Query 046189
Match_columns 139
No_of_seqs 156 out of 654
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 09:33:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046189.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046189hhsearch_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 1.1E-36 2.3E-41 223.9 9.2 68 51-118 36-103 (104)
2 PF02519 Auxin_inducible: Auxi 100.0 7.7E-37 1.7E-41 222.3 7.2 68 52-119 33-100 (100)
3 PLN03220 uncharacterized prote 100.0 3.6E-34 7.8E-39 210.7 5.9 95 6-117 3-102 (105)
4 PLN03219 uncharacterized prote 100.0 4.6E-32 1E-36 200.4 9.4 68 50-117 34-104 (108)
5 PF02214 BTB_2: BTB/POZ domain 91.3 0.28 6E-06 33.7 3.4 59 61-121 2-63 (94)
6 PRK02899 adaptor protein; Prov 81.9 1.2 2.6E-05 35.8 2.6 25 80-104 38-62 (197)
7 PRK02315 adaptor protein; Prov 76.0 2.1 4.6E-05 35.1 2.3 25 80-104 38-62 (233)
8 smart00666 PB1 PB1 domain. Pho 74.5 6.2 0.00014 26.1 4.0 53 62-119 6-69 (81)
9 cd05992 PB1 The PB1 domain is 71.8 8.9 0.00019 25.2 4.2 55 62-120 5-70 (81)
10 PF05389 MecA: Negative regula 68.8 1.6 3.5E-05 35.0 0.0 25 80-104 38-62 (220)
11 PF02100 ODC_AZ: Ornithine dec 57.6 22 0.00047 26.1 4.2 52 66-118 22-77 (108)
12 PF15387 DUF4611: Domain of un 49.7 21 0.00045 26.3 3.0 36 98-135 11-50 (96)
13 cd06407 PB1_NLP A PB1 domain i 47.9 35 0.00075 23.8 3.8 49 62-114 5-65 (82)
14 PF00651 BTB: BTB/POZ domain; 46.4 87 0.0019 20.9 5.7 57 60-121 13-74 (111)
15 cd01406 SIR2-like Sir2-like: P 46.4 33 0.00071 27.3 4.0 59 58-122 1-59 (242)
16 cd06410 PB1_UP2 Uncharacterize 45.3 47 0.001 24.0 4.3 34 61-98 17-50 (97)
17 PRK02797 4-alpha-L-fucosyltran 41.6 1.2E+02 0.0025 26.8 6.9 66 54-122 141-228 (322)
18 PF11822 DUF3342: Domain of un 36.3 25 0.00055 30.8 2.0 54 68-124 13-71 (317)
19 cd06398 PB1_Joka2 The PB1 doma 36.0 67 0.0014 22.9 3.8 55 62-116 5-72 (91)
20 PF02209 VHP: Villin headpiece 32.1 28 0.00062 21.1 1.2 19 77-95 1-19 (36)
21 KOG1733 Mitochondrial import i 31.6 16 0.00035 26.9 0.1 26 114-139 22-47 (97)
22 PRK10308 3-methyl-adenine DNA 31.4 1.5E+02 0.0032 25.0 5.8 65 57-121 45-124 (283)
23 PF00564 PB1: PB1 domain; Int 31.1 76 0.0017 20.7 3.3 54 62-120 6-71 (84)
24 PF07369 DUF1488: Protein of u 30.5 1E+02 0.0022 20.7 3.9 20 59-78 18-37 (83)
25 smart00153 VHP Villin headpiec 30.3 36 0.00079 20.5 1.5 18 77-94 1-18 (36)
26 PF12058 DUF3539: Protein of u 28.4 9.7 0.00021 27.7 -1.5 14 76-89 4-17 (88)
27 PF05194 UreE_C: UreE urease a 27.7 86 0.0019 21.6 3.2 26 59-90 26-51 (87)
28 PF10228 DUF2228: Uncharacteri 25.3 1.5E+02 0.0033 25.0 4.8 40 99-138 148-210 (253)
29 COG4862 MecA Negative regulato 24.8 55 0.0012 27.5 2.0 27 79-105 37-63 (224)
30 PRK09057 coproporphyrinogen II 24.5 1.1E+02 0.0024 26.3 4.0 48 58-111 55-102 (380)
31 COG2139 RPL21A Ribosomal prote 24.4 56 0.0012 24.2 1.8 21 60-80 73-93 (98)
32 cd04751 Commd3 COMM_Domain con 24.4 55 0.0012 23.2 1.8 23 99-121 64-86 (95)
33 PF11834 DUF3354: Domain of un 23.7 60 0.0013 22.2 1.8 17 81-97 26-42 (69)
34 PRK13347 coproporphyrinogen II 23.4 1.9E+02 0.004 25.6 5.2 57 57-119 102-159 (453)
35 PRK06582 coproporphyrinogen II 23.1 1.7E+02 0.0037 25.5 4.9 55 59-119 63-118 (390)
36 COG5431 Uncharacterized metal- 22.9 97 0.0021 23.5 2.9 62 57-119 32-102 (117)
37 PF14317 YcxB: YcxB-like prote 22.7 1.8E+02 0.0038 17.3 3.7 32 56-88 28-59 (62)
38 PF12062 HSNSD: heparan sulfat 22.4 69 0.0015 29.7 2.4 42 55-96 93-141 (487)
39 PF07429 Glyco_transf_56: 4-al 22.2 3.6E+02 0.0079 24.2 6.7 66 54-122 180-267 (360)
No 1
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=1.1e-36 Score=223.89 Aligned_cols=68 Identities=38% Similarity=0.806 Sum_probs=65.7
Q ss_pred CCCCCCCCeeEEEEcCCceEEEEecCCcCcHHHHHHHhhhhhhcCcccCCeEEecCcHHHHHHHHHHH
Q 046189 51 NSKPVPEGHVPVYVGDEMERFVVSAELLNHPVFVGLLNKSAQEYGYEQKGVLRIPCHVVVFERVVESL 118 (139)
Q Consensus 51 ~~~~vpkG~~~VyVG~e~~RfvVp~~yLnhP~F~~LL~~aeeEfG~~~~G~L~IPC~~~~Fe~vl~~l 118 (139)
.+.+||+||||||||++++||+||++|||||.|++||++|||||||+++|+|+|||+++.|++++|+|
T Consensus 36 ~~~~vpkG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfGf~~~G~L~IPC~~~~Fe~ll~~i 103 (104)
T PLN03090 36 LPLDVPKGHFPVYVGENRSRYIVPISFLTHPEFQSLLQQAEEEFGFDHDMGLTIPCEEVVFRSLTSMI 103 (104)
T ss_pred CCCCCCCCcEEEEECCCCEEEEEEHHHcCCHHHHHHHHHHHHHhCCCCCCcEEEeCCHHHHHHHHHHh
Confidence 35689999999999999999999999999999999999999999999999999999999999999998
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=7.7e-37 Score=222.31 Aligned_cols=68 Identities=49% Similarity=0.936 Sum_probs=66.0
Q ss_pred CCCCCCCeeEEEEcCCceEEEEecCCcCcHHHHHHHhhhhhhcCcccCCeEEecCcHHHHHHHHHHHH
Q 046189 52 SKPVPEGHVPVYVGDEMERFVVSAELLNHPVFVGLLNKSAQEYGYEQKGVLRIPCHVVVFERVVESLR 119 (139)
Q Consensus 52 ~~~vpkG~~~VyVG~e~~RfvVp~~yLnhP~F~~LL~~aeeEfG~~~~G~L~IPC~~~~Fe~vl~~l~ 119 (139)
..++|+||||||||++++||+||++|||||+|++||++|||||||+++|+|+|||+++.|+++||+|+
T Consensus 33 ~~~vp~G~~~VyVG~~~~Rfvvp~~~L~hp~f~~LL~~aeeEfG~~~~G~l~iPC~~~~Fe~~l~~le 100 (100)
T PF02519_consen 33 ESDVPKGHFAVYVGEERRRFVVPVSYLNHPLFQELLEQAEEEFGFDQDGPLTIPCDVVLFEHLLWLLE 100 (100)
T ss_pred cCCCCCCeEEEEeCccceEEEechHHcCchhHHHHHHHHhhhcCcCCCCcEEeeCCHHHHHHHHHHhC
Confidence 47899999999999999999999999999999999999999999999999999999999999999985
No 3
>PLN03220 uncharacterized protein; Provisional
Probab=100.00 E-value=3.6e-34 Score=210.67 Aligned_cols=95 Identities=35% Similarity=0.626 Sum_probs=76.2
Q ss_pred HHHhhhhhccccccccCcchhhhhccchhhhhHHHHHHhhhhCCCCCCCCCCCeeEEEEcC----CceEEEEecCCcCcH
Q 046189 6 RRLSRVADSSQYSLLRSDSTQAARRRPRRAESFRALKASLARRSPNSKPVPEGHVPVYVGD----EMERFVVSAELLNHP 81 (139)
Q Consensus 6 ~rl~rv~~ss~~~l~rs~s~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~vpkG~~~VyVG~----e~~RfvVp~~yLnhP 81 (139)
.++..+.+.-||++.|++..... ......+.+|||||||||||+ |++|||||++|||||
T Consensus 3 ~~~~~~~~~~k~~~~~~~~~~~~-----------------~~~~~~~~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP 65 (105)
T PLN03220 3 LSRFAISNATKQILKLNSLANRN-----------------RTSSSSSDHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHP 65 (105)
T ss_pred cchhhhHHHHHHHHHHHhhcccc-----------------cccccccCCCCCCeEEEEECCCCCccceEEEEEHHHcCCh
Confidence 34555655557887776522210 012234578999999999998 579999999999999
Q ss_pred HHHHHHhhhhhhcCccc-CCeEEecCcHHHHHHHHHH
Q 046189 82 VFVGLLNKSAQEYGYEQ-KGVLRIPCHVVVFERVVES 117 (139)
Q Consensus 82 ~F~~LL~~aeeEfG~~~-~G~L~IPC~~~~Fe~vl~~ 117 (139)
.|++||++|||||||+| +|+|+|||+++.|++++..
T Consensus 66 ~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~s 102 (105)
T PLN03220 66 SFKEFLSRAEEEFGFNHPMGGLTIPCREEVFLDLIAS 102 (105)
T ss_pred HHHHHHHHHHHHhCCCCCCCCEEeeCCHHHHHHHHHh
Confidence 99999999999999998 6999999999999999863
No 4
>PLN03219 uncharacterized protein; Provisional
Probab=99.97 E-value=4.6e-32 Score=200.37 Aligned_cols=68 Identities=46% Similarity=0.828 Sum_probs=63.6
Q ss_pred CCCCCCCCCeeEEEEcC--CceEEEEecCCcCcHHHHHHHhhhhhhcCccc-CCeEEecCcHHHHHHHHHH
Q 046189 50 PNSKPVPEGHVPVYVGD--EMERFVVSAELLNHPVFVGLLNKSAQEYGYEQ-KGVLRIPCHVVVFERVVES 117 (139)
Q Consensus 50 ~~~~~vpkG~~~VyVG~--e~~RfvVp~~yLnhP~F~~LL~~aeeEfG~~~-~G~L~IPC~~~~Fe~vl~~ 117 (139)
+.+..|||||+|||||+ |++||+||++|||||+|++||++|||||||++ +|+|+|||+++.|++||..
T Consensus 34 ~~~~~vpkGh~aVYVG~~~E~kRFvVPi~yL~hP~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~~ 104 (108)
T PLN03219 34 TTSGLVPKGHVAVYVGEQMEKKRFVVPISYLNHPLFREFLNRAEEECGFHHSMGGLTIPCREESFLHLITS 104 (108)
T ss_pred CCCCCCCCCeEEEEECCCCCceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEEeCCHHHHHHHHHh
Confidence 44578999999999997 58999999999999999999999999999997 6999999999999999975
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=91.34 E-value=0.28 Score=33.72 Aligned_cols=59 Identities=24% Similarity=0.318 Sum_probs=43.5
Q ss_pred EEEEcCCceEEEEecCCcC-cH--HHHHHHhhhhhhcCcccCCeEEecCcHHHHHHHHHHHHcC
Q 046189 61 PVYVGDEMERFVVSAELLN-HP--VFVGLLNKSAQEYGYEQKGVLRIPCHVVVFERVVESLRLG 121 (139)
Q Consensus 61 ~VyVG~e~~RfvVp~~yLn-hP--~F~~LL~~aeeEfG~~~~G~L~IPC~~~~Fe~vl~~l~~~ 121 (139)
.+=||. ++|.++.+-|. +| .|..++..-.....-+.+|.+-|.++...|++||..++.+
T Consensus 2 ~lNVGG--~~f~~~~~tL~~~~~s~l~~~~~~~~~~~~~~~~~~~fiDRdp~~F~~IL~ylr~~ 63 (94)
T PF02214_consen 2 RLNVGG--TIFETSRSTLTRYPDSLLARLFSGERSDDYDDDDGEYFIDRDPELFEYILNYLRTG 63 (94)
T ss_dssp EEEETT--EEEEEEHHHHHTSTTSTTTSHHHTGHGGGEETTTTEEEESS-HHHHHHHHHHHHHT
T ss_pred EEEECC--EEEEEcHHHHhhCCCChhhhHHhhccccccCCccceEEeccChhhhhHHHHHHhhc
Confidence 345775 68999987776 43 6777777642222234579999999999999999999994
No 6
>PRK02899 adaptor protein; Provisional
Probab=81.92 E-value=1.2 Score=35.80 Aligned_cols=25 Identities=24% Similarity=0.691 Sum_probs=21.6
Q ss_pred cHHHHHHHhhhhhhcCcccCCeEEe
Q 046189 80 HPVFVGLLNKSAQEYGYEQKGVLRI 104 (139)
Q Consensus 80 hP~F~~LL~~aeeEfG~~~~G~L~I 104 (139)
+-+|.++|++|..|+||..+|||+|
T Consensus 38 e~lF~~mm~Ea~~e~~F~~~~pl~~ 62 (197)
T PRK02899 38 HQLFRDMMQEANKELGFEADGPIAV 62 (197)
T ss_pred HHHHHHHHHHhhhccCcccCCeEEE
Confidence 4567788999999999998999976
No 7
>PRK02315 adaptor protein; Provisional
Probab=75.96 E-value=2.1 Score=35.10 Aligned_cols=25 Identities=16% Similarity=0.428 Sum_probs=22.7
Q ss_pred cHHHHHHHhhhhhhcCcccCCeEEe
Q 046189 80 HPVFVGLLNKSAQEYGYEQKGVLRI 104 (139)
Q Consensus 80 hP~F~~LL~~aeeEfG~~~~G~L~I 104 (139)
+-.|.++|++|..|+||..+|||+|
T Consensus 38 e~fF~~mm~Ea~~e~~F~~~~pl~~ 62 (233)
T PRK02315 38 EEFFYSMMDEVDEEDDFADEGPLWF 62 (233)
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 4689999999999999999999976
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=74.53 E-value=6.2 Score=26.14 Aligned_cols=53 Identities=23% Similarity=0.422 Sum_probs=37.9
Q ss_pred EEEcCCceEEEEecCCcCcHHHHHHHhhhhhhcCcc----------cCC-eEEecCcHHHHHHHHHHHH
Q 046189 62 VYVGDEMERFVVSAELLNHPVFVGLLNKSAQEYGYE----------QKG-VLRIPCHVVVFERVVESLR 119 (139)
Q Consensus 62 VyVG~e~~RfvVp~~yLnhP~F~~LL~~aeeEfG~~----------~~G-~L~IPC~~~~Fe~vl~~l~ 119 (139)
|+-|++.+||.||. ...|.+|..+..+.|+.. .+| .++|.++. .+..++.+.+
T Consensus 6 ~~~~~~~~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~-Dl~~a~~~~~ 69 (81)
T smart00666 6 LRYGGETRRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDE-DLEEAIEEYD 69 (81)
T ss_pred EEECCEEEEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHH-HHHHHHHHHH
Confidence 34477888999986 778999999999888774 133 67788865 4555555554
No 9
>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=71.78 E-value=8.9 Score=25.17 Aligned_cols=55 Identities=31% Similarity=0.511 Sum_probs=38.8
Q ss_pred EEEcCCceEEEEecCCcCcHHHHHHHhhhhhhcCcc----------cCC-eEEecCcHHHHHHHHHHHHc
Q 046189 62 VYVGDEMERFVVSAELLNHPVFVGLLNKSAQEYGYE----------QKG-VLRIPCHVVVFERVVESLRL 120 (139)
Q Consensus 62 VyVG~e~~RfvVp~~yLnhP~F~~LL~~aeeEfG~~----------~~G-~L~IPC~~~~Fe~vl~~l~~ 120 (139)
|+-+++..||.+|. .++.|.+|..+..+.|+.. .+| .++|-++ ..|+.++...+.
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 45566778999998 7888999999988888874 133 3555554 566766666654
No 10
>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=68.77 E-value=1.6 Score=34.96 Aligned_cols=25 Identities=28% Similarity=0.603 Sum_probs=0.0
Q ss_pred cHHHHHHHhhhhhhcCcccCCeEEe
Q 046189 80 HPVFVGLLNKSAQEYGYEQKGVLRI 104 (139)
Q Consensus 80 hP~F~~LL~~aeeEfG~~~~G~L~I 104 (139)
+-.|.++|++|.+|+||..+|+|+|
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 5689999999999999999999886
No 11
>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=57.56 E-value=22 Score=26.08 Aligned_cols=52 Identities=19% Similarity=0.247 Sum_probs=26.5
Q ss_pred CCceEEE-EecC---CcCcHHHHHHHhhhhhhcCcccCCeEEecCcHHHHHHHHHHH
Q 046189 66 DEMERFV-VSAE---LLNHPVFVGLLNKSAQEYGYEQKGVLRIPCHVVVFERVVESL 118 (139)
Q Consensus 66 ~e~~Rfv-Vp~~---yLnhP~F~~LL~~aeeEfG~~~~G~L~IPC~~~~Fe~vl~~l 118 (139)
+++.=|| ||-. -..-..|.+||+.|||.+|.++ -.++|+=+-.....++..|
T Consensus 22 ~~~~L~V~ip~~~~~~~~K~~lvaLLElAee~L~c~~-vvic~~k~~~d~~~Llr~l 77 (108)
T PF02100_consen 22 DERTLFVFIPSSALGQGSKESLVALLELAEEKLGCSH-VVICLDKNRPDRASLLRTL 77 (108)
T ss_dssp -TTEEEEE-SS---SS--SHHHHHHHHHHHHHH-----EEEEE---SS-HHHHHHHH
T ss_pred cCCEEEEEECCcccccccHHHHHHHHHHhcCcCCCCE-EEEEEECCchhHHHhhhhc
Confidence 4555566 4543 3445789999999999988866 4677765555544444433
No 12
>PF15387 DUF4611: Domain of unknown function (DUF4611)
Probab=49.72 E-value=21 Score=26.34 Aligned_cols=36 Identities=19% Similarity=0.393 Sum_probs=25.3
Q ss_pred cCCeEEecCc----HHHHHHHHHHHHcCCChHHHHHHHHhhh
Q 046189 98 QKGVLRIPCH----VVVFERVVESLRLGLESRDLQDLLSSVS 135 (139)
Q Consensus 98 ~~G~L~IPC~----~~~Fe~vl~~l~~~~~~~~~~~L~~~~~ 135 (139)
+..-|+|||+ ..-|+.||.-+..- .+.+-+|+..++
T Consensus 11 q~q~lrv~ce~p~~~d~~q~LlsGvaqm--~e~vsel~~~lV 50 (96)
T PF15387_consen 11 QPQRLRVPCEAPGDADPFQGLLSGVAQM--RELVSELFGPLV 50 (96)
T ss_pred CcceEEEeeecCCCcccHHHHHHHHHHH--HHHHHHHHHHHH
Confidence 4567999998 57899888877644 355666666553
No 13
>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=47.90 E-value=35 Score=23.80 Aligned_cols=49 Identities=18% Similarity=0.316 Sum_probs=33.9
Q ss_pred EEEcCCceEEEEecCCcCcHHHHHHHhhhhhhcCccc------------CCeEEecCcHHHHHHH
Q 046189 62 VYVGDEMERFVVSAELLNHPVFVGLLNKSAQEYGYEQ------------KGVLRIPCHVVVFERV 114 (139)
Q Consensus 62 VyVG~e~~RfvVp~~yLnhP~F~~LL~~aeeEfG~~~------------~G~L~IPC~~~~Fe~v 114 (139)
+..|++..||.+|... .|++|.++-.+-|+... +...+|.|+.++=|.+
T Consensus 5 ~~~~~d~~r~~l~~~~----~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai 65 (82)
T cd06407 5 ATYGEEKIRFRLPPSW----GFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEECI 65 (82)
T ss_pred EEeCCeEEEEEcCCCC----CHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHHH
Confidence 4457788899998643 68888888888776642 3456777887655543
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=46.41 E-value=87 Score=20.88 Aligned_cols=57 Identities=28% Similarity=0.507 Sum_probs=41.5
Q ss_pred eEEEEcCCceEEEEecCCc--CcHHHHHHHhhhhhhcCcccCC--eEEec-CcHHHHHHHHHHHHcC
Q 046189 60 VPVYVGDEMERFVVSAELL--NHPVFVGLLNKSAQEYGYEQKG--VLRIP-CHVVVFERVVESLRLG 121 (139)
Q Consensus 60 ~~VyVG~e~~RfvVp~~yL--nhP~F~~LL~~aeeEfG~~~~G--~L~IP-C~~~~Fe~vl~~l~~~ 121 (139)
+.+.||+ .++|-+.-..| ..|.|+.++... +....+ .+.++ |+...|+.++..+-.+
T Consensus 13 ~~i~v~d-~~~~~vhk~iL~~~S~~F~~~~~~~----~~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~ 74 (111)
T PF00651_consen 13 VTIRVGD-GKTFYVHKNILAARSPYFRNLFEGS----KFKESTVPEISLPDVSPEAFEAFLEYMYTG 74 (111)
T ss_dssp EEEEETT-TEEEEE-HHHHHHHBHHHHHHHTTT----TSTTSSEEEEEETTSCHHHHHHHHHHHHHS
T ss_pred EEEEECC-CEEEeechhhhhccchhhhhccccc----ccccccccccccccccccccccccccccCC
Confidence 4667776 57888887777 469999999988 112233 46555 8899999999988766
No 15
>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=46.40 E-value=33 Score=27.26 Aligned_cols=59 Identities=27% Similarity=0.326 Sum_probs=38.2
Q ss_pred CeeEEEEcCCceEEEEecCCcCcHHHHHHHhhhhhhcCcccCCeEEecCcHHHHHHHHHHHHcCC
Q 046189 58 GHVPVYVGDEMERFVVSAELLNHPVFVGLLNKSAQEYGYEQKGVLRIPCHVVVFERVVESLRLGL 122 (139)
Q Consensus 58 G~~~VyVG~e~~RfvVp~~yLnhP~F~~LL~~aeeEfG~~~~G~L~IPC~~~~Fe~vl~~l~~~~ 122 (139)
|+++++||-. |... .+-|...+|++...+++|.+......-.=+-..+..+...+.+..
T Consensus 1 g~lvlFiGAG-----~S~~-~glP~W~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~ 59 (242)
T cd01406 1 GRVVIFVGAG-----VSVS-SGLPDWKTLLDEIASELGLEIDGYSVEAKDENDYLELAELLEKEF 59 (242)
T ss_pred CCEEEEecCc-----cccc-cCCCChHHHHHHHHHHcCCccchhhccccchhhHHHHHHHHHHHh
Confidence 7899999976 3332 678999999999999998865422110012344555555555544
No 16
>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=45.31 E-value=47 Score=23.98 Aligned_cols=34 Identities=26% Similarity=0.326 Sum_probs=26.1
Q ss_pred EEEEcCCceEEEEecCCcCcHHHHHHHhhhhhhcCccc
Q 046189 61 PVYVGDEMERFVVSAELLNHPVFVGLLNKSAQEYGYEQ 98 (139)
Q Consensus 61 ~VyVG~e~~RfvVp~~yLnhP~F~~LL~~aeeEfG~~~ 98 (139)
.=|||.+.+--.|+-+ -.|.+|..+..+.++...
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 4699999888888866 367778888888777654
No 17
>PRK02797 4-alpha-L-fucosyltransferase; Provisional
Probab=41.59 E-value=1.2e+02 Score=26.77 Aligned_cols=66 Identities=17% Similarity=0.244 Sum_probs=45.7
Q ss_pred CCCCCeeEEEEcCC--------------------ceEEEEecCC--cCcHHHHHHHhhhhhhcCcccCCeEEecCcHHHH
Q 046189 54 PVPEGHVPVYVGDE--------------------MERFVVSAEL--LNHPVFVGLLNKSAQEYGYEQKGVLRIPCHVVVF 111 (139)
Q Consensus 54 ~vpkG~~~VyVG~e--------------------~~RfvVp~~y--LnhP~F~~LL~~aeeEfG~~~~G~L~IPC~~~~F 111 (139)
..+++.++|.||.. .-|++||.+| -|.--.++..+.+.+-||-+. ++|==+--.|
T Consensus 141 ~~~~~~~tIlvGNSgd~SN~Hie~L~~l~~~~~~~v~ii~PlsYp~gn~~Yi~~V~~~~~~lF~~~~---~~~L~e~l~f 217 (322)
T PRK02797 141 RQRAGKMTILVGNSGDRSNRHIEALRALHQQFGDNVKIIVPMGYPANNQAYIEEVRQAGLALFGAEN---FQILTEKLPF 217 (322)
T ss_pred ccCCCceEEEEeCCCCCcccHHHHHHHHHHHhCCCeEEEEECCcCCCCHHHHHHHHHHHHHhcCccc---EEehhhhCCH
Confidence 44677899999831 2399999999 676677777777777787543 4444455556
Q ss_pred HHHHHHHHcCC
Q 046189 112 ERVVESLRLGL 122 (139)
Q Consensus 112 e~vl~~l~~~~ 122 (139)
+.-+..|++.|
T Consensus 218 ~eYl~lL~~~D 228 (322)
T PRK02797 218 DDYLALLRQCD 228 (322)
T ss_pred HHHHHHHHhCC
Confidence 66666666654
No 18
>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=36.27 E-value=25 Score=30.75 Aligned_cols=54 Identities=20% Similarity=0.368 Sum_probs=40.9
Q ss_pred ceEEEEecCCcC--cHHHHHHHhh---hhhhcCcccCCeEEecCcHHHHHHHHHHHHcCCCh
Q 046189 68 MERFVVSAELLN--HPVFVGLLNK---SAQEYGYEQKGVLRIPCHVVVFERVVESLRLGLES 124 (139)
Q Consensus 68 ~~RfvVp~~yLn--hP~F~~LL~~---aeeEfG~~~~G~L~IPC~~~~Fe~vl~~l~~~~~~ 124 (139)
++=|..|.+.|- -..|++.|.. ..++. .+=.|.+-||+..|+.++..++...+.
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 566999988884 4679999965 33321 234588889999999999999987654
No 19
>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=35.97 E-value=67 Score=22.86 Aligned_cols=55 Identities=15% Similarity=0.141 Sum_probs=37.0
Q ss_pred EEEcCCceEEEEecC-CcCcHHHHHHHhhhhhhcCccc------------CCeEEecCcHHHHHHHHH
Q 046189 62 VYVGDEMERFVVSAE-LLNHPVFVGLLNKSAQEYGYEQ------------KGVLRIPCHVVVFERVVE 116 (139)
Q Consensus 62 VyVG~e~~RfvVp~~-yLnhP~F~~LL~~aeeEfG~~~------------~G~L~IPC~~~~Fe~vl~ 116 (139)
|.-|++.+||-+|.. --.+..|..|.++-++-|.... ...++|-|+.++-+-+-.
T Consensus 5 v~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~ 72 (91)
T cd06398 5 VKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQY 72 (91)
T ss_pred EEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHH
Confidence 444788899999964 0114578888888887766542 345788888876655443
No 20
>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=32.07 E-value=28 Score=21.10 Aligned_cols=19 Identities=21% Similarity=0.294 Sum_probs=15.2
Q ss_pred CcCcHHHHHHHhhhhhhcC
Q 046189 77 LLNHPVFVGLLNKSAQEYG 95 (139)
Q Consensus 77 yLnhP~F~~LL~~aeeEfG 95 (139)
||+.-.|+.++.+..+||.
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 7899999999999999874
No 21
>KOG1733 consensus Mitochondrial import inner membrane translocase, subunit TIM13 [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.63 E-value=16 Score=26.93 Aligned_cols=26 Identities=23% Similarity=0.501 Sum_probs=18.6
Q ss_pred HHHHHHcCCChHHHHHHHHhhhccCC
Q 046189 114 VVESLRLGLESRDLQDLLSSVSDEYF 139 (139)
Q Consensus 114 vl~~l~~~~~~~~~~~L~~~~~~~~~ 139 (139)
++..++....-...+|||+-|+|+||
T Consensus 22 ~m~qVkqqlAvAnAqeLv~kisekCf 47 (97)
T KOG1733|consen 22 LMNQVKQQLAVANAQELVSKISEKCF 47 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444445678899999999998
No 22
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=31.38 E-value=1.5e+02 Score=24.98 Aligned_cols=65 Identities=22% Similarity=0.204 Sum_probs=41.4
Q ss_pred CCeeEEEEcCCceEEEEecCCcCcHHHHHHHhhhhhhcCccc---------------CCeEEecCcHHHHHHHHHHHHcC
Q 046189 57 EGHVPVYVGDEMERFVVSAELLNHPVFVGLLNKSAQEYGYEQ---------------KGVLRIPCHVVVFERVVESLRLG 121 (139)
Q Consensus 57 kG~~~VyVG~e~~RfvVp~~yLnhP~F~~LL~~aeeEfG~~~---------------~G~L~IPC~~~~Fe~vl~~l~~~ 121 (139)
.|.|.|.-.++...+.|.++.-.-|....++.....-||.+. .-+|+||...+.||-+++.+-..
T Consensus 45 ~~~~~v~~~~~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L~~~~~~~~GlR~p~~~d~fE~lv~aIigQ 124 (283)
T PRK10308 45 RGVVTVIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGKLGAARPGLRLPGSVDAFEQGVRAILGQ 124 (283)
T ss_pred cEEEEEEEcCCCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCCcCCCCCCHHHHHHHHHHHh
Confidence 466666655554555555554333445556666666566543 34699999999999999876433
No 23
>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=31.09 E-value=76 Score=20.73 Aligned_cols=54 Identities=19% Similarity=0.370 Sum_probs=34.4
Q ss_pred EEEcCCceE-EEEecCCcCcHHHHHHHhhhhhhcCcc----------cCC-eEEecCcHHHHHHHHHHHHc
Q 046189 62 VYVGDEMER-FVVSAELLNHPVFVGLLNKSAQEYGYE----------QKG-VLRIPCHVVVFERVVESLRL 120 (139)
Q Consensus 62 VyVG~e~~R-fvVp~~yLnhP~F~~LL~~aeeEfG~~----------~~G-~L~IPC~~~~Fe~vl~~l~~ 120 (139)
++-+++..| +.+| ..+.|.+|..+.++.||.. .+| .++|.++.+ |+..+.....
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 445555555 5555 4579999999999999883 244 466666554 4555555543
No 24
>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=30.51 E-value=1e+02 Score=20.72 Aligned_cols=20 Identities=35% Similarity=0.380 Sum_probs=17.4
Q ss_pred eeEEEEcCCceEEEEecCCc
Q 046189 59 HVPVYVGDEMERFVVSAELL 78 (139)
Q Consensus 59 ~~~VyVG~e~~RfvVp~~yL 78 (139)
.|+++|+...-++.|+.+-|
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 68999999888999997766
No 25
>smart00153 VHP Villin headpiece domain.
Probab=30.27 E-value=36 Score=20.54 Aligned_cols=18 Identities=17% Similarity=0.377 Sum_probs=16.3
Q ss_pred CcCcHHHHHHHhhhhhhc
Q 046189 77 LLNHPVFVGLLNKSAQEY 94 (139)
Q Consensus 77 yLnhP~F~~LL~~aeeEf 94 (139)
||+.-.|+.++.++.+||
T Consensus 1 yLsdeeF~~vfgmsr~eF 18 (36)
T smart00153 1 YLSDEDFEEVFGMTREEF 18 (36)
T ss_pred CCCHHHHHHHHCCCHHHH
Confidence 789999999999999887
No 26
>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=28.39 E-value=9.7 Score=27.68 Aligned_cols=14 Identities=43% Similarity=0.553 Sum_probs=9.8
Q ss_pred CCcCcHHHHHHHhh
Q 046189 76 ELLNHPVFVGLLNK 89 (139)
Q Consensus 76 ~yLnhP~F~~LL~~ 89 (139)
.|||||.|.-|-.-
T Consensus 4 ~YLNHPtFGlLy~V 17 (88)
T PF12058_consen 4 TYLNHPTFGLLYRV 17 (88)
T ss_dssp -EEEETTTEEEEEE
T ss_pred ccccCCccchheee
Confidence 58999998766443
No 27
>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=27.71 E-value=86 Score=21.56 Aligned_cols=26 Identities=27% Similarity=0.523 Sum_probs=17.8
Q ss_pred eeEEEEcCCceEEEEecCCcCcHHHHHHHhhh
Q 046189 59 HVPVYVGDEMERFVVSAELLNHPVFVGLLNKS 90 (139)
Q Consensus 59 ~~~VyVG~e~~RfvVp~~yLnhP~F~~LL~~a 90 (139)
|+|++++++ +..|| ..+.+.+||++.
T Consensus 26 H~p~~i~~~--~l~v~----~d~~l~~~L~~l 51 (87)
T PF05194_consen 26 HWPLFIEED--ELYVP----YDHVLEELLRKL 51 (87)
T ss_dssp T--EEEETT--EEEEE------HHHHHHHHHT
T ss_pred ccceEEcCC--EEEec----CcHHHHHHHHHC
Confidence 899999987 78888 567778888774
No 28
>PF10228 DUF2228: Uncharacterised conserved protein (DUF2228); InterPro: IPR019361 This entry contains proteins that have no known function.
Probab=25.27 E-value=1.5e+02 Score=25.03 Aligned_cols=40 Identities=18% Similarity=0.319 Sum_probs=29.1
Q ss_pred CCeEEecCc-------------HHHHHHHHHHHHcCCCh-------HHHHHHHHhh--h-ccC
Q 046189 99 KGVLRIPCH-------------VVVFERVVESLRLGLES-------RDLQDLLSSV--S-DEY 138 (139)
Q Consensus 99 ~G~L~IPC~-------------~~~Fe~vl~~l~~~~~~-------~~~~~L~~~~--~-~~~ 138 (139)
.++|++|.+ -...++++..+.+..+. +.+++|++.+ + |+|
T Consensus 148 ~~GiVVP~d~k~~vGYR~L~~td~~Lk~il~~i~~a~~~~~~~~~~~~lqel~t~v~~AnDEc 210 (253)
T PF10228_consen 148 GAGIVVPVDRKNDVGYRELPETDAELKKILKKIVEAKNDEERQKAFAPLQELVTFVQIANDEC 210 (253)
T ss_pred CCeEEEeccCCCCcCceecCcccHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 467888888 34688899988885442 4677888887 4 777
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=24.76 E-value=55 Score=27.49 Aligned_cols=27 Identities=19% Similarity=0.405 Sum_probs=24.2
Q ss_pred CcHHHHHHHhhhhhhcCcccCCeEEec
Q 046189 79 NHPVFVGLLNKSAQEYGYEQKGVLRIP 105 (139)
Q Consensus 79 nhP~F~~LL~~aeeEfG~~~~G~L~IP 105 (139)
.|-.|-++++++..|-+|...|||.|-
T Consensus 37 ~EE~F~~mMdEl~~ee~F~~~GpL~iq 63 (224)
T COG4862 37 TEELFYEMMDELNLEEDFKDEGPLWIQ 63 (224)
T ss_pred HHHHHHHHHHhcCCccccccCCceEEE
Confidence 478999999999999999999999874
No 30
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=24.47 E-value=1.1e+02 Score=26.34 Aligned_cols=48 Identities=10% Similarity=0.193 Sum_probs=37.5
Q ss_pred CeeEEEEcCCceEEEEecCCcCcHHHHHHHhhhhhhcCcccCCeEEecCcHHHH
Q 046189 58 GHVPVYVGDEMERFVVSAELLNHPVFVGLLNKSAQEYGYEQKGVLRIPCHVVVF 111 (139)
Q Consensus 58 G~~~VyVG~e~~RfvVp~~yLnhP~F~~LL~~aeeEfG~~~~G~L~IPC~~~~F 111 (139)
..-.||+|... ..+|+...+..|++...+.|....+..++|=|....+
T Consensus 55 ~i~tiy~GGGT------Ps~l~~~~L~~ll~~i~~~f~~~~~~eit~E~~P~~i 102 (380)
T PRK09057 55 TLTSIFFGGGT------PSLMQPETVAALLDAIARLWPVADDIEITLEANPTSV 102 (380)
T ss_pred CcCeEEeCCCc------cccCCHHHHHHHHHHHHHhCCCCCCccEEEEECcCcC
Confidence 34599999763 4588889999999999999988776678887766433
No 31
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=24.42 E-value=56 Score=24.22 Aligned_cols=21 Identities=33% Similarity=0.544 Sum_probs=17.6
Q ss_pred eEEEEcCCceEEEEecCCcCc
Q 046189 60 VPVYVGDEMERFVVSAELLNH 80 (139)
Q Consensus 60 ~~VyVG~e~~RfvVp~~yLnh 80 (139)
|.||+|...++..|..++|.+
T Consensus 73 V~v~~G~k~K~liv~peHLk~ 93 (98)
T COG2139 73 VEVYDGNKEKTLIVRPEHLKP 93 (98)
T ss_pred EEEecCCceEEEEeCHHHccc
Confidence 578899988899999888875
No 32
>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=24.40 E-value=55 Score=23.23 Aligned_cols=23 Identities=17% Similarity=0.368 Sum_probs=20.3
Q ss_pred CCeEEecCcHHHHHHHHHHHHcC
Q 046189 99 KGVLRIPCHVVVFERVVESLRLG 121 (139)
Q Consensus 99 ~G~L~IPC~~~~Fe~vl~~l~~~ 121 (139)
.+.+.+-|+++.|.+++..|+.+
T Consensus 64 ~~~i~f~c~~e~L~~Li~~Lk~A 86 (95)
T cd04751 64 KPDINFTCTLEQLQDLVNKLKDA 86 (95)
T ss_pred cceEEEEeCHHHHHHHHHHHHHH
Confidence 35899999999999999999854
No 33
>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=23.71 E-value=60 Score=22.20 Aligned_cols=17 Identities=18% Similarity=0.518 Sum_probs=15.5
Q ss_pred HHHHHHHhhhhhhcCcc
Q 046189 81 PVFVGLLNKSAQEYGYE 97 (139)
Q Consensus 81 P~F~~LL~~aeeEfG~~ 97 (139)
-.+++||+.|++.||+.
T Consensus 26 ~SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 26 DSLEELLKIASEKFGFS 42 (69)
T ss_pred ccHHHHHHHHHHHhCCC
Confidence 47999999999999995
No 34
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=23.39 E-value=1.9e+02 Score=25.63 Aligned_cols=57 Identities=11% Similarity=0.205 Sum_probs=41.5
Q ss_pred CCeeEEEEcCCceEEEEecCCcCcHHHHHHHhhhhhhcCcccCCeEEecCcHHHH-HHHHHHHH
Q 046189 57 EGHVPVYVGDEMERFVVSAELLNHPVFVGLLNKSAQEYGYEQKGVLRIPCHVVVF-ERVVESLR 119 (139)
Q Consensus 57 kG~~~VyVG~e~~RfvVp~~yLnhP~F~~LL~~aeeEfG~~~~G~L~IPC~~~~F-e~vl~~l~ 119 (139)
.+...||+|... ..+|+.+.+.+|++...+.|++..+..++|-|+...+ +..+..|+
T Consensus 102 ~~v~~i~fgGGT------Ps~l~~~~l~~ll~~i~~~~~~~~~~e~tie~~p~~lt~e~l~~L~ 159 (453)
T PRK13347 102 RRVSQLHWGGGT------PTILNPDQFERLMAALRDAFDFAPEAEIAVEIDPRTVTAEMLQALA 159 (453)
T ss_pred CeEEEEEEcCcc------cccCCHHHHHHHHHHHHHhCCCCCCceEEEEeccccCCHHHHHHHH
Confidence 356788988752 4678899999999999999988766677887776655 33444444
No 35
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=23.10 E-value=1.7e+02 Score=25.53 Aligned_cols=55 Identities=13% Similarity=0.280 Sum_probs=41.7
Q ss_pred eeEEEEcCCceEEEEecCCcCcHHHHHHHhhhhhhcCcccCCeEEecCcHHHH-HHHHHHHH
Q 046189 59 HVPVYVGDEMERFVVSAELLNHPVFVGLLNKSAQEYGYEQKGVLRIPCHVVVF-ERVVESLR 119 (139)
Q Consensus 59 ~~~VyVG~e~~RfvVp~~yLnhP~F~~LL~~aeeEfG~~~~G~L~IPC~~~~F-e~vl~~l~ 119 (139)
.-.||+|... ..+|+...+..||+...+.|++.....++|=|....+ +..+..|+
T Consensus 63 i~tiy~GGGT------Ps~l~~~~l~~ll~~i~~~~~~~~~~eitiE~nP~~~~~e~l~~l~ 118 (390)
T PRK06582 63 IKSIFFGGGT------PSLMNPVIVEGIINKISNLAIIDNQTEITLETNPTSFETEKFKAFK 118 (390)
T ss_pred eeEEEECCCc------cccCCHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCcCCHHHHHHHH
Confidence 4589999863 4788899999999999998888766678888877655 34444444
No 36
>COG5431 Uncharacterized metal-binding protein [Function unknown]
Probab=22.88 E-value=97 Score=23.53 Aligned_cols=62 Identities=18% Similarity=0.269 Sum_probs=37.4
Q ss_pred CCeeEEEEcCCceEEEEecCCcCcHHHHHHHhhhh-----hhcCcc----cCCeEEecCcHHHHHHHHHHHH
Q 046189 57 EGHVPVYVGDEMERFVVSAELLNHPVFVGLLNKSA-----QEYGYE----QKGVLRIPCHVVVFERVVESLR 119 (139)
Q Consensus 57 kG~~~VyVG~e~~RfvVp~~yLnhP~F~~LL~~ae-----eEfG~~----~~G~L~IPC~~~~Fe~vl~~l~ 119 (139)
++-|-||||++ +-|++-.-|-+.|.|..-+..-- ---|.. .+--=.|.-..+.|.+||...-
T Consensus 32 ~~~~fVyvG~~-rdYIl~~gfCSCp~~~~svvl~Gk~~C~Hi~glk~A~~~gk~~~I~~y~~d~~~Il~e~y 102 (117)
T COG5431 32 KVKFFVYVGKE-RDYILEGGFCSCPDFLGSVVLKGKSPCAHIIGLKVAKITGKYDYIDAYYVDYPDILREKY 102 (117)
T ss_pred eEEEEEEEccc-cceEEEcCcccCHHHHhHhhhcCcccchhhhheeeeeecCcEEEEEEecccHHHHHHHHH
Confidence 34578999987 47888888999999984333210 001111 1222345666677777766544
No 37
>PF14317 YcxB: YcxB-like protein
Probab=22.73 E-value=1.8e+02 Score=17.32 Aligned_cols=32 Identities=9% Similarity=0.259 Sum_probs=24.0
Q ss_pred CCCeeEEEEcCCceEEEEecCCcCcHHHHHHHh
Q 046189 56 PEGHVPVYVGDEMERFVVSAELLNHPVFVGLLN 88 (139)
Q Consensus 56 pkG~~~VyVG~e~~RfvVp~~yLnhP~F~~LL~ 88 (139)
-+.++-+|+++. .-++||.+.++.-...++.+
T Consensus 28 ~~~~~~l~~~~~-~~~~iPk~~f~~~e~~~f~~ 59 (62)
T PF14317_consen 28 TKDYFYLYLGKN-QAFIIPKRAFSEEEKEEFRE 59 (62)
T ss_pred eCCEEEEEECCC-eEEEEEHHHCCHhHHHHHHH
Confidence 467888899876 79999999988555555443
No 38
>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=22.36 E-value=69 Score=29.74 Aligned_cols=42 Identities=29% Similarity=0.495 Sum_probs=36.0
Q ss_pred CC-CCeeEEEEcCCceEEEEec-----CCcCcHH-HHHHHhhhhhhcCc
Q 046189 55 VP-EGHVPVYVGDEMERFVVSA-----ELLNHPV-FVGLLNKSAQEYGY 96 (139)
Q Consensus 55 vp-kG~~~VyVG~e~~RfvVp~-----~yLnhP~-F~~LL~~aeeEfG~ 96 (139)
+| ||.+|+++-..+.||.|=+ .|+|-|. -++||++--.|||-
T Consensus 93 ~~~kg~lP~LT~~~kGRy~lII~ENl~kYlnld~wNR~LLdkYC~ey~V 141 (487)
T PF12062_consen 93 ASGKGDLPVLTDNDKGRYSLIIFENLLKYLNLDSWNRELLDKYCREYGV 141 (487)
T ss_pred ccCCCCCCccccCCCCcEEEEEehhHHHHcCChHHHHHHHHHHhHccCc
Confidence 44 5899999977788998875 9999998 89999999999876
No 39
>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=22.19 E-value=3.6e+02 Score=24.16 Aligned_cols=66 Identities=14% Similarity=0.259 Sum_probs=43.9
Q ss_pred CCCCCeeEEEEcC--------------------CceEEEEecCCcC--cHHHHHHHhhhhhhcCcccCCeEEecCcHHHH
Q 046189 54 PVPEGHVPVYVGD--------------------EMERFVVSAELLN--HPVFVGLLNKSAQEYGYEQKGVLRIPCHVVVF 111 (139)
Q Consensus 54 ~vpkG~~~VyVG~--------------------e~~RfvVp~~yLn--hP~F~~LL~~aeeEfG~~~~G~L~IPC~~~~F 111 (139)
..++|-+.|.||. +..|++||.+|=. .--.+.+.+.+++-||-+. +.+==+---|
T Consensus 180 ~~~~~~ltILvGNSgd~sNnHieaL~~L~~~~~~~~kIivPLsYg~~n~~Yi~~V~~~~~~lF~~~~---~~iL~e~mpf 256 (360)
T PF07429_consen 180 KKNKGKLTILVGNSGDPSNNHIEALEALKQQFGDDVKIIVPLSYGANNQAYIQQVIQAGKELFGAEN---FQILTEFMPF 256 (360)
T ss_pred cCCCCceEEEEcCCCCCCccHHHHHHHHHHhcCCCeEEEEECCCCCchHHHHHHHHHHHHHhcCccc---eeEhhhhCCH
Confidence 4567888888882 2469999999974 5677787777777788643 3332334446
Q ss_pred HHHHHHHHcCC
Q 046189 112 ERVVESLRLGL 122 (139)
Q Consensus 112 e~vl~~l~~~~ 122 (139)
+.=+..|++.|
T Consensus 257 ~eYl~lL~~cD 267 (360)
T PF07429_consen 257 DEYLALLSRCD 267 (360)
T ss_pred HHHHHHHHhCC
Confidence 66666666554
Done!