Query 043356
Match_columns 79
No_of_seqs 112 out of 620
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 04:13:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043356.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043356hhsearch_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 4.2E-37 9E-42 203.9 8.9 68 10-77 36-103 (104)
2 PF02519 Auxin_inducible: Auxi 100.0 3E-37 6.5E-42 202.3 8.1 68 11-78 33-100 (100)
3 PLN03220 uncharacterized prote 100.0 2.3E-35 5E-40 195.9 8.7 68 9-76 30-102 (105)
4 PLN03219 uncharacterized prote 100.0 3.2E-34 6.8E-39 191.2 8.4 67 11-77 36-105 (108)
5 PF02214 BTB_2: BTB/POZ domain 92.2 0.19 4.1E-06 30.9 3.0 57 20-78 2-61 (94)
6 PRK02899 adaptor protein; Prov 89.9 0.28 6E-06 35.3 2.5 24 40-63 39-62 (197)
7 PRK02315 adaptor protein; Prov 87.4 0.49 1.1E-05 34.7 2.3 25 39-63 38-62 (233)
8 PF05389 MecA: Negative regula 84.0 0.32 7E-06 34.8 0.0 25 39-63 38-62 (220)
9 smart00666 PB1 PB1 domain. Pho 81.0 5 0.00011 23.8 4.5 50 22-76 7-67 (81)
10 cd05992 PB1 The PB1 domain is 78.3 8.5 0.00018 22.6 4.9 52 21-76 5-67 (81)
11 PF02100 ODC_AZ: Ornithine dec 74.1 7.4 0.00016 25.6 4.1 50 24-74 21-74 (108)
12 cd06410 PB1_UP2 Uncharacterize 71.7 11 0.00024 24.4 4.4 46 20-69 17-75 (97)
13 PF00651 BTB: BTB/POZ domain; 63.0 24 0.00053 21.1 4.6 54 19-77 13-71 (111)
14 cd06407 PB1_NLP A PB1 domain i 54.5 35 0.00076 21.2 4.3 47 21-71 5-63 (82)
15 PF11834 DUF3354: Domain of un 49.8 14 0.0003 22.7 1.8 24 27-56 19-42 (69)
16 PF12058 DUF3539: Protein of u 48.0 2.7 5.8E-05 27.4 -1.6 11 35-45 4-14 (88)
17 TIGR03687 pupylate_cterm ubiqu 47.9 11 0.00023 20.5 1.0 19 42-60 12-32 (33)
18 PRK10308 3-methyl-adenine DNA 47.4 90 0.0019 23.5 6.2 62 16-77 45-121 (283)
19 smart00153 VHP Villin headpiec 45.8 9.4 0.0002 20.7 0.6 18 36-53 1-18 (36)
20 PF02209 VHP: Villin headpiece 45.1 7.3 0.00016 21.3 0.0 19 36-54 1-19 (36)
21 PF07369 DUF1488: Protein of u 42.3 43 0.00093 20.1 3.2 20 18-37 18-37 (83)
22 cd06398 PB1_Joka2 The PB1 doma 39.6 1E+02 0.0022 19.6 4.9 53 22-74 6-71 (91)
23 PF14317 YcxB: YcxB-like prote 38.1 67 0.0014 17.2 3.7 32 15-47 28-59 (62)
24 PF00564 PB1: PB1 domain; Int 37.1 87 0.0019 18.2 4.4 45 21-69 6-62 (84)
25 TIGR03793 TOMM_pelo TOMM prope 36.7 63 0.0014 20.1 3.4 27 37-63 14-44 (77)
26 COG4862 MecA Negative regulato 36.4 24 0.00053 26.5 1.7 27 38-64 37-63 (224)
27 KOG1290 Serine/threonine prote 35.9 23 0.0005 29.9 1.6 20 14-33 62-83 (590)
28 PF05194 UreE_C: UreE urease a 34.6 73 0.0016 19.6 3.4 26 18-49 26-51 (87)
29 PF11876 DUF3396: Protein of u 32.0 45 0.00097 24.1 2.4 38 26-63 23-63 (208)
30 cd04395 RhoGAP_ARHGAP21 RhoGAP 32.0 1E+02 0.0023 21.3 4.2 39 40-78 19-57 (196)
31 PF11822 DUF3342: Domain of un 31.9 67 0.0015 25.2 3.5 50 26-78 12-66 (317)
32 PRK02797 4-alpha-L-fucosyltran 31.3 2.3E+02 0.005 22.4 6.3 43 13-55 141-205 (322)
33 PLN02752 [acyl-carrier protein 30.8 44 0.00095 25.1 2.3 42 15-56 37-78 (343)
34 cd01783 DAGK_delta_RA Ubiquiti 29.7 1.2E+02 0.0026 19.9 4.0 45 16-60 2-47 (97)
35 cd04751 Commd3 COMM_Domain con 28.0 66 0.0014 20.3 2.5 20 59-78 65-84 (95)
36 PF06344 Parecho_VpG: Parechov 26.9 26 0.00057 16.9 0.3 11 11-21 8-18 (20)
37 cd06279 PBP1_LacI_like_3 Ligan 26.7 72 0.0016 22.2 2.7 26 31-56 5-36 (283)
38 PF08948 DUF1859: Domain of un 26.4 24 0.00052 24.1 0.2 28 15-43 86-123 (126)
39 PF10893 DUF2724: Protein of u 26.0 51 0.0011 20.5 1.6 29 37-66 3-31 (68)
40 PF07429 Glyco_transf_56: 4-al 25.9 2.9E+02 0.0062 22.2 6.1 43 13-55 180-244 (360)
41 cd01406 SIR2-like Sir2-like: P 25.7 95 0.0021 21.9 3.2 36 17-58 1-36 (242)
42 KOG4209 Splicing factor RNPS1, 25.4 21 0.00046 26.3 -0.2 43 26-68 95-138 (231)
43 PF04341 DUF485: Protein of un 25.0 59 0.0013 20.4 1.8 12 37-48 2-13 (91)
44 PF08740 BCS1_N: BCS1 N termin 24.8 1.7E+02 0.0037 19.7 4.2 37 27-63 127-163 (187)
45 COG1759 5-formaminoimidazole-4 24.0 37 0.0008 27.2 0.8 23 11-33 87-111 (361)
46 cd04404 RhoGAP-p50rhoGAP RhoGA 23.9 1.9E+02 0.0041 19.9 4.4 38 40-78 24-62 (195)
47 cd06399 PB1_P40 The PB1 domain 23.9 1.1E+02 0.0023 20.2 2.8 30 26-55 14-43 (92)
48 cd06080 MUM1_like Mutated mela 23.7 1.4E+02 0.0031 18.6 3.4 41 15-55 28-75 (80)
49 PRK07735 NADH dehydrogenase su 23.6 1.7E+02 0.0036 24.1 4.5 42 36-77 272-323 (430)
50 PF08861 DUF1828: Domain of un 23.4 1.9E+02 0.0041 17.7 4.8 38 39-76 44-82 (90)
51 PF13421 Band_7_1: SPFH domain 22.7 1.2E+02 0.0026 21.8 3.3 43 9-56 14-63 (211)
52 cd03397 PAP2_acid_phosphatase 22.6 60 0.0013 23.5 1.7 19 35-53 213-231 (232)
53 cd04373 RhoGAP_p190 RhoGAP_p19 22.3 2E+02 0.0043 19.9 4.2 28 51-78 27-54 (185)
54 PF12625 Arabinose_bd: Arabino 22.2 37 0.00081 22.0 0.5 23 19-41 166-188 (188)
55 PF11490 DNA_pol3_a_NII: DNA p 22.1 1.1E+02 0.0023 18.6 2.6 30 38-70 13-42 (117)
56 PF12062 HSNSD: heparan sulfat 21.9 82 0.0018 26.2 2.5 40 16-55 96-141 (487)
57 PF04304 DUF454: Protein of un 21.4 68 0.0015 18.7 1.5 20 36-55 5-24 (71)
58 TIGR02529 EutJ ethanolamine ut 21.4 1.1E+02 0.0024 22.0 2.9 29 40-68 44-73 (239)
59 cd04372 RhoGAP_chimaerin RhoGA 21.3 2.3E+02 0.005 19.6 4.4 39 40-78 17-55 (194)
60 PF02762 Cbl_N3: CBL proto-onc 20.7 84 0.0018 20.4 1.9 30 22-53 44-73 (86)
61 cd04407 RhoGAP_myosin_IXB RhoG 20.7 2.2E+02 0.0047 19.8 4.2 39 40-78 16-54 (186)
62 COG4378 Uncharacterized protei 20.5 1.1E+02 0.0023 20.5 2.4 25 27-51 45-69 (103)
63 KOG2813 Predicted molecular ch 20.5 89 0.0019 25.3 2.3 57 19-76 274-330 (406)
No 1
>PLN03090 auxin-responsive family protein; Provisional
Probab=100.00 E-value=4.2e-37 Score=203.94 Aligned_cols=68 Identities=43% Similarity=0.898 Sum_probs=66.0
Q ss_pred CCCCCCCceEEEEEcCCceEEEEeccCCCCHHHHHHHHHHHHhccccCCCceEeeCcHHHHHHHHHhh
Q 043356 10 GVRRAPKGHFVVYVGEEMRRFVIPLSYLKDPTFQKLLEKAAEEYMFSRESGIVLPCAESTFRRFLNLM 77 (79)
Q Consensus 10 ~~~~vpkG~~~VyVG~e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~l 77 (79)
.+.+||+||||||||++++||+||++|||||+|++||++|||||||+|+|+|+|||+++.|++++|+|
T Consensus 36 ~~~~vpkG~~aVyVG~~~~RfvVp~~~L~hP~F~~LL~~aeeEfGf~~~G~L~IPC~~~~Fe~ll~~i 103 (104)
T PLN03090 36 LPLDVPKGHFPVYVGENRSRYIVPISFLTHPEFQSLLQQAEEEFGFDHDMGLTIPCEEVVFRSLTSMI 103 (104)
T ss_pred CCCCCCCCcEEEEECCCCEEEEEEHHHcCCHHHHHHHHHHHHHhCCCCCCcEEEeCCHHHHHHHHHHh
Confidence 56689999999999999999999999999999999999999999999999999999999999999998
No 2
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=100.00 E-value=3e-37 Score=202.27 Aligned_cols=68 Identities=50% Similarity=0.953 Sum_probs=66.1
Q ss_pred CCCCCCceEEEEEcCCceEEEEeccCCCCHHHHHHHHHHHHhccccCCCceEeeCcHHHHHHHHHhhc
Q 043356 11 VRRAPKGHFVVYVGEEMRRFVIPLSYLKDPTFQKLLEKAAEEYMFSRESGIVLPCAESTFRRFLNLMD 78 (79)
Q Consensus 11 ~~~vpkG~~~VyVG~e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~l~ 78 (79)
..++|+||||||||++++||+||++|||||+|++||++|||||||+++|+|+|||+++.|++++|+|+
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 37899999999999999999999999999999999999999999999999999999999999999986
No 3
>PLN03220 uncharacterized protein; Provisional
Probab=100.00 E-value=2.3e-35 Score=195.88 Aligned_cols=68 Identities=41% Similarity=0.890 Sum_probs=63.6
Q ss_pred cCCCCCCCceEEEEEcC----CceEEEEeccCCCCHHHHHHHHHHHHhccccC-CCceEeeCcHHHHHHHHHh
Q 043356 9 EGVRRAPKGHFVVYVGE----EMRRFVIPLSYLKDPTFQKLLEKAAEEYMFSR-ESGIVLPCAESTFRRFLNL 76 (79)
Q Consensus 9 ~~~~~vpkG~~~VyVG~----e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~~-~G~L~iPC~~~~Fe~vl~~ 76 (79)
+.+.+|||||||||||+ +++||+||++|||||+|++||++|||||||+| +|+|+|||+++.|++++..
T Consensus 30 ~~~~~VPkGh~aVyVGe~~~~e~kRFVVPv~yL~hP~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~s 102 (105)
T PLN03220 30 SSSDHVPKGHVAVYVGEQIEMEKKRFVVPISFLNHPSFKEFLSRAEEEFGFNHPMGGLTIPCREEVFLDLIAS 102 (105)
T ss_pred cccCCCCCCeEEEEECCCCCccceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEeeCCHHHHHHHHHh
Confidence 46678999999999997 58999999999999999999999999999999 5999999999999999864
No 4
>PLN03219 uncharacterized protein; Provisional
Probab=100.00 E-value=3.2e-34 Score=191.20 Aligned_cols=67 Identities=43% Similarity=0.862 Sum_probs=62.8
Q ss_pred CCCCCCceEEEEEcC--CceEEEEeccCCCCHHHHHHHHHHHHhccccC-CCceEeeCcHHHHHHHHHhh
Q 043356 11 VRRAPKGHFVVYVGE--EMRRFVIPLSYLKDPTFQKLLEKAAEEYMFSR-ESGIVLPCAESTFRRFLNLM 77 (79)
Q Consensus 11 ~~~vpkG~~~VyVG~--e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~~-~G~L~iPC~~~~Fe~vl~~l 77 (79)
+.+|||||||||||+ |++||+||++|||||+|++||++|||||||+| +|+|+|||+++.|+++++.-
T Consensus 36 ~~~vpkGh~aVYVG~~~E~kRFvVPi~yL~hP~F~~LL~~AeEEfGf~~~~G~L~IPCd~~~F~~ll~~~ 105 (108)
T PLN03219 36 SGLVPKGHVAVYVGEQMEKKRFVVPISYLNHPLFREFLNRAEEECGFHHSMGGLTIPCREESFLHLITSH 105 (108)
T ss_pred CCCCCCCeEEEEECCCCCceEEEEEHHHcCChHHHHHHHHHHHHhCCCCCCCCEEEeCCHHHHHHHHHhh
Confidence 457999999999997 58999999999999999999999999999998 49999999999999999764
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=92.22 E-value=0.19 Score=30.95 Aligned_cols=57 Identities=16% Similarity=0.175 Sum_probs=42.4
Q ss_pred EEEEcCCceEEEEeccCCC-C--HHHHHHHHHHHHhccccCCCceEeeCcHHHHHHHHHhhc
Q 043356 20 VVYVGEEMRRFVIPLSYLK-D--PTFQKLLEKAAEEYMFSRESGIVLPCAESTFRRFLNLMD 78 (79)
Q Consensus 20 ~VyVG~e~~RfvVp~~yL~-h--P~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~l~ 78 (79)
-+-||. ++|.++.+-|. + ..|..+++.......-+.+|.+-|-++...|++|+..+.
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 356884 99999998887 4 488888886532223344599999999999999998764
No 6
>PRK02899 adaptor protein; Provisional
Probab=89.94 E-value=0.28 Score=35.31 Aligned_cols=24 Identities=21% Similarity=0.465 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHhccccCCCceEe
Q 043356 40 PTFQKLLEKAAEEYMFSRESGIVL 63 (79)
Q Consensus 40 P~F~~LL~~aeeEfG~~~~G~L~i 63 (79)
-+|.++|++|..|+||..+|+|+|
T Consensus 39 ~lF~~mm~Ea~~e~~F~~~~pl~~ 62 (197)
T PRK02899 39 QLFRDMMQEANKELGFEADGPIAV 62 (197)
T ss_pred HHHHHHHHHhhhccCcccCCeEEE
Confidence 467788999999999999999985
No 7
>PRK02315 adaptor protein; Provisional
Probab=87.37 E-value=0.49 Score=34.72 Aligned_cols=25 Identities=20% Similarity=0.381 Sum_probs=22.7
Q ss_pred CHHHHHHHHHHHHhccccCCCceEe
Q 043356 39 DPTFQKLLEKAAEEYMFSRESGIVL 63 (79)
Q Consensus 39 hP~F~~LL~~aeeEfG~~~~G~L~i 63 (79)
+-+|.++|++|..|+||..+|+|+|
T Consensus 38 e~fF~~mm~Ea~~e~~F~~~~pl~~ 62 (233)
T PRK02315 38 EEFFYSMMDEVDEEDDFADEGPLWF 62 (233)
T ss_pred HHHHHHHHHHhccccCcccCCeEEE
Confidence 3589999999999999999999986
No 8
>PF05389 MecA: Negative regulator of genetic competence (MecA); InterPro: IPR008681 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. This family contains several bacterial MecA proteins. In complex media competence development is poor, and there is little or no expression of late competence genes. Overexpression of MecA inhibits comG transcription [, , ]. MecA enables the recognition and targeting of unfolded and aggregated proteins to the ClpC protease or to other proteins involved in proteolysis. Acts negatively in the development of competence by binding ComK and recruiting it to the ClpCP protease. When overexpressed, inhibits sporulation. Also involved in Spx degradation by ClpC. ; PDB: 3JTP_C 2Y1R_O 3PXI_c 3PXG_b 3JTO_D 3JTN_A.
Probab=84.03 E-value=0.32 Score=34.81 Aligned_cols=25 Identities=28% Similarity=0.460 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHHhccccCCCceEe
Q 043356 39 DPTFQKLLEKAAEEYMFSRESGIVL 63 (79)
Q Consensus 39 hP~F~~LL~~aeeEfG~~~~G~L~i 63 (79)
+-+|.++|++|.+|+||..+|+|++
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 5689999999999999999999875
No 9
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=81.04 E-value=5 Score=23.80 Aligned_cols=50 Identities=24% Similarity=0.408 Sum_probs=35.9
Q ss_pred EEcCCceEEEEeccCCCCHHHHHHHHHHHHhcccc----------CCC-ceEeeCcHHHHHHHHHh
Q 043356 22 YVGEEMRRFVIPLSYLKDPTFQKLLEKAAEEYMFS----------RES-GIVLPCAESTFRRFLNL 76 (79)
Q Consensus 22 yVG~e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~----------~~G-~L~iPC~~~~Fe~vl~~ 76 (79)
+-|++.+||.+|- ...|.+|..+..+-|+.. .+| .++|.++. .++.++.+
T Consensus 7 ~~~~~~~~~~~~~----~~s~~dL~~~i~~~~~~~~~~~~l~Y~Dedgd~v~l~sd~-Dl~~a~~~ 67 (81)
T smart00666 7 RYGGETRRLSVPR----DISFEDLRSKVAKRFGLDNQSFTLKYQDEDGDLVSLTSDE-DLEEAIEE 67 (81)
T ss_pred EECCEEEEEEECC----CCCHHHHHHHHHHHhCCCCCCeEEEEECCCCCEEEecCHH-HHHHHHHH
Confidence 3477789999985 788999999999988874 233 57788865 34444443
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=78.30 E-value=8.5 Score=22.58 Aligned_cols=52 Identities=23% Similarity=0.417 Sum_probs=36.8
Q ss_pred EEEcCCceEEEEeccCCCCHHHHHHHHHHHHhcccc----------CCC-ceEeeCcHHHHHHHHHh
Q 043356 21 VYVGEEMRRFVIPLSYLKDPTFQKLLEKAAEEYMFS----------RES-GIVLPCAESTFRRFLNL 76 (79)
Q Consensus 21 VyVG~e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~----------~~G-~L~iPC~~~~Fe~vl~~ 76 (79)
++-+++.+||.+|. +++.|.+|..+-.+-|+.. .+| .++|.++ ..|+.++..
T Consensus 5 ~~~~~~~~~~~~~~---~~~s~~~L~~~i~~~~~~~~~~~~l~y~D~e~d~v~l~sd-~Dl~~a~~~ 67 (81)
T cd05992 5 VKYGGEIRRFVVVS---RSISFEDLRSKIAEKFGLDAVSFKLKYPDEDGDLVTISSD-EDLEEAIEE 67 (81)
T ss_pred EEecCCCEEEEEec---CCCCHHHHHHHHHHHhCCCCCcEEEEeeCCCCCEEEeCCH-HHHHHHHHH
Confidence 44455799999997 7899999999999988875 223 3556655 455555544
No 11
>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=74.15 E-value=7.4 Score=25.55 Aligned_cols=50 Identities=34% Similarity=0.350 Sum_probs=24.4
Q ss_pred cCCceEEE-EeccCC---CCHHHHHHHHHHHHhccccCCCceEeeCcHHHHHHHH
Q 043356 24 GEEMRRFV-IPLSYL---KDPTFQKLLEKAAEEYMFSRESGIVLPCAESTFRRFL 74 (79)
Q Consensus 24 G~e~~Rfv-Vp~~yL---~hP~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl 74 (79)
|+++.=|+ +|-..+ +-..|.+|||.|||.+|.++ -.+.++=+-.....++
T Consensus 21 ~~~~~L~V~ip~~~~~~~~K~~lvaLLElAee~L~c~~-vvic~~k~~~d~~~Ll 74 (108)
T PF02100_consen 21 GDERTLFVFIPSSALGQGSKESLVALLELAEEKLGCSH-VVICLDKNRPDRASLL 74 (108)
T ss_dssp --TTEEEEE-SS---SS--SHHHHHHHHHHHHHH-----EEEEE---SS-HHHHH
T ss_pred ccCCEEEEEECCcccccccHHHHHHHHHHhcCcCCCCE-EEEEEECCchhHHHhh
Confidence 34566777 565444 34679999999999999775 4555554444433333
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=71.66 E-value=11 Score=24.41 Aligned_cols=46 Identities=26% Similarity=0.328 Sum_probs=34.0
Q ss_pred EEEEcCCceEEEEeccCCCCHHHHHHHHHHHHhccccC-------------CCceEeeCcHHH
Q 043356 20 VVYVGEEMRRFVIPLSYLKDPTFQKLLEKAAEEYMFSR-------------ESGIVLPCAEST 69 (79)
Q Consensus 20 ~VyVG~e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~~-------------~G~L~iPC~~~~ 69 (79)
.=|||.+.+-..|+-+ -.|.+|..+..+.++... ++-+.|.||.+.
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 4699998888889876 467788888888776655 345667787743
No 13
>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=63.04 E-value=24 Score=21.10 Aligned_cols=54 Identities=30% Similarity=0.599 Sum_probs=37.2
Q ss_pred EEEEEcCCceEEEEeccCC--CCHHHHHHHHHHHHhccccCCC--ceEee-CcHHHHHHHHHhh
Q 043356 19 FVVYVGEEMRRFVIPLSYL--KDPTFQKLLEKAAEEYMFSRES--GIVLP-CAESTFRRFLNLM 77 (79)
Q Consensus 19 ~~VyVG~e~~RfvVp~~yL--~hP~F~~LL~~aeeEfG~~~~G--~L~iP-C~~~~Fe~vl~~l 77 (79)
+.+.||+ .++|-+.-..| ..|.|+.+++.. +....+ .+.++ |+...|+.++..+
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 3456675 78888887777 569999999887 212233 35555 7899999988754
No 14
>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=54.46 E-value=35 Score=21.24 Aligned_cols=47 Identities=28% Similarity=0.418 Sum_probs=33.7
Q ss_pred EEEcCCceEEEEeccCCCCHHHHHHHHHHHHhccccC------------CCceEeeCcHHHHH
Q 043356 21 VYVGEEMRRFVIPLSYLKDPTFQKLLEKAAEEYMFSR------------ESGIVLPCAESTFR 71 (79)
Q Consensus 21 VyVG~e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~~------------~G~L~iPC~~~~Fe 71 (79)
+..|++..||.+|.+ .-|++|.++-.+-|+.+. +..++|.|+.+.=+
T Consensus 5 ~~~~~d~~r~~l~~~----~~~~~L~~~i~~r~~~~~~~~f~LkY~Ddegd~v~ltsd~DL~e 63 (82)
T cd06407 5 ATYGEEKIRFRLPPS----WGFTELKQEIAKRFKLDDMSAFDLKYLDDDEEWVLLTCDADLEE 63 (82)
T ss_pred EEeCCeEEEEEcCCC----CCHHHHHHHHHHHhCCCCCCeeEEEEECCCCCeEEeecHHHHHH
Confidence 344777999998864 369999999888887653 24467888876544
No 15
>PF11834 DUF3354: Domain of unknown function (DUF3354); InterPro: IPR021789 Potassium channels take part in important processes of higher plants, including opening and closing of stomatal pores and leaf movement. Inward rectifying potassium (K(+)in) channels play an important role in turgor regulation and ion uptake in higher plants. All of them comprise, from their N-terminal to their C-terminal ends: a short hydrophilic region, a hydrophobic region structurally analogous and partially homologous to the transmembrane domain of voltage-gated animal channels from the Shaker superfamily, a putative cyclic nucleotide-binding domain, and a conserved C-terminal KHA domain. Between these last two regions, some of them (AKT1, AKT2 and SKT1) contain an ankyrin-repeat domain with six repeats homologous to those of human erythrocyte ankyrin. This entry represents the KHA domain which is unique to plant K(+)in channels. The KHA domain contains two high-homology blocks enriched for hydrophobic and acidic residues, respectively. The KHA domain is essential for interaction of plant K(+)in channels. The KHA domain mediates tetramerization and/or stabilisation of the heteromers [, , ].
Probab=49.83 E-value=14 Score=22.72 Aligned_cols=24 Identities=29% Similarity=0.527 Sum_probs=19.2
Q ss_pred ceEEEEeccCCCCHHHHHHHHHHHHhcccc
Q 043356 27 MRRFVIPLSYLKDPTFQKLLEKAAEEYMFS 56 (79)
Q Consensus 27 ~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~ 56 (79)
.+=..+| -.+++||+.|++.||+.
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 37999999999999985
No 16
>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=48.01 E-value=2.7 Score=27.44 Aligned_cols=11 Identities=55% Similarity=0.984 Sum_probs=7.7
Q ss_pred cCCCCHHHHHH
Q 043356 35 SYLKDPTFQKL 45 (79)
Q Consensus 35 ~yL~hP~F~~L 45 (79)
.|||||.|.-|
T Consensus 4 ~YLNHPtFGlL 14 (88)
T PF12058_consen 4 TYLNHPTFGLL 14 (88)
T ss_dssp -EEEETTTEEE
T ss_pred ccccCCccchh
Confidence 58999988543
No 17
>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=47.91 E-value=11 Score=20.53 Aligned_cols=19 Identities=37% Similarity=0.648 Sum_probs=14.6
Q ss_pred HHHHHHHHHHhc--cccCCCc
Q 043356 42 FQKLLEKAAEEY--MFSRESG 60 (79)
Q Consensus 42 F~~LL~~aeeEf--G~~~~G~ 60 (79)
+-.+|+..+|+| ||-|+|+
T Consensus 12 Id~vLe~NAe~FV~~fVQKGG 32 (33)
T TIGR03687 12 IDGVLESNAEEFVRGFVQKGG 32 (33)
T ss_pred HHHHHHHhHHHHHHHHHHccC
Confidence 456788888888 8888764
No 18
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=47.42 E-value=90 Score=23.45 Aligned_cols=62 Identities=19% Similarity=0.246 Sum_probs=42.2
Q ss_pred CceEEEEEcCCceEEEEeccCCCCHHHHHHHHHHHHhccccCC---------------CceEeeCcHHHHHHHHHhh
Q 043356 16 KGHFVVYVGEEMRRFVIPLSYLKDPTFQKLLEKAAEEYMFSRE---------------SGIVLPCAESTFRRFLNLM 77 (79)
Q Consensus 16 kG~~~VyVG~e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~~~---------------G~L~iPC~~~~Fe~vl~~l 77 (79)
.|.+.|.-......+.+.++.-.-+....++.....-|+.+.| -+|+||...+.||-+++.|
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 4555555544455666666553345556677777777777665 3589999999999988875
No 19
>smart00153 VHP Villin headpiece domain.
Probab=45.80 E-value=9.4 Score=20.73 Aligned_cols=18 Identities=33% Similarity=0.739 Sum_probs=16.3
Q ss_pred CCCCHHHHHHHHHHHHhc
Q 043356 36 YLKDPTFQKLLEKAAEEY 53 (79)
Q Consensus 36 yL~hP~F~~LL~~aeeEf 53 (79)
||+.--|+.++.++.+||
T Consensus 1 yLsdeeF~~vfgmsr~eF 18 (36)
T smart00153 1 YLSDEDFEEVFGMTREEF 18 (36)
T ss_pred CCCHHHHHHHHCCCHHHH
Confidence 788999999999999987
No 20
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=45.08 E-value=7.3 Score=21.27 Aligned_cols=19 Identities=37% Similarity=0.740 Sum_probs=14.9
Q ss_pred CCCCHHHHHHHHHHHHhcc
Q 043356 36 YLKDPTFQKLLEKAAEEYM 54 (79)
Q Consensus 36 yL~hP~F~~LL~~aeeEfG 54 (79)
||+.--|++++.++.+||.
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 7888999999999999873
No 21
>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=42.34 E-value=43 Score=20.14 Aligned_cols=20 Identities=25% Similarity=0.180 Sum_probs=17.8
Q ss_pred eEEEEEcCCceEEEEeccCC
Q 043356 18 HFVVYVGEEMRRFVIPLSYL 37 (79)
Q Consensus 18 ~~~VyVG~e~~RfvVp~~yL 37 (79)
.|+++|+...-++.|..+-|
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 58999998899999999877
No 22
>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=39.56 E-value=1e+02 Score=19.61 Aligned_cols=53 Identities=23% Similarity=0.289 Sum_probs=36.9
Q ss_pred EEcCCceEEEEeccC-CCCHHHHHHHHHHHHhccccC-----------C-CceEeeCcHHHHHHHH
Q 043356 22 YVGEEMRRFVIPLSY-LKDPTFQKLLEKAAEEYMFSR-----------E-SGIVLPCAESTFRRFL 74 (79)
Q Consensus 22 yVG~e~~RfvVp~~y-L~hP~F~~LL~~aeeEfG~~~-----------~-G~L~iPC~~~~Fe~vl 74 (79)
.-|++.+||-+|.+= -.+.-|..|.++-++-|.... + .-++|.|+.+.-+-+-
T Consensus 6 ~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~~~~~~l~Y~Dedgd~V~l~~D~DL~~a~~ 71 (91)
T cd06398 6 KYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSPDADLSLTYTDEDGDVVTLVDDNDLTDAIQ 71 (91)
T ss_pred EeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCCCCcEEEEEECCCCCEEEEccHHHHHHHHH
Confidence 347789999999640 114578899999888776653 2 3477889887666544
No 23
>PF14317 YcxB: YcxB-like protein
Probab=38.11 E-value=67 Score=17.18 Aligned_cols=32 Identities=25% Similarity=0.515 Sum_probs=23.7
Q ss_pred CCceEEEEEcCCceEEEEeccCCCCHHHHHHHH
Q 043356 15 PKGHFVVYVGEEMRRFVIPLSYLKDPTFQKLLE 47 (79)
Q Consensus 15 pkG~~~VyVG~e~~RfvVp~~yL~hP~F~~LL~ 47 (79)
-+.++-+|+++ ..-++||.+.++.--..++.+
T Consensus 28 ~~~~~~l~~~~-~~~~~iPk~~f~~~e~~~f~~ 59 (62)
T PF14317_consen 28 TKDYFYLYLGK-NQAFIIPKRAFSEEEKEEFRE 59 (62)
T ss_pred eCCEEEEEECC-CeEEEEEHHHCCHhHHHHHHH
Confidence 46678889986 699999999998554444443
No 24
>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=37.14 E-value=87 Score=18.23 Aligned_cols=45 Identities=24% Similarity=0.462 Sum_probs=30.2
Q ss_pred EEEcCCceE-EEEeccCCCCHHHHHHHHHHHHhcccc----------CCC-ceEeeCcHHH
Q 043356 21 VYVGEEMRR-FVIPLSYLKDPTFQKLLEKAAEEYMFS----------RES-GIVLPCAEST 69 (79)
Q Consensus 21 VyVG~e~~R-fvVp~~yL~hP~F~~LL~~aeeEfG~~----------~~G-~L~iPC~~~~ 69 (79)
++-+++.+| +.++ +.+.|.+|.++.++.||.. .+| .++|.++.+.
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 5679999999999999883 344 4667776543
No 25
>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=36.67 E-value=63 Score=20.10 Aligned_cols=27 Identities=19% Similarity=0.256 Sum_probs=18.8
Q ss_pred CCCHHHHHHH----HHHHHhccccCCCceEe
Q 043356 37 LKDPTFQKLL----EKAAEEYMFSRESGIVL 63 (79)
Q Consensus 37 L~hP~F~~LL----~~aeeEfG~~~~G~L~i 63 (79)
-..|.|++.| +.+-+||||+-...+.|
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 44557889987655544
No 26
>COG4862 MecA Negative regulator of genetic competence, sporulation and motility [Posttranslational modification, protein turnover, chaperones / Signal transduction mechanisms / Cell motility and secretion]
Probab=36.39 E-value=24 Score=26.49 Aligned_cols=27 Identities=15% Similarity=0.281 Sum_probs=24.0
Q ss_pred CCHHHHHHHHHHHHhccccCCCceEee
Q 043356 38 KDPTFQKLLEKAAEEYMFSRESGIVLP 64 (79)
Q Consensus 38 ~hP~F~~LL~~aeeEfG~~~~G~L~iP 64 (79)
.|-+|-++++.+..|-+|.-+|+|.|-
T Consensus 37 ~EE~F~~mMdEl~~ee~F~~~GpL~iq 63 (224)
T COG4862 37 TEELFYEMMDELNLEEDFKDEGPLWIQ 63 (224)
T ss_pred HHHHHHHHHHhcCCccccccCCceEEE
Confidence 367899999999999999999999874
No 27
>KOG1290 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=35.94 E-value=23 Score=29.91 Aligned_cols=20 Identities=20% Similarity=0.356 Sum_probs=16.4
Q ss_pred CCCceEEEEEcC--CceEEEEe
Q 043356 14 APKGHFVVYVGE--EMRRFVIP 33 (79)
Q Consensus 14 vpkG~~~VyVG~--e~~RfvVp 33 (79)
.+-||.||++|+ ...||+|-
T Consensus 62 ~kGGYHpV~IGD~F~~gRY~v~ 83 (590)
T KOG1290|consen 62 RKGGYHPVRIGDVFNGGRYHVQ 83 (590)
T ss_pred hcCCCceeeccccccCceEEEE
Confidence 678999999998 45788874
No 28
>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=34.59 E-value=73 Score=19.57 Aligned_cols=26 Identities=27% Similarity=0.668 Sum_probs=16.9
Q ss_pred eEEEEEcCCceEEEEeccCCCCHHHHHHHHHH
Q 043356 18 HFVVYVGEEMRRFVIPLSYLKDPTFQKLLEKA 49 (79)
Q Consensus 18 ~~~VyVG~e~~RfvVp~~yL~hP~F~~LL~~a 49 (79)
|+|++++++ +..|| ..+.+.+||++-
T Consensus 26 H~p~~i~~~--~l~v~----~d~~l~~~L~~l 51 (87)
T PF05194_consen 26 HWPLFIEED--ELYVP----YDHVLEELLRKL 51 (87)
T ss_dssp T--EEEETT--EEEEE------HHHHHHHHHT
T ss_pred ccceEEcCC--EEEec----CcHHHHHHHHHC
Confidence 789999874 78888 566777888763
No 29
>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=32.01 E-value=45 Score=24.07 Aligned_cols=38 Identities=26% Similarity=0.478 Sum_probs=29.1
Q ss_pred CceEEEEeccCCCC--HHHHHHHHHHHHhccccCC-CceEe
Q 043356 26 EMRRFVIPLSYLKD--PTFQKLLEKAAEEYMFSRE-SGIVL 63 (79)
Q Consensus 26 e~~RfvVp~~yL~h--P~F~~LL~~aeeEfG~~~~-G~L~i 63 (79)
+.-+|.+|++||.. -.|++|+....+.+-..|. +++.+
T Consensus 23 s~l~f~~P~~~l~~~~~~~~~l~~~~a~~L~~~~G~aGl~~ 63 (208)
T PF11876_consen 23 SYLSFSLPLEWLEEGPGHFRALFLELAERLPPSHGYAGLAF 63 (208)
T ss_pred cEEEEEeCHHHHhcCcHHHHHHHHHHHHHCCCCeEeeEEEE
Confidence 34689999999987 3599999999998766654 55553
No 30
>cd04395 RhoGAP_ARHGAP21 RhoGAP_ARHGAP21: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP21-like proteins. ArhGAP21 is a multi-domain protein, containing RhoGAP, PH and PDZ domains, and is believed to play a role in the organization of the cell-cell junction complex. It has been shown to function as a GAP of Cdc42 and RhoA, and to interact with alpha-catenin and Arf6. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=31.99 E-value=1e+02 Score=21.33 Aligned_cols=39 Identities=8% Similarity=0.083 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhccccCCCceEeeCcHHHHHHHHHhhc
Q 043356 40 PTFQKLLEKAAEEYMFSRESGIVLPCAESTFRRFLNLMD 78 (79)
Q Consensus 40 P~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~l~ 78 (79)
|.|-...-..-++.|.+.+|.-++|.+...-+.+...++
T Consensus 19 P~iv~~~~~~l~~~g~~~eGIFR~~g~~~~i~~l~~~l~ 57 (196)
T cd04395 19 PLIVEVCCNIVEARGLETVGIYRVPGNNAAISALQEELN 57 (196)
T ss_pred ChHHHHHHHHHHHcCCCCccceeCCCcHHHHHHHHHHHh
Confidence 555554555667889999999999999888888877765
No 31
>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=31.86 E-value=67 Score=25.18 Aligned_cols=50 Identities=22% Similarity=0.437 Sum_probs=36.9
Q ss_pred CceEEEEeccCCCC--HHHHHHHHH---HHHhccccCCCceEeeCcHHHHHHHHHhhc
Q 043356 26 EMRRFVIPLSYLKD--PTFQKLLEK---AAEEYMFSRESGIVLPCAESTFRRFLNLMD 78 (79)
Q Consensus 26 e~~RfvVp~~yL~h--P~F~~LL~~---aeeEfG~~~~G~L~iPC~~~~Fe~vl~~l~ 78 (79)
..+-|.-|.+.|-+ ..|++.|.. +.++.. +=.|.+-||+..|+.++..++
T Consensus 12 ~~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~~---~idisVhCDv~iF~WLm~yv~ 66 (317)
T PF11822_consen 12 EKRDFTCPRDLLVSEMRYFAEYLSRYINDSQRWE---EIDISVHCDVHIFEWLMRYVK 66 (317)
T ss_pred cceeeeccHHHHHHhhHHHHHHHhhcccccCcCC---CcceEEecChhHHHHHHHHhh
Confidence 46778888887754 679999976 333332 345888899999999987664
No 32
>PRK02797 4-alpha-L-fucosyltransferase; Provisional
Probab=31.28 E-value=2.3e+02 Score=22.38 Aligned_cols=43 Identities=14% Similarity=0.394 Sum_probs=31.0
Q ss_pred CCCCceEEEEEcC--------------------CceEEEEeccC--CCCHHHHHHHHHHHHhccc
Q 043356 13 RAPKGHFVVYVGE--------------------EMRRFVIPLSY--LKDPTFQKLLEKAAEEYMF 55 (79)
Q Consensus 13 ~vpkG~~~VyVG~--------------------e~~RfvVp~~y--L~hP~F~~LL~~aeeEfG~ 55 (79)
..+++.+.|.||. +.-|+.||.+| =|.-..++..+.+.+-||-
T Consensus 141 ~~~~~~~tIlvGNSgd~SN~Hie~L~~l~~~~~~~v~ii~PlsYp~gn~~Yi~~V~~~~~~lF~~ 205 (322)
T PRK02797 141 RQRAGKMTILVGNSGDRSNRHIEALRALHQQFGDNVKIIVPMGYPANNQAYIEEVRQAGLALFGA 205 (322)
T ss_pred ccCCCceEEEEeCCCCCcccHHHHHHHHHHHhCCCeEEEEECCcCCCCHHHHHHHHHHHHHhcCc
Confidence 4466789999985 23599999999 5555666666666667873
No 33
>PLN02752 [acyl-carrier protein] S-malonyltransferase
Probab=30.81 E-value=44 Score=25.05 Aligned_cols=42 Identities=14% Similarity=0.193 Sum_probs=26.8
Q ss_pred CCceEEEEEcCCceEEEEeccCCCCHHHHHHHHHHHHhcccc
Q 043356 15 PKGHFVVYVGEEMRRFVIPLSYLKDPTFQKLLEKAAEEYMFS 56 (79)
Q Consensus 15 pkG~~~VyVG~e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~ 56 (79)
+.-..-++-|...++.-.=..|.++|.|+++++++++-.|++
T Consensus 37 ~~~~a~lFpGQGsq~~gm~~~~~~~p~~~~~~~~~~~~lg~~ 78 (343)
T PLN02752 37 KPTTAFLFPGQGAQAVGMGKEAAEVPAAKALFDKASEILGYD 78 (343)
T ss_pred CCCEEEEECCCCcchhhHHHHHHhCHHHHHHHHHHHHHhCCC
Confidence 333444555653222222223778999999999999888865
No 34
>cd01783 DAGK_delta_RA Ubiquitin-like domain of Diacylgylcerol kinase (DAGK). DAGK_delta_RA Diacylgylcerol kinase (DAGK) phosphorylates the second messenger diacylglycerol to phosphatidic acid as part of a protein kinase C pathway. Nine mammalian DAGK isotypes have been identified, which are classified into five subgroups according to their domain architecture and the DAGK-delta and -theta isozymes, which fall into one such group, contain an RA (Ras-associated) domain. DAGKs also contain a conserved catalytic domain (DAGKc), an assesory domain (DAGKa), and an array of conserved motifs that are likely to play a role in lipid-protein and protein-protein interactions in various DAG/PA-dependent signalling pathways.
Probab=29.69 E-value=1.2e+02 Score=19.85 Aligned_cols=45 Identities=20% Similarity=0.193 Sum_probs=33.0
Q ss_pred CceEEEEEcC-CceEEEEeccCCCCHHHHHHHHHHHHhccccCCCc
Q 043356 16 KGHFVVYVGE-EMRRFVIPLSYLKDPTFQKLLEKAAEEYMFSRESG 60 (79)
Q Consensus 16 kG~~~VyVG~-e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~~~G~ 60 (79)
+|++=||-|. ...---+.+..-+.-.-++++.+|-+-||.++..+
T Consensus 2 ~g~iKVY~G~L~~~~~y~sv~V~~~tt~~dvv~eaL~kfGl~~~~~ 47 (97)
T cd01783 2 KEVVKVYPGWLRVGVAYVSIRVNKDTTVQDVILEVLPLFGLQAECP 47 (97)
T ss_pred CceEEEecCccccCcceEEEEecccchHHHHHHHHHHHhCcccCCc
Confidence 6899999996 11122225555677889999999999999988654
No 35
>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=27.97 E-value=66 Score=20.35 Aligned_cols=20 Identities=15% Similarity=0.433 Sum_probs=17.9
Q ss_pred CceEeeCcHHHHHHHHHhhc
Q 043356 59 SGIVLPCAESTFRRFLNLMD 78 (79)
Q Consensus 59 G~L~iPC~~~~Fe~vl~~l~ 78 (79)
..+.+-|+++.|+++++.|+
T Consensus 65 ~~i~f~c~~e~L~~Li~~Lk 84 (95)
T cd04751 65 PDINFTCTLEQLQDLVNKLK 84 (95)
T ss_pred ceEEEEeCHHHHHHHHHHHH
Confidence 48999999999999998775
No 36
>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=26.94 E-value=26 Score=16.92 Aligned_cols=11 Identities=45% Similarity=0.634 Sum_probs=8.5
Q ss_pred CCCCCCceEEE
Q 043356 11 VRRAPKGHFVV 21 (79)
Q Consensus 11 ~~~vpkG~~~V 21 (79)
+..-|||.|||
T Consensus 8 p~~kpkgtfpv 18 (20)
T PF06344_consen 8 PVAKPKGTFPV 18 (20)
T ss_pred cccccCCcccc
Confidence 45568999987
No 37
>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=26.67 E-value=72 Score=22.21 Aligned_cols=26 Identities=19% Similarity=0.261 Sum_probs=17.7
Q ss_pred EEecc---CCCCHHHHHHHH---HHHHhcccc
Q 043356 31 VIPLS---YLKDPTFQKLLE---KAAEEYMFS 56 (79)
Q Consensus 31 vVp~~---yL~hP~F~~LL~---~aeeEfG~~ 56 (79)
+||.. ++.||.|..+++ ++.+++||+
T Consensus 5 i~p~~~~~~~~~~~~~~~~~gi~~~a~~~g~~ 36 (283)
T cd06279 5 VLTDSLSYAFSDPVASQFLAGVAEVLDAAGVN 36 (283)
T ss_pred EeCCcccccccCccHHHHHHHHHHHHHHCCCE
Confidence 55643 378999999976 445567764
No 38
>PF08948 DUF1859: Domain of unknown function (DUF1859); InterPro: IPR015043 This entry is represented by Bacteriophage PRD1, P5. This protein has no known function though it is sometimes found in the N terminus of bacteriophage spike proteins []. ; PDB: 1W8X_N.
Probab=26.44 E-value=24 Score=24.10 Aligned_cols=28 Identities=29% Similarity=0.478 Sum_probs=7.6
Q ss_pred CCceEEEEEcCCceEEE----------EeccCCCCHHHH
Q 043356 15 PKGHFVVYVGEEMRRFV----------IPLSYLKDPTFQ 43 (79)
Q Consensus 15 pkG~~~VyVG~e~~Rfv----------Vp~~yL~hP~F~ 43 (79)
..|++|+.|-. +-+|+ +|+-+||.|+-+
T Consensus 86 ~QGYfPlL~~~-~~KFv~~~~~~GKks~P~~FlNF~IA~ 123 (126)
T PF08948_consen 86 KQGYFPLLVPG-RAKFVVRHTGSGKKSVPMFFLNFTIAQ 123 (126)
T ss_dssp --SS--EEE---SSSSEEEEEEEESS----S--------
T ss_pred Ccccceeeccc-hhhhhhhhccCCCcceeeEEEeceeee
Confidence 46999999843 34444 688888888644
No 39
>PF10893 DUF2724: Protein of unknown function (DUF2724); InterPro: IPR021221 This entry is represented by Bacteriophage 186, Fil. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.03 E-value=51 Score=20.54 Aligned_cols=29 Identities=31% Similarity=0.522 Sum_probs=20.0
Q ss_pred CCCHHHHHHHHHHHHhccccCCCceEeeCc
Q 043356 37 LKDPTFQKLLEKAAEEYMFSRESGIVLPCA 66 (79)
Q Consensus 37 L~hP~F~~LL~~aeeEfG~~~~G~L~iPC~ 66 (79)
-+.|.|..||++-.----|.| |-|.+||.
T Consensus 3 ~~epsfa~lLkkQSPamhyGH-GWI~l~~G 31 (68)
T PF10893_consen 3 TKEPSFASLLKKQSPAMHYGH-GWIELPDG 31 (68)
T ss_pred cccchHHHHHHhcCcccccCC-CeEECCCC
Confidence 467999999998554333434 78887653
No 40
>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=25.90 E-value=2.9e+02 Score=22.19 Aligned_cols=43 Identities=23% Similarity=0.497 Sum_probs=33.3
Q ss_pred CCCCceEEEEEcC--------------------CceEEEEeccCC--CCHHHHHHHHHHHHhccc
Q 043356 13 RAPKGHFVVYVGE--------------------EMRRFVIPLSYL--KDPTFQKLLEKAAEEYMF 55 (79)
Q Consensus 13 ~vpkG~~~VyVG~--------------------e~~RfvVp~~yL--~hP~F~~LL~~aeeEfG~ 55 (79)
..+++-..|.||. +..|++||.+|= |.-..+++.+.+.+-||-
T Consensus 180 ~~~~~~ltILvGNSgd~sNnHieaL~~L~~~~~~~~kIivPLsYg~~n~~Yi~~V~~~~~~lF~~ 244 (360)
T PF07429_consen 180 KKNKGKLTILVGNSGDPSNNHIEALEALKQQFGDDVKIIVPLSYGANNQAYIQQVIQAGKELFGA 244 (360)
T ss_pred cCCCCceEEEEcCCCCCCccHHHHHHHHHHhcCCCeEEEEECCCCCchHHHHHHHHHHHHHhcCc
Confidence 4567888999984 348999999996 456778877778878874
No 41
>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=25.72 E-value=95 Score=21.93 Aligned_cols=36 Identities=25% Similarity=0.433 Sum_probs=27.1
Q ss_pred ceEEEEEcCCceEEEEeccCCCCHHHHHHHHHHHHhccccCC
Q 043356 17 GHFVVYVGEEMRRFVIPLSYLKDPTFQKLLEKAAEEYMFSRE 58 (79)
Q Consensus 17 G~~~VyVG~e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~~~ 58 (79)
|.+++++|---.+= .+-|...+|++...++++.+.+
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 67889998622111 5789999999999999987654
No 42
>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]
Probab=25.44 E-value=21 Score=26.29 Aligned_cols=43 Identities=12% Similarity=0.174 Sum_probs=33.1
Q ss_pred CceEEEEeccCCCCHHHHHHHHHHHHhc-cccCCCceEeeCcHH
Q 043356 26 EMRRFVIPLSYLKDPTFQKLLEKAAEEY-MFSRESGIVLPCAES 68 (79)
Q Consensus 26 e~~RfvVp~~yL~hP~F~~LL~~aeeEf-G~~~~G~L~iPC~~~ 68 (79)
..+....|..|+++.-|...+++-+++| ++.+-..++||||-.
T Consensus 95 ~~~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~ 138 (231)
T KOG4209|consen 95 RQKEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKF 138 (231)
T ss_pred hhhccCCceEEEeccccccccchhhheeeccCCccceeeecccc
Confidence 3567778888999999999999977777 444445679999853
No 43
>PF04341 DUF485: Protein of unknown function, DUF485; InterPro: IPR007436 This family includes several putative integral membrane proteins.
Probab=24.98 E-value=59 Score=20.36 Aligned_cols=12 Identities=42% Similarity=0.958 Sum_probs=10.3
Q ss_pred CCCHHHHHHHHH
Q 043356 37 LKDPTFQKLLEK 48 (79)
Q Consensus 37 L~hP~F~~LL~~ 48 (79)
++||.|++|.++
T Consensus 2 ~~~p~f~~L~r~ 13 (91)
T PF04341_consen 2 LRSPEFQELVRR 13 (91)
T ss_pred CCCHHHHHHHHH
Confidence 589999999875
No 44
>PF08740 BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. This domain is found at the N terminus of the mitochondrial BSC1 subfamily, belonging to the AAA ATPase family. At2g21640 and BCS1 are both highly stress responsive genes which encode mitochondrial proteins. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA). The SA dependent pathway represented by BCS1 is one of at least three distinctive pathways to regulate mitochondrial stress response at a transcriptional level []. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III []. BCS1, a component of the inner membrane of mitochondria, belongs to the group of proteins with internal, noncleavable import signals. It has a transmembrane domain (amino acid residues 51 to 68), a presequence type helix (residues 69 to 83), and an import auxiliary region (residues 84 to 126) [].
Probab=24.77 E-value=1.7e+02 Score=19.68 Aligned_cols=37 Identities=16% Similarity=0.205 Sum_probs=26.0
Q ss_pred ceEEEEeccCCCCHHHHHHHHHHHHhccccCCCceEe
Q 043356 27 MRRFVIPLSYLKDPTFQKLLEKAAEEYMFSRESGIVL 63 (79)
Q Consensus 27 ~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~~~G~L~i 63 (79)
.+-..|..--.|...+++||+.|.+.+-=.++|.++|
T Consensus 127 ~e~l~l~~lg~s~~~l~~ll~ear~~~~~~~~~~t~I 163 (187)
T PF08740_consen 127 DETLTLSCLGRSPKPLKDLLEEAREYYLKKQKGKTTI 163 (187)
T ss_pred ceEEEEEEecCCHHHHHHHHHHHHHHHHHhcCCcEEE
Confidence 3455555555678899999999999885455565554
No 45
>COG1759 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]
Probab=24.00 E-value=37 Score=27.18 Aligned_cols=23 Identities=39% Similarity=0.741 Sum_probs=16.7
Q ss_pred CCCCCCceEEEEEcCC--ceEEEEe
Q 043356 11 VRRAPKGHFVVYVGEE--MRRFVIP 33 (79)
Q Consensus 11 ~~~vpkG~~~VyVG~e--~~RfvVp 33 (79)
..-+|.|.|++|||-+ -+.|.||
T Consensus 87 ~I~IP~gSfv~Y~G~d~ie~~~~vP 111 (361)
T COG1759 87 AIFIPHGSFVAYVGYDGIENEFEVP 111 (361)
T ss_pred eEEecCCceEEEecchhhhhcccCc
Confidence 3458999999999954 2446665
No 46
>cd04404 RhoGAP-p50rhoGAP RhoGAP-p50rhoGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP, also known as RhoGAP-1, contains a C-terminal RhoGAP domain and an N-terminal Sec14 domain which binds phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). It is ubiquitously expressed and preferentially active on Cdc42. This subgroup also contains closely related ARHGAP8. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=23.93 E-value=1.9e+02 Score=19.92 Aligned_cols=38 Identities=8% Similarity=0.087 Sum_probs=28.2
Q ss_pred HHHH-HHHHHHHHhccccCCCceEeeCcHHHHHHHHHhhc
Q 043356 40 PTFQ-KLLEKAAEEYMFSRESGIVLPCAESTFRRFLNLMD 78 (79)
Q Consensus 40 P~F~-~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~l~ 78 (79)
|.+- .+++-- ++.|.+.+|.-++|.+...-+.+...++
T Consensus 24 P~il~~~i~~l-~~~g~~~eGIFR~~g~~~~i~~l~~~~~ 62 (195)
T cd04404 24 PPVVRETVEYL-QAHALTTEGIFRRSANTQVVKEVQQKYN 62 (195)
T ss_pred ChHHHHHHHHH-HHcCCCCCCeeeCCCcHHHHHHHHHHHh
Confidence 4444 444444 4489999999999999998888887765
No 47
>cd06399 PB1_P40 The PB1 domain is essential part of the p40 adaptor protein which plays an important role in activating phagocyte NADPH oxidase during phagocytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes , such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domain of p40 represents a type I PB1 domain which interacts with the PB1 domain of oxidase activator p67 w
Probab=23.85 E-value=1.1e+02 Score=20.17 Aligned_cols=30 Identities=20% Similarity=0.345 Sum_probs=25.1
Q ss_pred CceEEEEeccCCCCHHHHHHHHHHHHhccc
Q 043356 26 EMRRFVIPLSYLKDPTFQKLLEKAAEEYMF 55 (79)
Q Consensus 26 e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~ 55 (79)
..+-..|.-+.-..|.|++||....++|+-
T Consensus 14 ~~rdi~vee~l~~~P~~kdLl~lmr~~f~~ 43 (92)
T cd06399 14 TIRDIAVEEDLSSTPLLKDLLELTRREFQR 43 (92)
T ss_pred cccceEeecccccCccHHHHHHHHHHHhch
Confidence 446667778888999999999999999863
No 48
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=23.67 E-value=1.4e+02 Score=18.64 Aligned_cols=41 Identities=27% Similarity=0.347 Sum_probs=32.3
Q ss_pred CCceEEEEEcCC----ceEEEEeccCCCCHHH---HHHHHHHHHhccc
Q 043356 15 PKGHFVVYVGEE----MRRFVIPLSYLKDPTF---QKLLEKAAEEYMF 55 (79)
Q Consensus 15 pkG~~~VyVG~e----~~RfvVp~~yL~hP~F---~~LL~~aeeEfG~ 55 (79)
++-+...+.|+. ..++-+...|+.|+.+ +.|+++|.|.|.-
T Consensus 28 ~~k~~V~FfG~~~~~a~~~~~~l~p~~~~~~~~ek~~~~~k~ke~~~~ 75 (80)
T cd06080 28 KQKARVNFIGDNMQSEKKGIRVVKRWLKHFDCTEKQKLTNKAKESYEQ 75 (80)
T ss_pred CCEEEEEEeCCCCceeccchhhcccccccHHHHHHHHHHHHHHHHHHH
Confidence 556667778874 4677788889999999 5899999998763
No 49
>PRK07735 NADH dehydrogenase subunit C; Validated
Probab=23.55 E-value=1.7e+02 Score=24.11 Aligned_cols=42 Identities=14% Similarity=0.173 Sum_probs=31.2
Q ss_pred CCCCHHHHHHHHHHHHhcccc----------CCCceEeeCcHHHHHHHHHhh
Q 043356 36 YLKDPTFQKLLEKAAEEYMFS----------RESGIVLPCAESTFRRFLNLM 77 (79)
Q Consensus 36 yL~hP~F~~LL~~aeeEfG~~----------~~G~L~iPC~~~~Fe~vl~~l 77 (79)
--|+|++..|++...+.||-. ..|.++|-++.+.+..++..|
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 346999999999988888732 235678888888877777654
No 50
>PF08861 DUF1828: Domain of unknown function DUF1828; InterPro: IPR014960 These proteins are functionally uncharacterised.
Probab=23.38 E-value=1.9e+02 Score=17.71 Aligned_cols=38 Identities=11% Similarity=0.191 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHHHhccccCC-CceEeeCcHHHHHHHHHh
Q 043356 39 DPTFQKLLEKAAEEYMFSRE-SGIVLPCAESTFRRFLNL 76 (79)
Q Consensus 39 hP~F~~LL~~aeeEfG~~~~-G~L~iPC~~~~Fe~vl~~ 76 (79)
.+.=+++|+.....||..-+ |.|.+.++.+.|-..+..
T Consensus 44 s~~R~~~l~~il~~~gv~~~~~el~~~~~~~~~~~~~~~ 82 (90)
T PF08861_consen 44 SKKRKKILNSILNGFGVELDEGELFIKTSEENFPQAKHR 82 (90)
T ss_pred chHHHHHHHHHHHHcCccccCCEEEEEeCHHHHHHHHHH
Confidence 67778999999999999776 999999999988766543
No 51
>PF13421 Band_7_1: SPFH domain-Band 7 family
Probab=22.73 E-value=1.2e+02 Score=21.82 Aligned_cols=43 Identities=16% Similarity=0.242 Sum_probs=31.8
Q ss_pred cCCCCCCCceEEEEE--cC-----CceEEEEeccCCCCHHHHHHHHHHHHhcccc
Q 043356 9 EGVRRAPKGHFVVYV--GE-----EMRRFVIPLSYLKDPTFQKLLEKAAEEYMFS 56 (79)
Q Consensus 9 ~~~~~vpkG~~~VyV--G~-----e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~ 56 (79)
.+.-.|++|..||.| |. +.-||.+-+. |.|++..|... -||++
T Consensus 14 GS~LiV~egQ~Avfv~~G~i~d~~~pG~y~l~T~--n~P~l~~l~~~---~~Gg~ 63 (211)
T PF13421_consen 14 GSQLIVREGQCAVFVNDGKIADVFGPGRYTLDTD--NIPILSTLKNW---KFGGE 63 (211)
T ss_pred CCEEEECCCCEEEEEECCEEEEEecCceEEEecC--CchHHHHHhhh---ccCCC
Confidence 444579999999999 32 4678888875 88999888653 35654
No 52
>cd03397 PAP2_acid_phosphatase PAP2, bacterial acid phosphatase or class A non-specific acid phosphatases. These enzymes catalyze phosphomonoester hydrolysis, with optimal activity in low pH conditions. They are secreted into the periplasmic space, and their physiological role remains to be determined.
Probab=22.65 E-value=60 Score=23.51 Aligned_cols=19 Identities=37% Similarity=0.510 Sum_probs=16.4
Q ss_pred cCCCCHHHHHHHHHHHHhc
Q 043356 35 SYLKDPTFQKLLEKAAEEY 53 (79)
Q Consensus 35 ~yL~hP~F~~LL~~aeeEf 53 (79)
..++.|.|++.|++|..|+
T Consensus 213 ~l~~~~~f~~~~~~A~~El 231 (232)
T cd03397 213 ALLADPAFAADLAAARAEL 231 (232)
T ss_pred HHhcCHHHHHHHHHHHHHh
Confidence 4678899999999999885
No 53
>cd04373 RhoGAP_p190 RhoGAP_p190: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p190-like proteins. p190, also named RhoGAP5, plays a role in neuritogenesis and axon branch stability. p190 shows a preference for Rho, over Rac and Cdc42, and consists of an N-terminal GTPase domain and a C-terminal GAP domain. The central portion of p190 contains important regulatory phosphorylation sites. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=22.32 E-value=2e+02 Score=19.86 Aligned_cols=28 Identities=11% Similarity=0.082 Sum_probs=23.3
Q ss_pred HhccccCCCceEeeCcHHHHHHHHHhhc
Q 043356 51 EEYMFSRESGIVLPCAESTFRRFLNLMD 78 (79)
Q Consensus 51 eEfG~~~~G~L~iPC~~~~Fe~vl~~l~ 78 (79)
++.|.+.+|.-++|.+....+++...++
T Consensus 27 ~~~gl~~eGIFR~~G~~~~i~~l~~~~~ 54 (185)
T cd04373 27 EATGLETEGIYRVSGNKTHLDSLQKQFD 54 (185)
T ss_pred HHcCCCCCCeeecCCcHHHHHHHHHHHh
Confidence 3489999999999999998888877655
No 54
>PF12625 Arabinose_bd: Arabinose-binding domain of AraC transcription regulator, N-term
Probab=22.20 E-value=37 Score=22.01 Aligned_cols=23 Identities=26% Similarity=0.352 Sum_probs=20.0
Q ss_pred EEEEEcCCceEEEEeccCCCCHH
Q 043356 19 FVVYVGEEMRRFVIPLSYLKDPT 41 (79)
Q Consensus 19 ~~VyVG~e~~RfvVp~~yL~hP~ 41 (79)
.+|..|....++++|.+.|+.|+
T Consensus 166 ~~v~f~~~~~~l~~~~~~L~~Pl 188 (188)
T PF12625_consen 166 CPVRFGQPFNALVFPREDLDLPL 188 (188)
T ss_pred CCCEeCCCcEEEEEeHHHhcCCC
Confidence 46788888999999999999985
No 55
>PF11490 DNA_pol3_a_NII: DNA polymerase III polC-type N-terminus II; InterPro: IPR024754 This domain is found in the N-terminal region of DNA polymerase III polC subunit A. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria []. The domain is also found in chromosomal replication initiator protein DnaA.
Probab=22.12 E-value=1.1e+02 Score=18.62 Aligned_cols=30 Identities=20% Similarity=0.456 Sum_probs=20.4
Q ss_pred CCHHHHHHHHHHHHhccccCCCceEeeCcHHHH
Q 043356 38 KDPTFQKLLEKAAEEYMFSRESGIVLPCAESTF 70 (79)
Q Consensus 38 ~hP~F~~LL~~aeeEfG~~~~G~L~iPC~~~~F 70 (79)
++|.++.+|..+.=++ .++-|+|.+.-...
T Consensus 13 ~~p~~~~~L~~~~~~~---~~~~l~i~v~~~~~ 42 (117)
T PF11490_consen 13 KSPSLKSLLKNAKPEF---EGNKLIIKVPNEIE 42 (117)
T ss_pred cCHHHHHHHHhCCeEE---ECCEEEEEeCCHHH
Confidence 5788888888777665 23667777765554
No 56
>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=21.94 E-value=82 Score=26.22 Aligned_cols=40 Identities=28% Similarity=0.473 Sum_probs=34.1
Q ss_pred CceEEEEEcCCceEEEEec-----cCCCCHH-HHHHHHHHHHhccc
Q 043356 16 KGHFVVYVGEEMRRFVIPL-----SYLKDPT-FQKLLEKAAEEYMF 55 (79)
Q Consensus 16 kG~~~VyVG~e~~RfvVp~-----~yL~hP~-F~~LL~~aeeEfG~ 55 (79)
||.+|+++-..+.||-+=+ .|+|-+. -++||++=-.|||-
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 5899999977788988775 8999998 89999998888853
No 57
>PF04304 DUF454: Protein of unknown function (DUF454); InterPro: IPR007401 This is a predicted membrane protein.
Probab=21.38 E-value=68 Score=18.72 Aligned_cols=20 Identities=15% Similarity=0.144 Sum_probs=16.4
Q ss_pred CCCCHHHHHHHHHHHHhccc
Q 043356 36 YLKDPTFQKLLEKAAEEYMF 55 (79)
Q Consensus 36 yL~hP~F~~LL~~aeeEfG~ 55 (79)
.+|||.|+..++.-+|.=|.
T Consensus 5 l~~h~~~g~~I~~w~~~r~i 24 (71)
T PF04304_consen 5 LLNHRLFGPYIRNWEEHRGI 24 (71)
T ss_pred HHcCchhHHHHHHHHHCCCc
Confidence 57999999999988876444
No 58
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein.
Probab=21.37 E-value=1.1e+02 Score=21.95 Aligned_cols=29 Identities=7% Similarity=0.140 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHhccccCC-CceEeeCcHH
Q 043356 40 PTFQKLLEKAAEEYMFSRE-SGIVLPCAES 68 (79)
Q Consensus 40 P~F~~LL~~aeeEfG~~~~-G~L~iPC~~~ 68 (79)
-+++.|++++++-.|...+ -.+++|++..
T Consensus 44 ~~l~~l~~~a~~~~g~~~~~vvisVP~~~~ 73 (239)
T TIGR02529 44 EIVRRLKDTLEQKLGIELTHAATAIPPGTI 73 (239)
T ss_pred HHHHHHHHHHHHHhCCCcCcEEEEECCCCC
Confidence 4688888888888887554 5689998754
No 59
>cd04372 RhoGAP_chimaerin RhoGAP_chimaerin: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of chimaerins. Chimaerins are a family of phorbolester- and diacylglycerol-responsive GAPs specific for the Rho-like GTPase Rac. Chimaerins exist in two alternative splice forms that each contain a C-terminal GAP domain, and a central C1 domain which binds phorbol esters, inducing a conformational change that activates the protein; one splice form is lacking the N-terminal Src homology-2 (SH2) domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GT
Probab=21.33 E-value=2.3e+02 Score=19.60 Aligned_cols=39 Identities=10% Similarity=0.035 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHhccccCCCceEeeCcHHHHHHHHHhhc
Q 043356 40 PTFQKLLEKAAEEYMFSRESGIVLPCAESTFRRFLNLMD 78 (79)
Q Consensus 40 P~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~l~ 78 (79)
|.+-.-+=..-++.|.+.+|.-++|-+...-+.+...++
T Consensus 17 P~iv~~ci~~l~~~gl~~EGIFR~sG~~~~i~~l~~~~d 55 (194)
T cd04372 17 PMVVDMCIREIEARGLQSEGLYRVSGFAEEIEDVKMAFD 55 (194)
T ss_pred ChHHHHHHHHHHHcCCCcCceeecCCcHHHHHHHHHHHc
Confidence 444433333335679999999999999888887776664
No 60
>PF02762 Cbl_N3: CBL proto-oncogene N-terminus, SH2-like domain; InterPro: IPR014742 Cbl (Casitas B-lineage lymphoma) is an adaptor protein that functions as a negative regulator of many signalling pathways that start from receptors at the cell surface. The N-terminal region of Cbl contains a Cbl-type phosphotyrosine-binding (Cbl-PTB) domain, which is composed of three evolutionarily conserved domains: an N-terminal four-helix bundle (4H) domain, an EF hand-like calcium-binding domain, and a divergent SH2-like domain. The calcium-bound EF-hand wedges between the 4H and SH2 domains, and roughly determines their relative orientation. The Cbl-PTB domain has also been named Cbl N-terminal (Cbl-N) or tyrosine kinase binding (TKB) domain [, ]. The N-terminal 4H domain contains four long alpha-helices. The C and D helices in this domain pack against the adjacent EF-hand-like domain, and a highly conserved loop connecting the A and B helices contacts the SH2-like domain. The EF-hand motif is similar to classical EF-hand proteins. The SH2-like domain retains the general helix-sheet-helix architecture of the SH2 fold, but lacks the secondary beta-sheet, comprising beta-strands D', E and F, and also a prominent BG loop []. This entry represents the SH2-like domain.; PDB: 3PFV_A 3VGO_A 3PLF_B 2Y1M_A 2CBL_A 3BUX_B 3BUN_B 3BUM_B 3OB1_B 3BUW_B ....
Probab=20.75 E-value=84 Score=20.35 Aligned_cols=30 Identities=17% Similarity=0.403 Sum_probs=19.6
Q ss_pred EEcCCceEEEEeccCCCCHHHHHHHHHHHHhc
Q 043356 22 YVGEEMRRFVIPLSYLKDPTFQKLLEKAAEEY 53 (79)
Q Consensus 22 yVG~e~~RfvVp~~yL~hP~F~~LL~~aeeEf 53 (79)
||-.+.+ ++-+-=-|-|++|+|++-+.|-|
T Consensus 44 yV~~dg~--I~QTIPqnk~L~qaLidG~reG~ 73 (86)
T PF02762_consen 44 YVTQDGK--ILQTIPQNKSLYQALIDGSREGF 73 (86)
T ss_dssp EEETTSE--EEEE--SSS-HHHHHHHHHHTTS
T ss_pred EEcCCCc--EEEecCCCchHHHHHHhccccce
Confidence 5654333 44555579999999999998865
No 61
>cd04407 RhoGAP_myosin_IXB RhoGAP_myosin_IXB: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in myosins IXB. Class IX myosins contain a characteristic head domain, a neck domain and a tail domain which contains a C6H2-zinc binding motif and a Rho-GAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell prolifer
Probab=20.74 E-value=2.2e+02 Score=19.79 Aligned_cols=39 Identities=13% Similarity=0.089 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHhccccCCCceEeeCcHHHHHHHHHhhc
Q 043356 40 PTFQKLLEKAAEEYMFSRESGIVLPCAESTFRRFLNLMD 78 (79)
Q Consensus 40 P~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~l~ 78 (79)
|.|-..+=..=+..|.+.+|.-++|.+....+.+...++
T Consensus 16 P~il~~~i~~l~~~gl~~EGIfR~~Gs~~~i~~l~~~~~ 54 (186)
T cd04407 16 PIVLEKLLEHVEMHGLYTEGIYRKSGSANRMKELHQLLQ 54 (186)
T ss_pred CcHHHHHHHHHHHcCCCCCceeecCCCHHHHHHHHHHHh
Confidence 344433333345678888999999999998888877665
No 62
>COG4378 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.55 E-value=1.1e+02 Score=20.47 Aligned_cols=25 Identities=12% Similarity=0.270 Sum_probs=21.2
Q ss_pred ceEEEEeccCCCCHHHHHHHHHHHH
Q 043356 27 MRRFVIPLSYLKDPTFQKLLEKAAE 51 (79)
Q Consensus 27 ~~RfvVp~~yL~hP~F~~LL~~aee 51 (79)
..-.+|=++|+||.+...+=++|.+
T Consensus 45 ~dlilvLtdf~nHNl~~~iK~eakk 69 (103)
T COG4378 45 TDLILVLTDFLNHNLMKKIKNEAKK 69 (103)
T ss_pred ccEEEEEhhhhcchHHHHHHHHHhh
Confidence 4567888999999999998888875
No 63
>KOG2813 consensus Predicted molecular chaperone, contains DnaJ domain [Posttranslational modification, protein turnover, chaperones]
Probab=20.54 E-value=89 Score=25.26 Aligned_cols=57 Identities=19% Similarity=0.260 Sum_probs=43.1
Q ss_pred EEEEEcCCceEEEEeccCCCCHHHHHHHHHHHHhccccCCCceEeeCcHHHHHHHHHh
Q 043356 19 FVVYVGEEMRRFVIPLSYLKDPTFQKLLEKAAEEYMFSRESGIVLPCAESTFRRFLNL 76 (79)
Q Consensus 19 ~~VyVG~e~~RfvVp~~yL~hP~F~~LL~~aeeEfG~~~~G~L~iPC~~~~Fe~vl~~ 76 (79)
+.||--.+.+|+ |...+++..+-.+||.+||-+-=|+.+..-.+||.-.-|+++-.+
T Consensus 274 ~vV~wKn~~krk-VSehr~~~~iPeell~~AeG~~~f~~en~~iypis~~~~~Dv~~~ 330 (406)
T KOG2813|consen 274 IVVYWKNEKKRK-VSEHRTESEIPEELLFQAEGKRIFEEENDYIYPISQYQEEDVNKM 330 (406)
T ss_pred EEEEeechhhhh-hhhhcccccCcHHHHHhhhcchhhhhccceEEeccccchhhHHHH
Confidence 344444456665 467888888899999999976557777889999998888877544
Done!