Query 036854
Match_columns 167
No_of_seqs 185 out of 640
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 06:05:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036854.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036854hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03090 auxin-responsive fami 100.0 1.1E-34 2.3E-39 219.6 10.5 93 47-151 11-103 (104)
2 PF02519 Auxin_inducible: Auxi 100.0 4.4E-34 9.5E-39 214.1 10.1 97 48-152 4-100 (100)
3 PLN03220 uncharacterized prote 100.0 1.4E-31 3.1E-36 202.8 10.1 69 81-149 31-101 (105)
4 PLN03219 uncharacterized prote 100.0 9.4E-31 2E-35 199.1 10.5 70 80-150 34-104 (108)
5 PRK02899 adaptor protein; Prov 84.9 0.74 1.6E-05 38.2 2.5 25 113-137 38-62 (197)
6 PF02214 BTB_2: BTB/POZ domain 84.8 1.5 3.2E-05 31.1 3.7 54 101-154 7-63 (94)
7 PRK02315 adaptor protein; Prov 79.7 1.4 3E-05 37.4 2.3 25 113-137 38-62 (233)
8 PF05389 MecA: Negative regula 75.0 0.94 2E-05 37.5 0.0 25 113-137 38-62 (220)
9 cd05992 PB1 The PB1 domain is 73.6 24 0.00051 23.9 6.8 50 100-153 10-70 (81)
10 smart00666 PB1 PB1 domain. Pho 68.9 11 0.00025 25.7 4.4 49 100-153 11-70 (81)
11 PF07429 Glyco_transf_56: 4-al 61.7 44 0.00095 30.8 7.8 69 84-155 180-267 (360)
12 PRK02797 4-alpha-L-fucosyltran 60.6 34 0.00073 31.1 6.8 69 84-155 141-228 (322)
13 cd06398 PB1_Joka2 The PB1 doma 53.0 52 0.0011 24.2 5.7 52 99-150 9-73 (91)
14 PF11834 DUF3354: Domain of un 51.2 26 0.00057 24.8 3.7 17 114-130 26-42 (69)
15 PF11822 DUF3342: Domain of un 49.7 24 0.00052 31.9 4.0 52 100-154 12-68 (317)
16 PF00651 BTB: BTB/POZ domain; 43.3 78 0.0017 21.8 5.2 51 100-154 19-74 (111)
17 PF02209 VHP: Villin headpiece 39.6 12 0.00026 23.5 0.4 19 110-128 1-19 (36)
18 smart00153 VHP Villin headpiec 38.0 15 0.00032 23.0 0.7 19 110-128 1-19 (36)
19 cd06397 PB1_UP1 Uncharacterize 37.1 83 0.0018 23.4 4.5 48 99-151 9-67 (82)
20 PF00564 PB1: PB1 domain; Int 33.8 1.4E+02 0.0031 20.0 5.2 50 100-153 11-71 (84)
21 PF14317 YcxB: YcxB-like prote 28.5 1.1E+02 0.0024 18.9 3.7 34 84-121 26-59 (62)
22 cd06410 PB1_UP2 Uncharacterize 28.3 1.1E+02 0.0024 22.8 4.1 46 91-143 17-75 (97)
23 cd06407 PB1_NLP A PB1 domain i 28.2 1E+02 0.0022 22.1 3.8 44 100-147 10-65 (82)
24 COG4862 MecA Negative regulato 27.9 39 0.00085 29.3 1.8 27 112-138 37-63 (224)
25 cd01406 SIR2-like Sir2-like: P 27.7 1.1E+02 0.0023 25.1 4.3 57 88-153 1-57 (242)
26 PF12058 DUF3539: Protein of u 27.5 14 0.0003 27.8 -0.9 14 109-122 4-17 (88)
27 PRK09057 coproporphyrinogen II 26.3 1.2E+02 0.0026 27.0 4.7 45 91-144 58-102 (380)
28 PF03460 NIR_SIR_ferr: Nitrite 26.3 89 0.0019 20.6 3.0 57 86-153 6-68 (69)
29 PRK06582 coproporphyrinogen II 25.3 1.4E+02 0.003 27.0 4.9 55 90-153 64-119 (390)
30 PRK13347 coproporphyrinogen II 25.0 1.7E+02 0.0036 26.8 5.4 58 87-153 102-160 (453)
31 cd06396 PB1_NBR1 The PB1 domai 24.6 2.9E+02 0.0062 20.2 6.1 52 100-154 10-70 (81)
32 PF13778 DUF4174: Domain of un 24.3 48 0.001 25.0 1.5 24 86-109 77-100 (118)
33 COG0635 HemN Coproporphyrinoge 22.4 1.8E+02 0.0038 26.7 5.1 57 87-152 86-145 (416)
34 PRK08898 coproporphyrinogen II 22.2 1.6E+02 0.0035 26.4 4.7 54 90-152 75-130 (394)
35 PRK10308 3-methyl-adenine DNA 21.9 3.2E+02 0.0069 23.8 6.3 62 87-151 45-121 (283)
36 PLN02752 [acyl-carrier protein 21.4 1.1E+02 0.0023 26.7 3.3 44 84-130 35-78 (343)
37 cd06080 MUM1_like Mutated mela 20.6 1.3E+02 0.0029 21.8 3.1 43 86-128 28-74 (80)
No 1
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=1.1e-34 Score=219.61 Aligned_cols=93 Identities=38% Similarity=0.687 Sum_probs=80.7
Q ss_pred chHHHHHHHHHHHhhcccccCCCCCCccccCCCCCCCCCCCCeEEEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHh
Q 036854 47 AMSKFLSMASCIRRGAKKLCFPSSNPGFIQLGQEKPAEVPKGHLAVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERV 126 (167)
Q Consensus 47 ~~~KL~~~~rKwqk~akrl~~~~s~~~~~~~~~~~~~~vpkG~~aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEE 126 (167)
.+..|++|.|+|.++++. + ++. ....+.++|+||||||||+ +++||+||++|||||+|++||++||||
T Consensus 11 ~~~~~kq~l~r~~s~~~~-----~--~~~--~~~~~~~vpkG~~aVyVG~---~~~RfvVp~~~L~hP~F~~LL~~aeeE 78 (104)
T PLN03090 11 QTAMLKQILKRCSSLGKK-----Q--GYD--EDGLPLDVPKGHFPVYVGE---NRSRYIVPISFLTHPEFQSLLQQAEEE 78 (104)
T ss_pred HHHHHHHHHHHHHHhccc-----C--Ccc--cccCCCCCCCCcEEEEECC---CCEEEEEEHHHcCCHHHHHHHHHHHHH
Confidence 367899999999988641 1 110 1125678999999999997 789999999999999999999999999
Q ss_pred cCccCCCceeecCcHHHHHHHHHHH
Q 036854 127 YGFNHPGGITIPCRISEFEKVKTRI 151 (167)
Q Consensus 127 fGf~~~G~L~IPC~~~~Fe~vl~~i 151 (167)
|||+++|+|+||||+++||+++|+|
T Consensus 79 fGf~~~G~L~IPC~~~~Fe~ll~~i 103 (104)
T PLN03090 79 FGFDHDMGLTIPCEEVVFRSLTSMI 103 (104)
T ss_pred hCCCCCCcEEEeCCHHHHHHHHHHh
Confidence 9999999999999999999999998
No 2
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=100.00 E-value=4.4e-34 Score=214.08 Aligned_cols=97 Identities=45% Similarity=0.716 Sum_probs=77.8
Q ss_pred hHHHHHHHHHHHhhcccccCCCCCCccccCCCCCCCCCCCCeEEEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHhc
Q 036854 48 MSKFLSMASCIRRGAKKLCFPSSNPGFIQLGQEKPAEVPKGHLAVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERVY 127 (167)
Q Consensus 48 ~~KL~~~~rKwqk~akrl~~~~s~~~~~~~~~~~~~~vpkG~~aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEEf 127 (167)
-.|..+.+++|+..+.......+. ...++..++|+||||||||+ +++||+||++|||||+|++||++|||||
T Consensus 4 ~~k~~~~~~k~~~~~~~~~~~~~~-----~~~~~~~~vp~G~~~VyVG~---~~~Rfvvp~~~L~hp~f~~LL~~aeeEf 75 (100)
T PF02519_consen 4 RLKSLASAKKWQSRARSKSSSSSS-----SRSSSESDVPKGHFAVYVGE---ERRRFVVPVSYLNHPLFQELLEQAEEEF 75 (100)
T ss_pred HHHHHHHHHhhhhhhhhccccccc-----ccccccCCCCCCeEEEEeCc---cceEEEechHHcCchhHHHHHHHHhhhc
Confidence 345566667888765311111110 01113468999999999997 7999999999999999999999999999
Q ss_pred CccCCCceeecCcHHHHHHHHHHHh
Q 036854 128 GFNHPGGITIPCRISEFEKVKTRID 152 (167)
Q Consensus 128 Gf~~~G~L~IPC~~~~Fe~vl~~i~ 152 (167)
||+++|+|+||||+++||+++|+|+
T Consensus 76 G~~~~G~l~iPC~~~~Fe~~l~~le 100 (100)
T PF02519_consen 76 GFDQDGPLTIPCDVVLFEHLLWLLE 100 (100)
T ss_pred CcCCCCcEEeeCCHHHHHHHHHHhC
Confidence 9999999999999999999999985
No 3
>PLN03220 uncharacterized protein; Provisional
Probab=99.97 E-value=1.4e-31 Score=202.75 Aligned_cols=69 Identities=51% Similarity=0.917 Sum_probs=63.3
Q ss_pred CCCCCCCCeEEEEEcccC-CCceeEEEeeeccCchHHHHHHHhhHHhcCccC-CCceeecCcHHHHHHHHH
Q 036854 81 KPAEVPKGHLAVYVGESD-DEARRVFVPVIYFNHPLFGELLKQAERVYGFNH-PGGITIPCRISEFEKVKT 149 (167)
Q Consensus 81 ~~~~vpkG~~aVYVG~~~-~~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~~-~G~L~IPC~~~~Fe~vl~ 149 (167)
.+.+|||||||||||+++ ++.+||+||++|||||+|++||++|||||||++ +|+|+||||++.|++++.
T Consensus 31 ~~~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~ 101 (105)
T PLN03220 31 SSDHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHPSFKEFLSRAEEEFGFNHPMGGLTIPCREEVFLDLIA 101 (105)
T ss_pred ccCCCCCCeEEEEECCCCCccceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEeeCCHHHHHHHHH
Confidence 466899999999999743 358999999999999999999999999999998 599999999999999975
No 4
>PLN03219 uncharacterized protein; Provisional
Probab=99.97 E-value=9.4e-31 Score=199.10 Aligned_cols=70 Identities=53% Similarity=0.935 Sum_probs=64.2
Q ss_pred CCCCCCCCCeEEEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHhcCccC-CCceeecCcHHHHHHHHHH
Q 036854 80 EKPAEVPKGHLAVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERVYGFNH-PGGITIPCRISEFEKVKTR 150 (167)
Q Consensus 80 ~~~~~vpkG~~aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~~-~G~L~IPC~~~~Fe~vl~~ 150 (167)
+.+.++||||||||||++ ++++||+||++|||||+|++||++|||||||++ +|+|+||||++.|++++..
T Consensus 34 ~~~~~vpkGh~aVYVG~~-~E~kRFvVPi~yL~hP~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~~ 104 (108)
T PLN03219 34 TTSGLVPKGHVAVYVGEQ-MEKKRFVVPISYLNHPLFREFLNRAEEECGFHHSMGGLTIPCREESFLHLITS 104 (108)
T ss_pred CCCCCCCCCeEEEEECCC-CCceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEEeCCHHHHHHHHHh
Confidence 356789999999999973 368999999999999999999999999999997 5999999999999999875
No 5
>PRK02899 adaptor protein; Provisional
Probab=84.95 E-value=0.74 Score=38.25 Aligned_cols=25 Identities=32% Similarity=0.761 Sum_probs=21.9
Q ss_pred chHHHHHHHhhHHhcCccCCCceee
Q 036854 113 HPLFGELLKQAERVYGFNHPGGITI 137 (167)
Q Consensus 113 hPlF~eLL~~AeEEfGf~~~G~L~I 137 (167)
+-+|.++|++|..|+||..+|||+|
T Consensus 38 e~lF~~mm~Ea~~e~~F~~~~pl~~ 62 (197)
T PRK02899 38 HQLFRDMMQEANKELGFEADGPIAV 62 (197)
T ss_pred HHHHHHHHHHhhhccCcccCCeEEE
Confidence 3578888999999999999999875
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=84.77 E-value=1.5 Score=31.06 Aligned_cols=54 Identities=11% Similarity=-0.027 Sum_probs=42.2
Q ss_pred ceeEEEeeeccC-c--hHHHHHHHhhHHhcCccCCCceeecCcHHHHHHHHHHHhcC
Q 036854 101 ARRVFVPVIYFN-H--PLFGELLKQAERVYGFNHPGGITIPCRISEFEKVKTRIDAW 154 (167)
Q Consensus 101 ~rRfvVP~~yLn-h--PlF~eLL~~AeEEfGf~~~G~L~IPC~~~~Fe~vl~~i~~~ 154 (167)
.+.|.++.+.|. + ..|..|+........-+.+|.+-|-++...|++|+..+..+
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 489999999887 4 48899988652222234569999999999999999999885
No 7
>PRK02315 adaptor protein; Provisional
Probab=79.74 E-value=1.4 Score=37.39 Aligned_cols=25 Identities=12% Similarity=0.314 Sum_probs=22.8
Q ss_pred chHHHHHHHhhHHhcCccCCCceee
Q 036854 113 HPLFGELLKQAERVYGFNHPGGITI 137 (167)
Q Consensus 113 hPlF~eLL~~AeEEfGf~~~G~L~I 137 (167)
+-+|.++|++|..|+||..+|||+|
T Consensus 38 e~fF~~mm~Ea~~e~~F~~~~pl~~ 62 (233)
T PRK02315 38 EEFFYSMMDEVDEEDDFADEGPLWF 62 (233)
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 4589999999999999999999985
No 8
>PF05389 MecA: Negative regulator of genetic competence (MecA); InterPro: IPR008681 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. This family contains several bacterial MecA proteins. In complex media competence development is poor, and there is little or no expression of late competence genes. Overexpression of MecA inhibits comG transcription [, , ]. MecA enables the recognition and targeting of unfolded and aggregated proteins to the ClpC protease or to other proteins involved in proteolysis. Acts negatively in the development of competence by binding ComK and recruiting it to the ClpCP protease. When overexpressed, inhibits sporulation. Also involved in Spx degradation by ClpC. ; PDB: 3JTP_C 2Y1R_O 3PXI_c 3PXG_b 3JTO_D 3JTN_A.
Probab=74.98 E-value=0.94 Score=37.47 Aligned_cols=25 Identities=28% Similarity=0.567 Sum_probs=0.0
Q ss_pred chHHHHHHHhhHHhcCccCCCceee
Q 036854 113 HPLFGELLKQAERVYGFNHPGGITI 137 (167)
Q Consensus 113 hPlF~eLL~~AeEEfGf~~~G~L~I 137 (167)
+-+|.++|++|.+|+||..+|||++
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 5689999999999999999999885
No 9
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=73.59 E-value=24 Score=23.88 Aligned_cols=50 Identities=20% Similarity=0.308 Sum_probs=38.7
Q ss_pred CceeEEEeeeccCchHHHHHHHhhHHhcCcc----------CC-CceeecCcHHHHHHHHHHHhc
Q 036854 100 EARRVFVPVIYFNHPLFGELLKQAERVYGFN----------HP-GGITIPCRISEFEKVKTRIDA 153 (167)
Q Consensus 100 ~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~----------~~-G~L~IPC~~~~Fe~vl~~i~~ 153 (167)
+.+||.||. .++-|.+|..+..+.|++. .+ ..|+|.++ +.|+.++.+...
T Consensus 10 ~~~~~~~~~---~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd-~Dl~~a~~~~~~ 70 (81)
T cd05992 10 EIRRFVVVS---RSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSD-EDLEEAIEEARR 70 (81)
T ss_pred CCEEEEEec---CCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCH-HHHHHHHHHHhh
Confidence 789999997 8899999999999998885 13 44667776 467777777654
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=68.93 E-value=11 Score=25.66 Aligned_cols=49 Identities=22% Similarity=0.448 Sum_probs=37.6
Q ss_pred CceeEEEeeeccCchHHHHHHHhhHHhcCcc----------CCC-ceeecCcHHHHHHHHHHHhc
Q 036854 100 EARRVFVPVIYFNHPLFGELLKQAERVYGFN----------HPG-GITIPCRISEFEKVKTRIDA 153 (167)
Q Consensus 100 ~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~----------~~G-~L~IPC~~~~Fe~vl~~i~~ 153 (167)
+.++|.||- .+-|.+|..+..+.|++. .+| .|+|.++. .++.++.+...
T Consensus 11 ~~~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~-Dl~~a~~~~~~ 70 (81)
T smart00666 11 ETRRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDE-DLEEAIEEYDS 70 (81)
T ss_pred EEEEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHH-HHHHHHHHHHH
Confidence 789999985 778999999999998875 234 68899976 55566666654
No 11
>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=61.71 E-value=44 Score=30.79 Aligned_cols=69 Identities=19% Similarity=0.420 Sum_probs=48.1
Q ss_pred CCCCCeEEEEEcccC-----------------CCceeEEEeeeccC--chHHHHHHHhhHHhcCccCCCceeecCcHHHH
Q 036854 84 EVPKGHLAVYVGESD-----------------DEARRVFVPVIYFN--HPLFGELLKQAERVYGFNHPGGITIPCRISEF 144 (167)
Q Consensus 84 ~vpkG~~aVYVG~~~-----------------~~~rRfvVP~~yLn--hPlF~eLL~~AeEEfGf~~~G~L~IPC~~~~F 144 (167)
..+++-..|.||..+ ++..|++||++|=. ..-.+++.+.+++-||- +-+.+==+---|
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 356788899998532 35689999999963 56777777778888873 334444455557
Q ss_pred HHHHHHHhcCC
Q 036854 145 EKVKTRIDAWD 155 (167)
Q Consensus 145 e~vl~~i~~~~ 155 (167)
+..+..|++.|
T Consensus 257 ~eYl~lL~~cD 267 (360)
T PF07429_consen 257 DEYLALLSRCD 267 (360)
T ss_pred HHHHHHHHhCC
Confidence 77777777665
No 12
>PRK02797 4-alpha-L-fucosyltransferase; Provisional
Probab=60.62 E-value=34 Score=31.08 Aligned_cols=69 Identities=19% Similarity=0.361 Sum_probs=47.2
Q ss_pred CCCCCeEEEEEcccC-----------------CCceeEEEeeec--cCchHHHHHHHhhHHhcCccCCCceeecCcHHHH
Q 036854 84 EVPKGHLAVYVGESD-----------------DEARRVFVPVIY--FNHPLFGELLKQAERVYGFNHPGGITIPCRISEF 144 (167)
Q Consensus 84 ~vpkG~~aVYVG~~~-----------------~~~rRfvVP~~y--LnhPlF~eLL~~AeEEfGf~~~G~L~IPC~~~~F 144 (167)
..+++-++|.||..+ ++.-|+.||++| =|..-.++..+.+.|-|| .+-+++==+--.|
T Consensus 141 ~~~~~~~tIlvGNSgd~SN~Hie~L~~l~~~~~~~v~ii~PlsYp~gn~~Yi~~V~~~~~~lF~---~~~~~~L~e~l~f 217 (322)
T PRK02797 141 RQRAGKMTILVGNSGDRSNRHIEALRALHQQFGDNVKIIVPMGYPANNQAYIEEVRQAGLALFG---AENFQILTEKLPF 217 (322)
T ss_pred ccCCCceEEEEeCCCCCcccHHHHHHHHHHHhCCCeEEEEECCcCCCCHHHHHHHHHHHHHhcC---cccEEehhhhCCH
Confidence 456778999999643 245599999999 454455555556666765 2345555566667
Q ss_pred HHHHHHHhcCC
Q 036854 145 EKVKTRIDAWD 155 (167)
Q Consensus 145 e~vl~~i~~~~ 155 (167)
+..+..|++.|
T Consensus 218 ~eYl~lL~~~D 228 (322)
T PRK02797 218 DDYLALLRQCD 228 (322)
T ss_pred HHHHHHHHhCC
Confidence 77788777665
No 13
>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=52.98 E-value=52 Score=24.19 Aligned_cols=52 Identities=13% Similarity=0.110 Sum_probs=36.7
Q ss_pred CCceeEEEeee-ccCchHHHHHHHhhHHhcCccC-----------C-CceeecCcHHHHHHHHHH
Q 036854 99 DEARRVFVPVI-YFNHPLFGELLKQAERVYGFNH-----------P-GGITIPCRISEFEKVKTR 150 (167)
Q Consensus 99 ~~~rRfvVP~~-yLnhPlF~eLL~~AeEEfGf~~-----------~-G~L~IPC~~~~Fe~vl~~ 150 (167)
++.+||-+|.. --.+.-|.+|.++-++-|.... + .-++|.||.++-+-+-.+
T Consensus 9 ~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~~ 73 (91)
T cd06398 9 GTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQYF 73 (91)
T ss_pred CEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHHH
Confidence 38999999963 0114578888888888777653 2 347899999887755443
No 14
>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=51.20 E-value=26 Score=24.79 Aligned_cols=17 Identities=41% Similarity=0.632 Sum_probs=15.2
Q ss_pred hHHHHHHHhhHHhcCcc
Q 036854 114 PLFGELLKQAERVYGFN 130 (167)
Q Consensus 114 PlF~eLL~~AeEEfGf~ 130 (167)
-.++|||+.|++.||+.
T Consensus 26 ~SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 26 DSLEELLKIASEKFGFS 42 (69)
T ss_pred ccHHHHHHHHHHHhCCC
Confidence 36899999999999985
No 15
>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=49.66 E-value=24 Score=31.89 Aligned_cols=52 Identities=19% Similarity=0.296 Sum_probs=39.7
Q ss_pred CceeEEEeeeccCc--hHHHHHHHh---hHHhcCccCCCceeecCcHHHHHHHHHHHhcC
Q 036854 100 EARRVFVPVIYFNH--PLFGELLKQ---AERVYGFNHPGGITIPCRISEFEKVKTRIDAW 154 (167)
Q Consensus 100 ~~rRfvVP~~yLnh--PlF~eLL~~---AeEEfGf~~~G~L~IPC~~~~Fe~vl~~i~~~ 154 (167)
..+=|..|.+.|-. ..|+++|.. +.++. .+=.|.+-||+..|+-++..++..
T Consensus 12 ~~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~---~~idisVhCDv~iF~WLm~yv~~~ 68 (317)
T PF11822_consen 12 EKRDFTCPRDLLVSEMRYFAEYLSRYINDSQRW---EEIDISVHCDVHIFEWLMRYVKGE 68 (317)
T ss_pred cceeeeccHHHHHHhhHHHHHHHhhcccccCcC---CCcceEEecChhHHHHHHHHhhcC
Confidence 45569999988865 569999965 33332 245688999999999999999873
No 16
>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=43.27 E-value=78 Score=21.84 Aligned_cols=51 Identities=18% Similarity=0.365 Sum_probs=36.2
Q ss_pred CceeEEEeeecc--CchHHHHHHHhhHHhcCccCCC--ceeec-CcHHHHHHHHHHHhcC
Q 036854 100 EARRVFVPVIYF--NHPLFGELLKQAERVYGFNHPG--GITIP-CRISEFEKVKTRIDAW 154 (167)
Q Consensus 100 ~~rRfvVP~~yL--nhPlF~eLL~~AeEEfGf~~~G--~L~IP-C~~~~Fe~vl~~i~~~ 154 (167)
+..+|-|.-.+| ..|.|..+++... ...++ .|.++ ++...|+.++..+=.+
T Consensus 19 d~~~~~vhk~iL~~~S~~F~~~~~~~~----~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~ 74 (111)
T PF00651_consen 19 DGKTFYVHKNILAARSPYFRNLFEGSK----FKESTVPEISLPDVSPEAFEAFLEYMYTG 74 (111)
T ss_dssp TTEEEEE-HHHHHHHBHHHHHHHTTTT----STTSSEEEEEETTSCHHHHHHHHHHHHHS
T ss_pred CCEEEeechhhhhccchhhhhcccccc----cccccccccccccccccccccccccccCC
Confidence 368888888877 4699999999881 12233 46655 7899999999877543
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=39.62 E-value=12 Score=23.49 Aligned_cols=19 Identities=11% Similarity=0.296 Sum_probs=15.3
Q ss_pred ccCchHHHHHHHhhHHhcC
Q 036854 110 YFNHPLFGELLKQAERVYG 128 (167)
Q Consensus 110 yLnhPlF~eLL~~AeEEfG 128 (167)
||+...|++++.|+.+||.
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 7899999999999999973
No 18
>smart00153 VHP Villin headpiece domain.
Probab=38.02 E-value=15 Score=22.98 Aligned_cols=19 Identities=16% Similarity=0.329 Sum_probs=17.0
Q ss_pred ccCchHHHHHHHhhHHhcC
Q 036854 110 YFNHPLFGELLKQAERVYG 128 (167)
Q Consensus 110 yLnhPlF~eLL~~AeEEfG 128 (167)
||+...|++++.|+.+||-
T Consensus 1 yLsdeeF~~vfgmsr~eF~ 19 (36)
T smart00153 1 YLSDEDFEEVFGMTREEFY 19 (36)
T ss_pred CCCHHHHHHHHCCCHHHHH
Confidence 7899999999999999973
No 19
>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=37.07 E-value=83 Score=23.36 Aligned_cols=48 Identities=19% Similarity=0.314 Sum_probs=36.5
Q ss_pred CCceeEEEeeeccCchHHHHHHHhhHHhcCcc----------CC-CceeecCcHHHHHHHHHHH
Q 036854 99 DEARRVFVPVIYFNHPLFGELLKQAERVYGFN----------HP-GGITIPCRISEFEKVKTRI 151 (167)
Q Consensus 99 ~~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~----------~~-G~L~IPC~~~~Fe~vl~~i 151 (167)
++.+||.+|. -|.+.+|-++-+.-|-++ +| ..|||.=+.++.+ ++...
T Consensus 9 g~~RRf~~~~----~pt~~~L~~kl~~Lf~lp~~~~~vtYiDeD~D~ITlssd~eL~d-~~~~~ 67 (82)
T cd06397 9 GDTRRIVFPD----IPTWEALASKLENLYNLPEIKVGVTYIDNDNDEITLSSNKELQD-FYRLS 67 (82)
T ss_pred CceEEEecCC----CccHHHHHHHHHHHhCCChhHeEEEEEcCCCCEEEecchHHHHH-HHHhc
Confidence 3899999998 899999999988877766 23 5688887777665 44443
No 20
>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=33.82 E-value=1.4e+02 Score=20.04 Aligned_cols=50 Identities=16% Similarity=0.232 Sum_probs=33.9
Q ss_pred CceeEEEeeeccCchHHHHHHHhhHHhcCcc----------CCC-ceeecCcHHHHHHHHHHHhc
Q 036854 100 EARRVFVPVIYFNHPLFGELLKQAERVYGFN----------HPG-GITIPCRISEFEKVKTRIDA 153 (167)
Q Consensus 100 ~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~----------~~G-~L~IPC~~~~Fe~vl~~i~~ 153 (167)
+.+| .+..-..+.|.+|..+.++.|+.. .+| .|+|.++.++ +.++.....
T Consensus 11 ~~~~---~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~Dl-~~a~~~~~~ 71 (84)
T PF00564_consen 11 DIRR---IISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDEDL-QEAIEQAKE 71 (84)
T ss_dssp EEEE---EEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHHH-HHHHHHHHH
T ss_pred eeEE---EEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHHH-HHHHHHHHh
Confidence 4555 334445679999999999999983 344 5778877654 446555554
No 21
>PF14317 YcxB: YcxB-like protein
Probab=28.49 E-value=1.1e+02 Score=18.89 Aligned_cols=34 Identities=18% Similarity=0.276 Sum_probs=26.1
Q ss_pred CCCCCeEEEEEcccCCCceeEEEeeeccCchHHHHHHH
Q 036854 84 EVPKGHLAVYVGESDDEARRVFVPVIYFNHPLFGELLK 121 (167)
Q Consensus 84 ~vpkG~~aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~ 121 (167)
...+.++.+|++ +..-++||-+.++.--..++.+
T Consensus 26 ~e~~~~~~l~~~----~~~~~~iPk~~f~~~e~~~f~~ 59 (62)
T PF14317_consen 26 VETKDYFYLYLG----KNQAFIIPKRAFSEEEKEEFRE 59 (62)
T ss_pred EEeCCEEEEEEC----CCeEEEEEHHHCCHhHHHHHHH
Confidence 346788999998 4688999999998655555554
No 22
>cd06410 PB1_UP2 Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=28.26 E-value=1.1e+02 Score=22.75 Aligned_cols=46 Identities=26% Similarity=0.279 Sum_probs=32.8
Q ss_pred EEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHhcCccC-------------CCceeecCcHHH
Q 036854 91 AVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERVYGFNH-------------PGGITIPCRISE 143 (167)
Q Consensus 91 aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~~-------------~G~L~IPC~~~~ 143 (167)
.=|||. +.+-..|+-+ .-|.||.....+.++... ++-|.|.||.++
T Consensus 17 l~Y~GG---~tr~i~V~r~----~s~~el~~kl~~~~~~~~~~~lky~Lp~edld~Lisv~~DeDl 75 (97)
T cd06410 17 LRYVGG---ETRIVSVDRS----ISFKELVSKLSELFGAGVVVTLKYQLPDEDLDALISVSNDEDL 75 (97)
T ss_pred EEEcCC---ceEEEEEcCC----CCHHHHHHHHHHHhCCCCceEEEEEcCCCCcceeEEecCcHHH
Confidence 469985 6777777766 467788888887776655 346778888754
No 23
>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=28.22 E-value=1e+02 Score=22.13 Aligned_cols=44 Identities=18% Similarity=0.224 Sum_probs=32.9
Q ss_pred CceeEEEeeeccCchHHHHHHHhhHHhcCccC------------CCceeecCcHHHHHHH
Q 036854 100 EARRVFVPVIYFNHPLFGELLKQAERVYGFNH------------PGGITIPCRISEFEKV 147 (167)
Q Consensus 100 ~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~~------------~G~L~IPC~~~~Fe~v 147 (167)
|..||-||.+ .-|++|.++-.+-|+++. +..++|.|+.++=|-+
T Consensus 10 d~~r~~l~~~----~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai 65 (82)
T cd06407 10 EKIRFRLPPS----WGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEECI 65 (82)
T ss_pred eEEEEEcCCC----CCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHHH
Confidence 7899998864 368888888888777642 2568899998876644
No 24
>COG4862 MecA Negative regulator of genetic competence, sporulation and motility [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Cell motility and secretion]
Probab=27.92 E-value=39 Score=29.26 Aligned_cols=27 Identities=22% Similarity=0.342 Sum_probs=24.1
Q ss_pred CchHHHHHHHhhHHhcCccCCCceeec
Q 036854 112 NHPLFGELLKQAERVYGFNHPGGITIP 138 (167)
Q Consensus 112 nhPlF~eLL~~AeEEfGf~~~G~L~IP 138 (167)
.+-+|-++++++.+|-+|..+|||.|-
T Consensus 37 ~EE~F~~mMdEl~~ee~F~~~GpL~iq 63 (224)
T COG4862 37 TEELFYEMMDELNLEEDFKDEGPLWIQ 63 (224)
T ss_pred HHHHHHHHHHhcCCccccccCCceEEE
Confidence 478999999999999999999999873
No 25
>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=27.66 E-value=1.1e+02 Score=25.14 Aligned_cols=57 Identities=14% Similarity=0.260 Sum_probs=34.6
Q ss_pred CeEEEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHhcCccCCCceeecCcHHHHHHHHHHHhc
Q 036854 88 GHLAVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERVYGFNHPGGITIPCRISEFEKVKTRIDA 153 (167)
Q Consensus 88 G~~aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~~~G~L~IPC~~~~Fe~vl~~i~~ 153 (167)
|.++++||.+ -... .+-|.+.+|++...++++.+.+....-.=+...+..+..++.+
T Consensus 1 g~lvlFiGAG--~S~~-------~glP~W~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~ 57 (242)
T cd01406 1 GRVVIFVGAG--VSVS-------SGLPDWKTLLDEIASELGLEIDGYSVEAKDENDYLELAELLEK 57 (242)
T ss_pred CCEEEEecCc--cccc-------cCCCChHHHHHHHHHHcCCccchhhccccchhhHHHHHHHHHH
Confidence 6789999952 1111 5789999999999999987654211100033444445544444
No 26
>PF12058 DUF3539: Protein of unknown function (DUF3539); InterPro: IPR021926 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved NHP sequence motif. ; PDB: 3N5B_B 2XKO_C 2XG8_F.
Probab=27.48 E-value=14 Score=27.79 Aligned_cols=14 Identities=50% Similarity=0.982 Sum_probs=9.9
Q ss_pred eccCchHHHHHHHh
Q 036854 109 IYFNHPLFGELLKQ 122 (167)
Q Consensus 109 ~yLnhPlF~eLL~~ 122 (167)
.|||||.|.-|..-
T Consensus 4 ~YLNHPtFGlLy~V 17 (88)
T PF12058_consen 4 TYLNHPTFGLLYRV 17 (88)
T ss_dssp -EEEETTTEEEEEE
T ss_pred ccccCCccchheee
Confidence 59999999766443
No 27
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=26.30 E-value=1.2e+02 Score=27.01 Aligned_cols=45 Identities=13% Similarity=0.248 Sum_probs=35.5
Q ss_pred EEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHhcCccCCCceeecCcHHHH
Q 036854 91 AVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERVYGFNHPGGITIPCRISEF 144 (167)
Q Consensus 91 aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~~~G~L~IPC~~~~F 144 (167)
.||+|. |+. .+|+...+.+||+...+.|.+..+..||+-|..+.+
T Consensus 58 tiy~GG--GTP-------s~l~~~~L~~ll~~i~~~f~~~~~~eit~E~~P~~i 102 (380)
T PRK09057 58 SIFFGG--GTP-------SLMQPETVAALLDAIARLWPVADDIEITLEANPTSV 102 (380)
T ss_pred eEEeCC--Ccc-------ccCCHHHHHHHHHHHHHhCCCCCCccEEEEECcCcC
Confidence 799984 232 578888999999999999988777779987766443
No 28
>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=26.26 E-value=89 Score=20.64 Aligned_cols=57 Identities=12% Similarity=0.204 Sum_probs=36.0
Q ss_pred CCCeEEEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHhcC-----ccCCCceeec-CcHHHHHHHHHHHhc
Q 036854 86 PKGHLAVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERVYG-----FNHPGGITIP-CRISEFEKVKTRIDA 153 (167)
Q Consensus 86 pkG~~aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEEfG-----f~~~G~L~IP-C~~~~Fe~vl~~i~~ 153 (167)
+.|++.|.+- +|.-.++-..+..|.+.| ++|| +.....|.|+ -+.+..+.|...|+.
T Consensus 6 ~~g~~~v~~~----------~~~G~i~~~~l~~la~ia-~~yg~~~irlT~~Q~l~l~~v~~~~~~~i~~~L~~ 68 (69)
T PF03460_consen 6 GDGFYMVRIR----------IPGGRISAEQLRALAEIA-EKYGDGEIRLTTRQNLQLRGVPEENLPAIFEELKE 68 (69)
T ss_dssp STTEEEEEEB-----------GGGEEEHHHHHHHHHHH-HHHSTSEEEEETTSCEEEEEEEGGGHHHHHHHHHH
T ss_pred CCeEEEEEEe----------CCCEEECHHHHHHHHHHH-HHhCCCeEEECCCCeEEEeCCCHHHHHHHHHHHHc
Confidence 3456666554 444557677777777777 4666 3445567766 777777777776653
No 29
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=25.30 E-value=1.4e+02 Score=26.97 Aligned_cols=55 Identities=9% Similarity=0.190 Sum_probs=40.6
Q ss_pred EEEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHhcCccCCCceeecCcHHHH-HHHHHHHhc
Q 036854 90 LAVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERVYGFNHPGGITIPCRISEF-EKVKTRIDA 153 (167)
Q Consensus 90 ~aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~~~G~L~IPC~~~~F-e~vl~~i~~ 153 (167)
-.||+|. |+. ++|+...+.+||+...+.|++..+-.||+-|....+ +..+..++.
T Consensus 64 ~tiy~GG--GTP-------s~l~~~~l~~ll~~i~~~~~~~~~~eitiE~nP~~~~~e~l~~l~~ 119 (390)
T PRK06582 64 KSIFFGG--GTP-------SLMNPVIVEGIINKISNLAIIDNQTEITLETNPTSFETEKFKAFKL 119 (390)
T ss_pred eEEEECC--Ccc-------ccCCHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCcCCHHHHHHHHH
Confidence 4799984 232 688899999999999998888776779998877655 344444443
No 30
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=24.99 E-value=1.7e+02 Score=26.83 Aligned_cols=58 Identities=12% Similarity=0.182 Sum_probs=41.6
Q ss_pred CCeEEEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHhcCccCCCceeecCcHHHH-HHHHHHHhc
Q 036854 87 KGHLAVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERVYGFNHPGGITIPCRISEF-EKVKTRIDA 153 (167)
Q Consensus 87 kG~~aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~~~G~L~IPC~~~~F-e~vl~~i~~ 153 (167)
.+...||+|. |+. ..|+.+.+.+|++...+.|++..+..+++-|+...+ +..+..++.
T Consensus 102 ~~v~~i~fgG--GTP-------s~l~~~~l~~ll~~i~~~~~~~~~~e~tie~~p~~lt~e~l~~L~~ 160 (453)
T PRK13347 102 RRVSQLHWGG--GTP-------TILNPDQFERLMAALRDAFDFAPEAEIAVEIDPRTVTAEMLQALAA 160 (453)
T ss_pred CeEEEEEEcC--ccc-------ccCCHHHHHHHHHHHHHhCCCCCCceEEEEeccccCCHHHHHHHHH
Confidence 3566788874 232 568899999999999999988766778888877655 334444444
No 31
>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=24.56 E-value=2.9e+02 Score=20.22 Aligned_cols=52 Identities=10% Similarity=0.096 Sum_probs=37.6
Q ss_pred CceeEEEeeeccCchHHHHHHHhhHHhcCcc---------CCCceeecCcHHHHHHHHHHHhcC
Q 036854 100 EARRVFVPVIYFNHPLFGELLKQAERVYGFN---------HPGGITIPCRISEFEKVKTRIDAW 154 (167)
Q Consensus 100 ~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~---------~~G~L~IPC~~~~Fe~vl~~i~~~ 154 (167)
+..||.+|- -.++-|.+|..+-+.-|+++ .+-+++|.|++++=| .+.+..+.
T Consensus 10 d~~rf~~~~--~~~~~~~~L~~ev~~rf~l~~f~lKYlDde~e~v~lssd~eLeE-~~rl~~~~ 70 (81)
T cd06396 10 ESQSFLVSD--SENTTWASVEAMVKVSFGLNDIQIKYVDEENEEVSVNSQGEYEE-ALKSAVRQ 70 (81)
T ss_pred eEEEEEecC--CCCCCHHHHHHHHHHHhCCCcceeEEEcCCCCEEEEEchhhHHH-HHHHHHhC
Confidence 789999874 22567999999999888854 236789999887644 55555544
No 32
>PF13778 DUF4174: Domain of unknown function (DUF4174)
Probab=24.26 E-value=48 Score=25.04 Aligned_cols=24 Identities=25% Similarity=0.357 Sum_probs=19.9
Q ss_pred CCCeEEEEEcccCCCceeEEEeee
Q 036854 86 PKGHLAVYVGESDDEARRVFVPVI 109 (167)
Q Consensus 86 pkG~~aVYVG~~~~~~rRfvVP~~ 109 (167)
+.++-+|.||++|+...||--|++
T Consensus 77 ~~~f~~vLiGKDG~vK~r~~~p~~ 100 (118)
T PF13778_consen 77 PGGFTVVLIGKDGGVKLRWPEPID 100 (118)
T ss_pred CCceEEEEEeCCCcEEEecCCCCC
Confidence 677788889998889999887764
No 33
>COG0635 HemN Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]
Probab=22.44 E-value=1.8e+02 Score=26.74 Aligned_cols=57 Identities=19% Similarity=0.294 Sum_probs=42.4
Q ss_pred CCeEEEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHhc-CccCCCceeecCcHHH--HHHHHHHHh
Q 036854 87 KGHLAVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERVY-GFNHPGGITIPCRISE--FEKVKTRID 152 (167)
Q Consensus 87 kG~~aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEEf-Gf~~~G~L~IPC~~~~--Fe~vl~~i~ 152 (167)
+-.-.||+|. |+. ++|+-..+..||+.-.+-| +.+.+--|||.++... .|.+..+-+
T Consensus 86 ~~v~ti~~GG--GTP-------slL~~~~l~~ll~~l~~~~~~~~~~~EitiE~nP~~~~~e~~~~l~~ 145 (416)
T COG0635 86 REVKTIYFGG--GTP-------SLLSPEQLERLLKALRELFNDLDPDAEITIEANPGTVEAEKFKALKE 145 (416)
T ss_pred CeEEEEEECC--Ccc-------ccCCHHHHHHHHHHHHHhcccCCCCceEEEEeCCCCCCHHHHHHHHH
Confidence 4567899984 243 7899999999999999999 5776788999987763 344433333
No 34
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=22.17 E-value=1.6e+02 Score=26.41 Aligned_cols=54 Identities=17% Similarity=0.256 Sum_probs=39.4
Q ss_pred EEEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHhcCccCCCceeecCcHHHH--HHHHHHHh
Q 036854 90 LAVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERVYGFNHPGGITIPCRISEF--EKVKTRID 152 (167)
Q Consensus 90 ~aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~~~G~L~IPC~~~~F--e~vl~~i~ 152 (167)
-.||+|. |+. .+|+...+.+|++...+.|.+..+-.|++-|....+ +.+..+.+
T Consensus 75 ~siy~GG--GTP-------s~L~~~~L~~ll~~i~~~~~~~~~~eit~E~~p~~~~~e~L~~l~~ 130 (394)
T PRK08898 75 HTVFIGG--GTP-------SLLSAAGLDRLLSDVRALLPLDPDAEITLEANPGTFEAEKFAQFRA 130 (394)
T ss_pred eEEEECC--CCc-------CCCCHHHHHHHHHHHHHhCCCCCCCeEEEEECCCCCCHHHHHHHHH
Confidence 3789984 233 678889999999999999988766788888865444 54444433
No 35
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=21.87 E-value=3.2e+02 Score=23.77 Aligned_cols=62 Identities=18% Similarity=0.313 Sum_probs=41.1
Q ss_pred CCeEEEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHhcCccCC---------------CceeecCcHHHHHHHHHHH
Q 036854 87 KGHLAVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERVYGFNHP---------------GGITIPCRISEFEKVKTRI 151 (167)
Q Consensus 87 kG~~aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~~~---------------G~L~IPC~~~~Fe~vl~~i 151 (167)
.|.+.|.-.. +...+.|-++.-.-|...+++.....-|+++.| -+|.||...+.||-+++.|
T Consensus 45 ~~~~~v~~~~---~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L~~~~~~~~GlR~p~~~d~fE~lv~aI 121 (283)
T PRK10308 45 RGVVTVIPDI---ARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGKLGAARPGLRLPGSVDAFEQGVRAI 121 (283)
T ss_pred cEEEEEEEcC---CCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCCcCCCCCCHHHHHHHHH
Confidence 4555555432 344555655553345566788888888887765 2488999999999887765
No 36
>PLN02752 [acyl-carrier protein] S-malonyltransferase
Probab=21.38 E-value=1.1e+02 Score=26.65 Aligned_cols=44 Identities=14% Similarity=0.224 Sum_probs=27.7
Q ss_pred CCCCCeEEEEEcccCCCceeEEEeeeccCchHHHHHHHhhHHhcCcc
Q 036854 84 EVPKGHLAVYVGESDDEARRVFVPVIYFNHPLFGELLKQAERVYGFN 130 (167)
Q Consensus 84 ~vpkG~~aVYVG~~~~~~rRfvVP~~yLnhPlF~eLL~~AeEEfGf~ 130 (167)
..+.-.+.+|-|++ . +..-.=-+|.++|.|+++++++++-.|++
T Consensus 35 ~~~~~~a~lFpGQG--s-q~~gm~~~~~~~p~~~~~~~~~~~~lg~~ 78 (343)
T PLN02752 35 DYKPTTAFLFPGQG--A-QAVGMGKEAAEVPAAKALFDKASEILGYD 78 (343)
T ss_pred CCCCCEEEEECCCC--c-chhhHHHHHHhCHHHHHHHHHHHHHhCCC
Confidence 33444555666752 1 11111123678999999999999988865
No 37
>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=20.60 E-value=1.3e+02 Score=21.75 Aligned_cols=43 Identities=16% Similarity=0.283 Sum_probs=34.2
Q ss_pred CCCeEEEEEccc-CCCceeEEEeeeccCchHH---HHHHHhhHHhcC
Q 036854 86 PKGHLAVYVGES-DDEARRVFVPVIYFNHPLF---GELLKQAERVYG 128 (167)
Q Consensus 86 pkG~~aVYVG~~-~~~~rRfvVP~~yLnhPlF---~eLL~~AeEEfG 128 (167)
++-+.+.|.|.. .-....+.+...|+.|+.+ |.|+++|.|.|.
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 666788888964 2334778888999999999 489999999875
Done!