Query 042279
Match_columns 92
No_of_seqs 114 out of 636
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 04:41:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042279.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042279hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03090 auxin-responsive fami 100.0 4.9E-41 1.1E-45 229.0 8.8 90 1-92 1-103 (104)
2 PLN03220 uncharacterized prote 100.0 6E-40 1.3E-44 223.9 9.2 90 1-91 1-102 (105)
3 PF02519 Auxin_inducible: Auxi 100.0 1.2E-36 2.7E-41 205.2 8.1 90 1-92 1-99 (100)
4 PLN03219 uncharacterized prote 100.0 1.8E-36 3.8E-41 207.7 8.8 91 1-91 1-104 (108)
5 PF02214 BTB_2: BTB/POZ domain 84.5 0.69 1.5E-05 29.3 1.7 55 33-91 2-59 (94)
6 PRK02899 adaptor protein; Prov 82.1 1.1 2.4E-05 33.2 2.2 23 55-78 40-62 (197)
7 PRK02315 adaptor protein; Prov 76.0 2 4.3E-05 32.5 2.0 24 54-78 39-62 (233)
8 smart00666 PB1 PB1 domain. Pho 74.1 12 0.00026 22.8 4.9 49 35-89 7-65 (81)
9 PF02100 ODC_AZ: Ornithine dec 73.5 3 6.5E-05 28.2 2.2 47 40-88 23-73 (108)
10 PF05389 MecA: Negative regula 71.7 1.3 2.7E-05 32.7 0.0 25 53-78 38-62 (220)
11 cd05992 PB1 The PB1 domain is 53.6 47 0.001 19.9 6.8 33 34-70 5-37 (81)
12 cd06410 PB1_UP2 Uncharacterize 52.1 36 0.00079 22.6 4.3 49 30-83 14-74 (97)
13 smart00153 VHP Villin headpiec 50.1 11 0.00023 21.1 1.3 19 50-68 1-19 (36)
14 PF02209 VHP: Villin headpiece 49.3 8.9 0.00019 21.5 0.8 19 50-68 1-19 (36)
15 PF08861 DUF1828: Domain of un 49.3 33 0.00071 21.9 3.6 39 53-91 44-82 (90)
16 PF11834 DUF3354: Domain of un 42.3 18 0.00039 22.8 1.6 24 41-70 19-42 (69)
17 PF12058 DUF3539: Protein of u 38.6 4.9 0.00011 27.0 -1.6 13 49-61 4-16 (88)
18 cd06407 PB1_NLP A PB1 domain i 37.6 1E+02 0.0022 19.7 4.6 48 34-86 5-63 (82)
19 PRK02797 4-alpha-L-fucosyltran 36.4 95 0.0021 25.2 5.1 45 26-70 141-206 (322)
20 PRK10308 3-methyl-adenine DNA 35.4 1E+02 0.0022 23.9 5.1 62 29-91 45-120 (283)
21 KOG1748 Acyl carrier protein/N 32.1 22 0.00048 25.3 0.8 26 64-89 98-124 (131)
22 PF00651 BTB: BTB/POZ domain; 30.6 1.3E+02 0.0028 18.4 4.2 52 32-90 13-69 (111)
23 TIGR02529 EutJ ethanolamine ut 29.1 55 0.0012 24.3 2.6 29 55-83 45-73 (239)
24 PF11876 DUF3396: Protein of u 26.7 45 0.00096 24.8 1.7 40 41-80 24-65 (208)
25 PF11822 DUF3342: Domain of un 26.7 65 0.0014 26.0 2.7 47 40-90 12-63 (317)
26 PF07429 Glyco_transf_56: 4-al 26.4 1.7E+02 0.0037 24.2 5.1 45 26-70 180-245 (360)
27 TIGR03793 TOMM_pelo TOMM prope 26.3 93 0.002 19.9 3.0 26 52-78 15-44 (77)
28 PF00564 PB1: PB1 domain; Int 26.3 1.5E+02 0.0033 17.7 4.0 44 34-82 6-60 (84)
29 PF14317 YcxB: YcxB-like prote 25.5 1.2E+02 0.0027 16.6 3.1 32 27-60 27-58 (62)
30 PRK14189 bifunctional 5,10-met 25.4 1.8E+02 0.0039 22.9 5.0 53 27-92 31-85 (285)
31 COG1759 5-formaminoimidazole-4 25.3 31 0.00068 28.4 0.7 24 25-48 88-112 (361)
32 PRK13277 5-formaminoimidazole- 24.4 22 0.00048 29.1 -0.3 27 25-53 88-115 (366)
33 cd04751 Commd3 COMM_Domain con 22.8 45 0.00097 21.8 1.0 56 35-92 28-83 (95)
34 PF12062 HSNSD: heparan sulfat 22.5 65 0.0014 27.6 2.1 44 25-69 91-141 (487)
35 cd06398 PB1_Joka2 The PB1 doma 21.6 2.4E+02 0.0053 18.3 5.8 54 34-88 5-70 (91)
36 cd06536 CIDE_N_ICAD CIDE_N dom 21.5 1.4E+02 0.0031 19.5 3.1 36 40-80 12-47 (80)
37 cd01406 SIR2-like Sir2-like: P 21.0 1.1E+02 0.0025 22.2 2.9 36 30-72 1-36 (242)
38 PF05194 UreE_C: UreE urease a 20.2 1.2E+02 0.0027 19.1 2.6 27 30-63 25-51 (87)
No 1
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=4.9e-41 Score=229.05 Aligned_cols=90 Identities=53% Similarity=0.872 Sum_probs=82.5
Q ss_pred Ccccchh----hHhHHHHHHhhhcCCCc---------cCCCCceEEEeecCCCceEEEEecCCCCchhHHHhhhhhHHhc
Q 042279 1 MAIRFLR----IVNSKQALRRALMVPEA---------STVPKGHFAVYVGETERSRFVVPVSYPKHPSFQKLLSPAEEEF 67 (92)
Q Consensus 1 m~~~~~~----~~~~k~~l~r~~~~~~~---------~~vpkG~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEf 67 (92)
|||+..+ ++++||+|+||.|.++. .+|||||||||||+ +++||+||++|||||.|++||++|||||
T Consensus 1 m~~~k~~ki~~~~~~kq~l~r~~s~~~~~~~~~~~~~~~vpkG~~aVyVG~-~~~RfvVp~~~L~hP~F~~LL~~aeeEf 79 (104)
T PLN03090 1 MAIKKSNKLTQTAMLKQILKRCSSLGKKQGYDEDGLPLDVPKGHFPVYVGE-NRSRYIVPISFLTHPEFQSLLQQAEEEF 79 (104)
T ss_pred CCcccccchhHHHHHHHHHHHHHHhcccCCcccccCCCCCCCCcEEEEECC-CCEEEEEEHHHcCCHHHHHHHHHHHHHh
Confidence 7887554 56899999999998643 47899999999998 8999999999999999999999999999
Q ss_pred CCccCCCceeeeCCHHHHHHHHhcC
Q 042279 68 GFHHPMGGLTIPCSEELFMDLTCRL 92 (92)
Q Consensus 68 G~~~~~G~L~IPC~~~~F~~vl~~L 92 (92)
||+|+ |+|+|||+++.|++++|+|
T Consensus 80 Gf~~~-G~L~IPC~~~~Fe~ll~~i 103 (104)
T PLN03090 80 GFDHD-MGLTIPCEEVVFRSLTSMI 103 (104)
T ss_pred CCCCC-CcEEEeCCHHHHHHHHHHh
Confidence 99998 8999999999999999986
No 2
>PLN03220 uncharacterized protein; Provisional
Probab=100.00 E-value=6e-40 Score=223.87 Aligned_cols=90 Identities=58% Similarity=1.021 Sum_probs=81.3
Q ss_pred CcccchhhHhH-HHHHHhhhcCCC--------ccCCCCceEEEeecCC---CceEEEEecCCCCchhHHHhhhhhHHhcC
Q 042279 1 MAIRFLRIVNS-KQALRRALMVPE--------ASTVPKGHFAVYVGET---ERSRFVVPVSYPKHPSFQKLLSPAEEEFG 68 (92)
Q Consensus 1 m~~~~~~~~~~-k~~l~r~~~~~~--------~~~vpkG~~aVyVG~~---~~~RfvVp~~~L~hP~F~~LL~~aeeEfG 68 (92)
||+++++|... ||+|+|++ .++ ..+|||||||||||++ +++||+||++|||||.|++||++||||||
T Consensus 1 ~~~~~~~~~~~~k~~~~~~~-~~~~~~~~~~~~~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP~F~~LL~~AeEEfG 79 (105)
T PLN03220 1 MGLSRFAISNATKQILKLNS-LANRNRTSSSSSDHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHPSFKEFLSRAEEEFG 79 (105)
T ss_pred CCcchhhhHHHHHHHHHHHh-hcccccccccccCCCCCCeEEEEECCCCCccceEEEEEHHHcCChHHHHHHHHHHHHhC
Confidence 99999999955 99999988 332 2589999999999972 58999999999999999999999999999
Q ss_pred CccCCCceeeeCCHHHHHHHHhc
Q 042279 69 FHHPMGGLTIPCSEELFMDLTCR 91 (92)
Q Consensus 69 ~~~~~G~L~IPC~~~~F~~vl~~ 91 (92)
|+|++|+|+|||+++.|++++++
T Consensus 80 f~~~~G~L~IPCd~~~F~~ll~s 102 (105)
T PLN03220 80 FNHPMGGLTIPCREEVFLDLIAS 102 (105)
T ss_pred CCCCCCCEEeeCCHHHHHHHHHh
Confidence 99966999999999999999874
No 3
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=100.00 E-value=1.2e-36 Score=205.17 Aligned_cols=90 Identities=58% Similarity=0.869 Sum_probs=76.6
Q ss_pred CcccchhhHhHHHHHHhhhcCC------C---ccCCCCceEEEeecCCCceEEEEecCCCCchhHHHhhhhhHHhcCCcc
Q 042279 1 MAIRFLRIVNSKQALRRALMVP------E---ASTVPKGHFAVYVGETERSRFVVPVSYPKHPSFQKLLSPAEEEFGFHH 71 (92)
Q Consensus 1 m~~~~~~~~~~k~~l~r~~~~~------~---~~~vpkG~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~ 71 (92)
|.-++.++..+++...++.+.. + ..++|+||+|||||+ +++||+||++|||||.|++||++|||||||+|
T Consensus 1 M~~~~k~~~~~~k~~~~~~~~~~~~~~~~~~~~~~vp~G~~~VyVG~-~~~Rfvvp~~~L~hp~f~~LL~~aeeEfG~~~ 79 (100)
T PF02519_consen 1 MASRLKSLASAKKWQSRARSKSSSSSSSRSSSESDVPKGHFAVYVGE-ERRRFVVPVSYLNHPLFQELLEQAEEEFGFDQ 79 (100)
T ss_pred CccHHHHHHHHHhhhhhhhhcccccccccccccCCCCCCeEEEEeCc-cceEEEechHHcCchhHHHHHHHHhhhcCcCC
Confidence 6666766666665555444321 1 277899999999998 99999999999999999999999999999999
Q ss_pred CCCceeeeCCHHHHHHHHhcC
Q 042279 72 PMGGLTIPCSEELFMDLTCRL 92 (92)
Q Consensus 72 ~~G~L~IPC~~~~F~~vl~~L 92 (92)
+ |+|+|||+++.|++++|+|
T Consensus 80 ~-G~l~iPC~~~~Fe~~l~~l 99 (100)
T PF02519_consen 80 D-GPLTIPCDVVLFEHLLWLL 99 (100)
T ss_pred C-CcEEeeCCHHHHHHHHHHh
Confidence 7 9999999999999999986
No 4
>PLN03219 uncharacterized protein; Provisional
Probab=100.00 E-value=1.8e-36 Score=207.70 Aligned_cols=91 Identities=53% Similarity=0.888 Sum_probs=75.2
Q ss_pred CcccchhhHhHHHHHHhhhcC------------CCccCCCCceEEEeecC-CCceEEEEecCCCCchhHHHhhhhhHHhc
Q 042279 1 MAIRFLRIVNSKQALRRALMV------------PEASTVPKGHFAVYVGE-TERSRFVVPVSYPKHPSFQKLLSPAEEEF 67 (92)
Q Consensus 1 m~~~~~~~~~~k~~l~r~~~~------------~~~~~vpkG~~aVyVG~-~~~~RfvVp~~~L~hP~F~~LL~~aeeEf 67 (92)
||.-..-...+||++|-.+-. +...+|||||+|||||+ ++++||+||++|||||.|++||++|||||
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vpkGh~aVYVG~~~E~kRFvVPi~yL~hP~F~~LL~~AeEEf 80 (108)
T PLN03219 1 MGLMRSMLPNAKQIFKSQSMRNKNGSSSPSSSTTTSGLVPKGHVAVYVGEQMEKKRFVVPISYLNHPLFREFLNRAEEEC 80 (108)
T ss_pred CchHHHHHhhHHHHHHHHHHhcccCCCCCccCCCCCCCCCCCeEEEEECCCCCceEEEEEHHHcCChHHHHHHHHHHHHh
Confidence 555555555777776622211 12367999999999998 46999999999999999999999999999
Q ss_pred CCccCCCceeeeCCHHHHHHHHhc
Q 042279 68 GFHHPMGGLTIPCSEELFMDLTCR 91 (92)
Q Consensus 68 G~~~~~G~L~IPC~~~~F~~vl~~ 91 (92)
||+|++|+|+|||+++.|++++++
T Consensus 81 Gf~~~~G~L~IPCd~~~F~~ll~~ 104 (108)
T PLN03219 81 GFHHSMGGLTIPCREESFLHLITS 104 (108)
T ss_pred CCCCCCCCEEEeCCHHHHHHHHHh
Confidence 999866999999999999999975
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=84.45 E-value=0.69 Score=29.27 Aligned_cols=55 Identities=22% Similarity=0.229 Sum_probs=39.0
Q ss_pred EEeecCCCceEEEEecCCCC-ch--hHHHhhhhhHHhcCCccCCCceeeeCCHHHHHHHHhc
Q 042279 33 AVYVGETERSRFVVPVSYPK-HP--SFQKLLSPAEEEFGFHHPMGGLTIPCSEELFMDLTCR 91 (92)
Q Consensus 33 aVyVG~~~~~RfvVp~~~L~-hP--~F~~LL~~aeeEfG~~~~~G~L~IPC~~~~F~~vl~~ 91 (92)
.+=||. ++|.++.+.|. +| .|..+++...... ++.++|.+-|-++...|++|+.-
T Consensus 2 ~lNVGG---~~f~~~~~tL~~~~~s~l~~~~~~~~~~~-~~~~~~~~fiDRdp~~F~~IL~y 59 (94)
T PF02214_consen 2 RLNVGG---TIFETSRSTLTRYPDSLLARLFSGERSDD-YDDDDGEYFIDRDPELFEYILNY 59 (94)
T ss_dssp EEEETT---EEEEEEHHHHHTSTTSTTTSHHHTGHGGG-EETTTTEEEESS-HHHHHHHHHH
T ss_pred EEEECC---EEEEEcHHHHhhCCCChhhhHHhhccccc-cCCccceEEeccChhhhhHHHHH
Confidence 345775 99999998887 54 6778877652222 22234899999999999999864
No 6
>PRK02899 adaptor protein; Provisional
Probab=82.14 E-value=1.1 Score=33.24 Aligned_cols=23 Identities=26% Similarity=0.671 Sum_probs=20.1
Q ss_pred hHHHhhhhhHHhcCCccCCCceee
Q 042279 55 SFQKLLSPAEEEFGFHHPMGGLTI 78 (92)
Q Consensus 55 ~F~~LL~~aeeEfG~~~~~G~L~I 78 (92)
.|.++|++|..|+||.-+ |||+|
T Consensus 40 lF~~mm~Ea~~e~~F~~~-~pl~~ 62 (197)
T PRK02899 40 LFRDMMQEANKELGFEAD-GPIAV 62 (197)
T ss_pred HHHHHHHHhhhccCcccC-CeEEE
Confidence 477789999999999976 99986
No 7
>PRK02315 adaptor protein; Provisional
Probab=75.98 E-value=2 Score=32.52 Aligned_cols=24 Identities=25% Similarity=0.361 Sum_probs=21.4
Q ss_pred hhHHHhhhhhHHhcCCccCCCceee
Q 042279 54 PSFQKLLSPAEEEFGFHHPMGGLTI 78 (92)
Q Consensus 54 P~F~~LL~~aeeEfG~~~~~G~L~I 78 (92)
-.|.++|++|..|+||..+ |+|+|
T Consensus 39 ~fF~~mm~Ea~~e~~F~~~-~pl~~ 62 (233)
T PRK02315 39 EFFYSMMDEVDEEDDFADE-GPLWF 62 (233)
T ss_pred HHHHHHHHHhccccCcccC-CeEEE
Confidence 4699999999999999975 99986
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=74.07 E-value=12 Score=22.80 Aligned_cols=49 Identities=24% Similarity=0.344 Sum_probs=34.8
Q ss_pred eecCCCceEEEEecCCCCchhHHHhhhhhHHhcCCc----------cCCCceeeeCCHHHHHHHH
Q 042279 35 YVGETERSRFVVPVSYPKHPSFQKLLSPAEEEFGFH----------HPMGGLTIPCSEELFMDLT 89 (92)
Q Consensus 35 yVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~----------~~~G~L~IPC~~~~F~~vl 89 (92)
+-|+ +.+||.+|- ...|.+|..+..+.|+.. .++..++|.++. ++...+
T Consensus 7 ~~~~-~~~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~-Dl~~a~ 65 (81)
T smart00666 7 RYGG-ETRRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDE-DLEEAI 65 (81)
T ss_pred EECC-EEEEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHH-HHHHHH
Confidence 3465 899999985 778999999999999874 122367777764 444433
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=73.46 E-value=3 Score=28.24 Aligned_cols=47 Identities=32% Similarity=0.356 Sum_probs=23.8
Q ss_pred CceEEE-EecCCCCc---hhHHHhhhhhHHhcCCccCCCceeeeCCHHHHHHH
Q 042279 40 ERSRFV-VPVSYPKH---PSFQKLLSPAEEEFGFHHPMGGLTIPCSEELFMDL 88 (92)
Q Consensus 40 ~~~Rfv-Vp~~~L~h---P~F~~LL~~aeeEfG~~~~~G~L~IPC~~~~F~~v 88 (92)
++.=|+ +|-+.+.+ ..|.+||+.|||++|.++ -.+.++=+-.....+
T Consensus 23 ~~~L~V~ip~~~~~~~~K~~lvaLLElAee~L~c~~--vvic~~k~~~d~~~L 73 (108)
T PF02100_consen 23 ERTLFVFIPSSALGQGSKESLVALLELAEEKLGCSH--VVICLDKNRPDRASL 73 (108)
T ss_dssp TTEEEEE-SS---SS--SHHHHHHHHHHHHHH------EEEEE---SS-HHHH
T ss_pred CCEEEEEECCcccccccHHHHHHHHHHhcCcCCCCE--EEEEEECCchhHHHh
Confidence 455666 46554444 459999999999999875 366666444443333
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=71.66 E-value=1.3 Score=32.75 Aligned_cols=25 Identities=40% Similarity=0.643 Sum_probs=0.0
Q ss_pred chhHHHhhhhhHHhcCCccCCCceee
Q 042279 53 HPSFQKLLSPAEEEFGFHHPMGGLTI 78 (92)
Q Consensus 53 hP~F~~LL~~aeeEfG~~~~~G~L~I 78 (92)
+-.|.++|++|.+|+||..+ |+|++
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
>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=53.62 E-value=47 Score=19.90 Aligned_cols=33 Identities=42% Similarity=0.580 Sum_probs=27.0
Q ss_pred EeecCCCceEEEEecCCCCchhHHHhhhhhHHhcCCc
Q 042279 34 VYVGETERSRFVVPVSYPKHPSFQKLLSPAEEEFGFH 70 (92)
Q Consensus 34 VyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~ 70 (92)
++-++ +.+||.+|. .++.|.+|..+-.+.|+..
T Consensus 5 ~~~~~-~~~~~~~~~---~~~s~~~L~~~i~~~~~~~ 37 (81)
T cd05992 5 VKYGG-EIRRFVVVS---RSISFEDLRSKIAEKFGLD 37 (81)
T ss_pred EEecC-CCEEEEEec---CCCCHHHHHHHHHHHhCCC
Confidence 44454 799999997 7888999999998888875
No 12
>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=52.07 E-value=36 Score=22.61 Aligned_cols=49 Identities=29% Similarity=0.282 Sum_probs=34.1
Q ss_pred ceEEEeecCCCceEEEEecCCCCchhHHHhhhhhHHhcCCccC------------CCceeeeCCHH
Q 042279 30 GHFAVYVGETERSRFVVPVSYPKHPSFQKLLSPAEEEFGFHHP------------MGGLTIPCSEE 83 (92)
Q Consensus 30 G~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~------------~G~L~IPC~~~ 83 (92)
+--.=|||. +.+-..|+-+ -.|.+|..+..+.++..+. ++-+.+.||.+
T Consensus 14 dg~l~Y~GG-~tr~i~V~r~----~s~~el~~kl~~~~~~~~~~~lky~Lp~edld~Lisv~~DeD 74 (97)
T cd06410 14 DGQLRYVGG-ETRIVSVDRS----ISFKELVSKLSELFGAGVVVTLKYQLPDEDLDALISVSNDED 74 (97)
T ss_pred CCCEEEcCC-ceEEEEEcCC----CCHHHHHHHHHHHhCCCCceEEEEEcCCCCcceeEEecCcHH
Confidence 333469997 8888888866 4677788887787776651 24667778864
No 13
>smart00153 VHP Villin headpiece domain.
Probab=50.09 E-value=11 Score=21.07 Aligned_cols=19 Identities=26% Similarity=0.508 Sum_probs=17.1
Q ss_pred CCCchhHHHhhhhhHHhcC
Q 042279 50 YPKHPSFQKLLSPAEEEFG 68 (92)
Q Consensus 50 ~L~hP~F~~LL~~aeeEfG 68 (92)
||+.-.|+..+.++.+||-
T Consensus 1 yLsdeeF~~vfgmsr~eF~ 19 (36)
T smart00153 1 YLSDEDFEEVFGMTREEFY 19 (36)
T ss_pred CCCHHHHHHHHCCCHHHHH
Confidence 7899999999999999983
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=49.31 E-value=8.9 Score=21.53 Aligned_cols=19 Identities=32% Similarity=0.551 Sum_probs=15.2
Q ss_pred CCCchhHHHhhhhhHHhcC
Q 042279 50 YPKHPSFQKLLSPAEEEFG 68 (92)
Q Consensus 50 ~L~hP~F~~LL~~aeeEfG 68 (92)
||+.-.|+++..++.+||-
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 7889999999999999984
No 15
>PF08861 DUF1828: Domain of unknown function DUF1828; InterPro: IPR014960 These proteins are functionally uncharacterised.
Probab=49.26 E-value=33 Score=21.86 Aligned_cols=39 Identities=31% Similarity=0.340 Sum_probs=33.5
Q ss_pred chhHHHhhhhhHHhcCCccCCCceeeeCCHHHHHHHHhc
Q 042279 53 HPSFQKLLSPAEEEFGFHHPMGGLTIPCSEELFMDLTCR 91 (92)
Q Consensus 53 hP~F~~LL~~aeeEfG~~~~~G~L~IPC~~~~F~~vl~~ 91 (92)
.|.=+++|+..-..||..-++|.|.+.++.+.|-....+
T Consensus 44 s~~R~~~l~~il~~~gv~~~~~el~~~~~~~~~~~~~~~ 82 (90)
T PF08861_consen 44 SKKRKKILNSILNGFGVELDEGELFIKTSEENFPQAKHR 82 (90)
T ss_pred chHHHHHHHHHHHHcCccccCCEEEEEeCHHHHHHHHHH
Confidence 677789999999999999888999999999988765543
No 16
>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=42.31 E-value=18 Score=22.85 Aligned_cols=24 Identities=38% Similarity=0.620 Sum_probs=19.4
Q ss_pred ceEEEEecCCCCchhHHHhhhhhHHhcCCc
Q 042279 41 RSRFVVPVSYPKHPSFQKLLSPAEEEFGFH 70 (92)
Q Consensus 41 ~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~ 70 (92)
.+=..+| -.+++||+.|++.||+.
T Consensus 19 GKvi~lP------~SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 19 GKVIWLP------DSLEELLKIASEKFGFS 42 (69)
T ss_pred CEEEEcC------ccHHHHHHHHHHHhCCC
Confidence 4555666 36999999999999995
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=38.57 E-value=4.9 Score=26.98 Aligned_cols=13 Identities=38% Similarity=0.784 Sum_probs=9.1
Q ss_pred CCCCchhHHHhhh
Q 042279 49 SYPKHPSFQKLLS 61 (92)
Q Consensus 49 ~~L~hP~F~~LL~ 61 (92)
.|||||.|--|-.
T Consensus 4 ~YLNHPtFGlLy~ 16 (88)
T PF12058_consen 4 TYLNHPTFGLLYR 16 (88)
T ss_dssp -EEEETTTEEEEE
T ss_pred ccccCCccchhee
Confidence 5899999865543
No 18
>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=37.61 E-value=1e+02 Score=19.72 Aligned_cols=48 Identities=25% Similarity=0.381 Sum_probs=33.4
Q ss_pred EeecCCCceEEEEecCCCCchhHHHhhhhhHHhcCCcc-----------CCCceeeeCCHHHHH
Q 042279 34 VYVGETERSRFVVPVSYPKHPSFQKLLSPAEEEFGFHH-----------PMGGLTIPCSEELFM 86 (92)
Q Consensus 34 VyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~-----------~~G~L~IPC~~~~F~ 86 (92)
+..|+ +..||.+|.+ ..|++|-++-++-|+.+. ++...+|.|+.+.=+
T Consensus 5 ~~~~~-d~~r~~l~~~----~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~e 63 (82)
T cd06407 5 ATYGE-EKIRFRLPPS----WGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEE 63 (82)
T ss_pred EEeCC-eEEEEEcCCC----CCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHH
Confidence 34465 8999999864 368999998888888753 224567778765433
No 19
>PRK02797 4-alpha-L-fucosyltransferase; Provisional
Probab=36.35 E-value=95 Score=25.22 Aligned_cols=45 Identities=18% Similarity=0.438 Sum_probs=33.2
Q ss_pred CCCCceEEEeecC-------------------CCceEEEEecCC--CCchhHHHhhhhhHHhcCCc
Q 042279 26 TVPKGHFAVYVGE-------------------TERSRFVVPVSY--PKHPSFQKLLSPAEEEFGFH 70 (92)
Q Consensus 26 ~vpkG~~aVyVG~-------------------~~~~RfvVp~~~--L~hP~F~~LL~~aeeEfG~~ 70 (92)
..+++-++|.||. ++.-|+.||.+| =|.--.++..+.+.+-||-+
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 4467889999986 134599999999 46556677777777788743
No 20
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=35.45 E-value=1e+02 Score=23.88 Aligned_cols=62 Identities=19% Similarity=0.221 Sum_probs=39.6
Q ss_pred CceEEEeecCCCceEEEEecCCCCchhHHHhhhhhHHhcCCccC--------------CCceeeeCCHHHHHHHHhc
Q 042279 29 KGHFAVYVGETERSRFVVPVSYPKHPSFQKLLSPAEEEFGFHHP--------------MGGLTIPCSEELFMDLTCR 91 (92)
Q Consensus 29 kG~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~--------------~G~L~IPC~~~~F~~vl~~ 91 (92)
.|++.|.-.+ ...++.+.++.-.-+....++.....-||.+.+ .-+|++|...+.||.+++.
T Consensus 45 ~~~~~v~~~~-~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L~~~~~~~~GlR~p~~~d~fE~lv~a 120 (283)
T PRK10308 45 RGVVTVIPDI-ARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGKLGAARPGLRLPGSVDAFEQGVRA 120 (283)
T ss_pred cEEEEEEEcC-CCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCCcCCCCCCHHHHHHHH
Confidence 4666665544 455666666653334455666666666666544 2469999999999988764
No 21
>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=32.07 E-value=22 Score=25.35 Aligned_cols=26 Identities=27% Similarity=0.298 Sum_probs=16.2
Q ss_pred HHhcCCccCCC-ceeeeCCHHHHHHHH
Q 042279 64 EEEFGFHHPMG-GLTIPCSEELFMDLT 89 (92)
Q Consensus 64 eeEfG~~~~~G-~L~IPC~~~~F~~vl 89 (92)
||||||+.+++ .=.|-|-.+.++.|.
T Consensus 98 EEEFgiEIpd~dAdki~t~~da~~yI~ 124 (131)
T KOG1748|consen 98 EEEFGIEIPDEDADKIKTVRDAADYIA 124 (131)
T ss_pred HHHhCCccCcchhhhhCCHHHHHHHHH
Confidence 89999997643 234555555555543
No 22
>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=30.62 E-value=1.3e+02 Score=18.36 Aligned_cols=52 Identities=23% Similarity=0.436 Sum_probs=34.2
Q ss_pred EEEeecCCCceEEEEecCCC--CchhHHHhhhhhHHhcCCccCCC--ceeee-CCHHHHHHHHh
Q 042279 32 FAVYVGETERSRFVVPVSYP--KHPSFQKLLSPAEEEFGFHHPMG--GLTIP-CSEELFMDLTC 90 (92)
Q Consensus 32 ~aVyVG~~~~~RfvVp~~~L--~hP~F~~LL~~aeeEfG~~~~~G--~L~IP-C~~~~F~~vl~ 90 (92)
+.+.|| +.++|-+.-..| ..|.|+.+++.. +.... + .+.++ |+.+.|+.+++
T Consensus 13 ~~i~v~--d~~~~~vhk~iL~~~S~~F~~~~~~~----~~~~~-~~~~i~~~~~~~~~~~~~l~ 69 (111)
T PF00651_consen 13 VTIRVG--DGKTFYVHKNILAARSPYFRNLFEGS----KFKES-TVPEISLPDVSPEAFEAFLE 69 (111)
T ss_dssp EEEEET--TTEEEEE-HHHHHHHBHHHHHHHTTT----TSTTS-SEEEEEETTSCHHHHHHHHH
T ss_pred EEEEEC--CCEEEeechhhhhccchhhhhccccc----ccccc-cccccccccccccccccccc
Confidence 345566 258888887777 468899999988 11112 3 35544 88889988875
No 23
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein.
Probab=29.11 E-value=55 Score=24.34 Aligned_cols=29 Identities=17% Similarity=0.273 Sum_probs=23.4
Q ss_pred hHHHhhhhhHHhcCCccCCCceeeeCCHH
Q 042279 55 SFQKLLSPAEEEFGFHHPMGGLTIPCSEE 83 (92)
Q Consensus 55 ~F~~LL~~aeeEfG~~~~~G~L~IPC~~~ 83 (92)
.++.|.++|++-.|...++-.+++|+...
T Consensus 45 ~l~~l~~~a~~~~g~~~~~vvisVP~~~~ 73 (239)
T TIGR02529 45 IVRRLKDTLEQKLGIELTHAATAIPPGTI 73 (239)
T ss_pred HHHHHHHHHHHHhCCCcCcEEEEECCCCC
Confidence 58888888888889877667899998653
No 24
>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=26.73 E-value=45 Score=24.85 Aligned_cols=40 Identities=20% Similarity=0.335 Sum_probs=31.6
Q ss_pred ceEEEEecCCCCch--hHHHhhhhhHHhcCCccCCCceeeeC
Q 042279 41 RSRFVVPVSYPKHP--SFQKLLSPAEEEFGFHHPMGGLTIPC 80 (92)
Q Consensus 41 ~~RfvVp~~~L~hP--~F~~LL~~aeeEfG~~~~~G~L~IPC 80 (92)
.=+|.+|++||..+ .|++|+....+++.+.|--+++.+-.
T Consensus 24 ~l~f~~P~~~l~~~~~~~~~l~~~~a~~L~~~~G~aGl~~~~ 65 (208)
T PF11876_consen 24 YLSFSLPLEWLEEGPGHFRALFLELAERLPPSHGYAGLAFNL 65 (208)
T ss_pred EEEEEeCHHHHhcCcHHHHHHHHHHHHHCCCCeEeeEEEEec
Confidence 46899999999873 49999999999887776556666654
No 25
>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=26.66 E-value=65 Score=26.04 Aligned_cols=47 Identities=19% Similarity=0.326 Sum_probs=35.1
Q ss_pred CceEEEEecCCCCc--hhHHHhhhh---hHHhcCCccCCCceeeeCCHHHHHHHHh
Q 042279 40 ERSRFVVPVSYPKH--PSFQKLLSP---AEEEFGFHHPMGGLTIPCSEELFMDLTC 90 (92)
Q Consensus 40 ~~~RfvVp~~~L~h--P~F~~LL~~---aeeEfG~~~~~G~L~IPC~~~~F~~vl~ 90 (92)
.++=|.-|.+.|-+ ..|++.|.. +.++.. + =.|.+-||+..|+.++.
T Consensus 12 ~~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~~---~-idisVhCDv~iF~WLm~ 63 (317)
T PF11822_consen 12 EKRDFTCPRDLLVSEMRYFAEYLSRYINDSQRWE---E-IDISVHCDVHIFEWLMR 63 (317)
T ss_pred cceeeeccHHHHHHhhHHHHHHHhhcccccCcCC---C-cceEEecChhHHHHHHH
Confidence 57789999888854 569999965 444332 2 35999999999999875
No 26
>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=26.37 E-value=1.7e+02 Score=24.16 Aligned_cols=45 Identities=27% Similarity=0.567 Sum_probs=34.8
Q ss_pred CCCCceEEEeecC-------------------CCceEEEEecCCCC--chhHHHhhhhhHHhcCCc
Q 042279 26 TVPKGHFAVYVGE-------------------TERSRFVVPVSYPK--HPSFQKLLSPAEEEFGFH 70 (92)
Q Consensus 26 ~vpkG~~aVyVG~-------------------~~~~RfvVp~~~L~--hP~F~~LL~~aeeEfG~~ 70 (92)
..++|-++|.||. ++..|++||.+|=. .-..+++.+.+++-||-+
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 4457899999985 14689999999974 567788888888888854
No 27
>TIGR03793 TOMM_pelo TOMM propeptide domain. This model represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM). Oddly, most of this seqence region appears homologous to nitrile hydratase subunits. This family is expanded especially in Pelotomaculum thermopropionicum SI.
Probab=26.35 E-value=93 Score=19.90 Aligned_cols=26 Identities=23% Similarity=0.433 Sum_probs=17.5
Q ss_pred CchhHHHhh-h---hhHHhcCCccCCCceee
Q 042279 52 KHPSFQKLL-S---PAEEEFGFHHPMGGLTI 78 (92)
Q Consensus 52 ~hP~F~~LL-~---~aeeEfG~~~~~G~L~I 78 (92)
..|.|++.| . .+=+||||+-+ ..+.|
T Consensus 15 ~Dp~Fr~~Ll~DPraaL~e~G~~~P-~~~~i 44 (77)
T TIGR03793 15 EDEAFKQALLTNPKEALEREGVQVP-AEVEV 44 (77)
T ss_pred cCHHHHHHHHHCHHHHHHHhCCCCC-CceEE
Confidence 578899855 4 44567899977 44444
No 28
>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=26.33 E-value=1.5e+02 Score=17.69 Aligned_cols=44 Identities=32% Similarity=0.426 Sum_probs=29.4
Q ss_pred EeecCCCceE-EEEecCCCCchhHHHhhhhhHHhcCCc----------cCCCceeeeCCH
Q 042279 34 VYVGETERSR-FVVPVSYPKHPSFQKLLSPAEEEFGFH----------HPMGGLTIPCSE 82 (92)
Q Consensus 34 VyVG~~~~~R-fvVp~~~L~hP~F~~LL~~aeeEfG~~----------~~~G~L~IPC~~ 82 (92)
++-++ +.+| +.+| +.+.|.+|.++.++.||.. .++-.++|.++.
T Consensus 6 ~~~~~-~~~~~~~~~----~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~ 60 (84)
T PF00564_consen 6 VRYGG-DIRRIISLP----SDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDE 60 (84)
T ss_dssp EEETT-EEEEEEEEC----STSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHH
T ss_pred EEECC-eeEEEEEcC----CCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHH
Confidence 34454 5555 5555 5679999999999999983 221256777764
No 29
>PF14317 YcxB: YcxB-like protein
Probab=25.49 E-value=1.2e+02 Score=16.56 Aligned_cols=32 Identities=19% Similarity=0.373 Sum_probs=23.3
Q ss_pred CCCceEEEeecCCCceEEEEecCCCCchhHHHhh
Q 042279 27 VPKGHFAVYVGETERSRFVVPVSYPKHPSFQKLL 60 (92)
Q Consensus 27 vpkG~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL 60 (92)
.-+.++-+|++. ..-++||-+.++.-...++.
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 69999999988844444443
No 30
>PRK14189 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=25.44 E-value=1.8e+02 Score=22.89 Aligned_cols=53 Identities=23% Similarity=0.247 Sum_probs=37.9
Q ss_pred CCCceEEEeecCCCceEEEEecCCCCchhHHHhhhhhHHhcCCccCCCceeee--CCHHHHHHHHhcC
Q 042279 27 VPKGHFAVYVGETERSRFVVPVSYPKHPSFQKLLSPAEEEFGFHHPMGGLTIP--CSEELFMDLTCRL 92 (92)
Q Consensus 27 vpkG~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~~G~L~IP--C~~~~F~~vl~~L 92 (92)
.+.+...|.||+ +. ..-....--.++.+|.|++.+ .+.+| ++.+.|+..+..|
T Consensus 31 ~~p~Laii~vg~-d~----------as~~Yv~~k~k~~~~~Gi~~~--~~~l~~~~~~~~l~~~I~~l 85 (285)
T PRK14189 31 HQPGLAVILVGD-NP----------ASQVYVRNKVKACEDNGFHSL--KDRYPADLSEAELLARIDEL 85 (285)
T ss_pred CCCeEEEEEeCC-Cc----------hHHHHHHHHHHHHHHcCCEEE--EEECCCCCCHHHHHHHHHHH
Confidence 345888999997 22 233455667788999999865 57777 7788888877653
No 31
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=25.29 E-value=31 Score=28.36 Aligned_cols=24 Identities=38% Similarity=0.732 Sum_probs=17.9
Q ss_pred cCCCCceEEEeecCC-CceEEEEec
Q 042279 25 STVPKGHFAVYVGET-ERSRFVVPV 48 (92)
Q Consensus 25 ~~vpkG~~aVyVG~~-~~~RfvVp~ 48 (92)
.-+|.|-|++|||-+ --+.|.||+
T Consensus 88 I~IP~gSfv~Y~G~d~ie~~~~vP~ 112 (361)
T COG1759 88 IFIPHGSFVAYVGYDGIENEFEVPM 112 (361)
T ss_pred EEecCCceEEEecchhhhhcccCcc
Confidence 468999999999962 235577774
No 32
>PRK13277 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase-like protein; Provisional
Probab=24.41 E-value=22 Score=29.12 Aligned_cols=27 Identities=41% Similarity=0.551 Sum_probs=19.7
Q ss_pred cCCCCceEEEeecCCCce-EEEEecCCCCc
Q 042279 25 STVPKGHFAVYVGETERS-RFVVPVSYPKH 53 (92)
Q Consensus 25 ~~vpkG~~aVyVG~~~~~-RfvVp~~~L~h 53 (92)
.-+|.|-|++|||-+.-. .|-|| .+.+
T Consensus 88 i~iPh~sf~~y~g~~~ie~~~~vp--~fGn 115 (366)
T PRK13277 88 IFVPNRSFAVYVGYDAIENEFKVP--IFGN 115 (366)
T ss_pred EEecCCCeEEEecHHHHhhcCCCC--cccC
Confidence 468999999999973323 68888 4444
No 33
>cd04751 Commd3 COMM_Domain containing protein 3. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=22.79 E-value=45 Score=21.80 Aligned_cols=56 Identities=20% Similarity=0.186 Sum_probs=31.4
Q ss_pred eecCCCceEEEEecCCCCchhHHHhhhhhHHhcCCccCCCceeeeCCHHHHHHHHhcC
Q 042279 35 YVGETERSRFVVPVSYPKHPSFQKLLSPAEEEFGFHHPMGGLTIPCSEELFMDLTCRL 92 (92)
Q Consensus 35 yVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~~G~L~IPC~~~~F~~vl~~L 92 (92)
+++-+=+--|.|..+.++++.+--.+-+-.-+-|=. . ..+.+-|+++.|+++++.|
T Consensus 28 l~dv~WRld~~lsS~~l~~~~~p~~~i~L~~~~~~~-~-~~i~f~c~~e~L~~Li~~L 83 (95)
T cd04751 28 ITDVNWRLDYVVSSKHLGKVNQPIYLIQLSTENGEN-K-PDINFTCTLEQLQDLVNKL 83 (95)
T ss_pred eecCceEEEEEEcccccCcccceeEEEEEeccCCCC-c-ceEEEEeCHHHHHHHHHHH
Confidence 444423556666666665433332222222221211 2 4799999999999998764
No 34
>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=22.46 E-value=65 Score=27.60 Aligned_cols=44 Identities=23% Similarity=0.440 Sum_probs=37.3
Q ss_pred cCCC-CceEEEeecCCCceEEEEec-----CCCCchh-HHHhhhhhHHhcCC
Q 042279 25 STVP-KGHFAVYVGETERSRFVVPV-----SYPKHPS-FQKLLSPAEEEFGF 69 (92)
Q Consensus 25 ~~vp-kG~~aVyVG~~~~~RfvVp~-----~~L~hP~-F~~LL~~aeeEfG~ 69 (92)
.-+| ||.+|+++-. ++.||-|-+ .|+|-+. -++||++=-.|||-
T Consensus 91 ei~~~kg~lP~LT~~-~kGRy~lII~ENl~kYlnld~wNR~LLdkYC~ey~V 141 (487)
T PF12062_consen 91 EIASGKGDLPVLTDN-DKGRYSLIIFENLLKYLNLDSWNRELLDKYCREYGV 141 (487)
T ss_pred EEccCCCCCCccccC-CCCcEEEEEehhHHHHcCChHHHHHHHHHHhHccCc
Confidence 4455 6999999976 788999887 8999998 89999999888874
No 35
>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=21.58 E-value=2.4e+02 Score=18.34 Aligned_cols=54 Identities=22% Similarity=0.225 Sum_probs=35.2
Q ss_pred EeecCCCceEEEEecCCC-CchhHHHhhhhhHHhcCCcc-----------CCCceeeeCCHHHHHHH
Q 042279 34 VYVGETERSRFVVPVSYP-KHPSFQKLLSPAEEEFGFHH-----------PMGGLTIPCSEELFMDL 88 (92)
Q Consensus 34 VyVG~~~~~RfvVp~~~L-~hP~F~~LL~~aeeEfG~~~-----------~~G~L~IPC~~~~F~~v 88 (92)
|.-|+ +.+||-+|.+=. .+..|..|.++-++-|.... ++.-++|.|+.+.-+.+
T Consensus 5 v~y~~-~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~ 70 (91)
T cd06398 5 VKYGG-TLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAI 70 (91)
T ss_pred EEeCC-EEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHH
Confidence 33465 899999996411 14478888888888776653 22357888886655443
No 36
>cd06536 CIDE_N_ICAD CIDE_N domain of ICAD. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD (DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and release of active DFF40/CAD nuclease.
Probab=21.46 E-value=1.4e+02 Score=19.45 Aligned_cols=36 Identities=25% Similarity=0.319 Sum_probs=25.0
Q ss_pred CceEEEEecCCCCchhHHHhhhhhHHhcCCccCCCceeeeC
Q 042279 40 ERSRFVVPVSYPKHPSFQKLLSPAEEEFGFHHPMGGLTIPC 80 (92)
Q Consensus 40 ~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~~G~L~IPC 80 (92)
..+||=|=.+ .+++|+.++.+-|....++++++|=+
T Consensus 12 r~~k~GV~A~-----sL~eL~~K~~~~l~l~~~~~~~~lvL 47 (80)
T cd06536 12 RQKQHGVAAS-----SLEELRIKACESLGFDSSSAPITLVL 47 (80)
T ss_pred CCeeEeEEcC-----CHHHHHHHHHHHhCCCCCCCceEEEE
Confidence 4566666544 46799999999999985433566654
No 37
>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=20.99 E-value=1.1e+02 Score=22.21 Aligned_cols=36 Identities=22% Similarity=0.473 Sum_probs=27.8
Q ss_pred ceEEEeecCCCceEEEEecCCCCchhHHHhhhhhHHhcCCccC
Q 042279 30 GHFAVYVGETERSRFVVPVSYPKHPSFQKLLSPAEEEFGFHHP 72 (92)
Q Consensus 30 G~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~aeeEfG~~~~ 72 (92)
|.++++||-+-..+ .+-|...+|++...+++|.+.+
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 77899999732222 5789999999999999987644
No 38
>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=20.21 E-value=1.2e+02 Score=19.09 Aligned_cols=27 Identities=22% Similarity=0.514 Sum_probs=17.5
Q ss_pred ceEEEeecCCCceEEEEecCCCCchhHHHhhhhh
Q 042279 30 GHFAVYVGETERSRFVVPVSYPKHPSFQKLLSPA 63 (92)
Q Consensus 30 G~~aVyVG~~~~~RfvVp~~~L~hP~F~~LL~~a 63 (92)
=|+|+++++ .+..|| ..+.+.++|++-
T Consensus 25 rH~p~~i~~---~~l~v~----~d~~l~~~L~~l 51 (87)
T PF05194_consen 25 RHWPLFIEE---DELYVP----YDHVLEELLRKL 51 (87)
T ss_dssp TT--EEEET---TEEEEE------HHHHHHHHHT
T ss_pred CccceEEcC---CEEEec----CcHHHHHHHHHC
Confidence 478999997 388888 666777787763
Done!