Query 034598
Match_columns 90
No_of_seqs 108 out of 623
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 04:30:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034598.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034598hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03220 uncharacterized prote 100.0 4.6E-39 1E-43 219.4 9.8 90 1-90 1-102 (105)
2 PLN03090 auxin-responsive fami 100.0 1.5E-37 3.2E-42 211.8 9.1 86 1-89 1-101 (104)
3 PLN03219 uncharacterized prote 100.0 3.1E-35 6.8E-40 201.4 9.2 83 7-89 6-103 (108)
4 PF02519 Auxin_inducible: Auxi 100.0 3.2E-35 6.9E-40 198.0 8.6 64 24-89 34-97 (100)
5 PRK02899 adaptor protein; Prov 84.3 0.91 2E-05 33.6 2.5 24 53-77 39-62 (197)
6 PF02214 BTB_2: BTB/POZ domain 79.6 2 4.4E-05 27.0 2.5 53 33-89 3-58 (94)
7 PRK02315 adaptor protein; Prov 77.5 1.9 4.2E-05 32.5 2.3 24 53-77 39-62 (233)
8 smart00666 PB1 PB1 domain. Pho 77.3 12 0.00026 22.7 5.5 42 35-81 8-59 (81)
9 PF02100 ODC_AZ: Ornithine dec 75.6 2.7 5.8E-05 28.4 2.4 38 39-78 23-64 (108)
10 PF05389 MecA: Negative regula 72.7 1.2 2.5E-05 32.9 0.0 25 52-77 38-62 (220)
11 cd06410 PB1_UP2 Uncharacterize 51.5 45 0.00097 22.1 4.7 46 32-82 17-74 (97)
12 smart00153 VHP Villin headpiec 46.3 10 0.00023 21.1 0.8 19 49-67 1-19 (36)
13 PF12058 DUF3539: Protein of u 46.3 4 8.6E-05 27.4 -1.1 11 48-58 4-14 (88)
14 PF02209 VHP: Villin headpiece 46.0 9 0.00019 21.5 0.5 19 49-67 1-19 (36)
15 PF11834 DUF3354: Domain of un 44.4 19 0.00042 22.7 1.9 16 54-69 27-42 (69)
16 cd05992 PB1 The PB1 domain is 40.8 79 0.0017 18.8 7.0 33 33-69 5-37 (81)
17 PF05041 Pecanex_C: Pecanex pr 39.8 20 0.00043 27.7 1.7 27 10-37 194-220 (232)
18 PF08861 DUF1828: Domain of un 37.2 73 0.0016 20.2 3.9 37 52-88 44-80 (90)
19 PF12062 HSNSD: heparan sulfat 36.8 28 0.00062 29.7 2.3 40 28-68 96-141 (487)
20 cd06396 PB1_NBR1 The PB1 domai 36.2 1.2E+02 0.0027 19.7 5.2 43 39-83 10-60 (81)
21 PF11876 DUF3396: Protein of u 35.4 34 0.00074 25.4 2.3 41 39-79 23-65 (208)
22 cd06407 PB1_NLP A PB1 domain i 33.2 1.3E+02 0.0029 19.2 5.0 45 34-83 6-61 (82)
23 PF11470 TUG-UBL1: GLUT4 regul 31.9 74 0.0016 19.7 3.1 34 40-75 6-39 (65)
24 PF14317 YcxB: YcxB-like prote 31.3 96 0.0021 17.0 3.6 32 26-59 27-58 (62)
25 PF00564 PB1: PB1 domain; Int 30.9 1.2E+02 0.0027 18.1 5.1 46 33-82 6-61 (84)
26 TIGR02529 EutJ ethanolamine ut 30.1 60 0.0013 24.1 2.9 29 54-82 45-73 (239)
27 PRK10308 3-methyl-adenine DNA 29.9 1.8E+02 0.0039 22.5 5.6 61 28-89 45-119 (283)
28 cd01406 SIR2-like Sir2-like: P 29.0 75 0.0016 23.1 3.2 36 29-71 1-36 (242)
29 PF08948 DUF1859: Domain of un 28.7 19 0.00042 25.2 0.1 29 26-56 85-123 (126)
30 TIGR03687 pupylate_cterm ubiqu 27.4 33 0.00073 19.1 0.9 18 55-72 12-31 (33)
31 TIGR03793 TOMM_pelo TOMM prope 26.6 1.1E+02 0.0025 19.5 3.4 27 50-77 14-44 (77)
32 PRK02797 4-alpha-L-fucosyltran 26.5 1.9E+02 0.0041 23.5 5.3 45 25-69 141-206 (322)
33 PF11822 DUF3342: Domain of un 26.3 75 0.0016 25.7 3.0 46 39-88 12-62 (317)
34 PF05194 UreE_C: UreE urease a 23.6 1.2E+02 0.0025 19.2 3.0 28 28-62 24-51 (87)
35 COG4862 MecA Negative regulato 23.4 57 0.0012 25.3 1.7 27 51-78 37-63 (224)
36 cd06080 MUM1_like Mutated mela 23.3 1.4E+02 0.0031 19.2 3.4 42 27-68 28-75 (80)
37 COG1759 5-formaminoimidazole-4 22.8 38 0.00082 27.9 0.7 26 22-47 86-112 (361)
38 PF07429 Glyco_transf_56: 4-al 22.4 2.4E+02 0.0052 23.3 5.2 45 25-69 180-245 (360)
39 KOG1748 Acyl carrier protein/N 22.0 45 0.00097 23.8 0.9 30 59-88 94-124 (131)
40 cd06279 PBP1_LacI_like_3 Ligan 21.5 1E+02 0.0022 22.1 2.7 26 44-69 5-36 (283)
41 PF04341 DUF485: Protein of un 21.0 72 0.0016 20.5 1.7 12 50-61 2-13 (91)
42 PRK13277 5-formaminoimidazole- 20.2 31 0.00067 28.3 -0.3 30 22-53 86-116 (366)
No 1
>PLN03220 uncharacterized protein; Provisional
Probab=100.00 E-value=4.6e-39 Score=219.43 Aligned_cols=90 Identities=64% Similarity=1.100 Sum_probs=81.5
Q ss_pred CccchhhhHHHHHHHHhhhc---------CCCCCCCcceEEEEecCC---cceEEEEEccCcCchhHHHHHHHHHHhhCC
Q 034598 1 MGIRLPAMIHNAKQILKLHS---------KDQSGVPKGHVVVYVGEL---QKTRFVVPISYLNHPSFIDLLNRAEEEFGF 68 (90)
Q Consensus 1 m~~~~~~~~~~~~~~~~~~~---------~~~~~vpkG~~aVyVG~~---~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~ 68 (90)
||+++.+|....||++++|+ ..+.+|||||||||||++ +++||+||++|||||.|++||++|||||||
T Consensus 1 ~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP~F~~LL~~AeEEfGf 80 (105)
T PLN03220 1 MGLSRFAISNATKQILKLNSLANRNRTSSSSSDHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHPSFKEFLSRAEEEFGF 80 (105)
T ss_pred CCcchhhhHHHHHHHHHHHhhcccccccccccCCCCCCeEEEEECCCCCccceEEEEEHHHcCChHHHHHHHHHHHHhCC
Confidence 89999999977799999884 134589999999999972 589999999999999999999999999999
Q ss_pred ccCCCcEEeeCcHHHHHhhhcC
Q 034598 69 NHPMGGLTIPCREDAFINITFN 90 (90)
Q Consensus 69 ~~~~G~L~IPC~~~~F~~vl~~ 90 (90)
+|++|+|+|||+++.|++++++
T Consensus 81 ~~~~G~L~IPCd~~~F~~ll~s 102 (105)
T PLN03220 81 NHPMGGLTIPCREEVFLDLIAS 102 (105)
T ss_pred CCCCCCEEeeCCHHHHHHHHHh
Confidence 9966999999999999999864
No 2
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=1.5e-37 Score=211.80 Aligned_cols=86 Identities=55% Similarity=0.871 Sum_probs=76.6
Q ss_pred Cccchhh----hHHHHHHHHhhhc----C-------CCCCCCcceEEEEecCCcceEEEEEccCcCchhHHHHHHHHHHh
Q 034598 1 MGIRLPA----MIHNAKQILKLHS----K-------DQSGVPKGHVVVYVGELQKTRFVVPISYLNHPSFIDLLNRAEEE 65 (90)
Q Consensus 1 m~~~~~~----~~~~~~~~~~~~~----~-------~~~~vpkG~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeE 65 (90)
|||+-.+ ++ ++||+|+||+ + .+.+||+||||||||+ +++||+||++|||||.|++||++||||
T Consensus 1 m~~~k~~ki~~~~-~~kq~l~r~~s~~~~~~~~~~~~~~~vpkG~~aVyVG~-~~~RfvVp~~~L~hP~F~~LL~~aeeE 78 (104)
T PLN03090 1 MAIKKSNKLTQTA-MLKQILKRCSSLGKKQGYDEDGLPLDVPKGHFPVYVGE-NRSRYIVPISFLTHPEFQSLLQQAEEE 78 (104)
T ss_pred CCcccccchhHHH-HHHHHHHHHHHhcccCCcccccCCCCCCCCcEEEEECC-CCEEEEEEHHHcCCHHHHHHHHHHHHH
Confidence 7776444 43 8899999993 2 2347999999999998 899999999999999999999999999
Q ss_pred hCCccCCCcEEeeCcHHHHHhhhc
Q 034598 66 FGFNHPMGGLTIPCREDAFINITF 89 (90)
Q Consensus 66 fG~~~~~G~L~IPC~~~~F~~vl~ 89 (90)
|||+|+ |+|+|||+++.|++++|
T Consensus 79 fGf~~~-G~L~IPC~~~~Fe~ll~ 101 (104)
T PLN03090 79 FGFDHD-MGLTIPCEEVVFRSLTS 101 (104)
T ss_pred hCCCCC-CcEEEeCCHHHHHHHHH
Confidence 999998 89999999999999997
No 3
>PLN03219 uncharacterized protein; Provisional
Probab=100.00 E-value=3.1e-35 Score=201.44 Aligned_cols=83 Identities=66% Similarity=1.111 Sum_probs=71.6
Q ss_pred hhHHHHHHHHhhhc---C-----------CCCCCCcceEEEEecC-CcceEEEEEccCcCchhHHHHHHHHHHhhCCccC
Q 034598 7 AMIHNAKQILKLHS---K-----------DQSGVPKGHVVVYVGE-LQKTRFVVPISYLNHPSFIDLLNRAEEEFGFNHP 71 (90)
Q Consensus 7 ~~~~~~~~~~~~~~---~-----------~~~~vpkG~~aVyVG~-~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~ 71 (90)
+++..+||+++..+ + .+.+|||||+|||||+ ++++||+||++|||||.|++||++|||||||+|+
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vpkGh~aVYVG~~~E~kRFvVPi~yL~hP~F~~LL~~AeEEfGf~~~ 85 (108)
T PLN03219 6 SMLPNAKQIFKSQSMRNKNGSSSPSSSTTTSGLVPKGHVAVYVGEQMEKKRFVVPISYLNHPLFREFLNRAEEECGFHHS 85 (108)
T ss_pred HHHhhHHHHHHHHHHhcccCCCCCccCCCCCCCCCCCeEEEEECCCCCceEEEEEHHHcCChHHHHHHHHHHHHhCCCCC
Confidence 34458888887331 1 2267999999999997 3699999999999999999999999999999986
Q ss_pred CCcEEeeCcHHHHHhhhc
Q 034598 72 MGGLTIPCREDAFINITF 89 (90)
Q Consensus 72 ~G~L~IPC~~~~F~~vl~ 89 (90)
+|+|+|||+++.|+++|+
T Consensus 86 ~G~L~IPCd~~~F~~ll~ 103 (108)
T PLN03219 86 MGGLTIPCREESFLHLIT 103 (108)
T ss_pred CCCEEEeCCHHHHHHHHH
Confidence 699999999999999987
No 4
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=100.00 E-value=3.2e-35 Score=197.98 Aligned_cols=64 Identities=61% Similarity=1.095 Sum_probs=62.4
Q ss_pred CCCCcceEEEEecCCcceEEEEEccCcCchhHHHHHHHHHHhhCCccCCCcEEeeCcHHHHHhhhc
Q 034598 24 SGVPKGHVVVYVGELQKTRFVVPISYLNHPSFIDLLNRAEEEFGFNHPMGGLTIPCREDAFINITF 89 (90)
Q Consensus 24 ~~vpkG~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~~G~L~IPC~~~~F~~vl~ 89 (90)
.++|+||||||||+ +++||+||++|||||+|++||++|||||||+++ |+|+|||+++.|++++|
T Consensus 34 ~~vp~G~~~VyVG~-~~~Rfvvp~~~L~hp~f~~LL~~aeeEfG~~~~-G~l~iPC~~~~Fe~~l~ 97 (100)
T PF02519_consen 34 SDVPKGHFAVYVGE-ERRRFVVPVSYLNHPLFQELLEQAEEEFGFDQD-GPLTIPCDVVLFEHLLW 97 (100)
T ss_pred CCCCCCeEEEEeCc-cceEEEechHHcCchhHHHHHHHHhhhcCcCCC-CcEEeeCCHHHHHHHHH
Confidence 78999999999998 899999999999999999999999999999997 99999999999999998
No 5
>PRK02899 adaptor protein; Provisional
Probab=84.29 E-value=0.91 Score=33.62 Aligned_cols=24 Identities=29% Similarity=0.671 Sum_probs=20.7
Q ss_pred hhHHHHHHHHHHhhCCccCCCcEEe
Q 034598 53 PSFIDLLNRAEEEFGFNHPMGGLTI 77 (90)
Q Consensus 53 P~F~~LL~~aeeEfG~~~~~G~L~I 77 (90)
-+|.++|++|..|+||..+ |||+|
T Consensus 39 ~lF~~mm~Ea~~e~~F~~~-~pl~~ 62 (197)
T PRK02899 39 QLFRDMMQEANKELGFEAD-GPIAV 62 (197)
T ss_pred HHHHHHHHHhhhccCcccC-CeEEE
Confidence 3577889999999999987 89986
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=79.58 E-value=2 Score=27.01 Aligned_cols=53 Identities=23% Similarity=0.243 Sum_probs=38.4
Q ss_pred EEecCCcceEEEEEccCcC-ch--hHHHHHHHHHHhhCCccCCCcEEeeCcHHHHHhhhc
Q 034598 33 VYVGELQKTRFVVPISYLN-HP--SFIDLLNRAEEEFGFNHPMGGLTIPCREDAFINITF 89 (90)
Q Consensus 33 VyVG~~~~~RfvVp~~~L~-hP--~F~~LL~~aeeEfG~~~~~G~L~IPC~~~~F~~vl~ 89 (90)
+=||. ++|.++.+.|. +| .|..+++...... .+.+.|.+-|-++...|++||.
T Consensus 3 lNVGG---~~f~~~~~tL~~~~~s~l~~~~~~~~~~~-~~~~~~~~fiDRdp~~F~~IL~ 58 (94)
T PF02214_consen 3 LNVGG---TIFETSRSTLTRYPDSLLARLFSGERSDD-YDDDDGEYFIDRDPELFEYILN 58 (94)
T ss_dssp EEETT---EEEEEEHHHHHTSTTSTTTSHHHTGHGGG-EETTTTEEEESS-HHHHHHHHH
T ss_pred EEECC---EEEEEcHHHHhhCCCChhhhHHhhccccc-cCCccceEEeccChhhhhHHHH
Confidence 44775 99999999888 54 6888888652221 2223489999999999999973
No 7
>PRK02315 adaptor protein; Provisional
Probab=77.54 E-value=1.9 Score=32.51 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=21.5
Q ss_pred hhHHHHHHHHHHhhCCccCCCcEEe
Q 034598 53 PSFIDLLNRAEEEFGFNHPMGGLTI 77 (90)
Q Consensus 53 P~F~~LL~~aeeEfG~~~~~G~L~I 77 (90)
-.|.++|++|..|+||..+ |+|+|
T Consensus 39 ~fF~~mm~Ea~~e~~F~~~-~pl~~ 62 (233)
T PRK02315 39 EFFYSMMDEVDEEDDFADE-GPLWF 62 (233)
T ss_pred HHHHHHHHHhccccCcccC-CeEEE
Confidence 4699999999999999985 99987
No 8
>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=77.33 E-value=12 Score=22.75 Aligned_cols=42 Identities=26% Similarity=0.445 Sum_probs=32.1
Q ss_pred ecCCcceEEEEEccCcCchhHHHHHHHHHHhhCCc----------cCCCcEEeeCcH
Q 034598 35 VGELQKTRFVVPISYLNHPSFIDLLNRAEEEFGFN----------HPMGGLTIPCRE 81 (90)
Q Consensus 35 VG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~----------~~~G~L~IPC~~ 81 (90)
-|+ +.+||.+|- ...|.+|..+..+-|+.. .++..++|.++.
T Consensus 8 ~~~-~~~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~ 59 (81)
T smart00666 8 YGG-ETRRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDE 59 (81)
T ss_pred ECC-EEEEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHH
Confidence 365 789999986 778999999999999874 232367777766
No 9
>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=75.59 E-value=2.7 Score=28.44 Aligned_cols=38 Identities=37% Similarity=0.580 Sum_probs=21.3
Q ss_pred cceEEE-EEccCcCc---hhHHHHHHHHHHhhCCccCCCcEEee
Q 034598 39 QKTRFV-VPISYLNH---PSFIDLLNRAEEEFGFNHPMGGLTIP 78 (90)
Q Consensus 39 ~~~Rfv-Vp~~~L~h---P~F~~LL~~aeeEfG~~~~~G~L~IP 78 (90)
++.=|| +|-..+.+ ..|.+|||.|||.++.++ -.+.++
T Consensus 23 ~~~L~V~ip~~~~~~~~K~~lvaLLElAee~L~c~~--vvic~~ 64 (108)
T PF02100_consen 23 ERTLFVFIPSSALGQGSKESLVALLELAEEKLGCSH--VVICLD 64 (108)
T ss_dssp TTEEEEE-SS---SS--SHHHHHHHHHHHHHH------EEEEE-
T ss_pred CCEEEEEECCcccccccHHHHHHHHHHhcCcCCCCE--EEEEEE
Confidence 456666 56555444 559999999999999876 355555
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=72.66 E-value=1.2 Score=32.86 Aligned_cols=25 Identities=40% Similarity=0.689 Sum_probs=0.0
Q ss_pred chhHHHHHHHHHHhhCCccCCCcEEe
Q 034598 52 HPSFIDLLNRAEEEFGFNHPMGGLTI 77 (90)
Q Consensus 52 hP~F~~LL~~aeeEfG~~~~~G~L~I 77 (90)
+-.|.++|++|.+|+||..+ |+|++
T Consensus 38 e~fF~~ileea~~e~~F~~~-~~l~~ 62 (220)
T PF05389_consen 38 EEFFYSILEEADEEHGFEND-GPLTF 62 (220)
T ss_dssp --------------------------
T ss_pred HHHHHHHHHHhccccCcccC-CeEEE
Confidence 34699999999999999985 88875
No 11
>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=51.47 E-value=45 Score=22.13 Aligned_cols=46 Identities=28% Similarity=0.356 Sum_probs=32.3
Q ss_pred EEEecCCcceEEEEEccCcCchhHHHHHHHHHHhhCCccC------------CCcEEeeCcHH
Q 034598 32 VVYVGELQKTRFVVPISYLNHPSFIDLLNRAEEEFGFNHP------------MGGLTIPCRED 82 (90)
Q Consensus 32 aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~------------~G~L~IPC~~~ 82 (90)
.=|||. +.+--.|+-+ ..|.+|..+..+.++..+. ++-+.|.||.+
T Consensus 17 l~Y~GG-~tr~i~V~r~----~s~~el~~kl~~~~~~~~~~~lky~Lp~edld~Lisv~~DeD 74 (97)
T cd06410 17 LRYVGG-ETRIVSVDRS----ISFKELVSKLSELFGAGVVVTLKYQLPDEDLDALISVSNDED 74 (97)
T ss_pred EEEcCC-ceEEEEEcCC----CCHHHHHHHHHHHhCCCCceEEEEEcCCCCcceeEEecCcHH
Confidence 469997 7777778776 3677788888888876651 14566777774
No 12
>smart00153 VHP Villin headpiece domain.
Probab=46.29 E-value=10 Score=21.15 Aligned_cols=19 Identities=32% Similarity=0.593 Sum_probs=16.9
Q ss_pred CcCchhHHHHHHHHHHhhC
Q 034598 49 YLNHPSFIDLLNRAEEEFG 67 (90)
Q Consensus 49 ~L~hP~F~~LL~~aeeEfG 67 (90)
||+...|+.++.++.+||-
T Consensus 1 yLsdeeF~~vfgmsr~eF~ 19 (36)
T smart00153 1 YLSDEDFEEVFGMTREEFY 19 (36)
T ss_pred CCCHHHHHHHHCCCHHHHH
Confidence 7899999999999999883
No 13
>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=46.28 E-value=4 Score=27.41 Aligned_cols=11 Identities=64% Similarity=1.050 Sum_probs=7.9
Q ss_pred cCcCchhHHHH
Q 034598 48 SYLNHPSFIDL 58 (90)
Q Consensus 48 ~~L~hP~F~~L 58 (90)
.|||||.|--|
T Consensus 4 ~YLNHPtFGlL 14 (88)
T PF12058_consen 4 TYLNHPTFGLL 14 (88)
T ss_dssp -EEEETTTEEE
T ss_pred ccccCCccchh
Confidence 58999988544
No 14
>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=45.99 E-value=9 Score=21.51 Aligned_cols=19 Identities=32% Similarity=0.564 Sum_probs=15.1
Q ss_pred CcCchhHHHHHHHHHHhhC
Q 034598 49 YLNHPSFIDLLNRAEEEFG 67 (90)
Q Consensus 49 ~L~hP~F~~LL~~aeeEfG 67 (90)
||+...|+++..++.+||.
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 7899999999999999884
No 15
>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=44.45 E-value=19 Score=22.70 Aligned_cols=16 Identities=50% Similarity=0.823 Sum_probs=14.9
Q ss_pred hHHHHHHHHHHhhCCc
Q 034598 54 SFIDLLNRAEEEFGFN 69 (90)
Q Consensus 54 ~F~~LL~~aeeEfG~~ 69 (90)
.+++||+.|++.||+.
T Consensus 27 SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 27 SLEELLKIASEKFGFS 42 (69)
T ss_pred cHHHHHHHHHHHhCCC
Confidence 6999999999999995
No 16
>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=40.77 E-value=79 Score=18.81 Aligned_cols=33 Identities=39% Similarity=0.568 Sum_probs=26.8
Q ss_pred EEecCCcceEEEEEccCcCchhHHHHHHHHHHhhCCc
Q 034598 33 VYVGELQKTRFVVPISYLNHPSFIDLLNRAEEEFGFN 69 (90)
Q Consensus 33 VyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~ 69 (90)
++-++ +.+||.+|. .++.|.+|..+-.+.|+..
T Consensus 5 ~~~~~-~~~~~~~~~---~~~s~~~L~~~i~~~~~~~ 37 (81)
T cd05992 5 VKYGG-EIRRFVVVS---RSISFEDLRSKIAEKFGLD 37 (81)
T ss_pred EEecC-CCEEEEEec---CCCCHHHHHHHHHHHhCCC
Confidence 34444 689999998 8888999999999989885
No 17
>PF05041 Pecanex_C: Pecanex protein (C-terminus); InterPro: IPR007735 This family consists of pecanex protein homologues. The pecanex protein is a maternal-effect neurogenic gene found in Drosophila [].; GO: 0016021 integral to membrane
Probab=39.79 E-value=20 Score=27.65 Aligned_cols=27 Identities=30% Similarity=0.452 Sum_probs=19.7
Q ss_pred HHHHHHHhhhcCCCCCCCcceEEEEecC
Q 034598 10 HNAKQILKLHSKDQSGVPKGHVVVYVGE 37 (90)
Q Consensus 10 ~~~~~~~~~~~~~~~~vpkG~~aVyVG~ 37 (90)
+..++.|+.--..+.+.|=|| |+||..
T Consensus 194 Q~~~~~LRNl~~qs~d~PlGY-PiYvSP 220 (232)
T PF05041_consen 194 QNHKQLLRNLINQSADPPLGY-PIYVSP 220 (232)
T ss_pred cchHHHHHHHHHhhccCCCCc-ceEecc
Confidence 455555555545667999999 999986
No 18
>PF08861 DUF1828: Domain of unknown function DUF1828; InterPro: IPR014960 These proteins are functionally uncharacterised.
Probab=37.19 E-value=73 Score=20.17 Aligned_cols=37 Identities=24% Similarity=0.291 Sum_probs=31.8
Q ss_pred chhHHHHHHHHHHhhCCccCCCcEEeeCcHHHHHhhh
Q 034598 52 HPSFIDLLNRAEEEFGFNHPMGGLTIPCREDAFINIT 88 (90)
Q Consensus 52 hP~F~~LL~~aeeEfG~~~~~G~L~IPC~~~~F~~vl 88 (90)
.|.=+++|+..-..||+.-++|.|.+.++.+.|-...
T Consensus 44 s~~R~~~l~~il~~~gv~~~~~el~~~~~~~~~~~~~ 80 (90)
T PF08861_consen 44 SKKRKKILNSILNGFGVELDEGELFIKTSEENFPQAK 80 (90)
T ss_pred chHHHHHHHHHHHHcCccccCCEEEEEeCHHHHHHHH
Confidence 5777899999999999998889999999998886543
No 19
>PF12062 HSNSD: heparan sulfate-N-deacetylase; InterPro: IPR021930 This family of proteins is are heparan sulphate N-deacetylase enzymes. This protein is found in eukaryotes. This enzyme is often found associated with PF00685 from PFAM. ; GO: 0015016 [heparan sulfate]-glucosamine N-sulfotransferase activity, 0016787 hydrolase activity
Probab=36.80 E-value=28 Score=29.67 Aligned_cols=40 Identities=35% Similarity=0.547 Sum_probs=35.5
Q ss_pred cceEEEEecCCcceEEEEEc-----cCcCchh-HHHHHHHHHHhhCC
Q 034598 28 KGHVVVYVGELQKTRFVVPI-----SYLNHPS-FIDLLNRAEEEFGF 68 (90)
Q Consensus 28 kG~~aVyVG~~~~~RfvVp~-----~~L~hP~-F~~LL~~aeeEfG~ 68 (90)
||.+|+++-. ++.||-+-+ .|+|-+. -++||++=..|||.
T Consensus 96 kg~lP~LT~~-~kGRy~lII~ENl~kYlnld~wNR~LLdkYC~ey~V 141 (487)
T PF12062_consen 96 KGDLPVLTDN-DKGRYSLIIFENLLKYLNLDSWNRELLDKYCREYGV 141 (487)
T ss_pred CCCCCccccC-CCCcEEEEEehhHHHHcCChHHHHHHHHHHhHccCc
Confidence 6899999976 788998886 8999998 89999999999975
No 20
>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=36.15 E-value=1.2e+02 Score=19.70 Aligned_cols=43 Identities=14% Similarity=0.300 Sum_probs=32.6
Q ss_pred cceEEEEEccCcCchhHHHHHHHHHHhhCCc--------cCCCcEEeeCcHHH
Q 034598 39 QKTRFVVPISYLNHPSFIDLLNRAEEEFGFN--------HPMGGLTIPCREDA 83 (90)
Q Consensus 39 ~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~--------~~~G~L~IPC~~~~ 83 (90)
+..||.++-+ .++.|.+|..+-+.-|+++ .++-+++|.|+.+.
T Consensus 10 d~~rf~~~~~--~~~~~~~L~~ev~~rf~l~~f~lKYlDde~e~v~lssd~eL 60 (81)
T cd06396 10 ESQSFLVSDS--ENTTWASVEAMVKVSFGLNDIQIKYVDEENEEVSVNSQGEY 60 (81)
T ss_pred eEEEEEecCC--CCCCHHHHHHHHHHHhCCCcceeEEEcCCCCEEEEEchhhH
Confidence 6899988752 2557999999999989853 44457899998853
No 21
>PF11876 DUF3396: Protein of unknown function (DUF3396); InterPro: IPR021815 This family of proteins are functionally uncharacterised. This protein is found in bacteria and viruses. Proteins in this family are typically between 302 to 382 amino acids in length.
Probab=35.38 E-value=34 Score=25.42 Aligned_cols=41 Identities=22% Similarity=0.368 Sum_probs=32.2
Q ss_pred cceEEEEEccCcCch--hHHHHHHHHHHhhCCccCCCcEEeeC
Q 034598 39 QKTRFVVPISYLNHP--SFIDLLNRAEEEFGFNHPMGGLTIPC 79 (90)
Q Consensus 39 ~~~RfvVp~~~L~hP--~F~~LL~~aeeEfG~~~~~G~L~IPC 79 (90)
+--+|.+|++||..+ .|++|+...++.+...|.-+++.+-.
T Consensus 23 s~l~f~~P~~~l~~~~~~~~~l~~~~a~~L~~~~G~aGl~~~~ 65 (208)
T PF11876_consen 23 SYLSFSLPLEWLEEGPGHFRALFLELAERLPPSHGYAGLAFNL 65 (208)
T ss_pred cEEEEEeCHHHHhcCcHHHHHHHHHHHHHCCCCeEeeEEEEec
Confidence 457899999999872 49999999999998777555665543
No 22
>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=33.19 E-value=1.3e+02 Score=19.15 Aligned_cols=45 Identities=27% Similarity=0.510 Sum_probs=32.1
Q ss_pred EecCCcceEEEEEccCcCchhHHHHHHHHHHhhCCcc-----------CCCcEEeeCcHHH
Q 034598 34 YVGELQKTRFVVPISYLNHPSFIDLLNRAEEEFGFNH-----------PMGGLTIPCREDA 83 (90)
Q Consensus 34 yVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~-----------~~G~L~IPC~~~~ 83 (90)
..|+ +..||.+|.+- -|++|.++-.+-|+.+. ++...+|.|+.+.
T Consensus 6 ~~~~-d~~r~~l~~~~----~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL 61 (82)
T cd06407 6 TYGE-EKIRFRLPPSW----GFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADL 61 (82)
T ss_pred EeCC-eEEEEEcCCCC----CHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHH
Confidence 3355 78999888744 68888888888887753 2345777887754
No 23
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=31.85 E-value=74 Score=19.69 Aligned_cols=34 Identities=24% Similarity=0.399 Sum_probs=20.3
Q ss_pred ceEEEEEccCcCchhHHHHHHHHHHhhCCccCCCcE
Q 034598 40 KTRFVVPISYLNHPSFIDLLNRAEEEFGFNHPMGGL 75 (90)
Q Consensus 40 ~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~~G~L 75 (90)
.+|+.|++. ..-.+.++|++|-+.||++.+.+.|
T Consensus 6 ~rr~~vkvt--p~~~l~~VL~eac~k~~l~~~~~~L 39 (65)
T PF11470_consen 6 FRRFKVKVT--PNTTLNQVLEEACKKFGLDPSSYDL 39 (65)
T ss_dssp S-EEEE-----TTSBHHHHHHHHHHHTT--GGG-EE
T ss_pred CcEEEEEEC--CCCCHHHHHHHHHHHcCCCccceEE
Confidence 478877775 3446889999999999998753333
No 24
>PF14317 YcxB: YcxB-like protein
Probab=31.34 E-value=96 Score=17.00 Aligned_cols=32 Identities=16% Similarity=0.350 Sum_probs=23.8
Q ss_pred CCcceEEEEecCCcceEEEEEccCcCchhHHHHH
Q 034598 26 VPKGHVVVYVGELQKTRFVVPISYLNHPSFIDLL 59 (90)
Q Consensus 26 vpkG~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL 59 (90)
.-+.++-+|++. ..-++||-+.++.-...++.
T Consensus 27 e~~~~~~l~~~~--~~~~~iPk~~f~~~e~~~f~ 58 (62)
T PF14317_consen 27 ETKDYFYLYLGK--NQAFIIPKRAFSEEEKEEFR 58 (62)
T ss_pred EeCCEEEEEECC--CeEEEEEHHHCCHhHHHHHH
Confidence 346788889985 69999999999854444444
No 25
>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=30.90 E-value=1.2e+02 Score=18.08 Aligned_cols=46 Identities=35% Similarity=0.375 Sum_probs=29.5
Q ss_pred EEecCCcceEEEEEccCcCchhHHHHHHHHHHhhCCc----------cCCCcEEeeCcHH
Q 034598 33 VYVGELQKTRFVVPISYLNHPSFIDLLNRAEEEFGFN----------HPMGGLTIPCRED 82 (90)
Q Consensus 33 VyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~----------~~~G~L~IPC~~~ 82 (90)
++-++ +.+| .+..-..+.|.+|..+.++.||.. .++-.++|.++.+
T Consensus 6 ~~~~~-~~~~---~~~~~~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~D 61 (84)
T PF00564_consen 6 VRYGG-DIRR---IISLPSDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDED 61 (84)
T ss_dssp EEETT-EEEE---EEEECSTSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHH
T ss_pred EEECC-eeEE---EEEcCCCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHH
Confidence 33444 4555 333345679999999999999983 2323577777663
No 26
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein.
Probab=30.13 E-value=60 Score=24.08 Aligned_cols=29 Identities=17% Similarity=0.187 Sum_probs=23.2
Q ss_pred hHHHHHHHHHHhhCCccCCCcEEeeCcHH
Q 034598 54 SFIDLLNRAEEEFGFNHPMGGLTIPCRED 82 (90)
Q Consensus 54 ~F~~LL~~aeeEfG~~~~~G~L~IPC~~~ 82 (90)
.++.|.+++++-.|...+.-.+++|+...
T Consensus 45 ~l~~l~~~a~~~~g~~~~~vvisVP~~~~ 73 (239)
T TIGR02529 45 IVRRLKDTLEQKLGIELTHAATAIPPGTI 73 (239)
T ss_pred HHHHHHHHHHHHhCCCcCcEEEEECCCCC
Confidence 58889999988888876657899998653
No 27
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=29.88 E-value=1.8e+02 Score=22.47 Aligned_cols=61 Identities=21% Similarity=0.234 Sum_probs=39.4
Q ss_pred cceEEEEecCCcceEEEEEccCcCchhHHHHHHHHHHhhCCccC--------------CCcEEeeCcHHHHHhhhc
Q 034598 28 KGHVVVYVGELQKTRFVVPISYLNHPSFIDLLNRAEEEFGFNHP--------------MGGLTIPCREDAFINITF 89 (90)
Q Consensus 28 kG~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~--------------~G~L~IPC~~~~F~~vl~ 89 (90)
.|++.|.-.. ...++.+.++.-.-+....++.+...-|+.+.+ .-+|+||...+-||-+++
T Consensus 45 ~~~~~v~~~~-~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L~~~~~~~~GlR~p~~~d~fE~lv~ 119 (283)
T PRK10308 45 RGVVTVIPDI-ARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGKLGAARPGLRLPGSVDAFEQGVR 119 (283)
T ss_pred cEEEEEEEcC-CCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCCcCCCCCCHHHHHHH
Confidence 4566665544 445566655553334555677777777776654 246899998999997765
No 28
>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=29.03 E-value=75 Score=23.12 Aligned_cols=36 Identities=28% Similarity=0.505 Sum_probs=28.2
Q ss_pred ceEEEEecCCcceEEEEEccCcCchhHHHHHHHHHHhhCCccC
Q 034598 29 GHVVVYVGELQKTRFVVPISYLNHPSFIDLLNRAEEEFGFNHP 71 (90)
Q Consensus 29 G~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~ 71 (90)
|.++++||.+-..+ .+-|...+|++...++++.+.+
T Consensus 1 g~lvlFiGAG~S~~-------~glP~W~~Ll~~l~~~~~~~~~ 36 (242)
T cd01406 1 GRVVIFVGAGVSVS-------SGLPDWKTLLDEIASELGLEID 36 (242)
T ss_pred CCEEEEecCccccc-------cCCCChHHHHHHHHHHcCCccc
Confidence 68899999752222 5789999999999999987654
No 29
>PF08948 DUF1859: Domain of unknown function (DUF1859); InterPro: IPR015043 This entry is represented by Bacteriophage PRD1, P5. This protein has no known function though it is sometimes found in the N terminus of bacteriophage spike proteins []. ; PDB: 1W8X_N.
Probab=28.70 E-value=19 Score=25.24 Aligned_cols=29 Identities=28% Similarity=0.427 Sum_probs=7.8
Q ss_pred CCcceEEEEecCCcceEEE----------EEccCcCchhHH
Q 034598 26 VPKGHVVVYVGELQKTRFV----------VPISYLNHPSFI 56 (90)
Q Consensus 26 vpkG~~aVyVG~~~~~Rfv----------Vp~~~L~hP~F~ 56 (90)
-.+||+|+.|-. +-+|+ +|+-+||.|.-+
T Consensus 85 G~QGYfPlL~~~--~~KFv~~~~~~GKks~P~~FlNF~IA~ 123 (126)
T PF08948_consen 85 GKQGYFPLLVPG--RAKFVVRHTGSGKKSVPMFFLNFTIAQ 123 (126)
T ss_dssp ---SS--EEE----SSSSEEEEEEEESS----S--------
T ss_pred CCcccceeeccc--hhhhhhhhccCCCcceeeEEEeceeee
Confidence 357999999963 44444 688888887643
No 30
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=27.41 E-value=33 Score=19.13 Aligned_cols=18 Identities=33% Similarity=0.486 Sum_probs=14.2
Q ss_pred HHHHHHHHHHhh--CCccCC
Q 034598 55 FIDLLNRAEEEF--GFNHPM 72 (90)
Q Consensus 55 F~~LL~~aeeEf--G~~~~~ 72 (90)
+-.+|+..+||| ||-|++
T Consensus 12 Id~vLe~NAe~FV~~fVQKG 31 (33)
T TIGR03687 12 IDGVLESNAEEFVRGFVQKG 31 (33)
T ss_pred HHHHHHHhHHHHHHHHHHcc
Confidence 456788888998 888873
No 31
>TIGR03793 TOMM_pelo TOMM propeptide domain. This model represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM). Oddly, most of this seqence region appears homologous to nitrile hydratase subunits. This family is expanded especially in Pelotomaculum thermopropionicum SI.
Probab=26.61 E-value=1.1e+02 Score=19.50 Aligned_cols=27 Identities=22% Similarity=0.350 Sum_probs=18.4
Q ss_pred cCchhHHHHH----HHHHHhhCCccCCCcEEe
Q 034598 50 LNHPSFIDLL----NRAEEEFGFNHPMGGLTI 77 (90)
Q Consensus 50 L~hP~F~~LL----~~aeeEfG~~~~~G~L~I 77 (90)
-..|.|++.| ..+=+||||+-+ ..+.|
T Consensus 14 w~Dp~Fr~~Ll~DPraaL~e~G~~~P-~~~~i 44 (77)
T TIGR03793 14 WEDEAFKQALLTNPKEALEREGVQVP-AEVEV 44 (77)
T ss_pred HcCHHHHHHHHHCHHHHHHHhCCCCC-CceEE
Confidence 3578899866 455668899876 44443
No 32
>PRK02797 4-alpha-L-fucosyltransferase; Provisional
Probab=26.52 E-value=1.9e+02 Score=23.49 Aligned_cols=45 Identities=20% Similarity=0.394 Sum_probs=33.7
Q ss_pred CCCcceEEEEecC-------------------CcceEEEEEccC--cCchhHHHHHHHHHHhhCCc
Q 034598 25 GVPKGHVVVYVGE-------------------LQKTRFVVPISY--LNHPSFIDLLNRAEEEFGFN 69 (90)
Q Consensus 25 ~vpkG~~aVyVG~-------------------~~~~RfvVp~~~--L~hP~F~~LL~~aeeEfG~~ 69 (90)
..+++.+.+.||. ++.-|+.||.+| =|.-..++..+.+.+-||-+
T Consensus 141 ~~~~~~~tIlvGNSgd~SN~Hie~L~~l~~~~~~~v~ii~PlsYp~gn~~Yi~~V~~~~~~lF~~~ 206 (322)
T PRK02797 141 RQRAGKMTILVGNSGDRSNRHIEALRALHQQFGDNVKIIVPMGYPANNQAYIEEVRQAGLALFGAE 206 (322)
T ss_pred ccCCCceEEEEeCCCCCcccHHHHHHHHHHHhCCCeEEEEECCcCCCCHHHHHHHHHHHHHhcCcc
Confidence 4467789999995 134599999999 56666777777778888743
No 33
>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=26.33 E-value=75 Score=25.66 Aligned_cols=46 Identities=20% Similarity=0.381 Sum_probs=34.4
Q ss_pred cceEEEEEccCcCc--hhHHHHHHH---HHHhhCCccCCCcEEeeCcHHHHHhhh
Q 034598 39 QKTRFVVPISYLNH--PSFIDLLNR---AEEEFGFNHPMGGLTIPCREDAFINIT 88 (90)
Q Consensus 39 ~~~RfvVp~~~L~h--P~F~~LL~~---aeeEfG~~~~~G~L~IPC~~~~F~~vl 88 (90)
..+=|..|...|-. ..|++.|.. +.++.. + =.|.+-||+..|+.++
T Consensus 12 ~~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~~---~-idisVhCDv~iF~WLm 62 (317)
T PF11822_consen 12 EKRDFTCPRDLLVSEMRYFAEYLSRYINDSQRWE---E-IDISVHCDVHIFEWLM 62 (317)
T ss_pred cceeeeccHHHHHHhhHHHHHHHhhcccccCcCC---C-cceEEecChhHHHHHH
Confidence 56789999888854 559999966 333322 2 4589999999999886
No 34
>PF05194 UreE_C: UreE urease accessory protein, C-terminal domain; InterPro: IPR007864 Urease and other nickel metalloenzymes are synthesised as precursors devoid of the metalloenzyme active site. These precursors then undergo a complex post-translational maturation process that requires a number of accessory proteins. Members of this group are nickel-binding proteins required for urease metallocentre assembly []. They are believed to function as metallochaperones to deliver nickel to urease apoprotein [, ]. It has been shown by yeast two-hybrid analysis that UreE forms a dimeric complex with UreG in Helicobacter pylori []. The UreDFG-apoenzyme complex has also been shown to exist [, ] and is believed to be, with the addition of UreE, the assembly system for active urease []. The complexes, rather than the individual proteins, presumably bind to UreB via UreE/H recognition sites. The structure of Klebsiella aerogenes UreE reveals a unique two-domain architecture.The N-terminal domain is structurally related to a heat shock protein, while the C-terminal domain shows homology to the Atx1 copper metallochaperone [, ]. Significantly, the metal-binding sites in UreE and Atx1 are distinct in location and types of residues despite the relationship between these proteins and the mechanism for UreE activation of urease is proposed to be different from the thiol ligand exchange mechanism used by the copper metallochaperones. The C-terminal domain of this protein is the metal-binding region, which can bind up to six Ni molecules per dimer. Most members of this group contain a histidine-rich C-terminal motif that is involved in, but not solely responsible for, binding nickel ions in K. aerogenes UreE []. However, internal ligands, not the histidine residues at the C terminus, are necessary for UreE to assist in urease activation in K. aerogenes [], even though the truncated protein lacking the His-rich region binds two nickel ions instead of six. In H. pylori and some other organisms, the terminal histidine-rich binding sites are absent, but the internal histidine sites are present, and the latter probably function as nickel donors. Deletion analysis shows that this domain alone is sufficient for metal-binding and activation of urease [].; GO: 0016151 nickel ion binding, 0006461 protein complex assembly, 0019627 urea metabolic process; PDB: 3NXZ_B 3TJA_B 3LA0_B 3TJ9_B 3NY0_A 3L9Z_A 3TJ8_A 1EAR_A 1EB0_A 1GMU_B ....
Probab=23.61 E-value=1.2e+02 Score=19.21 Aligned_cols=28 Identities=21% Similarity=0.420 Sum_probs=18.1
Q ss_pred cceEEEEecCCcceEEEEEccCcCchhHHHHHHHH
Q 034598 28 KGHVVVYVGELQKTRFVVPISYLNHPSFIDLLNRA 62 (90)
Q Consensus 28 kG~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~a 62 (90)
.-|+|+++++ .+..|| ..+.+.+||++-
T Consensus 24 NrH~p~~i~~---~~l~v~----~d~~l~~~L~~l 51 (87)
T PF05194_consen 24 NRHWPLFIEE---DELYVP----YDHVLEELLRKL 51 (87)
T ss_dssp HTT--EEEET---TEEEEE------HHHHHHHHHT
T ss_pred CCccceEEcC---CEEEec----CcHHHHHHHHHC
Confidence 3588999997 378888 666777888764
No 35
>COG4862 MecA Negative regulator of genetic competence, sporulation and motility [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Cell motility and secretion]
Probab=23.38 E-value=57 Score=25.26 Aligned_cols=27 Identities=22% Similarity=0.362 Sum_probs=23.5
Q ss_pred CchhHHHHHHHHHHhhCCccCCCcEEee
Q 034598 51 NHPSFIDLLNRAEEEFGFNHPMGGLTIP 78 (90)
Q Consensus 51 ~hP~F~~LL~~aeeEfG~~~~~G~L~IP 78 (90)
.|-.|-++++.+.+|-+|... |+|.|-
T Consensus 37 ~EE~F~~mMdEl~~ee~F~~~-GpL~iq 63 (224)
T COG4862 37 TEELFYEMMDELNLEEDFKDE-GPLWIQ 63 (224)
T ss_pred HHHHHHHHHHhcCCccccccC-CceEEE
Confidence 467899999999999999987 999874
No 36
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=23.29 E-value=1.4e+02 Score=19.17 Aligned_cols=42 Identities=24% Similarity=0.340 Sum_probs=33.7
Q ss_pred CcceEEEEecCC---cceEEEEEccCcCchhH---HHHHHHHHHhhCC
Q 034598 27 PKGHVVVYVGEL---QKTRFVVPISYLNHPSF---IDLLNRAEEEFGF 68 (90)
Q Consensus 27 pkG~~aVyVG~~---~~~RfvVp~~~L~hP~F---~~LL~~aeeEfG~ 68 (90)
++-+.+.+.|+. ...++-+...|+.|+.+ +.|+++|.|.|.-
T Consensus 28 ~~k~~V~FfG~~~~~a~~~~~~l~p~~~~~~~~ek~~~~~k~ke~~~~ 75 (80)
T cd06080 28 KQKARVNFIGDNMQSEKKGIRVVKRWLKHFDCTEKQKLTNKAKESYEQ 75 (80)
T ss_pred CCEEEEEEeCCCCceeccchhhcccccccHHHHHHHHHHHHHHHHHHH
Confidence 666778888973 24778888899999999 5899999998763
No 37
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=22.82 E-value=38 Score=27.90 Aligned_cols=26 Identities=35% Similarity=0.593 Sum_probs=19.2
Q ss_pred CCCCCCcceEEEEecCC-cceEEEEEc
Q 034598 22 DQSGVPKGHVVVYVGEL-QKTRFVVPI 47 (90)
Q Consensus 22 ~~~~vpkG~~aVyVG~~-~~~RfvVp~ 47 (90)
..--+|.|.|++|||-+ -...|.||+
T Consensus 86 n~I~IP~gSfv~Y~G~d~ie~~~~vP~ 112 (361)
T COG1759 86 NAIFIPHGSFVAYVGYDGIENEFEVPM 112 (361)
T ss_pred CeEEecCCceEEEecchhhhhcccCcc
Confidence 45679999999999962 235577764
No 38
>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=22.40 E-value=2.4e+02 Score=23.27 Aligned_cols=45 Identities=27% Similarity=0.508 Sum_probs=34.9
Q ss_pred CCCcceEEEEecC-------------------CcceEEEEEccCc--CchhHHHHHHHHHHhhCCc
Q 034598 25 GVPKGHVVVYVGE-------------------LQKTRFVVPISYL--NHPSFIDLLNRAEEEFGFN 69 (90)
Q Consensus 25 ~vpkG~~aVyVG~-------------------~~~~RfvVp~~~L--~hP~F~~LL~~aeeEfG~~ 69 (90)
..+++-+.+.||. ++..|+.||.+|= |.-...++.+.+++-||-+
T Consensus 180 ~~~~~~ltILvGNSgd~sNnHieaL~~L~~~~~~~~kIivPLsYg~~n~~Yi~~V~~~~~~lF~~~ 245 (360)
T PF07429_consen 180 KKNKGKLTILVGNSGDPSNNHIEALEALKQQFGDDVKIIVPLSYGANNQAYIQQVIQAGKELFGAE 245 (360)
T ss_pred cCCCCceEEEEcCCCCCCccHHHHHHHHHHhcCCCeEEEEECCCCCchHHHHHHHHHHHHHhcCcc
Confidence 4567889999985 1468999999996 4567888888888888853
No 39
>KOG1748 consensus Acyl carrier protein/NADH-ubiquinone oxidoreductase, NDUFAB1/SDAP subunit [Energy production and conversion; Lipid transport and metabolism; Secondary metabolites biosynthesis, transport and catabolism]
Probab=21.98 E-value=45 Score=23.79 Aligned_cols=30 Identities=33% Similarity=0.310 Sum_probs=17.5
Q ss_pred HHHHHHhhCCccCCC-cEEeeCcHHHHHhhh
Q 034598 59 LNRAEEEFGFNHPMG-GLTIPCREDAFINIT 88 (90)
Q Consensus 59 L~~aeeEfG~~~~~G-~L~IPC~~~~F~~vl 88 (90)
+---||||||+-+++ .=.|-|-.+.++.+.
T Consensus 94 VMAlEEEFgiEIpd~dAdki~t~~da~~yI~ 124 (131)
T KOG1748|consen 94 VMALEEEFGIEIPDEDADKIKTVRDAADYIA 124 (131)
T ss_pred hhhhHHHhCCccCcchhhhhCCHHHHHHHHH
Confidence 334489999987532 334555555555443
No 40
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=21.51 E-value=1e+02 Score=22.05 Aligned_cols=26 Identities=23% Similarity=0.290 Sum_probs=17.8
Q ss_pred EEEcc---CcCchhHHHHHH---HHHHhhCCc
Q 034598 44 VVPIS---YLNHPSFIDLLN---RAEEEFGFN 69 (90)
Q Consensus 44 vVp~~---~L~hP~F~~LL~---~aeeEfG~~ 69 (90)
+||.. ++.+|.|..+++ ++.+++||+
T Consensus 5 i~p~~~~~~~~~~~~~~~~~gi~~~a~~~g~~ 36 (283)
T cd06279 5 VLTDSLSYAFSDPVASQFLAGVAEVLDAAGVN 36 (283)
T ss_pred EeCCcccccccCccHHHHHHHHHHHHHHCCCE
Confidence 45543 378999999876 555667764
No 41
>PF04341 DUF485: Protein of unknown function, DUF485; InterPro: IPR007436 This family includes several putative integral membrane proteins.
Probab=20.98 E-value=72 Score=20.52 Aligned_cols=12 Identities=42% Similarity=0.847 Sum_probs=10.2
Q ss_pred cCchhHHHHHHH
Q 034598 50 LNHPSFIDLLNR 61 (90)
Q Consensus 50 L~hP~F~~LL~~ 61 (90)
++||.|++|.++
T Consensus 2 ~~~p~f~~L~r~ 13 (91)
T PF04341_consen 2 LRSPEFQELVRR 13 (91)
T ss_pred CCCHHHHHHHHH
Confidence 589999999875
No 42
>PRK13277 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase-like protein; Provisional
Probab=20.21 E-value=31 Score=28.26 Aligned_cols=30 Identities=30% Similarity=0.408 Sum_probs=21.3
Q ss_pred CCCCCCcceEEEEecCCcce-EEEEEccCcCch
Q 034598 22 DQSGVPKGHVVVYVGELQKT-RFVVPISYLNHP 53 (90)
Q Consensus 22 ~~~~vpkG~~aVyVG~~~~~-RfvVp~~~L~hP 53 (90)
..--+|.|-|++|||-+.-. .|-|| ++++-
T Consensus 86 n~i~iPh~sf~~y~g~~~ie~~~~vp--~fGnr 116 (366)
T PRK13277 86 NAIFVPNRSFAVYVGYDAIENEFKVP--IFGNR 116 (366)
T ss_pred CeEEecCCCeEEEecHHHHhhcCCCC--cccCH
Confidence 45679999999999963223 68888 45443
Done!