Query 040904
Match_columns 92
No_of_seqs 121 out of 599
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 12:57:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040904.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040904hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03090 auxin-responsive fami 100.0 1.2E-42 2.7E-47 236.7 9.9 90 2-91 14-103 (104)
2 PLN03220 uncharacterized prote 100.0 1.5E-37 3.2E-42 211.9 9.8 87 2-90 11-102 (105)
3 PF02519 Auxin_inducible: Auxi 100.0 3.3E-37 7.2E-42 207.8 8.9 67 25-91 33-99 (100)
4 PLN03219 uncharacterized prote 100.0 3.9E-36 8.5E-41 205.7 9.8 89 2-90 10-104 (108)
5 PF02214 BTB_2: BTB/POZ domain 89.3 0.44 9.6E-06 30.2 2.8 56 34-91 2-60 (94)
6 PRK02899 adaptor protein; Prov 88.2 0.45 9.8E-06 35.3 2.6 25 53-77 38-62 (197)
7 PRK02315 adaptor protein; Prov 84.7 0.76 1.7E-05 34.7 2.3 25 53-77 38-62 (233)
8 PF05389 MecA: Negative regula 81.4 0.47 1E-05 35.0 0.0 25 53-77 38-62 (220)
9 smart00666 PB1 PB1 domain. Pho 78.5 6.3 0.00014 24.1 4.5 49 36-89 7-66 (81)
10 cd05992 PB1 The PB1 domain is 75.2 11 0.00024 22.8 4.9 51 35-89 5-66 (81)
11 cd06410 PB1_UP2 Uncharacterize 66.8 16 0.00034 24.3 4.5 45 34-82 17-74 (97)
12 PF02100 ODC_AZ: Ornithine dec 66.8 12 0.00027 25.2 4.1 51 38-89 21-75 (108)
13 PRK10308 3-methyl-adenine DNA 63.1 23 0.0005 27.4 5.5 63 30-92 45-122 (283)
14 PF00651 BTB: BTB/POZ domain; 59.6 31 0.00068 21.3 4.8 54 33-91 13-71 (111)
15 cd06398 PB1_Joka2 The PB1 doma 56.8 49 0.0011 21.6 5.5 52 37-88 7-71 (91)
16 PF00564 PB1: PB1 domain; Int 54.1 36 0.00077 20.6 4.2 43 36-82 7-61 (84)
17 cd06407 PB1_NLP A PB1 domain i 45.1 60 0.0013 20.8 4.4 47 35-85 5-63 (82)
18 PF11834 DUF3354: Domain of un 44.3 20 0.00044 22.6 2.0 23 42-70 20-42 (69)
19 PF02209 VHP: Villin headpiece 43.3 10 0.00023 21.2 0.5 18 50-67 1-18 (36)
20 PF12058 DUF3539: Protein of u 42.4 4.2 9.2E-05 27.2 -1.4 9 49-57 4-12 (88)
21 cd06396 PB1_NBR1 The PB1 domai 41.6 89 0.0019 20.3 4.8 46 38-85 8-62 (81)
22 smart00153 VHP Villin headpiec 41.3 14 0.0003 20.6 0.8 18 50-67 1-18 (36)
23 PRK02797 4-alpha-L-fucosyltran 36.4 1.2E+02 0.0025 24.7 5.6 44 27-70 141-206 (322)
24 TIGR03687 pupylate_cterm ubiqu 36.3 19 0.0004 20.1 0.8 19 56-74 12-32 (33)
25 PLN02752 [acyl-carrier protein 35.2 36 0.00077 26.4 2.5 49 22-70 30-78 (343)
26 TIGR03793 TOMM_pelo TOMM prope 34.9 69 0.0015 20.5 3.4 27 51-77 14-44 (77)
27 cd06397 PB1_UP1 Uncharacterize 32.0 1.5E+02 0.0033 19.5 5.4 46 36-85 6-62 (82)
28 PF14317 YcxB: YcxB-like prote 31.4 97 0.0021 17.0 3.8 32 29-61 28-59 (62)
29 COG4862 MecA Negative regulato 31.0 34 0.00074 26.4 1.8 27 52-78 37-63 (224)
30 COG5431 Uncharacterized metal- 29.9 64 0.0014 22.6 2.8 28 30-58 32-59 (117)
31 PF07429 Glyco_transf_56: 4-al 28.3 1.7E+02 0.0038 24.1 5.4 43 28-70 181-245 (360)
32 TIGR02529 EutJ ethanolamine ut 27.7 79 0.0017 23.5 3.2 40 42-82 33-73 (239)
33 PF05194 UreE_C: UreE urease a 26.9 1.1E+02 0.0025 19.2 3.5 27 31-63 25-51 (87)
34 cd01406 SIR2-like Sir2-like: P 26.8 81 0.0018 23.0 3.1 36 31-72 1-36 (242)
35 COG1759 5-formaminoimidazole-4 26.7 31 0.00067 28.4 0.9 22 27-48 89-112 (361)
36 COG2139 RPL21A Ribosomal prote 24.8 62 0.0013 22.1 2.0 21 33-53 73-93 (98)
37 PF06344 Parecho_VpG: Parechov 24.7 33 0.00072 17.0 0.5 12 24-35 7-18 (20)
38 KOG1748 Acyl carrier protein/N 24.5 48 0.001 23.6 1.5 30 60-89 94-125 (131)
39 PF07369 DUF1488: Protein of u 24.3 1.3E+02 0.0029 18.5 3.3 20 32-51 18-37 (83)
40 cd04751 Commd3 COMM_Domain con 24.2 82 0.0018 20.5 2.4 19 73-91 65-83 (95)
41 PF12062 HSNSD: heparan sulfat 23.8 69 0.0015 27.4 2.5 40 30-69 96-141 (487)
42 cd06401 PB1_TFG The PB1 domain 23.7 1.9E+02 0.0042 18.9 4.1 42 38-82 8-63 (81)
43 PF00356 LacI: Bacterial regul 23.5 1E+02 0.0022 17.6 2.5 20 53-72 27-46 (46)
44 cd01615 CIDE_N CIDE_N domain, 23.3 1.2E+02 0.0026 19.7 3.0 34 40-79 12-45 (78)
45 PF08861 DUF1828: Domain of un 23.0 2.1E+02 0.0045 18.1 4.3 40 53-92 44-84 (90)
46 cd06279 PBP1_LacI_like_3 Ligan 21.4 1.1E+02 0.0023 22.1 2.8 26 45-70 5-36 (283)
47 cd06399 PB1_P40 The PB1 domain 21.3 1.2E+02 0.0026 20.5 2.8 28 42-69 16-43 (92)
48 COG0763 LpxB Lipid A disacchar 21.3 45 0.00098 27.5 0.9 32 42-73 152-188 (381)
49 PF11876 DUF3396: Protein of u 20.8 95 0.0021 23.1 2.5 31 41-71 24-56 (208)
50 PF06307 Herpes_IR6: Herpesvir 20.7 60 0.0013 24.8 1.4 41 1-47 15-55 (214)
51 PF08740 BCS1_N: BCS1 N termin 20.7 2E+02 0.0043 20.0 4.0 35 42-76 128-162 (187)
52 PF08948 DUF1859: Domain of un 20.7 37 0.0008 23.8 0.2 28 29-57 86-123 (126)
53 KOG2813 Predicted molecular ch 20.7 1.2E+02 0.0027 25.1 3.3 55 33-88 274-328 (406)
54 PRK13277 5-formaminoimidazole- 20.5 34 0.00074 28.0 0.1 25 27-53 89-115 (366)
55 PF04341 DUF485: Protein of un 20.5 77 0.0017 20.4 1.7 12 51-62 2-13 (91)
56 cd04395 RhoGAP_ARHGAP21 RhoGAP 20.4 2.2E+02 0.0048 20.3 4.3 38 53-90 18-55 (196)
No 1
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=1.2e-42 Score=236.65 Aligned_cols=90 Identities=59% Similarity=1.134 Sum_probs=85.6
Q ss_pred hhHHHHhhhccCCCCccCCCCCCCCCCCCCeEEEEEcCCceEEEEeccCCCcHHHHHHHHHHHHhcCccCCCcEEecCcH
Q 040904 2 AIQEIFKQCSSFGKKCSCDQDGHPNDVPKGHCVVYVGENRSRYIIPITWLNHPKFKNLLEKAAEEYGYKHDLGIILPCDE 81 (92)
Q Consensus 2 ~~k~~lkr~~s~~~~~~~~~~~~~~~vpkG~~~VyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~g~L~IPC~~ 81 (92)
.+|++||||+|.+++++++....|.+|||||||||||++++||+||++|||||+|++||++|||||||+|+|+|+|||++
T Consensus 14 ~~kq~l~r~~s~~~~~~~~~~~~~~~vpkG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfGf~~~G~L~IPC~~ 93 (104)
T PLN03090 14 MLKQILKRCSSLGKKQGYDEDGLPLDVPKGHFPVYVGENRSRYIVPISFLTHPEFQSLLQQAEEEFGFDHDMGLTIPCEE 93 (104)
T ss_pred HHHHHHHHHHHhcccCCcccccCCCCCCCCcEEEEECCCCEEEEEEHHHcCCHHHHHHHHHHHHHhCCCCCCcEEEeCCH
Confidence 36899999999999987766678999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhh
Q 040904 82 RVFRQLTSWL 91 (92)
Q Consensus 82 ~~F~~~l~~l 91 (92)
+.|++++|||
T Consensus 94 ~~Fe~ll~~i 103 (104)
T PLN03090 94 VVFRSLTSMI 103 (104)
T ss_pred HHHHHHHHHh
Confidence 9999999997
No 2
>PLN03220 uncharacterized protein; Provisional
Probab=100.00 E-value=1.5e-37 Score=211.90 Aligned_cols=87 Identities=41% Similarity=0.846 Sum_probs=75.4
Q ss_pred hhHHHHhhhccCCCCccCCCCCCCCCCCCCeEEEEEcC----CceEEEEeccCCCcHHHHHHHHHHHHhcCccC-CCcEE
Q 040904 2 AIQEIFKQCSSFGKKCSCDQDGHPNDVPKGHCVVYVGE----NRSRYIIPITWLNHPKFKNLLEKAAEEYGYKH-DLGII 76 (92)
Q Consensus 2 ~~k~~lkr~~s~~~~~~~~~~~~~~~vpkG~~~VyVG~----~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~-~g~L~ 76 (92)
+.|++++|++ ++++.. .....+.+|||||||||||+ +++||+||++|||||.|++||++|||||||+| +|+|+
T Consensus 11 ~~k~~~~~~~-~~~~~~-~~~~~~~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP~F~~LL~~AeEEfGf~~~~G~L~ 88 (105)
T PLN03220 11 ATKQILKLNS-LANRNR-TSSSSSDHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHPSFKEFLSRAEEEFGFNHPMGGLT 88 (105)
T ss_pred HHHHHHHHHh-hccccc-ccccccCCCCCCeEEEEECCCCCccceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEE
Confidence 3589999999 555422 12346779999999999997 58999999999999999999999999999998 59999
Q ss_pred ecCcHHHHHHHHHh
Q 040904 77 LPCDERVFRQLTSW 90 (92)
Q Consensus 77 IPC~~~~F~~~l~~ 90 (92)
|||+++.|+++++.
T Consensus 89 IPCd~~~F~~ll~s 102 (105)
T PLN03220 89 IPCREEVFLDLIAS 102 (105)
T ss_pred eeCCHHHHHHHHHh
Confidence 99999999999875
No 3
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=100.00 E-value=3.3e-37 Score=207.79 Aligned_cols=67 Identities=49% Similarity=0.996 Sum_probs=65.2
Q ss_pred CCCCCCCeEEEEEcCCceEEEEeccCCCcHHHHHHHHHHHHhcCccCCCcEEecCcHHHHHHHHHhh
Q 040904 25 PNDVPKGHCVVYVGENRSRYIIPITWLNHPKFKNLLEKAAEEYGYKHDLGIILPCDERVFRQLTSWL 91 (92)
Q Consensus 25 ~~~vpkG~~~VyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~g~L~IPC~~~~F~~~l~~l 91 (92)
..++|+||||||||++++||+||++|||||+|++||++|||||||+++|+|+|||+++.|++++|+|
T Consensus 33 ~~~vp~G~~~VyVG~~~~Rfvvp~~~L~hp~f~~LL~~aeeEfG~~~~G~l~iPC~~~~Fe~~l~~l 99 (100)
T PF02519_consen 33 ESDVPKGHFAVYVGEERRRFVVPVSYLNHPLFQELLEQAEEEFGFDQDGPLTIPCDVVLFEHLLWLL 99 (100)
T ss_pred cCCCCCCeEEEEeCccceEEEechHHcCchhHHHHHHHHhhhcCcCCCCcEEeeCCHHHHHHHHHHh
Confidence 3689999999999999999999999999999999999999999999999999999999999999987
No 4
>PLN03219 uncharacterized protein; Provisional
Probab=100.00 E-value=3.9e-36 Score=205.74 Aligned_cols=89 Identities=40% Similarity=0.755 Sum_probs=77.4
Q ss_pred hhHHHHhhhccCCCCccC---CCCCCCCCCCCCeEEEEEcC--CceEEEEeccCCCcHHHHHHHHHHHHhcCccC-CCcE
Q 040904 2 AIQEIFKQCSSFGKKCSC---DQDGHPNDVPKGHCVVYVGE--NRSRYIIPITWLNHPKFKNLLEKAAEEYGYKH-DLGI 75 (92)
Q Consensus 2 ~~k~~lkr~~s~~~~~~~---~~~~~~~~vpkG~~~VyVG~--~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~-~g~L 75 (92)
+.|+|||..+...++.+. +..+.+.+|||||+|||||+ |++||+||++|||||+|++||++|||||||+| +|+|
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vpkGh~aVYVG~~~E~kRFvVPi~yL~hP~F~~LL~~AeEEfGf~~~~G~L 89 (108)
T PLN03219 10 NAKQIFKSQSMRNKNGSSSPSSSTTTSGLVPKGHVAVYVGEQMEKKRFVVPISYLNHPLFREFLNRAEEECGFHHSMGGL 89 (108)
T ss_pred hHHHHHHHHHHhcccCCCCCccCCCCCCCCCCCeEEEEECCCCCceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCE
Confidence 468899877777776442 22356778999999999997 58999999999999999999999999999998 5999
Q ss_pred EecCcHHHHHHHHHh
Q 040904 76 ILPCDERVFRQLTSW 90 (92)
Q Consensus 76 ~IPC~~~~F~~~l~~ 90 (92)
+|||+++.|+++++.
T Consensus 90 ~IPCd~~~F~~ll~~ 104 (108)
T PLN03219 90 TIPCREESFLHLITS 104 (108)
T ss_pred EEeCCHHHHHHHHHh
Confidence 999999999999975
No 5
>PF02214 BTB_2: BTB/POZ domain; InterPro: IPR003131 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. The Kv family can be divided into several subfamilies on the basis of sequence similarity and function. Four of these subfamilies, Kv1 (Shaker), Kv2 (Shab), Kv3 (Shaw) and Kv4 (Shal), consist of pore-forming alpha subunits that associate with different types of beta subunit. Each alpha subunit comprises six hydrophobic TM domains with a P-domain between the fifth and sixth, which partially resides in the membrane. The fourth TM domain has positively charged residues at every third residue and acts as a voltage sensor, which triggers the conformational change that opens the channel pore in response to a displacement in membrane potential []. More recently, 4 new electrically-silent alpha subunits have been cloned: Kv5 (KCNF), Kv6 (KCNG), Kv8 and Kv9 (KCNS). These subunits do not themselves possess any functional activity, but appear to form heteromeric channels with Kv2 subunits, and thus modulate Shab channel activity []. When highly expressed, they inhibit channel activity, but at lower levels show more specific modulatory actions. The N-terminal, cytoplasmic tetramerization domain (T1) of voltage-gated potassium channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels []. This domain is found in a subset of a larger group of proteins that contain the BTB/POZ domain.; GO: 0005249 voltage-gated potassium channel activity, 0006813 potassium ion transport, 0008076 voltage-gated potassium channel complex, 0016020 membrane; PDB: 1NN7_A 3KVT_A 1EXB_E 1QDV_A 1DSX_E 1QDW_F 3LUT_B 3LNM_B 2A79_B 3DRY_C ....
Probab=89.28 E-value=0.44 Score=30.15 Aligned_cols=56 Identities=16% Similarity=0.211 Sum_probs=41.0
Q ss_pred EEEEcCCceEEEEeccCCC-cH--HHHHHHHHHHHhcCccCCCcEEecCcHHHHHHHHHhh
Q 040904 34 VVYVGENRSRYIIPITWLN-HP--KFKNLLEKAAEEYGYKHDLGIILPCDERVFRQLTSWL 91 (92)
Q Consensus 34 ~VyVG~~~~RfvVp~~~L~-hP--~F~~LL~~aeeEfG~~~~g~L~IPC~~~~F~~~l~~l 91 (92)
.+-||. ++|.++.+.|. +| .|..+++.......-+.+|.+-|-++...|++||.-|
T Consensus 2 ~lNVGG--~~f~~~~~tL~~~~~s~l~~~~~~~~~~~~~~~~~~~fiDRdp~~F~~IL~yl 60 (94)
T PF02214_consen 2 RLNVGG--TIFETSRSTLTRYPDSLLARLFSGERSDDYDDDDGEYFIDRDPELFEYILNYL 60 (94)
T ss_dssp EEEETT--EEEEEEHHHHHTSTTSTTTSHHHTGHGGGEETTTTEEEESS-HHHHHHHHHHH
T ss_pred EEEECC--EEEEEcHHHHhhCCCChhhhHHhhccccccCCccceEEeccChhhhhHHHHHH
Confidence 456786 69999998887 44 7888888653222234567899999999999999754
No 6
>PRK02899 adaptor protein; Provisional
Probab=88.24 E-value=0.45 Score=35.26 Aligned_cols=25 Identities=28% Similarity=0.624 Sum_probs=21.5
Q ss_pred cHHHHHHHHHHHHhcCccCCCcEEe
Q 040904 53 HPKFKNLLEKAAEEYGYKHDLGIIL 77 (92)
Q Consensus 53 hP~F~~LL~~aeeEfG~~~~g~L~I 77 (92)
+-+|.++|++|..|+||..+|+|+|
T Consensus 38 e~lF~~mm~Ea~~e~~F~~~~pl~~ 62 (197)
T PRK02899 38 HQLFRDMMQEANKELGFEADGPIAV 62 (197)
T ss_pred HHHHHHHHHHhhhccCcccCCeEEE
Confidence 3467778999999999999999875
No 7
>PRK02315 adaptor protein; Provisional
Probab=84.73 E-value=0.76 Score=34.73 Aligned_cols=25 Identities=12% Similarity=0.282 Sum_probs=22.6
Q ss_pred cHHHHHHHHHHHHhcCccCCCcEEe
Q 040904 53 HPKFKNLLEKAAEEYGYKHDLGIIL 77 (92)
Q Consensus 53 hP~F~~LL~~aeeEfG~~~~g~L~I 77 (92)
+-+|.++|++|..|+||..+|+|+|
T Consensus 38 e~fF~~mm~Ea~~e~~F~~~~pl~~ 62 (233)
T PRK02315 38 EEFFYSMMDEVDEEDDFADEGPLWF 62 (233)
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 4589999999999999999999876
No 8
>PF05389 MecA: Negative regulator of genetic competence (MecA); InterPro: IPR008681 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. This family contains several bacterial MecA proteins. In complex media competence development is poor, and there is little or no expression of late competence genes. Overexpression of MecA inhibits comG transcription [, , ]. MecA enables the recognition and targeting of unfolded and aggregated proteins to the ClpC protease or to other proteins involved in proteolysis. Acts negatively in the development of competence by binding ComK and recruiting it to the ClpCP protease. When overexpressed, inhibits sporulation. Also involved in Spx degradation by ClpC. ; PDB: 3JTP_C 2Y1R_O 3PXI_c 3PXG_b 3JTO_D 3JTN_A.
Probab=81.37 E-value=0.47 Score=35.03 Aligned_cols=25 Identities=32% Similarity=0.509 Sum_probs=0.0
Q ss_pred cHHHHHHHHHHHHhcCccCCCcEEe
Q 040904 53 HPKFKNLLEKAAEEYGYKHDLGIIL 77 (92)
Q Consensus 53 hP~F~~LL~~aeeEfG~~~~g~L~I 77 (92)
+-.|.++|++|.+|+||+.+|+|++
T Consensus 38 e~fF~~ileea~~e~~F~~~~~l~~ 62 (220)
T PF05389_consen 38 EEFFYSILEEADEEHGFENDGPLTF 62 (220)
T ss_dssp -------------------------
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 5679999999999999999998875
No 9
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=78.54 E-value=6.3 Score=24.06 Aligned_cols=49 Identities=24% Similarity=0.369 Sum_probs=36.5
Q ss_pred EEcCCceEEEEeccCCCcHHHHHHHHHHHHhcCcc----------CCC-cEEecCcHHHHHHHHH
Q 040904 36 YVGENRSRYIIPITWLNHPKFKNLLEKAAEEYGYK----------HDL-GIILPCDERVFRQLTS 89 (92)
Q Consensus 36 yVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~----------~~g-~L~IPC~~~~F~~~l~ 89 (92)
+-|++.+||.+|- ...|.+|..+..+.|+.. .+| .++|.++. .+..++.
T Consensus 7 ~~~~~~~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~-Dl~~a~~ 66 (81)
T smart00666 7 RYGGETRRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDE-DLEEAIE 66 (81)
T ss_pred EECCEEEEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHH-HHHHHHH
Confidence 3377788999985 788999999999999875 245 68888876 4444443
No 10
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=75.16 E-value=11 Score=22.77 Aligned_cols=51 Identities=24% Similarity=0.384 Sum_probs=37.0
Q ss_pred EEEcCCceEEEEeccCCCcHHHHHHHHHHHHhcCcc----------CCC-cEEecCcHHHHHHHHH
Q 040904 35 VYVGENRSRYIIPITWLNHPKFKNLLEKAAEEYGYK----------HDL-GIILPCDERVFRQLTS 89 (92)
Q Consensus 35 VyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~----------~~g-~L~IPC~~~~F~~~l~ 89 (92)
++-+++.+||.+|- .++.|.+|..+-++.|+.. .+| -++|.++. .++..+.
T Consensus 5 ~~~~~~~~~~~~~~---~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd~-Dl~~a~~ 66 (81)
T cd05992 5 VKYGGEIRRFVVVS---RSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSDE-DLEEAIE 66 (81)
T ss_pred EEecCCCEEEEEec---CCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCHH-HHHHHHH
Confidence 44456679999997 7899999999999999885 234 56677664 5555444
No 11
>cd06410 PB1_UP2 Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=66.80 E-value=16 Score=24.33 Aligned_cols=45 Identities=29% Similarity=0.358 Sum_probs=33.1
Q ss_pred EEEEcCCceEEEEeccCCCcHHHHHHHHHHHHhcCccC-------------CCcEEecCcHH
Q 040904 34 VVYVGENRSRYIIPITWLNHPKFKNLLEKAAEEYGYKH-------------DLGIILPCDER 82 (92)
Q Consensus 34 ~VyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~-------------~g~L~IPC~~~ 82 (92)
.=|||.+.+-..|+-+ -.|.+|..+..+.++... ++-+.|.||.+
T Consensus 17 l~Y~GG~tr~i~V~r~----~s~~el~~kl~~~~~~~~~~~lky~Lp~edld~Lisv~~DeD 74 (97)
T cd06410 17 LRYVGGETRIVSVDRS----ISFKELVSKLSELFGAGVVVTLKYQLPDEDLDALISVSNDED 74 (97)
T ss_pred EEEcCCceEEEEEcCC----CCHHHHHHHHHHHhCCCCceEEEEEcCCCCcceeEEecCcHH
Confidence 4699999888888876 467778888888877665 33456777774
No 12
>PF02100 ODC_AZ: Ornithine decarboxylase antizyme; InterPro: IPR002993 Ornithine decarboxylase antizyme (ODC-AZ) [] binds to, and destabilises, ornithine decarboxylase (ODC), a key enzyme in polyamine synthesis. ODC is then rapidly degraded. The expression of ODC-AZ requires programmed, ribosomal frameshifting which is modulated according to the cellular concentration of polyamines. High levels of polyamines induce a +1 ribosomal frameshift in the translation of mRNA for the antizyme leading to the expression of a full-length protein. At least two forms of ODC-AZ exist in mammals [] and the protein has been found in Drosophila (protein Gutfeeling).; GO: 0004857 enzyme inhibitor activity, 0008073 ornithine decarboxylase inhibitor activity; PDB: 1ZO0_A.
Probab=66.77 E-value=12 Score=25.20 Aligned_cols=51 Identities=29% Similarity=0.417 Sum_probs=24.9
Q ss_pred cCCceEEE-EeccCC---CcHHHHHHHHHHHHhcCccCCCcEEecCcHHHHHHHHH
Q 040904 38 GENRSRYI-IPITWL---NHPKFKNLLEKAAEEYGYKHDLGIILPCDERVFRQLTS 89 (92)
Q Consensus 38 G~~~~Rfv-Vp~~~L---~hP~F~~LL~~aeeEfG~~~~g~L~IPC~~~~F~~~l~ 89 (92)
|+++.=|| +|-..+ .-..|.+|||.|||.+|.++ -.+.++=+-.....++.
T Consensus 21 ~~~~~L~V~ip~~~~~~~~K~~lvaLLElAee~L~c~~-vvic~~k~~~d~~~Llr 75 (108)
T PF02100_consen 21 GDERTLFVFIPSSALGQGSKESLVALLELAEEKLGCSH-VVICLDKNRPDRASLLR 75 (108)
T ss_dssp --TTEEEEE-SS---SS--SHHHHHHHHHHHHHH-----EEEEE---SS-HHHHHH
T ss_pred ccCCEEEEEECCcccccccHHHHHHHHHHhcCcCCCCE-EEEEEECCchhHHHhhh
Confidence 34566666 565444 44679999999999988765 35566644444444443
No 13
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=63.15 E-value=23 Score=27.43 Aligned_cols=63 Identities=19% Similarity=0.212 Sum_probs=44.7
Q ss_pred CCeEEEEEcCCceEEEEeccCCCcHHHHHHHHHHHHhcCccCC---------------CcEEecCcHHHHHHHHHhhC
Q 040904 30 KGHCVVYVGENRSRYIIPITWLNHPKFKNLLEKAAEEYGYKHD---------------LGIILPCDERVFRQLTSWLI 92 (92)
Q Consensus 30 kG~~~VyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~---------------g~L~IPC~~~~F~~~l~~l~ 92 (92)
.|.+.|.-.++..++.+.++.-.-|....++.....-||.+.| -+|++|...+.||.+++.||
T Consensus 45 ~~~~~v~~~~~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L~~~~~~~~GlR~p~~~d~fE~lv~aIi 122 (283)
T PRK10308 45 RGVVTVIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGKLGAARPGLRLPGSVDAFEQGVRAIL 122 (283)
T ss_pred cEEEEEEEcCCCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCCcCCCCCCHHHHHHHHHH
Confidence 4666666655555666666654345566778888887777754 26999999999999988764
No 14
>PF00651 BTB: BTB/POZ domain; InterPro: IPR013069 The BTB (for BR-C, ttk and bab) [] or POZ (for Pox virus and Zinc finger) [] domain is present near the N terminus of a fraction of zinc finger (IPR007087 from INTERPRO) proteins and in proteins that contain the IPR006652 from INTERPRO motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation []. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule []. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [, , ]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.; GO: 0005515 protein binding; PDB: 3M5B_A 1R28_B 3LBZ_A 3E4U_F 3BIM_B 1R2B_A 1R29_A 2VPK_A 2YY9_B 3GA1_A ....
Probab=59.63 E-value=31 Score=21.26 Aligned_cols=54 Identities=24% Similarity=0.519 Sum_probs=37.5
Q ss_pred EEEEEcCCceEEEEeccCC--CcHHHHHHHHHHHHhcCccCCC--cEEec-CcHHHHHHHHHhh
Q 040904 33 CVVYVGENRSRYIIPITWL--NHPKFKNLLEKAAEEYGYKHDL--GIILP-CDERVFRQLTSWL 91 (92)
Q Consensus 33 ~~VyVG~~~~RfvVp~~~L--~hP~F~~LL~~aeeEfG~~~~g--~L~IP-C~~~~F~~~l~~l 91 (92)
+.+.||+ .++|-++-..| ..|.|+.+++.. +...++ .+.++ ++.+.|+.++..+
T Consensus 13 ~~i~v~d-~~~~~vhk~iL~~~S~~F~~~~~~~----~~~~~~~~~i~~~~~~~~~~~~~l~~~ 71 (111)
T PF00651_consen 13 VTIRVGD-GKTFYVHKNILAARSPYFRNLFEGS----KFKESTVPEISLPDVSPEAFEAFLEYM 71 (111)
T ss_dssp EEEEETT-TEEEEE-HHHHHHHBHHHHHHHTTT----TSTTSSEEEEEETTSCHHHHHHHHHHH
T ss_pred EEEEECC-CEEEeechhhhhccchhhhhccccc----ccccccccccccccccccccccccccc
Confidence 3556665 57898888887 569999999988 222233 35555 7899999988754
No 15
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=56.81 E-value=49 Score=21.65 Aligned_cols=52 Identities=19% Similarity=0.236 Sum_probs=37.4
Q ss_pred EcCCceEEEEeccC-CCcHHHHHHHHHHHHhcCccC-----------CC-cEEecCcHHHHHHHH
Q 040904 37 VGENRSRYIIPITW-LNHPKFKNLLEKAAEEYGYKH-----------DL-GIILPCDERVFRQLT 88 (92)
Q Consensus 37 VG~~~~RfvVp~~~-L~hP~F~~LL~~aeeEfG~~~-----------~g-~L~IPC~~~~F~~~l 88 (92)
-|++.+||-+|..- -.+..|..|.++-++-|.... +| -++|.|+.+.-+.+-
T Consensus 7 y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~ 71 (91)
T cd06398 7 YGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQ 71 (91)
T ss_pred eCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHH
Confidence 37788999999640 114578899999888876653 45 688999987766553
No 16
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=54.09 E-value=36 Score=20.58 Aligned_cols=43 Identities=26% Similarity=0.410 Sum_probs=30.5
Q ss_pred EEcCCceE-EEEeccCCCcHHHHHHHHHHHHhcCcc----------CCC-cEEecCcHH
Q 040904 36 YVGENRSR-YIIPITWLNHPKFKNLLEKAAEEYGYK----------HDL-GIILPCDER 82 (92)
Q Consensus 36 yVG~~~~R-fvVp~~~L~hP~F~~LL~~aeeEfG~~----------~~g-~L~IPC~~~ 82 (92)
+-+++.+| +.++ ..+.|.+|.++.++.||.. .+| .++|.++.+
T Consensus 7 ~~~~~~~~~~~~~----~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~D 61 (84)
T PF00564_consen 7 RYGGDIRRIISLP----SDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDED 61 (84)
T ss_dssp EETTEEEEEEEEC----STSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHH
T ss_pred EECCeeEEEEEcC----CCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHH
Confidence 34555455 4444 5679999999999999984 355 577887764
No 17
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=45.11 E-value=60 Score=20.76 Aligned_cols=47 Identities=23% Similarity=0.446 Sum_probs=34.2
Q ss_pred EEEcCCceEEEEeccCCCcHHHHHHHHHHHHhcCccC-----------CC-cEEecCcHHHHH
Q 040904 35 VYVGENRSRYIIPITWLNHPKFKNLLEKAAEEYGYKH-----------DL-GIILPCDERVFR 85 (92)
Q Consensus 35 VyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~-----------~g-~L~IPC~~~~F~ 85 (92)
+..|++..||.+|.+ ..|++|.++-++-|+... +| ..+|.|+.+.=+
T Consensus 5 ~~~~~d~~r~~l~~~----~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~e 63 (82)
T cd06407 5 ATYGEEKIRFRLPPS----WGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEE 63 (82)
T ss_pred EEeCCeEEEEEcCCC----CCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHH
Confidence 344777889998864 368999999888887652 34 678888886544
No 18
>PF11834 DUF3354: Domain of unknown function (DUF3354); InterPro: IPR021789 Potassium channels take part in important processes of higher plants, including opening and closing of stomatal pores and leaf movement. Inward rectifying potassium (K(+)in) channels play an important role in turgor regulation and ion uptake in higher plants. All of them comprise, from their N-terminal to their C-terminal ends: a short hydrophilic region, a hydrophobic region structurally analogous and partially homologous to the transmembrane domain of voltage-gated animal channels from the Shaker superfamily, a putative cyclic nucleotide-binding domain, and a conserved C-terminal KHA domain. Between these last two regions, some of them (AKT1, AKT2 and SKT1) contain an ankyrin-repeat domain with six repeats homologous to those of human erythrocyte ankyrin. This entry represents the KHA domain which is unique to plant K(+)in channels. The KHA domain contains two high-homology blocks enriched for hydrophobic and acidic residues, respectively. The KHA domain is essential for interaction of plant K(+)in channels. The KHA domain mediates tetramerization and/or stabilisation of the heteromers [, , ].
Probab=44.28 E-value=20 Score=22.60 Aligned_cols=23 Identities=26% Similarity=0.606 Sum_probs=18.8
Q ss_pred eEEEEeccCCCcHHHHHHHHHHHHhcCcc
Q 040904 42 SRYIIPITWLNHPKFKNLLEKAAEEYGYK 70 (92)
Q Consensus 42 ~RfvVp~~~L~hP~F~~LL~~aeeEfG~~ 70 (92)
+=..+| -.+.+||+.|++.||+.
T Consensus 20 Kvi~lP------~SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 20 KVIWLP------DSLEELLKIASEKFGFS 42 (69)
T ss_pred EEEEcC------ccHHHHHHHHHHHhCCC
Confidence 455666 36899999999999995
No 19
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=43.31 E-value=10 Score=21.20 Aligned_cols=18 Identities=22% Similarity=0.608 Sum_probs=14.6
Q ss_pred CCCcHHHHHHHHHHHHhc
Q 040904 50 WLNHPKFKNLLEKAAEEY 67 (92)
Q Consensus 50 ~L~hP~F~~LL~~aeeEf 67 (92)
||+.-.|.++..++.+||
T Consensus 1 YLsd~dF~~vFgm~~~eF 18 (36)
T PF02209_consen 1 YLSDEDFEKVFGMSREEF 18 (36)
T ss_dssp GS-HHHHHHHHSS-HHHH
T ss_pred CcCHHHHHHHHCCCHHHH
Confidence 788999999999999997
No 20
>PF12058 DUF3539: Protein of unknown function (DUF3539); InterPro: IPR021926 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved NHP sequence motif. ; PDB: 3N5B_B 2XKO_C 2XG8_F.
Probab=42.39 E-value=4.2 Score=27.23 Aligned_cols=9 Identities=67% Similarity=1.257 Sum_probs=6.7
Q ss_pred cCCCcHHHH
Q 040904 49 TWLNHPKFK 57 (92)
Q Consensus 49 ~~L~hP~F~ 57 (92)
.|||||.|-
T Consensus 4 ~YLNHPtFG 12 (88)
T PF12058_consen 4 TYLNHPTFG 12 (88)
T ss_dssp -EEEETTTE
T ss_pred ccccCCccc
Confidence 589999874
No 21
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=41.59 E-value=89 Score=20.35 Aligned_cols=46 Identities=2% Similarity=0.131 Sum_probs=34.0
Q ss_pred cCCceEEEEeccCCCcHHHHHHHHHHHHhcCcc--------CCC-cEEecCcHHHHH
Q 040904 38 GENRSRYIIPITWLNHPKFKNLLEKAAEEYGYK--------HDL-GIILPCDERVFR 85 (92)
Q Consensus 38 G~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~--------~~g-~L~IPC~~~~F~ 85 (92)
|++..||.++- -.++.|.+|.++-+.-|+++ .+| .++|.|+++.=|
T Consensus 8 ~~d~~rf~~~~--~~~~~~~~L~~ev~~rf~l~~f~lKYlDde~e~v~lssd~eLeE 62 (81)
T cd06396 8 NGESQSFLVSD--SENTTWASVEAMVKVSFGLNDIQIKYVDEENEEVSVNSQGEYEE 62 (81)
T ss_pred CCeEEEEEecC--CCCCCHHHHHHHHHHHhCCCcceeEEEcCCCCEEEEEchhhHHH
Confidence 55678999874 12557999999999999864 344 789999886533
No 22
>smart00153 VHP Villin headpiece domain.
Probab=41.34 E-value=14 Score=20.63 Aligned_cols=18 Identities=22% Similarity=0.600 Sum_probs=16.4
Q ss_pred CCCcHHHHHHHHHHHHhc
Q 040904 50 WLNHPKFKNLLEKAAEEY 67 (92)
Q Consensus 50 ~L~hP~F~~LL~~aeeEf 67 (92)
||+.-.|+.++.++.+||
T Consensus 1 yLsdeeF~~vfgmsr~eF 18 (36)
T smart00153 1 YLSDEDFEEVFGMTREEF 18 (36)
T ss_pred CCCHHHHHHHHCCCHHHH
Confidence 788999999999999997
No 23
>PRK02797 4-alpha-L-fucosyltransferase; Provisional
Probab=36.42 E-value=1.2e+02 Score=24.70 Aligned_cols=44 Identities=16% Similarity=0.397 Sum_probs=32.3
Q ss_pred CCCCCeEEEEEcC--------------------CceEEEEeccC--CCcHHHHHHHHHHHHhcCcc
Q 040904 27 DVPKGHCVVYVGE--------------------NRSRYIIPITW--LNHPKFKNLLEKAAEEYGYK 70 (92)
Q Consensus 27 ~vpkG~~~VyVG~--------------------~~~RfvVp~~~--L~hP~F~~LL~~aeeEfG~~ 70 (92)
..+++-+.+.||. +.-|++||.+| =|.--.++..+.+.+-||-+
T Consensus 141 ~~~~~~~tIlvGNSgd~SN~Hie~L~~l~~~~~~~v~ii~PlsYp~gn~~Yi~~V~~~~~~lF~~~ 206 (322)
T PRK02797 141 RQRAGKMTILVGNSGDRSNRHIEALRALHQQFGDNVKIIVPMGYPANNQAYIEEVRQAGLALFGAE 206 (322)
T ss_pred ccCCCceEEEEeCCCCCcccHHHHHHHHHHHhCCCeEEEEECCcCCCCHHHHHHHHHHHHHhcCcc
Confidence 3467789999984 12599999999 56666666777777778743
No 24
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=36.28 E-value=19 Score=20.10 Aligned_cols=19 Identities=37% Similarity=0.697 Sum_probs=14.4
Q ss_pred HHHHHHHHHHhc--CccCCCc
Q 040904 56 FKNLLEKAAEEY--GYKHDLG 74 (92)
Q Consensus 56 F~~LL~~aeeEf--G~~~~g~ 74 (92)
+-.+|+..+||| ||-|.|+
T Consensus 12 Id~vLe~NAe~FV~~fVQKGG 32 (33)
T TIGR03687 12 IDGVLESNAEEFVRGFVQKGG 32 (33)
T ss_pred HHHHHHHhHHHHHHHHHHccC
Confidence 456788888888 7777764
No 25
>PLN02752 [acyl-carrier protein] S-malonyltransferase
Probab=35.18 E-value=36 Score=26.35 Aligned_cols=49 Identities=22% Similarity=0.272 Sum_probs=32.4
Q ss_pred CCCCCCCCCCeEEEEEcCCceEEEEeccCCCcHHHHHHHHHHHHhcCcc
Q 040904 22 DGHPNDVPKGHCVVYVGENRSRYIIPITWLNHPKFKNLLEKAAEEYGYK 70 (92)
Q Consensus 22 ~~~~~~vpkG~~~VyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~ 70 (92)
++.+.+.+.-.+.++-|...++.-.=.+|.++|.|+++++++++-.|++
T Consensus 30 ~~~~~~~~~~~a~lFpGQGsq~~gm~~~~~~~p~~~~~~~~~~~~lg~~ 78 (343)
T PLN02752 30 DALFADYKPTTAFLFPGQGAQAVGMGKEAAEVPAAKALFDKASEILGYD 78 (343)
T ss_pred cccccCCCCCEEEEECCCCcchhhHHHHHHhCHHHHHHHHHHHHHhCCC
Confidence 3455555555666666764333222233678999999999999988865
No 26
>TIGR03793 TOMM_pelo TOMM propeptide domain. This model represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM). Oddly, most of this seqence region appears homologous to nitrile hydratase subunits. This family is expanded especially in Pelotomaculum thermopropionicum SI.
Probab=34.93 E-value=69 Score=20.49 Aligned_cols=27 Identities=22% Similarity=0.262 Sum_probs=18.2
Q ss_pred CCcHHHHHHH-HH---HHHhcCccCCCcEEe
Q 040904 51 LNHPKFKNLL-EK---AAEEYGYKHDLGIIL 77 (92)
Q Consensus 51 L~hP~F~~LL-~~---aeeEfG~~~~g~L~I 77 (92)
-..|.|++.| .. +=+||||.-+..+.|
T Consensus 14 w~Dp~Fr~~Ll~DPraaL~e~G~~~P~~~~i 44 (77)
T TIGR03793 14 WEDEAFKQALLTNPKEALEREGVQVPAEVEV 44 (77)
T ss_pred HcCHHHHHHHHHCHHHHHHHhCCCCCCceEE
Confidence 3578999955 43 446889987665544
No 27
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=31.98 E-value=1.5e+02 Score=19.54 Aligned_cols=46 Identities=20% Similarity=0.292 Sum_probs=34.6
Q ss_pred EEcCCceEEEEeccCCCcHHHHHHHHHHHHhcCcc----------CCC-cEEecCcHHHHH
Q 040904 36 YVGENRSRYIIPITWLNHPKFKNLLEKAAEEYGYK----------HDL-GIILPCDERVFR 85 (92)
Q Consensus 36 yVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~----------~~g-~L~IPC~~~~F~ 85 (92)
--|...+||..|. .|.+.+|-++-+.=|-+. .+| .|||.=+.+..+
T Consensus 6 ~~~g~~RRf~~~~----~pt~~~L~~kl~~Lf~lp~~~~~vtYiDeD~D~ITlssd~eL~d 62 (82)
T cd06397 6 SFLGDTRRIVFPD----IPTWEALASKLENLYNLPEIKVGVTYIDNDNDEITLSSNKELQD 62 (82)
T ss_pred EeCCceEEEecCC----CccHHHHHHHHHHHhCCChhHeEEEEEcCCCCEEEecchHHHHH
Confidence 3456679999998 899999999998877766 344 688876665444
No 28
>PF14317 YcxB: YcxB-like protein
Probab=31.36 E-value=97 Score=17.03 Aligned_cols=32 Identities=25% Similarity=0.448 Sum_probs=24.0
Q ss_pred CCCeEEEEEcCCceEEEEeccCCCcHHHHHHHH
Q 040904 29 PKGHCVVYVGENRSRYIIPITWLNHPKFKNLLE 61 (92)
Q Consensus 29 pkG~~~VyVG~~~~RfvVp~~~L~hP~F~~LL~ 61 (92)
-+.++-+|+++. .-++||.+.++.-...++.+
T Consensus 28 ~~~~~~l~~~~~-~~~~iPk~~f~~~e~~~f~~ 59 (62)
T PF14317_consen 28 TKDYFYLYLGKN-QAFIIPKRAFSEEEKEEFRE 59 (62)
T ss_pred eCCEEEEEECCC-eEEEEEHHHCCHhHHHHHHH
Confidence 467888899875 89999999998555554443
No 29
>COG4862 MecA Negative regulator of genetic competence, sporulation and motility [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Cell motility and secretion]
Probab=31.02 E-value=34 Score=26.43 Aligned_cols=27 Identities=11% Similarity=0.240 Sum_probs=24.1
Q ss_pred CcHHHHHHHHHHHHhcCccCCCcEEec
Q 040904 52 NHPKFKNLLEKAAEEYGYKHDLGIILP 78 (92)
Q Consensus 52 ~hP~F~~LL~~aeeEfG~~~~g~L~IP 78 (92)
.|-+|.++++.+.+|-+|..+|+|.|-
T Consensus 37 ~EE~F~~mMdEl~~ee~F~~~GpL~iq 63 (224)
T COG4862 37 TEELFYEMMDELNLEEDFKDEGPLWIQ 63 (224)
T ss_pred HHHHHHHHHHhcCCccccccCCceEEE
Confidence 367899999999999999999999873
No 30
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=29.90 E-value=64 Score=22.57 Aligned_cols=28 Identities=32% Similarity=0.551 Sum_probs=23.2
Q ss_pred CCeEEEEEcCCceEEEEeccCCCcHHHHH
Q 040904 30 KGHCVVYVGENRSRYIIPITWLNHPKFKN 58 (92)
Q Consensus 30 kG~~~VyVG~~~~RfvVp~~~L~hP~F~~ 58 (92)
++-|.||||++ +-|++-..|-+-|.|..
T Consensus 32 ~~~~fVyvG~~-rdYIl~~gfCSCp~~~~ 59 (117)
T COG5431 32 KVKFFVYVGKE-RDYILEGGFCSCPDFLG 59 (117)
T ss_pred eEEEEEEEccc-cceEEEcCcccCHHHHh
Confidence 45689999997 46888888999999973
No 31
>PF07429 Glyco_transf_56: 4-alpha-L-fucosyltransferase glycosyl transferase group 56; InterPro: IPR009993 This family contains the bacterial enzyme 4-alpha-L-fucosyltransferase (Fuc4NAc transferase) (approximately 360 residues long). This catalyses the synthesis of Fuc4NAc-ManNAcA-GlcNAc-PP-Und (lipid III) as part of the biosynthetic pathway of enterobacterial common antigen (ECA), a polysaccharide comprised of the trisaccharide repeat unit Fuc4NAc-ManNAcA-GlcNAc [].; GO: 0008417 fucosyltransferase activity, 0009246 enterobacterial common antigen biosynthetic process, 0009276 Gram-negative-bacterium-type cell wall
Probab=28.32 E-value=1.7e+02 Score=24.08 Aligned_cols=43 Identities=21% Similarity=0.511 Sum_probs=33.3
Q ss_pred CCCCeEEEEEcC--------------------CceEEEEeccCC--CcHHHHHHHHHHHHhcCcc
Q 040904 28 VPKGHCVVYVGE--------------------NRSRYIIPITWL--NHPKFKNLLEKAAEEYGYK 70 (92)
Q Consensus 28 vpkG~~~VyVG~--------------------~~~RfvVp~~~L--~hP~F~~LL~~aeeEfG~~ 70 (92)
.+++-..+.||. +..|++||++|= |.-...++.+.+++-||-+
T Consensus 181 ~~~~~ltILvGNSgd~sNnHieaL~~L~~~~~~~~kIivPLsYg~~n~~Yi~~V~~~~~~lF~~~ 245 (360)
T PF07429_consen 181 KNKGKLTILVGNSGDPSNNHIEALEALKQQFGDDVKIIVPLSYGANNQAYIQQVIQAGKELFGAE 245 (360)
T ss_pred CCCCceEEEEcCCCCCCccHHHHHHHHHHhcCCCeEEEEECCCCCchHHHHHHHHHHHHHhcCcc
Confidence 457889999983 348999999996 4567777777788888743
No 32
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein.
Probab=27.73 E-value=79 Score=23.47 Aligned_cols=40 Identities=8% Similarity=0.092 Sum_probs=27.7
Q ss_pred eEEEEeccCCCcHHHHHHHHHHHHhcCccCCC-cEEecCcHH
Q 040904 42 SRYIIPITWLNHPKFKNLLEKAAEEYGYKHDL-GIILPCDER 82 (92)
Q Consensus 42 ~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~g-~L~IPC~~~ 82 (92)
++-++..+-.. -.++.|.+++++-.|...+. .+++|++..
T Consensus 33 ~g~I~d~~~~~-~~l~~l~~~a~~~~g~~~~~vvisVP~~~~ 73 (239)
T TIGR02529 33 DGIVVDFLGAV-EIVRRLKDTLEQKLGIELTHAATAIPPGTI 73 (239)
T ss_pred CCeEEEhHHHH-HHHHHHHHHHHHHhCCCcCcEEEEECCCCC
Confidence 45555544433 36788888888888887655 799998653
No 33
>PF05194 UreE_C: UreE urease accessory protein, C-terminal domain; InterPro: IPR007864 Urease and other nickel metalloenzymes are synthesised as precursors devoid of the metalloenzyme active site. These precursors then undergo a complex post-translational maturation process that requires a number of accessory proteins. Members of this group are nickel-binding proteins required for urease metallocentre assembly []. They are believed to function as metallochaperones to deliver nickel to urease apoprotein [, ]. It has been shown by yeast two-hybrid analysis that UreE forms a dimeric complex with UreG in Helicobacter pylori []. The UreDFG-apoenzyme complex has also been shown to exist [, ] and is believed to be, with the addition of UreE, the assembly system for active urease []. The complexes, rather than the individual proteins, presumably bind to UreB via UreE/H recognition sites. The structure of Klebsiella aerogenes UreE reveals a unique two-domain architecture.The N-terminal domain is structurally related to a heat shock protein, while the C-terminal domain shows homology to the Atx1 copper metallochaperone [, ]. Significantly, the metal-binding sites in UreE and Atx1 are distinct in location and types of residues despite the relationship between these proteins and the mechanism for UreE activation of urease is proposed to be different from the thiol ligand exchange mechanism used by the copper metallochaperones. The C-terminal domain of this protein is the metal-binding region, which can bind up to six Ni molecules per dimer. Most members of this group contain a histidine-rich C-terminal motif that is involved in, but not solely responsible for, binding nickel ions in K. aerogenes UreE []. However, internal ligands, not the histidine residues at the C terminus, are necessary for UreE to assist in urease activation in K. aerogenes [], even though the truncated protein lacking the His-rich region binds two nickel ions instead of six. In H. pylori and some other organisms, the terminal histidine-rich binding sites are absent, but the internal histidine sites are present, and the latter probably function as nickel donors. Deletion analysis shows that this domain alone is sufficient for metal-binding and activation of urease [].; GO: 0016151 nickel ion binding, 0006461 protein complex assembly, 0019627 urea metabolic process; PDB: 3NXZ_B 3TJA_B 3LA0_B 3TJ9_B 3NY0_A 3L9Z_A 3TJ8_A 1EAR_A 1EB0_A 1GMU_B ....
Probab=26.86 E-value=1.1e+02 Score=19.24 Aligned_cols=27 Identities=22% Similarity=0.474 Sum_probs=17.5
Q ss_pred CeEEEEEcCCceEEEEeccCCCcHHHHHHHHHH
Q 040904 31 GHCVVYVGENRSRYIIPITWLNHPKFKNLLEKA 63 (92)
Q Consensus 31 G~~~VyVG~~~~RfvVp~~~L~hP~F~~LL~~a 63 (92)
-|+|++++++ +..|| ..+.+.+||++-
T Consensus 25 rH~p~~i~~~--~l~v~----~d~~l~~~L~~l 51 (87)
T PF05194_consen 25 RHWPLFIEED--ELYVP----YDHVLEELLRKL 51 (87)
T ss_dssp TT--EEEETT--EEEEE------HHHHHHHHHT
T ss_pred CccceEEcCC--EEEec----CcHHHHHHHHHC
Confidence 3789999886 88888 566677777763
No 34
>cd01406 SIR2-like Sir2-like: Prokaryotic group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines; and are members of the SIR2 superfamily of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation.
Probab=26.83 E-value=81 Score=23.00 Aligned_cols=36 Identities=36% Similarity=0.601 Sum_probs=27.9
Q ss_pred CeEEEEEcCCceEEEEeccCCCcHHHHHHHHHHHHhcCccCC
Q 040904 31 GHCVVYVGENRSRYIIPITWLNHPKFKNLLEKAAEEYGYKHD 72 (92)
Q Consensus 31 G~~~VyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~ 72 (92)
|.+++++|..-.+= .+-|...+|++...+++|.+.+
T Consensus 1 g~lvlFiGAG~S~~------~glP~W~~Ll~~l~~~~~~~~~ 36 (242)
T cd01406 1 GRVVIFVGAGVSVS------SGLPDWKTLLDEIASELGLEID 36 (242)
T ss_pred CCEEEEecCccccc------cCCCChHHHHHHHHHHcCCccc
Confidence 67899998752221 5789999999999999987654
No 35
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=26.72 E-value=31 Score=28.37 Aligned_cols=22 Identities=32% Similarity=0.765 Sum_probs=16.6
Q ss_pred CCCCCeEEEEEcCC--ceEEEEec
Q 040904 27 DVPKGHCVVYVGEN--RSRYIIPI 48 (92)
Q Consensus 27 ~vpkG~~~VyVG~~--~~RfvVp~ 48 (92)
-+|.|.|++|||-+ -+.|.||+
T Consensus 89 ~IP~gSfv~Y~G~d~ie~~~~vP~ 112 (361)
T COG1759 89 FIPHGSFVAYVGYDGIENEFEVPM 112 (361)
T ss_pred EecCCceEEEecchhhhhcccCcc
Confidence 47999999999953 25577764
No 36
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=24.78 E-value=62 Score=22.08 Aligned_cols=21 Identities=24% Similarity=0.341 Sum_probs=16.8
Q ss_pred EEEEEcCCceEEEEeccCCCc
Q 040904 33 CVVYVGENRSRYIIPITWLNH 53 (92)
Q Consensus 33 ~~VyVG~~~~RfvVp~~~L~h 53 (92)
+.||+|+..++..|...+|.+
T Consensus 73 V~v~~G~k~K~liv~peHLk~ 93 (98)
T COG2139 73 VEVYDGNKEKTLIVRPEHLKP 93 (98)
T ss_pred EEEecCCceEEEEeCHHHccc
Confidence 567788888888888888765
No 37
>PF06344 Parecho_VpG: Parechovirus Genome-linked protein; InterPro: IPR009407 The viral polyprotein of parechoviruses contains: coat protein VP0 (P1AB); coat protein VP3 (P1C); coat protein VP1 (P1D); picornain 2A (3.4.22.29 from EC, core protein P2A); core protein P2B; core protein P2C; core protein P3A; genome-linked protein VPg (P3B); picornain 3C (3.4.22.28 from EC, MEROPS peptidase subfamily 3CF: parechovirus picornain 3C (P3C)) []. This entry consists of the genome-linked protein Vpg type P3B.; GO: 0019015 viral genome
Probab=24.71 E-value=33 Score=16.99 Aligned_cols=12 Identities=42% Similarity=0.540 Sum_probs=9.6
Q ss_pred CCCCCCCCeEEE
Q 040904 24 HPNDVPKGHCVV 35 (92)
Q Consensus 24 ~~~~vpkG~~~V 35 (92)
.|..-|||-|||
T Consensus 7 lp~~kpkgtfpv 18 (20)
T PF06344_consen 7 LPVAKPKGTFPV 18 (20)
T ss_pred ccccccCCcccc
Confidence 566679999997
No 38
>KOG1748 consensus Acyl carrier protein/NADH-ubiquinone oxidoreductase, NDUFAB1/SDAP subunit [Energy production and conversion; Lipid transport and metabolism; Secondary metabolites biosynthesis, transport and catabolism]
Probab=24.50 E-value=48 Score=23.61 Aligned_cols=30 Identities=10% Similarity=0.046 Sum_probs=19.7
Q ss_pred HHHHHHhcCccCCC--cEEecCcHHHHHHHHH
Q 040904 60 LEKAAEEYGYKHDL--GIILPCDERVFRQLTS 89 (92)
Q Consensus 60 L~~aeeEfG~~~~g--~L~IPC~~~~F~~~l~ 89 (92)
+=--||||||+.+. +=.|-|-.+.+++|-.
T Consensus 94 VMAlEEEFgiEIpd~dAdki~t~~da~~yI~~ 125 (131)
T KOG1748|consen 94 VMALEEEFGIEIPDEDADKIKTVRDAADYIAD 125 (131)
T ss_pred hhhhHHHhCCccCcchhhhhCCHHHHHHHHHh
Confidence 33457999998643 4556676777776643
No 39
>PF07369 DUF1488: Protein of unknown function (DUF1488); InterPro: IPR009962 This family consists of several hypothetical bacterial proteins of around 85 residues in length. The function of this family is unknown.; PDB: 2GPI_A.
Probab=24.27 E-value=1.3e+02 Score=18.49 Aligned_cols=20 Identities=20% Similarity=0.067 Sum_probs=17.8
Q ss_pred eEEEEEcCCceEEEEeccCC
Q 040904 32 HCVVYVGENRSRYIIPITWL 51 (92)
Q Consensus 32 ~~~VyVG~~~~RfvVp~~~L 51 (92)
.|+++|+...-++.|..+-|
T Consensus 18 ~F~a~~~g~~i~C~Is~~aL 37 (83)
T PF07369_consen 18 RFPAQVDGMQIRCAISAEAL 37 (83)
T ss_dssp EEEEEETTEEEEEEEEHHHH
T ss_pred EEEEEECCEEEEEEEeHHHH
Confidence 68999998889999999877
No 40
>cd04751 Commd3 COMM_Domain containing protein 3. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=24.17 E-value=82 Score=20.52 Aligned_cols=19 Identities=21% Similarity=0.326 Sum_probs=16.8
Q ss_pred CcEEecCcHHHHHHHHHhh
Q 040904 73 LGIILPCDERVFRQLTSWL 91 (92)
Q Consensus 73 g~L~IPC~~~~F~~~l~~l 91 (92)
..+..-|+++.|+++++.|
T Consensus 65 ~~i~f~c~~e~L~~Li~~L 83 (95)
T cd04751 65 PDINFTCTLEQLQDLVNKL 83 (95)
T ss_pred ceEEEEeCHHHHHHHHHHH
Confidence 4799999999999999865
No 41
>PF12062 HSNSD: heparan sulfate-N-deacetylase; InterPro: IPR021930 This family of proteins is are heparan sulphate N-deacetylase enzymes. This protein is found in eukaryotes. This enzyme is often found associated with PF00685 from PFAM. ; GO: 0015016 [heparan sulfate]-glucosamine N-sulfotransferase activity, 0016787 hydrolase activity
Probab=23.83 E-value=69 Score=27.40 Aligned_cols=40 Identities=35% Similarity=0.592 Sum_probs=34.3
Q ss_pred CCeEEEEEcCCceEEEEec-----cCCCcHH-HHHHHHHHHHhcCc
Q 040904 30 KGHCVVYVGENRSRYIIPI-----TWLNHPK-FKNLLEKAAEEYGY 69 (92)
Q Consensus 30 kG~~~VyVG~~~~RfvVp~-----~~L~hP~-F~~LL~~aeeEfG~ 69 (92)
||.+|+++-..+.||.+=+ .|+|-|. -++||++=-.|||-
T Consensus 96 kg~lP~LT~~~kGRy~lII~ENl~kYlnld~wNR~LLdkYC~ey~V 141 (487)
T PF12062_consen 96 KGDLPVLTDNDKGRYSLIIFENLLKYLNLDSWNRELLDKYCREYGV 141 (487)
T ss_pred CCCCCccccCCCCcEEEEEehhHHHHcCChHHHHHHHHHHhHccCc
Confidence 6899999977778888775 8999999 89999998888864
No 42
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=23.68 E-value=1.9e+02 Score=18.91 Aligned_cols=42 Identities=19% Similarity=0.124 Sum_probs=28.4
Q ss_pred cCCceEEEEeccCCCcHHHHHHHHHHHHhcCcc-------------CCC-cEEecCcHH
Q 040904 38 GENRSRYIIPITWLNHPKFKNLLEKAAEEYGYK-------------HDL-GIILPCDER 82 (92)
Q Consensus 38 G~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~-------------~~g-~L~IPC~~~ 82 (92)
|++-+|+.+|.. .=.|.+|.++....|... .+| -+||.++.+
T Consensus 8 g~DiR~~~~~~~---~~t~~~L~~~v~~~F~~~~~~~~~flIKYkD~dGDlVTIts~~d 63 (81)
T cd06401 8 GDDIRRIPIHNE---DITYDELLLMMQRVFRGKLGSSDDVLIKYKDEDGDLITIFDSSD 63 (81)
T ss_pred CCeEEEEeccCc---cccHHHHHHHHHHHhccccCCcccEEEEEECCCCCEEEeccHHH
Confidence 677788766631 126888888888777633 356 578888754
No 43
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=23.47 E-value=1e+02 Score=17.64 Aligned_cols=20 Identities=30% Similarity=0.519 Sum_probs=14.4
Q ss_pred cHHHHHHHHHHHHhcCccCC
Q 040904 53 HPKFKNLLEKAAEEYGYKHD 72 (92)
Q Consensus 53 hP~F~~LL~~aeeEfG~~~~ 72 (92)
.|.-++-..++.+|.||..+
T Consensus 27 s~~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 27 SEETRERILEAAEELGYRPN 46 (46)
T ss_dssp THHHHHHHHHHHHHHTB-SS
T ss_pred CHHHHHHHHHHHHHHCCCCC
Confidence 35667778889999999653
No 44
>cd01615 CIDE_N CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein.
Probab=23.34 E-value=1.2e+02 Score=19.67 Aligned_cols=34 Identities=18% Similarity=0.216 Sum_probs=23.3
Q ss_pred CceEEEEeccCCCcHHHHHHHHHHHHhcCccCCCcEEecC
Q 040904 40 NRSRYIIPITWLNHPKFKNLLEKAAEEYGYKHDLGIILPC 79 (92)
Q Consensus 40 ~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~g~L~IPC 79 (92)
..+|+=|-+. .+++|+.++.+-|+... .+++|=+
T Consensus 12 r~~k~GV~A~-----sL~eL~~K~~~~l~l~~-~~~~lvL 45 (78)
T cd01615 12 RSRKKGVAAS-----SLEELLSKACEKLKLPS-APVTLVL 45 (78)
T ss_pred CCeeEEEEcC-----CHHHHHHHHHHHcCCCC-CCeEEEE
Confidence 3466666654 46899999999999973 3444433
No 45
>PF08861 DUF1828: Domain of unknown function DUF1828; InterPro: IPR014960 These proteins are functionally uncharacterised.
Probab=23.01 E-value=2.1e+02 Score=18.05 Aligned_cols=40 Identities=25% Similarity=0.336 Sum_probs=33.0
Q ss_pred cHHHHHHHHHHHHhcCccCC-CcEEecCcHHHHHHHHHhhC
Q 040904 53 HPKFKNLLEKAAEEYGYKHD-LGIILPCDERVFRQLTSWLI 92 (92)
Q Consensus 53 hP~F~~LL~~aeeEfG~~~~-g~L~IPC~~~~F~~~l~~l~ 92 (92)
.|.=+++|+..-..||.+-+ |.|.+.++.+.|-.....+|
T Consensus 44 s~~R~~~l~~il~~~gv~~~~~el~~~~~~~~~~~~~~~li 84 (90)
T PF08861_consen 44 SKKRKKILNSILNGFGVELDEGELFIKTSEENFPQAKHRLI 84 (90)
T ss_pred chHHHHHHHHHHHHcCccccCCEEEEEeCHHHHHHHHHHHH
Confidence 67778999999999999754 68999999999987776653
No 46
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=21.41 E-value=1.1e+02 Score=22.06 Aligned_cols=26 Identities=12% Similarity=0.267 Sum_probs=17.4
Q ss_pred EEecc---CCCcHHHHHHHH---HHHHhcCcc
Q 040904 45 IIPIT---WLNHPKFKNLLE---KAAEEYGYK 70 (92)
Q Consensus 45 vVp~~---~L~hP~F~~LL~---~aeeEfG~~ 70 (92)
+||.. ++.||.|..+++ ++.+++||+
T Consensus 5 i~p~~~~~~~~~~~~~~~~~gi~~~a~~~g~~ 36 (283)
T cd06279 5 VLTDSLSYAFSDPVASQFLAGVAEVLDAAGVN 36 (283)
T ss_pred EeCCcccccccCccHHHHHHHHHHHHHHCCCE
Confidence 55643 378999999876 445567764
No 47
>cd06399 PB1_P40 The PB1 domain is essential part of the p40 adaptor protein which plays an important role in activating phagocyte NADPH oxidase during phagocytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes , such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domain of p40 represents a type I PB1 domain which interacts with the PB1 domain of oxidase activator p67 w
Probab=21.31 E-value=1.2e+02 Score=20.45 Aligned_cols=28 Identities=21% Similarity=0.292 Sum_probs=23.1
Q ss_pred eEEEEeccCCCcHHHHHHHHHHHHhcCc
Q 040904 42 SRYIIPITWLNHPKFKNLLEKAAEEYGY 69 (92)
Q Consensus 42 ~RfvVp~~~L~hP~F~~LL~~aeeEfG~ 69 (92)
+-..|.-+.-..|.|++||.....+|+-
T Consensus 16 rdi~vee~l~~~P~~kdLl~lmr~~f~~ 43 (92)
T cd06399 16 RDIAVEEDLSSTPLLKDLLELTRREFQR 43 (92)
T ss_pred cceEeecccccCccHHHHHHHHHHHhch
Confidence 4456666777899999999999999864
No 48
>COG0763 LpxB Lipid A disaccharide synthetase [Cell envelope biogenesis, outer membrane]
Probab=21.25 E-value=45 Score=27.54 Aligned_cols=32 Identities=31% Similarity=0.590 Sum_probs=26.4
Q ss_pred eEEEEeccCCCcHHHHHH--H---HHHHHhcCccCCC
Q 040904 42 SRYIIPITWLNHPKFKNL--L---EKAAEEYGYKHDL 73 (92)
Q Consensus 42 ~RfvVp~~~L~hP~F~~L--L---~~aeeEfG~~~~g 73 (92)
+|+=+|+.|+.||+-.+. . +.+.+++|.+.++
T Consensus 152 ~k~g~~~~yVGHpl~d~i~~~~~r~~ar~~l~~~~~~ 188 (381)
T COG0763 152 DKFGLPCTYVGHPLADEIPLLPDREAAREKLGIDADE 188 (381)
T ss_pred HhcCCCeEEeCChhhhhccccccHHHHHHHhCCCCCC
Confidence 788899999999998776 2 4477889998887
No 49
>PF11876 DUF3396: Protein of unknown function (DUF3396); InterPro: IPR021815 This family of proteins are functionally uncharacterised. This protein is found in bacteria and viruses. Proteins in this family are typically between 302 to 382 amino acids in length.
Probab=20.84 E-value=95 Score=23.07 Aligned_cols=31 Identities=29% Similarity=0.650 Sum_probs=25.3
Q ss_pred ceEEEEeccCCCc-H-HHHHHHHHHHHhcCccC
Q 040904 41 RSRYIIPITWLNH-P-KFKNLLEKAAEEYGYKH 71 (92)
Q Consensus 41 ~~RfvVp~~~L~h-P-~F~~LL~~aeeEfG~~~ 71 (92)
.=+|.+|++||.. | .|++|+....+.+-+.|
T Consensus 24 ~l~f~~P~~~l~~~~~~~~~l~~~~a~~L~~~~ 56 (208)
T PF11876_consen 24 YLSFSLPLEWLEEGPGHFRALFLELAERLPPSH 56 (208)
T ss_pred EEEEEeCHHHHhcCcHHHHHHHHHHHHHCCCCe
Confidence 3589999999987 2 49999999998876655
No 50
>PF06307 Herpes_IR6: Herpesvirus IR6 protein; InterPro: IPR010447 This family consists of several Herpesvirus IR6 proteins. The equine herpesvirus 1 (EHV-1) IR6 protein forms typical rod-like structures in infected cells, influences virus growth at elevated temperatures, and determines the virulence of EHV-1 Rac strains [].
Probab=20.74 E-value=60 Score=24.78 Aligned_cols=41 Identities=22% Similarity=0.237 Sum_probs=23.3
Q ss_pred ChhHHHHhhhccCCCCccCCCCCCCCCCCCCeEEEEEcCCceEEEEe
Q 040904 1 MAIQEIFKQCSSFGKKCSCDQDGHPNDVPKGHCVVYVGENRSRYIIP 47 (92)
Q Consensus 1 m~~k~~lkr~~s~~~~~~~~~~~~~~~vpkG~~~VyVG~~~~RfvVp 47 (92)
|.....+|||+--... +.=+.||.|||||-=.+..-|.-|+
T Consensus 15 ~~g~~yFrrCR~E~ne------G~yA~vPpgYFPV~Ps~~P~lv~V~ 55 (214)
T PF06307_consen 15 MLGRSYFRRCREEMNE------GYYAKVPPGYFPVRPSEKPLLVPVE 55 (214)
T ss_pred cccHHHHHHHHHHhhc------CeeeecCCCccccCCCCcceeeecc
Confidence 3445556666533332 2335789999998755444444444
No 51
>PF08740 BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. This domain is found at the N terminus of the mitochondrial BSC1 subfamily, belonging to the AAA ATPase family. At2g21640 and BCS1 are both highly stress responsive genes which encode mitochondrial proteins. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA). The SA dependent pathway represented by BCS1 is one of at least three distinctive pathways to regulate mitochondrial stress response at a transcriptional level []. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III []. BCS1, a component of the inner membrane of mitochondria, belongs to the group of proteins with internal, noncleavable import signals. It has a transmembrane domain (amino acid residues 51 to 68), a presequence type helix (residues 69 to 83), and an import auxiliary region (residues 84 to 126) [].
Probab=20.70 E-value=2e+02 Score=19.98 Aligned_cols=35 Identities=23% Similarity=0.145 Sum_probs=24.8
Q ss_pred eEEEEeccCCCcHHHHHHHHHHHHhcCccCCCcEE
Q 040904 42 SRYIIPITWLNHPKFKNLLEKAAEEYGYKHDLGII 76 (92)
Q Consensus 42 ~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~g~L~ 76 (92)
+-..|..--.|...+++||+.|.+.+-=.+.+..+
T Consensus 128 e~l~l~~lg~s~~~l~~ll~ear~~~~~~~~~~t~ 162 (187)
T PF08740_consen 128 ETLTLSCLGRSPKPLKDLLEEAREYYLKKQKGKTT 162 (187)
T ss_pred eEEEEEEecCCHHHHHHHHHHHHHHHHHhcCCcEE
Confidence 45555555567889999999999987545555433
No 52
>PF08948 DUF1859: Domain of unknown function (DUF1859); InterPro: IPR015043 This entry is represented by Bacteriophage PRD1, P5. This protein has no known function though it is sometimes found in the N terminus of bacteriophage spike proteins []. ; PDB: 1W8X_N.
Probab=20.70 E-value=37 Score=23.81 Aligned_cols=28 Identities=18% Similarity=0.445 Sum_probs=7.1
Q ss_pred CCCeEEEEEcCCceEEE----------EeccCCCcHHHH
Q 040904 29 PKGHCVVYVGENRSRYI----------IPITWLNHPKFK 57 (92)
Q Consensus 29 pkG~~~VyVG~~~~Rfv----------Vp~~~L~hP~F~ 57 (92)
..||+|+.|-.- -.|+ +|+-|||.|+-+
T Consensus 86 ~QGYfPlL~~~~-~KFv~~~~~~GKks~P~~FlNF~IA~ 123 (126)
T PF08948_consen 86 KQGYFPLLVPGR-AKFVVRHTGSGKKSVPMFFLNFTIAQ 123 (126)
T ss_dssp --SS--EEE--S-SSSEEEEEEEESS----S--------
T ss_pred Ccccceeeccch-hhhhhhhccCCCcceeeEEEeceeee
Confidence 479999998431 2333 788899988644
No 53
>KOG2813 consensus Predicted molecular chaperone, contains DnaJ domain [Posttranslational modification, protein turnover, chaperones]
Probab=20.65 E-value=1.2e+02 Score=25.12 Aligned_cols=55 Identities=16% Similarity=0.172 Sum_probs=41.5
Q ss_pred EEEEEcCCceEEEEeccCCCcHHHHHHHHHHHHhcCccCCCcEEecCcHHHHHHHH
Q 040904 33 CVVYVGENRSRYIIPITWLNHPKFKNLLEKAAEEYGYKHDLGIILPCDERVFRQLT 88 (92)
Q Consensus 33 ~~VyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~g~L~IPC~~~~F~~~l 88 (92)
+.||--.+.+|+ |...+++...=.+||.+||-+-=|+.+.-..+||..-.|+.+-
T Consensus 274 ~vV~wKn~~krk-VSehr~~~~iPeell~~AeG~~~f~~en~~iypis~~~~~Dv~ 328 (406)
T KOG2813|consen 274 IVVYWKNEKKRK-VSEHRTESEIPEELLFQAEGKRIFEEENDYIYPISQYQEEDVN 328 (406)
T ss_pred EEEEeechhhhh-hhhhcccccCcHHHHHhhhcchhhhhccceEEeccccchhhHH
Confidence 455555566676 4677888888899999999765566666789999888777653
No 54
>PRK13277 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase-like protein; Provisional
Probab=20.55 E-value=34 Score=28.03 Aligned_cols=25 Identities=28% Similarity=0.565 Sum_probs=18.6
Q ss_pred CCCCCeEEEEEcCCc--eEEEEeccCCCc
Q 040904 27 DVPKGHCVVYVGENR--SRYIIPITWLNH 53 (92)
Q Consensus 27 ~vpkG~~~VyVG~~~--~RfvVp~~~L~h 53 (92)
-||.|-|++|||-+. +.|.|| ++.+
T Consensus 89 ~iPh~sf~~y~g~~~ie~~~~vp--~fGn 115 (366)
T PRK13277 89 FVPNRSFAVYVGYDAIENEFKVP--IFGN 115 (366)
T ss_pred EecCCCeEEEecHHHHhhcCCCC--cccC
Confidence 479999999999642 368888 4444
No 55
>PF04341 DUF485: Protein of unknown function, DUF485; InterPro: IPR007436 This family includes several putative integral membrane proteins.
Probab=20.53 E-value=77 Score=20.40 Aligned_cols=12 Identities=33% Similarity=0.866 Sum_probs=10.2
Q ss_pred CCcHHHHHHHHH
Q 040904 51 LNHPKFKNLLEK 62 (92)
Q Consensus 51 L~hP~F~~LL~~ 62 (92)
++||.|++|.++
T Consensus 2 ~~~p~f~~L~r~ 13 (91)
T PF04341_consen 2 LRSPEFQELVRR 13 (91)
T ss_pred CCCHHHHHHHHH
Confidence 589999999875
No 56
>cd04395 RhoGAP_ARHGAP21 RhoGAP_ARHGAP21: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP21-like proteins. ArhGAP21 is a multi-domain protein, containing RhoGAP, PH and PDZ domains, and is believed to play a role in the organization of the cell-cell junction complex. It has been shown to function as a GAP of Cdc42 and RhoA, and to interact with alpha-catenin and Arf6. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=20.38 E-value=2.2e+02 Score=20.29 Aligned_cols=38 Identities=13% Similarity=0.055 Sum_probs=27.7
Q ss_pred cHHHHHHHHHHHHhcCccCCCcEEecCcHHHHHHHHHh
Q 040904 53 HPKFKNLLEKAAEEYGYKHDLGIILPCDERVFRQLTSW 90 (92)
Q Consensus 53 hP~F~~LL~~aeeEfG~~~~g~L~IPC~~~~F~~~l~~ 90 (92)
=|.|....-..-++.|.+.+|.-++|.+...-+++...
T Consensus 18 vP~iv~~~~~~l~~~g~~~eGIFR~~g~~~~i~~l~~~ 55 (196)
T cd04395 18 VPLIVEVCCNIVEARGLETVGIYRVPGNNAAISALQEE 55 (196)
T ss_pred CChHHHHHHHHHHHcCCCCccceeCCCcHHHHHHHHHH
Confidence 35666555556678899999999999987776666543
Done!