL~~F~~~~~~~ql~LL~k-v 131 (154)
-=.++||.++-+++..++++..|+=....+.-+++=| -++|. =.++-..+.++..---..|++. -.++..|.+ +
T Consensus 63 qcs~~ii~ell~lm~kn~i~~~didan~vs~fLK~~~~inkKd---YklvfeiiN~~~~e~lnLttek-Inei~eIFk~l 138 (225)
T PHA03074 63 QCSGEIISELLELMNKNQISTKDVDANFVSSFLKAKERINKKD---YKLVFEIINQVKDEKLNLTTEK-INEVVEIFKHL 138 (225)
T ss_pred HhhHHHHHHHHHHHHHccCChhhhhHHHHHHHHHHHHhcCchh---HHHHHHHHHHhhhhcccccHHH-HHHHHHHHHHH
Confidence 3377999999999999999999999999999998864 35553 1244555666665555567776 666655554 5
Q ss_pred HHHhHhhh
Q psy8743 132 QEFCYENM 139 (154)
Q Consensus 132 Q~~Cye~~ 139 (154)
=-+||+|.
T Consensus 139 vfF~qent 146 (225)
T PHA03074 139 VFFCQENT 146 (225)
T ss_pred HHHHhccC
Confidence 56899974
No 56
>PF12554 MOZART1: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR022214 This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 105 amino acids in length. There is a single completely conserved residue L that may be functionally important.
Probab=26.48 E-value=1.4e+02 Score=18.86 Aligned_cols=29 Identities=21% Similarity=0.241 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Q psy8743 39 KKELQEQLEEQISEGASIKDIVADIREIA 67 (154)
Q Consensus 39 ~kel~~~l~~~i~~~~~~~~ii~~ik~~~ 67 (154)
-+|--+..-+.++.|.+|+.+..-||+++
T Consensus 20 d~etL~ici~L~e~GVnPeaLA~vI~elr 48 (48)
T PF12554_consen 20 DRETLSICIELCENGVNPEALAAVIKELR 48 (48)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHHHhC
Confidence 35566777888999999998888888753
No 57
>PF01452 Rota_NSP4: Rotavirus non structural protein; InterPro: IPR002107 This entry contains rotaviral non-structural protein 4 (NSP4) as well as related proteins: NSP5, NS28, and NCVP5. The final steps in the assembly of rotavirus occur in the lumen of the endoplasmic reticulum (ER). Targeting of the immature inner capsid particle (ICP) to this compartment is mediated by the cytoplasmic tail of NSP4, located in the ER membrane [, ].; PDB: 2O1J_D 1G1J_B 1G1I_B 2O1K_B 3MIW_A.
Probab=25.88 E-value=1.1e+02 Score=24.28 Aligned_cols=58 Identities=16% Similarity=0.302 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHhhhh----ccchH--HHHHHHHHHHHhhHhhHHHHhcCCCcHHHHHHHHHHHHH
Q psy8743 76 ELIVLIWSTVMAQVE----WNKKE--ELVAEQALKHLKQFTPLFGAFTDTAPRAELALMLKVQEF 134 (154)
Q Consensus 76 evi~~iw~~lM~~ve----ws~k~--~~~~e~a~~~lkk~~pLL~~F~~~~~~~ql~LL~kvQ~~ 134 (154)
=||..|+.++|+.+- -..++ +...+..++++++=-......++.. =+|++||-.|.+.
T Consensus 70 y~ivTI~N~llklaGykeqittkDeie~qmdrivkemrrQlemidkLTtRE-iEQVeLLkrI~d~ 133 (173)
T PF01452_consen 70 YCIVTIFNTLLKLAGYKEQITTKDEIEKQMDRIVKEMRRQLEMIDKLTTRE-IEQVELLKRIYDM 133 (173)
T ss_dssp -------------------------HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
T ss_pred EEEEeehhhHHHHhcccccCCcHHHHHHHHHHHHHHHHHHHHHHHhhhhhH-HHHHHHHHHHHHH
Confidence 367788999998872 23332 3334456666666677788889988 9999999988654
No 58
>PF10265 DUF2217: Uncharacterized conserved protein (DUF2217); InterPro: IPR019392 This is a family of conserved proteins varying in length from 500-600 residues. Their function is not known.
Probab=25.71 E-value=79 Score=29.32 Aligned_cols=75 Identities=12% Similarity=0.295 Sum_probs=52.9
Q ss_pred CCCHHHHHHHHhhcCchhHHHHHHHhhH-HHHHHHHHHH---------------HHHHHHc-CCCHHHHHHHHHHHHhhc
Q psy8743 8 KRSDEYFRTVFEEKGLADIVKLHMAQAS-QEAKKELQEQ---------------LEEQISE-GASIKDIVADIREIANKH 70 (154)
Q Consensus 8 kRs~~~~~~~f~~~gL~~l~~~~~~~~~-~~~~kel~~~---------------l~~~i~~-~~~~~~ii~~ik~~~~~~ 70 (154)
.+++..|.+.| +++++|.....+ ...+.||.+. |.+++++ +.||..|..-|+-.=.+.
T Consensus 335 ~~~p~~f~~~y-----e~m~~f~~~~~~~~~~~~EL~~rgV~~~~fyDvvlDfillDaFedL~~PPssv~aV~~Nrwls~ 409 (514)
T PF10265_consen 335 DKDPKDFLEAY-----EEMMEFLQDPENWDTMEEELESRGVKCMNFYDVVLDFILLDAFEDLENPPSSVLAVVQNRWLSD 409 (514)
T ss_pred CCCcHHHHHHH-----HHHHHHHcCcccHHHHHHHHhhCCceeeeHHHHHHHHHHHHHHhhhcCCcHHHHHHHHcchhhh
Confidence 34556666665 346666665444 4555555432 5566655 588999999999999999
Q ss_pred CCChHHHHHHHHHHHHh
Q psy8743 71 CIPDQELIVLIWSTVMA 87 (154)
Q Consensus 71 ~~~~~evi~~iw~~lM~ 87 (154)
++.+.-+..+||+.+-.
T Consensus 410 sfKetal~ta~Wsvlka 426 (514)
T PF10265_consen 410 SFKETALATAVWSVLKA 426 (514)
T ss_pred hhhhhccCCcchhhhHH
Confidence 99999999999998853
No 59
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=25.60 E-value=1.1e+02 Score=23.42 Aligned_cols=36 Identities=17% Similarity=0.355 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCC
Q psy8743 37 EAKKELQEQLEEQISEGASIKDIVADIREIANKHCI 72 (154)
Q Consensus 37 ~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~ 72 (154)
..=+++...+.+++.+|.+.++|+.+..+.=-+.-+
T Consensus 57 ~~A~dmR~~I~~~l~~G~s~~eI~~~~v~rYG~~Vl 92 (148)
T PF03918_consen 57 PIARDMRREIREMLAEGKSDEEIIDYFVERYGEFVL 92 (148)
T ss_dssp HHHHHHHHHHHHHHHHT--HHHHHHHHHHHHTTT-E
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCccee
Confidence 445678888999999999999999888776555443
No 60
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=25.43 E-value=1.4e+02 Score=16.80 Aligned_cols=27 Identities=11% Similarity=0.251 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHH
Q psy8743 40 KELQEQLEEQISEGASIKDIVADIREI 66 (154)
Q Consensus 40 kel~~~l~~~i~~~~~~~~ii~~ik~~ 66 (154)
+.+...+...+.++.+.++|+..++..
T Consensus 8 ~~~v~~i~~~l~~~~t~~~I~~~l~~~ 34 (39)
T PF05184_consen 8 KFVVKEIEKLLKNNKTEEEIKKALEKA 34 (39)
T ss_dssp HHHHHHHHHHHHSTCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCccHHHHHHHHHHH
Confidence 456667777887788888888777653
No 61
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=25.26 E-value=2.9e+02 Score=22.36 Aligned_cols=63 Identities=14% Similarity=0.232 Sum_probs=44.0
Q ss_pred CHHHHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHH---------HHHHHhhcCCChHHHH
Q psy8743 10 SDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVAD---------IREIANKHCIPDQELI 78 (154)
Q Consensus 10 s~~~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~---------ik~~~~~~~~~~~evi 78 (154)
|..+|...|++.|.+ +.+|...++-+..++.| .. ...+.++.+|... -+.+++.+.+|..+..
T Consensus 227 S~r~L~r~Fk~~G~T-~~~yi~~~RL~~A~~lL-~~----~~~~~sI~eIA~~~GF~d~s~Fsr~Fkk~~G~sP~~yR 298 (302)
T PRK09685 227 SVRSLYRLFAEQGLV-VAQYIRNRRLDRCADDL-RP----AADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSPGEYR 298 (302)
T ss_pred CHHHHHHHHHHcCCC-HHHHHHHHHHHHHHHHh-hh----hccCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHHHHH
Confidence 678899999998875 78888888887777776 22 1134566666543 4677777777776654
No 62
>KOG2580|consensus
Probab=24.41 E-value=3e+02 Score=25.15 Aligned_cols=23 Identities=22% Similarity=0.593 Sum_probs=18.0
Q ss_pred Hhh-HHHHhcCCCcHHHHHHHHHHHHHhHhh
Q psy8743 109 FTP-LFGAFTDTAPRAELALMLKVQEFCYEN 138 (154)
Q Consensus 109 ~~p-LL~~F~~~~~~~ql~LL~kvQ~~Cye~ 138 (154)
.-| +|++|..++ ++ .++.||+|-
T Consensus 328 IiPnVLeAyvkGD----~e---vLK~wcsea 351 (459)
T KOG2580|consen 328 IIPNVLEAYVKGD----LE---VLKKWCSEA 351 (459)
T ss_pred hhHHHHHHHHhcc----HH---HHHHHHhhh
Confidence 357 899999998 44 568899994
No 63
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=23.37 E-value=4.4e+02 Score=21.95 Aligned_cols=62 Identities=10% Similarity=0.137 Sum_probs=41.1
Q ss_pred CHHHHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHH---------HHHHhhcCCChHHHHHH
Q psy8743 10 SDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADI---------REIANKHCIPDQELIVL 80 (154)
Q Consensus 10 s~~~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~i---------k~~~~~~~~~~~evi~~ 80 (154)
|+.+|...|++.|.+ ..+|....+-+.+++-+ ..+.++.+|...+ +.+++...+|..+....
T Consensus 163 S~s~l~R~FK~~G~T-~~eyl~~~Rl~~A~~LL--------~~~~sI~eIA~~~GF~s~S~Fsr~FKr~~G~TPs~yRk~ 233 (253)
T PRK09940 163 SESLLKKKLKQEQTT-FSQILLDARMQHAKNLI--------RVEGSVNKIAEQCGYASTSYFIYAFRKHFGNSPKRVSKE 233 (253)
T ss_pred CHHHHHHHHHHcCCC-HHHHHHHHHHHHHHHHH--------ccCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHHHHHHH
Confidence 677899999998865 67888766655554422 2245777776543 66677777777665543
No 64
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=23.10 E-value=4.5e+02 Score=22.50 Aligned_cols=67 Identities=10% Similarity=0.152 Sum_probs=43.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHH----HHHHHHHHHhhhhccchHHHHHHHHHHHHhhHhhHHHHh
Q psy8743 43 QEQLEEQISEGASIKDIVADIREIANKHCIPDQEL----IVLIWSTVMAQVEWNKKEELVAEQALKHLKQFTPLFGAF 116 (154)
Q Consensus 43 ~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~ev----i~~iw~~lM~~vews~k~~~~~e~a~~~lkk~~pLL~~F 116 (154)
...|..+.. +.+.+.++..++.+.. .+++..=+ ||.....+=+ + + .+.+...|...|++|..++..=
T Consensus 8 ~k~L~k~~~-~~~~~~~l~~L~~L~~-~~~t~~lL~~T~IG~~Vn~lrk---h-~-~~~I~~lAk~li~~WK~~v~~~ 78 (299)
T TIGR01385 8 AKALDKNKS-SKNVEQCLDILHQLKE-FPPTEELLQETKVGVKVNKLRK---H-P-NEDISKLAKKIIKSWKKVVDKN 78 (299)
T ss_pred HHHhhhhcc-CCCHHHHHHHHHHHhc-CCCcHHHHhhCchhHHHHHHHc---C-C-cHHHHHHHHHHHHHHHHHHhhh
Confidence 334555544 5778889999999986 77776433 2333222222 1 1 3457889999999999999874
No 65
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=22.99 E-value=2e+02 Score=18.05 Aligned_cols=31 Identities=10% Similarity=0.238 Sum_probs=18.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHhhcC-CChHHHHHHH
Q psy8743 44 EQLEEQISEGASIKDIVADIREIANKHC-IPDQELIVLI 81 (154)
Q Consensus 44 ~~l~~~i~~~~~~~~ii~~ik~~~~~~~-~~~~evi~~i 81 (154)
.++.+.++.|.++++|. ..++ ++..++-.++
T Consensus 22 ~~i~~~~~~G~s~eeI~-------~~yp~Lt~~~i~aAl 53 (56)
T PF04255_consen 22 RDILDLLAAGESPEEIA-------EDYPSLTLEDIRAAL 53 (56)
T ss_dssp HHHHHHHHTT--HHHHH-------HHSTT--HHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHH-------HHCCCCCHHHHHHHH
Confidence 45666778888888887 3466 7777776665
No 66
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=22.98 E-value=3.1e+02 Score=23.13 Aligned_cols=62 Identities=10% Similarity=0.083 Sum_probs=36.1
Q ss_pred CHHHHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHH---------HHHHHhhcCCChHHHHH
Q psy8743 10 SDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVAD---------IREIANKHCIPDQELIV 79 (154)
Q Consensus 10 s~~~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~---------ik~~~~~~~~~~~evi~ 79 (154)
|..+|..+|++.|.+. -+|+...+-...++-|. ..+.++.+|... .+.+++-..+|..+...
T Consensus 210 S~stl~R~Fk~~g~s~-~~~~~~~Rl~~A~~lL~-------~~~~sI~~IA~~~GY~s~S~Fsr~FK~~~G~TP~~yr~ 280 (291)
T PRK15186 210 SCSTLKRKLKQENTSF-SEVYLNARMNKATKLLR-------NSEYNITRVAYMCGYDSASYFTCVFKKHFKTTPSEFLA 280 (291)
T ss_pred CHHHHHHHHHHcCCCH-HHHHHHHHHHHHHHHHH-------cCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHHHHHH
Confidence 6788999999987644 44554333333333332 234566655543 46666667777666554
No 67
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=22.73 E-value=3.4e+02 Score=20.51 Aligned_cols=66 Identities=15% Similarity=0.099 Sum_probs=41.1
Q ss_pred HHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHH
Q psy8743 13 YFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVL 80 (154)
Q Consensus 13 ~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~ 80 (154)
.++...++-.|.+|-+.+.|-....-++.-. ....-.+.....+.+..|++++.++.++-.|+.+.
T Consensus 13 ~lra~~re~~~e~Lee~~ekl~~vv~er~~~--~~~~~~~~~er~~~l~~i~~~~~~~Git~eeL~~~ 78 (134)
T PRK10328 13 TLRAMAREFSIDVLEEMLEKFRVVTKERREE--EEQQQRELAERQEKINTWLELMKADGINPEELLGN 78 (134)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHhhh
Confidence 4556666677777777777654433322221 11111222336688999999999999999999653
No 68
>PRK08402 replication factor A; Reviewed
Probab=22.54 E-value=2.6e+02 Score=24.55 Aligned_cols=42 Identities=31% Similarity=0.520 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCChHHHHHHH
Q psy8743 38 AKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLI 81 (154)
Q Consensus 38 ~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~~~~~~evi~~i 81 (154)
.+.++.+.|.+.. |.+.++|-..|+++...+++++.+-+..|
T Consensus 5 ~~~~i~e~~~~~~--~vs~eei~~~l~~lv~~~~~~e~~A~~~i 46 (355)
T PRK08402 5 TKEEIIERIERKT--GMSREEIEEKIREIMKEEGISEHAAALLL 46 (355)
T ss_pred cHHHHHHHHHHhh--CCCHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 3567778888885 79999999999999999998888776665
No 69
>PF01372 Melittin: Melittin; InterPro: IPR002116 Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an Arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Api m 3. Melittin is the principal protein component of the venom of the honeybee, Apis mellifera. It inhibits protein kinase C, Ca2+/calmodulin-dependent protein kinase II, myosin light chain kinase and Na+/K+-ATPase (synaptosomal membrane) and is a cell membrane lytic factor. Melittin is a small peptide with no disulphide bridge; the N-terminal part of the molecule is predominantly hydrophobic and the C-terminal part is hydrophilic and strongly basic. The molecular mechanisms underlying the various effects of melittin on membranes have not been completely defined and much of the evidence indicates that different molecular mechanisms may underlie different actions of the peptide []. Extensive work with melittin has shown that the venom has multiple effects, probably, as a result of its interaction with negatively changed phospholipids. It inhibits well known transport pumps such as the Na+-K+-ATPase and the H+-K+-ATPase. Melittin increases the permeability of cell membranes to ions, particularly Na+ and indirectly Ca2+, because of the Na+-Ca2+-exchange. This effect results in marked morphological and functional changes, particularly in excitable tissues such as cardiac myocytes. In some other tissues, e.g., cornea, not only Na+ but Cl- permeability is also increased by melittin. Similar effects to melittin on H+-K+-ATPase have been found with the synthetic amphipathic polypeptide Trp-3 []. The study of melittin in model membranes has been useful for the development of methodology for determination of membrane protein structures. A molecular dynamics simulation of melittin in a hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer was carried out. The effect of melittin on the surrounding membrane was localised to its immediate vicinity, and its asymmetry with respect to the two layers may be a result of the fact that it is not fully transmembranal. Melittin's hydrophilic C terminus anchors it at the extracellular interface, leaving the N terminus "loose" in the lower layer of the membrane [].; GO: 0004860 protein kinase inhibitor activity, 0005576 extracellular region; PDB: 3QRX_B 2MLT_A 1BH1_A.
Probab=22.33 E-value=56 Score=18.04 Aligned_cols=15 Identities=13% Similarity=0.297 Sum_probs=11.6
Q ss_pred hcCchhHHHHHHHhh
Q psy8743 20 EKGLADIVKLHMAQA 34 (154)
Q Consensus 20 ~~gL~~l~~~~~~~~ 34 (154)
+.||+.++.|.+.++
T Consensus 10 a~~LP~lISWIK~kr 24 (26)
T PF01372_consen 10 ATGLPTLISWIKNKR 24 (26)
T ss_dssp HTHHHHHHHHHHHHH
T ss_pred HhcChHHHHHHHHHh
Confidence 468889999988664
No 70
>KOG1900|consensus
Probab=22.16 E-value=6.8e+02 Score=26.14 Aligned_cols=109 Identities=11% Similarity=0.167 Sum_probs=67.0
Q ss_pred hHHHHHHHhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHh------------------------hcCCChHHHHHH
Q psy8743 25 DIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIAN------------------------KHCIPDQELIVL 80 (154)
Q Consensus 25 ~l~~~~~~~~~~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~------------------------~~~~~~~evi~~ 80 (154)
.+.+...|-.-+...+++..+++++-.+....++++.++..... =.+..|+.+|..
T Consensus 1071 f~~~i~dklevA~iQ~dvl~a~~d~~~~~~~~~el~k~Ld~el~~~t~Lyn~fAdPf~l~Ei~L~I~~~a~y~D~~~I~~ 1150 (1311)
T KOG1900|consen 1071 FLIEIEDKLEVASIQDDVLVAMQDDRIDASAANELVKELDGELLSLTQLYNEFADPFDLWEICLSIFKCADYSDPSLIQE 1150 (1311)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHhhcchhHHHHHHHHhccccccHHHHHHhccCcchHHHHHHHHhhhccCCChHHHHH
Confidence 34445555566666777777777665554555566655544322 256779999999
Q ss_pred HHHHHHhhhh--ccchHHHHHHHHHHHHhhHhhHHHHhcCCCcHHHH-----HHHHHHHHHhHh
Q psy8743 81 IWSTVMAQVE--WNKKEELVAEQALKHLKQFTPLFGAFTDTAPRAEL-----ALMLKVQEFCYE 137 (154)
Q Consensus 81 iw~~lM~~ve--ws~k~~~~~e~a~~~lkk~~pLL~~F~~~~~~~ql-----~LL~kvQ~~Cye 137 (154)
.|.-+++++- -+..+ +--.+.+.+..+++..+..++...+. .|..++-++-++
T Consensus 1151 ~W~~li~s~~~~~~~~~----~~~~~~~~~I~~~~~~~~~~~~~~~~~F~i~~l~~~~~~~~~d 1210 (1311)
T KOG1900|consen 1151 TWARLIDSALSQPGITS----EVLKRLGSKISNTLKVYGKTDVDSEFVFPIAELESKVCELFFD 1210 (1311)
T ss_pred HHHHHHHHHHhcCCCcH----HHHhhHHHHHhhhhhhhcCCcccCchhhhHHHHHHHHHHHhcc
Confidence 9999999982 22223 34456677778888888777633332 244444444444
No 71
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=21.98 E-value=2.8e+02 Score=19.26 Aligned_cols=61 Identities=16% Similarity=0.426 Sum_probs=35.4
Q ss_pred CHHHHHHHHhhcC-----chhHHHHHHHhhH--------HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhc
Q psy8743 10 SDEYFRTVFEEKG-----LADIVKLHMAQAS--------QEAKKELQEQLEEQISEGASIKDIVADIREIANKH 70 (154)
Q Consensus 10 s~~~~~~~f~~~g-----L~~l~~~~~~~~~--------~~~~kel~~~l~~~i~~~~~~~~ii~~ik~~~~~~ 70 (154)
+++.+.+..+..| +++|+++..+++. ..-++++...+......|.+.++++..+++.+.+-
T Consensus 10 n~e~v~~~l~~R~~~~~~vd~i~~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i 83 (108)
T PF02403_consen 10 NPEEVRENLKKRGGDEEDVDEIIELDQERRELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEI 83 (108)
T ss_dssp HHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCHhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHH
Confidence 3566677777775 4556666655532 22334445555555555666777777777665543
No 72
>PF03271 EB1: EB1-like C-terminal motif; InterPro: IPR004953 A group of microtubule-associated proteins called +TIPs (plus end tracking proteins), including EB1 (end-binding protein 1) family proteins, label growing microtubules ends specifically in diverse organisms and are implicated in spindle dynamics, chromosome segregation, and directing microtubules toward cortical sites. EB1 members have a bipartite composition: the N-terminal CH domain (IPR001715 from INTERPRO) mediates microtubule plus end localization and a C-terminal cargo binding domain (EB1-C) that captures cell polarity determinants. The EB1-C domain comprises a unique EB1-like sequence motif that acts as a binding site for other +TIP proteins. It interacts with the carboxy terminus of the adenomatous polyposis coli (APC) tumor suppressor, a well conserved +TIP phosphoprotein with a pivotal function in cell cycle regulation. Another binding partner of the EB1-C domain is the well conserved +TIP protein dynactin, a component of the large cytoplasmic dynein/dynactin complex [, , ]. The ~80-residue EB1-C domain starts with a long smoothly curved helix (alpha1), which is followed by a hairpin connection leading to a short second helix (alpha2) running antiparallel to alpha1. The two parallel alpha1 helices of the EB1-C domain dimer wrap around each other in a slightly left-handed supercoil. The two alpha2 helices run antiparallel to helices alpha1 and form a similar fork in the opposite orientation and rotated by 90 degrees. As a result, two helical segments from each monomer form a four-helix bundle. The side chain forming the hydrophobic core of this bundle are highly conserved [, , ]. Some protein known to contain an EB1-C domain are listed below: Yeast protein BIM1. Fission yeast microtubule integrity protein mal3. Vertebrate microtubule-associated protein RP/EB family member 1 (EB1). Vertebrate microtubule-associated protein RP/EB family member 2 (EB2 or RP1). Vertebrate microtubule-associated protein RP/EB family member 3 (EBF3). ; GO: 0008017 microtubule binding; PDB: 3TQ7_B 4E61_B 2HKQ_A 1YIG_B 3GJO_B 2HL5_B 1YIB_A 1WU9_A 1TXQ_B.
Probab=21.85 E-value=1.1e+02 Score=18.71 Aligned_cols=28 Identities=18% Similarity=0.351 Sum_probs=18.5
Q ss_pred HHHHHHHHhHhh-h-hh--hHHHHHHHHhhcC
Q psy8743 127 LMLKVQEFCYEN-M-NL--MRVFQKIILLFYK 154 (154)
Q Consensus 127 LL~kvQ~~Cye~-~-~~--mk~F~kIl~~LY~ 154 (154)
=|..|+..|.+. . .- ..+-.+|..+||.
T Consensus 12 KLR~IE~l~q~~~~~~~~~~~~~~~I~~ILYa 43 (43)
T PF03271_consen 12 KLRDIEILCQEANESENEPKDLIKKIQEILYA 43 (43)
T ss_dssp HHHHHHHHHHHHCHHCCTC--HHHHHHHHHHC
T ss_pred HHHHHHHHHhhccccCcchhHHHHHHHHHhcC
Confidence 367788899882 2 21 1255899999985
No 73
>PF06109 HlyE: Haemolysin E (HlyE); InterPro: IPR010356 This family consists of several enterobacterial haemolysin (HlyE) proteins. Haemolysin E (HlyE) is a novel pore-forming toxin of Escherichia coli, Salmonella typhi, and Shigella flexneri. HlyE is unrelated to the well characterised pore-forming E. coli haemolysins of the RTX family, haemolysin A (HlyA), and the enterohaemolysin encoded by the plasmid borne ehxA gene of E. coli 0157. However, it is evident that expression of HlyE in the absence of the RTX toxins is sufficient to give a haemolytic phenotype in E. coli. HlyE is a protein of 34 kDa that is expressed during anaerobic growth of E. coli. Anaerobic expression is controlled by the transcription factor, FNR, such that, upon ingestion and entry into the anaerobic mammalian intestine, HlyE is produced and may then contribute to the colonisation of the host [].; PDB: 2WCD_P 1QOY_A.
Probab=21.68 E-value=2.9e+02 Score=22.91 Aligned_cols=68 Identities=19% Similarity=0.368 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHhhcCCChHHHHHHHHHHHHhhh-----------hccchHHHHHHHHHHHHhhHhhHHHHhcCCCcHHHH
Q psy8743 57 KDIVADIREIANKHCIPDQELIVLIWSTVMAQV-----------EWNKKEELVAEQALKHLKQFTPLFGAFTDTAPRAEL 125 (154)
Q Consensus 57 ~~ii~~ik~~~~~~~~~~~evi~~iw~~lM~~v-----------ews~k~~~~~e~a~~~lkk~~pLL~~F~~~~~~~ql 125 (154)
++-|.++-.++.+++-+-.-++|-|=+-+|++- +|-+. +...+..|-.||..|-.....+|-
T Consensus 38 ~~tikelsrfk~eysq~as~lvg~ik~llm~sqd~yfeatq~vyewcgv-------~tqll~ay~~lf~ey~ekkasaqk 110 (299)
T PF06109_consen 38 NDTIKELSRFKQEYSQSASTLVGDIKSLLMNSQDRYFEATQTVYEWCGV-------TTQLLTAYISLFNEYNEKKASAQK 110 (299)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHTSS--TTTHHHHH
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcchHhHHHHHHHHHHHHhH-------HHHHHHHHHHHHHHhhhhhhhhcc
Confidence 344444555555666555666666666666653 24433 233344555666555543325666
Q ss_pred HHHHHH
Q psy8743 126 ALMLKV 131 (154)
Q Consensus 126 ~LL~kv 131 (154)
.+|.||
T Consensus 111 ~ilikv 116 (299)
T PF06109_consen 111 DILIKV 116 (299)
T ss_dssp HHHHHH
T ss_pred ceehhh
Confidence 666555
No 74
>PF00745 GlutR_dimer: Glutamyl-tRNAGlu reductase, dimerisation domain; InterPro: IPR015896 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents the helical dimerisation domain of glutamyl-tRNA reductase (1.2.1.70 from EC) []. This enzyme reduces glutamyl-tRNA to glutamate-1-semialdehyde during the first stage of tetrapyrrole biosynthesis by the C5 pathway [, ]. The enzyme requires NADPH as a cofactor.; GO: 0008883 glutamyl-tRNA reductase activity, 0050661 NADP binding, 0033014 tetrapyrrole biosynthetic process, 0055114 oxidation-reduction process; PDB: 1GPJ_A.
Probab=21.10 E-value=92 Score=21.21 Aligned_cols=36 Identities=17% Similarity=0.282 Sum_probs=16.3
Q ss_pred HHHHHHhhcCchhHHHHHHHhhHHHHHHHHHHHHHH
Q psy8743 13 YFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEE 48 (154)
Q Consensus 13 ~~~~~f~~~gL~~l~~~~~~~~~~~~~kel~~~l~~ 48 (154)
.|...++.....+++.=++.+...-...|++..+.+
T Consensus 13 ~f~~w~~~~~~~p~I~~l~~~~e~i~~~el~~~~~~ 48 (101)
T PF00745_consen 13 EFMRWLKSRKVDPVIKALREKAEEIRDEELERALKK 48 (101)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-
T ss_pred HHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 344444444444444444444444444444444444
No 75
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=20.25 E-value=1.8e+02 Score=16.31 Aligned_cols=28 Identities=18% Similarity=0.160 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHhhcCCChHHHHHHHHH
Q psy8743 56 IKDIVADIREIANKHCIPDQELIVLIWS 83 (154)
Q Consensus 56 ~~~ii~~ik~~~~~~~~~~~evi~~iw~ 83 (154)
+++....++....+.++|-.++|..+..
T Consensus 7 ~~~~~~~l~~~a~~~g~s~s~~ir~ai~ 34 (39)
T PF01402_consen 7 PDELYERLDELAKELGRSRSELIREAIR 34 (39)
T ss_dssp EHHHHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 3567778888888888888888776544
Done!