Query 046487
Match_columns 106
No_of_seqs 121 out of 626
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 12:38:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046487.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046487hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03090 auxin-responsive fami 100.0 1.4E-47 3E-52 267.4 11.0 104 1-106 1-104 (104)
2 PLN03220 uncharacterized prote 100.0 7.9E-37 1.7E-41 213.4 10.2 96 1-103 1-101 (105)
3 PF02519 Auxin_inducible: Auxi 100.0 7.4E-37 1.6E-41 211.4 9.4 68 39-106 33-100 (100)
4 PLN03219 uncharacterized prote 100.0 3.4E-36 7.3E-41 211.1 9.5 100 1-104 1-104 (108)
5 PF02214 BTB_2: BTB/POZ domain 90.8 0.18 3.8E-06 32.9 1.9 57 48-106 2-61 (94)
6 PRK02899 adaptor protein; Prov 88.1 0.46 9.9E-06 36.2 2.7 25 67-91 38-62 (197)
7 PRK02315 adaptor protein; Prov 85.5 0.67 1.4E-05 36.0 2.3 25 67-91 38-62 (233)
8 smart00666 PB1 PB1 domain. Pho 81.2 4.7 0.0001 25.3 4.7 48 50-102 7-65 (81)
9 PF05389 MecA: Negative regula 80.3 0.54 1.2E-05 35.7 0.0 25 67-91 38-62 (220)
10 cd05992 PB1 The PB1 domain is 78.3 8.6 0.00019 23.9 5.2 51 49-103 5-66 (81)
11 cd06398 PB1_Joka2 The PB1 doma 64.4 30 0.00066 23.3 5.6 54 50-103 6-72 (91)
12 cd06410 PB1_UP2 Uncharacterize 63.4 18 0.00038 24.7 4.4 46 48-97 17-75 (97)
13 cd06397 PB1_UP1 Uncharacterize 55.8 50 0.0011 22.4 5.4 47 50-100 6-63 (82)
14 PF02100 ODC_AZ: Ornithine dec 53.4 28 0.00062 24.0 4.1 50 53-103 22-75 (108)
15 PF00564 PB1: PB1 domain; Int 53.1 41 0.00088 20.9 4.5 45 49-97 6-62 (84)
16 cd06396 PB1_NBR1 The PB1 domai 51.4 51 0.0011 22.1 4.9 46 52-99 8-62 (81)
17 cd06407 PB1_NLP A PB1 domain i 45.4 59 0.0013 21.4 4.5 48 49-100 5-64 (82)
18 PRK10308 3-methyl-adenine DNA 45.3 77 0.0017 25.2 5.9 62 44-105 45-121 (283)
19 PF12058 DUF3539: Protein of u 45.1 3.4 7.4E-05 28.4 -1.6 11 63-73 4-14 (88)
20 PF07369 DUF1488: Protein of u 44.2 44 0.00096 21.3 3.7 20 46-65 18-37 (83)
21 PF00651 BTB: BTB/POZ domain; 42.4 73 0.0016 20.1 4.6 54 47-105 13-71 (111)
22 PF11834 DUF3354: Domain of un 38.1 27 0.00058 22.6 1.9 16 69-84 27-42 (69)
23 TIGR03687 pupylate_cterm ubiqu 32.8 22 0.00047 20.3 0.7 19 70-88 12-32 (33)
24 smart00153 VHP Villin headpiec 32.1 23 0.0005 20.2 0.8 19 64-82 1-19 (36)
25 PF02209 VHP: Villin headpiece 31.9 20 0.00044 20.5 0.5 19 64-82 1-19 (36)
26 TIGR03793 TOMM_pelo TOMM prope 31.7 81 0.0018 20.7 3.4 27 65-91 14-44 (77)
27 PF11822 DUF3342: Domain of un 31.0 59 0.0013 27.0 3.2 49 54-105 12-65 (317)
28 COG4862 MecA Negative regulato 29.5 39 0.00084 26.8 1.9 27 66-92 37-63 (224)
29 PF12062 HSNSD: heparan sulfat 28.9 45 0.00098 29.2 2.3 40 44-83 96-141 (487)
30 PF06544 DUF1115: Protein of u 27.9 2.1E+02 0.0045 19.8 5.2 26 59-84 3-28 (128)
31 PF06344 Parecho_VpG: Parechov 27.8 24 0.00053 17.9 0.3 12 38-49 7-18 (20)
32 PLN02752 [acyl-carrier protein 27.6 53 0.0012 26.1 2.4 47 38-84 32-78 (343)
33 cd01406 SIR2-like Sir2-like: P 26.8 80 0.0017 23.7 3.2 36 45-86 1-36 (242)
34 PRK02797 4-alpha-L-fucosyltran 24.3 3.2E+02 0.0069 22.8 6.4 42 42-83 142-205 (322)
35 TIGR02529 EutJ ethanolamine ut 23.7 96 0.0021 23.7 3.1 40 56-96 33-73 (239)
36 PF05194 UreE_C: UreE urease a 23.3 1.3E+02 0.0028 19.5 3.3 27 45-77 25-51 (87)
37 COG5389 Uncharacterized protei 23.0 45 0.00098 25.5 1.1 18 78-96 78-95 (181)
38 PRK13347 coproporphyrinogen II 22.8 1.9E+02 0.0041 24.2 4.9 48 45-98 103-150 (453)
39 PRK07735 NADH dehydrogenase su 22.6 1.4E+02 0.0031 25.8 4.2 42 64-105 272-323 (430)
40 PF04341 DUF485: Protein of un 21.9 69 0.0015 21.2 1.8 12 65-76 2-13 (91)
41 COG1759 5-formaminoimidazole-4 21.7 44 0.00096 28.2 0.9 37 41-78 89-136 (361)
42 PF14317 YcxB: YcxB-like prote 21.3 1.7E+02 0.0037 16.4 3.8 32 43-75 28-59 (62)
43 cd04751 Commd3 COMM_Domain con 21.2 96 0.0021 20.7 2.4 19 87-105 65-83 (95)
44 cd06401 PB1_TFG The PB1 domain 21.0 2.3E+02 0.0049 19.1 4.1 42 52-96 8-63 (81)
45 PRK13277 5-formaminoimidazole- 20.9 33 0.00071 28.9 0.0 21 41-61 89-111 (366)
No 1
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=1.4e-47 Score=267.37 Aligned_cols=104 Identities=88% Similarity=1.390 Sum_probs=97.8
Q ss_pred CCccccCCcchhHHHHHHHhhhhccccCCCCCCCCCCCCccCCCceEEEEEcCcceEEEEeccCCCcHHHHHHHHHHHHh
Q 046487 1 MAIRKSSKLPQAAVLKQILKRCSSLGKKQHSSYDEDGLPLDVPKGHFAVYVGEHRSRYIVPISFLSHPEFQCLLRQAEEE 80 (106)
Q Consensus 1 m~~~~~~~~~~~~~lk~~lkr~~S~~~~~~~~~~~~~~~~~vpkG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeE 80 (106)
|+++|++||++++++||+|+||+|+++++ +++.+..|.+||+||||||||++++||+||++|||||+|++||++||||
T Consensus 1 m~~~k~~ki~~~~~~kq~l~r~~s~~~~~--~~~~~~~~~~vpkG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeE 78 (104)
T PLN03090 1 MAIKKSNKLTQTAMLKQILKRCSSLGKKQ--GYDEDGLPLDVPKGHFPVYVGENRSRYIVPISFLTHPEFQSLLQQAEEE 78 (104)
T ss_pred CCcccccchhHHHHHHHHHHHHHHhcccC--CcccccCCCCCCCCcEEEEECCCCEEEEEEHHHcCCHHHHHHHHHHHHH
Confidence 89999999999999999999999999864 3444557889999999999999999999999999999999999999999
Q ss_pred cCCcCCCceEeeCcHHHHHHHHhhhC
Q 046487 81 FGFDHDMGLTIPCEEVVFRSLTSMLR 106 (106)
Q Consensus 81 ~G~~~~G~l~IpC~~~~Fe~vl~~l~ 106 (106)
|||+|+|+|+|||+++.|++++|||+
T Consensus 79 fGf~~~G~L~IPC~~~~Fe~ll~~i~ 104 (104)
T PLN03090 79 FGFDHDMGLTIPCEEVVFRSLTSMIR 104 (104)
T ss_pred hCCCCCCcEEEeCCHHHHHHHHHHhC
Confidence 99999999999999999999999985
No 2
>PLN03220 uncharacterized protein; Provisional
Probab=100.00 E-value=7.9e-37 Score=213.37 Aligned_cols=96 Identities=50% Similarity=0.835 Sum_probs=79.5
Q ss_pred CCccccCCcchhHHHHHHHhhhhccccCCCCCCCCCCCCccCCCceEEEEEcC----cceEEEEeccCCCcHHHHHHHHH
Q 046487 1 MAIRKSSKLPQAAVLKQILKRCSSLGKKQHSSYDEDGLPLDVPKGHFAVYVGE----HRSRYIVPISFLSHPEFQCLLRQ 76 (106)
Q Consensus 1 m~~~~~~~~~~~~~lk~~lkr~~S~~~~~~~~~~~~~~~~~vpkG~~aVyVG~----~~~RfvVp~~~L~hP~F~~LL~~ 76 (106)
|++++.+. ....||+|+||. ++++.. . ....+.+|||||||||||+ +++||+||++|||||.|++||++
T Consensus 1 ~~~~~~~~---~~~~k~~~~~~~-~~~~~~-~--~~~~~~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP~F~~LL~~ 73 (105)
T PLN03220 1 MGLSRFAI---SNATKQILKLNS-LANRNR-T--SSSSSDHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHPSFKEFLSR 73 (105)
T ss_pred CCcchhhh---HHHHHHHHHHHh-hccccc-c--cccccCCCCCCeEEEEECCCCCccceEEEEEHHHcCChHHHHHHHH
Confidence 55555432 446799999998 655422 1 1224568999999999997 58999999999999999999999
Q ss_pred HHHhcCCcC-CCceEeeCcHHHHHHHHh
Q 046487 77 AEEEFGFDH-DMGLTIPCEEVVFRSLTS 103 (106)
Q Consensus 77 aeeE~G~~~-~G~l~IpC~~~~Fe~vl~ 103 (106)
|||||||+| +|+|+|||+++.|++++.
T Consensus 74 AeEEfGf~~~~G~L~IPCd~~~F~~ll~ 101 (105)
T PLN03220 74 AEEEFGFNHPMGGLTIPCREEVFLDLIA 101 (105)
T ss_pred HHHHhCCCCCCCCEEeeCCHHHHHHHHH
Confidence 999999998 599999999999999986
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=7.4e-37 Score=211.39 Aligned_cols=68 Identities=65% Similarity=1.099 Sum_probs=65.7
Q ss_pred CccCCCceEEEEEcCcceEEEEeccCCCcHHHHHHHHHHHHhcCCcCCCceEeeCcHHHHHHHHhhhC
Q 046487 39 PLDVPKGHFAVYVGEHRSRYIVPISFLSHPEFQCLLRQAEEEFGFDHDMGLTIPCEEVVFRSLTSMLR 106 (106)
Q Consensus 39 ~~~vpkG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeE~G~~~~G~l~IpC~~~~Fe~vl~~l~ 106 (106)
..++|+||||||||++++||+||++|||||+|++||++|||||||+++|+|+|||+++.|+++||+|.
T Consensus 33 ~~~vp~G~~~VyVG~~~~Rfvvp~~~L~hp~f~~LL~~aeeEfG~~~~G~l~iPC~~~~Fe~~l~~le 100 (100)
T PF02519_consen 33 ESDVPKGHFAVYVGEERRRFVVPVSYLNHPLFQELLEQAEEEFGFDQDGPLTIPCDVVLFEHLLWLLE 100 (100)
T ss_pred cCCCCCCeEEEEeCccceEEEechHHcCchhHHHHHHHHhhhcCcCCCCcEEeeCCHHHHHHHHHHhC
Confidence 36899999999999999999999999999999999999999999999999999999999999999983
No 4
>PLN03219 uncharacterized protein; Provisional
Probab=100.00 E-value=3.4e-36 Score=211.07 Aligned_cols=100 Identities=46% Similarity=0.666 Sum_probs=82.8
Q ss_pred CCccccCCcchhHHHHHHHhhhhccccCCCC-CCCCCCCCccCCCceEEEEEcC--cceEEEEeccCCCcHHHHHHHHHH
Q 046487 1 MAIRKSSKLPQAAVLKQILKRCSSLGKKQHS-SYDEDGLPLDVPKGHFAVYVGE--HRSRYIVPISFLSHPEFQCLLRQA 77 (106)
Q Consensus 1 m~~~~~~~~~~~~~lk~~lkr~~S~~~~~~~-~~~~~~~~~~vpkG~~aVyVG~--~~~RfvVp~~~L~hP~F~~LL~~a 77 (106)
|+++++... +.|||+|.-...++..++ ...+.+.+.+|||||||||||+ +++||+||++|||||+|++||++|
T Consensus 1 ~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vpkGh~aVYVG~~~E~kRFvVPi~yL~hP~F~~LL~~A 76 (108)
T PLN03219 1 MGLMRSMLP----NAKQIFKSQSMRNKNGSSSPSSSTTTSGLVPKGHVAVYVGEQMEKKRFVVPISYLNHPLFREFLNRA 76 (108)
T ss_pred CchHHHHHh----hHHHHHHHHHHhcccCCCCCccCCCCCCCCCCCeEEEEECCCCCceEEEEEHHHcCChHHHHHHHHH
Confidence 666776543 788888766555555433 2334456678999999999997 589999999999999999999999
Q ss_pred HHhcCCcC-CCceEeeCcHHHHHHHHhh
Q 046487 78 EEEFGFDH-DMGLTIPCEEVVFRSLTSM 104 (106)
Q Consensus 78 eeE~G~~~-~G~l~IpC~~~~Fe~vl~~ 104 (106)
||||||++ +|+|+|||+++.|++||+.
T Consensus 77 eEEfGf~~~~G~L~IPCd~~~F~~ll~~ 104 (108)
T PLN03219 77 EEECGFHHSMGGLTIPCREESFLHLITS 104 (108)
T ss_pred HHHhCCCCCCCCEEEeCCHHHHHHHHHh
Confidence 99999997 5999999999999999974
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=90.82 E-value=0.18 Score=32.91 Aligned_cols=57 Identities=21% Similarity=0.202 Sum_probs=40.9
Q ss_pred EEEEcCcceEEEEeccCCC-cH--HHHHHHHHHHHhcCCcCCCceEeeCcHHHHHHHHhhhC
Q 046487 48 AVYVGEHRSRYIVPISFLS-HP--EFQCLLRQAEEEFGFDHDMGLTIPCEEVVFRSLTSMLR 106 (106)
Q Consensus 48 aVyVG~~~~RfvVp~~~L~-hP--~F~~LL~~aeeE~G~~~~G~l~IpC~~~~Fe~vl~~l~ 106 (106)
.+-||. ++|.++.+-|. +| .|..+++.......-+.+|.+-|-++...|++||.-|+
T Consensus 2 ~lNVGG--~~f~~~~~tL~~~~~s~l~~~~~~~~~~~~~~~~~~~fiDRdp~~F~~IL~ylr 61 (94)
T PF02214_consen 2 RLNVGG--TIFETSRSTLTRYPDSLLARLFSGERSDDYDDDDGEYFIDRDPELFEYILNYLR 61 (94)
T ss_dssp EEEETT--EEEEEEHHHHHTSTTSTTTSHHHTGHGGGEETTTTEEEESS-HHHHHHHHHHHH
T ss_pred EEEECC--EEEEEcHHHHhhCCCChhhhHHhhccccccCCccceEEeccChhhhhHHHHHHh
Confidence 456786 58999987776 44 78888886522222234688999999999999998764
No 6
>PRK02899 adaptor protein; Provisional
Probab=88.14 E-value=0.46 Score=36.21 Aligned_cols=25 Identities=28% Similarity=0.651 Sum_probs=21.3
Q ss_pred cHHHHHHHHHHHHhcCCcCCCceEe
Q 046487 67 HPEFQCLLRQAEEEFGFDHDMGLTI 91 (106)
Q Consensus 67 hP~F~~LL~~aeeE~G~~~~G~l~I 91 (106)
+-+|.++|++|..|+||..+|||+|
T Consensus 38 e~lF~~mm~Ea~~e~~F~~~~pl~~ 62 (197)
T PRK02899 38 HQLFRDMMQEANKELGFEADGPIAV 62 (197)
T ss_pred HHHHHHHHHHhhhccCcccCCeEEE
Confidence 3467777999999999999999875
No 7
>PRK02315 adaptor protein; Provisional
Probab=85.47 E-value=0.67 Score=36.03 Aligned_cols=25 Identities=20% Similarity=0.271 Sum_probs=22.6
Q ss_pred cHHHHHHHHHHHHhcCCcCCCceEe
Q 046487 67 HPEFQCLLRQAEEEFGFDHDMGLTI 91 (106)
Q Consensus 67 hP~F~~LL~~aeeE~G~~~~G~l~I 91 (106)
+-.|.++|++|..|+||..+|+|+|
T Consensus 38 e~fF~~mm~Ea~~e~~F~~~~pl~~ 62 (233)
T PRK02315 38 EEFFYSMMDEVDEEDDFADEGPLWF 62 (233)
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 3579999999999999999999986
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=81.16 E-value=4.7 Score=25.31 Aligned_cols=48 Identities=23% Similarity=0.353 Sum_probs=35.5
Q ss_pred EEcCcceEEEEeccCCCcHHHHHHHHHHHHhcCCc----------CCC-ceEeeCcHHHHHHHH
Q 046487 50 YVGEHRSRYIVPISFLSHPEFQCLLRQAEEEFGFD----------HDM-GLTIPCEEVVFRSLT 102 (106)
Q Consensus 50 yVG~~~~RfvVp~~~L~hP~F~~LL~~aeeE~G~~----------~~G-~l~IpC~~~~Fe~vl 102 (106)
+-|++.+||.+|. .+.|.+|..+..+-|+.. .+| .++|.++.+ ++.++
T Consensus 7 ~~~~~~~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~D-l~~a~ 65 (81)
T smart00666 7 RYGGETRRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDED-LEEAI 65 (81)
T ss_pred EECCEEEEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHHH-HHHHH
Confidence 3377889999985 778999999999988874 245 688888654 34333
No 9
>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=80.27 E-value=0.54 Score=35.69 Aligned_cols=25 Identities=40% Similarity=0.628 Sum_probs=0.0
Q ss_pred cHHHHHHHHHHHHhcCCcCCCceEe
Q 046487 67 HPEFQCLLRQAEEEFGFDHDMGLTI 91 (106)
Q Consensus 67 hP~F~~LL~~aeeE~G~~~~G~l~I 91 (106)
+-.|.++|++|.+|+||+.+|+|++
T Consensus 38 e~fF~~ileea~~e~~F~~~~~l~~ 62 (220)
T PF05389_consen 38 EEFFYSILEEADEEHGFENDGPLTF 62 (220)
T ss_dssp -------------------------
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 5679999999999999999998875
No 10
>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=78.35 E-value=8.6 Score=23.90 Aligned_cols=51 Identities=25% Similarity=0.338 Sum_probs=36.6
Q ss_pred EEEcCcceEEEEeccCCCcHHHHHHHHHHHHhcCCc----------CCC-ceEeeCcHHHHHHHHh
Q 046487 49 VYVGEHRSRYIVPISFLSHPEFQCLLRQAEEEFGFD----------HDM-GLTIPCEEVVFRSLTS 103 (106)
Q Consensus 49 VyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeE~G~~----------~~G-~l~IpC~~~~Fe~vl~ 103 (106)
++-+++.+||.+|. .++.|.+|..+..+-|++. .+| .++|.++ +.|+..+.
T Consensus 5 ~~~~~~~~~~~~~~---~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd-~Dl~~a~~ 66 (81)
T cd05992 5 VKYGGEIRRFVVVS---RSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSD-EDLEEAIE 66 (81)
T ss_pred EEecCCCEEEEEec---CCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCH-HHHHHHHH
Confidence 44455679999997 7889999999999988875 244 4667665 35555544
No 11
>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=64.43 E-value=30 Score=23.26 Aligned_cols=54 Identities=17% Similarity=0.199 Sum_probs=38.5
Q ss_pred EEcCcceEEEEeccC-CCcHHHHHHHHHHHHhcCCcC-----------CC-ceEeeCcHHHHHHHHh
Q 046487 50 YVGEHRSRYIVPISF-LSHPEFQCLLRQAEEEFGFDH-----------DM-GLTIPCEEVVFRSLTS 103 (106)
Q Consensus 50 yVG~~~~RfvVp~~~-L~hP~F~~LL~~aeeE~G~~~-----------~G-~l~IpC~~~~Fe~vl~ 103 (106)
.-|++.+||-+|..- -.+.-|..|.++-++-|.... +| .++|.|+.+.-+.+-.
T Consensus 6 ~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~~ 72 (91)
T cd06398 6 KYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQY 72 (91)
T ss_pred EeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHHH
Confidence 347788999999640 114578899998888776642 45 5889999887766543
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=63.41 E-value=18 Score=24.75 Aligned_cols=46 Identities=26% Similarity=0.300 Sum_probs=32.6
Q ss_pred EEEEcCcceEEEEeccCCCcHHHHHHHHHHHHhcCCcC-------------CCceEeeCcHHH
Q 046487 48 AVYVGEHRSRYIVPISFLSHPEFQCLLRQAEEEFGFDH-------------DMGLTIPCEEVV 97 (106)
Q Consensus 48 aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeE~G~~~-------------~G~l~IpC~~~~ 97 (106)
.=|||.+.+-..|+-+ -.|.+|..+..+.++... ++-+.|.||.++
T Consensus 17 l~Y~GG~tr~i~V~r~----~s~~el~~kl~~~~~~~~~~~lky~Lp~edld~Lisv~~DeDl 75 (97)
T cd06410 17 LRYVGGETRIVSVDRS----ISFKELVSKLSELFGAGVVVTLKYQLPDEDLDALISVSNDEDL 75 (97)
T ss_pred EEEcCCceEEEEEcCC----CCHHHHHHHHHHHhCCCCceEEEEEcCCCCcceeEEecCcHHH
Confidence 4699999888888876 356777778777776654 234567777643
No 13
>cd06397 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions.
Probab=55.79 E-value=50 Score=22.38 Aligned_cols=47 Identities=15% Similarity=0.245 Sum_probs=35.6
Q ss_pred EEcCcceEEEEeccCCCcHHHHHHHHHHHHhcCCc----------CCC-ceEeeCcHHHHHH
Q 046487 50 YVGEHRSRYIVPISFLSHPEFQCLLRQAEEEFGFD----------HDM-GLTIPCEEVVFRS 100 (106)
Q Consensus 50 yVG~~~~RfvVp~~~L~hP~F~~LL~~aeeE~G~~----------~~G-~l~IpC~~~~Fe~ 100 (106)
--|...|||+.|. .|.+.+|-++-+.-|-+. ++| .|||.=+.++.+.
T Consensus 6 ~~~g~~RRf~~~~----~pt~~~L~~kl~~Lf~lp~~~~~vtYiDeD~D~ITlssd~eL~d~ 63 (82)
T cd06397 6 SFLGDTRRIVFPD----IPTWEALASKLENLYNLPEIKVGVTYIDNDNDEITLSSNKELQDF 63 (82)
T ss_pred EeCCceEEEecCC----CccHHHHHHHHHHHhCCChhHeEEEEEcCCCCEEEecchHHHHHH
Confidence 3455679999998 899999999999877665 454 6888877666543
No 14
>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=53.42 E-value=28 Score=24.05 Aligned_cols=50 Identities=26% Similarity=0.349 Sum_probs=25.5
Q ss_pred CcceEEE-Eecc---CCCcHHHHHHHHHHHHhcCCcCCCceEeeCcHHHHHHHHh
Q 046487 53 EHRSRYI-VPIS---FLSHPEFQCLLRQAEEEFGFDHDMGLTIPCEEVVFRSLTS 103 (106)
Q Consensus 53 ~~~~Rfv-Vp~~---~L~hP~F~~LL~~aeeE~G~~~~G~l~IpC~~~~Fe~vl~ 103 (106)
+++.=|| +|-. ...-.-|.+|||.|||.+|.++ -.++++=+-.....++.
T Consensus 22 ~~~~L~V~ip~~~~~~~~K~~lvaLLElAee~L~c~~-vvic~~k~~~d~~~Llr 75 (108)
T PF02100_consen 22 DERTLFVFIPSSALGQGSKESLVALLELAEEKLGCSH-VVICLDKNRPDRASLLR 75 (108)
T ss_dssp -TTEEEEE-SS---SS--SHHHHHHHHHHHHHH-----EEEEE---SS-HHHHHH
T ss_pred cCCEEEEEECCcccccccHHHHHHHHHHhcCcCCCCE-EEEEEECCchhHHHhhh
Confidence 4556676 5643 3445789999999999998753 35666654444444443
No 15
>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=53.09 E-value=41 Score=20.89 Aligned_cols=45 Identities=31% Similarity=0.384 Sum_probs=31.1
Q ss_pred EEEcCcceE-EEEeccCCCcHHHHHHHHHHHHhcCCc----------CCC-ceEeeCcHHH
Q 046487 49 VYVGEHRSR-YIVPISFLSHPEFQCLLRQAEEEFGFD----------HDM-GLTIPCEEVV 97 (106)
Q Consensus 49 VyVG~~~~R-fvVp~~~L~hP~F~~LL~~aeeE~G~~----------~~G-~l~IpC~~~~ 97 (106)
++-+++.+| +.+| ..+.|.+|..+.++.||.. .+| .++|.++.++
T Consensus 6 ~~~~~~~~~~~~~~----~~~s~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD~V~i~sd~Dl 62 (84)
T PF00564_consen 6 VRYGGDIRRIISLP----SDVSFDDLRSKIREKFGLLDEDFQLKYKDEDGDLVTISSDEDL 62 (84)
T ss_dssp EEETTEEEEEEEEC----STSHHHHHHHHHHHHHTTSTSSEEEEEEETTSSEEEESSHHHH
T ss_pred EEECCeeEEEEEcC----CCCCHHHHHHHHHHHhCCCCccEEEEeeCCCCCEEEeCCHHHH
Confidence 344555555 4444 4679999999999999983 355 5777777654
No 16
>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=51.41 E-value=51 Score=22.05 Aligned_cols=46 Identities=7% Similarity=0.186 Sum_probs=34.2
Q ss_pred cCcceEEEEeccCCCcHHHHHHHHHHHHhcCCc--------CCC-ceEeeCcHHHHH
Q 046487 52 GEHRSRYIVPISFLSHPEFQCLLRQAEEEFGFD--------HDM-GLTIPCEEVVFR 99 (106)
Q Consensus 52 G~~~~RfvVp~~~L~hP~F~~LL~~aeeE~G~~--------~~G-~l~IpC~~~~Fe 99 (106)
|++..||.++- -.++.|.+|..+-+.-|+++ .+| +++|.|+.++=|
T Consensus 8 ~~d~~rf~~~~--~~~~~~~~L~~ev~~rf~l~~f~lKYlDde~e~v~lssd~eLeE 62 (81)
T cd06396 8 NGESQSFLVSD--SENTTWASVEAMVKVSFGLNDIQIKYVDEENEEVSVNSQGEYEE 62 (81)
T ss_pred CCeEEEEEecC--CCCCCHHHHHHHHHHHhCCCcceeEEEcCCCCEEEEEchhhHHH
Confidence 55678999884 12557999999999988853 455 789999887544
No 17
>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=45.42 E-value=59 Score=21.35 Aligned_cols=48 Identities=23% Similarity=0.435 Sum_probs=34.6
Q ss_pred EEEcCcceEEEEeccCCCcHHHHHHHHHHHHhcCCcC-----------CC-ceEeeCcHHHHHH
Q 046487 49 VYVGEHRSRYIVPISFLSHPEFQCLLRQAEEEFGFDH-----------DM-GLTIPCEEVVFRS 100 (106)
Q Consensus 49 VyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeE~G~~~-----------~G-~l~IpC~~~~Fe~ 100 (106)
+..|++..||.+|..- -|++|.++-.+-|+++. +| .++|.|+.++=|.
T Consensus 5 ~~~~~d~~r~~l~~~~----~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~ea 64 (82)
T cd06407 5 ATYGEEKIRFRLPPSW----GFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEEC 64 (82)
T ss_pred EEeCCeEEEEEcCCCC----CHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHHH
Confidence 3447778999998643 68888888888877642 34 6788888876553
No 18
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=45.26 E-value=77 Score=25.21 Aligned_cols=62 Identities=18% Similarity=0.190 Sum_probs=42.7
Q ss_pred CceEEEEEcCcceEEEEeccCCCcHHHHHHHHHHHHhcCCcCC---------------CceEeeCcHHHHHHHHhhh
Q 046487 44 KGHFAVYVGEHRSRYIVPISFLSHPEFQCLLRQAEEEFGFDHD---------------MGLTIPCEEVVFRSLTSML 105 (106)
Q Consensus 44 kG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeE~G~~~~---------------G~l~IpC~~~~Fe~vl~~l 105 (106)
.|.+.|.-.+....+.+.++.-.-|....++.....-||.+.| -+|+||...+.||.+++.|
T Consensus 45 ~~~~~v~~~~~~~~l~~~~~~~~~~~~~~~~~~vrr~fdLd~d~~~i~~~L~~~~~~~~GlR~p~~~d~fE~lv~aI 121 (283)
T PRK10308 45 RGVVTVIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGKLGAARPGLRLPGSVDAFEQGVRAI 121 (283)
T ss_pred cEEEEEEEcCCCceEEEEEcCCccccHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCCCcCCCCCCHHHHHHHHH
Confidence 4667666655545566655553335556677777777777665 2599999999999988864
No 19
>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=45.06 E-value=3.4 Score=28.36 Aligned_cols=11 Identities=45% Similarity=1.014 Sum_probs=7.9
Q ss_pred cCCCcHHHHHH
Q 046487 63 SFLSHPEFQCL 73 (106)
Q Consensus 63 ~~L~hP~F~~L 73 (106)
.|||||.|.-|
T Consensus 4 ~YLNHPtFGlL 14 (88)
T PF12058_consen 4 TYLNHPTFGLL 14 (88)
T ss_dssp -EEEETTTEEE
T ss_pred ccccCCccchh
Confidence 58999988544
No 20
>PF07369 DUF1488: Protein of unknown function (DUF1488); InterPro: IPR009962 This family consists of several hypothetical bacterial proteins of around 85 residues in length. The function of this family is unknown.; PDB: 2GPI_A.
Probab=44.21 E-value=44 Score=21.29 Aligned_cols=20 Identities=20% Similarity=0.258 Sum_probs=17.7
Q ss_pred eEEEEEcCcceEEEEeccCC
Q 046487 46 HFAVYVGEHRSRYIVPISFL 65 (106)
Q Consensus 46 ~~aVyVG~~~~RfvVp~~~L 65 (106)
.|+++|+...-++.|+.+-|
T Consensus 18 ~F~a~~~g~~i~C~Is~~aL 37 (83)
T PF07369_consen 18 RFPAQVDGMQIRCAISAEAL 37 (83)
T ss_dssp EEEEEETTEEEEEEEEHHHH
T ss_pred EEEEEECCEEEEEEEeHHHH
Confidence 68999998889999998776
No 21
>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=42.35 E-value=73 Score=20.10 Aligned_cols=54 Identities=19% Similarity=0.447 Sum_probs=36.2
Q ss_pred EEEEEcCcceEEEEeccCC--CcHHHHHHHHHHHHhcCCcCCC--ceEee-CcHHHHHHHHhhh
Q 046487 47 FAVYVGEHRSRYIVPISFL--SHPEFQCLLRQAEEEFGFDHDM--GLTIP-CEEVVFRSLTSML 105 (106)
Q Consensus 47 ~aVyVG~~~~RfvVp~~~L--~hP~F~~LL~~aeeE~G~~~~G--~l~Ip-C~~~~Fe~vl~~l 105 (106)
+.+.||+ .++|-+.-..| ..|.|+.+++.. +....+ .+.++ ++.+.|+.+++.+
T Consensus 13 ~~i~v~d-~~~~~vhk~iL~~~S~~F~~~~~~~----~~~~~~~~~i~~~~~~~~~~~~~l~~~ 71 (111)
T PF00651_consen 13 VTIRVGD-GKTFYVHKNILAARSPYFRNLFEGS----KFKESTVPEISLPDVSPEAFEAFLEYM 71 (111)
T ss_dssp EEEEETT-TEEEEE-HHHHHHHBHHHHHHHTTT----TSTTSSEEEEEETTSCHHHHHHHHHHH
T ss_pred EEEEECC-CEEEeechhhhhccchhhhhccccc----ccccccccccccccccccccccccccc
Confidence 3455665 46888887766 469999999888 212333 35545 8899999888653
No 22
>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=38.12 E-value=27 Score=22.62 Aligned_cols=16 Identities=44% Similarity=0.796 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHhcCCc
Q 046487 69 EFQCLLRQAEEEFGFD 84 (106)
Q Consensus 69 ~F~~LL~~aeeE~G~~ 84 (106)
.+++||+.|++.||+.
T Consensus 27 SleeLl~ia~~kfg~~ 42 (69)
T PF11834_consen 27 SLEELLKIASEKFGFS 42 (69)
T ss_pred cHHHHHHHHHHHhCCC
Confidence 6999999999999985
No 23
>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=32.82 E-value=22 Score=20.31 Aligned_cols=19 Identities=37% Similarity=0.627 Sum_probs=14.6
Q ss_pred HHHHHHHHHHhc--CCcCCCc
Q 046487 70 FQCLLRQAEEEF--GFDHDMG 88 (106)
Q Consensus 70 F~~LL~~aeeE~--G~~~~G~ 88 (106)
+-.+|+.-+||| ||-|.|+
T Consensus 12 Id~vLe~NAe~FV~~fVQKGG 32 (33)
T TIGR03687 12 IDGVLESNAEEFVRGFVQKGG 32 (33)
T ss_pred HHHHHHHhHHHHHHHHHHccC
Confidence 457788888888 8877764
No 24
>smart00153 VHP Villin headpiece domain.
Probab=32.05 E-value=23 Score=20.18 Aligned_cols=19 Identities=32% Similarity=0.572 Sum_probs=16.5
Q ss_pred CCCcHHHHHHHHHHHHhcC
Q 046487 64 FLSHPEFQCLLRQAEEEFG 82 (106)
Q Consensus 64 ~L~hP~F~~LL~~aeeE~G 82 (106)
||+.-.|++++.++.+||-
T Consensus 1 yLsdeeF~~vfgmsr~eF~ 19 (36)
T smart00153 1 YLSDEDFEEVFGMTREEFY 19 (36)
T ss_pred CCCHHHHHHHHCCCHHHHH
Confidence 7888999999999998873
No 25
>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=31.90 E-value=20 Score=20.53 Aligned_cols=19 Identities=32% Similarity=0.585 Sum_probs=14.8
Q ss_pred CCCcHHHHHHHHHHHHhcC
Q 046487 64 FLSHPEFQCLLRQAEEEFG 82 (106)
Q Consensus 64 ~L~hP~F~~LL~~aeeE~G 82 (106)
||+.-.|+++..++.+||.
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 7888999999999998873
No 26
>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=31.69 E-value=81 Score=20.70 Aligned_cols=27 Identities=19% Similarity=0.256 Sum_probs=18.5
Q ss_pred CCcHHHHHHH----HHHHHhcCCcCCCceEe
Q 046487 65 LSHPEFQCLL----RQAEEEFGFDHDMGLTI 91 (106)
Q Consensus 65 L~hP~F~~LL----~~aeeE~G~~~~G~l~I 91 (106)
-..|.|++.| ..+-+||||+-+..+.|
T Consensus 14 w~Dp~Fr~~Ll~DPraaL~e~G~~~P~~~~i 44 (77)
T TIGR03793 14 WEDEAFKQALLTNPKEALEREGVQVPAEVEV 44 (77)
T ss_pred HcCHHHHHHHHHCHHHHHHHhCCCCCCceEE
Confidence 3578999966 44556889987665444
No 27
>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=31.04 E-value=59 Score=26.96 Aligned_cols=49 Identities=14% Similarity=0.430 Sum_probs=35.3
Q ss_pred cceEEEEeccCC--CcHHHHHHHHH---HHHhcCCcCCCceEeeCcHHHHHHHHhhh
Q 046487 54 HRSRYIVPISFL--SHPEFQCLLRQ---AEEEFGFDHDMGLTIPCEEVVFRSLTSML 105 (106)
Q Consensus 54 ~~~RfvVp~~~L--~hP~F~~LL~~---aeeE~G~~~~G~l~IpC~~~~Fe~vl~~l 105 (106)
..+=|.-|...| +.+.|++.|.. ..++. .+-.|.+-||+..|+.++.-+
T Consensus 12 ~~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~---~~idisVhCDv~iF~WLm~yv 65 (317)
T PF11822_consen 12 EKRDFTCPRDLLVSEMRYFAEYLSRYINDSQRW---EEIDISVHCDVHIFEWLMRYV 65 (317)
T ss_pred cceeeeccHHHHHHhhHHHHHHHhhcccccCcC---CCcceEEecChhHHHHHHHHh
Confidence 346688887766 45789999976 33332 234699999999999998643
No 28
>COG4862 MecA Negative regulator of genetic competence, sporulation and motility [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Cell motility and secretion]
Probab=29.46 E-value=39 Score=26.82 Aligned_cols=27 Identities=19% Similarity=0.180 Sum_probs=23.9
Q ss_pred CcHHHHHHHHHHHHhcCCcCCCceEee
Q 046487 66 SHPEFQCLLRQAEEEFGFDHDMGLTIP 92 (106)
Q Consensus 66 ~hP~F~~LL~~aeeE~G~~~~G~l~Ip 92 (106)
.|-.|-++++++..|-+|...|+|.|-
T Consensus 37 ~EE~F~~mMdEl~~ee~F~~~GpL~iq 63 (224)
T COG4862 37 TEELFYEMMDELNLEEDFKDEGPLWIQ 63 (224)
T ss_pred HHHHHHHHHHhcCCccccccCCceEEE
Confidence 377999999999999999999999873
No 29
>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=28.92 E-value=45 Score=29.22 Aligned_cols=40 Identities=28% Similarity=0.478 Sum_probs=34.5
Q ss_pred CceEEEEEcCcceEEEEec-----cCCCcHH-HHHHHHHHHHhcCC
Q 046487 44 KGHFAVYVGEHRSRYIVPI-----SFLSHPE-FQCLLRQAEEEFGF 83 (106)
Q Consensus 44 kG~~aVyVG~~~~RfvVp~-----~~L~hP~-F~~LL~~aeeE~G~ 83 (106)
||.+|+++-..+.||.|=+ .|+|-|. -++||++=..|||-
T Consensus 96 kg~lP~LT~~~kGRy~lII~ENl~kYlnld~wNR~LLdkYC~ey~V 141 (487)
T PF12062_consen 96 KGDLPVLTDNDKGRYSLIIFENLLKYLNLDSWNRELLDKYCREYGV 141 (487)
T ss_pred CCCCCccccCCCCcEEEEEehhHHHHcCChHHHHHHHHHHhHccCc
Confidence 5899999977778888775 8999998 89999999999863
No 30
>PF06544 DUF1115: Protein of unknown function (DUF1115); InterPro: IPR010541 This entry represents the C terminus of several eukaryotic RWD domain-containing proteins of unknown function.
Probab=27.92 E-value=2.1e+02 Score=19.81 Aligned_cols=26 Identities=15% Similarity=0.284 Sum_probs=21.7
Q ss_pred EEeccCCCcHHHHHHHHHHHHhcCCc
Q 046487 59 IVPISFLSHPEFQCLLRQAEEEFGFD 84 (106)
Q Consensus 59 vVp~~~L~hP~F~~LL~~aeeE~G~~ 84 (106)
+-.+..|.||.-+--++.-++|++..
T Consensus 3 ~~~I~~L~~p~~R~kI~~nA~ql~Lt 28 (128)
T PF06544_consen 3 VHHIKSLSNPKKRFKIDKNAKQLHLT 28 (128)
T ss_pred EEEeCcccCHHHHHHHHHHHHHhCCe
Confidence 44567889999999999999998664
No 31
>PF06344 Parecho_VpG: Parechovirus Genome-linked protein; InterPro: IPR009407 The viral polyprotein of parechoviruses contains: coat protein VP0 (P1AB); coat protein VP3 (P1C); coat protein VP1 (P1D); picornain 2A (3.4.22.29 from EC, core protein P2A); core protein P2B; core protein P2C; core protein P3A; genome-linked protein VPg (P3B); picornain 3C (3.4.22.28 from EC, MEROPS peptidase subfamily 3CF: parechovirus picornain 3C (P3C)) []. This entry consists of the genome-linked protein Vpg type P3B.; GO: 0019015 viral genome
Probab=27.79 E-value=24 Score=17.86 Aligned_cols=12 Identities=58% Similarity=1.088 Sum_probs=9.5
Q ss_pred CCccCCCceEEE
Q 046487 38 LPLDVPKGHFAV 49 (106)
Q Consensus 38 ~~~~vpkG~~aV 49 (106)
.|..-|||.|||
T Consensus 7 lp~~kpkgtfpv 18 (20)
T PF06344_consen 7 LPVAKPKGTFPV 18 (20)
T ss_pred ccccccCCcccc
Confidence 456678999997
No 32
>PLN02752 [acyl-carrier protein] S-malonyltransferase
Probab=27.56 E-value=53 Score=26.11 Aligned_cols=47 Identities=19% Similarity=0.214 Sum_probs=29.4
Q ss_pred CCccCCCceEEEEEcCcceEEEEeccCCCcHHHHHHHHHHHHhcCCc
Q 046487 38 LPLDVPKGHFAVYVGEHRSRYIVPISFLSHPEFQCLLRQAEEEFGFD 84 (106)
Q Consensus 38 ~~~~vpkG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeE~G~~ 84 (106)
.+.+.+.-..-++-|....+.-.=..|.++|.|+++++++++-.|++
T Consensus 32 ~~~~~~~~~a~lFpGQGsq~~gm~~~~~~~p~~~~~~~~~~~~lg~~ 78 (343)
T PLN02752 32 LFADYKPTTAFLFPGQGAQAVGMGKEAAEVPAAKALFDKASEILGYD 78 (343)
T ss_pred cccCCCCCEEEEECCCCcchhhHHHHHHhCHHHHHHHHHHHHHhCCC
Confidence 33343444555555653332222233678999999999999888864
No 33
>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=26.81 E-value=80 Score=23.69 Aligned_cols=36 Identities=28% Similarity=0.577 Sum_probs=27.8
Q ss_pred ceEEEEEcCcceEEEEeccCCCcHHHHHHHHHHHHhcCCcCC
Q 046487 45 GHFAVYVGEHRSRYIVPISFLSHPEFQCLLRQAEEEFGFDHD 86 (106)
Q Consensus 45 G~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeE~G~~~~ 86 (106)
|.+++++|-..-+ + .+-|.+.+|++...+++|.+.+
T Consensus 1 g~lvlFiGAG~S~---~---~glP~W~~Ll~~l~~~~~~~~~ 36 (242)
T cd01406 1 GRVVIFVGAGVSV---S---SGLPDWKTLLDEIASELGLEID 36 (242)
T ss_pred CCEEEEecCcccc---c---cCCCChHHHHHHHHHHcCCccc
Confidence 6788999874211 1 5789999999999999987654
No 34
>PRK02797 4-alpha-L-fucosyltransferase; Provisional
Probab=24.28 E-value=3.2e+02 Score=22.82 Aligned_cols=42 Identities=19% Similarity=0.389 Sum_probs=32.3
Q ss_pred CCCceEEEEEcC--------------------cceEEEEeccC--CCcHHHHHHHHHHHHhcCC
Q 046487 42 VPKGHFAVYVGE--------------------HRSRYIVPISF--LSHPEFQCLLRQAEEEFGF 83 (106)
Q Consensus 42 vpkG~~aVyVG~--------------------~~~RfvVp~~~--L~hP~F~~LL~~aeeE~G~ 83 (106)
.+++.+.+.||. +.-|++||.+| =|.-..++..+.+.+-||-
T Consensus 142 ~~~~~~tIlvGNSgd~SN~Hie~L~~l~~~~~~~v~ii~PlsYp~gn~~Yi~~V~~~~~~lF~~ 205 (322)
T PRK02797 142 QRAGKMTILVGNSGDRSNRHIEALRALHQQFGDNVKIIVPMGYPANNQAYIEEVRQAGLALFGA 205 (322)
T ss_pred cCCCceEEEEeCCCCCcccHHHHHHHHHHHhCCCeEEEEECCcCCCCHHHHHHHHHHHHHhcCc
Confidence 466889999984 22599999999 6766777777777777873
No 35
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein.
Probab=23.72 E-value=96 Score=23.67 Aligned_cols=40 Identities=15% Similarity=0.159 Sum_probs=26.8
Q ss_pred eEEEEeccCCCcHHHHHHHHHHHHhcCCcCCC-ceEeeCcHH
Q 046487 56 SRYIVPISFLSHPEFQCLLRQAEEEFGFDHDM-GLTIPCEEV 96 (106)
Q Consensus 56 ~RfvVp~~~L~hP~F~~LL~~aeeE~G~~~~G-~l~IpC~~~ 96 (106)
.+-++..+-.. -.++.|.+.+++-.|...+. .+++|+...
T Consensus 33 ~g~I~d~~~~~-~~l~~l~~~a~~~~g~~~~~vvisVP~~~~ 73 (239)
T TIGR02529 33 DGIVVDFLGAV-EIVRRLKDTLEQKLGIELTHAATAIPPGTI 73 (239)
T ss_pred CCeEEEhHHHH-HHHHHHHHHHHHHhCCCcCcEEEEECCCCC
Confidence 34444443332 36888888888888886655 699998754
No 36
>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=23.26 E-value=1.3e+02 Score=19.50 Aligned_cols=27 Identities=26% Similarity=0.519 Sum_probs=17.0
Q ss_pred ceEEEEEcCcceEEEEeccCCCcHHHHHHHHHH
Q 046487 45 GHFAVYVGEHRSRYIVPISFLSHPEFQCLLRQA 77 (106)
Q Consensus 45 G~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~a 77 (106)
-|+|++++++ +..|| ..+.+.+||++-
T Consensus 25 rH~p~~i~~~--~l~v~----~d~~l~~~L~~l 51 (87)
T PF05194_consen 25 RHWPLFIEED--ELYVP----YDHVLEELLRKL 51 (87)
T ss_dssp TT--EEEETT--EEEEE------HHHHHHHHHT
T ss_pred CccceEEcCC--EEEec----CcHHHHHHHHHC
Confidence 3678999886 77888 566667777764
No 37
>COG5389 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.02 E-value=45 Score=25.50 Aligned_cols=18 Identities=39% Similarity=0.449 Sum_probs=13.5
Q ss_pred HHhcCCcCCCceEeeCcHH
Q 046487 78 EEEFGFDHDMGLTIPCEEV 96 (106)
Q Consensus 78 eeE~G~~~~G~l~IpC~~~ 96 (106)
.||-+| +.|+|+|.|+--
T Consensus 78 ~~eg~~-~pgvL~iaceG~ 95 (181)
T COG5389 78 REEGPF-QPGVLVIACEGA 95 (181)
T ss_pred cccCCC-CCceEEEEeccH
Confidence 456667 579999999843
No 38
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=22.80 E-value=1.9e+02 Score=24.23 Aligned_cols=48 Identities=13% Similarity=0.234 Sum_probs=36.1
Q ss_pred ceEEEEEcCcceEEEEeccCCCcHHHHHHHHHHHHhcCCcCCCceEeeCcHHHH
Q 046487 45 GHFAVYVGEHRSRYIVPISFLSHPEFQCLLRQAEEEFGFDHDMGLTIPCEEVVF 98 (106)
Q Consensus 45 G~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeE~G~~~~G~l~IpC~~~~F 98 (106)
+...+|+|... -..|+.+.+.+|++...+.|++..+..+++-|+...+
T Consensus 103 ~v~~i~fgGGT------Ps~l~~~~l~~ll~~i~~~~~~~~~~e~tie~~p~~l 150 (453)
T PRK13347 103 RVSQLHWGGGT------PTILNPDQFERLMAALRDAFDFAPEAEIAVEIDPRTV 150 (453)
T ss_pred eEEEEEEcCcc------cccCCHHHHHHHHHHHHHhCCCCCCceEEEEeccccC
Confidence 56677776642 3567899999999999999988655567777776544
No 39
>PRK07735 NADH dehydrogenase subunit C; Validated
Probab=22.62 E-value=1.4e+02 Score=25.81 Aligned_cols=42 Identities=17% Similarity=0.230 Sum_probs=30.2
Q ss_pred CCCcHHHHHHHHHHHHhcCCc----------CCCceEeeCcHHHHHHHHhhh
Q 046487 64 FLSHPEFQCLLRQAEEEFGFD----------HDMGLTIPCEEVVFRSLTSML 105 (106)
Q Consensus 64 ~L~hP~F~~LL~~aeeE~G~~----------~~G~l~IpC~~~~Fe~vl~~l 105 (106)
--|+|.+..|++...+.||-. ..|.++|-++.+.+..|+..|
T Consensus 272 ~pn~p~l~~l~~~L~e~fg~~i~~~~~i~~~~~d~lti~V~~e~L~eV~~~L 323 (430)
T PRK07735 272 SVNQPYLNKYVEVIKEKLGEDVLEDSYINKLSKDVPTLVVEPEKYYEVAELL 323 (430)
T ss_pred CCCchHHHHHHHHHHHHhhhhhhhhhhhccccCCceEEEEcHHHHHHHHHHH
Confidence 356999999999888888622 234577888888777776544
No 40
>PF04341 DUF485: Protein of unknown function, DUF485; InterPro: IPR007436 This family includes several putative integral membrane proteins.
Probab=21.93 E-value=69 Score=21.20 Aligned_cols=12 Identities=58% Similarity=0.930 Sum_probs=10.4
Q ss_pred CCcHHHHHHHHH
Q 046487 65 LSHPEFQCLLRQ 76 (106)
Q Consensus 65 L~hP~F~~LL~~ 76 (106)
++||.|++|.++
T Consensus 2 ~~~p~f~~L~r~ 13 (91)
T PF04341_consen 2 LRSPEFQELVRR 13 (91)
T ss_pred CCCHHHHHHHHH
Confidence 589999999876
No 41
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=21.68 E-value=44 Score=28.19 Aligned_cols=37 Identities=32% Similarity=0.513 Sum_probs=23.8
Q ss_pred cCCCceEEEEEcCc--ceEEEEeccCC---------CcHHHHHHHHHHH
Q 046487 41 DVPKGHFAVYVGEH--RSRYIVPISFL---------SHPEFQCLLRQAE 78 (106)
Q Consensus 41 ~vpkG~~aVyVG~~--~~RfvVp~~~L---------~hP~F~~LL~~ae 78 (106)
-||.|-|++|||-+ -+.|.||+ |- ..-.-..||++|.
T Consensus 89 ~IP~gSfv~Y~G~d~ie~~~~vP~-fGnR~lLrwE~~~~~~~~lLekAg 136 (361)
T COG1759 89 FIPHGSFVAYVGYDGIENEFEVPM-FGNRELLRWEEDRKLEYKLLEKAG 136 (361)
T ss_pred EecCCceEEEecchhhhhcccCcc-cccHhHhhhhcchhhHHHHHHHcC
Confidence 47999999999943 35677773 11 2223356777764
No 42
>PF14317 YcxB: YcxB-like protein
Probab=21.26 E-value=1.7e+02 Score=16.43 Aligned_cols=32 Identities=25% Similarity=0.464 Sum_probs=23.9
Q ss_pred CCceEEEEEcCcceEEEEeccCCCcHHHHHHHH
Q 046487 43 PKGHFAVYVGEHRSRYIVPISFLSHPEFQCLLR 75 (106)
Q Consensus 43 pkG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~ 75 (106)
-+.++-+|+++. .-++||.+.++.-...++.+
T Consensus 28 ~~~~~~l~~~~~-~~~~iPk~~f~~~e~~~f~~ 59 (62)
T PF14317_consen 28 TKDYFYLYLGKN-QAFIIPKRAFSEEEKEEFRE 59 (62)
T ss_pred eCCEEEEEECCC-eEEEEEHHHCCHhHHHHHHH
Confidence 368888999876 89999999888544444443
No 43
>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=21.23 E-value=96 Score=20.74 Aligned_cols=19 Identities=16% Similarity=0.331 Sum_probs=17.0
Q ss_pred CceEeeCcHHHHHHHHhhh
Q 046487 87 MGLTIPCEEVVFRSLTSML 105 (106)
Q Consensus 87 G~l~IpC~~~~Fe~vl~~l 105 (106)
..+.+-|+++.|+++++-|
T Consensus 65 ~~i~f~c~~e~L~~Li~~L 83 (95)
T cd04751 65 PDINFTCTLEQLQDLVNKL 83 (95)
T ss_pred ceEEEEeCHHHHHHHHHHH
Confidence 4799999999999999866
No 44
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction 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. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=20.98 E-value=2.3e+02 Score=19.07 Aligned_cols=42 Identities=21% Similarity=0.086 Sum_probs=28.0
Q ss_pred cCcceEEEEeccCCCcHHHHHHHHHHHHhcCC-------------cCCC-ceEeeCcHH
Q 046487 52 GEHRSRYIVPISFLSHPEFQCLLRQAEEEFGF-------------DHDM-GLTIPCEEV 96 (106)
Q Consensus 52 G~~~~RfvVp~~~L~hP~F~~LL~~aeeE~G~-------------~~~G-~l~IpC~~~ 96 (106)
|++-||+.+|..- =.|.+|.+.....|.. +++| -+||.++.+
T Consensus 8 g~DiR~~~~~~~~---~t~~~L~~~v~~~F~~~~~~~~~flIKYkD~dGDlVTIts~~d 63 (81)
T cd06401 8 GDDIRRIPIHNED---ITYDELLLMMQRVFRGKLGSSDDVLIKYKDEDGDLITIFDSSD 63 (81)
T ss_pred CCeEEEEeccCcc---ccHHHHHHHHHHHhccccCCcccEEEEEECCCCCEEEeccHHH
Confidence 6677887766321 2678888888776652 3456 478888744
No 45
>PRK13277 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase-like protein; Provisional
Probab=20.89 E-value=33 Score=28.87 Aligned_cols=21 Identities=48% Similarity=0.779 Sum_probs=16.7
Q ss_pred cCCCceEEEEEcCcc--eEEEEe
Q 046487 41 DVPKGHFAVYVGEHR--SRYIVP 61 (106)
Q Consensus 41 ~vpkG~~aVyVG~~~--~RfvVp 61 (106)
-||.|-|++|||-+. ..|.||
T Consensus 89 ~iPh~sf~~y~g~~~ie~~~~vp 111 (366)
T PRK13277 89 FVPNRSFAVYVGYDAIENEFKVP 111 (366)
T ss_pred EecCCCeEEEecHHHHhhcCCCC
Confidence 479999999999532 268888
Done!