Query 048112
Match_columns 94
No_of_seqs 122 out of 645
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 06:22:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048112.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048112hhsearch_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 6.8E-37 1.5E-41 209.2 8.6 91 1-92 1-104 (104)
2 PLN03220 uncharacterized prote 100.0 5.1E-35 1.1E-39 200.2 8.3 89 1-90 1-102 (105)
3 PF02519 Auxin_inducible: Auxi 100.0 5.2E-32 1.1E-36 183.2 7.3 91 1-92 1-100 (100)
4 PLN03219 uncharacterized prote 100.0 7.3E-32 1.6E-36 185.4 8.1 91 1-91 1-105 (108)
5 PRK02899 adaptor protein; Prov 86.6 0.57 1.2E-05 34.9 2.4 25 52-77 38-62 (197)
6 PRK02315 adaptor protein; Prov 82.9 1 2.2E-05 34.2 2.4 24 53-77 39-62 (233)
7 PF05389 MecA: Negative regula 77.8 0.71 1.5E-05 34.2 0.0 25 52-77 38-62 (220)
8 PF02214 BTB_2: BTB/POZ domain 73.7 1.6 3.5E-05 27.6 0.9 51 42-93 9-62 (94)
9 PF03460 NIR_SIR_ferr: Nitrite 49.2 24 0.00052 21.0 2.8 54 36-91 6-66 (69)
10 PF11834 DUF3354: Domain of un 47.7 13 0.00029 23.5 1.6 17 53-69 26-42 (69)
11 PF08861 DUF1828: Domain of un 43.8 57 0.0012 20.8 4.1 39 52-90 44-82 (90)
12 PF12058 DUF3539: Protein of u 41.9 4.2 9.1E-05 27.3 -1.5 12 48-59 4-15 (88)
13 KOG1785 Tyrosine kinase negati 40.5 43 0.00094 28.7 3.9 32 49-81 310-346 (563)
14 PF11822 DUF3342: Domain of un 39.9 45 0.00097 27.0 3.8 39 51-93 26-67 (317)
15 PF09277 Erythro-docking: Eryt 39.9 27 0.00058 21.7 2.0 16 10-25 34-49 (58)
16 smart00153 VHP Villin headpiec 39.6 16 0.00035 20.4 0.9 19 49-67 1-19 (36)
17 PF02209 VHP: Villin headpiece 37.6 15 0.00032 20.7 0.5 19 49-67 1-19 (36)
18 PF02100 ODC_AZ: Ornithine dec 37.2 29 0.00064 23.4 2.1 38 51-90 39-76 (108)
19 TIGR03687 pupylate_cterm ubiqu 34.2 17 0.00037 20.3 0.4 17 55-71 12-30 (33)
20 COG4862 MecA Negative regulato 33.2 33 0.00071 26.6 2.0 26 52-78 38-63 (224)
21 smart00666 PB1 PB1 domain. Pho 33.2 83 0.0018 19.0 3.5 45 42-91 14-68 (81)
22 PF12588 PSDC: Phophatidylseri 28.6 61 0.0013 23.2 2.6 38 4-41 94-132 (141)
23 PF02762 Cbl_N3: CBL proto-onc 26.9 66 0.0014 21.5 2.3 29 38-66 43-73 (86)
24 cd06279 PBP1_LacI_like_3 Ligan 26.2 68 0.0015 23.2 2.6 26 44-69 5-36 (283)
25 cd06536 CIDE_N_ICAD CIDE_N dom 25.6 94 0.002 20.4 2.9 27 53-79 21-47 (80)
26 cd06399 PB1_P40 The PB1 domain 25.5 71 0.0015 21.6 2.3 25 43-67 18-42 (92)
27 TIGR03793 TOMM_pelo TOMM prope 25.4 99 0.0021 19.8 3.0 25 51-76 15-43 (77)
28 PF11876 DUF3396: Protein of u 24.9 57 0.0012 24.4 2.0 36 42-77 26-63 (208)
29 PF04341 DUF485: Protein of un 24.6 55 0.0012 21.2 1.7 12 50-61 2-13 (91)
30 cd04893 ACT_GcvR_1 ACT domains 24.5 1.3E+02 0.0029 18.3 3.4 34 36-69 37-71 (77)
31 PF00651 BTB: BTB/POZ domain; 24.1 1.8E+02 0.0039 17.8 4.3 36 51-91 33-71 (111)
32 cd04751 Commd3 COMM_Domain con 23.8 82 0.0018 20.6 2.4 20 73-92 65-84 (95)
33 PF05419 GUN4: GUN4-like ; In 23.5 7.9 0.00017 27.3 -2.7 24 33-56 109-132 (132)
34 PF10945 DUF2629: Protein of u 23.4 61 0.0013 19.1 1.5 17 6-22 24-40 (44)
35 PF12451 VPS11_C: Vacuolar pro 23.4 43 0.00094 19.6 0.9 18 51-68 20-37 (49)
36 TIGR02529 EutJ ethanolamine ut 22.9 81 0.0018 23.5 2.5 40 42-82 34-73 (239)
37 cd01615 CIDE_N CIDE_N domain, 22.8 1.1E+02 0.0023 20.0 2.7 25 53-79 21-45 (78)
38 cd05992 PB1 The PB1 domain is 22.5 1.8E+02 0.004 17.3 5.5 50 38-91 9-68 (81)
39 PF04304 DUF454: Protein of un 21.2 60 0.0013 19.6 1.3 21 49-69 5-25 (71)
40 PF11731 Cdd1: Pathogenicity l 20.7 1.4E+02 0.003 20.0 3.1 32 56-93 45-76 (93)
No 1
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=6.8e-37 Score=209.24 Aligned_cols=91 Identities=44% Similarity=0.751 Sum_probs=81.2
Q ss_pred Ccccch----hHHhHHHHHHHhHHHhhhhhc-cccccccCCCCcee--------EEEEecCCCCchHHHHHHHhhhhhcC
Q 048112 1 MAIRFP----SALNAKHILRQLKLLANQAAA-TASVSADVPKGHLA--------RLIIPVSFLNHPSFQELLTKAGEDFG 67 (94)
Q Consensus 1 m~~~~~----~~~~lk~~lrr~~s~~~~~~~-~~s~~~~vpkG~~a--------RfvVp~~~L~hP~F~~LL~~aeeEfG 67 (94)
|||+.+ +++++||+||||+|.+++++. ....+.+||||||| ||+||++|||||+|++||++||||||
T Consensus 1 m~~~k~~ki~~~~~~kq~l~r~~s~~~~~~~~~~~~~~~vpkG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG 80 (104)
T PLN03090 1 MAIKKSNKLTQTAMLKQILKRCSSLGKKQGYDEDGLPLDVPKGHFPVYVGENRSRYIVPISFLTHPEFQSLLQQAEEEFG 80 (104)
T ss_pred CCcccccchhHHHHHHHHHHHHHHhcccCCcccccCCCCCCCCcEEEEECCCCEEEEEEHHHcCCHHHHHHHHHHHHHhC
Confidence 777754 467999999999999877543 24577899999999 99999999999999999999999999
Q ss_pred cccCCCceeeeCcHHHHHHHHHhhc
Q 048112 68 YYHPMGGLTIPCRKDAFINLTSRLN 92 (94)
Q Consensus 68 ~~~~~G~L~iPC~~~~F~~vl~~l~ 92 (94)
|+|+ |+|+||||++.|++++|+|+
T Consensus 81 f~~~-G~L~IPC~~~~Fe~ll~~i~ 104 (104)
T PLN03090 81 FDHD-MGLTIPCEEVVFRSLTSMIR 104 (104)
T ss_pred CCCC-CcEEEeCCHHHHHHHHHHhC
Confidence 9998 89999999999999999983
No 2
>PLN03220 uncharacterized protein; Provisional
Probab=100.00 E-value=5.1e-35 Score=200.15 Aligned_cols=89 Identities=51% Similarity=0.942 Sum_probs=80.2
Q ss_pred CcccchhHHh-HHHHHHHhHHHhhhhhccccccccCCCCcee------------EEEEecCCCCchHHHHHHHhhhhhcC
Q 048112 1 MAIRFPSALN-AKHILRQLKLLANQAAATASVSADVPKGHLA------------RLIIPVSFLNHPSFQELLTKAGEDFG 67 (94)
Q Consensus 1 m~~~~~~~~~-lk~~lrr~~s~~~~~~~~~s~~~~vpkG~~a------------RfvVp~~~L~hP~F~~LL~~aeeEfG 67 (94)
||++++.|.. .||++||++ .+++.+..++.+.+||||||| |||||++|||||+|++||++||||||
T Consensus 1 ~~~~~~~~~~~~k~~~~~~~-~~~~~~~~~~~~~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP~F~~LL~~AeEEfG 79 (105)
T PLN03220 1 MGLSRFAISNATKQILKLNS-LANRNRTSSSSSDHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHPSFKEFLSRAEEEFG 79 (105)
T ss_pred CCcchhhhHHHHHHHHHHHh-hcccccccccccCCCCCCeEEEEECCCCCccceEEEEEHHHcCChHHHHHHHHHHHHhC
Confidence 8999999984 599999999 666555556678899999999 99999999999999999999999999
Q ss_pred cccCCCceeeeCcHHHHHHHHHh
Q 048112 68 YYHPMGGLTIPCRKDAFINLTSR 90 (94)
Q Consensus 68 ~~~~~G~L~iPC~~~~F~~vl~~ 90 (94)
|+|++|+|+||||++.|++++..
T Consensus 80 f~~~~G~L~IPCd~~~F~~ll~s 102 (105)
T PLN03220 80 FNHPMGGLTIPCREEVFLDLIAS 102 (105)
T ss_pred CCCCCCCEEeeCCHHHHHHHHHh
Confidence 99855999999999999999864
No 3
>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=99.97 E-value=5.2e-32 Score=183.21 Aligned_cols=91 Identities=44% Similarity=0.702 Sum_probs=70.5
Q ss_pred CcccchhHHhHHHHHHHhHHHhhhh-hccccccccCCCCcee--------EEEEecCCCCchHHHHHHHhhhhhcCcccC
Q 048112 1 MAIRFPSALNAKHILRQLKLLANQA-AATASVSADVPKGHLA--------RLIIPVSFLNHPSFQELLTKAGEDFGYYHP 71 (94)
Q Consensus 1 m~~~~~~~~~lk~~lrr~~s~~~~~-~~~~s~~~~vpkG~~a--------RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~ 71 (94)
|+-++.++..+++...++....+.. .+.++...++|+|||| ||+||++|||||+|++||++|||||||+++
T Consensus 1 M~~~~k~~~~~~k~~~~~~~~~~~~~~~~~~~~~~vp~G~~~VyVG~~~~Rfvvp~~~L~hp~f~~LL~~aeeEfG~~~~ 80 (100)
T PF02519_consen 1 MASRLKSLASAKKWQSRARSKSSSSSSSRSSSESDVPKGHFAVYVGEERRRFVVPVSYLNHPLFQELLEQAEEEFGFDQD 80 (100)
T ss_pred CccHHHHHHHHHhhhhhhhhcccccccccccccCCCCCCeEEEEeCccceEEEechHHcCchhHHHHHHHHhhhcCcCCC
Confidence 4555555554444444433322221 1123345899999999 999999999999999999999999999997
Q ss_pred CCceeeeCcHHHHHHHHHhhc
Q 048112 72 MGGLTIPCRKDAFINLTSRLN 92 (94)
Q Consensus 72 ~G~L~iPC~~~~F~~vl~~l~ 92 (94)
|+|+||||++.|++++|+|+
T Consensus 81 -G~l~iPC~~~~Fe~~l~~le 100 (100)
T PF02519_consen 81 -GPLTIPCDVVLFEHLLWLLE 100 (100)
T ss_pred -CcEEeeCCHHHHHHHHHHhC
Confidence 99999999999999999986
No 4
>PLN03219 uncharacterized protein; Provisional
Probab=99.97 E-value=7.3e-32 Score=185.37 Aligned_cols=91 Identities=41% Similarity=0.802 Sum_probs=77.6
Q ss_pred CcccchhHHhHHHHHHHhHHHhhhhhc----cccccccCCCCcee----------EEEEecCCCCchHHHHHHHhhhhhc
Q 048112 1 MAIRFPSALNAKHILRQLKLLANQAAA----TASVSADVPKGHLA----------RLIIPVSFLNHPSFQELLTKAGEDF 66 (94)
Q Consensus 1 m~~~~~~~~~lk~~lrr~~s~~~~~~~----~~s~~~~vpkG~~a----------RfvVp~~~L~hP~F~~LL~~aeeEf 66 (94)
||...+-+...||+.|-.+...+.+++ +++.+.+|||||+| ||+||++|||||+|++||++|||||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vpkGh~aVYVG~~~E~kRFvVPi~yL~hP~F~~LL~~AeEEf 80 (108)
T PLN03219 1 MGLMRSMLPNAKQIFKSQSMRNKNGSSSPSSSTTTSGLVPKGHVAVYVGEQMEKKRFVVPISYLNHPLFREFLNRAEEEC 80 (108)
T ss_pred CchHHHHHhhHHHHHHHHHHhcccCCCCCccCCCCCCCCCCCeEEEEECCCCCceEEEEEHHHcCChHHHHHHHHHHHHh
Confidence 777787888999998766655554433 24566789999999 9999999999999999999999999
Q ss_pred CcccCCCceeeeCcHHHHHHHHHhh
Q 048112 67 GYYHPMGGLTIPCRKDAFINLTSRL 91 (94)
Q Consensus 67 G~~~~~G~L~iPC~~~~F~~vl~~l 91 (94)
||+|++|+|+||||++.|+++++.-
T Consensus 81 Gf~~~~G~L~IPCd~~~F~~ll~~~ 105 (108)
T PLN03219 81 GFHHSMGGLTIPCREESFLHLITSH 105 (108)
T ss_pred CCCCCCCCEEEeCCHHHHHHHHHhh
Confidence 9998559999999999999999763
No 5
>PRK02899 adaptor protein; Provisional
Probab=86.63 E-value=0.57 Score=34.86 Aligned_cols=25 Identities=20% Similarity=0.659 Sum_probs=21.6
Q ss_pred chHHHHHHHhhhhhcCcccCCCceee
Q 048112 52 HPSFQELLTKAGEDFGYYHPMGGLTI 77 (94)
Q Consensus 52 hP~F~~LL~~aeeEfG~~~~~G~L~i 77 (94)
+-+|.++|++|..|+||..+ |+|+|
T Consensus 38 e~lF~~mm~Ea~~e~~F~~~-~pl~~ 62 (197)
T PRK02899 38 HQLFRDMMQEANKELGFEAD-GPIAV 62 (197)
T ss_pred HHHHHHHHHHhhhccCcccC-CeEEE
Confidence 35788889999999999987 89875
No 6
>PRK02315 adaptor protein; Provisional
Probab=82.90 E-value=1 Score=34.16 Aligned_cols=24 Identities=17% Similarity=0.285 Sum_probs=21.9
Q ss_pred hHHHHHHHhhhhhcCcccCCCceee
Q 048112 53 PSFQELLTKAGEDFGYYHPMGGLTI 77 (94)
Q Consensus 53 P~F~~LL~~aeeEfG~~~~~G~L~i 77 (94)
-+|.++|++|..|+||..+ |+|+|
T Consensus 39 ~fF~~mm~Ea~~e~~F~~~-~pl~~ 62 (233)
T PRK02315 39 EFFYSMMDEVDEEDDFADE-GPLWF 62 (233)
T ss_pred HHHHHHHHHhccccCcccC-CeEEE
Confidence 5899999999999999986 89986
No 7
>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=77.83 E-value=0.71 Score=34.21 Aligned_cols=25 Identities=32% Similarity=0.550 Sum_probs=0.0
Q ss_pred chHHHHHHHhhhhhcCcccCCCceee
Q 048112 52 HPSFQELLTKAGEDFGYYHPMGGLTI 77 (94)
Q Consensus 52 hP~F~~LL~~aeeEfG~~~~~G~L~i 77 (94)
+-+|.++|++|.+|+||..+ |+|++
T Consensus 38 e~fF~~ileea~~e~~F~~~-~~l~~ 62 (220)
T PF05389_consen 38 EEFFYSILEEADEEHGFEND-GPLTF 62 (220)
T ss_dssp --------------------------
T ss_pred HHHHHHHHHHhccccCcccC-CeEEE
Confidence 46899999999999999996 88874
No 8
>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=73.73 E-value=1.6 Score=27.63 Aligned_cols=51 Identities=16% Similarity=0.021 Sum_probs=31.9
Q ss_pred EEEEecCCCC-c--hHHHHHHHhhhhhcCcccCCCceeeeCcHHHHHHHHHhhcc
Q 048112 42 RLIIPVSFLN-H--PSFQELLTKAGEDFGYYHPMGGLTIPCRKDAFINLTSRLNW 93 (94)
Q Consensus 42 RfvVp~~~L~-h--P~F~~LL~~aeeEfG~~~~~G~L~iPC~~~~F~~vl~~l~~ 93 (94)
+|.++.+.|. + ..|..+++....... +.+.|.+-|-++...|++||..++.
T Consensus 9 ~f~~~~~tL~~~~~s~l~~~~~~~~~~~~-~~~~~~~fiDRdp~~F~~IL~ylr~ 62 (94)
T PF02214_consen 9 IFETSRSTLTRYPDSLLARLFSGERSDDY-DDDDGEYFIDRDPELFEYILNYLRT 62 (94)
T ss_dssp EEEEEHHHHHTSTTSTTTSHHHTGHGGGE-ETTTTEEEESS-HHHHHHHHHHHHH
T ss_pred EEEEcHHHHhhCCCChhhhHHhhcccccc-CCccceEEeccChhhhhHHHHHHhh
Confidence 4555555544 3 366677765421111 2223889999999999999998864
No 9
>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=49.18 E-value=24 Score=20.98 Aligned_cols=54 Identities=19% Similarity=0.306 Sum_probs=34.4
Q ss_pred CCCcee-EEEEecCCCCchHHHHHHHhhhhhcC-----cccCCCceeee-CcHHHHHHHHHhh
Q 048112 36 PKGHLA-RLIIPVSFLNHPSFQELLTKAGEDFG-----YYHPMGGLTIP-CRKDAFINLTSRL 91 (94)
Q Consensus 36 pkG~~a-RfvVp~~~L~hP~F~~LL~~aeeEfG-----~~~~~G~L~iP-C~~~~F~~vl~~l 91 (94)
+.|++. |+-+|.-.++-..++.|.+.| ++|| +... ..|.|+ -+.+.-..+...|
T Consensus 6 ~~g~~~v~~~~~~G~i~~~~l~~la~ia-~~yg~~~irlT~~-Q~l~l~~v~~~~~~~i~~~L 66 (69)
T PF03460_consen 6 GDGFYMVRIRIPGGRISAEQLRALAEIA-EKYGDGEIRLTTR-QNLQLRGVPEENLPAIFEEL 66 (69)
T ss_dssp STTEEEEEEB-GGGEEEHHHHHHHHHHH-HHHSTSEEEEETT-SCEEEEEEEGGGHHHHHHHH
T ss_pred CCeEEEEEEeCCCEEECHHHHHHHHHHH-HHhCCCeEEECCC-CeEEEeCCCHHHHHHHHHHH
Confidence 467645 999999999888888888877 5676 2222 335544 5555555555544
No 10
>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=47.74 E-value=13 Score=23.53 Aligned_cols=17 Identities=47% Similarity=0.755 Sum_probs=15.3
Q ss_pred hHHHHHHHhhhhhcCcc
Q 048112 53 PSFQELLTKAGEDFGYY 69 (94)
Q Consensus 53 P~F~~LL~~aeeEfG~~ 69 (94)
-.++|||+.|++.||+.
T Consensus 26 ~SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 26 DSLEELLKIASEKFGFS 42 (69)
T ss_pred ccHHHHHHHHHHHhCCC
Confidence 36999999999999985
No 11
>PF08861 DUF1828: Domain of unknown function DUF1828; InterPro: IPR014960 These proteins are functionally uncharacterised.
Probab=43.83 E-value=57 Score=20.80 Aligned_cols=39 Identities=21% Similarity=0.255 Sum_probs=32.4
Q ss_pred chHHHHHHHhhhhhcCcccCCCceeeeCcHHHHHHHHHh
Q 048112 52 HPSFQELLTKAGEDFGYYHPMGGLTIPCRKDAFINLTSR 90 (94)
Q Consensus 52 hP~F~~LL~~aeeEfG~~~~~G~L~iPC~~~~F~~vl~~ 90 (94)
.|-=+++|+..-..||..-++|.|.+.++.+.|-.....
T Consensus 44 s~~R~~~l~~il~~~gv~~~~~el~~~~~~~~~~~~~~~ 82 (90)
T PF08861_consen 44 SKKRKKILNSILNGFGVELDEGELFIKTSEENFPQAKHR 82 (90)
T ss_pred chHHHHHHHHHHHHcCccccCCEEEEEeCHHHHHHHHHH
Confidence 466678899999999999887899999999988776654
No 12
>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=41.90 E-value=4.2 Score=27.34 Aligned_cols=12 Identities=50% Similarity=1.018 Sum_probs=8.7
Q ss_pred CCCCchHHHHHH
Q 048112 48 SFLNHPSFQELL 59 (94)
Q Consensus 48 ~~L~hP~F~~LL 59 (94)
.|||||.|.-|-
T Consensus 4 ~YLNHPtFGlLy 15 (88)
T PF12058_consen 4 TYLNHPTFGLLY 15 (88)
T ss_dssp -EEEETTTEEEE
T ss_pred ccccCCccchhe
Confidence 689999986553
No 13
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=40.46 E-value=43 Score=28.68 Aligned_cols=32 Identities=38% Similarity=0.446 Sum_probs=22.1
Q ss_pred CCCchHHHHHHHhhhhhc-----CcccCCCceeeeCcH
Q 048112 49 FLNHPSFQELLTKAGEDF-----GYYHPMGGLTIPCRK 81 (94)
Q Consensus 49 ~L~hP~F~~LL~~aeeEf-----G~~~~~G~L~iPC~~ 81 (94)
=-|.|+||+||+-..|-| |=+|+ -.|+=-|++
T Consensus 310 P~NKpL~QaL~eG~keGFYlyPdGr~~n-pdLt~l~~~ 346 (563)
T KOG1785|consen 310 PQNKPLFQALLEGHKEGFYLYPDGRDQN-PDLTGLCQP 346 (563)
T ss_pred CCCcHHHHHHHhccccceEECCCCccCC-CChhhccCC
Confidence 358899999999998877 43443 236555554
No 14
>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=39.93 E-value=45 Score=27.04 Aligned_cols=39 Identities=15% Similarity=0.266 Sum_probs=28.1
Q ss_pred CchHHHHHHHh---hhhhcCcccCCCceeeeCcHHHHHHHHHhhcc
Q 048112 51 NHPSFQELLTK---AGEDFGYYHPMGGLTIPCRKDAFINLTSRLNW 93 (94)
Q Consensus 51 ~hP~F~~LL~~---aeeEfG~~~~~G~L~iPC~~~~F~~vl~~l~~ 93 (94)
....|++.|.. +..+.. + =.|.+-||+..|+.++..+++
T Consensus 26 ~M~YF~~~l~~~~~~~~~~~---~-idisVhCDv~iF~WLm~yv~~ 67 (317)
T PF11822_consen 26 EMRYFAEYLSRYINDSQRWE---E-IDISVHCDVHIFEWLMRYVKG 67 (317)
T ss_pred hhHHHHHHHhhcccccCcCC---C-cceEEecChhHHHHHHHHhhc
Confidence 34679999965 333322 2 359999999999999987653
No 15
>PF09277 Erythro-docking: Erythronolide synthase, docking; InterPro: IPR015357 Docking domains are found in prokaryotic erythronolide synthase. They adopt a structure consisting of a bundle of four alpha-helices, and mediate homodimerisation of the protein, stabilising the resulting complex []. ; PDB: 1PZQ_A.
Probab=39.92 E-value=27 Score=21.72 Aligned_cols=16 Identities=19% Similarity=0.177 Sum_probs=12.2
Q ss_pred hHHHHHHHhHHHhhhh
Q 048112 10 NAKHILRQLKLLANQA 25 (94)
Q Consensus 10 ~lk~~lrr~~s~~~~~ 25 (94)
||..+||+|++.....
T Consensus 34 RLeaLLR~Wq~~r~~~ 49 (58)
T PF09277_consen 34 RLEALLRRWQDRRAPA 49 (58)
T ss_dssp HHHHHHHHHHHHHH-S
T ss_pred HHHHHHHHHHhccCCC
Confidence 8889999999875443
No 16
>smart00153 VHP Villin headpiece domain.
Probab=39.64 E-value=16 Score=20.40 Aligned_cols=19 Identities=26% Similarity=0.578 Sum_probs=16.8
Q ss_pred CCCchHHHHHHHhhhhhcC
Q 048112 49 FLNHPSFQELLTKAGEDFG 67 (94)
Q Consensus 49 ~L~hP~F~~LL~~aeeEfG 67 (94)
||+.-.|++.+.++.+||-
T Consensus 1 yLsdeeF~~vfgmsr~eF~ 19 (36)
T smart00153 1 YLSDEDFEEVFGMTREEFY 19 (36)
T ss_pred CCCHHHHHHHHCCCHHHHH
Confidence 7888999999999999983
No 17
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=37.61 E-value=15 Score=20.68 Aligned_cols=19 Identities=21% Similarity=0.544 Sum_probs=15.0
Q ss_pred CCCchHHHHHHHhhhhhcC
Q 048112 49 FLNHPSFQELLTKAGEDFG 67 (94)
Q Consensus 49 ~L~hP~F~~LL~~aeeEfG 67 (94)
||+.-.|++++.++.+||.
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 7888999999999999884
No 18
>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=37.15 E-value=29 Score=23.44 Aligned_cols=38 Identities=21% Similarity=0.209 Sum_probs=21.0
Q ss_pred CchHHHHHHHhhhhhcCcccCCCceeeeCcHHHHHHHHHh
Q 048112 51 NHPSFQELLTKAGEDFGYYHPMGGLTIPCRKDAFINLTSR 90 (94)
Q Consensus 51 ~hP~F~~LL~~aeeEfG~~~~~G~L~iPC~~~~F~~vl~~ 90 (94)
.-..|.+|||.|||.+|-++ =.+.++=+-.....++..
T Consensus 39 ~K~~lvaLLElAee~L~c~~--vvic~~k~~~d~~~Llr~ 76 (108)
T PF02100_consen 39 SKESLVALLELAEEKLGCSH--VVICLDKNRPDRASLLRT 76 (108)
T ss_dssp -SHHHHHHHHHHHHHH------EEEEE---SS-HHHHHHH
T ss_pred cHHHHHHHHHHhcCcCCCCE--EEEEEECCchhHHHhhhh
Confidence 44789999999999999765 356666555555555543
No 19
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=34.22 E-value=17 Score=20.32 Aligned_cols=17 Identities=24% Similarity=0.620 Sum_probs=13.9
Q ss_pred HHHHHHhhhhhc--CcccC
Q 048112 55 FQELLTKAGEDF--GYYHP 71 (94)
Q Consensus 55 F~~LL~~aeeEf--G~~~~ 71 (94)
+-++|+.-+||| ||-|+
T Consensus 12 Id~vLe~NAe~FV~~fVQK 30 (33)
T TIGR03687 12 IDGVLESNAEEFVRGFVQK 30 (33)
T ss_pred HHHHHHHhHHHHHHHHHHc
Confidence 457888888998 88888
No 20
>COG4862 MecA Negative regulator of genetic competence, sporulation and motility [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Cell motility and secretion]
Probab=33.22 E-value=33 Score=26.63 Aligned_cols=26 Identities=19% Similarity=0.271 Sum_probs=23.3
Q ss_pred chHHHHHHHhhhhhcCcccCCCceeee
Q 048112 52 HPSFQELLTKAGEDFGYYHPMGGLTIP 78 (94)
Q Consensus 52 hP~F~~LL~~aeeEfG~~~~~G~L~iP 78 (94)
|-+|-++++.+.+|=+|..+ |+|+|-
T Consensus 38 EE~F~~mMdEl~~ee~F~~~-GpL~iq 63 (224)
T COG4862 38 EELFYEMMDELNLEEDFKDE-GPLWIQ 63 (224)
T ss_pred HHHHHHHHHhcCCccccccC-CceEEE
Confidence 57899999999999999998 999873
No 21
>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=33.21 E-value=83 Score=19.00 Aligned_cols=45 Identities=20% Similarity=0.324 Sum_probs=30.8
Q ss_pred EEEEecCCCCchHHHHHHHhhhhhcCcc----------cCCCceeeeCcHHHHHHHHHhh
Q 048112 42 RLIIPVSFLNHPSFQELLTKAGEDFGYY----------HPMGGLTIPCRKDAFINLTSRL 91 (94)
Q Consensus 42 RfvVp~~~L~hP~F~~LL~~aeeEfG~~----------~~~G~L~iPC~~~~F~~vl~~l 91 (94)
||.||. ...|.+|..+..+-|+.. .++..++|.++. .++..+.+.
T Consensus 14 ~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~-Dl~~a~~~~ 68 (81)
T smart00666 14 RLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDE-DLEEAIEEY 68 (81)
T ss_pred EEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHH-HHHHHHHHH
Confidence 677765 678999999999988874 232357788865 445554443
No 22
>PF12588 PSDC: Phophatidylserine decarboxylase ; InterPro: IPR022237 This domain family is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF02666 from PFAM. Phosphatidylserine decarboxylase (PSD) is an important enzyme in the synthesis of phosphatidylethanolamine in both prokaryotes and eukaryotes.
Probab=28.64 E-value=61 Score=23.16 Aligned_cols=38 Identities=21% Similarity=0.320 Sum_probs=24.1
Q ss_pred cchhHH-hHHHHHHHhHHHhhhhhccccccccCCCCcee
Q 048112 4 RFPSAL-NAKHILRQLKLLANQAAATASVSADVPKGHLA 41 (94)
Q Consensus 4 ~~~~~~-~lk~~lrr~~s~~~~~~~~~s~~~~vpkG~~a 41 (94)
+.+.+. ++|++|.-|..+-...+|.+.-..+.|.|.|.
T Consensus 94 ~~p~vN~~lK~ILn~W~~fL~sp~S~~vL~~~~~~GWfs 132 (141)
T PF12588_consen 94 LDPDVNAQLKKILNEWGEFLSSPASRSVLNTDPPNGWFS 132 (141)
T ss_pred cCHHHHHHHHHHHHHHHHHcCChhhhccccCCCCCCccC
Confidence 333433 89999999998776554444444444667663
No 23
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=26.92 E-value=66 Score=21.47 Aligned_cols=29 Identities=24% Similarity=0.347 Sum_probs=19.8
Q ss_pred Ccee--EEEEecCCCCchHHHHHHHhhhhhc
Q 048112 38 GHLA--RLIIPVSFLNHPSFQELLTKAGEDF 66 (94)
Q Consensus 38 G~~a--RfvVp~~~L~hP~F~~LL~~aeeEf 66 (94)
||++ .=++-+---|-|++|+|++-.+|-|
T Consensus 43 GyV~~dg~I~QTIPqnk~L~qaLidG~reG~ 73 (86)
T PF02762_consen 43 GYVTQDGKILQTIPQNKSLYQALIDGSREGF 73 (86)
T ss_dssp EEEETTSEEEEE--SSS-HHHHHHHHHHTTS
T ss_pred EEEcCCCcEEEecCCCchHHHHHHhccccce
Confidence 4444 4556666789999999999988866
No 24
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=26.19 E-value=68 Score=23.19 Aligned_cols=26 Identities=15% Similarity=0.261 Sum_probs=18.5
Q ss_pred EEecC---CCCchHHHHHHH---hhhhhcCcc
Q 048112 44 IIPVS---FLNHPSFQELLT---KAGEDFGYY 69 (94)
Q Consensus 44 vVp~~---~L~hP~F~~LL~---~aeeEfG~~ 69 (94)
+||.. ++.||.|.++++ ++.+++||.
T Consensus 5 i~p~~~~~~~~~~~~~~~~~gi~~~a~~~g~~ 36 (283)
T cd06279 5 VLTDSLSYAFSDPVASQFLAGVAEVLDAAGVN 36 (283)
T ss_pred EeCCcccccccCccHHHHHHHHHHHHHHCCCE
Confidence 56643 378999999976 556677764
No 25
>cd06536 CIDE_N_ICAD CIDE_N domain of ICAD. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD (DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and release of active DFF40/CAD nuclease.
Probab=25.58 E-value=94 Score=20.36 Aligned_cols=27 Identities=30% Similarity=0.399 Sum_probs=19.7
Q ss_pred hHHHHHHHhhhhhcCcccCCCceeeeC
Q 048112 53 PSFQELLTKAGEDFGYYHPMGGLTIPC 79 (94)
Q Consensus 53 P~F~~LL~~aeeEfG~~~~~G~L~iPC 79 (94)
...++|+.++.+-|.....+++++|=+
T Consensus 21 ~sL~eL~~K~~~~l~l~~~~~~~~lvL 47 (80)
T cd06536 21 SSLEELRIKACESLGFDSSSAPITLVL 47 (80)
T ss_pred CCHHHHHHHHHHHhCCCCCCCceEEEE
Confidence 457999999999999875423455544
No 26
>cd06399 PB1_P40 The PB1 domain is essential part of the p40 adaptor protein which plays an important role in activating phagocyte NADPH oxidase during phagocytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes , such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domain of p40 represents a type I PB1 domain which interacts with the PB1 domain of oxidase activator p67 w
Probab=25.51 E-value=71 Score=21.64 Aligned_cols=25 Identities=16% Similarity=0.400 Sum_probs=21.6
Q ss_pred EEEecCCCCchHHHHHHHhhhhhcC
Q 048112 43 LIIPVSFLNHPSFQELLTKAGEDFG 67 (94)
Q Consensus 43 fvVp~~~L~hP~F~~LL~~aeeEfG 67 (94)
..|.-+.-..|.|++||.....+|+
T Consensus 18 i~vee~l~~~P~~kdLl~lmr~~f~ 42 (92)
T cd06399 18 IAVEEDLSSTPLLKDLLELTRREFQ 42 (92)
T ss_pred eEeecccccCccHHHHHHHHHHHhc
Confidence 4566777889999999999999997
No 27
>TIGR03793 TOMM_pelo TOMM propeptide domain. This model represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM). Oddly, most of this seqence region appears homologous to nitrile hydratase subunits. This family is expanded especially in Pelotomaculum thermopropionicum SI.
Probab=25.45 E-value=99 Score=19.84 Aligned_cols=25 Identities=24% Similarity=0.327 Sum_probs=17.3
Q ss_pred CchHHHHHH----HhhhhhcCcccCCCcee
Q 048112 51 NHPSFQELL----TKAGEDFGYYHPMGGLT 76 (94)
Q Consensus 51 ~hP~F~~LL----~~aeeEfG~~~~~G~L~ 76 (94)
..|.|++.| +.+=+||||+-+ ..+.
T Consensus 15 ~Dp~Fr~~Ll~DPraaL~e~G~~~P-~~~~ 43 (77)
T TIGR03793 15 EDEAFKQALLTNPKEALEREGVQVP-AEVE 43 (77)
T ss_pred cCHHHHHHHHHCHHHHHHHhCCCCC-CceE
Confidence 458899966 456678899876 4443
No 28
>PF11876 DUF3396: Protein of unknown function (DUF3396); InterPro: IPR021815 This family of proteins are functionally uncharacterised. This protein is found in bacteria and viruses. Proteins in this family are typically between 302 to 382 amino acids in length.
Probab=24.87 E-value=57 Score=24.36 Aligned_cols=36 Identities=25% Similarity=0.538 Sum_probs=28.1
Q ss_pred EEEEecCCCCc-h-HHHHHHHhhhhhcCcccCCCceee
Q 048112 42 RLIIPVSFLNH-P-SFQELLTKAGEDFGYYHPMGGLTI 77 (94)
Q Consensus 42 RfvVp~~~L~h-P-~F~~LL~~aeeEfG~~~~~G~L~i 77 (94)
+|.+|++||.. | .|++|+....+.+-..|--+++.+
T Consensus 26 ~f~~P~~~l~~~~~~~~~l~~~~a~~L~~~~G~aGl~~ 63 (208)
T PF11876_consen 26 SFSLPLEWLEEGPGHFRALFLELAERLPPSHGYAGLAF 63 (208)
T ss_pred EEEeCHHHHhcCcHHHHHHHHHHHHHCCCCeEeeEEEE
Confidence 99999999986 2 599999999998876664345443
No 29
>PF04341 DUF485: Protein of unknown function, DUF485; InterPro: IPR007436 This family includes several putative integral membrane proteins.
Probab=24.64 E-value=55 Score=21.20 Aligned_cols=12 Identities=50% Similarity=0.930 Sum_probs=10.3
Q ss_pred CCchHHHHHHHh
Q 048112 50 LNHPSFQELLTK 61 (94)
Q Consensus 50 L~hP~F~~LL~~ 61 (94)
++||.|++|.++
T Consensus 2 ~~~p~f~~L~r~ 13 (91)
T PF04341_consen 2 LRSPEFQELVRR 13 (91)
T ss_pred CCCHHHHHHHHH
Confidence 689999999875
No 30
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int
Probab=24.53 E-value=1.3e+02 Score=18.28 Aligned_cols=34 Identities=9% Similarity=0.098 Sum_probs=25.6
Q ss_pred CCCcee-EEEEecCCCCchHHHHHHHhhhhhcCcc
Q 048112 36 PKGHLA-RLIIPVSFLNHPSFQELLTKAGEDFGYY 69 (94)
Q Consensus 36 pkG~~a-RfvVp~~~L~hP~F~~LL~~aeeEfG~~ 69 (94)
-.|+|. |.++-.+..+-..+++.|+.-+++||.+
T Consensus 37 ~~~~F~m~~~~~~~~~~~~~l~~~l~~~~~~~~l~ 71 (77)
T cd04893 37 LGTEFALTMLVEGSWDAIAKLEAALPGLARRLDLT 71 (77)
T ss_pred EcCEEEEEEEEEeccccHHHHHHHHHHHHHHcCCE
Confidence 567777 7666666567778888888888888864
No 31
>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=24.08 E-value=1.8e+02 Score=17.77 Aligned_cols=36 Identities=17% Similarity=0.434 Sum_probs=22.6
Q ss_pred CchHHHHHHHhhhhhcCcccCCC--ceeee-CcHHHHHHHHHhh
Q 048112 51 NHPSFQELLTKAGEDFGYYHPMG--GLTIP-CRKDAFINLTSRL 91 (94)
Q Consensus 51 ~hP~F~~LL~~aeeEfG~~~~~G--~L~iP-C~~~~F~~vl~~l 91 (94)
.-|.|+.+++... .... + .+.++ ++.+.|+.++..+
T Consensus 33 ~S~~F~~~~~~~~----~~~~-~~~~i~~~~~~~~~~~~~l~~~ 71 (111)
T PF00651_consen 33 RSPYFRNLFEGSK----FKES-TVPEISLPDVSPEAFEAFLEYM 71 (111)
T ss_dssp HBHHHHHHHTTTT----STTS-SEEEEEETTSCHHHHHHHHHHH
T ss_pred cchhhhhcccccc----cccc-cccccccccccccccccccccc
Confidence 3488888888771 1111 2 25444 6788888888754
No 32
>cd04751 Commd3 COMM_Domain containing protein 3. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=23.76 E-value=82 Score=20.60 Aligned_cols=20 Identities=15% Similarity=0.489 Sum_probs=18.1
Q ss_pred CceeeeCcHHHHHHHHHhhc
Q 048112 73 GGLTIPCRKDAFINLTSRLN 92 (94)
Q Consensus 73 G~L~iPC~~~~F~~vl~~l~ 92 (94)
..+.+-|+++.|++++..|+
T Consensus 65 ~~i~f~c~~e~L~~Li~~Lk 84 (95)
T cd04751 65 PDINFTCTLEQLQDLVNKLK 84 (95)
T ss_pred ceEEEEeCHHHHHHHHHHHH
Confidence 47999999999999999875
No 33
>PF05419 GUN4: GUN4-like ; InterPro: IPR008629 In Arabidopsis, GUN4 is required for the functioning of the plastid mediated repression of nuclear transcription that is involved in controlling the levels of magnesium- protoporphyrin IX. GUN4 binds the product and substrate of Mg-chelatase, an enzyme that produces Mg-Proto, and activates Mg-chelatase. GUN4 is thought to participate in plastid-to-nucleus signalling by regulating magnesium-protoporphyrin IX synthesis or trafficking.; PDB: 1Y6I_A 1Z3X_A 1Z3Y_A.
Probab=23.49 E-value=7.9 Score=27.27 Aligned_cols=24 Identities=42% Similarity=0.739 Sum_probs=10.9
Q ss_pred ccCCCCceeEEEEecCCCCchHHH
Q 048112 33 ADVPKGHLARLIIPVSFLNHPSFQ 56 (94)
Q Consensus 33 ~~vpkG~~aRfvVp~~~L~hP~F~ 56 (94)
..+|+||+|=.-+--.+++||.|+
T Consensus 109 l~AP~GHLP~~~~~~~~~~~~~~~ 132 (132)
T PF05419_consen 109 LNAPKGHLPAVWWLSSLLSHPAWQ 132 (132)
T ss_dssp TTS-TT--S-THHHHHHHTSCHHH
T ss_pred CCCCCCCCccHHHHHHHHcCCCcC
Confidence 448999997222223456666553
No 34
>PF10945 DUF2629: Protein of unknown function (DUF2629); InterPro: IPR024487 Some members in this family of proteins are annotated as YhjR however currently no function is known.
Probab=23.41 E-value=61 Score=19.14 Aligned_cols=17 Identities=24% Similarity=0.272 Sum_probs=13.0
Q ss_pred hhHHhHHHHHHHhHHHh
Q 048112 6 PSALNAKHILRQLKLLA 22 (94)
Q Consensus 6 ~~~~~lk~~lrr~~s~~ 22 (94)
+...++.+++.||+-..
T Consensus 24 sr~e~l~~~~~RWPLLa 40 (44)
T PF10945_consen 24 SREERLNQALQRWPLLA 40 (44)
T ss_pred HHHHHHHHHHHHChhHH
Confidence 34448999999999764
No 35
>PF12451 VPS11_C: Vacuolar protein sorting protein 11 C terminal; InterPro: IPR024763 Vps 11 is one of the evolutionarily conserved class C vacuolar protein sorting genes (c-vps: vps11, vps16, vps18, and vps33), whose products physically associate to form the c-vps protein complex required for vesicle docking and fusion. This entry represents the C-terminal domain of vps11.
Probab=23.37 E-value=43 Score=19.61 Aligned_cols=18 Identities=22% Similarity=0.409 Sum_probs=14.9
Q ss_pred CchHHHHHHHhhhhhcCc
Q 048112 51 NHPSFQELLTKAGEDFGY 68 (94)
Q Consensus 51 ~hP~F~~LL~~aeeEfG~ 68 (94)
+|-+|...|+.+++-|+.
T Consensus 20 ~~d~F~~~L~~s~D~F~v 37 (49)
T PF12451_consen 20 QHDLFFKQLEESEDRFSV 37 (49)
T ss_pred cHHHHHHHHHhCCCCchh
Confidence 578999999999888864
No 36
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein.
Probab=22.92 E-value=81 Score=23.50 Aligned_cols=40 Identities=10% Similarity=0.042 Sum_probs=27.5
Q ss_pred EEEEecCCCCchHHHHHHHhhhhhcCcccCCCceeeeCcHH
Q 048112 42 RLIIPVSFLNHPSFQELLTKAGEDFGYYHPMGGLTIPCRKD 82 (94)
Q Consensus 42 RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~~G~L~iPC~~~ 82 (94)
+.++..+-.. -.++.|.+++|+-.|...+.-.+++|++..
T Consensus 34 g~I~d~~~~~-~~l~~l~~~a~~~~g~~~~~vvisVP~~~~ 73 (239)
T TIGR02529 34 GIVVDFLGAV-EIVRRLKDTLEQKLGIELTHAATAIPPGTI 73 (239)
T ss_pred CeEEEhHHHH-HHHHHHHHHHHHHhCCCcCcEEEEECCCCC
Confidence 4444444433 368889999988888866545689998653
No 37
>cd01615 CIDE_N CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein.
Probab=22.76 E-value=1.1e+02 Score=19.99 Aligned_cols=25 Identities=32% Similarity=0.367 Sum_probs=18.6
Q ss_pred hHHHHHHHhhhhhcCcccCCCceeeeC
Q 048112 53 PSFQELLTKAGEDFGYYHPMGGLTIPC 79 (94)
Q Consensus 53 P~F~~LL~~aeeEfG~~~~~G~L~iPC 79 (94)
...++|+.++.+-|+... .+++|=+
T Consensus 21 ~sL~eL~~K~~~~l~l~~--~~~~lvL 45 (78)
T cd01615 21 SSLEELLSKACEKLKLPS--APVTLVL 45 (78)
T ss_pred CCHHHHHHHHHHHcCCCC--CCeEEEE
Confidence 357899999999999974 3454444
No 38
>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=22.49 E-value=1.8e+02 Score=17.25 Aligned_cols=50 Identities=24% Similarity=0.426 Sum_probs=34.0
Q ss_pred CceeEEEEecCCCCchHHHHHHHhhhhhcCcc---------cCCCc-eeeeCcHHHHHHHHHhh
Q 048112 38 GHLARLIIPVSFLNHPSFQELLTKAGEDFGYY---------HPMGG-LTIPCRKDAFINLTSRL 91 (94)
Q Consensus 38 G~~aRfvVp~~~L~hP~F~~LL~~aeeEfG~~---------~~~G~-L~iPC~~~~F~~vl~~l 91 (94)
|..-||.+|. .++.|.+|..+-.+.|+.. .+.|- ++|.++ +.++..+...
T Consensus 9 ~~~~~~~~~~---~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd-~Dl~~a~~~~ 68 (81)
T cd05992 9 GEIRRFVVVS---RSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSD-EDLEEAIEEA 68 (81)
T ss_pred CCCEEEEEec---CCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCH-HHHHHHHHHH
Confidence 4444888887 7889999999988888874 12233 566665 4566666554
No 39
>PF04304 DUF454: Protein of unknown function (DUF454); InterPro: IPR007401 This is a predicted membrane protein.
Probab=21.19 E-value=60 Score=19.60 Aligned_cols=21 Identities=29% Similarity=0.333 Sum_probs=17.4
Q ss_pred CCCchHHHHHHHhhhhhcCcc
Q 048112 49 FLNHPSFQELLTKAGEDFGYY 69 (94)
Q Consensus 49 ~L~hP~F~~LL~~aeeEfG~~ 69 (94)
.+|||.|+..++.-+|.=|..
T Consensus 5 l~~h~~~g~~I~~w~~~r~i~ 25 (71)
T PF04304_consen 5 LLNHRLFGPYIRNWEEHRGIP 25 (71)
T ss_pred HHcCchhHHHHHHHHHCCCcC
Confidence 479999999999988875544
No 40
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=20.74 E-value=1.4e+02 Score=19.98 Aligned_cols=32 Identities=28% Similarity=0.270 Sum_probs=25.8
Q ss_pred HHHHHhhhhhcCcccCCCceeeeCcHHHHHHHHHhhcc
Q 048112 56 QELLTKAGEDFGYYHPMGGLTIPCRKDAFINLTSRLNW 93 (94)
Q Consensus 56 ~~LL~~aeeEfG~~~~~G~L~iPC~~~~F~~vl~~l~~ 93 (94)
.+|-++-++-.|+.++ ||-.+.|..++...++
T Consensus 45 ~~Ly~~lc~~~G~~~D------pCvldvfr~av~~a~~ 76 (93)
T PF11731_consen 45 EELYERLCALTGQRHD------PCVLDVFRCAVYFANG 76 (93)
T ss_pred HHHHHHHHHHcCCcCC------cHHHHHHHHHHHHHcC
Confidence 5677777887888887 8999999999877653
Done!