Query 040086
Match_columns 146
No_of_seqs 107 out of 699
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 04:59:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040086.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040086hhsearch_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 1.7E-42 3.6E-47 256.1 11.1 101 1-101 3-103 (104)
2 PF02519 Auxin_inducible: Auxi 100.0 2.7E-35 5.9E-40 215.6 9.1 91 12-102 6-100 (100)
3 PLN03220 uncharacterized prote 100.0 5.3E-34 1.1E-38 210.9 8.2 86 13-100 12-102 (105)
4 PLN03219 uncharacterized prote 100.0 3.9E-31 8.4E-36 196.5 9.5 69 33-101 34-105 (108)
5 PRK02899 adaptor protein; Prov 80.7 1.4 3E-05 35.7 2.5 25 63-87 38-62 (197)
6 PF02214 BTB_2: BTB/POZ domain 80.5 1.3 2.8E-05 30.6 2.0 58 45-104 3-63 (94)
7 PRK02315 adaptor protein; Prov 73.6 2.4 5.3E-05 35.0 2.1 25 63-87 38-62 (233)
8 smart00666 PB1 PB1 domain. Pho 72.3 7.6 0.00017 25.9 4.0 53 46-103 7-70 (81)
9 PF05389 MecA: Negative regula 68.4 1.6 3.6E-05 35.2 0.0 25 63-87 38-62 (220)
10 cd05992 PB1 The PB1 domain is 65.8 17 0.00037 24.0 4.6 55 45-103 5-70 (81)
11 cd06398 PB1_Joka2 The PB1 doma 48.8 51 0.0011 23.6 4.9 56 45-100 5-73 (91)
12 cd06410 PB1_UP2 Uncharacterize 39.9 60 0.0013 23.6 4.2 34 44-81 17-50 (97)
13 PF02100 ODC_AZ: Ornithine dec 38.3 58 0.0013 24.0 4.0 51 48-99 21-75 (108)
14 PF00651 BTB: BTB/POZ domain; 37.9 71 0.0015 21.5 4.2 58 43-105 13-75 (111)
15 PF02209 VHP: Villin headpiece 37.5 14 0.0003 22.6 0.5 19 60-78 1-19 (36)
16 cd06407 PB1_NLP A PB1 domain i 35.8 76 0.0016 22.2 4.1 48 45-96 5-64 (82)
17 PF12058 DUF3539: Protein of u 35.4 6.9 0.00015 28.6 -1.3 10 59-68 4-13 (88)
18 smart00153 VHP Villin headpiec 34.2 19 0.00041 21.9 0.7 19 60-78 1-19 (36)
19 PF11834 DUF3354: Domain of un 31.8 41 0.00089 23.2 2.1 17 64-80 26-42 (69)
20 PF00564 PB1: PB1 domain; Int 30.4 1.1E+02 0.0024 20.1 4.1 54 45-103 6-71 (84)
21 PRK10308 3-methyl-adenine DNA 29.5 2E+02 0.0044 24.3 6.4 62 40-101 45-121 (283)
22 PRK02797 4-alpha-L-fucosyltran 27.5 2.3E+02 0.005 25.1 6.5 65 38-105 142-228 (322)
23 cd04395 RhoGAP_ARHGAP21 RhoGAP 26.3 1.5E+02 0.0033 23.2 4.8 44 63-106 18-61 (196)
24 PF11822 DUF3342: Domain of un 26.2 98 0.0021 27.3 4.0 54 51-107 13-71 (317)
25 PF08948 DUF1859: Domain of un 24.6 39 0.00085 25.8 1.1 28 39-67 86-123 (126)
26 cd01406 SIR2-like Sir2-like: P 22.9 1.1E+02 0.0023 24.5 3.4 36 41-82 1-36 (242)
27 COG1759 5-formaminoimidazole-4 22.6 43 0.00094 30.0 1.1 37 37-74 89-136 (361)
28 cd04404 RhoGAP-p50rhoGAP RhoGA 22.6 2.5E+02 0.0054 21.8 5.4 44 64-108 24-68 (195)
29 PF06344 Parecho_VpG: Parechov 21.5 54 0.0012 17.7 0.9 14 32-45 5-18 (20)
30 PF14062 DUF4253: Domain of un 21.4 2.6E+02 0.0056 20.5 4.9 73 10-103 29-102 (111)
31 cd06399 PB1_P40 The PB1 domain 20.9 1.1E+02 0.0024 22.5 2.8 28 51-78 15-42 (92)
32 PF05194 UreE_C: UreE urease a 20.4 1.4E+02 0.0031 20.6 3.2 27 41-73 25-51 (87)
No 1
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=1.7e-42 Score=256.10 Aligned_cols=101 Identities=38% Similarity=0.695 Sum_probs=92.9
Q ss_pred CCcccchhhHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCcEEEEecCCceeeeeecccCCcHHHHHHHHHHHHhcCCC
Q 040086 1 MSKCNKIRHIVRIRQMLRQWRRKARIAASASRATPSDVPAGHVAVCVGSSSRRFIVRATYLNHPMFKKLLVQAEEEYGFS 80 (146)
Q Consensus 1 m~k~~ki~~i~kL~~~~rkW~~~a~~~~~~~~~~~~~vpkG~~aVyVG~e~~RfvVp~~~L~hP~F~~LL~~aeEEfG~~ 80 (146)
|.|++||+++++|+||+|||+++++.+.......|.+||+||||||||++++||+||++|||||+|++||++|||||||.
T Consensus 3 ~~k~~ki~~~~~~kq~l~r~~s~~~~~~~~~~~~~~~vpkG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfGf~ 82 (104)
T PLN03090 3 IKKSNKLTQTAMLKQILKRCSSLGKKQGYDEDGLPLDVPKGHFPVYVGENRSRYIVPISFLTHPEFQSLLQQAEEEFGFD 82 (104)
T ss_pred cccccchhHHHHHHHHHHHHHHhcccCCcccccCCCCCCCCcEEEEECCCCEEEEEEHHHcCCHHHHHHHHHHHHHhCCC
Confidence 35899999999999999999999876443224578899999999999999999999999999999999999999999999
Q ss_pred CCCCeeecCChHHHHHHHHHh
Q 040086 81 HVGPLTIPCDESTFEEILRVV 101 (146)
Q Consensus 81 ~~G~L~IPC~~~~Fe~vl~~i 101 (146)
|+|+|+||||++.|++++|+|
T Consensus 83 ~~G~L~IPC~~~~Fe~ll~~i 103 (104)
T PLN03090 83 HDMGLTIPCEEVVFRSLTSMI 103 (104)
T ss_pred CCCcEEEeCCHHHHHHHHHHh
Confidence 999999999999999999998
No 2
>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=2.7e-35 Score=215.62 Aligned_cols=91 Identities=49% Similarity=0.902 Sum_probs=77.3
Q ss_pred HHHHHHHHHHHHHHhhcccC----CCCCCCCCCCcEEEEecCCceeeeeecccCCcHHHHHHHHHHHHhcCCCCCCCeee
Q 040086 12 RIRQMLRQWRRKARIAASAS----RATPSDVPAGHVAVCVGSSSRRFIVRATYLNHPMFKKLLVQAEEEYGFSHVGPLTI 87 (146)
Q Consensus 12 kL~~~~rkW~~~a~~~~~~~----~~~~~~vpkG~~aVyVG~e~~RfvVp~~~L~hP~F~~LL~~aeEEfG~~~~G~L~I 87 (146)
+....+++|++.++..++.. +....++|+||||||||++++||+||++|||||+|++||++|||||||+++|+|+|
T Consensus 6 k~~~~~~k~~~~~~~~~~~~~~~~~~~~~~vp~G~~~VyVG~~~~Rfvvp~~~L~hp~f~~LL~~aeeEfG~~~~G~l~i 85 (100)
T PF02519_consen 6 KSLASAKKWQSRARSKSSSSSSSRSSSESDVPKGHFAVYVGEERRRFVVPVSYLNHPLFQELLEQAEEEFGFDQDGPLTI 85 (100)
T ss_pred HHHHHHHhhhhhhhhcccccccccccccCCCCCCeEEEEeCccceEEEechHHcCchhHHHHHHHHhhhcCcCCCCcEEe
Confidence 33445677777765533321 12237899999999999999999999999999999999999999999999999999
Q ss_pred cCChHHHHHHHHHhc
Q 040086 88 PCDESTFEEILRVVS 102 (146)
Q Consensus 88 PC~~~~Fe~vl~~i~ 102 (146)
|||++.|++++|+|+
T Consensus 86 PC~~~~Fe~~l~~le 100 (100)
T PF02519_consen 86 PCDVVLFEHLLWLLE 100 (100)
T ss_pred eCCHHHHHHHHHHhC
Confidence 999999999999986
No 3
>PLN03220 uncharacterized protein; Provisional
Probab=100.00 E-value=5.3e-34 Score=210.91 Aligned_cols=86 Identities=44% Similarity=0.809 Sum_probs=70.5
Q ss_pred HHHHHHHHHHHHHhhcccCCCCCCCCCCCcEEEEecC----CceeeeeecccCCcHHHHHHHHHHHHhcCCCC-CCCeee
Q 040086 13 IRQMLRQWRRKARIAASASRATPSDVPAGHVAVCVGS----SSRRFIVRATYLNHPMFKKLLVQAEEEYGFSH-VGPLTI 87 (146)
Q Consensus 13 L~~~~rkW~~~a~~~~~~~~~~~~~vpkG~~aVyVG~----e~~RfvVp~~~L~hP~F~~LL~~aeEEfG~~~-~G~L~I 87 (146)
.||++++.. .+...++ ++..+.+||+||||||||+ +++||+||++|||||+|++||++|||||||.| +|+|+|
T Consensus 12 ~k~~~~~~~-~~~~~~~-~~~~~~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP~F~~LL~~AeEEfGf~~~~G~L~I 89 (105)
T PLN03220 12 TKQILKLNS-LANRNRT-SSSSSDHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHPSFKEFLSRAEEEFGFNHPMGGLTI 89 (105)
T ss_pred HHHHHHHHh-hcccccc-cccccCCCCCCeEEEEECCCCCccceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEe
Confidence 355555555 3322111 2345678999999999997 48999999999999999999999999999998 699999
Q ss_pred cCChHHHHHHHHH
Q 040086 88 PCDESTFEEILRV 100 (146)
Q Consensus 88 PC~~~~Fe~vl~~ 100 (146)
|||++.|++++..
T Consensus 90 PCd~~~F~~ll~s 102 (105)
T PLN03220 90 PCREEVFLDLIAS 102 (105)
T ss_pred eCCHHHHHHHHHh
Confidence 9999999999863
No 4
>PLN03219 uncharacterized protein; Provisional
Probab=99.97 E-value=3.9e-31 Score=196.49 Aligned_cols=69 Identities=51% Similarity=0.924 Sum_probs=64.0
Q ss_pred CCCCCCCCCcEEEEecC--CceeeeeecccCCcHHHHHHHHHHHHhcCCCC-CCCeeecCChHHHHHHHHHh
Q 040086 33 ATPSDVPAGHVAVCVGS--SSRRFIVRATYLNHPMFKKLLVQAEEEYGFSH-VGPLTIPCDESTFEEILRVV 101 (146)
Q Consensus 33 ~~~~~vpkG~~aVyVG~--e~~RfvVp~~~L~hP~F~~LL~~aeEEfG~~~-~G~L~IPC~~~~Fe~vl~~i 101 (146)
+.+.++|+||+|||||+ |++||+||++|||||+|++||++|||||||.+ +|+|+||||++.|++++..-
T Consensus 34 ~~~~~vpkGh~aVYVG~~~E~kRFvVPi~yL~hP~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~~~ 105 (108)
T PLN03219 34 TTSGLVPKGHVAVYVGEQMEKKRFVVPISYLNHPLFREFLNRAEEECGFHHSMGGLTIPCREESFLHLITSH 105 (108)
T ss_pred CCCCCCCCCeEEEEECCCCCceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEEeCCHHHHHHHHHhh
Confidence 45578999999999997 58999999999999999999999999999997 69999999999999999753
No 5
>PRK02899 adaptor protein; Provisional
Probab=80.72 E-value=1.4 Score=35.74 Aligned_cols=25 Identities=32% Similarity=0.846 Sum_probs=21.5
Q ss_pred cHHHHHHHHHHHHhcCCCCCCCeee
Q 040086 63 HPMFKKLLVQAEEEYGFSHVGPLTI 87 (146)
Q Consensus 63 hP~F~~LL~~aeEEfG~~~~G~L~I 87 (146)
+-+|.++|++|..|+||..+|||+|
T Consensus 38 e~lF~~mm~Ea~~e~~F~~~~pl~~ 62 (197)
T PRK02899 38 HQLFRDMMQEANKELGFEADGPIAV 62 (197)
T ss_pred HHHHHHHHHHhhhccCcccCCeEEE
Confidence 3467888999999999999999974
No 6
>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=80.47 E-value=1.3 Score=30.61 Aligned_cols=58 Identities=21% Similarity=0.218 Sum_probs=42.6
Q ss_pred EEecCCceeeeeecccCC-c--HHHHHHHHHHHHhcCCCCCCCeeecCChHHHHHHHHHhcCC
Q 040086 45 VCVGSSSRRFIVRATYLN-H--PMFKKLLVQAEEEYGFSHVGPLTIPCDESTFEEILRVVSRP 104 (146)
Q Consensus 45 VyVG~e~~RfvVp~~~L~-h--P~F~~LL~~aeEEfG~~~~G~L~IPC~~~~Fe~vl~~i~~~ 104 (146)
.-|| .++|.++.+.|. + ..|..++........-..+|.+-|-++...|++||..+..+
T Consensus 3 lNVG--G~~f~~~~~tL~~~~~s~l~~~~~~~~~~~~~~~~~~~fiDRdp~~F~~IL~ylr~~ 63 (94)
T PF02214_consen 3 LNVG--GTIFETSRSTLTRYPDSLLARLFSGERSDDYDDDDGEYFIDRDPELFEYILNYLRTG 63 (94)
T ss_dssp EEET--TEEEEEEHHHHHTSTTSTTTSHHHTGHGGGEETTTTEEEESS-HHHHHHHHHHHHHT
T ss_pred EEEC--CEEEEEcHHHHhhCCCChhhhHHhhccccccCCccceEEeccChhhhhHHHHHHhhc
Confidence 3465 588999988776 4 47888887653222223468999999999999999999984
No 7
>PRK02315 adaptor protein; Provisional
Probab=73.59 E-value=2.4 Score=35.01 Aligned_cols=25 Identities=28% Similarity=0.541 Sum_probs=22.5
Q ss_pred cHHHHHHHHHHHHhcCCCCCCCeee
Q 040086 63 HPMFKKLLVQAEEEYGFSHVGPLTI 87 (146)
Q Consensus 63 hP~F~~LL~~aeEEfG~~~~G~L~I 87 (146)
+-+|.++|+++..|+||..+|||+|
T Consensus 38 e~fF~~mm~Ea~~e~~F~~~~pl~~ 62 (233)
T PRK02315 38 EEFFYSMMDEVDEEDDFADEGPLWF 62 (233)
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 4589999999999999999999985
No 8
>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=72.28 E-value=7.6 Score=25.91 Aligned_cols=53 Identities=23% Similarity=0.418 Sum_probs=38.7
Q ss_pred EecCCceeeeeecccCCcHHHHHHHHHHHHhcCCCC----------CC-CeeecCChHHHHHHHHHhcC
Q 040086 46 CVGSSSRRFIVRATYLNHPMFKKLLVQAEEEYGFSH----------VG-PLTIPCDESTFEEILRVVSR 103 (146)
Q Consensus 46 yVG~e~~RfvVp~~~L~hP~F~~LL~~aeEEfG~~~----------~G-~L~IPC~~~~Fe~vl~~i~~ 103 (146)
+-|++.+||.+|. ...|.+|..+..+.|+... +| .++|.++. .++.++.+...
T Consensus 7 ~~~~~~~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~-Dl~~a~~~~~~ 70 (81)
T smart00666 7 RYGGETRRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDE-DLEEAIEEYDS 70 (81)
T ss_pred EECCEEEEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHH-HHHHHHHHHHH
Confidence 3477889999985 7789999999999998751 34 66777755 45566665544
No 9
>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=68.39 E-value=1.6 Score=35.17 Aligned_cols=25 Identities=44% Similarity=0.760 Sum_probs=0.0
Q ss_pred cHHHHHHHHHHHHhcCCCCCCCeee
Q 040086 63 HPMFKKLLVQAEEEYGFSHVGPLTI 87 (146)
Q Consensus 63 hP~F~~LL~~aeEEfG~~~~G~L~I 87 (146)
+-.|.++|++|.+|+||..+|||++
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 5689999999999999999999885
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=65.80 E-value=17 Score=23.96 Aligned_cols=55 Identities=31% Similarity=0.498 Sum_probs=40.4
Q ss_pred EEecCCceeeeeecccCCcHHHHHHHHHHHHhcCCC----------CCC-CeeecCChHHHHHHHHHhcC
Q 040086 45 VCVGSSSRRFIVRATYLNHPMFKKLLVQAEEEYGFS----------HVG-PLTIPCDESTFEEILRVVSR 103 (146)
Q Consensus 45 VyVG~e~~RfvVp~~~L~hP~F~~LL~~aeEEfG~~----------~~G-~L~IPC~~~~Fe~vl~~i~~ 103 (146)
++-+.+.+||.+|. .++.|.+|..+..+.|++. .+| .++|.++ ..|+..+....+
T Consensus 5 ~~~~~~~~~~~~~~---~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd-~Dl~~a~~~~~~ 70 (81)
T cd05992 5 VKYGGEIRRFVVVS---RSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSD-EDLEEAIEEARR 70 (81)
T ss_pred EEecCCCEEEEEec---CCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCH-HHHHHHHHHHhh
Confidence 44556789999997 8999999999999999885 133 4445554 567777777665
No 11
>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=48.81 E-value=51 Score=23.61 Aligned_cols=56 Identities=23% Similarity=0.222 Sum_probs=38.3
Q ss_pred EEecCCceeeeeecc-cCCcHHHHHHHHHHHHhcCCCC-----------CC-CeeecCChHHHHHHHHH
Q 040086 45 VCVGSSSRRFIVRAT-YLNHPMFKKLLVQAEEEYGFSH-----------VG-PLTIPCDESTFEEILRV 100 (146)
Q Consensus 45 VyVG~e~~RfvVp~~-~L~hP~F~~LL~~aeEEfG~~~-----------~G-~L~IPC~~~~Fe~vl~~ 100 (146)
|.-|++.+||-+|.. --.+.-|..|.++-++-|.... +| .++|.||.++-+-+-..
T Consensus 5 v~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~~ 73 (91)
T cd06398 5 VKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQYF 73 (91)
T ss_pred EEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHHH
Confidence 334778999999963 0125689999999999886653 23 56688887766555443
No 12
>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=39.85 E-value=60 Score=23.56 Aligned_cols=34 Identities=26% Similarity=0.338 Sum_probs=26.6
Q ss_pred EEEecCCceeeeeecccCCcHHHHHHHHHHHHhcCCCC
Q 040086 44 AVCVGSSSRRFIVRATYLNHPMFKKLLVQAEEEYGFSH 81 (146)
Q Consensus 44 aVyVG~e~~RfvVp~~~L~hP~F~~LL~~aeEEfG~~~ 81 (146)
.=|||.+.+-..|+-+ -.|.+|..+..+.++...
T Consensus 17 l~Y~GG~tr~i~V~r~----~s~~el~~kl~~~~~~~~ 50 (97)
T cd06410 17 LRYVGGETRIVSVDRS----ISFKELVSKLSELFGAGV 50 (97)
T ss_pred EEEcCCceEEEEEcCC----CCHHHHHHHHHHHhCCCC
Confidence 4699998887788865 477888888888887655
No 13
>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=38.28 E-value=58 Score=23.97 Aligned_cols=51 Identities=24% Similarity=0.327 Sum_probs=23.8
Q ss_pred cCCceeee-eeccc---CCcHHHHHHHHHHHHhcCCCCCCCeeecCChHHHHHHHH
Q 040086 48 GSSSRRFI-VRATY---LNHPMFKKLLVQAEEEYGFSHVGPLTIPCDESTFEEILR 99 (146)
Q Consensus 48 G~e~~Rfv-Vp~~~---L~hP~F~~LL~~aeEEfG~~~~G~L~IPC~~~~Fe~vl~ 99 (146)
|+++.=|+ +|-.. ..-.-|..|||.|||.++.++ -.++++=+-.....+++
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 34556666 45433 344679999999999988765 34445443333444443
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=37.92 E-value=71 Score=21.52 Aligned_cols=58 Identities=26% Similarity=0.517 Sum_probs=41.0
Q ss_pred EEEEecCCceeeeeecccC--CcHHHHHHHHHHHHhcCCCCCC--Ceeec-CChHHHHHHHHHhcCCC
Q 040086 43 VAVCVGSSSRRFIVRATYL--NHPMFKKLLVQAEEEYGFSHVG--PLTIP-CDESTFEEILRVVSRPE 105 (146)
Q Consensus 43 ~aVyVG~e~~RfvVp~~~L--~hP~F~~LL~~aeEEfG~~~~G--~L~IP-C~~~~Fe~vl~~i~~~~ 105 (146)
+.+.||+ ..+|-++-..| ..|.|+.+++.. +....+ .+.++ ++...|+.++..+-.++
T Consensus 13 ~~i~v~d-~~~~~vhk~iL~~~S~~F~~~~~~~----~~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~~ 75 (111)
T PF00651_consen 13 VTIRVGD-GKTFYVHKNILAARSPYFRNLFEGS----KFKESTVPEISLPDVSPEAFEAFLEYMYTGE 75 (111)
T ss_dssp EEEEETT-TEEEEE-HHHHHHHBHHHHHHHTTT----TSTTSSEEEEEETTSCHHHHHHHHHHHHHSE
T ss_pred EEEEECC-CEEEeechhhhhccchhhhhccccc----ccccccccccccccccccccccccccccCCc
Confidence 4556654 68888888776 569999999888 222233 35555 88999999999997654
No 15
>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=37.46 E-value=14 Score=22.58 Aligned_cols=19 Identities=32% Similarity=0.532 Sum_probs=15.2
Q ss_pred cCCcHHHHHHHHHHHHhcC
Q 040086 60 YLNHPMFKKLLVQAEEEYG 78 (146)
Q Consensus 60 ~L~hP~F~~LL~~aeEEfG 78 (146)
||+.-.|++++.++.+||-
T Consensus 1 YLsd~dF~~vFgm~~~eF~ 19 (36)
T PF02209_consen 1 YLSDEDFEKVFGMSREEFY 19 (36)
T ss_dssp GS-HHHHHHHHSS-HHHHH
T ss_pred CcCHHHHHHHHCCCHHHHH
Confidence 7899999999999999974
No 16
>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=35.80 E-value=76 Score=22.21 Aligned_cols=48 Identities=17% Similarity=0.228 Sum_probs=33.6
Q ss_pred EEecCCceeeeeecccCCcHHHHHHHHHHHHhcCCCC------------CCCeeecCChHHHHH
Q 040086 45 VCVGSSSRRFIVRATYLNHPMFKKLLVQAEEEYGFSH------------VGPLTIPCDESTFEE 96 (146)
Q Consensus 45 VyVG~e~~RfvVp~~~L~hP~F~~LL~~aeEEfG~~~------------~G~L~IPC~~~~Fe~ 96 (146)
+..|++..||.+|.. .-|++|.++-.+-|++.. +..++|.|+.++=|.
T Consensus 5 ~~~~~d~~r~~l~~~----~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~ea 64 (82)
T cd06407 5 ATYGEEKIRFRLPPS----WGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEEC 64 (82)
T ss_pred EEeCCeEEEEEcCCC----CCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHH
Confidence 344778889988853 369999999999887642 235667777765443
No 17
>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=35.43 E-value=6.9 Score=28.56 Aligned_cols=10 Identities=70% Similarity=1.162 Sum_probs=6.9
Q ss_pred ccCCcHHHHH
Q 040086 59 TYLNHPMFKK 68 (146)
Q Consensus 59 ~~L~hP~F~~ 68 (146)
.|||||.|--
T Consensus 4 ~YLNHPtFGl 13 (88)
T PF12058_consen 4 TYLNHPTFGL 13 (88)
T ss_dssp -EEEETTTEE
T ss_pred ccccCCccch
Confidence 5899998743
No 18
>smart00153 VHP Villin headpiece domain.
Probab=34.21 E-value=19 Score=21.91 Aligned_cols=19 Identities=26% Similarity=0.488 Sum_probs=16.6
Q ss_pred cCCcHHHHHHHHHHHHhcC
Q 040086 60 YLNHPMFKKLLVQAEEEYG 78 (146)
Q Consensus 60 ~L~hP~F~~LL~~aeEEfG 78 (146)
||+.-.|++.+.++.+||-
T Consensus 1 yLsdeeF~~vfgmsr~eF~ 19 (36)
T smart00153 1 YLSDEDFEEVFGMTREEFY 19 (36)
T ss_pred CCCHHHHHHHHCCCHHHHH
Confidence 7888999999999999973
No 19
>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=31.76 E-value=41 Score=23.16 Aligned_cols=17 Identities=41% Similarity=0.686 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHhcCCC
Q 040086 64 PMFKKLLVQAEEEYGFS 80 (146)
Q Consensus 64 P~F~~LL~~aeEEfG~~ 80 (146)
-.++|||+.|++.||+.
T Consensus 26 ~SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 26 DSLEELLKIASEKFGFS 42 (69)
T ss_pred ccHHHHHHHHHHHhCCC
Confidence 37999999999999985
No 20
>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=30.40 E-value=1.1e+02 Score=20.12 Aligned_cols=54 Identities=26% Similarity=0.420 Sum_probs=34.5
Q ss_pred EEecCCcee-eeeecccCCcHHHHHHHHHHHHhcCCC----------CCC-CeeecCChHHHHHHHHHhcC
Q 040086 45 VCVGSSSRR-FIVRATYLNHPMFKKLLVQAEEEYGFS----------HVG-PLTIPCDESTFEEILRVVSR 103 (146)
Q Consensus 45 VyVG~e~~R-fvVp~~~L~hP~F~~LL~~aeEEfG~~----------~~G-~L~IPC~~~~Fe~vl~~i~~ 103 (146)
++-+++.+| +.+| ..+.|.+|.++.++.||.. .+| .++|.++.+ |+..+....+
T Consensus 6 ~~~~~~~~~~~~~~----~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~D-l~~a~~~~~~ 71 (84)
T PF00564_consen 6 VRYGGDIRRIISLP----SDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDED-LQEAIEQAKE 71 (84)
T ss_dssp EEETTEEEEEEEEC----STSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHH-HHHHHHHHHH
T ss_pred EEECCeeEEEEEcC----CCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHH-HHHHHHHHHh
Confidence 344555555 4444 5679999999999999984 245 455666554 5555555544
No 21
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=29.53 E-value=2e+02 Score=24.34 Aligned_cols=62 Identities=16% Similarity=0.224 Sum_probs=42.8
Q ss_pred CCcEEEEecCCceeeeeecccCCcHHHHHHHHHHHHhcCCCCC---------------CCeeecCChHHHHHHHHHh
Q 040086 40 AGHVAVCVGSSSRRFIVRATYLNHPMFKKLLVQAEEEYGFSHV---------------GPLTIPCDESTFEEILRVV 101 (146)
Q Consensus 40 kG~~aVyVG~e~~RfvVp~~~L~hP~F~~LL~~aeEEfG~~~~---------------G~L~IPC~~~~Fe~vl~~i 101 (146)
.|++.|.-..++..+.+.++.-.-+....++.....-|+.+.| -+|+||...+.||.+++.|
T Consensus 45 ~~~~~v~~~~~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L~~~~~~~~GlR~p~~~d~fE~lv~aI 121 (283)
T PRK10308 45 RGVVTVIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGKLGAARPGLRLPGSVDAFEQGVRAI 121 (283)
T ss_pred cEEEEEEEcCCCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCCcCCCCCCHHHHHHHHH
Confidence 4666666545555666666554445566677777777766543 3689999999999888876
No 22
>PRK02797 4-alpha-L-fucosyltransferase; Provisional
Probab=27.51 E-value=2.3e+02 Score=25.15 Aligned_cols=65 Identities=20% Similarity=0.360 Sum_probs=45.3
Q ss_pred CCCCcEEEEecCC--------------------ceeeeeeccc--CCcHHHHHHHHHHHHhcCCCCCCCeeecCChHHHH
Q 040086 38 VPAGHVAVCVGSS--------------------SRRFIVRATY--LNHPMFKKLLVQAEEEYGFSHVGPLTIPCDESTFE 95 (146)
Q Consensus 38 vpkG~~aVyVG~e--------------------~~RfvVp~~~--L~hP~F~~LL~~aeEEfG~~~~G~L~IPC~~~~Fe 95 (146)
.+++.+.|.||.+ .-|++||++| =|.--.++..+.+++-||- +-+++-=+---|+
T Consensus 142 ~~~~~~tIlvGNSgd~SN~Hie~L~~l~~~~~~~v~ii~PlsYp~gn~~Yi~~V~~~~~~lF~~---~~~~~L~e~l~f~ 218 (322)
T PRK02797 142 QRAGKMTILVGNSGDRSNRHIEALRALHQQFGDNVKIIVPMGYPANNQAYIEEVRQAGLALFGA---ENFQILTEKLPFD 218 (322)
T ss_pred cCCCceEEEEeCCCCCcccHHHHHHHHHHHhCCCeEEEEECCcCCCCHHHHHHHHHHHHHhcCc---ccEEehhhhCCHH
Confidence 4677899999853 3499999999 5655666666777777773 3444444555677
Q ss_pred HHHHHhcCCC
Q 040086 96 EILRVVSRPE 105 (146)
Q Consensus 96 ~vl~~i~~~~ 105 (146)
..+.+|.+-|
T Consensus 219 eYl~lL~~~D 228 (322)
T PRK02797 219 DYLALLRQCD 228 (322)
T ss_pred HHHHHHHhCC
Confidence 7777776655
No 23
>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=26.31 E-value=1.5e+02 Score=23.17 Aligned_cols=44 Identities=16% Similarity=0.319 Sum_probs=36.2
Q ss_pred cHHHHHHHHHHHHhcCCCCCCCeeecCChHHHHHHHHHhcCCCC
Q 040086 63 HPMFKKLLVQAEEEYGFSHVGPLTIPCDESTFEEILRVVSRPET 106 (146)
Q Consensus 63 hP~F~~LL~~aeEEfG~~~~G~L~IPC~~~~Fe~vl~~i~~~~~ 106 (146)
=|.|.+..-..-++.|...+|.-++|.+...-+.+...++++..
T Consensus 18 vP~iv~~~~~~l~~~g~~~eGIFR~~g~~~~i~~l~~~l~~~~~ 61 (196)
T cd04395 18 VPLIVEVCCNIVEARGLETVGIYRVPGNNAAISALQEELNRGGF 61 (196)
T ss_pred CChHHHHHHHHHHHcCCCCccceeCCCcHHHHHHHHHHHhcCCC
Confidence 45666555556678899999999999999999999999998763
No 24
>PF11822 DUF3342: Domain of unknown function (DUF3342); InterPro: IPR021777 This family of proteins are functionally uncharacterised. This family is found in bacteria. This presumed domain is typically between 170 to 303 amino acids in length. The N-terminal half of this family is a BTB-like domain.
Probab=26.16 E-value=98 Score=27.33 Aligned_cols=54 Identities=20% Similarity=0.358 Sum_probs=41.0
Q ss_pred ceeeeeecccCC--cHHHHHHHHH---HHHhcCCCCCCCeeecCChHHHHHHHHHhcCCCCC
Q 040086 51 SRRFIVRATYLN--HPMFKKLLVQ---AEEEYGFSHVGPLTIPCDESTFEEILRVVSRPETG 107 (146)
Q Consensus 51 ~~RfvVp~~~L~--hP~F~~LL~~---aeEEfG~~~~G~L~IPC~~~~Fe~vl~~i~~~~~~ 107 (146)
.+=|..|.+.|- ..-|++.|.. ..++. .+=.|.+-||+..|+.++..+++..+.
T Consensus 13 ~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~---~~idisVhCDv~iF~WLm~yv~~~~p~ 71 (317)
T PF11822_consen 13 KRDFTCPRDLLVSEMRYFAEYLSRYINDSQRW---EEIDISVHCDVHIFEWLMRYVKGEPPS 71 (317)
T ss_pred ceeeeccHHHHHHhhHHHHHHHhhcccccCcC---CCcceEEecChhHHHHHHHHhhcCCCc
Confidence 577999988875 4669999965 33321 135778889999999999999997664
No 25
>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=24.62 E-value=39 Score=25.76 Aligned_cols=28 Identities=21% Similarity=0.414 Sum_probs=8.3
Q ss_pred CCCcEEEEecCCceeee----------eecccCCcHHHH
Q 040086 39 PAGHVAVCVGSSSRRFI----------VRATYLNHPMFK 67 (146)
Q Consensus 39 pkG~~aVyVG~e~~Rfv----------Vp~~~L~hP~F~ 67 (146)
..|++|+.| ..+-+|+ +|+-|||.|+-+
T Consensus 86 ~QGYfPlL~-~~~~KFv~~~~~~GKks~P~~FlNF~IA~ 123 (126)
T PF08948_consen 86 KQGYFPLLV-PGRAKFVVRHTGSGKKSVPMFFLNFTIAQ 123 (126)
T ss_dssp --SS--EEE---SSSSEEEEEEEESS----S--------
T ss_pred Ccccceeec-cchhhhhhhhccCCCcceeeEEEeceeee
Confidence 379999999 3455555 678888887643
No 26
>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=22.89 E-value=1.1e+02 Score=24.49 Aligned_cols=36 Identities=31% Similarity=0.445 Sum_probs=28.3
Q ss_pred CcEEEEecCCceeeeeecccCCcHHHHHHHHHHHHhcCCCCC
Q 040086 41 GHVAVCVGSSSRRFIVRATYLNHPMFKKLLVQAEEEYGFSHV 82 (146)
Q Consensus 41 G~~aVyVG~e~~RfvVp~~~L~hP~F~~LL~~aeEEfG~~~~ 82 (146)
|++++++|..-. ++ .+-|.+.+|++...++++...+
T Consensus 1 g~lvlFiGAG~S---~~---~glP~W~~Ll~~l~~~~~~~~~ 36 (242)
T cd01406 1 GRVVIFVGAGVS---VS---SGLPDWKTLLDEIASELGLEID 36 (242)
T ss_pred CCEEEEecCccc---cc---cCCCChHHHHHHHHHHcCCccc
Confidence 688999997632 12 5789999999999999987643
No 27
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=22.64 E-value=43 Score=30.03 Aligned_cols=37 Identities=27% Similarity=0.324 Sum_probs=25.4
Q ss_pred CCCCCcEEEEecCC--ceeeeeec---------ccCCcHHHHHHHHHHH
Q 040086 37 DVPAGHVAVCVGSS--SRRFIVRA---------TYLNHPMFKKLLVQAE 74 (146)
Q Consensus 37 ~vpkG~~aVyVG~e--~~RfvVp~---------~~L~hP~F~~LL~~ae 74 (146)
-+|.|-|++|||-| -..|.||+ +- ..-.-..||++|.
T Consensus 89 ~IP~gSfv~Y~G~d~ie~~~~vP~fGnR~lLrwE~-~~~~~~~lLekAg 136 (361)
T COG1759 89 FIPHGSFVAYVGYDGIENEFEVPMFGNRELLRWEE-DRKLEYKLLEKAG 136 (361)
T ss_pred EecCCceEEEecchhhhhcccCcccccHhHhhhhc-chhhHHHHHHHcC
Confidence 48999999999966 25577775 11 2334467888775
No 28
>cd04404 RhoGAP-p50rhoGAP RhoGAP-p50rhoGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP, also known as RhoGAP-1, contains a C-terminal RhoGAP domain and an N-terminal Sec14 domain which binds phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). It is ubiquitously expressed and preferentially active on Cdc42. This subgroup also contains closely related ARHGAP8. 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=22.63 E-value=2.5e+02 Score=21.84 Aligned_cols=44 Identities=9% Similarity=0.089 Sum_probs=34.3
Q ss_pred HHHH-HHHHHHHHhcCCCCCCCeeecCChHHHHHHHHHhcCCCCCC
Q 040086 64 PMFK-KLLVQAEEEYGFSHVGPLTIPCDESTFEEILRVVSRPETGT 108 (146)
Q Consensus 64 P~F~-~LL~~aeEEfG~~~~G~L~IPC~~~~Fe~vl~~i~~~~~~~ 108 (146)
|.+. .+++..++ .|.+.+|.-++|-+...-+.+...++++++.+
T Consensus 24 P~il~~~i~~l~~-~g~~~eGIFR~~g~~~~i~~l~~~~~~~~~~~ 68 (195)
T cd04404 24 PPVVRETVEYLQA-HALTTEGIFRRSANTQVVKEVQQKYNMGEPVD 68 (195)
T ss_pred ChHHHHHHHHHHH-cCCCCCCeeeCCCcHHHHHHHHHHHhCCCCCC
Confidence 4444 55555544 89999999999999999999999998876443
No 29
>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=21.46 E-value=54 Score=17.68 Aligned_cols=14 Identities=29% Similarity=0.484 Sum_probs=10.6
Q ss_pred CCCCCCCCCCcEEE
Q 040086 32 RATPSDVPAGHVAV 45 (146)
Q Consensus 32 ~~~~~~vpkG~~aV 45 (146)
...|..-|||.|||
T Consensus 5 ptlp~~kpkgtfpv 18 (20)
T PF06344_consen 5 PTLPVAKPKGTFPV 18 (20)
T ss_pred ccccccccCCcccc
Confidence 34566779999987
No 30
>PF14062 DUF4253: Domain of unknown function (DUF4253)
Probab=21.37 E-value=2.6e+02 Score=20.48 Aligned_cols=73 Identities=21% Similarity=0.245 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCcEEEEecCCceeeeeecccCCcH-HHHHHHHHHHHhcCCCCCCCeeec
Q 040086 10 IVRIRQMLRQWRRKARIAASASRATPSDVPAGHVAVCVGSSSRRFIVRATYLNHP-MFKKLLVQAEEEYGFSHVGPLTIP 88 (146)
Q Consensus 10 i~kL~~~~rkW~~~a~~~~~~~~~~~~~vpkG~~aVyVG~e~~RfvVp~~~L~hP-~F~~LL~~aeEEfG~~~~G~L~IP 88 (146)
...+..++|.|+.+- |..+|.+|.+ .|-...-+-| ...+.+..|.|-|.|..|-.- --
T Consensus 29 ~~~~~a~lr~W~er~----------------ga~i~~i~~d----~le~~v~~pP~~~~ea~~lA~E~y~fCpD~v~-qg 87 (111)
T PF14062_consen 29 TADIIAVLRYWEERY----------------GAEIVGIGFD----TLELSVARPPQTPEEAEALAAEHYAFCPDIVD-QG 87 (111)
T ss_pred HHHHHHHHHHHHHHh----------------CEEEEEEECC----EEEEEECCCCCCHHHHHHHHHHHHHhCccHHh-cC
Confidence 345667788887543 6677777765 2444444566 688999999999999875111 12
Q ss_pred CChHHHHHHHHHhcC
Q 040086 89 CDESTFEEILRVVSR 103 (146)
Q Consensus 89 C~~~~Fe~vl~~i~~ 103 (146)
++...++.+-..|.+
T Consensus 88 ~~~~~l~~la~~L~~ 102 (111)
T PF14062_consen 88 YGNFTLEELAEELRK 102 (111)
T ss_pred CCCCCHHHHHHHHhC
Confidence 333355555555543
No 31
>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=20.91 E-value=1.1e+02 Score=22.52 Aligned_cols=28 Identities=25% Similarity=0.415 Sum_probs=23.5
Q ss_pred ceeeeeecccCCcHHHHHHHHHHHHhcC
Q 040086 51 SRRFIVRATYLNHPMFKKLLVQAEEEYG 78 (146)
Q Consensus 51 ~~RfvVp~~~L~hP~F~~LL~~aeEEfG 78 (146)
.+=..|.-+.-..|.|++||....++|+
T Consensus 15 ~rdi~vee~l~~~P~~kdLl~lmr~~f~ 42 (92)
T cd06399 15 IRDIAVEEDLSSTPLLKDLLELTRREFQ 42 (92)
T ss_pred ccceEeecccccCccHHHHHHHHHHHhc
Confidence 3455677788889999999999999986
No 32
>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=20.38 E-value=1.4e+02 Score=20.61 Aligned_cols=27 Identities=15% Similarity=0.262 Sum_probs=16.6
Q ss_pred CcEEEEecCCceeeeeecccCCcHHHHHHHHHH
Q 040086 41 GHVAVCVGSSSRRFIVRATYLNHPMFKKLLVQA 73 (146)
Q Consensus 41 G~~aVyVG~e~~RfvVp~~~L~hP~F~~LL~~a 73 (146)
=|+|++++++ +..|| ..+.+.++|++.
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 3889999765 77777 566667777763
Done!