Query 048575
Match_columns 172
No_of_seqs 171 out of 656
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 10:48:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048575.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048575hhsearch_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 8.5E-43 1.8E-47 264.5 11.3 103 1-131 1-103 (104)
2 PF02519 Auxin_inducible: Auxi 100.0 5.3E-35 1.2E-39 219.8 10.1 67 66-132 34-100 (100)
3 PLN03220 uncharacterized prote 100.0 1E-33 2.2E-38 214.9 7.6 64 66-129 33-101 (105)
4 PLN03219 uncharacterized prote 100.0 7.6E-31 1.6E-35 200.1 9.3 66 65-130 36-104 (108)
5 PRK02899 adaptor protein; Prov 84.3 0.94 2E-05 37.8 2.9 25 93-117 38-62 (197)
6 PF02214 BTB_2: BTB/POZ domain 81.3 0.84 1.8E-05 32.5 1.3 55 80-134 6-63 (94)
7 smart00666 PB1 PB1 domain. Pho 80.4 3.8 8.2E-05 28.3 4.4 52 77-133 8-70 (81)
8 PRK02315 adaptor protein; Prov 78.3 1.7 3.7E-05 37.0 2.4 25 93-117 38-62 (233)
9 cd05992 PB1 The PB1 domain is 74.1 8.5 0.00018 26.2 4.7 55 75-133 5-70 (81)
10 PF05389 MecA: Negative regula 73.5 1.1 2.3E-05 37.3 0.0 25 93-117 38-62 (220)
11 PRK02797 4-alpha-L-fucosyltran 63.5 31 0.00066 31.4 7.1 70 67-139 141-232 (322)
12 cd06398 PB1_Joka2 The PB1 doma 56.1 37 0.00081 25.1 5.3 53 77-129 7-72 (91)
13 PF07429 Glyco_transf_56: 4-al 56.1 43 0.00094 30.9 6.8 68 68-138 181-270 (360)
14 cd06407 PB1_NLP A PB1 domain i 53.5 31 0.00068 24.9 4.5 53 76-133 6-70 (82)
15 cd06410 PB1_UP2 Uncharacterize 49.0 34 0.00074 25.6 4.2 46 74-123 17-75 (97)
16 PF02209 VHP: Villin headpiece 42.4 11 0.00025 23.7 0.6 19 90-108 1-19 (36)
17 smart00153 VHP Villin headpiec 42.4 13 0.00028 23.3 0.9 19 90-108 1-19 (36)
18 cd06401 PB1_TFG The PB1 domain 40.5 60 0.0013 24.0 4.3 31 75-109 6-36 (81)
19 PF00564 PB1: PB1 domain; Int 39.8 71 0.0015 21.7 4.4 54 75-133 6-71 (84)
20 cd01406 SIR2-like Sir2-like: P 39.3 47 0.001 27.4 4.0 59 71-135 1-59 (242)
21 cd06397 PB1_UP1 Uncharacterize 38.0 1.3E+02 0.0028 22.4 5.7 54 75-133 5-69 (82)
22 COG4923 Predicted nuclease (RN 35.6 27 0.00058 30.3 2.0 18 112-129 86-103 (245)
23 PF08948 DUF1859: Domain of un 34.7 17 0.00038 28.5 0.7 28 69-97 86-123 (126)
24 PF11834 DUF3354: Domain of un 34.6 32 0.00069 24.4 2.0 16 95-110 27-42 (69)
25 PF00651 BTB: BTB/POZ domain; 34.2 68 0.0015 22.3 3.7 57 74-135 14-75 (111)
26 PF11822 DUF3342: Domain of un 31.3 70 0.0015 29.1 4.0 57 80-139 12-73 (317)
27 PF14317 YcxB: YcxB-like prote 30.8 78 0.0017 19.7 3.2 34 68-102 27-60 (62)
28 PF02100 ODC_AZ: Ornithine dec 28.5 1E+02 0.0022 23.3 4.0 43 80-123 23-69 (108)
29 cd06396 PB1_NBR1 The PB1 domai 27.7 2.3E+02 0.005 20.8 5.6 56 78-136 8-72 (81)
30 COG1759 5-formaminoimidazole-4 26.8 31 0.00068 31.8 1.1 38 66-104 88-136 (361)
31 PF07369 DUF1488: Protein of u 26.4 88 0.0019 21.8 3.1 20 72-91 18-37 (83)
32 PRK10308 3-methyl-adenine DNA 26.4 2E+02 0.0043 25.1 6.0 63 70-132 45-122 (283)
33 COG4862 MecA Negative regulato 22.1 61 0.0013 28.2 1.9 38 80-118 26-63 (224)
34 KOG1748 Acyl carrier protein/N 21.8 48 0.001 26.6 1.1 40 88-130 85-126 (131)
35 cd04395 RhoGAP_ARHGAP21 RhoGAP 21.4 2.3E+02 0.005 22.9 5.1 44 94-137 19-62 (196)
36 PF09475 Dot_icm_IcmQ: Dot/Icm 21.3 31 0.00068 28.9 0.0 14 65-78 112-125 (179)
37 PF03460 NIR_SIR_ferr: Nitrite 21.0 1.3E+02 0.0029 19.9 3.1 55 69-131 6-66 (69)
38 TIGR02527 dot_icm_IcmQ Dot/Icm 20.5 38 0.00081 28.5 0.3 13 66-78 113-125 (182)
No 1
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=8.5e-43 Score=264.50 Aligned_cols=103 Identities=42% Similarity=0.683 Sum_probs=92.5
Q ss_pred CCCccccchhHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCCcchhhhhhhhcccccCCCCCCCCCCCCCCceEEEEeccc
Q 048575 1 MESKKSNKIREIVRLQQILRKWRKLANSPKTSTGGNNNNNSASKSIKFLKRTLSLSDNPLHNASTSTVPKGYLAVCVGEE 80 (172)
Q Consensus 1 ~~~~k~~ki~~i~rL~qilKKWq~~a~~~r~~~~~~~~~~~~s~s~~~~~r~is~~~~~~~~~ss~~vpkG~~~VYVG~e 80 (172)
|+++|++||+||++|+||+|||++++..+... . + ..+.++|+||||||||++
T Consensus 1 m~~~k~~ki~~~~~~kq~l~r~~s~~~~~~~~-------------------------~-~--~~~~~vpkG~~aVyVG~~ 52 (104)
T PLN03090 1 MAIKKSNKLTQTAMLKQILKRCSSLGKKQGYD-------------------------E-D--GLPLDVPKGHFPVYVGEN 52 (104)
T ss_pred CCcccccchhHHHHHHHHHHHHHHhcccCCcc-------------------------c-c--cCCCCCCCCcEEEEECCC
Confidence 89999999999999999999999886543210 0 0 134578999999999999
Q ss_pred ceeEEEccCCCChHHHHHHHHHHHHhcCcccCCceEecCcHHHHHHHHHHH
Q 048575 81 LKRFIIPTDYLSHQAFHILLREAEEEFGFQQTGVLRIPCEVAVFESILKMV 131 (172)
Q Consensus 81 ~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~~~G~L~iPCd~~~Fe~vl~~l 131 (172)
++||+||++|||||+|++||++|||||||.++|+|+||||+++|++++|+|
T Consensus 53 ~~RfvVp~~~L~hP~F~~LL~~aeeEfGf~~~G~L~IPC~~~~Fe~ll~~i 103 (104)
T PLN03090 53 RSRYIVPISFLTHPEFQSLLQQAEEEFGFDHDMGLTIPCEEVVFRSLTSMI 103 (104)
T ss_pred CEEEEEEHHHcCCHHHHHHHHHHHHHhCCCCCCcEEEeCCHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999998
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=5.3e-35 Score=219.83 Aligned_cols=67 Identities=57% Similarity=1.012 Sum_probs=65.4
Q ss_pred CCCCCceEEEEecccceeEEEccCCCChHHHHHHHHHHHHhcCcccCCceEecCcHHHHHHHHHHHh
Q 048575 66 STVPKGYLAVCVGEELKRFIIPTDYLSHQAFHILLREAEEEFGFQQTGVLRIPCEVAVFESILKMVE 132 (172)
Q Consensus 66 ~~vpkG~~~VYVG~e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~~~G~L~iPCd~~~Fe~vl~~l~ 132 (172)
..+|+||||||||++++||+||++|||||+|++||++|||||||+++|+|+||||+++|+++||+||
T Consensus 34 ~~vp~G~~~VyVG~~~~Rfvvp~~~L~hp~f~~LL~~aeeEfG~~~~G~l~iPC~~~~Fe~~l~~le 100 (100)
T PF02519_consen 34 SDVPKGHFAVYVGEERRRFVVPVSYLNHPLFQELLEQAEEEFGFDQDGPLTIPCDVVLFEHLLWLLE 100 (100)
T ss_pred CCCCCCeEEEEeCccceEEEechHHcCchhHHHHHHHHhhhcCcCCCCcEEeeCCHHHHHHHHHHhC
Confidence 5789999999999999999999999999999999999999999999999999999999999999986
No 3
>PLN03220 uncharacterized protein; Provisional
Probab=100.00 E-value=1e-33 Score=214.88 Aligned_cols=64 Identities=50% Similarity=0.909 Sum_probs=60.7
Q ss_pred CCCCCceEEEEecc----cceeEEEccCCCChHHHHHHHHHHHHhcCccc-CCceEecCcHHHHHHHHH
Q 048575 66 STVPKGYLAVCVGE----ELKRFIIPTDYLSHQAFHILLREAEEEFGFQQ-TGVLRIPCEVAVFESILK 129 (172)
Q Consensus 66 ~~vpkG~~~VYVG~----e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~~-~G~L~iPCd~~~Fe~vl~ 129 (172)
.+|||||||||||+ +++||+||++|||||+|++||++|||||||.+ +|+|+||||++.|++++.
T Consensus 33 ~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~ 101 (105)
T PLN03220 33 DHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHPSFKEFLSRAEEEFGFNHPMGGLTIPCREEVFLDLIA 101 (105)
T ss_pred CCCCCCeEEEEECCCCCccceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEeeCCHHHHHHHHH
Confidence 47999999999997 58999999999999999999999999999998 699999999999999985
No 4
>PLN03219 uncharacterized protein; Provisional
Probab=99.97 E-value=7.6e-31 Score=200.10 Aligned_cols=66 Identities=47% Similarity=0.821 Sum_probs=62.1
Q ss_pred CCCCCCceEEEEecc--cceeEEEccCCCChHHHHHHHHHHHHhcCccc-CCceEecCcHHHHHHHHHH
Q 048575 65 TSTVPKGYLAVCVGE--ELKRFIIPTDYLSHQAFHILLREAEEEFGFQQ-TGVLRIPCEVAVFESILKM 130 (172)
Q Consensus 65 s~~vpkG~~~VYVG~--e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~~-~G~L~iPCd~~~Fe~vl~~ 130 (172)
+..+||||||||||+ |++||+||++|||||+|++||++|||||||.+ +|+|+||||++.|++||..
T Consensus 36 ~~~vpkGh~aVYVG~~~E~kRFvVPi~yL~hP~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~~ 104 (108)
T PLN03219 36 SGLVPKGHVAVYVGEQMEKKRFVVPISYLNHPLFREFLNRAEEECGFHHSMGGLTIPCREESFLHLITS 104 (108)
T ss_pred CCCCCCCeEEEEECCCCCceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEEeCCHHHHHHHHHh
Confidence 457999999999996 59999999999999999999999999999997 6999999999999999874
No 5
>PRK02899 adaptor protein; Provisional
Probab=84.27 E-value=0.94 Score=37.78 Aligned_cols=25 Identities=36% Similarity=0.764 Sum_probs=21.9
Q ss_pred hHHHHHHHHHHHHhcCcccCCceEe
Q 048575 93 HQAFHILLREAEEEFGFQQTGVLRI 117 (172)
Q Consensus 93 hP~F~~LL~~aeEEfG~~~~G~L~i 117 (172)
+-+|.++|++|..|+||..+|||+|
T Consensus 38 e~lF~~mm~Ea~~e~~F~~~~pl~~ 62 (197)
T PRK02899 38 HQLFRDMMQEANKELGFEADGPIAV 62 (197)
T ss_pred HHHHHHHHHHhhhccCcccCCeEEE
Confidence 4578888999999999999999985
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=81.29 E-value=0.84 Score=32.46 Aligned_cols=55 Identities=16% Similarity=0.105 Sum_probs=40.6
Q ss_pred cceeEEEccCCCC-h--HHHHHHHHHHHHhcCcccCCceEecCcHHHHHHHHHHHhcc
Q 048575 80 ELKRFIIPTDYLS-H--QAFHILLREAEEEFGFQQTGVLRIPCEVAVFESILKMVEQK 134 (172)
Q Consensus 80 e~~RFvVp~~yLn-h--P~F~~LL~~aeEEfG~~~~G~L~iPCd~~~Fe~vl~~l~~~ 134 (172)
.+++|.++.+-|. + ..|..|+........-..+|.+-|-++...|++||..++.+
T Consensus 6 GG~~f~~~~~tL~~~~~s~l~~~~~~~~~~~~~~~~~~~fiDRdp~~F~~IL~ylr~~ 63 (94)
T PF02214_consen 6 GGTIFETSRSTLTRYPDSLLARLFSGERSDDYDDDDGEYFIDRDPELFEYILNYLRTG 63 (94)
T ss_dssp TTEEEEEEHHHHHTSTTSTTTSHHHTGHGGGEETTTTEEEESS-HHHHHHHHHHHHHT
T ss_pred CCEEEEEcHHHHhhCCCChhhhHHhhccccccCCccceEEeccChhhhhHHHHHHhhc
Confidence 4678888887665 3 47777777542222333479999999999999999999995
No 7
>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=80.44 E-value=3.8 Score=28.25 Aligned_cols=52 Identities=19% Similarity=0.471 Sum_probs=39.2
Q ss_pred ecccceeEEEccCCCChHHHHHHHHHHHHhcCcc----------cCC-ceEecCcHHHHHHHHHHHhc
Q 048575 77 VGEELKRFIIPTDYLSHQAFHILLREAEEEFGFQ----------QTG-VLRIPCEVAVFESILKMVEQ 133 (172)
Q Consensus 77 VG~e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~----------~~G-~L~iPCd~~~Fe~vl~~l~~ 133 (172)
-|.+.+||.||- ..-|.+|..+..+.|++. .+| .++|.+|.+ ++.++.+...
T Consensus 8 ~~~~~~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~D-l~~a~~~~~~ 70 (81)
T smart00666 8 YGGETRRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDED-LEEAIEEYDS 70 (81)
T ss_pred ECCEEEEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHHH-HHHHHHHHHH
Confidence 378999999986 566999999999999885 134 788999775 4456666654
No 8
>PRK02315 adaptor protein; Provisional
Probab=78.30 E-value=1.7 Score=37.01 Aligned_cols=25 Identities=28% Similarity=0.442 Sum_probs=22.7
Q ss_pred hHHHHHHHHHHHHhcCcccCCceEe
Q 048575 93 HQAFHILLREAEEEFGFQQTGVLRI 117 (172)
Q Consensus 93 hP~F~~LL~~aeEEfG~~~~G~L~i 117 (172)
+-+|.++|+++..|+||..+|||+|
T Consensus 38 e~fF~~mm~Ea~~e~~F~~~~pl~~ 62 (233)
T PRK02315 38 EEFFYSMMDEVDEEDDFADEGPLWF 62 (233)
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 4689999999999999999999985
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=74.09 E-value=8.5 Score=26.24 Aligned_cols=55 Identities=22% Similarity=0.440 Sum_probs=40.5
Q ss_pred EEecccceeEEEccCCCChHHHHHHHHHHHHhcCcc-----------cCCceEecCcHHHHHHHHHHHhc
Q 048575 75 VCVGEELKRFIIPTDYLSHQAFHILLREAEEEFGFQ-----------QTGVLRIPCEVAVFESILKMVEQ 133 (172)
Q Consensus 75 VYVG~e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~-----------~~G~L~iPCd~~~Fe~vl~~l~~ 133 (172)
|+-+.+.+||.+|. .++-|.+|..+..+.|++. .+..++|-+|. -|+.++....+
T Consensus 5 ~~~~~~~~~~~~~~---~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd~-Dl~~a~~~~~~ 70 (81)
T cd05992 5 VKYGGEIRRFVVVS---RSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSDE-DLEEAIEEARR 70 (81)
T ss_pred EEecCCCEEEEEec---CCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCHH-HHHHHHHHHhh
Confidence 44456899999997 7788999999999998885 23456677764 55667766654
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=73.48 E-value=1.1 Score=37.30 Aligned_cols=25 Identities=40% Similarity=0.685 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHHhcCcccCCceEe
Q 048575 93 HQAFHILLREAEEEFGFQQTGVLRI 117 (172)
Q Consensus 93 hP~F~~LL~~aeEEfG~~~~G~L~i 117 (172)
+-.|.++|++|.+|+||..+|||++
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 5679999999999999999999986
No 11
>PRK02797 4-alpha-L-fucosyltransferase; Provisional
Probab=63.49 E-value=31 Score=31.42 Aligned_cols=70 Identities=20% Similarity=0.326 Sum_probs=51.6
Q ss_pred CCCCceEEEEec--------------------ccceeEEEccCC--CChHHHHHHHHHHHHhcCcccCCceEecCcHHHH
Q 048575 67 TVPKGYLAVCVG--------------------EELKRFIIPTDY--LSHQAFHILLREAEEEFGFQQTGVLRIPCEVAVF 124 (172)
Q Consensus 67 ~vpkG~~~VYVG--------------------~e~~RFvVp~~y--LnhP~F~~LL~~aeEEfG~~~~G~L~iPCd~~~F 124 (172)
..++|-++|.|| .+.-|++||+.| =|.--.++..+.+.|-||- +-+++-=+---|
T Consensus 141 ~~~~~~~tIlvGNSgd~SN~Hie~L~~l~~~~~~~v~ii~PlsYp~gn~~Yi~~V~~~~~~lF~~---~~~~~L~e~l~f 217 (322)
T PRK02797 141 RQRAGKMTILVGNSGDRSNRHIEALRALHQQFGDNVKIIVPMGYPANNQAYIEEVRQAGLALFGA---ENFQILTEKLPF 217 (322)
T ss_pred ccCCCceEEEEeCCCCCcccHHHHHHHHHHHhCCCeEEEEECCcCCCCHHHHHHHHHHHHHhcCc---ccEEehhhhCCH
Confidence 346677889888 245699999999 6766777777777888873 456666666778
Q ss_pred HHHHHHHhccCCccc
Q 048575 125 ESILKMVEQKKDTFF 139 (172)
Q Consensus 125 e~vl~~l~~~~~~~~ 139 (172)
+..+.+|.+.|=.+.
T Consensus 218 ~eYl~lL~~~Dl~~f 232 (322)
T PRK02797 218 DDYLALLRQCDLGYF 232 (322)
T ss_pred HHHHHHHHhCCEEEE
Confidence 888999988775443
No 12
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=56.14 E-value=37 Score=25.06 Aligned_cols=53 Identities=21% Similarity=0.282 Sum_probs=37.6
Q ss_pred ecccceeEEEccC-CCChHHHHHHHHHHHHhcCccc------------CCceEecCcHHHHHHHHH
Q 048575 77 VGEELKRFIIPTD-YLSHQAFHILLREAEEEFGFQQ------------TGVLRIPCEVAVFESILK 129 (172)
Q Consensus 77 VG~e~~RFvVp~~-yLnhP~F~~LL~~aeEEfG~~~------------~G~L~iPCd~~~Fe~vl~ 129 (172)
-|++.+||-+|.. --.+.-|..|.++-++-|.... ..-++|-||.++-+-+-.
T Consensus 7 y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~ 72 (91)
T cd06398 7 YGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQY 72 (91)
T ss_pred eCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHH
Confidence 3789999999974 0113468888888888777653 335789999987764443
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=56.10 E-value=43 Score=30.92 Aligned_cols=68 Identities=22% Similarity=0.365 Sum_probs=48.9
Q ss_pred CCCceEEEEec--------------------ccceeEEEccCCCC--hHHHHHHHHHHHHhcCcccCCceEecCcHHHHH
Q 048575 68 VPKGYLAVCVG--------------------EELKRFIIPTDYLS--HQAFHILLREAEEEFGFQQTGVLRIPCEVAVFE 125 (172)
Q Consensus 68 vpkG~~~VYVG--------------------~e~~RFvVp~~yLn--hP~F~~LL~~aeEEfG~~~~G~L~iPCd~~~Fe 125 (172)
.++|-..|.|| .+..|++||+.|=. .--..++.+.+++-||- +-+.+==|---|+
T Consensus 181 ~~~~~ltILvGNSgd~sNnHieaL~~L~~~~~~~~kIivPLsYg~~n~~Yi~~V~~~~~~lF~~---~~~~iL~e~mpf~ 257 (360)
T PF07429_consen 181 KNKGKLTILVGNSGDPSNNHIEALEALKQQFGDDVKIIVPLSYGANNQAYIQQVIQAGKELFGA---ENFQILTEFMPFD 257 (360)
T ss_pred CCCCceEEEEcCCCCCCccHHHHHHHHHHhcCCCeEEEEECCCCCchHHHHHHHHHHHHHhcCc---cceeEhhhhCCHH
Confidence 45677777777 25689999999974 56777888888888883 3454444555678
Q ss_pred HHHHHHhccCCcc
Q 048575 126 SILKMVEQKKDTF 138 (172)
Q Consensus 126 ~vl~~l~~~~~~~ 138 (172)
..+.+|++.|-.+
T Consensus 258 eYl~lL~~cDl~i 270 (360)
T PF07429_consen 258 EYLALLSRCDLGI 270 (360)
T ss_pred HHHHHHHhCCEEE
Confidence 8888888877543
No 14
>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=53.54 E-value=31 Score=24.91 Aligned_cols=53 Identities=23% Similarity=0.455 Sum_probs=38.0
Q ss_pred EecccceeEEEccCCCChHHHHHHHHHHHHhcCccc------------CCceEecCcHHHHHHHHHHHhc
Q 048575 76 CVGEELKRFIIPTDYLSHQAFHILLREAEEEFGFQQ------------TGVLRIPCEVAVFESILKMVEQ 133 (172)
Q Consensus 76 YVG~e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~~------------~G~L~iPCd~~~Fe~vl~~l~~ 133 (172)
..|+|..||.+|... -|++|.++-.+-|++.. +..++|.||.++=| .+.+.+.
T Consensus 6 ~~~~d~~r~~l~~~~----~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~e-ai~i~~~ 70 (82)
T cd06407 6 TYGEEKIRFRLPPSW----GFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEE-CIDVYRS 70 (82)
T ss_pred EeCCeEEEEEcCCCC----CHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHH-HHHHHHH
Confidence 347899999999864 48888888888777642 35678899988765 4444444
No 15
>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=49.03 E-value=34 Score=25.58 Aligned_cols=46 Identities=17% Similarity=0.307 Sum_probs=33.5
Q ss_pred EEEecccceeEEEccCCCChHHHHHHHHHHHHhcCccc-------------CCceEecCcHHH
Q 048575 74 AVCVGEELKRFIIPTDYLSHQAFHILLREAEEEFGFQQ-------------TGVLRIPCEVAV 123 (172)
Q Consensus 74 ~VYVG~e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~~-------------~G~L~iPCd~~~ 123 (172)
.=|||.+.+--.|+-+ . -|.+|..+..+.++... ++-+.|-||.++
T Consensus 17 l~Y~GG~tr~i~V~r~-~---s~~el~~kl~~~~~~~~~~~lky~Lp~edld~Lisv~~DeDl 75 (97)
T cd06410 17 LRYVGGETRIVSVDRS-I---SFKELVSKLSELFGAGVVVTLKYQLPDEDLDALISVSNDEDL 75 (97)
T ss_pred EEEcCCceEEEEEcCC-C---CHHHHHHHHHHHhCCCCceEEEEEcCCCCcceeEEecCcHHH
Confidence 4699999999999988 4 45667777777776654 445678888754
No 16
>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=42.43 E-value=11 Score=23.65 Aligned_cols=19 Identities=37% Similarity=0.590 Sum_probs=15.4
Q ss_pred CCChHHHHHHHHHHHHhcC
Q 048575 90 YLSHQAFHILLREAEEEFG 108 (172)
Q Consensus 90 yLnhP~F~~LL~~aeEEfG 108 (172)
||+...|.+++.|+.+||.
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 8999999999999999974
No 17
>smart00153 VHP Villin headpiece domain.
Probab=42.42 E-value=13 Score=23.28 Aligned_cols=19 Identities=37% Similarity=0.571 Sum_probs=17.1
Q ss_pred CCChHHHHHHHHHHHHhcC
Q 048575 90 YLSHQAFHILLREAEEEFG 108 (172)
Q Consensus 90 yLnhP~F~~LL~~aeEEfG 108 (172)
||+...|++++.|+.+||-
T Consensus 1 yLsdeeF~~vfgmsr~eF~ 19 (36)
T smart00153 1 YLSDEDFEEVFGMTREEFY 19 (36)
T ss_pred CCCHHHHHHHHCCCHHHHH
Confidence 8999999999999999973
No 18
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=40.49 E-value=60 Score=23.97 Aligned_cols=31 Identities=19% Similarity=0.337 Sum_probs=22.0
Q ss_pred EEecccceeEEEccCCCChHHHHHHHHHHHHhcCc
Q 048575 75 VCVGEELKRFIIPTDYLSHQAFHILLREAEEEFGF 109 (172)
Q Consensus 75 VYVG~e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~ 109 (172)
|| |.|-||+.+|..-+ -|.+|..+....|..
T Consensus 6 ~~-g~DiR~~~~~~~~~---t~~~L~~~v~~~F~~ 36 (81)
T cd06401 6 QL-GDDIRRIPIHNEDI---TYDELLLMMQRVFRG 36 (81)
T ss_pred Ee-CCeEEEEeccCccc---cHHHHHHHHHHHhcc
Confidence 44 78999977775222 578888888877763
No 19
>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=39.76 E-value=71 Score=21.72 Aligned_cols=54 Identities=22% Similarity=0.497 Sum_probs=36.7
Q ss_pred EEeccccee-EEEccCCCChHHHHHHHHHHHHhcCcc----------cCC-ceEecCcHHHHHHHHHHHhc
Q 048575 75 VCVGEELKR-FIIPTDYLSHQAFHILLREAEEEFGFQ----------QTG-VLRIPCEVAVFESILKMVEQ 133 (172)
Q Consensus 75 VYVG~e~~R-FvVp~~yLnhP~F~~LL~~aeEEfG~~----------~~G-~L~iPCd~~~Fe~vl~~l~~ 133 (172)
++-|.+.+| +.+|.. +-|.+|..+.++.||.. .+| .++|.++.++= .++....+
T Consensus 6 ~~~~~~~~~~~~~~~~----~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~Dl~-~a~~~~~~ 71 (84)
T PF00564_consen 6 VRYGGDIRRIISLPSD----VSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDEDLQ-EAIEQAKE 71 (84)
T ss_dssp EEETTEEEEEEEECST----SHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHHHH-HHHHHHHH
T ss_pred EEECCeeEEEEEcCCC----CCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHHHH-HHHHHHHh
Confidence 344556666 655544 58999999999999983 244 57788887654 45555544
No 20
>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=39.26 E-value=47 Score=27.41 Aligned_cols=59 Identities=17% Similarity=0.263 Sum_probs=38.1
Q ss_pred ceEEEEecccceeEEEccCCCChHHHHHHHHHHHHhcCcccCCceEecCcHHHHHHHHHHHhccC
Q 048575 71 GYLAVCVGEELKRFIIPTDYLSHQAFHILLREAEEEFGFQQTGVLRIPCEVAVFESILKMVEQKK 135 (172)
Q Consensus 71 G~~~VYVG~e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~~~G~L~iPCd~~~Fe~vl~~l~~~~ 135 (172)
|++++++|..-.+= .+-|.+.+|++...+|+|...+....--=+...+..+..++++..
T Consensus 1 g~lvlFiGAG~S~~------~glP~W~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~ 59 (242)
T cd01406 1 GRVVIFVGAGVSVS------SGLPDWKTLLDEIASELGLEIDGYSVEAKDENDYLELAELLEKEF 59 (242)
T ss_pred CCEEEEecCccccc------cCCCChHHHHHHHHHHcCCccchhhccccchhhHHHHHHHHHHHh
Confidence 78899998663331 577899999999999998765421110003445555666666543
No 21
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=38.01 E-value=1.3e+02 Score=22.39 Aligned_cols=54 Identities=7% Similarity=0.242 Sum_probs=39.8
Q ss_pred EEecccceeEEEccCCCChHHHHHHHHHHHHhcCccc----------C-CceEecCcHHHHHHHHHHHhc
Q 048575 75 VCVGEELKRFIIPTDYLSHQAFHILLREAEEEFGFQQ----------T-GVLRIPCEVAVFESILKMVEQ 133 (172)
Q Consensus 75 VYVG~e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~~----------~-G~L~iPCd~~~Fe~vl~~l~~ 133 (172)
|--|.+.|||.+|. .|-+.+|-++.+.=|-+.. | ..|||.=+.++.+. +....+
T Consensus 5 v~~~g~~RRf~~~~----~pt~~~L~~kl~~Lf~lp~~~~~vtYiDeD~D~ITlssd~eL~d~-~~~~~~ 69 (82)
T cd06397 5 SSFLGDTRRIVFPD----IPTWEALASKLENLYNLPEIKVGVTYIDNDNDEITLSSNKELQDF-YRLSHR 69 (82)
T ss_pred EEeCCceEEEecCC----CccHHHHHHHHHHHhCCChhHeEEEEEcCCCCEEEecchHHHHHH-HHhccc
Confidence 33467999999998 7999999999988777762 3 57888887777664 444433
No 22
>COG4923 Predicted nuclease (RNAse H fold) [General function prediction only]
Probab=35.61 E-value=27 Score=30.34 Aligned_cols=18 Identities=28% Similarity=0.790 Sum_probs=13.5
Q ss_pred CCceEecCcHHHHHHHHH
Q 048575 112 TGVLRIPCEVAVFESILK 129 (172)
Q Consensus 112 ~G~L~iPCd~~~Fe~vl~ 129 (172)
....++||.+.++..+-.
T Consensus 86 sSvF~vPcR~A~Y~~~y~ 103 (245)
T COG4923 86 SSVFSVPCRAALYSDIYG 103 (245)
T ss_pred cceeccchHHHHHHHHHH
Confidence 445789999998876644
No 23
>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=34.74 E-value=17 Score=28.45 Aligned_cols=28 Identities=21% Similarity=0.522 Sum_probs=9.2
Q ss_pred CCceEEEEecccceeEE----------EccCCCChHHHH
Q 048575 69 PKGYLAVCVGEELKRFI----------IPTDYLSHQAFH 97 (172)
Q Consensus 69 pkG~~~VYVG~e~~RFv----------Vp~~yLnhP~F~ 97 (172)
..|||||.| ..+-.|+ ||+-|||.|+-+
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 479999999 5666776 688889888743
No 24
>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=34.55 E-value=32 Score=24.42 Aligned_cols=16 Identities=44% Similarity=0.771 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHhcCcc
Q 048575 95 AFHILLREAEEEFGFQ 110 (172)
Q Consensus 95 ~F~~LL~~aeEEfG~~ 110 (172)
-++|||+.|++.||+.
T Consensus 27 SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 27 SLEELLKIASEKFGFS 42 (69)
T ss_pred cHHHHHHHHHHHhCCC
Confidence 5899999999999995
No 25
>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=34.24 E-value=68 Score=22.26 Aligned_cols=57 Identities=21% Similarity=0.417 Sum_probs=39.8
Q ss_pred EEEecccceeEEEccCCC--ChHHHHHHHHHHHHhcCcccCC--ceEec-CcHHHHHHHHHHHhccC
Q 048575 74 AVCVGEELKRFIIPTDYL--SHQAFHILLREAEEEFGFQQTG--VLRIP-CEVAVFESILKMVEQKK 135 (172)
Q Consensus 74 ~VYVG~e~~RFvVp~~yL--nhP~F~~LL~~aeEEfG~~~~G--~L~iP-Cd~~~Fe~vl~~l~~~~ 135 (172)
.+.|| +.++|-|.-..| ..|.|+.+++.. +....+ .|.++ ++...|+.++..+-.++
T Consensus 14 ~i~v~-d~~~~~vhk~iL~~~S~~F~~~~~~~----~~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~~ 75 (111)
T PF00651_consen 14 TIRVG-DGKTFYVHKNILAARSPYFRNLFEGS----KFKESTVPEISLPDVSPEAFEAFLEYMYTGE 75 (111)
T ss_dssp EEEET-TTEEEEE-HHHHHHHBHHHHHHHTTT----TSTTSSEEEEEETTSCHHHHHHHHHHHHHSE
T ss_pred EEEEC-CCEEEeechhhhhccchhhhhccccc----ccccccccccccccccccccccccccccCCc
Confidence 45554 478888888777 459999999877 222333 46555 68999999999997543
No 26
>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=31.26 E-value=70 Score=29.07 Aligned_cols=57 Identities=21% Similarity=0.437 Sum_probs=43.1
Q ss_pred cceeEEEccCCCC--hHHHHHHHHH---HHHhcCcccCCceEecCcHHHHHHHHHHHhccCCccc
Q 048575 80 ELKRFIIPTDYLS--HQAFHILLRE---AEEEFGFQQTGVLRIPCEVAVFESILKMVEQKKDTFF 139 (172)
Q Consensus 80 e~~RFvVp~~yLn--hP~F~~LL~~---aeEEfG~~~~G~L~iPCd~~~Fe~vl~~l~~~~~~~~ 139 (172)
..+=|..|.+.|- ...|+++|.. ..++. .+-.|.+-||+..|+.++.-+++..+.+.
T Consensus 12 ~~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~---~~idisVhCDv~iF~WLm~yv~~~~p~l~ 73 (317)
T PF11822_consen 12 EKRDFTCPRDLLVSEMRYFAEYLSRYINDSQRW---EEIDISVHCDVHIFEWLMRYVKGEPPSLT 73 (317)
T ss_pred cceeeeccHHHHHHhhHHHHHHHhhcccccCcC---CCcceEEecChhHHHHHHHHhhcCCCcCC
Confidence 3567888888774 4679999965 33332 24679999999999999999999766543
No 27
>PF14317 YcxB: YcxB-like protein
Probab=30.82 E-value=78 Score=19.72 Aligned_cols=34 Identities=24% Similarity=0.345 Sum_probs=25.8
Q ss_pred CCCceEEEEecccceeEEEccCCCChHHHHHHHHH
Q 048575 68 VPKGYLAVCVGEELKRFIIPTDYLSHQAFHILLRE 102 (172)
Q Consensus 68 vpkG~~~VYVG~e~~RFvVp~~yLnhP~F~~LL~~ 102 (172)
--+.++.+|++ +..-++||.+.++.-...+|.+.
T Consensus 27 e~~~~~~l~~~-~~~~~~iPk~~f~~~e~~~f~~~ 60 (62)
T PF14317_consen 27 ETKDYFYLYLG-KNQAFIIPKRAFSEEEKEEFREF 60 (62)
T ss_pred EeCCEEEEEEC-CCeEEEEEHHHCCHhHHHHHHHH
Confidence 34788999995 66999999999986655555543
No 28
>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=28.50 E-value=1e+02 Score=23.33 Aligned_cols=43 Identities=28% Similarity=0.339 Sum_probs=21.2
Q ss_pred cceeEE-EccC---CCChHHHHHHHHHHHHhcCcccCCceEecCcHHH
Q 048575 80 ELKRFI-IPTD---YLSHQAFHILLREAEEEFGFQQTGVLRIPCEVAV 123 (172)
Q Consensus 80 e~~RFv-Vp~~---yLnhP~F~~LL~~aeEEfG~~~~G~L~iPCd~~~ 123 (172)
++.=|+ +|-. -..-.-|.+||+.|||++|.++ -.|.|+=+-..
T Consensus 23 ~~~L~V~ip~~~~~~~~K~~lvaLLElAee~L~c~~-vvic~~k~~~d 69 (108)
T PF02100_consen 23 ERTLFVFIPSSALGQGSKESLVALLELAEEKLGCSH-VVICLDKNRPD 69 (108)
T ss_dssp TTEEEEE-SS---SS--SHHHHHHHHHHHHHH-----EEEEE---SS-
T ss_pred CCEEEEEECCcccccccHHHHHHHHHHhcCcCCCCE-EEEEEECCchh
Confidence 445555 4543 3455789999999999988654 34445444333
No 29
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=27.71 E-value=2.3e+02 Score=20.75 Aligned_cols=56 Identities=13% Similarity=0.259 Sum_probs=42.0
Q ss_pred cccceeEEEccCCCChHHHHHHHHHHHHhcCcc---------cCCceEecCcHHHHHHHHHHHhccCC
Q 048575 78 GEELKRFIIPTDYLSHQAFHILLREAEEEFGFQ---------QTGVLRIPCEVAVFESILKMVEQKKD 136 (172)
Q Consensus 78 G~e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~---------~~G~L~iPCd~~~Fe~vl~~l~~~~~ 136 (172)
|+|..||.++-+ .++-|.+|.++-+.-||+. .+.+++|.|++++ +..+.+.++...
T Consensus 8 ~~d~~rf~~~~~--~~~~~~~L~~ev~~rf~l~~f~lKYlDde~e~v~lssd~eL-eE~~rl~~~~~~ 72 (81)
T cd06396 8 NGESQSFLVSDS--ENTTWASVEAMVKVSFGLNDIQIKYVDEENEEVSVNSQGEY-EEALKSAVRQGN 72 (81)
T ss_pred CCeEEEEEecCC--CCCCHHHHHHHHHHHhCCCcceeEEEcCCCCEEEEEchhhH-HHHHHHHHhCCC
Confidence 679999999862 2445899999998888864 2457899998875 557777777653
No 30
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=26.83 E-value=31 Score=31.77 Aligned_cols=38 Identities=24% Similarity=0.370 Sum_probs=26.0
Q ss_pred CCCCCceEEEEeccc--ceeEEEccCCCC---------hHHHHHHHHHHH
Q 048575 66 STVPKGYLAVCVGEE--LKRFIIPTDYLS---------HQAFHILLREAE 104 (172)
Q Consensus 66 ~~vpkG~~~VYVG~e--~~RFvVp~~yLn---------hP~F~~LL~~ae 104 (172)
-.+|.|-|++|||-| -..|.||. |-| .-.-..||++|.
T Consensus 88 I~IP~gSfv~Y~G~d~ie~~~~vP~-fGnR~lLrwE~~~~~~~~lLekAg 136 (361)
T COG1759 88 IFIPHGSFVAYVGYDGIENEFEVPM-FGNRELLRWEEDRKLEYKLLEKAG 136 (361)
T ss_pred EEecCCceEEEecchhhhhcccCcc-cccHhHhhhhcchhhHHHHHHHcC
Confidence 468999999999976 45577775 222 223456777764
No 31
>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=26.39 E-value=88 Score=21.83 Aligned_cols=20 Identities=20% Similarity=0.132 Sum_probs=17.6
Q ss_pred eEEEEecccceeEEEccCCC
Q 048575 72 YLAVCVGEELKRFIIPTDYL 91 (172)
Q Consensus 72 ~~~VYVG~e~~RFvVp~~yL 91 (172)
.|+++||...-++.|..+-|
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 68999998999999998766
No 32
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=26.38 E-value=2e+02 Score=25.12 Aligned_cols=63 Identities=19% Similarity=0.164 Sum_probs=42.7
Q ss_pred CceEEEEecccceeEEEccCCCChHHHHHHHHHHHHhcCcccC---------------CceEecCcHHHHHHHHHHHh
Q 048575 70 KGYLAVCVGEELKRFIIPTDYLSHQAFHILLREAEEEFGFQQT---------------GVLRIPCEVAVFESILKMVE 132 (172)
Q Consensus 70 kG~~~VYVG~e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~~~---------------G~L~iPCd~~~Fe~vl~~l~ 132 (172)
.|.|.|.-..++.++.|.++.-.-+....++.....-||++.| -+|+||...+.||-+++.|=
T Consensus 45 ~~~~~v~~~~~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L~~~~~~~~GlR~p~~~d~fE~lv~aIi 122 (283)
T PRK10308 45 RGVVTVIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGKLGAARPGLRLPGSVDAFEQGVRAIL 122 (283)
T ss_pred cEEEEEEEcCCCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCCcCCCCCCHHHHHHHHHH
Confidence 5777777655555666666543334555667666666666554 46899999999998888763
No 33
>COG4862 MecA Negative regulator of genetic competence, sporulation and motility [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Cell motility and secretion]
Probab=22.15 E-value=61 Score=28.17 Aligned_cols=38 Identities=24% Similarity=0.323 Sum_probs=29.5
Q ss_pred cceeEEEccCCCChHHHHHHHHHHHHhcCcccCCceEec
Q 048575 80 ELKRFIIPTDYLSHQAFHILLREAEEEFGFQQTGVLRIP 118 (172)
Q Consensus 80 e~~RFvVp~~yLnhP~F~~LL~~aeEEfG~~~~G~L~iP 118 (172)
++.=|..|-. -.+-+|-+++..+.+|-+|..+|||.|-
T Consensus 26 ~~eD~w~n~e-k~EE~F~~mMdEl~~ee~F~~~GpL~iq 63 (224)
T COG4862 26 EREDFWYNRE-KTEELFYEMMDELNLEEDFKDEGPLWIQ 63 (224)
T ss_pred CHHHhccchH-HHHHHHHHHHHhcCCccccccCCceEEE
Confidence 4444555443 4688999999999999999999999873
No 34
>KOG1748 consensus Acyl carrier protein/NADH-ubiquinone oxidoreductase, NDUFAB1/SDAP subunit [Energy production and conversion; Lipid transport and metabolism; Secondary metabolites biosynthesis, transport and catabolism]
Probab=21.82 E-value=48 Score=26.57 Aligned_cols=40 Identities=23% Similarity=0.222 Sum_probs=26.7
Q ss_pred cCCCChHHHHHHHHHHHHhcCccc--CCceEecCcHHHHHHHHHH
Q 048575 88 TDYLSHQAFHILLREAEEEFGFQQ--TGVLRIPCEVAVFESILKM 130 (172)
Q Consensus 88 ~~yLnhP~F~~LL~~aeEEfG~~~--~G~L~iPCd~~~Fe~vl~~ 130 (172)
++-|.|- |++-..||||||+- ...=.|-|-.+.++||...
T Consensus 85 lDSLD~V---EiVMAlEEEFgiEIpd~dAdki~t~~da~~yI~~~ 126 (131)
T KOG1748|consen 85 LDSLDTV---EIVMALEEEFGIEIPDEDADKIKTVRDAADYIADK 126 (131)
T ss_pred Ccccccc---hhhhhhHHHhCCccCcchhhhhCCHHHHHHHHHhc
Confidence 3456553 45556689999985 3455677777777777654
No 35
>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=21.44 E-value=2.3e+02 Score=22.88 Aligned_cols=44 Identities=14% Similarity=0.202 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHhcCcccCCceEecCcHHHHHHHHHHHhccCCc
Q 048575 94 QAFHILLREAEEEFGFQQTGVLRIPCEVAVFESILKMVEQKKDT 137 (172)
Q Consensus 94 P~F~~LL~~aeEEfG~~~~G~L~iPCd~~~Fe~vl~~l~~~~~~ 137 (172)
|.|-+..-..-++.|...+|--++|.+....+.+...++++...
T Consensus 19 P~iv~~~~~~l~~~g~~~eGIFR~~g~~~~i~~l~~~l~~~~~~ 62 (196)
T cd04395 19 PLIVEVCCNIVEARGLETVGIYRVPGNNAAISALQEELNRGGFD 62 (196)
T ss_pred ChHHHHHHHHHHHcCCCCccceeCCCcHHHHHHHHHHHhcCCCC
Confidence 45554444455788999999999999999999999999987643
No 36
>PF09475 Dot_icm_IcmQ: Dot/Icm secretion system protein (dot_icm_IcmQ); InterPro: IPR013365 Proteins in this entry are the IcmQ component of Dot/Icm secretion systems, as found in the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favor calling this the Dot/Icm system. This protein was shown to be essential for translocation ().; PDB: 3FXE_A 3FXD_C.
Probab=21.32 E-value=31 Score=28.94 Aligned_cols=14 Identities=14% Similarity=0.515 Sum_probs=0.0
Q ss_pred CCCCCCceEEEEec
Q 048575 65 TSTVPKGYLAVCVG 78 (172)
Q Consensus 65 s~~vpkG~~~VYVG 78 (172)
...+.++|++|||-
T Consensus 112 enk~NEAYVaiyIn 125 (179)
T PF09475_consen 112 ENKLNEAYVAIYIN 125 (179)
T ss_dssp --------------
T ss_pred hcccceeEEEEEEc
Confidence 35688999999994
No 37
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=21.01 E-value=1.3e+02 Score=19.86 Aligned_cols=55 Identities=20% Similarity=0.356 Sum_probs=33.1
Q ss_pred CCceEEEEecccceeEEEccCCCChHHHHHHHHHHHHhcC-----cccCCceEec-CcHHHHHHHHHHH
Q 048575 69 PKGYLAVCVGEELKRFIIPTDYLSHQAFHILLREAEEEFG-----FQQTGVLRIP-CEVAVFESILKMV 131 (172)
Q Consensus 69 pkG~~~VYVG~e~~RFvVp~~yLnhP~F~~LL~~aeEEfG-----~~~~G~L~iP-Cd~~~Fe~vl~~l 131 (172)
+.|++.|.+ .+|.--++-..++.|.+.+ ++|| +.....|.|+ -+....+.|...|
T Consensus 6 ~~g~~~v~~-------~~~~G~i~~~~l~~la~ia-~~yg~~~irlT~~Q~l~l~~v~~~~~~~i~~~L 66 (69)
T PF03460_consen 6 GDGFYMVRI-------RIPGGRISAEQLRALAEIA-EKYGDGEIRLTTRQNLQLRGVPEENLPAIFEEL 66 (69)
T ss_dssp STTEEEEEE-------B-GGGEEEHHHHHHHHHHH-HHHSTSEEEEETTSCEEEEEEEGGGHHHHHHHH
T ss_pred CCeEEEEEE-------eCCCEEECHHHHHHHHHHH-HHhCCCeEEECCCCeEEEeCCCHHHHHHHHHHH
Confidence 456677765 4666677777888888877 6777 2234445554 4454455555444
No 38
>TIGR02527 dot_icm_IcmQ Dot/Icm secretion system protein IcmQ. Members of this protein family are the IcmQ component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favor calling this the Dot/Icm system. This protein was shown to be essential for translocation (PubMed:15661013).
Probab=20.51 E-value=38 Score=28.54 Aligned_cols=13 Identities=8% Similarity=0.363 Sum_probs=11.2
Q ss_pred CCCCCceEEEEec
Q 048575 66 STVPKGYLAVCVG 78 (172)
Q Consensus 66 ~~vpkG~~~VYVG 78 (172)
..+.++|++|||-
T Consensus 113 nk~NEAYVaiyI~ 125 (182)
T TIGR02527 113 NKLNEACVAIAID 125 (182)
T ss_pred ccccceEEEEEEc
Confidence 4689999999994
Done!