Query 047125
Match_columns 166
No_of_seqs 117 out of 597
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 07:53:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047125.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047125hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02519 Auxin_inducible: Auxi 100.0 3.9E-33 8.4E-38 208.6 8.4 68 94-164 33-100 (100)
2 PLN03090 auxin-responsive fami 100.0 1.6E-32 3.5E-37 208.6 8.1 68 93-163 36-103 (104)
3 PLN03219 uncharacterized prote 100.0 3.7E-32 8E-37 208.1 7.9 71 93-163 35-105 (108)
4 PLN03220 uncharacterized prote 100.0 7.8E-31 1.7E-35 200.0 8.5 70 93-162 31-102 (105)
5 PRK02899 adaptor protein; Prov 77.7 1.9 4.1E-05 35.8 2.4 25 124-149 38-62 (197)
6 PF02214 BTB_2: BTB/POZ domain 71.3 4.1 9E-05 28.5 2.6 56 104-164 3-61 (94)
7 PRK02315 adaptor protein; Prov 70.5 3.4 7.3E-05 35.0 2.3 25 124-149 38-62 (233)
8 PF05389 MecA: Negative regula 64.2 2.2 4.8E-05 35.1 0.0 25 124-149 38-62 (220)
9 smart00666 PB1 PB1 domain. Pho 43.3 92 0.002 21.0 5.3 50 107-163 9-68 (81)
10 cd05992 PB1 The PB1 domain is 34.2 1.4E+02 0.0031 19.9 6.9 47 113-163 12-68 (81)
11 PF11834 DUF3354: Domain of un 32.8 34 0.00073 24.5 1.9 16 126-141 27-42 (69)
12 KOG2523 Predicted RNA-binding 30.6 90 0.002 26.6 4.3 72 54-142 86-160 (181)
13 PF07429 Glyco_transf_56: 4-al 28.5 1.5E+02 0.0032 27.6 5.7 46 96-141 180-245 (360)
14 PRK10308 3-methyl-adenine DNA 27.4 2.3E+02 0.005 24.6 6.4 62 100-163 46-121 (283)
15 PF08861 DUF1828: Domain of un 26.9 1.5E+02 0.0032 21.2 4.4 39 124-162 44-82 (90)
16 PF12342 DUF3640: Protein of u 24.6 26 0.00056 21.4 0.1 8 32-39 16-23 (26)
17 COG1759 5-formaminoimidazole-4 24.4 32 0.0007 31.9 0.7 24 96-119 89-112 (361)
18 cd06410 PB1_UP2 Uncharacterize 22.5 1.8E+02 0.004 21.7 4.3 51 103-161 17-80 (97)
19 PF11287 DUF3088: Protein of u 22.1 54 0.0012 25.8 1.4 20 7-26 2-28 (112)
20 smart00153 VHP Villin headpiec 21.9 45 0.00097 21.1 0.8 19 121-139 1-19 (36)
21 PF11822 DUF3342: Domain of un 21.7 1.2E+02 0.0027 27.6 3.8 59 103-165 2-67 (317)
22 PF02209 VHP: Villin headpiece 20.8 38 0.00083 21.6 0.3 19 121-139 1-19 (36)
No 1
>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=3.9e-33 Score=208.57 Aligned_cols=68 Identities=40% Similarity=0.579 Sum_probs=65.5
Q ss_pred CCCCCCceEEEEEcCCCCceEEEEeccCCCCHHHHHHHHhHHHhcCCcCCCCceEeeccHHHHHHHHHhhc
Q 047125 94 TRSIRSFLLEVEVGRPENQKLASTPVSFLSQPPFQELLSKAEEEFGYNNPMGGLTIPYREDIFINLTSGLN 164 (166)
Q Consensus 94 ~~~VPKG~faVYVG~e~e~rRFVVPv~yLnHPlFqeLLeqAEEEfGf~~~~G~LtIPCdv~~FE~VL~~I~ 164 (166)
..+||+||||||||+++ +||+||++|||||+|++||++|||||||+|+ |+|+|||+++.|++++++|+
T Consensus 33 ~~~vp~G~~~VyVG~~~--~Rfvvp~~~L~hp~f~~LL~~aeeEfG~~~~-G~l~iPC~~~~Fe~~l~~le 100 (100)
T PF02519_consen 33 ESDVPKGHFAVYVGEER--RRFVVPVSYLNHPLFQELLEQAEEEFGFDQD-GPLTIPCDVVLFEHLLWLLE 100 (100)
T ss_pred cCCCCCCeEEEEeCccc--eEEEechHHcCchhHHHHHHHHhhhcCcCCC-CcEEeeCCHHHHHHHHHHhC
Confidence 36899999999999987 9999999999999999999999999999998 99999999999999999985
No 2
>PLN03090 auxin-responsive family protein; Provisional
Probab=99.97 E-value=1.6e-32 Score=208.57 Aligned_cols=68 Identities=41% Similarity=0.606 Sum_probs=65.5
Q ss_pred CCCCCCCceEEEEEcCCCCceEEEEeccCCCCHHHHHHHHhHHHhcCCcCCCCceEeeccHHHHHHHHHhh
Q 047125 93 PTRSIRSFLLEVEVGRPENQKLASTPVSFLSQPPFQELLSKAEEEFGYNNPMGGLTIPYREDIFINLTSGL 163 (166)
Q Consensus 93 ~~~~VPKG~faVYVG~e~e~rRFVVPv~yLnHPlFqeLLeqAEEEfGf~~~~G~LtIPCdv~~FE~VL~~I 163 (166)
.|.+|||||||||||+++ +||+||++|||||+|++||++|||||||+|+ |+|+|||+++.|++|+++|
T Consensus 36 ~~~~vpkG~~aVyVG~~~--~RfvVp~~~L~hP~F~~LL~~aeeEfGf~~~-G~L~IPC~~~~Fe~ll~~i 103 (104)
T PLN03090 36 LPLDVPKGHFPVYVGENR--SRYIVPISFLTHPEFQSLLQQAEEEFGFDHD-MGLTIPCEEVVFRSLTSMI 103 (104)
T ss_pred CCCCCCCCcEEEEECCCC--EEEEEEHHHcCCHHHHHHHHHHHHHhCCCCC-CcEEEeCCHHHHHHHHHHh
Confidence 466899999999999987 9999999999999999999999999999998 9999999999999999998
No 3
>PLN03219 uncharacterized protein; Provisional
Probab=99.97 E-value=3.7e-32 Score=208.11 Aligned_cols=71 Identities=38% Similarity=0.663 Sum_probs=65.2
Q ss_pred CCCCCCCceEEEEEcCCCCceEEEEeccCCCCHHHHHHHHhHHHhcCCcCCCCceEeeccHHHHHHHHHhh
Q 047125 93 PTRSIRSFLLEVEVGRPENQKLASTPVSFLSQPPFQELLSKAEEEFGYNNPMGGLTIPYREDIFINLTSGL 163 (166)
Q Consensus 93 ~~~~VPKG~faVYVG~e~e~rRFVVPv~yLnHPlFqeLLeqAEEEfGf~~~~G~LtIPCdv~~FE~VL~~I 163 (166)
.+..|||||||||||++.|.+|||||++|||||+|++||++|||||||+|++|+|+|||+++.|++|++.-
T Consensus 35 ~~~~vpkGh~aVYVG~~~E~kRFvVPi~yL~hP~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~~~ 105 (108)
T PLN03219 35 TSGLVPKGHVAVYVGEQMEKKRFVVPISYLNHPLFREFLNRAEEECGFHHSMGGLTIPCREESFLHLITSH 105 (108)
T ss_pred CCCCCCCCeEEEEECCCCCceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEEeCCHHHHHHHHHhh
Confidence 35689999999999996556999999999999999999999999999998559999999999999999864
No 4
>PLN03220 uncharacterized protein; Provisional
Probab=99.97 E-value=7.8e-31 Score=199.98 Aligned_cols=70 Identities=46% Similarity=0.830 Sum_probs=63.6
Q ss_pred CCCCCCCceEEEEEcCCC--CceEEEEeccCCCCHHHHHHHHhHHHhcCCcCCCCceEeeccHHHHHHHHHh
Q 047125 93 PTRSIRSFLLEVEVGRPE--NQKLASTPVSFLSQPPFQELLSKAEEEFGYNNPMGGLTIPYREDIFINLTSG 162 (166)
Q Consensus 93 ~~~~VPKG~faVYVG~e~--e~rRFVVPv~yLnHPlFqeLLeqAEEEfGf~~~~G~LtIPCdv~~FE~VL~~ 162 (166)
.+.+|||||||||||++. +.+|||||++|||||+|++||++|||||||+|++|+|+|||+++.|++++..
T Consensus 31 ~~~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~s 102 (105)
T PLN03220 31 SSDHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHPSFKEFLSRAEEEFGFNHPMGGLTIPCREEVFLDLIAS 102 (105)
T ss_pred ccCCCCCCeEEEEECCCCCccceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEeeCCHHHHHHHHHh
Confidence 456899999999999853 3499999999999999999999999999999955999999999999999864
No 5
>PRK02899 adaptor protein; Provisional
Probab=77.66 E-value=1.9 Score=35.81 Aligned_cols=25 Identities=20% Similarity=0.668 Sum_probs=21.5
Q ss_pred CHHHHHHHHhHHHhcCCcCCCCceEe
Q 047125 124 QPPFQELLSKAEEEFGYNNPMGGLTI 149 (166)
Q Consensus 124 HPlFqeLLeqAEEEfGf~~~~G~LtI 149 (166)
+-+|.++|++|..|+||..+ |+|+|
T Consensus 38 e~lF~~mm~Ea~~e~~F~~~-~pl~~ 62 (197)
T PRK02899 38 HQLFRDMMQEANKELGFEAD-GPIAV 62 (197)
T ss_pred HHHHHHHHHHhhhccCcccC-CeEEE
Confidence 34677779999999999988 99876
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=71.30 E-value=4.1 Score=28.54 Aligned_cols=56 Identities=21% Similarity=0.257 Sum_probs=40.1
Q ss_pred EEEcCCCCceEEEEeccCCC-CH--HHHHHHHhHHHhcCCcCCCCceEeeccHHHHHHHHHhhc
Q 047125 104 VEVGRPENQKLASTPVSFLS-QP--PFQELLSKAEEEFGYNNPMGGLTIPYREDIFINLTSGLN 164 (166)
Q Consensus 104 VYVG~e~e~rRFVVPv~yLn-HP--lFqeLLeqAEEEfGf~~~~G~LtIPCdv~~FE~VL~~I~ 164 (166)
+-||. ++|.++.+-|. +| .|..|++.......-+.+ |.+-|-++...|++||..+.
T Consensus 3 lNVGG----~~f~~~~~tL~~~~~s~l~~~~~~~~~~~~~~~~-~~~fiDRdp~~F~~IL~ylr 61 (94)
T PF02214_consen 3 LNVGG----TIFETSRSTLTRYPDSLLARLFSGERSDDYDDDD-GEYFIDRDPELFEYILNYLR 61 (94)
T ss_dssp EEETT----EEEEEEHHHHHTSTTSTTTSHHHTGHGGGEETTT-TEEEESS-HHHHHHHHHHHH
T ss_pred EEECC----EEEEEcHHHHhhCCCChhhhHHhhccccccCCcc-ceEEeccChhhhhHHHHHHh
Confidence 34655 78999988877 44 788888865222222334 89999999999999998765
No 7
>PRK02315 adaptor protein; Provisional
Probab=70.54 E-value=3.4 Score=34.98 Aligned_cols=25 Identities=20% Similarity=0.385 Sum_probs=22.5
Q ss_pred CHHHHHHHHhHHHhcCCcCCCCceEe
Q 047125 124 QPPFQELLSKAEEEFGYNNPMGGLTI 149 (166)
Q Consensus 124 HPlFqeLLeqAEEEfGf~~~~G~LtI 149 (166)
+-+|.++|++|..|+||..+ |+|+|
T Consensus 38 e~fF~~mm~Ea~~e~~F~~~-~pl~~ 62 (233)
T PRK02315 38 EEFFYSMMDEVDEEDDFADE-GPLWF 62 (233)
T ss_pred HHHHHHHHHHhccccCcccC-CeEEE
Confidence 35899999999999999997 99987
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=64.24 E-value=2.2 Score=35.06 Aligned_cols=25 Identities=40% Similarity=0.687 Sum_probs=0.0
Q ss_pred CHHHHHHHHhHHHhcCCcCCCCceEe
Q 047125 124 QPPFQELLSKAEEEFGYNNPMGGLTI 149 (166)
Q Consensus 124 HPlFqeLLeqAEEEfGf~~~~G~LtI 149 (166)
+-+|.++|++|.+|+||..+ |+|+|
T Consensus 38 e~fF~~ileea~~e~~F~~~-~~l~~ 62 (220)
T PF05389_consen 38 EEFFYSILEEADEEHGFEND-GPLTF 62 (220)
T ss_dssp --------------------------
T ss_pred HHHHHHHHHHhccccCcccC-CeEEE
Confidence 56899999999999999997 88875
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=43.28 E-value=92 Score=21.03 Aligned_cols=50 Identities=22% Similarity=0.294 Sum_probs=35.0
Q ss_pred cCCCCceEEEEeccCCCCHHHHHHHHhHHHhcCCcC----------CCCceEeeccHHHHHHHHHhh
Q 047125 107 GRPENQKLASTPVSFLSQPPFQELLSKAEEEFGYNN----------PMGGLTIPYREDIFINLTSGL 163 (166)
Q Consensus 107 G~e~e~rRFVVPv~yLnHPlFqeLLeqAEEEfGf~~----------~~G~LtIPCdv~~FE~VL~~I 163 (166)
|++. +||.||- ...|.+|..+..+.|+... +...++|.++. +++.++.+.
T Consensus 9 ~~~~--~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~-Dl~~a~~~~ 68 (81)
T smart00666 9 GGET--RRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDE-DLEEAIEEY 68 (81)
T ss_pred CCEE--EEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHH-HHHHHHHHH
Confidence 4443 8888875 7789999999999998851 21357888865 455555543
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=34.25 E-value=1.4e+02 Score=19.87 Aligned_cols=47 Identities=21% Similarity=0.222 Sum_probs=34.1
Q ss_pred eEEEEeccCCCCHHHHHHHHhHHHhcCCcC---------CCC-ceEeeccHHHHHHHHHhh
Q 047125 113 KLASTPVSFLSQPPFQELLSKAEEEFGYNN---------PMG-GLTIPYREDIFINLTSGL 163 (166)
Q Consensus 113 rRFVVPv~yLnHPlFqeLLeqAEEEfGf~~---------~~G-~LtIPCdv~~FE~VL~~I 163 (166)
+||.+|. .++.|.+|..+.++.|+... +.| -++|.++ ++|+.++...
T Consensus 12 ~~~~~~~---~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd-~Dl~~a~~~~ 68 (81)
T cd05992 12 RRFVVVS---RSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSD-EDLEEAIEEA 68 (81)
T ss_pred EEEEEec---CCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCH-HHHHHHHHHH
Confidence 8999997 88999999999999999851 113 3556554 5666666654
No 11
>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=32.78 E-value=34 Score=24.47 Aligned_cols=16 Identities=44% Similarity=0.848 Sum_probs=15.0
Q ss_pred HHHHHHHhHHHhcCCc
Q 047125 126 PFQELLSKAEEEFGYN 141 (166)
Q Consensus 126 lFqeLLeqAEEEfGf~ 141 (166)
.+++||+.|++.||+.
T Consensus 27 SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 27 SLEELLKIASEKFGFS 42 (69)
T ss_pred cHHHHHHHHHHHhCCC
Confidence 6899999999999996
No 12
>KOG2523 consensus Predicted RNA-binding protein with PUA domain [Translation, ribosomal structure and biogenesis]
Probab=30.56 E-value=90 Score=26.56 Aligned_cols=72 Identities=11% Similarity=-0.007 Sum_probs=47.7
Q ss_pred CCcCcceeehhhhccccccccccccC---CCCCCCCCCCCCCCCCCCCCceEEEEEcCCCCceEEEEeccCCCCHHHHHH
Q 047125 54 SRIPRIGIFYRSLVAGEYEQDYSARS---RMYPPRGHSRSRPPTRSIRSFLLEVEVGRPENQKLASTPVSFLSQPPFQEL 130 (166)
Q Consensus 54 ~~~~~~~i~~r~l~~~a~~~~~~~~s---~gy~~~g~~~~~~~~~~VPKG~faVYVG~e~e~rRFVVPv~yLnHPlFqeL 130 (166)
|+.|.+. .-+++-+||-++-|+.+. +|....|.. .+..+++|-.+|--.++. .|++=-.|
T Consensus 86 hk~p~~~-~~~qvD~GAIkfvlsGAnIMcPGlts~g~~----l~~~~ekd~~V~i~aeGK------------~~alAiG~ 148 (181)
T KOG2523|consen 86 HKYPFIF-PHVQVDRGAIKFVLSGANIMCPGLTSPGAK----LPPGVEKDTIVAIMAEGK------------EHALAIGL 148 (181)
T ss_pred hhCCCcc-ceEEecCcceeeeecCCceEcccCCCCccc----CCCCccCCCEEEEEecCc------------hhhhhhhh
Confidence 5667766 667788899888888776 555555543 234677766555443332 47888889
Q ss_pred HHhHHHhcCCcC
Q 047125 131 LSKAEEEFGYNN 142 (166)
Q Consensus 131 LeqAEEEfGf~~ 142 (166)
+.++.+|.---+
T Consensus 149 ~~ms~kei~s~n 160 (181)
T KOG2523|consen 149 TKMSAKEIKSVN 160 (181)
T ss_pred hhhcHHHHHhhc
Confidence 999888864433
No 13
>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=28.51 E-value=1.5e+02 Score=27.59 Aligned_cols=46 Identities=22% Similarity=0.289 Sum_probs=36.4
Q ss_pred CCCCceEEEEEcCCC------------------CceEEEEeccCC--CCHHHHHHHHhHHHhcCCc
Q 047125 96 SIRSFLLEVEVGRPE------------------NQKLASTPVSFL--SQPPFQELLSKAEEEFGYN 141 (166)
Q Consensus 96 ~VPKG~faVYVG~e~------------------e~rRFVVPv~yL--nHPlFqeLLeqAEEEfGf~ 141 (166)
..+++-+.|.||.+. +..|++||++|= |.--.+++.+++++-||-+
T Consensus 180 ~~~~~~ltILvGNSgd~sNnHieaL~~L~~~~~~~~kIivPLsYg~~n~~Yi~~V~~~~~~lF~~~ 245 (360)
T PF07429_consen 180 KKNKGKLTILVGNSGDPSNNHIEALEALKQQFGDDVKIIVPLSYGANNQAYIQQVIQAGKELFGAE 245 (360)
T ss_pred cCCCCceEEEEcCCCCCCccHHHHHHHHHHhcCCCeEEEEECCCCCchHHHHHHHHHHHHHhcCcc
Confidence 456889999999764 248999999996 4567788888888888854
No 14
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=27.36 E-value=2.3e+02 Score=24.62 Aligned_cols=62 Identities=19% Similarity=0.126 Sum_probs=40.3
Q ss_pred ceEEEEEcCCCCceEEEEeccCCCCHHHHHHHHhHHHhcCCcCCC--------------CceEeeccHHHHHHHHHhh
Q 047125 100 FLLEVEVGRPENQKLASTPVSFLSQPPFQELLSKAEEEFGYNNPM--------------GGLTIPYREDIFINLTSGL 163 (166)
Q Consensus 100 G~faVYVG~e~e~rRFVVPv~yLnHPlFqeLLeqAEEEfGf~~~~--------------G~LtIPCdv~~FE~VL~~I 163 (166)
|.|.|.-..++ .++.|-+..-.-+....++.+...-|+.+.+. -+|+||...+.||-+++.|
T Consensus 46 ~~~~v~~~~~~--~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L~~~~~~~~GlR~p~~~d~fE~lv~aI 121 (283)
T PRK10308 46 GVVTVIPDIAR--HTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGKLGAARPGLRLPGSVDAFEQGVRAI 121 (283)
T ss_pred EEEEEEEcCCC--ceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCCcCCCCCCHHHHHHHHH
Confidence 55555544433 34444444432345556777777777777651 4699999999999998876
No 15
>PF08861 DUF1828: Domain of unknown function DUF1828; InterPro: IPR014960 These proteins are functionally uncharacterised.
Probab=26.87 E-value=1.5e+02 Score=21.19 Aligned_cols=39 Identities=21% Similarity=0.221 Sum_probs=33.3
Q ss_pred CHHHHHHHHhHHHhcCCcCCCCceEeeccHHHHHHHHHh
Q 047125 124 QPPFQELLSKAEEEFGYNNPMGGLTIPYREDIFINLTSG 162 (166)
Q Consensus 124 HPlFqeLLeqAEEEfGf~~~~G~LtIPCdv~~FE~VL~~ 162 (166)
.+.=+++|+..-..||+.-+.|.|.+.++.+.|-..+..
T Consensus 44 s~~R~~~l~~il~~~gv~~~~~el~~~~~~~~~~~~~~~ 82 (90)
T PF08861_consen 44 SKKRKKILNSILNGFGVELDEGELFIKTSEENFPQAKHR 82 (90)
T ss_pred chHHHHHHHHHHHHcCccccCCEEEEEeCHHHHHHHHHH
Confidence 677789999999999999877999999999988766544
No 16
>PF12342 DUF3640: Protein of unknown function (DUF3640) ; InterPro: IPR022101 This entry defines the N-terminal domain of the polyprotein of GB virus C; its function is not known.
Probab=24.60 E-value=26 Score=21.37 Aligned_cols=8 Identities=63% Similarity=1.556 Sum_probs=7.3
Q ss_pred CccceeeE
Q 047125 32 NWGTGVWG 39 (166)
Q Consensus 32 ~~~~~~~~ 39 (166)
.||.||||
T Consensus 16 qwG~gv~G 23 (26)
T PF12342_consen 16 QWGPGVHG 23 (26)
T ss_pred ccCCCcCC
Confidence 69999998
No 17
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=24.40 E-value=32 Score=31.89 Aligned_cols=24 Identities=17% Similarity=0.016 Sum_probs=17.8
Q ss_pred CCCCceEEEEEcCCCCceEEEEec
Q 047125 96 SIRSFLLEVEVGRPENQKLASTPV 119 (166)
Q Consensus 96 ~VPKG~faVYVG~e~e~rRFVVPv 119 (166)
-||.|-|++|||-++-...|.||+
T Consensus 89 ~IP~gSfv~Y~G~d~ie~~~~vP~ 112 (361)
T COG1759 89 FIPHGSFVAYVGYDGIENEFEVPM 112 (361)
T ss_pred EecCCceEEEecchhhhhcccCcc
Confidence 589999999999663225666664
No 18
>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=22.48 E-value=1.8e+02 Score=21.74 Aligned_cols=51 Identities=29% Similarity=0.363 Sum_probs=35.0
Q ss_pred EEEEcCCCCceEEEEeccCCCCHHHHHHHHhHHHhcCCcC-------------CCCceEeeccHHHHHHHHH
Q 047125 103 EVEVGRPENQKLASTPVSFLSQPPFQELLSKAEEEFGYNN-------------PMGGLTIPYREDIFINLTS 161 (166)
Q Consensus 103 aVYVG~e~e~rRFVVPv~yLnHPlFqeLLeqAEEEfGf~~-------------~~G~LtIPCdv~~FE~VL~ 161 (166)
.=|||.+. +-..|+-. -.|.+|..+..+.++..+ + +-+.|.||.+. .+++.
T Consensus 17 l~Y~GG~t--r~i~V~r~----~s~~el~~kl~~~~~~~~~~~lky~Lp~edld-~Lisv~~DeDl-~~M~~ 80 (97)
T cd06410 17 LRYVGGET--RIVSVDRS----ISFKELVSKLSELFGAGVVVTLKYQLPDEDLD-ALISVSNDEDL-KNMME 80 (97)
T ss_pred EEEcCCce--EEEEEcCC----CCHHHHHHHHHHHhCCCCceEEEEEcCCCCcc-eeEEecCcHHH-HHHHH
Confidence 46999886 66667655 467888888888887775 2 45678888743 34443
No 19
>PF11287 DUF3088: Protein of unknown function (DUF3088); InterPro: IPR021439 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=22.08 E-value=54 Score=25.85 Aligned_cols=20 Identities=30% Similarity=0.727 Sum_probs=16.6
Q ss_pred cceEEeeccccee-------eeeeecc
Q 047125 7 KPLLILYEPELLN-------FYCWSTT 26 (166)
Q Consensus 7 ~~~~~~~~~~~~~-------~~~~~~~ 26 (166)
++.|.|-+|...+ ||||.-.
T Consensus 2 ~d~LfLL~pgF~D~~~PG~~f~Cp~c~ 28 (112)
T PF11287_consen 2 RDILFLLRPGFEDPAGPGQRFYCPHCA 28 (112)
T ss_pred CcEEEEecCCCcCCCCCCceEECCchH
Confidence 6789999998887 9999754
No 20
>smart00153 VHP Villin headpiece domain.
Probab=21.89 E-value=45 Score=21.14 Aligned_cols=19 Identities=37% Similarity=0.655 Sum_probs=16.5
Q ss_pred CCCCHHHHHHHHhHHHhcC
Q 047125 121 FLSQPPFQELLSKAEEEFG 139 (166)
Q Consensus 121 yLnHPlFqeLLeqAEEEfG 139 (166)
||+.-.|++++.++.+||-
T Consensus 1 yLsdeeF~~vfgmsr~eF~ 19 (36)
T smart00153 1 YLSDEDFEEVFGMTREEFY 19 (36)
T ss_pred CCCHHHHHHHHCCCHHHHH
Confidence 7888899999999998873
No 21
>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=21.66 E-value=1.2e+02 Score=27.57 Aligned_cols=59 Identities=19% Similarity=0.249 Sum_probs=41.2
Q ss_pred EEEEcCCCC--ceEEEEeccCCC--CHHHHHHHHh---HHHhcCCcCCCCceEeeccHHHHHHHHHhhcC
Q 047125 103 EVEVGRPEN--QKLASTPVSFLS--QPPFQELLSK---AEEEFGYNNPMGGLTIPYREDIFINLTSGLNG 165 (166)
Q Consensus 103 aVYVG~e~e--~rRFVVPv~yLn--HPlFqeLLeq---AEEEfGf~~~~G~LtIPCdv~~FE~VL~~I~~ 165 (166)
.|-|=++.. .+=|..|...|- ..-|+++|.. +..+.. + =.|.+-||+..|+.++.-+++
T Consensus 2 ~ihV~De~~~~~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~~---~-idisVhCDv~iF~WLm~yv~~ 67 (317)
T PF11822_consen 2 VIHVCDEARNEKRDFTCPRDLLVSEMRYFAEYLSRYINDSQRWE---E-IDISVHCDVHIFEWLMRYVKG 67 (317)
T ss_pred EEEEEcCCCCcceeeeccHHHHHHhhHHHHHHHhhcccccCcCC---C-cceEEecChhHHHHHHHHhhc
Confidence 455544432 377888888774 4669999965 333322 2 479999999999999987764
No 22
>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=20.79 E-value=38 Score=21.56 Aligned_cols=19 Identities=32% Similarity=0.621 Sum_probs=14.7
Q ss_pred CCCCHHHHHHHHhHHHhcC
Q 047125 121 FLSQPPFQELLSKAEEEFG 139 (166)
Q Consensus 121 yLnHPlFqeLLeqAEEEfG 139 (166)
||+.-.|++++.++.+||-
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 7888899999999998873
Done!