Query 030768
Match_columns 171
No_of_seqs 190 out of 631
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 04:17:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030768.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030768hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02519 Auxin_inducible: Auxi 100.0 1.6E-34 3.4E-39 217.2 9.6 95 49-155 6-100 (100)
2 PLN03090 auxin-responsive fami 100.0 3.3E-34 7.2E-39 217.7 10.2 92 47-154 12-103 (104)
3 PLN03220 uncharacterized prote 100.0 2E-31 4.3E-36 202.6 9.7 69 84-152 31-101 (105)
4 PLN03219 uncharacterized prote 100.0 6.1E-31 1.3E-35 200.8 11.1 71 82-153 33-104 (108)
5 PF02214 BTB_2: BTB/POZ domain 87.4 1.1 2.3E-05 31.9 4.1 54 104-157 7-63 (94)
6 PRK02899 adaptor protein; Prov 82.7 0.97 2.1E-05 37.7 2.3 25 116-140 38-62 (197)
7 cd05992 PB1 The PB1 domain is 77.8 15 0.00033 24.9 6.7 50 103-156 10-70 (81)
8 PRK02315 adaptor protein; Prov 76.9 1.8 3.9E-05 36.8 2.2 25 116-140 38-62 (233)
9 smart00666 PB1 PB1 domain. Pho 74.9 15 0.00032 25.2 6.1 50 103-157 11-71 (81)
10 PF05389 MecA: Negative regula 72.7 1.2 2.5E-05 37.1 0.0 25 116-140 38-62 (220)
11 PRK02797 4-alpha-L-fucosyltran 65.7 24 0.00052 32.1 6.8 69 87-158 141-228 (322)
12 PF07429 Glyco_transf_56: 4-al 64.8 24 0.00051 32.6 6.7 69 87-158 180-267 (360)
13 PF11834 DUF3354: Domain of un 50.9 28 0.00061 24.7 3.8 17 117-133 26-42 (69)
14 cd06398 PB1_Joka2 The PB1 doma 49.9 73 0.0016 23.5 6.0 51 102-152 9-72 (91)
15 PF02209 VHP: Villin headpiece 41.2 10 0.00022 23.9 0.3 19 113-131 1-19 (36)
16 smart00153 VHP Villin headpiec 39.9 12 0.00026 23.5 0.4 19 113-131 1-19 (36)
17 PF12058 DUF3539: Protein of u 34.0 11 0.00023 28.5 -0.5 13 112-124 4-16 (88)
18 cd01406 SIR2-like Sir2-like: P 33.3 92 0.002 25.7 4.8 60 91-159 1-60 (242)
19 cd06397 PB1_UP1 Uncharacterize 32.7 1.2E+02 0.0025 22.7 4.7 48 102-154 9-67 (82)
20 cd06407 PB1_NLP A PB1 domain i 31.9 94 0.002 22.4 4.1 45 103-151 10-66 (82)
21 cd06396 PB1_NBR1 The PB1 domai 30.5 2.2E+02 0.0048 20.9 6.2 54 102-158 9-71 (81)
22 cd06410 PB1_UP2 Uncharacterize 30.1 1.1E+02 0.0024 22.9 4.4 46 94-146 17-75 (97)
23 PF00651 BTB: BTB/POZ domain; 27.1 1.7E+02 0.0037 20.1 4.8 50 104-157 20-74 (111)
24 PF11822 DUF3342: Domain of un 26.4 81 0.0017 28.7 3.6 53 103-158 12-69 (317)
25 cd02393 PNPase_KH Polynucleoti 25.0 2E+02 0.0043 19.1 4.6 50 86-154 6-60 (61)
26 PF14317 YcxB: YcxB-like prote 24.1 1.3E+02 0.0028 18.6 3.4 33 88-124 27-59 (62)
27 cd06399 PB1_P40 The PB1 domain 24.1 3.3E+02 0.0071 20.7 6.9 64 105-170 16-88 (92)
28 PF10087 DUF2325: Uncharacteri 23.9 2.5E+02 0.0054 20.0 5.2 46 105-154 50-96 (97)
29 PLN02752 [acyl-carrier protein 23.8 67 0.0015 28.0 2.5 46 85-133 33-78 (343)
30 PF09186 DUF1949: Domain of un 22.9 50 0.0011 20.7 1.2 49 110-160 2-55 (56)
31 COG4862 MecA Negative regulato 22.7 50 0.0011 28.7 1.5 27 115-141 37-63 (224)
32 PF04304 DUF454: Protein of un 22.4 62 0.0013 22.0 1.7 21 113-133 5-25 (71)
33 KOG4209 Splicing factor RNPS1, 22.2 33 0.00071 29.4 0.3 44 103-146 95-139 (231)
34 PRK10308 3-methyl-adenine DNA 20.7 3.5E+02 0.0076 23.6 6.4 64 90-156 45-123 (283)
35 PF07104 DUF1366: Protein of u 20.3 1.5E+02 0.0033 23.1 3.6 41 88-130 16-56 (116)
36 PF02100 ODC_AZ: Ornithine dec 20.2 67 0.0015 24.4 1.6 38 113-151 37-74 (108)
No 1
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=100.00 E-value=1.6e-34 Score=217.24 Aligned_cols=95 Identities=41% Similarity=0.723 Sum_probs=77.9
Q ss_pred HHHHHHHHHHhhHhhhccCCCCCCCccCCCCCCCcCCCCCCCCeEEEEEcccCCcceEEEEEeeccCChhHHHHHHHHHH
Q 030768 49 KLISWGRRLTNGAKSLCLAKPASGYVPMDQDPIREKPVSVPKGHLAVYVGQKDGDFHRVLVPVIYFNHPLFGKLLRDAEE 128 (171)
Q Consensus 49 KL~~~~rKwq~~A~~~rk~~s~~~~~r~~~~~~~s~~~~vpkG~~aVYVG~~~~d~rRFvVP~~yLnhPlF~eLL~~aeE 128 (171)
|.++.++||++.++..++..+ . .+ .++..++|+||||||||+ +++||+||++|||||+|++||++|||
T Consensus 6 k~~~~~~k~~~~~~~~~~~~~---~----~~--~~~~~~vp~G~~~VyVG~---~~~Rfvvp~~~L~hp~f~~LL~~aee 73 (100)
T PF02519_consen 6 KSLASAKKWQSRARSKSSSSS---S----SR--SSSESDVPKGHFAVYVGE---ERRRFVVPVSYLNHPLFQELLEQAEE 73 (100)
T ss_pred HHHHHHHhhhhhhhhcccccc---c----cc--ccccCCCCCCeEEEEeCc---cceEEEechHHcCchhHHHHHHHHhh
Confidence 445555788777655544322 0 00 112367999999999997 79999999999999999999999999
Q ss_pred hcCccCCCceEecCcHHHHHHHHHHHH
Q 030768 129 EYGFNQQGGITIPCRFSEFEQVQTRIA 155 (171)
Q Consensus 129 EfGf~~~G~LtIPCd~~~Fe~vl~~i~ 155 (171)
||||+++|+|+||||+++||+++|+|+
T Consensus 74 EfG~~~~G~l~iPC~~~~Fe~~l~~le 100 (100)
T PF02519_consen 74 EFGFDQDGPLTIPCDVVLFEHLLWLLE 100 (100)
T ss_pred hcCcCCCCcEEeeCCHHHHHHHHHHhC
Confidence 999999999999999999999999985
No 2
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=3.3e-34 Score=217.69 Aligned_cols=92 Identities=41% Similarity=0.767 Sum_probs=79.3
Q ss_pred hhHHHHHHHHHHhhHhhhccCCCCCCCccCCCCCCCcCCCCCCCCeEEEEEcccCCcceEEEEEeeccCChhHHHHHHHH
Q 030768 47 ISKLISWGRRLTNGAKSLCLAKPASGYVPMDQDPIREKPVSVPKGHLAVYVGQKDGDFHRVLVPVIYFNHPLFGKLLRDA 126 (171)
Q Consensus 47 l~KL~~~~rKwq~~A~~~rk~~s~~~~~r~~~~~~~s~~~~vpkG~~aVYVG~~~~d~rRFvVP~~yLnhPlF~eLL~~a 126 (171)
+..|+++.++|.++++.. ++ +++. .+.+||+||||||||+ +++||+||++|||||+|++||++|
T Consensus 12 ~~~~kq~l~r~~s~~~~~-------~~---~~~~---~~~~vpkG~~aVyVG~---~~~RfvVp~~~L~hP~F~~LL~~a 75 (104)
T PLN03090 12 TAMLKQILKRCSSLGKKQ-------GY---DEDG---LPLDVPKGHFPVYVGE---NRSRYIVPISFLTHPEFQSLLQQA 75 (104)
T ss_pred HHHHHHHHHHHHHhcccC-------Cc---cccc---CCCCCCCCcEEEEECC---CCEEEEEEHHHcCCHHHHHHHHHH
Confidence 567889999998774421 11 1111 4678999999999997 689999999999999999999999
Q ss_pred HHhcCccCCCceEecCcHHHHHHHHHHH
Q 030768 127 EEEYGFNQQGGITIPCRFSEFEQVQTRI 154 (171)
Q Consensus 127 eEEfGf~~~G~LtIPCd~~~Fe~vl~~i 154 (171)
||||||+|+|+|+||||+++||+++|+|
T Consensus 76 eeEfGf~~~G~L~IPC~~~~Fe~ll~~i 103 (104)
T PLN03090 76 EEEFGFDHDMGLTIPCEEVVFRSLTSMI 103 (104)
T ss_pred HHHhCCCCCCcEEEeCCHHHHHHHHHHh
Confidence 9999999999999999999999999998
No 3
>PLN03220 uncharacterized protein; Provisional
Probab=99.97 E-value=2e-31 Score=202.59 Aligned_cols=69 Identities=48% Similarity=0.877 Sum_probs=63.2
Q ss_pred CCCCCCCCeEEEEEcccC-CcceEEEEEeeccCChhHHHHHHHHHHhcCccC-CCceEecCcHHHHHHHHH
Q 030768 84 KPVSVPKGHLAVYVGQKD-GDFHRVLVPVIYFNHPLFGKLLRDAEEEYGFNQ-QGGITIPCRFSEFEQVQT 152 (171)
Q Consensus 84 ~~~~vpkG~~aVYVG~~~-~d~rRFvVP~~yLnhPlF~eLL~~aeEEfGf~~-~G~LtIPCd~~~Fe~vl~ 152 (171)
.+++|||||||||||+++ .+++||+||++|||||+|++||++|||||||+| +|+|+||||++.|++++.
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 456899999999999732 358999999999999999999999999999998 599999999999999985
No 4
>PLN03219 uncharacterized protein; Provisional
Probab=99.97 E-value=6.1e-31 Score=200.76 Aligned_cols=71 Identities=49% Similarity=0.883 Sum_probs=64.7
Q ss_pred CcCCCCCCCCeEEEEEcccCCcceEEEEEeeccCChhHHHHHHHHHHhcCccC-CCceEecCcHHHHHHHHHH
Q 030768 82 REKPVSVPKGHLAVYVGQKDGDFHRVLVPVIYFNHPLFGKLLRDAEEEYGFNQ-QGGITIPCRFSEFEQVQTR 153 (171)
Q Consensus 82 ~s~~~~vpkG~~aVYVG~~~~d~rRFvVP~~yLnhPlF~eLL~~aeEEfGf~~-~G~LtIPCd~~~Fe~vl~~ 153 (171)
++++.+|||||||||||+. ++++||+||++|||||+|++||++|||||||+| +|+|+||||++.|++++..
T Consensus 33 ~~~~~~vpkGh~aVYVG~~-~E~kRFvVPi~yL~hP~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~~ 104 (108)
T PLN03219 33 TTTSGLVPKGHVAVYVGEQ-MEKKRFVVPISYLNHPLFREFLNRAEEECGFHHSMGGLTIPCREESFLHLITS 104 (108)
T ss_pred CCCCCCCCCCeEEEEECCC-CCceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEEeCCHHHHHHHHHh
Confidence 3356789999999999973 368999999999999999999999999999997 5999999999999999875
No 5
>PF02214 BTB_2: BTB/POZ domain; InterPro: IPR003131 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. The Kv family can be divided into several subfamilies on the basis of sequence similarity and function. Four of these subfamilies, Kv1 (Shaker), Kv2 (Shab), Kv3 (Shaw) and Kv4 (Shal), consist of pore-forming alpha subunits that associate with different types of beta subunit. Each alpha subunit comprises six hydrophobic TM domains with a P-domain between the fifth and sixth, which partially resides in the membrane. The fourth TM domain has positively charged residues at every third residue and acts as a voltage sensor, which triggers the conformational change that opens the channel pore in response to a displacement in membrane potential []. More recently, 4 new electrically-silent alpha subunits have been cloned: Kv5 (KCNF), Kv6 (KCNG), Kv8 and Kv9 (KCNS). These subunits do not themselves possess any functional activity, but appear to form heteromeric channels with Kv2 subunits, and thus modulate Shab channel activity []. When highly expressed, they inhibit channel activity, but at lower levels show more specific modulatory actions. The N-terminal, cytoplasmic tetramerization domain (T1) of voltage-gated potassium channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels []. This domain is found in a subset of a larger group of proteins that contain the BTB/POZ domain.; GO: 0005249 voltage-gated potassium channel activity, 0006813 potassium ion transport, 0008076 voltage-gated potassium channel complex, 0016020 membrane; PDB: 1NN7_A 3KVT_A 1EXB_E 1QDV_A 1DSX_E 1QDW_F 3LUT_B 3LNM_B 2A79_B 3DRY_C ....
Probab=87.43 E-value=1.1 Score=31.92 Aligned_cols=54 Identities=13% Similarity=0.074 Sum_probs=42.4
Q ss_pred ceEEEEEeeccC-C--hhHHHHHHHHHHhcCccCCCceEecCcHHHHHHHHHHHHcC
Q 030768 104 FHRVLVPVIYFN-H--PLFGKLLRDAEEEYGFNQQGGITIPCRFSEFEQVQTRIAAG 157 (171)
Q Consensus 104 ~rRFvVP~~yLn-h--PlF~eLL~~aeEEfGf~~~G~LtIPCd~~~Fe~vl~~i~~~ 157 (171)
.+.|.++.+.|. + ..|..|+........-+.+|.+-|-++...|++|+.-+..+
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 389999999888 4 48999988653222234569999999999999999999985
No 6
>PRK02899 adaptor protein; Provisional
Probab=82.72 E-value=0.97 Score=37.70 Aligned_cols=25 Identities=36% Similarity=0.828 Sum_probs=21.6
Q ss_pred ChhHHHHHHHHHHhcCccCCCceEe
Q 030768 116 HPLFGKLLRDAEEEYGFNQQGGITI 140 (171)
Q Consensus 116 hPlF~eLL~~aeEEfGf~~~G~LtI 140 (171)
+-+|.++|++|..|+||..+|||+|
T Consensus 38 e~lF~~mm~Ea~~e~~F~~~~pl~~ 62 (197)
T PRK02899 38 HQLFRDMMQEANKELGFEADGPIAV 62 (197)
T ss_pred HHHHHHHHHHhhhccCcccCCeEEE
Confidence 3577888999999999999999875
No 7
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=77.77 E-value=15 Score=24.93 Aligned_cols=50 Identities=18% Similarity=0.337 Sum_probs=39.0
Q ss_pred cceEEEEEeeccCChhHHHHHHHHHHhcCcc----------CC-CceEecCcHHHHHHHHHHHHc
Q 030768 103 DFHRVLVPVIYFNHPLFGKLLRDAEEEYGFN----------QQ-GGITIPCRFSEFEQVQTRIAA 156 (171)
Q Consensus 103 d~rRFvVP~~yLnhPlF~eLL~~aeEEfGf~----------~~-G~LtIPCd~~~Fe~vl~~i~~ 156 (171)
+.+||.+|. .++.|.+|..+..+.|++. .+ ..++|.++ +.|+.++.....
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 789999998 8999999999999999875 13 34667666 567777777765
No 8
>PRK02315 adaptor protein; Provisional
Probab=76.90 E-value=1.8 Score=36.84 Aligned_cols=25 Identities=20% Similarity=0.466 Sum_probs=22.7
Q ss_pred ChhHHHHHHHHHHhcCccCCCceEe
Q 030768 116 HPLFGKLLRDAEEEYGFNQQGGITI 140 (171)
Q Consensus 116 hPlF~eLL~~aeEEfGf~~~G~LtI 140 (171)
+-+|.++|++|..|+||..+|||+|
T Consensus 38 e~fF~~mm~Ea~~e~~F~~~~pl~~ 62 (233)
T PRK02315 38 EEFFYSMMDEVDEEDDFADEGPLWF 62 (233)
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 4589999999999999999999986
No 9
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=74.88 E-value=15 Score=25.22 Aligned_cols=50 Identities=16% Similarity=0.328 Sum_probs=38.3
Q ss_pred cceEEEEEeeccCChhHHHHHHHHHHhcCcc----------CCC-ceEecCcHHHHHHHHHHHHcC
Q 030768 103 DFHRVLVPVIYFNHPLFGKLLRDAEEEYGFN----------QQG-GITIPCRFSEFEQVQTRIAAG 157 (171)
Q Consensus 103 d~rRFvVP~~yLnhPlF~eLL~~aeEEfGf~----------~~G-~LtIPCd~~~Fe~vl~~i~~~ 157 (171)
+.++|.||- .+.|.+|..+..+.|++. .+| .++|.++. .++.++.+....
T Consensus 11 ~~~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~-Dl~~a~~~~~~~ 71 (81)
T smart00666 11 ETRRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDE-DLEEAIEEYDSL 71 (81)
T ss_pred EEEEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHH-HHHHHHHHHHHc
Confidence 789999885 888999999999998874 234 68899976 556666666543
No 10
>PF05389 MecA: Negative regulator of genetic competence (MecA); InterPro: IPR008681 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. This family contains several bacterial MecA proteins. In complex media competence development is poor, and there is little or no expression of late competence genes. Overexpression of MecA inhibits comG transcription [, , ]. MecA enables the recognition and targeting of unfolded and aggregated proteins to the ClpC protease or to other proteins involved in proteolysis. Acts negatively in the development of competence by binding ComK and recruiting it to the ClpCP protease. When overexpressed, inhibits sporulation. Also involved in Spx degradation by ClpC. ; PDB: 3JTP_C 2Y1R_O 3PXI_c 3PXG_b 3JTO_D 3JTN_A.
Probab=72.68 E-value=1.2 Score=37.08 Aligned_cols=25 Identities=36% Similarity=0.699 Sum_probs=0.0
Q ss_pred ChhHHHHHHHHHHhcCccCCCceEe
Q 030768 116 HPLFGKLLRDAEEEYGFNQQGGITI 140 (171)
Q Consensus 116 hPlF~eLL~~aeEEfGf~~~G~LtI 140 (171)
+-+|.++|++|.+|+||..+|||++
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 11
>PRK02797 4-alpha-L-fucosyltransferase; Provisional
Probab=65.74 E-value=24 Score=32.11 Aligned_cols=69 Identities=17% Similarity=0.329 Sum_probs=48.5
Q ss_pred CCCCCeEEEEEcccC-----------------CcceEEEEEeec--cCChhHHHHHHHHHHhcCccCCCceEecCcHHHH
Q 030768 87 SVPKGHLAVYVGQKD-----------------GDFHRVLVPVIY--FNHPLFGKLLRDAEEEYGFNQQGGITIPCRFSEF 147 (171)
Q Consensus 87 ~vpkG~~aVYVG~~~-----------------~d~rRFvVP~~y--LnhPlF~eLL~~aeEEfGf~~~G~LtIPCd~~~F 147 (171)
..+++.+.|.||..+ ++.-|++||++| =|..-.++..+.+.|-|| .+-+++==+.-.|
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 456788999999743 355699999999 454455555555666676 3456665666778
Q ss_pred HHHHHHHHcCC
Q 030768 148 EQVQTRIAAGN 158 (171)
Q Consensus 148 e~vl~~i~~~~ 158 (171)
+..+..|++.|
T Consensus 218 ~eYl~lL~~~D 228 (322)
T PRK02797 218 DDYLALLRQCD 228 (322)
T ss_pred HHHHHHHHhCC
Confidence 88888887765
No 12
>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=64.76 E-value=24 Score=32.62 Aligned_cols=69 Identities=22% Similarity=0.455 Sum_probs=50.1
Q ss_pred CCCCCeEEEEEcccC-----------------CcceEEEEEeeccC--ChhHHHHHHHHHHhcCccCCCceEecCcHHHH
Q 030768 87 SVPKGHLAVYVGQKD-----------------GDFHRVLVPVIYFN--HPLFGKLLRDAEEEYGFNQQGGITIPCRFSEF 147 (171)
Q Consensus 87 ~vpkG~~aVYVG~~~-----------------~d~rRFvVP~~yLn--hPlF~eLL~~aeEEfGf~~~G~LtIPCd~~~F 147 (171)
..+++-..|.||..+ ++..+++||++|=. ..-..++.+.+++-|| ++-+.+==+.--|
T Consensus 180 ~~~~~~ltILvGNSgd~sNnHieaL~~L~~~~~~~~kIivPLsYg~~n~~Yi~~V~~~~~~lF~---~~~~~iL~e~mpf 256 (360)
T PF07429_consen 180 KKNKGKLTILVGNSGDPSNNHIEALEALKQQFGDDVKIIVPLSYGANNQAYIQQVIQAGKELFG---AENFQILTEFMPF 256 (360)
T ss_pred cCCCCceEEEEcCCCCCCccHHHHHHHHHHhcCCCeEEEEECCCCCchHHHHHHHHHHHHHhcC---ccceeEhhhhCCH
Confidence 356788999998743 46789999999963 5677777777777787 3344444456667
Q ss_pred HHHHHHHHcCC
Q 030768 148 EQVQTRIAAGN 158 (171)
Q Consensus 148 e~vl~~i~~~~ 158 (171)
+..+..+++.+
T Consensus 257 ~eYl~lL~~cD 267 (360)
T PF07429_consen 257 DEYLALLSRCD 267 (360)
T ss_pred HHHHHHHHhCC
Confidence 88888887776
No 13
>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=50.89 E-value=28 Score=24.74 Aligned_cols=17 Identities=35% Similarity=0.657 Sum_probs=15.3
Q ss_pred hhHHHHHHHHHHhcCcc
Q 030768 117 PLFGKLLRDAEEEYGFN 133 (171)
Q Consensus 117 PlF~eLL~~aeEEfGf~ 133 (171)
-.++|||+.|++.||+.
T Consensus 26 ~SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 26 DSLEELLKIASEKFGFS 42 (69)
T ss_pred ccHHHHHHHHHHHhCCC
Confidence 47899999999999985
No 14
>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=49.90 E-value=73 Score=23.52 Aligned_cols=51 Identities=20% Similarity=0.219 Sum_probs=36.4
Q ss_pred CcceEEEEEee-ccCChhHHHHHHHHHHhcCccC-----------CC-ceEecCcHHHHHHHHH
Q 030768 102 GDFHRVLVPVI-YFNHPLFGKLLRDAEEEYGFNQ-----------QG-GITIPCRFSEFEQVQT 152 (171)
Q Consensus 102 ~d~rRFvVP~~-yLnhPlF~eLL~~aeEEfGf~~-----------~G-~LtIPCd~~~Fe~vl~ 152 (171)
++.+||-+|.. --.+.-|.+|.++-++-|.... +| -++|.||.++-+-+-.
T Consensus 9 ~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~ 72 (91)
T cd06398 9 GTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQY 72 (91)
T ss_pred CEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHH
Confidence 48999999974 0114588999999888777653 23 4789999887765443
No 15
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=41.19 E-value=10 Score=23.88 Aligned_cols=19 Identities=26% Similarity=0.450 Sum_probs=15.4
Q ss_pred ccCChhHHHHHHHHHHhcC
Q 030768 113 YFNHPLFGKLLRDAEEEYG 131 (171)
Q Consensus 113 yLnhPlF~eLL~~aeEEfG 131 (171)
||+...|++++.|+.+||.
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 7899999999999999974
No 16
>smart00153 VHP Villin headpiece domain.
Probab=39.94 E-value=12 Score=23.52 Aligned_cols=19 Identities=21% Similarity=0.406 Sum_probs=17.0
Q ss_pred ccCChhHHHHHHHHHHhcC
Q 030768 113 YFNHPLFGKLLRDAEEEYG 131 (171)
Q Consensus 113 yLnhPlF~eLL~~aeEEfG 131 (171)
||+...|++++.|+.+||-
T Consensus 1 yLsdeeF~~vfgmsr~eF~ 19 (36)
T smart00153 1 YLSDEDFEEVFGMTREEFY 19 (36)
T ss_pred CCCHHHHHHHHCCCHHHHH
Confidence 7899999999999999973
No 17
>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=34.03 E-value=11 Score=28.45 Aligned_cols=13 Identities=62% Similarity=1.165 Sum_probs=9.7
Q ss_pred eccCChhHHHHHH
Q 030768 112 IYFNHPLFGKLLR 124 (171)
Q Consensus 112 ~yLnhPlF~eLL~ 124 (171)
.|||||.|.-|..
T Consensus 4 ~YLNHPtFGlLy~ 16 (88)
T PF12058_consen 4 TYLNHPTFGLLYR 16 (88)
T ss_dssp -EEEETTTEEEEE
T ss_pred ccccCCccchhee
Confidence 5999999976643
No 18
>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=33.31 E-value=92 Score=25.66 Aligned_cols=60 Identities=17% Similarity=0.281 Sum_probs=37.9
Q ss_pred CeEEEEEcccCCcceEEEEEeeccCChhHHHHHHHHHHhcCccCCCceEecCcHHHHHHHHHHHHcCCC
Q 030768 91 GHLAVYVGQKDGDFHRVLVPVIYFNHPLFGKLLRDAEEEYGFNQQGGITIPCRFSEFEQVQTRIAAGNG 159 (171)
Q Consensus 91 G~~aVYVG~~~~d~rRFvVP~~yLnhPlF~eLL~~aeEEfGf~~~G~LtIPCd~~~Fe~vl~~i~~~~~ 159 (171)
|+++++||-+ -+.. .+-|.+.+|++...+|++.+.+....-.=+...+..+..++....+
T Consensus 1 g~lvlFiGAG-~S~~--------~glP~W~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ 60 (242)
T cd01406 1 GRVVIFVGAG-VSVS--------SGLPDWKTLLDEIASELGLEIDGYSVEAKDENDYLELAELLEKEFG 60 (242)
T ss_pred CCEEEEecCc-cccc--------cCCCChHHHHHHHHHHcCCccchhhccccchhhHHHHHHHHHHHhc
Confidence 7889999962 1211 5789999999999999987644211100134555566666655443
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=32.75 E-value=1.2e+02 Score=22.67 Aligned_cols=48 Identities=21% Similarity=0.299 Sum_probs=36.3
Q ss_pred CcceEEEEEeeccCChhHHHHHHHHHHhcCcc----------CC-CceEecCcHHHHHHHHHHH
Q 030768 102 GDFHRVLVPVIYFNHPLFGKLLRDAEEEYGFN----------QQ-GGITIPCRFSEFEQVQTRI 154 (171)
Q Consensus 102 ~d~rRFvVP~~yLnhPlF~eLL~~aeEEfGf~----------~~-G~LtIPCd~~~Fe~vl~~i 154 (171)
++.+||.+|. -|.+.+|-++-+.=|-+. .| ..|||.=+.++.+ ++...
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 4899999998 899999999998877665 23 4688887776665 44433
No 20
>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=31.88 E-value=94 Score=22.42 Aligned_cols=45 Identities=13% Similarity=0.227 Sum_probs=33.5
Q ss_pred cceEEEEEeeccCChhHHHHHHHHHHhcCccC------------CCceEecCcHHHHHHHH
Q 030768 103 DFHRVLVPVIYFNHPLFGKLLRDAEEEYGFNQ------------QGGITIPCRFSEFEQVQ 151 (171)
Q Consensus 103 d~rRFvVP~~yLnhPlF~eLL~~aeEEfGf~~------------~G~LtIPCd~~~Fe~vl 151 (171)
|..||-||. ..-|++|.++-.+-|++.. +..++|.|+.++=|-+-
T Consensus 10 d~~r~~l~~----~~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~eai~ 66 (82)
T cd06407 10 EKIRFRLPP----SWGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEECID 66 (82)
T ss_pred eEEEEEcCC----CCCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHHHH
Confidence 789998885 3479999999888877642 24688999988766443
No 21
>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=30.46 E-value=2.2e+02 Score=20.88 Aligned_cols=54 Identities=9% Similarity=0.145 Sum_probs=38.9
Q ss_pred CcceEEEEEeeccCChhHHHHHHHHHHhcCcc---------CCCceEecCcHHHHHHHHHHHHcCC
Q 030768 102 GDFHRVLVPVIYFNHPLFGKLLRDAEEEYGFN---------QQGGITIPCRFSEFEQVQTRIAAGN 158 (171)
Q Consensus 102 ~d~rRFvVP~~yLnhPlF~eLL~~aeEEfGf~---------~~G~LtIPCd~~~Fe~vl~~i~~~~ 158 (171)
+|..||.+|- -.++.|.+|..+-+.-|+++ .+-+++|.|++++= ..+.+..+..
T Consensus 9 ~d~~rf~~~~--~~~~~~~~L~~ev~~rf~l~~f~lKYlDde~e~v~lssd~eLe-E~~rl~~~~~ 71 (81)
T cd06396 9 GESQSFLVSD--SENTTWASVEAMVKVSFGLNDIQIKYVDEENEEVSVNSQGEYE-EALKSAVRQG 71 (81)
T ss_pred CeEEEEEecC--CCCCCHHHHHHHHHHHhCCCcceeEEEcCCCCEEEEEchhhHH-HHHHHHHhCC
Confidence 3789999874 23668999999999988854 23578999988754 4555555443
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=30.08 E-value=1.1e+02 Score=22.85 Aligned_cols=46 Identities=22% Similarity=0.196 Sum_probs=33.4
Q ss_pred EEEEcccCCcceEEEEEeeccCChhHHHHHHHHHHhcCccC-------------CCceEecCcHHH
Q 030768 94 AVYVGQKDGDFHRVLVPVIYFNHPLFGKLLRDAEEEYGFNQ-------------QGGITIPCRFSE 146 (171)
Q Consensus 94 aVYVG~~~~d~rRFvVP~~yLnhPlF~eLL~~aeEEfGf~~-------------~G~LtIPCd~~~ 146 (171)
.=|||. +.+-..||-+ ..|.||..+..+.++... ++-+.|.||.++
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 579985 6777777765 477888888888877655 346778888743
No 23
>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=27.10 E-value=1.7e+02 Score=20.13 Aligned_cols=50 Identities=20% Similarity=0.349 Sum_probs=35.6
Q ss_pred ceEEEEEeecc--CChhHHHHHHHHHHhcCccCCC--ceEec-CcHHHHHHHHHHHHcC
Q 030768 104 FHRVLVPVIYF--NHPLFGKLLRDAEEEYGFNQQG--GITIP-CRFSEFEQVQTRIAAG 157 (171)
Q Consensus 104 ~rRFvVP~~yL--nhPlF~eLL~~aeEEfGf~~~G--~LtIP-Cd~~~Fe~vl~~i~~~ 157 (171)
..+|-|.-..| ..|.|..+++... ...++ .|.++ ++...|+.++..+=.+
T Consensus 20 ~~~~~vhk~iL~~~S~~F~~~~~~~~----~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~ 74 (111)
T PF00651_consen 20 GKTFYVHKNILAARSPYFRNLFEGSK----FKESTVPEISLPDVSPEAFEAFLEYMYTG 74 (111)
T ss_dssp TEEEEE-HHHHHHHBHHHHHHHTTTT----STTSSEEEEEETTSCHHHHHHHHHHHHHS
T ss_pred CEEEeechhhhhccchhhhhcccccc----cccccccccccccccccccccccccccCC
Confidence 58888887777 4699999998881 12233 46655 8899999999887544
No 24
>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=26.35 E-value=81 Score=28.68 Aligned_cols=53 Identities=13% Similarity=0.256 Sum_probs=40.6
Q ss_pred cceEEEEEeeccCC--hhHHHHHHH---HHHhcCccCCCceEecCcHHHHHHHHHHHHcCC
Q 030768 103 DFHRVLVPVIYFNH--PLFGKLLRD---AEEEYGFNQQGGITIPCRFSEFEQVQTRIAAGN 158 (171)
Q Consensus 103 d~rRFvVP~~yLnh--PlF~eLL~~---aeEEfGf~~~G~LtIPCd~~~Fe~vl~~i~~~~ 158 (171)
..+=|..|.+.|-. .-|+++|.. ..++. .+=.|.+-||+..|+-+|.-++...
T Consensus 12 ~~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~---~~idisVhCDv~iF~WLm~yv~~~~ 69 (317)
T PF11822_consen 12 EKRDFTCPRDLLVSEMRYFAEYLSRYINDSQRW---EEIDISVHCDVHIFEWLMRYVKGEP 69 (317)
T ss_pred cceeeeccHHHHHHhhHHHHHHHhhcccccCcC---CCcceEEecChhHHHHHHHHhhcCC
Confidence 56779999988854 669999965 33332 2457899999999999999998743
No 25
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=25.03 E-value=2e+02 Score=19.13 Aligned_cols=50 Identities=20% Similarity=0.357 Sum_probs=37.0
Q ss_pred CCCCCCeEEEEEcccCCcceEEEEEeeccCChhHHHHHHHHHHhcCc----cCCCceEecCc-HHHHHHHHHHH
Q 030768 86 VSVPKGHLAVYVGQKDGDFHRVLVPVIYFNHPLFGKLLRDAEEEYGF----NQQGGITIPCR-FSEFEQVQTRI 154 (171)
Q Consensus 86 ~~vpkG~~aVYVG~~~~d~rRFvVP~~yLnhPlF~eLL~~aeEEfGf----~~~G~LtIPCd-~~~Fe~vl~~i 154 (171)
..+|.-.+...+|..+ +-+++-++++|- +.+|.++|-+. .+..+.+..+|
T Consensus 6 i~Ip~~~ig~iIGkgG-------------------~~ik~I~~~tg~~I~i~~~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 6 MKIPPDKIRDVIGPGG-------------------KTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred EEeChhheeeeECCCc-------------------hHHHHHHHHHCCEEEeCCCCEEEEEeCCHHHHHHHHHHh
Confidence 3577888888888754 567777777764 35688999997 77777777665
No 26
>PF14317 YcxB: YcxB-like protein
Probab=24.14 E-value=1.3e+02 Score=18.64 Aligned_cols=33 Identities=15% Similarity=0.251 Sum_probs=25.3
Q ss_pred CCCCeEEEEEcccCCcceEEEEEeeccCChhHHHHHH
Q 030768 88 VPKGHLAVYVGQKDGDFHRVLVPVIYFNHPLFGKLLR 124 (171)
Q Consensus 88 vpkG~~aVYVG~~~~d~rRFvVP~~yLnhPlF~eLL~ 124 (171)
.-+.++.+|++ +..-++||-..++.-...++.+
T Consensus 27 e~~~~~~l~~~----~~~~~~iPk~~f~~~e~~~f~~ 59 (62)
T PF14317_consen 27 ETKDYFYLYLG----KNQAFIIPKRAFSEEEKEEFRE 59 (62)
T ss_pred EeCCEEEEEEC----CCeEEEEEHHHCCHhHHHHHHH
Confidence 45788999997 4699999999998655555554
No 27
>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=24.12 E-value=3.3e+02 Score=20.73 Aligned_cols=64 Identities=17% Similarity=0.305 Sum_probs=38.1
Q ss_pred eEEEEEeeccCChhHHHHHHHHHHhcCcc--------CCCceE-ecCcHHHHHHHHHHHHcCCCCCccccccccc
Q 030768 105 HRVLVPVIYFNHPLFGKLLRDAEEEYGFN--------QQGGIT-IPCRFSEFEQVQTRIAAGNGARTRKLTWKRN 170 (171)
Q Consensus 105 rRFvVP~~yLnhPlF~eLL~~aeEEfGf~--------~~G~Lt-IPCd~~~Fe~vl~~i~~~~~~~~~~~~~~~~ 170 (171)
+=..|.-+.-..|.|.+||.....||+-+ .+|-|. |-=| +..+=++...+ +.++-.+-|+|+.|
T Consensus 16 rdi~vee~l~~~P~~kdLl~lmr~~f~~~dIaLNYrD~EGDLIRlldd-eDv~LMV~~~r-~~~~~k~~fPWeLh 88 (92)
T cd06399 16 RDIAVEEDLSSTPLLKDLLELTRREFQREDIALNYRDAEGDLIRLLSD-EDVALMVRQSR-GLPSQKRLFPWKLH 88 (92)
T ss_pred cceEeecccccCccHHHHHHHHHHHhchhheeeeeecCCCCEEEEcch-hhHHHHHHHHh-cCCCcccccceeEE
Confidence 44455556778999999999999998732 245543 4333 22222233332 22333358999875
No 28
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.92 E-value=2.5e+02 Score=20.03 Aligned_cols=46 Identities=26% Similarity=0.308 Sum_probs=30.5
Q ss_pred eEEEEEeeccCChhHHHHHHHHHHhcCccCCCceEec-CcHHHHHHHHHHH
Q 030768 105 HRVLVPVIYFNHPLFGKLLRDAEEEYGFNQQGGITIP-CRFSEFEQVQTRI 154 (171)
Q Consensus 105 rRFvVP~~yLnhPlF~eLL~~aeEEfGf~~~G~LtIP-Cd~~~Fe~vl~~i 154 (171)
.=.+|+++|++|-.....-+.|. .+|-+ .+... +.+..|+..|..+
T Consensus 50 D~VIv~t~~vsH~~~~~vk~~ak-k~~ip---~~~~~~~~~~~l~~~l~~~ 96 (97)
T PF10087_consen 50 DLVIVFTDYVSHNAMWKVKKAAK-KYGIP---IIYSRSRGVSSLERALERL 96 (97)
T ss_pred CEEEEEeCCcChHHHHHHHHHHH-HcCCc---EEEECCCCHHHHHHHHHhh
Confidence 45677888999999887777666 43321 23344 6677787777654
No 29
>PLN02752 [acyl-carrier protein] S-malonyltransferase
Probab=23.76 E-value=67 Score=28.03 Aligned_cols=46 Identities=15% Similarity=0.080 Sum_probs=28.9
Q ss_pred CCCCCCCeEEEEEcccCCcceEEEEEeeccCChhHHHHHHHHHHhcCcc
Q 030768 85 PVSVPKGHLAVYVGQKDGDFHRVLVPVIYFNHPLFGKLLRDAEEEYGFN 133 (171)
Q Consensus 85 ~~~vpkG~~aVYVG~~~~d~rRFvVP~~yLnhPlF~eLL~~aeEEfGf~ 133 (171)
..+.+.-.+.++-|++ .+.-=+.. +|.++|.|+++++++++-.|++
T Consensus 33 ~~~~~~~~a~lFpGQG--sq~~gm~~-~~~~~p~~~~~~~~~~~~lg~~ 78 (343)
T PLN02752 33 FADYKPTTAFLFPGQG--AQAVGMGK-EAAEVPAAKALFDKASEILGYD 78 (343)
T ss_pred ccCCCCCEEEEECCCC--cchhhHHH-HHHhCHHHHHHHHHHHHHhCCC
Confidence 3344455666777762 11111111 2678999999999999888765
No 30
>PF09186 DUF1949: Domain of unknown function (DUF1949); InterPro: IPR015269 Members of this entry are a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement []. This entry contains the protein Impact, which is a translational regulator that ensures constant high levels of translation under amino acid starvation. It acts by interacting with Gcn1/Gcn1L1, thereby preventing activation of Gcn2 protein kinases (EIF2AK1 to 4) and subsequent down-regulation of protein synthesis. It is evolutionary conserved from eukaryotes to archaea []. ; PDB: 2CVE_A 1VI7_A.
Probab=22.91 E-value=50 Score=20.74 Aligned_cols=49 Identities=16% Similarity=0.232 Sum_probs=30.7
Q ss_pred EeeccCChhHHHHHHHHH-----HhcCccCCCceEecCcHHHHHHHHHHHHcCCCC
Q 030768 110 PVIYFNHPLFGKLLRDAE-----EEYGFNQQGGITIPCRFSEFEQVQTRIAAGNGA 160 (171)
Q Consensus 110 P~~yLnhPlF~eLL~~ae-----EEfGf~~~G~LtIPCd~~~Fe~vl~~i~~~~~~ 160 (171)
-++|=....++-+|++.. ++|+ .+=.++|.++.+.-+.+...|.+-.+|
T Consensus 2 ~~~Y~~~~~v~~~l~~~~~~i~~~~y~--~~V~~~v~v~~~~~~~f~~~l~~~t~G 55 (56)
T PF09186_consen 2 SCDYSQYGKVERLLEQNGIEIVDEDYT--DDVTLTVAVPEEEVEEFKAQLTDLTSG 55 (56)
T ss_dssp EE-CCCHHHHHHHHHHTTTEEEEEEEC--TTEEEEEEEECCCHHHHHHHHHHHTTT
T ss_pred EechhhHHHHHHHHHHCCCEEEcceec--ceEEEEEEECHHHHHHHHHHHHHHcCC
Confidence 456777778888888763 4554 555677777766666666555544443
No 31
>COG4862 MecA Negative regulator of genetic competence, sporulation and motility [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Cell motility and secretion]
Probab=22.73 E-value=50 Score=28.71 Aligned_cols=27 Identities=22% Similarity=0.409 Sum_probs=24.0
Q ss_pred CChhHHHHHHHHHHhcCccCCCceEec
Q 030768 115 NHPLFGKLLRDAEEEYGFNQQGGITIP 141 (171)
Q Consensus 115 nhPlF~eLL~~aeEEfGf~~~G~LtIP 141 (171)
.|-+|-++++++.+|-+|..+|||.|-
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 32
>PF04304 DUF454: Protein of unknown function (DUF454); InterPro: IPR007401 This is a predicted membrane protein.
Probab=22.36 E-value=62 Score=21.99 Aligned_cols=21 Identities=43% Similarity=0.738 Sum_probs=17.4
Q ss_pred ccCChhHHHHHHHHHHhcCcc
Q 030768 113 YFNHPLFGKLLRDAEEEYGFN 133 (171)
Q Consensus 113 yLnhPlF~eLL~~aeEEfGf~ 133 (171)
.+|||.|+..++.-+|.=|.+
T Consensus 5 l~~h~~~g~~I~~w~~~r~i~ 25 (71)
T PF04304_consen 5 LLNHRLFGPYIRNWEEHRGIP 25 (71)
T ss_pred HHcCchhHHHHHHHHHCCCcC
Confidence 579999999999998775544
No 33
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=22.20 E-value=33 Score=29.36 Aligned_cols=44 Identities=16% Similarity=0.159 Sum_probs=33.4
Q ss_pred cceEEEEEeeccCChhHHHHHHHHHHhc-CccCCCceEecCcHHH
Q 030768 103 DFHRVLVPVIYFNHPLFGKLLRDAEEEY-GFNQQGGITIPCRFSE 146 (171)
Q Consensus 103 d~rRFvVP~~yLnhPlF~eLL~~aeEEf-Gf~~~G~LtIPCd~~~ 146 (171)
..+-.-.|..|+++.-|...+++.+++| ++.+-..++||||-..
T Consensus 95 ~~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~ 139 (231)
T KOG4209|consen 95 RQKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFR 139 (231)
T ss_pred hhhccCCceEEEeccccccccchhhheeeccCCccceeeeccccC
Confidence 4666778888999999999999987776 3334455799998644
No 34
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=20.69 E-value=3.5e+02 Score=23.60 Aligned_cols=64 Identities=17% Similarity=0.237 Sum_probs=42.0
Q ss_pred CCeEEEEEcccCCcceEEEEEeeccCChhHHHHHHHHHHhcCccCC---------------CceEecCcHHHHHHHHHHH
Q 030768 90 KGHLAVYVGQKDGDFHRVLVPVIYFNHPLFGKLLRDAEEEYGFNQQ---------------GGITIPCRFSEFEQVQTRI 154 (171)
Q Consensus 90 kG~~aVYVG~~~~d~rRFvVP~~yLnhPlF~eLL~~aeEEfGf~~~---------------G~LtIPCd~~~Fe~vl~~i 154 (171)
.|.+.|.-.. +...+.|-++.-.-|...+++.....-|+++.| -+|.||...+.||-+++.|
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 4555554432 345566655553345566788888888887765 3488999899999888876
Q ss_pred Hc
Q 030768 155 AA 156 (171)
Q Consensus 155 ~~ 156 (171)
-.
T Consensus 122 ig 123 (283)
T PRK10308 122 LG 123 (283)
T ss_pred HH
Confidence 43
No 35
>PF07104 DUF1366: Protein of unknown function (DUF1366); InterPro: IPR009796 This entry is represented by Streptococcus phage 7201, Orf40. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Streptococcus thermophilus bacteriophage proteins of around 130 residues in length. One of the sequences in this family, from phage Sfi11 (O80186 from SWISSPROT) is known as Gp149. The function of this family is unknown.
Probab=20.33 E-value=1.5e+02 Score=23.12 Aligned_cols=41 Identities=15% Similarity=0.145 Sum_probs=30.1
Q ss_pred CCCCeEEEEEcccCCcceEEEEEeeccCChhHHHHHHHHHHhc
Q 030768 88 VPKGHLAVYVGQKDGDFHRVLVPVIYFNHPLFGKLLRDAEEEY 130 (171)
Q Consensus 88 vpkG~~aVYVG~~~~d~rRFvVP~~yLnhPlF~eLL~~aeEEf 130 (171)
+..+.-++.+|.. +.---+.+|.++.+.+ +.|||++++|+|
T Consensus 16 sv~~T~ViL~~~d-Ga~ip~~L~~D~~~ks-~~ELi~~ale~i 56 (116)
T PF07104_consen 16 SVSKTKVILTNDD-GAYIPVFLPGDKIDKS-NTELIELALEMI 56 (116)
T ss_pred CeeeeEEEEEcCC-CcEEEeeCChhhhcCC-HHHHHHHHHHHH
Confidence 4567777777763 3556667777887765 789999999876
No 36
>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=20.18 E-value=67 Score=24.36 Aligned_cols=38 Identities=18% Similarity=0.064 Sum_probs=20.0
Q ss_pred ccCChhHHHHHHHHHHhcCccCCCceEecCcHHHHHHHH
Q 030768 113 YFNHPLFGKLLRDAEEEYGFNQQGGITIPCRFSEFEQVQ 151 (171)
Q Consensus 113 yLnhPlF~eLL~~aeEEfGf~~~G~LtIPCd~~~Fe~vl 151 (171)
-.+-.-|.+|||.|||+++.++ -.|.++=+-.....++
T Consensus 37 ~~~K~~lvaLLElAee~L~c~~-vvic~~k~~~d~~~Ll 74 (108)
T PF02100_consen 37 QGSKESLVALLELAEEKLGCSH-VVICLDKNRPDRASLL 74 (108)
T ss_dssp S--SHHHHHHHHHHHHHH-----EEEEE---SS-HHHHH
T ss_pred cccHHHHHHHHHHhcCcCCCCE-EEEEEECCchhHHHhh
Confidence 3355789999999999988764 4555664444444444
Done!