Query 047136
Match_columns 142
No_of_seqs 129 out of 671
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 08:01:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047136.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047136hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02519 Auxin_inducible: Auxi 100.0 3.9E-38 8.6E-43 229.5 9.9 99 1-102 1-100 (100)
2 PLN03090 auxin-responsive fami 100.0 3E-36 6.6E-41 221.7 10.1 91 4-101 12-103 (104)
3 PLN03220 uncharacterized prote 100.0 4.1E-32 9E-37 199.9 9.6 86 5-99 10-101 (105)
4 PLN03219 uncharacterized prote 100.0 1.5E-31 3.3E-36 197.7 9.1 89 12-101 13-105 (108)
5 PRK02899 adaptor protein; Prov 83.8 0.95 2.1E-05 36.5 2.6 25 63-87 38-62 (197)
6 PF02214 BTB_2: BTB/POZ domain 82.2 0.62 1.3E-05 32.0 0.8 54 51-104 7-63 (94)
7 cd05992 PB1 The PB1 domain is 78.6 8.1 0.00017 25.4 5.4 53 47-103 7-70 (81)
8 PRK02315 adaptor protein; Prov 77.8 1.8 3.8E-05 35.7 2.3 25 63-87 38-62 (233)
9 PF05389 MecA: Negative regula 72.3 1.2 2.6E-05 35.8 0.0 25 63-87 38-62 (220)
10 smart00666 PB1 PB1 domain. Pho 71.5 6.4 0.00014 26.1 3.5 51 47-102 8-69 (81)
11 PF00651 BTB: BTB/POZ domain; 66.7 17 0.00037 24.5 4.9 57 44-104 13-74 (111)
12 cd06407 PB1_NLP A PB1 domain i 51.5 26 0.00057 24.4 3.7 47 45-95 5-63 (82)
13 TIGR02527 dot_icm_IcmQ Dot/Icm 51.1 11 0.00024 30.6 1.9 55 11-65 78-146 (182)
14 cd06396 PB1_NBR1 The PB1 domai 49.5 65 0.0014 22.8 5.5 57 45-104 5-70 (81)
15 PF08948 DUF1859: Domain of un 49.5 7.5 0.00016 29.5 0.7 28 40-67 86-123 (126)
16 PF14317 YcxB: YcxB-like prote 49.1 33 0.00071 20.8 3.6 33 39-71 27-59 (62)
17 cd06397 PB1_UP1 Uncharacterize 43.9 47 0.001 23.8 4.0 46 47-96 7-63 (82)
18 PF02209 VHP: Villin headpiece 41.4 15 0.00032 22.3 1.0 19 60-78 1-19 (36)
19 PF09475 Dot_icm_IcmQ: Dot/Icm 39.7 9.7 0.00021 30.9 0.0 56 11-66 78-147 (179)
20 smart00153 VHP Villin headpiec 39.4 20 0.00042 21.7 1.3 19 60-78 1-19 (36)
21 PF11822 DUF3342: Domain of un 38.0 28 0.00061 30.5 2.6 63 51-117 13-80 (317)
22 PF00564 PB1: PB1 domain; Int 36.5 38 0.00082 22.3 2.5 51 48-102 9-70 (84)
23 PF07429 Glyco_transf_56: 4-al 33.7 79 0.0017 28.3 4.7 64 38-104 180-266 (360)
24 COG3769 Predicted hydrolase (H 32.3 66 0.0014 27.6 3.8 73 3-80 46-120 (274)
25 PF12058 DUF3539: Protein of u 32.2 6.9 0.00015 28.4 -1.8 13 59-71 4-16 (88)
26 cd06401 PB1_TFG The PB1 domain 32.1 78 0.0017 22.6 3.6 31 45-78 5-35 (81)
27 cd06398 PB1_Joka2 The PB1 doma 31.5 81 0.0018 22.4 3.7 51 47-97 7-70 (91)
28 KOG1290 Serine/threonine prote 30.4 30 0.00065 32.6 1.6 19 39-57 62-83 (590)
29 cd04751 Commd3 COMM_Domain con 28.5 59 0.0013 23.1 2.6 30 82-112 64-93 (95)
30 COG1759 5-formaminoimidazole-4 27.8 30 0.00065 30.8 1.1 79 36-115 87-199 (361)
31 PF14974 DUF4511: Domain of un 26.9 2E+02 0.0044 21.4 5.2 41 64-110 47-87 (105)
32 PF11834 DUF3354: Domain of un 26.7 51 0.0011 22.6 1.8 17 64-80 26-42 (69)
33 COG4862 MecA Negative regulato 26.1 51 0.0011 27.7 2.1 26 62-87 37-62 (224)
34 PRK02797 4-alpha-L-fucosyltran 25.6 1.6E+02 0.0034 26.0 5.1 64 38-104 141-227 (322)
35 cd01406 SIR2-like Sir2-like: P 25.1 1.2E+02 0.0025 24.2 4.0 56 42-104 1-58 (242)
36 PF06849 DUF1246: Protein of u 24.5 4 8.7E-05 31.3 -4.3 23 36-58 67-92 (124)
37 PF05194 UreE_C: UreE urease a 24.4 1.1E+02 0.0023 21.1 3.2 27 42-73 25-51 (87)
38 COG4923 Predicted nuclease (RN 24.2 1E+02 0.0022 25.9 3.5 15 83-97 87-101 (245)
39 PF11126 Phage_DsbA: Transcrip 23.9 1.7E+02 0.0037 20.4 4.1 37 64-110 17-53 (69)
40 PF04332 DUF475: Protein of un 23.5 51 0.0011 28.7 1.7 16 2-17 6-21 (294)
41 cd06080 MUM1_like Mutated mela 23.0 1.2E+02 0.0025 21.3 3.2 39 40-78 28-74 (80)
42 PRK10308 3-methyl-adenine DNA 22.6 3E+02 0.0066 23.2 6.2 61 41-101 45-121 (283)
43 COG2899 Uncharacterized protei 22.0 45 0.00097 29.4 1.0 16 2-17 56-71 (346)
44 cd04395 RhoGAP_ARHGAP21 RhoGAP 20.8 1.9E+02 0.0042 22.5 4.4 42 64-105 19-60 (196)
No 1
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=100.00 E-value=3.9e-38 Score=229.53 Aligned_cols=99 Identities=38% Similarity=0.704 Sum_probs=88.1
Q ss_pred CCCHHHHHHHHHHHhhhhhcccCcccccccccccCCCCCCCCeEEEEecc-ccEEeEeccCCCcHHHHHHHHhhhHhcCC
Q 047136 1 MTNSKRLIQLARKWQKMAAMKRKRISFPRRAAAQNSSVANKGHFVVYTTD-NMRFTVPLEYLSRNVFIELLRMSEEEFGL 79 (142)
Q Consensus 1 m~~~~KL~~~~kKWq~~a~~~r~r~s~~~~~~~~~~~~vpkG~~~VyVGe-~~RfvVp~~yL~hp~F~~LL~~aeeEfG~ 79 (142)
||+.+|....++||++.++..+++.+..... +..++|+||||||||+ ++||+||++|||||+|++||++|+|||||
T Consensus 1 M~~~~k~~~~~~k~~~~~~~~~~~~~~~~~~---~~~~vp~G~~~VyVG~~~~Rfvvp~~~L~hp~f~~LL~~aeeEfG~ 77 (100)
T PF02519_consen 1 MASRLKSLASAKKWQSRARSKSSSSSSSRSS---SESDVPKGHFAVYVGEERRRFVVPVSYLNHPLFQELLEQAEEEFGF 77 (100)
T ss_pred CccHHHHHHHHHhhhhhhhhccccccccccc---ccCCCCCCeEEEEeCccceEEEechHHcCchhHHHHHHHHhhhcCc
Confidence 9999999999999999877666544433222 1368999999999998 89999999999999999999999999999
Q ss_pred CCCCCeeecCchHHHHHHHHHHh
Q 047136 80 PSNGPITLPCDSTFLNYVMTLVK 102 (142)
Q Consensus 80 ~~~G~L~iPC~~~~Fe~vl~~i~ 102 (142)
+++|+|+||||+++|++++|+|+
T Consensus 78 ~~~G~l~iPC~~~~Fe~~l~~le 100 (100)
T PF02519_consen 78 DQDGPLTIPCDVVLFEHLLWLLE 100 (100)
T ss_pred CCCCcEEeeCCHHHHHHHHHHhC
Confidence 99999999999999999999985
No 2
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=3e-36 Score=221.71 Aligned_cols=91 Identities=25% Similarity=0.544 Sum_probs=78.8
Q ss_pred HHHHHHHHHHHhhhhhcccCcccccccccccCCCCCCCCeEEEEecc-ccEEeEeccCCCcHHHHHHHHhhhHhcCCCCC
Q 047136 4 SKRLIQLARKWQKMAAMKRKRISFPRRAAAQNSSVANKGHFVVYTTD-NMRFTVPLEYLSRNVFIELLRMSEEEFGLPSN 82 (142)
Q Consensus 4 ~~KL~~~~kKWq~~a~~~r~r~s~~~~~~~~~~~~vpkG~~~VyVGe-~~RfvVp~~yL~hp~F~~LL~~aeeEfG~~~~ 82 (142)
..+|++|+|||+++++.+. + ..+..+.++|+||||||||+ ++||+||++|||||+|++||++|||||||+++
T Consensus 12 ~~~~kq~l~r~~s~~~~~~----~---~~~~~~~~vpkG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfGf~~~ 84 (104)
T PLN03090 12 TAMLKQILKRCSSLGKKQG----Y---DEDGLPLDVPKGHFPVYVGENRSRYIVPISFLTHPEFQSLLQQAEEEFGFDHD 84 (104)
T ss_pred HHHHHHHHHHHHHhcccCC----c---ccccCCCCCCCCcEEEEECCCCEEEEEEHHHcCCHHHHHHHHHHHHHhCCCCC
Confidence 4678999999998754321 1 01113668999999999998 58999999999999999999999999999999
Q ss_pred CCeeecCchHHHHHHHHHH
Q 047136 83 GPITLPCDSTFLNYVMTLV 101 (142)
Q Consensus 83 G~L~iPC~~~~Fe~vl~~i 101 (142)
|+|+||||+++|++++|+|
T Consensus 85 G~L~IPC~~~~Fe~ll~~i 103 (104)
T PLN03090 85 MGLTIPCEEVVFRSLTSMI 103 (104)
T ss_pred CcEEEeCCHHHHHHHHHHh
Confidence 9999999999999999998
No 3
>PLN03220 uncharacterized protein; Provisional
Probab=99.97 E-value=4.1e-32 Score=199.85 Aligned_cols=86 Identities=33% Similarity=0.581 Sum_probs=71.1
Q ss_pred HHHHHHHHHHhhhhhcccCcccccccccccCCCCCCCCeEEEEecc-----ccEEeEeccCCCcHHHHHHHHhhhHhcCC
Q 047136 5 KRLIQLARKWQKMAAMKRKRISFPRRAAAQNSSVANKGHFVVYTTD-----NMRFTVPLEYLSRNVFIELLRMSEEEFGL 79 (142)
Q Consensus 5 ~KL~~~~kKWq~~a~~~r~r~s~~~~~~~~~~~~vpkG~~~VyVGe-----~~RfvVp~~yL~hp~F~~LL~~aeeEfG~ 79 (142)
.+++|++|+.. ++. |.+.+ ...+.+|||||||||||+ ++||+||++|||||+|++||++|||||||
T Consensus 10 ~~~k~~~~~~~-~~~--~~~~~------~~~~~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP~F~~LL~~AeEEfGf 80 (105)
T PLN03220 10 NATKQILKLNS-LAN--RNRTS------SSSSDHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHPSFKEFLSRAEEEFGF 80 (105)
T ss_pred HHHHHHHHHHh-hcc--ccccc------ccccCCCCCCeEEEEECCCCCccceEEEEEHHHcCChHHHHHHHHHHHHhCC
Confidence 46788888776 432 21111 112557999999999997 58999999999999999999999999999
Q ss_pred CC-CCCeeecCchHHHHHHHH
Q 047136 80 PS-NGPITLPCDSTFLNYVMT 99 (142)
Q Consensus 80 ~~-~G~L~iPC~~~~Fe~vl~ 99 (142)
++ +|+|+||||++.|++++.
T Consensus 81 ~~~~G~L~IPCd~~~F~~ll~ 101 (105)
T PLN03220 81 NHPMGGLTIPCREEVFLDLIA 101 (105)
T ss_pred CCCCCCEEeeCCHHHHHHHHH
Confidence 98 699999999999999985
No 4
>PLN03219 uncharacterized protein; Provisional
Probab=99.97 E-value=1.5e-31 Score=197.68 Aligned_cols=89 Identities=29% Similarity=0.533 Sum_probs=72.5
Q ss_pred HHHhhhhhcccCcccccccccccCCCCCCCCeEEEEecc---ccEEeEeccCCCcHHHHHHHHhhhHhcCCCC-CCCeee
Q 047136 12 RKWQKMAAMKRKRISFPRRAAAQNSSVANKGHFVVYTTD---NMRFTVPLEYLSRNVFIELLRMSEEEFGLPS-NGPITL 87 (142)
Q Consensus 12 kKWq~~a~~~r~r~s~~~~~~~~~~~~vpkG~~~VyVGe---~~RfvVp~~yL~hp~F~~LL~~aeeEfG~~~-~G~L~i 87 (142)
+-|+..+..+|+-.+.+++. .+.+..+||||||||||+ ++||+||++|||||+|++||++|||||||++ +|+|+|
T Consensus 13 ~~~~~~~~~~~~~~~~~~~~-~~~~~~vpkGh~aVYVG~~~E~kRFvVPi~yL~hP~F~~LL~~AeEEfGf~~~~G~L~I 91 (108)
T PLN03219 13 QIFKSQSMRNKNGSSSPSSS-TTTSGLVPKGHVAVYVGEQMEKKRFVVPISYLNHPLFREFLNRAEEECGFHHSMGGLTI 91 (108)
T ss_pred HHHHHHHHhcccCCCCCccC-CCCCCCCCCCeEEEEECCCCCceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEE
Confidence 45775555555544433322 223668999999999996 6999999999999999999999999999997 699999
Q ss_pred cCchHHHHHHHHHH
Q 047136 88 PCDSTFLNYVMTLV 101 (142)
Q Consensus 88 PC~~~~Fe~vl~~i 101 (142)
|||++.|++++..-
T Consensus 92 PCd~~~F~~ll~~~ 105 (108)
T PLN03219 92 PCREESFLHLITSH 105 (108)
T ss_pred eCCHHHHHHHHHhh
Confidence 99999999998753
No 5
>PRK02899 adaptor protein; Provisional
Probab=83.76 E-value=0.95 Score=36.49 Aligned_cols=25 Identities=24% Similarity=0.751 Sum_probs=21.4
Q ss_pred cHHHHHHHHhhhHhcCCCCCCCeee
Q 047136 63 RNVFIELLRMSEEEFGLPSNGPITL 87 (142)
Q Consensus 63 hp~F~~LL~~aeeEfG~~~~G~L~i 87 (142)
+-+|.++|++|..|+||..+|||+|
T Consensus 38 e~lF~~mm~Ea~~e~~F~~~~pl~~ 62 (197)
T PRK02899 38 HQLFRDMMQEANKELGFEADGPIAV 62 (197)
T ss_pred HHHHHHHHHHhhhccCcccCCeEEE
Confidence 3578888999999999999999863
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=82.16 E-value=0.62 Score=32.05 Aligned_cols=54 Identities=11% Similarity=0.204 Sum_probs=40.2
Q ss_pred ccEEeEeccCCC-c--HHHHHHHHhhhHhcCCCCCCCeeecCchHHHHHHHHHHhcc
Q 047136 51 NMRFTVPLEYLS-R--NVFIELLRMSEEEFGLPSNGPITLPCDSTFLNYVMTLVKGC 104 (142)
Q Consensus 51 ~~RfvVp~~yL~-h--p~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~i~~~ 104 (142)
+++|.++.+.|. + ..|..++........-+.+|.+-|-++...|++|+..++.+
T Consensus 7 G~~f~~~~~tL~~~~~s~l~~~~~~~~~~~~~~~~~~~fiDRdp~~F~~IL~ylr~~ 63 (94)
T PF02214_consen 7 GTIFETSRSTLTRYPDSLLARLFSGERSDDYDDDDGEYFIDRDPELFEYILNYLRTG 63 (94)
T ss_dssp TEEEEEEHHHHHTSTTSTTTSHHHTGHGGGEETTTTEEEESS-HHHHHHHHHHHHHT
T ss_pred CEEEEEcHHHHhhCCCChhhhHHhhccccccCCccceEEeccChhhhhHHHHHHhhc
Confidence 578888887776 4 47888888652222224579999999999999999999984
No 7
>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=78.59 E-value=8.1 Score=25.45 Aligned_cols=53 Identities=26% Similarity=0.372 Sum_probs=37.7
Q ss_pred EeccccEEeEeccCCCcHHHHHHHHhhhHhcCCC----------CCCC-eeecCchHHHHHHHHHHhc
Q 047136 47 YTTDNMRFTVPLEYLSRNVFIELLRMSEEEFGLP----------SNGP-ITLPCDSTFLNYVMTLVKG 103 (142)
Q Consensus 47 yVGe~~RfvVp~~yL~hp~F~~LL~~aeeEfG~~----------~~G~-L~iPC~~~~Fe~vl~~i~~ 103 (142)
|-|+.+||.+|. .++.|.+|..+.++.|++. .+|- ++|.++ ..|+.++....+
T Consensus 7 ~~~~~~~~~~~~---~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd-~Dl~~a~~~~~~ 70 (81)
T cd05992 7 YGGEIRRFVVVS---RSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSD-EDLEEAIEEARR 70 (81)
T ss_pred ecCCCEEEEEec---CCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCH-HHHHHHHHHHhh
Confidence 446789999998 8888999999988888874 2333 455555 466666666553
No 8
>PRK02315 adaptor protein; Provisional
Probab=77.82 E-value=1.8 Score=35.65 Aligned_cols=25 Identities=20% Similarity=0.466 Sum_probs=22.4
Q ss_pred cHHHHHHHHhhhHhcCCCCCCCeee
Q 047136 63 RNVFIELLRMSEEEFGLPSNGPITL 87 (142)
Q Consensus 63 hp~F~~LL~~aeeEfG~~~~G~L~i 87 (142)
+-+|.++|+++..|+||..+|||+|
T Consensus 38 e~fF~~mm~Ea~~e~~F~~~~pl~~ 62 (233)
T PRK02315 38 EEFFYSMMDEVDEEDDFADEGPLWF 62 (233)
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 4589999999999999999999864
No 9
>PF05389 MecA: Negative regulator of genetic competence (MecA); InterPro: IPR008681 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. This family contains several bacterial MecA proteins. In complex media competence development is poor, and there is little or no expression of late competence genes. Overexpression of MecA inhibits comG transcription [, , ]. MecA enables the recognition and targeting of unfolded and aggregated proteins to the ClpC protease or to other proteins involved in proteolysis. Acts negatively in the development of competence by binding ComK and recruiting it to the ClpCP protease. When overexpressed, inhibits sporulation. Also involved in Spx degradation by ClpC. ; PDB: 3JTP_C 2Y1R_O 3PXI_c 3PXG_b 3JTO_D 3JTN_A.
Probab=72.27 E-value=1.2 Score=35.77 Aligned_cols=25 Identities=32% Similarity=0.756 Sum_probs=0.0
Q ss_pred cHHHHHHHHhhhHhcCCCCCCCeee
Q 047136 63 RNVFIELLRMSEEEFGLPSNGPITL 87 (142)
Q Consensus 63 hp~F~~LL~~aeeEfG~~~~G~L~i 87 (142)
+-+|.++|+++.+|+||..+|||++
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 5689999999999999999999875
No 10
>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=71.46 E-value=6.4 Score=26.14 Aligned_cols=51 Identities=25% Similarity=0.406 Sum_probs=35.8
Q ss_pred EeccccEEeEeccCCCcHHHHHHHHhhhHhcCCC----------CCC-CeeecCchHHHHHHHHHHh
Q 047136 47 YTTDNMRFTVPLEYLSRNVFIELLRMSEEEFGLP----------SNG-PITLPCDSTFLNYVMTLVK 102 (142)
Q Consensus 47 yVGe~~RfvVp~~yL~hp~F~~LL~~aeeEfG~~----------~~G-~L~iPC~~~~Fe~vl~~i~ 102 (142)
|.|+.+||.||- ...|.+|..+..+.|+.. .+| .++|.++. .++.++.+..
T Consensus 8 ~~~~~~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~-Dl~~a~~~~~ 69 (81)
T smart00666 8 YGGETRRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDE-DLEEAIEEYD 69 (81)
T ss_pred ECCEEEEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHH-HHHHHHHHHH
Confidence 445678999986 777999999999988874 234 46777755 4555555554
No 11
>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=66.69 E-value=17 Score=24.52 Aligned_cols=57 Identities=18% Similarity=0.217 Sum_probs=41.8
Q ss_pred EEEEeccccEEeEeccCC--CcHHHHHHHHhhhHhcCCCCCC--Ceeec-CchHHHHHHHHHHhcc
Q 047136 44 FVVYTTDNMRFTVPLEYL--SRNVFIELLRMSEEEFGLPSNG--PITLP-CDSTFLNYVMTLVKGC 104 (142)
Q Consensus 44 ~~VyVGe~~RfvVp~~yL--~hp~F~~LL~~aeeEfG~~~~G--~L~iP-C~~~~Fe~vl~~i~~~ 104 (142)
+.+.||++++|-+.-..| ..|.|+.+++.. +....+ .+.++ ++...|+.++..+-.+
T Consensus 13 ~~i~v~d~~~~~vhk~iL~~~S~~F~~~~~~~----~~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~ 74 (111)
T PF00651_consen 13 VTIRVGDGKTFYVHKNILAARSPYFRNLFEGS----KFKESTVPEISLPDVSPEAFEAFLEYMYTG 74 (111)
T ss_dssp EEEEETTTEEEEE-HHHHHHHBHHHHHHHTTT----TSTTSSEEEEEETTSCHHHHHHHHHHHHHS
T ss_pred EEEEECCCEEEeechhhhhccchhhhhccccc----ccccccccccccccccccccccccccccCC
Confidence 455667789999998887 459999999987 122233 35555 8899999999998755
No 12
>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=51.51 E-value=26 Score=24.43 Aligned_cols=47 Identities=26% Similarity=0.509 Sum_probs=32.1
Q ss_pred EEEeccccEEeEeccCCCcHHHHHHHHhhhHhcCCCC------------CCCeeecCchHHHH
Q 047136 45 VVYTTDNMRFTVPLEYLSRNVFIELLRMSEEEFGLPS------------NGPITLPCDSTFLN 95 (142)
Q Consensus 45 ~VyVGe~~RfvVp~~yL~hp~F~~LL~~aeeEfG~~~------------~G~L~iPC~~~~Fe 95 (142)
+.|-||..||-+|..- -|++|.++-++-|++.. +..++|.|+.++=|
T Consensus 5 ~~~~~d~~r~~l~~~~----~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~e 63 (82)
T cd06407 5 ATYGEEKIRFRLPPSW----GFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEE 63 (82)
T ss_pred EEeCCeEEEEEcCCCC----CHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHH
Confidence 3455677899988743 58888888887776532 34567888876544
No 13
>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=51.12 E-value=11 Score=30.64 Aligned_cols=55 Identities=18% Similarity=0.320 Sum_probs=34.4
Q ss_pred HHHHhh-hhhcccCcccccccccccC--------CCCCCCCeEEEEecccc-----EEeEeccCCCcHH
Q 047136 11 ARKWQK-MAAMKRKRISFPRRAAAQN--------SSVANKGHFVVYTTDNM-----RFTVPLEYLSRNV 65 (142)
Q Consensus 11 ~kKWq~-~a~~~r~r~s~~~~~~~~~--------~~~vpkG~~~VyVGe~~-----RfvVp~~yL~hp~ 65 (142)
++.|.+ ++++.|..+|-|=-.+..| ...+.++|++|||-... -=-+|++=|+.|+
T Consensus 78 lqsWerilanLprqmisRPIYanE~dvk~~IksKenk~NEAYVaiyI~q~dIl~~~~dk~p~Dk~GkpL 146 (182)
T TIGR02527 78 LKQWAKILASLERQMIGRPIYADEADAKAAIKQKENKLNEACVAIAIDQSDIIHLSADKAPKDKLGKLL 146 (182)
T ss_pred HHHHHHHHHhChhhhhCCCCcCCHHHHHHHHHhhhccccceEEEEEEchHhcccCCcccCcccccCCcc
Confidence 578997 6668877766553333222 56789999999997422 1224555555554
No 14
>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=49.48 E-value=65 Score=22.81 Aligned_cols=57 Identities=16% Similarity=0.276 Sum_probs=39.6
Q ss_pred EEEeccccEEeEeccCCCcHHHHHHHHhhhHhcCCC---------CCCCeeecCchHHHHHHHHHHhcc
Q 047136 45 VVYTTDNMRFTVPLEYLSRNVFIELLRMSEEEFGLP---------SNGPITLPCDSTFLNYVMTLVKGC 104 (142)
Q Consensus 45 ~VyVGe~~RfvVp~~yL~hp~F~~LL~~aeeEfG~~---------~~G~L~iPC~~~~Fe~vl~~i~~~ 104 (142)
|-|-||..||.+|- -.++.|.+|..+-+.-|+++ .+.+++|.|++++ +..+.+.++.
T Consensus 5 aty~~d~~rf~~~~--~~~~~~~~L~~ev~~rf~l~~f~lKYlDde~e~v~lssd~eL-eE~~rl~~~~ 70 (81)
T cd06396 5 VTYNGESQSFLVSD--SENTTWASVEAMVKVSFGLNDIQIKYVDEENEEVSVNSQGEY-EEALKSAVRQ 70 (81)
T ss_pred EEECCeEEEEEecC--CCCCCHHHHHHHHHHHhCCCcceeEEEcCCCCEEEEEchhhH-HHHHHHHHhC
Confidence 44667889999875 22456899999988888864 3457899998765 4444555543
No 15
>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=49.48 E-value=7.5 Score=29.45 Aligned_cols=28 Identities=21% Similarity=0.469 Sum_probs=8.8
Q ss_pred CCCeEEEEeccccEEe----------EeccCCCcHHHH
Q 047136 40 NKGHFVVYTTDNMRFT----------VPLEYLSRNVFI 67 (142)
Q Consensus 40 pkG~~~VyVGe~~Rfv----------Vp~~yL~hp~F~ 67 (142)
..||||+.|-.+.+|+ ||+-|||.|+-+
T Consensus 86 ~QGYfPlL~~~~~KFv~~~~~~GKks~P~~FlNF~IA~ 123 (126)
T PF08948_consen 86 KQGYFPLLVPGRAKFVVRHTGSGKKSVPMFFLNFTIAQ 123 (126)
T ss_dssp --SS--EEE--SSSSEEEEEEEESS----S--------
T ss_pred CcccceeeccchhhhhhhhccCCCcceeeEEEeceeee
Confidence 5799999997766665 688888888643
No 16
>PF14317 YcxB: YcxB-like protein
Probab=49.14 E-value=33 Score=20.78 Aligned_cols=33 Identities=24% Similarity=0.325 Sum_probs=26.1
Q ss_pred CCCCeEEEEeccccEEeEeccCCCcHHHHHHHH
Q 047136 39 ANKGHFVVYTTDNMRFTVPLEYLSRNVFIELLR 71 (142)
Q Consensus 39 vpkG~~~VyVGe~~RfvVp~~yL~hp~F~~LL~ 71 (142)
.-+.++-+|+++..-++||.+.++.-...++.+
T Consensus 27 e~~~~~~l~~~~~~~~~iPk~~f~~~e~~~f~~ 59 (62)
T PF14317_consen 27 ETKDYFYLYLGKNQAFIIPKRAFSEEEKEEFRE 59 (62)
T ss_pred EeCCEEEEEECCCeEEEEEHHHCCHhHHHHHHH
Confidence 346789999999999999999999655555544
No 17
>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=43.92 E-value=47 Score=23.84 Aligned_cols=46 Identities=22% Similarity=0.398 Sum_probs=34.4
Q ss_pred EeccccEEeEeccCCCcHHHHHHHHhhhHhcCCC----------CC-CCeeecCchHHHHH
Q 047136 47 YTTDNMRFTVPLEYLSRNVFIELLRMSEEEFGLP----------SN-GPITLPCDSTFLNY 96 (142)
Q Consensus 47 yVGe~~RfvVp~~yL~hp~F~~LL~~aeeEfG~~----------~~-G~L~iPC~~~~Fe~ 96 (142)
|-|+.|||..|. -|.+.+|-++.+.=|.+. .| ..|||.=+.++.+.
T Consensus 7 ~~g~~RRf~~~~----~pt~~~L~~kl~~Lf~lp~~~~~vtYiDeD~D~ITlssd~eL~d~ 63 (82)
T cd06397 7 FLGDTRRIVFPD----IPTWEALASKLENLYNLPEIKVGVTYIDNDNDEITLSSNKELQDF 63 (82)
T ss_pred eCCceEEEecCC----CccHHHHHHHHHHHhCCChhHeEEEEEcCCCCEEEecchHHHHHH
Confidence 456789999998 899999999999877765 33 34677766555543
No 18
>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=41.41 E-value=15 Score=22.31 Aligned_cols=19 Identities=47% Similarity=0.651 Sum_probs=15.4
Q ss_pred CCCcHHHHHHHHhhhHhcC
Q 047136 60 YLSRNVFIELLRMSEEEFG 78 (142)
Q Consensus 60 yL~hp~F~~LL~~aeeEfG 78 (142)
||+...|.+++.++.+||.
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 7899999999999999984
No 19
>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=39.68 E-value=9.7 Score=30.87 Aligned_cols=56 Identities=20% Similarity=0.441 Sum_probs=0.0
Q ss_pred HHHHhh-hhhcccCcccccccccccC--------CCCCCCCeEEEEeccccEE-----eEeccCCCcHHH
Q 047136 11 ARKWQK-MAAMKRKRISFPRRAAAQN--------SSVANKGHFVVYTTDNMRF-----TVPLEYLSRNVF 66 (142)
Q Consensus 11 ~kKWq~-~a~~~r~r~s~~~~~~~~~--------~~~vpkG~~~VyVGe~~Rf-----vVp~~yL~hp~F 66 (142)
++.|.+ ++++.|..+|-|=-.+..| ...+.++|++|||-...=+ -+|++=|+.|+.
T Consensus 78 lqsWerilanLprqmisRPIY~nE~dvk~~IksKenk~NEAYVaiyInq~dIl~~~~dk~~~Dk~GkpLl 147 (179)
T PF09475_consen 78 LQSWERILANLPRQMISRPIYANEEDVKAAIKSKENKLNEAYVAIYINQSDILSLSPDKIPTDKLGKPLL 147 (179)
T ss_dssp ----------------------------------------------------------------------
T ss_pred HHHHHHHHHhCchhhhCCCCcCCHHHHHHHHHhhhcccceeEEEEEEchHhcccCCcccccccccCCccc
Confidence 578997 6668877766553333322 5568899999999743222 245555555543
No 20
>smart00153 VHP Villin headpiece domain.
Probab=39.44 E-value=20 Score=21.71 Aligned_cols=19 Identities=47% Similarity=0.681 Sum_probs=17.1
Q ss_pred CCCcHHHHHHHHhhhHhcC
Q 047136 60 YLSRNVFIELLRMSEEEFG 78 (142)
Q Consensus 60 yL~hp~F~~LL~~aeeEfG 78 (142)
||+.-.|++.+.++.+||-
T Consensus 1 yLsdeeF~~vfgmsr~eF~ 19 (36)
T smart00153 1 YLSDEDFEEVFGMTREEFY 19 (36)
T ss_pred CCCHHHHHHHHCCCHHHHH
Confidence 7899999999999999973
No 21
>PF11822 DUF3342: Domain of unknown function (DUF3342); InterPro: IPR021777 This family of proteins are functionally uncharacterised. This family is found in bacteria. This presumed domain is typically between 170 to 303 amino acids in length. The N-terminal half of this family is a BTB-like domain.
Probab=38.03 E-value=28 Score=30.51 Aligned_cols=63 Identities=25% Similarity=0.436 Sum_probs=46.4
Q ss_pred ccEEeEeccCCC--cHHHHHHHHh---hhHhcCCCCCCCeeecCchHHHHHHHHHHhccChhhHHHHHHhhc
Q 047136 51 NMRFTVPLEYLS--RNVFIELLRM---SEEEFGLPSNGPITLPCDSTFLNYVMTLVKGCIPEDLGKALITSL 117 (142)
Q Consensus 51 ~~RfvVp~~yL~--hp~F~~LL~~---aeeEfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~~~~~e~~~l~s~ 117 (142)
++=|..|.+.|- -..|++.|.. ..++. .+=.|.+-||+..|+.++.-+++.. ..+|-....||
T Consensus 13 ~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~---~~idisVhCDv~iF~WLm~yv~~~~-p~l~~~NvvsI 80 (317)
T PF11822_consen 13 KRDFTCPRDLLVSEMRYFAEYLSRYINDSQRW---EEIDISVHCDVHIFEWLMRYVKGEP-PSLTPSNVVSI 80 (317)
T ss_pred ceeeeccHHHHHHhhHHHHHHHhhcccccCcC---CCcceEEecChhHHHHHHHHhhcCC-CcCCcCcEEEe
Confidence 477999998884 4689999966 33332 2456889999999999999998843 55665555554
No 22
>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=36.53 E-value=38 Score=22.30 Aligned_cols=51 Identities=27% Similarity=0.345 Sum_probs=31.3
Q ss_pred eccccEEeEeccCCCcHHHHHHHHhhhHhcCCC----------CCCC-eeecCchHHHHHHHHHHh
Q 047136 48 TTDNMRFTVPLEYLSRNVFIELLRMSEEEFGLP----------SNGP-ITLPCDSTFLNYVMTLVK 102 (142)
Q Consensus 48 VGe~~RfvVp~~yL~hp~F~~LL~~aeeEfG~~----------~~G~-L~iPC~~~~Fe~vl~~i~ 102 (142)
-|+.+| .+..-..+.|.+|.++.++.||.. .+|- ++|.++.+ |+..+...+
T Consensus 9 ~~~~~~---~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~D-l~~a~~~~~ 70 (84)
T PF00564_consen 9 GGDIRR---IISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDED-LQEAIEQAK 70 (84)
T ss_dssp TTEEEE---EEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHH-HHHHHHHHH
T ss_pred CCeeEE---EEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHH-HHHHHHHHH
Confidence 345555 333345569999999999999883 3554 55666544 444444443
No 23
>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=33.65 E-value=79 Score=28.29 Aligned_cols=64 Identities=20% Similarity=0.436 Sum_probs=43.6
Q ss_pred CCCCCeEEEEec---------------------cccEEeEeccCCC--cHHHHHHHHhhhHhcCCCCCCCeeecCchHHH
Q 047136 38 VANKGHFVVYTT---------------------DNMRFTVPLEYLS--RNVFIELLRMSEEEFGLPSNGPITLPCDSTFL 94 (142)
Q Consensus 38 ~vpkG~~~VyVG---------------------e~~RfvVp~~yL~--hp~F~~LL~~aeeEfG~~~~G~L~iPC~~~~F 94 (142)
..++|-..|.|| +..|++||+.|=. ..-..++.+.+++-||- +-+.+-=+---|
T Consensus 180 ~~~~~~ltILvGNSgd~sNnHieaL~~L~~~~~~~~kIivPLsYg~~n~~Yi~~V~~~~~~lF~~---~~~~iL~e~mpf 256 (360)
T PF07429_consen 180 KKNKGKLTILVGNSGDPSNNHIEALEALKQQFGDDVKIIVPLSYGANNQAYIQQVIQAGKELFGA---ENFQILTEFMPF 256 (360)
T ss_pred cCCCCceEEEEcCCCCCCccHHHHHHHHHHhcCCCeEEEEECCCCCchHHHHHHHHHHHHHhcCc---cceeEhhhhCCH
Confidence 345678888887 1379999999974 56777777777777873 334444455556
Q ss_pred HHHHHHHhcc
Q 047136 95 NYVMTLVKGC 104 (142)
Q Consensus 95 e~vl~~i~~~ 104 (142)
+..+.++.+-
T Consensus 257 ~eYl~lL~~c 266 (360)
T PF07429_consen 257 DEYLALLSRC 266 (360)
T ss_pred HHHHHHHHhC
Confidence 6667666654
No 24
>COG3769 Predicted hydrolase (HAD superfamily) [General function prediction only]
Probab=32.31 E-value=66 Score=27.62 Aligned_cols=73 Identities=16% Similarity=0.035 Sum_probs=46.0
Q ss_pred CHHHHHHHHHHHhhhhhcccCcccccccccccCCCCCCCCeEEEEeccc--cEEeEeccCCCcHHHHHHHHhhhHhcCCC
Q 047136 3 NSKRLIQLARKWQKMAAMKRKRISFPRRAAAQNSSVANKGHFVVYTTDN--MRFTVPLEYLSRNVFIELLRMSEEEFGLP 80 (142)
Q Consensus 3 ~~~KL~~~~kKWq~~a~~~r~r~s~~~~~~~~~~~~vpkG~~~VyVGe~--~RfvVp~~yL~hp~F~~LL~~aeeEfG~~ 80 (142)
|+|-..+|.--|.++..-++ +-+ ..+....-.|+|++|.=++-+ .=+.+-.-=+--..++++|++.||-|||.
T Consensus 46 SSKT~aE~~~l~~~l~v~~~--p~i---aEnG~aI~~p~~~~~~~~~~r~~~g~~~~elg~~l~~ire~l~kLee~~g~~ 120 (274)
T COG3769 46 SSKTRAEMLYLQKSLGVQGL--PLI---AENGAAIYLPKGWFPFDGKPREISGISHIELGKVLEKIREKLDKLEEHFGFT 120 (274)
T ss_pred ccchHHHHHHHHHhcCCCCC--cee---ecCCceEEecccccccCCCCceecceEeeehhhhHHHHHHHHHHHHHHhCee
Confidence 66778889989998766552 211 222234567999999876543 12222111122345899999999999985
No 25
>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=32.19 E-value=6.9 Score=28.43 Aligned_cols=13 Identities=38% Similarity=0.531 Sum_probs=9.4
Q ss_pred cCCCcHHHHHHHH
Q 047136 59 EYLSRNVFIELLR 71 (142)
Q Consensus 59 ~yL~hp~F~~LL~ 71 (142)
.|||||.|.-|-.
T Consensus 4 ~YLNHPtFGlLy~ 16 (88)
T PF12058_consen 4 TYLNHPTFGLLYR 16 (88)
T ss_dssp -EEEETTTEEEEE
T ss_pred ccccCCccchhee
Confidence 5899999976644
No 26
>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=32.09 E-value=78 Score=22.57 Aligned_cols=31 Identities=26% Similarity=0.220 Sum_probs=20.4
Q ss_pred EEEeccccEEeEeccCCCcHHHHHHHHhhhHhcC
Q 047136 45 VVYTTDNMRFTVPLEYLSRNVFIELLRMSEEEFG 78 (142)
Q Consensus 45 ~VyVGe~~RfvVp~~yL~hp~F~~LL~~aeeEfG 78 (142)
+||-||-||+-+|.+- =.|.+|.++.+..|.
T Consensus 5 ~~~g~DiR~~~~~~~~---~t~~~L~~~v~~~F~ 35 (81)
T cd06401 5 AQLGDDIRRIPIHNED---ITYDELLLMMQRVFR 35 (81)
T ss_pred EEeCCeEEEEeccCcc---ccHHHHHHHHHHHhc
Confidence 4565677886666422 267788888876665
No 27
>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=31.50 E-value=81 Score=22.44 Aligned_cols=51 Identities=27% Similarity=0.325 Sum_probs=33.3
Q ss_pred EeccccEEeEecc-CCCcHHHHHHHHhhhHhcCCCC-----------CCC-eeecCchHHHHHH
Q 047136 47 YTTDNMRFTVPLE-YLSRNVFIELLRMSEEEFGLPS-----------NGP-ITLPCDSTFLNYV 97 (142)
Q Consensus 47 yVGe~~RfvVp~~-yL~hp~F~~LL~~aeeEfG~~~-----------~G~-L~iPC~~~~Fe~v 97 (142)
|=|+-+||-+|.. --.+.-|..|.++-++-|.... +|- ++|.||.++-+-+
T Consensus 7 y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~ 70 (91)
T cd06398 7 YGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAI 70 (91)
T ss_pred eCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHH
Confidence 3356799999974 0114478888888888776542 333 5788877665543
No 28
>KOG1290 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=30.35 E-value=30 Score=32.63 Aligned_cols=19 Identities=26% Similarity=0.279 Sum_probs=15.9
Q ss_pred CCCCeEEEEecc---ccEEeEe
Q 047136 39 ANKGHFVVYTTD---NMRFTVP 57 (142)
Q Consensus 39 vpkG~~~VyVGe---~~RfvVp 57 (142)
.+-||.||++|| ..||+|-
T Consensus 62 ~kGGYHpV~IGD~F~~gRY~v~ 83 (590)
T KOG1290|consen 62 RKGGYHPVRIGDVFNGGRYHVQ 83 (590)
T ss_pred hcCCCceeeccccccCceEEEE
Confidence 467999999998 3899884
No 29
>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=28.54 E-value=59 Score=23.10 Aligned_cols=30 Identities=17% Similarity=0.356 Sum_probs=23.6
Q ss_pred CCCeeecCchHHHHHHHHHHhccChhhHHHH
Q 047136 82 NGPITLPCDSTFLNYVMTLVKGCIPEDLGKA 112 (142)
Q Consensus 82 ~G~L~iPC~~~~Fe~vl~~i~~~~~~~~e~~ 112 (142)
.+++.+-|+++.|.+++.-|+.. .+.+|++
T Consensus 64 ~~~i~f~c~~e~L~~Li~~Lk~A-~~~~e~~ 93 (95)
T cd04751 64 KPDINFTCTLEQLQDLVNKLKDA-AKNIERA 93 (95)
T ss_pred cceEEEEeCHHHHHHHHHHHHHH-HHHHHHh
Confidence 35899999999999999999644 4666653
No 30
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=27.78 E-value=30 Score=30.84 Aligned_cols=79 Identities=24% Similarity=0.362 Sum_probs=45.5
Q ss_pred CCCCCCCeEEEEec-c--ccEEeEeccCC---------CcHHHHHHHHhhhH----hcCC--CCCCCe------------
Q 047136 36 SSVANKGHFVVYTT-D--NMRFTVPLEYL---------SRNVFIELLRMSEE----EFGL--PSNGPI------------ 85 (142)
Q Consensus 36 ~~~vpkG~~~VyVG-e--~~RfvVp~~yL---------~hp~F~~LL~~aee----EfG~--~~~G~L------------ 85 (142)
..-+|.|-|++||| | ...|.||+ |= ..-.-..||++|-= .|.= +.||++
T Consensus 87 ~I~IP~gSfv~Y~G~d~ie~~~~vP~-fGnR~lLrwE~~~~~~~~lLekAgi~~P~~~~~PeeIdr~VIVK~pgAkggRG 165 (361)
T COG1759 87 AIFIPHGSFVAYVGYDGIENEFEVPM-FGNRELLRWEEDRKLEYKLLEKAGLRIPKKYKSPEEIDRPVIVKLPGAKGGRG 165 (361)
T ss_pred eEEecCCceEEEecchhhhhcccCcc-cccHhHhhhhcchhhHHHHHHHcCCCCCcccCChHHcCCceEEecCCccCCce
Confidence 45689999999999 4 36677774 11 22234578887752 2220 123443
Q ss_pred -eecCchHHHH-HHHHHHhccCh--hhHHHHHHh
Q 047136 86 -TLPCDSTFLN-YVMTLVKGCIP--EDLGKALIT 115 (142)
Q Consensus 86 -~iPC~~~~Fe-~vl~~i~~~~~--~~~e~~~l~ 115 (142)
-+.=+...|. .+-.+++++.- +|++++-+-
T Consensus 166 yFiA~s~eef~ek~e~l~~~gvi~~edlkna~Ie 199 (361)
T COG1759 166 YFIASSPEEFYEKAERLLKRGVITEEDLKNARIE 199 (361)
T ss_pred EEEEcCHHHHHHHHHHHHHcCCcchhhhhhceee
Confidence 3344555565 45566776653 666666543
No 31
>PF14974 DUF4511: Domain of unknown function (DUF4511)
Probab=26.91 E-value=2e+02 Score=21.40 Aligned_cols=41 Identities=7% Similarity=0.124 Sum_probs=26.3
Q ss_pred HHHHHHHHhhhHhcCCCCCCCeeecCchHHHHHHHHHHhccChhhHH
Q 047136 64 NVFIELLRMSEEEFGLPSNGPITLPCDSTFLNYVMTLVKGCIPEDLG 110 (142)
Q Consensus 64 p~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~~~~~e 110 (142)
|+..++--..=+.|||..+|. .+..|.+++..+++++ .|+.
T Consensus 47 Pva~qiq~~VIk~yGF~~~~e-----G~~~f~~~i~~~e~~D-~eva 87 (105)
T PF14974_consen 47 PVATQIQMEVIKKYGFPESRE-----GVMQFAQLIRELEKDD-PEVA 87 (105)
T ss_pred HHHHHHHHHHHHHcCCCCCcc-----hHHHHHHHHHHHHccC-HHHH
Confidence 334444444556799985332 2568999999998876 5555
No 32
>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=26.65 E-value=51 Score=22.58 Aligned_cols=17 Identities=35% Similarity=0.772 Sum_probs=15.2
Q ss_pred HHHHHHHHhhhHhcCCC
Q 047136 64 NVFIELLRMSEEEFGLP 80 (142)
Q Consensus 64 p~F~~LL~~aeeEfG~~ 80 (142)
-.++|||+.|++.||+.
T Consensus 26 ~SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 26 DSLEELLKIASEKFGFS 42 (69)
T ss_pred ccHHHHHHHHHHHhCCC
Confidence 36999999999999985
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=26.07 E-value=51 Score=27.68 Aligned_cols=26 Identities=19% Similarity=0.420 Sum_probs=23.6
Q ss_pred CcHHHHHHHHhhhHhcCCCCCCCeee
Q 047136 62 SRNVFIELLRMSEEEFGLPSNGPITL 87 (142)
Q Consensus 62 ~hp~F~~LL~~aeeEfG~~~~G~L~i 87 (142)
.|-+|-++++.+..|-+|..+|||.|
T Consensus 37 ~EE~F~~mMdEl~~ee~F~~~GpL~i 62 (224)
T COG4862 37 TEELFYEMMDELNLEEDFKDEGPLWI 62 (224)
T ss_pred HHHHHHHHHHhcCCccccccCCceEE
Confidence 47899999999999999999999876
No 34
>PRK02797 4-alpha-L-fucosyltransferase; Provisional
Probab=25.65 E-value=1.6e+02 Score=26.03 Aligned_cols=64 Identities=16% Similarity=0.351 Sum_probs=42.8
Q ss_pred CCCCCeEEEEecc---------------------ccEEeEeccC--CCcHHHHHHHHhhhHhcCCCCCCCeeecCchHHH
Q 047136 38 VANKGHFVVYTTD---------------------NMRFTVPLEY--LSRNVFIELLRMSEEEFGLPSNGPITLPCDSTFL 94 (142)
Q Consensus 38 ~vpkG~~~VyVGe---------------------~~RfvVp~~y--L~hp~F~~LL~~aeeEfG~~~~G~L~iPC~~~~F 94 (142)
..++|-+.|.||. .-|++||+.| =|.--.++..+.+.+-||- +-+++-=+---|
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 3467789999982 1499999999 4555555555556666763 345555566667
Q ss_pred HHHHHHHhcc
Q 047136 95 NYVMTLVKGC 104 (142)
Q Consensus 95 e~vl~~i~~~ 104 (142)
+..+.+|.+.
T Consensus 218 ~eYl~lL~~~ 227 (322)
T PRK02797 218 DDYLALLRQC 227 (322)
T ss_pred HHHHHHHHhC
Confidence 7777777654
No 35
>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=25.14 E-value=1.2e+02 Score=24.20 Aligned_cols=56 Identities=18% Similarity=0.173 Sum_probs=35.4
Q ss_pred CeEEEEeccc--cEEeEeccCCCcHHHHHHHHhhhHhcCCCCCCCeeecCchHHHHHHHHHHhcc
Q 047136 42 GHFVVYTTDN--MRFTVPLEYLSRNVFIELLRMSEEEFGLPSNGPITLPCDSTFLNYVMTLVKGC 104 (142)
Q Consensus 42 G~~~VyVGe~--~RfvVp~~yL~hp~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~i~~~ 104 (142)
|.+++++|-+ .+ .+-|.+.+|++...+++|...+....-.=+...+..+..++.+.
T Consensus 1 g~lvlFiGAG~S~~-------~glP~W~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ 58 (242)
T cd01406 1 GRVVIFVGAGVSVS-------SGLPDWKTLLDEIASELGLEIDGYSVEAKDENDYLELAELLEKE 58 (242)
T ss_pred CCEEEEecCccccc-------cCCCChHHHHHHHHHHcCCccchhhccccchhhHHHHHHHHHHH
Confidence 6789999864 33 57889999999999999865432111000234455555555544
No 36
>PF06849 DUF1246: Protein of unknown function (DUF1246); InterPro: IPR010672 The last two steps of de novo purine biosynthesis are: i) conversion of 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (AICAR) to 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate (FAICAR) ii) conversion of FAICAR to inosine5'-monophopsphate (IMP) In bacteria and eukaryotes, these steps are catalysed by the well-characterised bifunctional enzyme PurH []. Archaea do not appear to posses PurH, however, and perform these reactions by a different mecahnism []. In archaea, step i) is catalysed by the well-conserved PurP protein, while step ii) is catalysed by the PurO enzyme in some (though not all) species [, ]. This entry represents the N-terminal domain of PurP. Its function is not known, though it is almost always found in association with IPR009720 from INTERPRO.; GO: 0000287 magnesium ion binding, 0005524 ATP binding, 0016879 ligase activity, forming carbon-nitrogen bonds, 0006188 IMP biosynthetic process; PDB: 2PBZ_C 2R85_B 2R87_E 2R84_A 2R86_A 2R7L_A 2R7N_A 2R7K_A 2R7M_A.
Probab=24.53 E-value=4 Score=31.28 Aligned_cols=23 Identities=35% Similarity=0.689 Sum_probs=13.7
Q ss_pred CCCCCCCeEEEEec-c--ccEEeEec
Q 047136 36 SSVANKGHFVVYTT-D--NMRFTVPL 58 (142)
Q Consensus 36 ~~~vpkG~~~VyVG-e--~~RfvVp~ 58 (142)
..-||.|-|++|+| | .++|.||+
T Consensus 67 ~I~VPhgSfv~Y~G~d~ie~~~~vP~ 92 (124)
T PF06849_consen 67 AIFVPHGSFVAYVGYDRIENEFKVPI 92 (124)
T ss_dssp EEE--BTTHHHHH-HHHHHHT-SS-E
T ss_pred eEEecCCCeeEeecHHHHhhcCCCCe
Confidence 55699999999999 4 35577775
No 37
>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=24.39 E-value=1.1e+02 Score=21.13 Aligned_cols=27 Identities=30% Similarity=0.543 Sum_probs=17.3
Q ss_pred CeEEEEeccccEEeEeccCCCcHHHHHHHHhh
Q 047136 42 GHFVVYTTDNMRFTVPLEYLSRNVFIELLRMS 73 (142)
Q Consensus 42 G~~~VyVGe~~RfvVp~~yL~hp~F~~LL~~a 73 (142)
=|+|+++++. +..|| ..+.+.+||++.
T Consensus 25 rH~p~~i~~~-~l~v~----~d~~l~~~L~~l 51 (87)
T PF05194_consen 25 RHWPLFIEED-ELYVP----YDHVLEELLRKL 51 (87)
T ss_dssp TT--EEEETT-EEEEE------HHHHHHHHHT
T ss_pred CccceEEcCC-EEEec----CcHHHHHHHHHC
Confidence 4889999877 77777 666677777773
No 38
>COG4923 Predicted nuclease (RNAse H fold) [General function prediction only]
Probab=24.17 E-value=1e+02 Score=25.90 Aligned_cols=15 Identities=13% Similarity=0.592 Sum_probs=11.7
Q ss_pred CCeeecCchHHHHHH
Q 047136 83 GPITLPCDSTFLNYV 97 (142)
Q Consensus 83 G~L~iPC~~~~Fe~v 97 (142)
...+|||.+..+..+
T Consensus 87 SvF~vPcR~A~Y~~~ 101 (245)
T COG4923 87 SVFSVPCRAALYSDI 101 (245)
T ss_pred ceeccchHHHHHHHH
Confidence 346899999888766
No 39
>PF11126 Phage_DsbA: Transcriptional regulator DsbA; InterPro: IPR020313 DsbA is a double stranded binding protein found in bacteriophage T4 which is involved in transcriptional regulation. DsbA, along with other viral proteins, interacts with the host RNA polymerase core enzyme enabling initiation of transcription. DsbA acts as an enhancer protein of late genes in vitro. The protein consists of mainly alpha helices [].
Probab=23.90 E-value=1.7e+02 Score=20.35 Aligned_cols=37 Identities=14% Similarity=0.321 Sum_probs=28.9
Q ss_pred HHHHHHHHhhhHhcCCCCCCCeeecCchHHHHHHHHHHhccChhhHH
Q 047136 64 NVFIELLRMSEEEFGLPSNGPITLPCDSTFLNYVMTLVKGCIPEDLG 110 (142)
Q Consensus 64 p~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~~~~~e 110 (142)
..++++=+.|.+|+|.++ ..|-.++.+-.+..-.+.|
T Consensus 17 e~IKdik~~AK~ElGv~g----------k~Fnkl~~lyHk~~Re~fE 53 (69)
T PF11126_consen 17 EMIKDIKDRAKDELGVDG----------KMFNKLLKLYHKQEREEFE 53 (69)
T ss_pred HHHHHHHHHHHHHcCCCH----------HHHHHHHHHHHHhhHHHHH
Confidence 356677788999999854 6899999999887766555
No 40
>PF04332 DUF475: Protein of unknown function (DUF475); InterPro: IPR007427 This entry contains proteins that are predicted to be an integral membrane proteins with multiple transmembrane domains.
Probab=23.46 E-value=51 Score=28.70 Aligned_cols=16 Identities=25% Similarity=0.501 Sum_probs=14.6
Q ss_pred CCHHHHHHHHHHHhhh
Q 047136 2 TNSKRLIQLARKWQKM 17 (142)
Q Consensus 2 ~~~~KL~~~~kKWq~~ 17 (142)
+|++.|+.|..+||+.
T Consensus 6 VNA~vLk~Ms~~Wq~~ 21 (294)
T PF04332_consen 6 VNATVLKRMSPFWQRR 21 (294)
T ss_pred hhHHHHHhhhHHHHHH
Confidence 6899999999999983
No 41
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=23.04 E-value=1.2e+02 Score=21.33 Aligned_cols=39 Identities=18% Similarity=0.189 Sum_probs=32.5
Q ss_pred CCCeEEEEeccc-----cEEeEeccCCCcHHH---HHHHHhhhHhcC
Q 047136 40 NKGHFVVYTTDN-----MRFTVPLEYLSRNVF---IELLRMSEEEFG 78 (142)
Q Consensus 40 pkG~~~VyVGe~-----~RfvVp~~yL~hp~F---~~LL~~aeeEfG 78 (142)
++-+.+.+.|+. .++-+...|+.|+.+ +.|++++.|.|.
T Consensus 28 ~~k~~V~FfG~~~~~a~~~~~~l~p~~~~~~~~ek~~~~~k~ke~~~ 74 (80)
T cd06080 28 KQKARVNFIGDNMQSEKKGIRVVKRWLKHFDCTEKQKLTNKAKESYE 74 (80)
T ss_pred CCEEEEEEeCCCCceeccchhhcccccccHHHHHHHHHHHHHHHHHH
Confidence 556778888974 788888999999999 489999999875
No 42
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=22.65 E-value=3e+02 Score=23.17 Aligned_cols=61 Identities=18% Similarity=0.150 Sum_probs=41.5
Q ss_pred CCeEEEEecc-ccEEeEeccCCCcHHHHHHHHhhhHhcCCCCC---------------CCeeecCchHHHHHHHHHH
Q 047136 41 KGHFVVYTTD-NMRFTVPLEYLSRNVFIELLRMSEEEFGLPSN---------------GPITLPCDSTFLNYVMTLV 101 (142)
Q Consensus 41 kG~~~VyVGe-~~RfvVp~~yL~hp~F~~LL~~aeeEfG~~~~---------------G~L~iPC~~~~Fe~vl~~i 101 (142)
.|++.|.-.. +.++.|.+..-.-|...+++.+...-||++.| -+|++|...+.||-+++.|
T Consensus 45 ~~~~~v~~~~~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L~~~~~~~~GlR~p~~~d~fE~lv~aI 121 (283)
T PRK10308 45 RGVVTVIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGKLGAARPGLRLPGSVDAFEQGVRAI 121 (283)
T ss_pred cEEEEEEEcCCCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCCcCCCCCCHHHHHHHHH
Confidence 4666665433 34555555553345566777777777777644 4589999999999988876
No 43
>COG2899 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.98 E-value=45 Score=29.43 Aligned_cols=16 Identities=31% Similarity=0.480 Sum_probs=14.5
Q ss_pred CCHHHHHHHHHHHhhh
Q 047136 2 TNSKRLIQLARKWQKM 17 (142)
Q Consensus 2 ~~~~KL~~~~kKWq~~ 17 (142)
+|+.+|+.|..+||++
T Consensus 56 vNA~iLk~MS~~Wqk~ 71 (346)
T COG2899 56 VNAAILKDMSPFWQKR 71 (346)
T ss_pred hhHHHHHhccHHHHHH
Confidence 6889999999999984
No 44
>cd04395 RhoGAP_ARHGAP21 RhoGAP_ARHGAP21: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP21-like proteins. ArhGAP21 is a multi-domain protein, containing RhoGAP, PH and PDZ domains, and is believed to play a role in the organization of the cell-cell junction complex. It has been shown to function as a GAP of Cdc42 and RhoA, and to interact with alpha-catenin and Arf6. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=20.84 E-value=1.9e+02 Score=22.49 Aligned_cols=42 Identities=14% Similarity=0.137 Sum_probs=34.0
Q ss_pred HHHHHHHHhhhHhcCCCCCCCeeecCchHHHHHHHHHHhccC
Q 047136 64 NVFIELLRMSEEEFGLPSNGPITLPCDSTFLNYVMTLVKGCI 105 (142)
Q Consensus 64 p~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~i~~~~ 105 (142)
|.|.+..-..-++.|.+.+|.-++|.+...-+.+...++++.
T Consensus 19 P~iv~~~~~~l~~~g~~~eGIFR~~g~~~~i~~l~~~l~~~~ 60 (196)
T cd04395 19 PLIVEVCCNIVEARGLETVGIYRVPGNNAAISALQEELNRGG 60 (196)
T ss_pred ChHHHHHHHHHHHcCCCCccceeCCCcHHHHHHHHHHHhcCC
Confidence 455544444557789999999999999999999999999875
Done!