Query psy5445
Match_columns 315
No_of_seqs 54 out of 56
Neff 2.9
Searched_HMMs 46136
Date Fri Aug 16 17:45:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5445.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5445hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03185 CaKB: Calcium-activat 99.8 5.7E-21 1.2E-25 171.6 0.0 157 70-240 21-189 (201)
2 PF15050 SCIMP: SCIMP protein 64.8 3 6.6E-05 36.7 0.9 58 210-271 2-62 (133)
3 PF04906 Tweety: Tweety; Inte 60.2 7.6 0.00016 38.7 2.9 41 208-249 7-50 (406)
4 PF12158 DUF3592: Protein of u 53.4 33 0.00072 27.6 5.1 20 189-208 94-113 (148)
5 PF10999 DUF2839: Protein of u 52.5 7.6 0.00017 30.7 1.2 15 37-51 3-17 (68)
6 PF15102 TMEM154: TMEM154 prot 52.1 7.3 0.00016 34.8 1.2 15 216-230 55-69 (146)
7 PF10577 UPF0560: Uncharacteri 50.0 15 0.00032 40.5 3.2 52 200-252 255-308 (807)
8 PF05510 Sarcoglycan_2: Sarcog 47.2 14 0.00031 37.3 2.5 25 217-241 284-308 (386)
9 PF02038 ATP1G1_PLM_MAT8: ATP1 46.3 16 0.00034 27.7 2.0 40 208-252 8-47 (50)
10 PF12606 RELT: Tumour necrosis 44.5 19 0.00042 27.0 2.2 19 222-240 4-22 (50)
11 PHA02954 EEV membrane glycopro 43.7 4.1 8.9E-05 39.8 -1.9 27 211-237 274-300 (317)
12 PF02402 Lysis_col: Lysis prot 43.3 10 0.00022 28.3 0.5 16 264-279 21-36 (46)
13 PRK13865 type IV secretion sys 41.4 56 0.0012 30.5 5.2 28 62-89 38-65 (229)
14 KOG4482|consensus 40.3 27 0.00058 36.1 3.1 78 196-281 279-365 (449)
15 TIGR00267 conserved hypothetic 38.4 68 0.0015 28.3 5.1 41 26-66 46-86 (169)
16 KOG3970|consensus 36.4 61 0.0013 31.7 4.7 35 47-86 236-271 (299)
17 PRK13872 conjugal transfer pro 36.2 48 0.001 30.2 3.9 28 61-88 38-65 (228)
18 PF11952 DUF3469: Protein of u 35.9 4.6 0.0001 32.7 -2.4 16 162-177 40-57 (87)
19 KOG4544|consensus 34.4 57 0.0012 29.4 3.9 34 56-89 44-84 (144)
20 PF08018 Antimicrobial_1: Frog 34.0 15 0.00033 24.0 0.2 13 284-296 11-23 (24)
21 PRK13887 conjugal transfer pro 33.0 1.5E+02 0.0033 27.5 6.7 27 62-88 53-79 (250)
22 PF07234 DUF1426: Protein of u 31.7 54 0.0012 28.4 3.2 40 58-97 10-49 (117)
23 PF09925 DUF2157: Predicted me 30.7 1.5E+02 0.0032 25.0 5.7 24 59-82 31-54 (145)
24 PRK13836 conjugal transfer pro 29.9 80 0.0017 28.7 4.2 26 62-87 30-55 (220)
25 PF13908 Shisa: Wnt and FGF in 29.0 32 0.0007 29.9 1.5 17 222-238 80-96 (179)
26 PF00957 Synaptobrevin: Synapt 28.9 35 0.00076 26.4 1.5 10 58-67 61-70 (89)
27 KOG3088|consensus 28.8 79 0.0017 31.6 4.2 25 60-84 130-154 (313)
28 PF02439 Adeno_E3_CR2: Adenovi 28.4 29 0.00063 25.0 0.9 26 224-250 9-34 (38)
29 PF10166 DUF2368: Uncharacteri 28.1 78 0.0017 27.7 3.6 29 60-89 47-81 (131)
30 PF13253 DUF4044: Protein of u 27.0 1.4E+02 0.003 21.1 4.0 26 56-81 5-30 (35)
31 COG1459 PulF Type II secretory 26.2 58 0.0013 32.8 2.9 32 60-91 159-190 (397)
32 TIGR00964 secE_bact preprotein 25.5 2E+02 0.0044 21.0 5.0 28 57-84 17-44 (55)
33 PRK07597 secE preprotein trans 24.2 1.3E+02 0.0027 22.5 3.7 27 58-84 27-53 (64)
34 PF00957 Synaptobrevin: Synapt 24.1 1E+02 0.0022 23.8 3.3 31 57-87 55-86 (89)
35 PF03904 DUF334: Domain of unk 23.8 2.5E+02 0.0053 27.2 6.3 24 62-85 146-169 (230)
36 COG3736 VirB8 Type IV secretor 23.5 98 0.0021 29.7 3.7 27 62-88 41-67 (239)
37 COG5393 Predicted membrane pro 22.4 1.6E+02 0.0034 26.3 4.4 43 44-95 38-81 (131)
38 COG4038 Predicted membrane pro 22.3 51 0.0011 27.3 1.4 33 62-98 5-37 (87)
39 TIGR01195 oadG_fam sodium pump 22.2 1E+02 0.0022 24.6 3.0 41 64-105 3-44 (82)
40 PF00690 Cation_ATPase_N: Cati 22.1 90 0.002 23.0 2.6 18 23-40 13-30 (69)
41 PF14143 YrhC: YrhC-like prote 21.8 1.7E+02 0.0037 23.5 4.2 42 58-99 2-44 (72)
42 COG5528 Predicted integral mem 21.0 3.5E+02 0.0075 24.6 6.4 49 36-84 102-150 (155)
43 TIGR02976 phageshock_pspB phag 20.7 69 0.0015 25.6 1.8 22 220-241 4-26 (75)
44 PF01200 Ribosomal_S28e: Ribos 20.4 1.5E+02 0.0033 23.8 3.6 29 132-170 20-48 (69)
45 PF04246 RseC_MucC: Positive r 20.3 1.4E+02 0.003 24.9 3.6 38 203-240 56-93 (135)
No 1
>PF03185 CaKB: Calcium-activated potassium channel, beta subunit; InterPro: IPR003930 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. Ca2+-activated K+ channels are a diverse group of channels that are activated by an increase in intracellular Ca2+ concentration. They are found in the majority of nerve cells, where they modulate cell excitability and action potential. Three types of Ca2+-activated K+ channel have been characterised, termed small-conductance (SK), intermediate conductance (IK) and large conductance (BK) respectively []. BK channels (also referred to as maxi-K channels) are widely expressed in the body, being found in glandular tissue, smooth and skeletal muscle, as well as in neural tissues. They have been demonstrated to regulate arteriolar and airway diameter, and also neurotransmitter release. Each channel complex is thought to be composed of 2 types of subunit: the pore- forming (alpha) subunits and smaller accessory (beta) subunits. The beta subunit (which is thought to possess 2 TM domains) increases the Ca2+ sensitivity of the BK channel []. It does this by enhancing the time spent by the channel in burst-like open states. However, it has little effect on the durations of closed intervals between bursts, or on the numbers of open and closed states entered during gating []. ; GO: 0015269 calcium-activated potassium channel activity, 0006813 potassium ion transport, 0016020 membrane; PDB: 1JO6_A.
Probab=99.80 E-value=5.7e-21 Score=171.55 Aligned_cols=157 Identities=22% Similarity=0.477 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHhhhccceeechhhhhhhcCCCCCCeeEEEeeecccCCccCCcccccccccc-cCCccceEEEEEeecC
Q psy5445 70 FFAMTAVSTGSSLLFLVPLYVDPAISTLTSDFNPNPVTCVTILNRTETGIFNCTWSSCREGCT-SDMYKCFQIFVKYVDY 148 (315)
Q Consensus 70 ~l~~~av~S~fafLFLVPfvVdPAisTi~adFdp~Pv~CvTt~~~~~~Gl~NCTWsSCREGCT-sd~y~C~QI~VnY~~~ 148 (315)
.+++.++++.|.+++ .++-|++...+ .++++|++......+...+|+. ||+-.|. ...|+|.||+|||+..
T Consensus 21 ~m~~~svlm~~vlGi---tiv~P~l~s~~----~~et~Ctvl~s~i~~~~v~Cs~-~cg~~c~~~s~yPCLqV~Vn~t~s 92 (201)
T PF03185_consen 21 AMMICSVLMLFVLGI---TIVKPYLKSLW----FEETNCTVLSSHIVGEWVDCSF-SCGSDCRGVSKYPCLQVFVNYTHS 92 (201)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHH---hccchhhhhcc----cccceEEEEEEEeecccccccc-cCCCCCCCcCCCCceEEEEEecCC
Confidence 344445555555555 89999999886 5899999999988888899999 9999998 6799999999999776
Q ss_pred CCCCCCCCCCCcCceEeeccCCcCCCCcc---------chHHHHHHhCCC-CCcceeeeecCC-CceEEeecCHHHHHHH
Q psy5445 149 NVTFSEEPLYVDNAILLVNIKGCGYPPEV---------QCANFASSYGMQ-DKSYPCYYSRKN-TTIVMDKYDEEEQMYI 217 (315)
Q Consensus 149 n~~~~e~~~~~~earLliNikGCGYpP~v---------nC~~F~k~YG~d-Ga~FPCYYSr~~-p~~VVaryd~d~t~~~ 217 (315)
+. ....+.+|..+..|.| |.|.|.+ +=.+|.+.||.. |+.|||||+..+ |+.|+.+...++..
T Consensus 93 g~---~a~L~~~E~~l~~n~k-CsY~P~C~~d~~~~~~~V~~~~~~~~~~~gq~f~Cfy~P~~~~~~Vil~r~y~~~~-- 166 (201)
T PF03185_consen 93 GQ---TALLHHDEETLDSNPK-CSYIPKCHRDRQDNRAEVEDFQENFGQQNGQTFPCFYDPDNQPEDVILRRKYDPSV-- 166 (201)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred Cc---eEEEEEchHhhccCCc-ceecCcccccHHHHHHHHHHHHHHhhhccCcceeeeecCCCCcceEEEEEecCHhH--
Confidence 42 2346889999999999 9999965 233488888888 899999999976 58899888887666
Q ss_pred hhhhhhhhhhHHHHhhhhhhhhh
Q psy5445 218 IIHYFIIPFIICVVCSIVLCVMH 240 (315)
Q Consensus 218 Ll~a~~VP~vlFvISvi~L~i~h 240 (315)
++|+|.||..+|+.+++++.+.-
T Consensus 167 ~fhslfWP~l~lvgG~liv~mvk 189 (201)
T PF03185_consen 167 LFHSLFWPSLMLVGGVLIVAMVK 189 (201)
T ss_dssp -----------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999998888877
No 2
>PF15050 SCIMP: SCIMP protein
Probab=64.80 E-value=3 Score=36.73 Aligned_cols=58 Identities=21% Similarity=0.280 Sum_probs=33.9
Q ss_pred CHHHHHHHhhhhhhhhhhHHHHhhhhhhhhhcccccccccccC---CCCCCCCCccccccccccC
Q psy5445 210 DEEEQMYIIIHYFIIPFIICVVCSIVLCVMHCECQCNDNIATS---LPPSKQRPDDEQNYVKDVG 271 (315)
Q Consensus 210 d~d~t~~~Ll~a~~VP~vlFvISvi~L~i~hc~C~C~~~~~~~---~~psk~~~~~~~~~~~~~~ 271 (315)
|||...--+|.|++| .+||++.-.+++|-||+.-+.-.. -.|.|++-+||..--..|+
T Consensus 2 ~WWr~nFWiiLAVaI----I~vS~~lglIlyCvcR~~lRqGkkweiakp~k~~~rdeEkmYENv~ 62 (133)
T PF15050_consen 2 SWWRDNFWIILAVAI----ILVSVVLGLILYCVCRWQLRQGKKWEIAKPLKQKQRDEEKMYENVL 62 (133)
T ss_pred chHHhchHHHHHHHH----HHHHHHHHHHHHHHHHHHHHccccceeccchhhhcccHHHHHHHhh
Confidence 566655445666653 345566666678777654443333 4677777777754444443
No 3
>PF04906 Tweety: Tweety; InterPro: IPR006990 None of the members of the tweety (tty) family have been functionally characterised. However, they are considered to be transmembrane proteins with five potential membrane-spanning regions. A number of potential functions have been suggested on the basis of homology to the yeast FTR1 and FTH1 iron transporter proteins and the mammalian neurotensin receptors 1 and 2 in that they have a similar hydrophobicity profiles although there is no detectable sequence homology to the tweety-related proteins. It has been proposed that the tweety-related proteins could be involved in transport of iron or other divalent cations or alternatively that they may be membrane-bound receptors [].
Probab=60.17 E-value=7.6 Score=38.67 Aligned_cols=41 Identities=12% Similarity=0.349 Sum_probs=26.9
Q ss_pred ecCHH-HHHHH-hhhhhhhhhhHHHHhhhhh-hhhhccccccccc
Q psy5445 208 KYDEE-EQMYI-IIHYFIIPFIICVVCSIVL-CVMHCECQCNDNI 249 (315)
Q Consensus 208 ryd~d-~t~~~-Ll~a~~VP~vlFvISvi~L-~i~hc~C~C~~~~ 249 (315)
.|+.+ ++|.+ |++.-.||.+.++++.+.| +++-|.| |.++.
T Consensus 7 ~F~p~~~~Y~qsL~~la~v~~~~l~l~Ll~ll~yl~~~C-C~r~~ 50 (406)
T PF04906_consen 7 TFNPQDEEYQQSLLILASVAAACLALSLLFLLIYLICRC-CCRRP 50 (406)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hCCCC
Confidence 35555 35555 5666778999999998774 4556677 54443
No 4
>PF12158 DUF3592: Protein of unknown function (DUF3592); InterPro: IPR021994 This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length.
Probab=53.36 E-value=33 Score=27.62 Aligned_cols=20 Identities=15% Similarity=0.207 Sum_probs=16.3
Q ss_pred CCCcceeeeecCCCceEEee
Q psy5445 189 QDKSYPCYYSRKNTTIVMDK 208 (315)
Q Consensus 189 dGa~FPCYYSr~~p~~VVar 208 (315)
.|+..+-||+.+||+.+...
T Consensus 94 ~G~~V~V~Y~P~~P~~~~l~ 113 (148)
T PF12158_consen 94 IGDTVTVYYNPNNPEEARLE 113 (148)
T ss_pred CcCEEEEEECCcCCCeEEEe
Confidence 79999999999999754333
No 5
>PF10999 DUF2839: Protein of unknown function (DUF2839); InterPro: IPR021262 This bacterial family of unknown function appear to be restricted to Cyanobacteria.
Probab=52.53 E-value=7.6 Score=30.75 Aligned_cols=15 Identities=27% Similarity=0.386 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHhhc
Q psy5445 37 QLRKRKLLELAQNKN 51 (315)
Q Consensus 37 ~~r~rk~~ela~~k~ 51 (315)
|++|||=+-|.+..+
T Consensus 3 EAKRRke~Gl~pr~~ 17 (68)
T PF10999_consen 3 EAKRRKELGLPPRYK 17 (68)
T ss_pred chhhhhhccCCCccC
Confidence 567777665555544
No 6
>PF15102 TMEM154: TMEM154 protein family
Probab=52.08 E-value=7.3 Score=34.84 Aligned_cols=15 Identities=27% Similarity=0.565 Sum_probs=10.7
Q ss_pred HHhhhhhhhhhhHHH
Q psy5445 216 YIIIHYFIIPFIICV 230 (315)
Q Consensus 216 ~~Ll~a~~VP~vlFv 230 (315)
.++++..+||+|+++
T Consensus 55 ~efiLmIlIP~VLLv 69 (146)
T PF15102_consen 55 LEFILMILIPLVLLV 69 (146)
T ss_pred cceEEEEeHHHHHHH
Confidence 345888899977663
No 7
>PF10577 UPF0560: Uncharacterised protein family UPF0560; InterPro: IPR018890 This family of proteins has no known function.
Probab=49.99 E-value=15 Score=40.51 Aligned_cols=52 Identities=10% Similarity=0.171 Sum_probs=32.9
Q ss_pred CCCceEEeecCHHHHHHHhhh--hhhhhhhHHHHhhhhhhhhhcccccccccccC
Q psy5445 200 KNTTIVMDKYDEEEQMYIIIH--YFIIPFIICVVCSIVLCVMHCECQCNDNIATS 252 (315)
Q Consensus 200 ~~p~~VVaryd~d~t~~~Ll~--a~~VP~vlFvISvi~L~i~hc~C~C~~~~~~~ 252 (315)
..++.++.. +.|=+.++-++ +++==+++.+|.++-|+++||.++|.+.+.+.
T Consensus 255 ~~~G~~~~~-~~Di~~YHT~fLl~ILG~~~livl~lL~vLl~yCrrkc~~~r~~~ 308 (807)
T PF10577_consen 255 SSSGPVVST-GSDITTYHTVFLLAILGGTALIVLILLCVLLCYCRRKCLKPRQRH 308 (807)
T ss_pred cccCccccc-CCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCccccc
Confidence 445666666 44555655444 44444566666666667778888898877554
No 8
>PF05510 Sarcoglycan_2: Sarcoglycan alpha/epsilon; InterPro: IPR008908 Sarcoglycans are a subcomplex of transmembrane proteins which are part of the dystrophin-glycoprotein complex. They are expressed in the skeletal, cardiac and smooth muscle. Although numerous studies have been conducted on the sarcoglycan subcomplex in skeletal and cardiac muscle, the manner of the distribution and localisation of these proteins along the nonjunctional sarcolemma is not clear []. This family contains alpha and epsilon members.; GO: 0016012 sarcoglycan complex
Probab=47.19 E-value=14 Score=37.33 Aligned_cols=25 Identities=24% Similarity=0.530 Sum_probs=23.4
Q ss_pred HhhhhhhhhhhHHHHhhhhhhhhhc
Q psy5445 217 IIIHYFIIPFIICVVCSIVLCVMHC 241 (315)
Q Consensus 217 ~Ll~a~~VP~vlFvISvi~L~i~hc 241 (315)
++++.++||.+++++-+++|.++-|
T Consensus 284 d~~vtl~iPl~i~llL~llLs~Imc 308 (386)
T PF05510_consen 284 DFLVTLAIPLIIALLLLLLLSYIMC 308 (386)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhe
Confidence 4789999999999999999999998
No 9
>PF02038 ATP1G1_PLM_MAT8: ATP1G1/PLM/MAT8 family; InterPro: IPR000272 The FXYD protein family contains at least seven members in mammals []. Two other family members that are not obvious orthologs of any identified mammalian FXYD protein exist in zebrafish. All these proteins share a signature sequence of six conserved amino acids comprising the FXYD motif in the NH2-terminus, and two glycines and one serine residue in the transmembrane domain. FXYD proteins are widely distributed in mammalian tissues with prominent expression in tissues that perform fluid and solute transport or that are electrically excitable. Initial functional characterisation suggested that FXYD proteins act as channels or as modulators of ion channels however studies have revealed that most FXYD proteins have another specific function and act as tissue-specific regulatory subunits of the Na,K-ATPase. Each of these auxiliary subunits produces a distinct functional effect on the transport characteristics of the Na,K-ATPase that is adjusted to the specific functional demands of the tissue in which the FXYD protein is expressed. FXYD proteins appear to preferentially associate with Na,K-ATPase alpha1-beta isozymes, and affect their function in a way that render them operationally complementary or supplementary to coexisting isozymes.; GO: 0005216 ion channel activity, 0006811 ion transport, 0016020 membrane; PDB: 2JO1_A 2JP3_A 2ZXE_G 3A3Y_G 3N23_E 3B8E_H 3KDP_G 3N2F_E.
Probab=46.26 E-value=16 Score=27.67 Aligned_cols=40 Identities=20% Similarity=0.374 Sum_probs=24.0
Q ss_pred ecCHHHHHHHhhhhhhhhhhHHHHhhhhhhhhhcccccccccccC
Q psy5445 208 KYDEEEQMYIIIHYFIIPFIICVVCSIVLCVMHCECQCNDNIATS 252 (315)
Q Consensus 208 ryd~d~t~~~Ll~a~~VP~vlFvISvi~L~i~hc~C~C~~~~~~~ 252 (315)
.||++ +++ +-.+++-.++|+++++++.-=- |+|..+...+
T Consensus 8 ~YDy~-tLr--igGLi~A~vlfi~Gi~iils~k--ckCk~~qk~~ 47 (50)
T PF02038_consen 8 YYDYE-TLR--IGGLIFAGVLFILGILIILSGK--CKCKFNQKPR 47 (50)
T ss_dssp GGCHH-HHH--HHHHHHHHHHHHHHHHHHCTTH--HHHHHSTTTT
T ss_pred ccchh-Hhh--ccchHHHHHHHHHHHHHHHcCc--cccCCCCCCC
Confidence 47875 443 3455666788999886665544 5554444333
No 10
>PF12606 RELT: Tumour necrosis factor receptor superfamily member 19; InterPro: IPR022248 The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). RELT (receptor expressed in lymphoid tissues) is a member of the TNFR superfamily. The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1 []. RELT like proteins 1 and 2 (RELL1 and RELL2) are two RELT homologues that bind to RELT. The expression of RELL1 at the mRNA level is ubiquitous, whereas expression of RELL2 mRNA is more restricted to particular tissues [].
Probab=44.52 E-value=19 Score=26.96 Aligned_cols=19 Identities=26% Similarity=0.343 Sum_probs=12.7
Q ss_pred hhhhhhHHHHhhhhhhhhh
Q psy5445 222 FIIPFIICVVCSIVLCVMH 240 (315)
Q Consensus 222 ~~VP~vlFvISvi~L~i~h 240 (315)
|++=.++||..++.+.++|
T Consensus 4 ~~iV~i~iv~~lLg~~I~~ 22 (50)
T PF12606_consen 4 FLIVSIFIVMGLLGLSICT 22 (50)
T ss_pred hHHHHHHHHHHHHHHHHHH
Confidence 4444556777777777776
No 11
>PHA02954 EEV membrane glycoprotein; Provisional
Probab=43.73 E-value=4.1 Score=39.82 Aligned_cols=27 Identities=33% Similarity=0.319 Sum_probs=22.2
Q ss_pred HHHHHHHhhhhhhhhhhHHHHhhhhhh
Q psy5445 211 EEEQMYIIIHYFIIPFIICVVCSIVLC 237 (315)
Q Consensus 211 ~d~t~~~Ll~a~~VP~vlFvISvi~L~ 237 (315)
++.++..+|+|+.|--|+|+||+|+|.
T Consensus 274 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 300 (317)
T PHA02954 274 LEATYHIIIVALTIMGVIFLISVIVLV 300 (317)
T ss_pred hhceeeEeeeehhhhHHHHhheeeEEE
Confidence 445666688899999999999999885
No 12
>PF02402 Lysis_col: Lysis protein; InterPro: IPR003059 The DNA sequence of the entire colicin E2 operon has been determined []. The operon comprises the colicin activity gene (ceaB), the colicin immunity gene (ceiB) and the lysis gene (celB), which is essential for colicin release from producing cells []. A putative LexA binding site is located upstream from ceaB, and a rho-independent terminator structure is located downstream from celB []. Comparison of the amino acid sequences of colicin E2 and cloacin DF13 reveal extensive similarity. These colicins have different modes of action and recognise different cell surface receptors; the two major regions of heterology at the C terminus, and in the C-terminal end of the central region are thought to correspond to the catalytic and receptor-recognition domains, respectively []. Sequence similarities between colicins E2, A and E1 [] are less striking. The colicin E2 (pyocin) immunity protein does not share similarity with either the colicin E3 or cloacin DF13 [] immunity proteins. By contrast, the lysis proteins of the ColE2, ColE1 and CloDF13 plasmids are almost identical except in the N-terminal regions, which themselves are similar to lipoprotein signal peptides []. Processing of the ColE2 prolysis protein to the mature form is prevented by globomycin, a specific inhibitor of the lipoprotein signal peptidase []. The mature ColE2 lysis protein is located in the cell envelope [].; GO: 0009405 pathogenesis, 0019835 cytolysis, 0019867 outer membrane
Probab=43.29 E-value=10 Score=28.34 Aligned_cols=16 Identities=38% Similarity=0.850 Sum_probs=13.4
Q ss_pred cccccccCCCCCCCCC
Q psy5445 264 QNYVKDVGGTDLGPQN 279 (315)
Q Consensus 264 ~~~~~~~~~~~~~~~~ 279 (315)
-||+|||||-...|..
T Consensus 21 aN~iRDvqGGtVaPSS 36 (46)
T PF02402_consen 21 ANYIRDVQGGTVAPSS 36 (46)
T ss_pred hcceecCCCceECCCc
Confidence 4899999998888864
No 13
>PRK13865 type IV secretion system protein VirB8; Provisional
Probab=41.42 E-value=56 Score=30.53 Aligned_cols=28 Identities=14% Similarity=0.194 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcccee
Q psy5445 62 KIWFYTTSFFAMTAVSTGSSLLFLVPLY 89 (315)
Q Consensus 62 k~~FYtT~~l~~~av~S~fafLFLVPfv 89 (315)
|..+-.....++++++|++|+..|+|+-
T Consensus 38 k~aw~va~~~~~~~~~~~~Av~~l~PLK 65 (229)
T PRK13865 38 RVLAAVAGIAVAGNVAQAFAIATMVPLE 65 (229)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcccC
Confidence 3334355667888889999999998874
No 14
>KOG4482|consensus
Probab=40.31 E-value=27 Score=36.06 Aligned_cols=78 Identities=14% Similarity=0.283 Sum_probs=52.1
Q ss_pred eeecCCCceEEeecCHHHHHHHhhhhhhhhhhHHHHhhhhhhhhhcccccccccccCCCCCC---------CCCcccccc
Q psy5445 196 YYSRKNTTIVMDKYDEEEQMYIIIHYFIIPFIICVVCSIVLCVMHCECQCNDNIATSLPPSK---------QRPDDEQNY 266 (315)
Q Consensus 196 YYSr~~p~~VVaryd~d~t~~~Ll~a~~VP~vlFvISvi~L~i~hc~C~C~~~~~~~~~psk---------~~~~~~~~~ 266 (315)
+++-+-|..+-.| +-+-.++|+|+||..++++=++.|.++-| |++.-. .++-+| =++.+.+..
T Consensus 279 ~~~~~~~~e~p~R----dyy~df~~tfaIpl~Valll~~~La~imc---~rrEg~-~~rd~~ts~~q~fh~c~i~~ntke 350 (449)
T KOG4482|consen 279 FQNLNPPPEQPPR----DYYGDFLHTFAIPLGVALLLVLALAYIMC---CRREGQ-KKRDDKTSDIQNFHHCSIRDNTKE 350 (449)
T ss_pred hhccCCCccCCch----hHHHHHHHHHHHHHHHHHHHHHHHHHHHh---hhhhcc-ccccccchhhhheeeeeecCCHHH
Confidence 4444455555543 34566899999999999999999999998 443221 111111 134455667
Q ss_pred ccccCCCCCCCCCCC
Q psy5445 267 VKDVGGTDLGPQNYK 281 (315)
Q Consensus 267 ~~~~~~~~~~~~~~~ 281 (315)
+|+..|.|.||..-.
T Consensus 351 lr~mS~~~~g~~~ns 365 (449)
T KOG4482|consen 351 LREMSLQSMGPDTNS 365 (449)
T ss_pred HHhhhccccCCcccc
Confidence 899999999997533
No 15
>TIGR00267 conserved hypothetical protein TIGR00267. This family is represented in three of the first four completed archaeal genomes, with two members in A. fulgidus.
Probab=38.39 E-value=68 Score=28.32 Aligned_cols=41 Identities=15% Similarity=0.031 Sum_probs=20.5
Q ss_pred CCcccccchHHHHHHHHHHHHHHhhcCcccchhHHHHHHHH
Q psy5445 26 SSSELLLDPQQQLRKRKLLELAQNKNKKKVKRTCKQKIWFY 66 (315)
Q Consensus 26 ~sselll~~~~~~r~rk~~ela~~k~~~~~~~t~rek~~FY 66 (315)
...|++-|+.|+.|.|+-+|-....+|.-.+.+..+|..+.
T Consensus 46 a~GeYv~e~ae~~~e~~ele~~~~~~~g~~~~~~~~~~~~~ 86 (169)
T TIGR00267 46 AFGAFTAERAEEEREMRELEKSMLMDEGKLDDTIIYKQARR 86 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCchhhHHHHHHh
Confidence 44577766665555544444433333333344556665553
No 16
>KOG3970|consensus
Probab=36.42 E-value=61 Score=31.74 Aligned_cols=35 Identities=14% Similarity=0.224 Sum_probs=23.4
Q ss_pred HHhhc-CcccchhHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q psy5445 47 AQNKN-KKKVKRTCKQKIWFYTTSFFAMTAVSTGSSLLFLV 86 (315)
Q Consensus 47 a~~k~-~~~~~~t~rek~~FYtT~~l~~~av~S~fafLFLV 86 (315)
-.+|- +.+++++..++++| ++++|+++..+|+.|.
T Consensus 236 ~R~~~g~s~rP~~~~~ra~f-----li~lgvLafi~~i~lM 271 (299)
T KOG3970|consen 236 WRAKHGGSGRPQEAKKRALF-----LIFLGVLAFITIIMLM 271 (299)
T ss_pred HHHhhCCCCCCHHHHHHHHH-----HHHHHHHHHHHHHHHH
Confidence 34443 55667888888776 5667777777777654
No 17
>PRK13872 conjugal transfer protein TrbF; Provisional
Probab=36.20 E-value=48 Score=30.21 Aligned_cols=28 Identities=7% Similarity=0.064 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccce
Q psy5445 61 QKIWFYTTSFFAMTAVSTGSSLLFLVPL 88 (315)
Q Consensus 61 ek~~FYtT~~l~~~av~S~fafLFLVPf 88 (315)
+|+|+...+..+++++++++|+.++.|+
T Consensus 38 ~~~w~~va~~~l~i~~~~v~av~~l~pl 65 (228)
T PRK13872 38 ARNWRLMAFGCLALSAGLAGGLVWQSAR 65 (228)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4467766666777778888888888774
No 18
>PF11952 DUF3469: Protein of unknown function (DUF3469); InterPro: IPR021859 This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 108 to 439 amino acids in length.
Probab=35.94 E-value=4.6 Score=32.71 Aligned_cols=16 Identities=50% Similarity=1.144 Sum_probs=13.1
Q ss_pred ceEeeccC--CcCCCCcc
Q psy5445 162 AILLVNIK--GCGYPPEV 177 (315)
Q Consensus 162 arLliNik--GCGYpP~v 177 (315)
|.+++|.+ ||+||+.+
T Consensus 40 s~v~~N~~fLGC~Yp~~~ 57 (87)
T PF11952_consen 40 SQVWANMEFLGCRYPPEV 57 (87)
T ss_pred HHHHHhHHHHhcCCCHHH
Confidence 46788987 99999866
No 19
>KOG4544|consensus
Probab=34.43 E-value=57 Score=29.39 Aligned_cols=34 Identities=24% Similarity=0.304 Sum_probs=23.1
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHH-------hhhcccee
Q psy5445 56 KRTCKQKIWFYTTSFFAMTAVSTGSS-------LLFLVPLY 89 (315)
Q Consensus 56 ~~t~rek~~FYtT~~l~~~av~S~fa-------fLFLVPfv 89 (315)
.+-..++-+||--++|+.+++.++.| .++|||.+
T Consensus 44 ~~Ia~~RE~f~w~~~f~~~avv~laa~~~~~Kr~~~liPIv 84 (144)
T KOG4544|consen 44 FKIAEEREKFNWIACFGSLAVVLLAASSFHHKRLLHLIPIV 84 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccchheech
Confidence 34445666777778888888877766 35677754
No 20
>PF08018 Antimicrobial_1: Frog antimicrobial peptide ; InterPro: IPR012520 This family includes antimicrobial peptides secreted from skins of frogs. The secretion of antimicrobial peptides from the skins of frogs plays an important role in the self defence of these frogs. Structural characterisation of these peptides showed that they belonged to four known families: the brevinin-1 family, the esculentin-2 family, the ranatuerin-2 family and the temporin family [].; GO: 0005576 extracellular region
Probab=33.99 E-value=15 Score=24.03 Aligned_cols=13 Identities=46% Similarity=1.035 Sum_probs=10.6
Q ss_pred ccchhhhhhhhcc
Q psy5445 284 ELLPTILCAISYR 296 (315)
Q Consensus 284 ~~~~~~~~~~~~~ 296 (315)
+++|+|+|+|+-+
T Consensus 11 ~~lp~i~C~ItKK 23 (24)
T PF08018_consen 11 NVLPKIFCAITKK 23 (24)
T ss_pred HhcchhHhhhccc
Confidence 5799999999853
No 21
>PRK13887 conjugal transfer protein TrbF; Provisional
Probab=33.02 E-value=1.5e+02 Score=27.51 Aligned_cols=27 Identities=7% Similarity=0.186 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccce
Q psy5445 62 KIWFYTTSFFAMTAVSTGSSLLFLVPL 88 (315)
Q Consensus 62 k~~FYtT~~l~~~av~S~fafLFLVPf 88 (315)
|.|....+..++++++|++|+.+|.|+
T Consensus 53 ~~w~v~a~~~~~ia~~~v~av~~l~pl 79 (250)
T PRK13887 53 QTWQVVGILSLLIALAAVGGVIHIGSQ 79 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 356665666677788888888888776
No 22
>PF07234 DUF1426: Protein of unknown function (DUF1426); InterPro: IPR009871 This family consists of several Banana bunchy top virus proteins of around 120 residues in length. Q9IGU4 from SWISSPROT is annotated a movement protein whereas most other family members are hypothetical. The function of this family is unknown.
Probab=31.73 E-value=54 Score=28.38 Aligned_cols=40 Identities=28% Similarity=0.394 Sum_probs=34.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhhccceeechhhhhh
Q psy5445 58 TCKQKIWFYTTSFFAMTAVSTGSSLLFLVPLYVDPAISTL 97 (315)
Q Consensus 58 t~rek~~FYtT~~l~~~av~S~fafLFLVPfvVdPAisTi 97 (315)
-+.|=++|+...|.+++-+--+.|+||=||=||---+.-+
T Consensus 10 lfFEwFLF~~AIFiAItIlYILLalL~EvPkYIK~~VrYl 49 (117)
T PF07234_consen 10 LFFEWFLFFGAIFIAITILYILLALLFEVPKYIKELVRYL 49 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 4678889999999999999999999999999887665544
No 23
>PF09925 DUF2157: Predicted membrane protein (DUF2157); InterPro: IPR018677 This family of various hypothetical prokaryotic proteins has no known function.
Probab=30.66 E-value=1.5e+02 Score=25.03 Aligned_cols=24 Identities=8% Similarity=0.049 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q psy5445 59 CKQKIWFYTTSFFAMTAVSTGSSL 82 (315)
Q Consensus 59 ~rek~~FYtT~~l~~~av~S~faf 82 (315)
.--+++.|..+.++.+|++..+|.
T Consensus 31 ~~~~~l~~lGall~~~gii~fvA~ 54 (145)
T PF09925_consen 31 WLARILLYLGALLLGLGIILFVAA 54 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 667888999999999998888775
No 24
>PRK13836 conjugal transfer protein TrbF; Provisional
Probab=29.93 E-value=80 Score=28.67 Aligned_cols=26 Identities=15% Similarity=0.031 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccc
Q psy5445 62 KIWFYTTSFFAMTAVSTGSSLLFLVP 87 (315)
Q Consensus 62 k~~FYtT~~l~~~av~S~fafLFLVP 87 (315)
++|+...+..++++++|+++++++-|
T Consensus 30 ~~W~~~a~~~l~~a~~~v~~~~~l~~ 55 (220)
T PRK13836 30 AAWRIVGILGLTMAVIGFGYALYQST 55 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 77888777555557777777777543
No 25
>PF13908 Shisa: Wnt and FGF inhibitory regulator
Probab=29.03 E-value=32 Score=29.94 Aligned_cols=17 Identities=35% Similarity=0.501 Sum_probs=7.5
Q ss_pred hhhhhhHHHHhhhhhhh
Q psy5445 222 FIIPFIICVVCSIVLCV 238 (315)
Q Consensus 222 ~~VP~vlFvISvi~L~i 238 (315)
+++=+++|||.++++++
T Consensus 80 iivgvi~~Vi~Iv~~Iv 96 (179)
T PF13908_consen 80 IIVGVICGVIAIVVLIV 96 (179)
T ss_pred eeeehhhHHHHHHHhHh
Confidence 44444444444444433
No 26
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain []. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins []. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.; GO: 0016192 vesicle-mediated transport, 0016021 integral to membrane; PDB: 3EGX_C 2NUP_C 3EGD_C 2NUT_C 1IOU_A 1H8M_A 3B5N_A 3ZYM_A 2NPS_A 1SFC_E ....
Probab=28.93 E-value=35 Score=26.44 Aligned_cols=10 Identities=10% Similarity=0.076 Sum_probs=4.4
Q ss_pred hHHHHHHHHH
Q psy5445 58 TCKQKIWFYT 67 (315)
Q Consensus 58 t~rek~~FYt 67 (315)
.+.++.+.|.
T Consensus 61 ~~~~~~k~~~ 70 (89)
T PF00957_consen 61 MWWRNYKLYI 70 (89)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 3444444443
No 27
>KOG3088|consensus
Probab=28.84 E-value=79 Score=31.60 Aligned_cols=25 Identities=16% Similarity=-0.060 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5445 60 KQKIWFYTTSFFAMTAVSTGSSLLF 84 (315)
Q Consensus 60 rek~~FYtT~~l~~~av~S~fafLF 84 (315)
..|..||+=.+..++.++-++|-|.
T Consensus 130 ~vk~~yylwm~~~~tL~~Niia~la 154 (313)
T KOG3088|consen 130 LVKRAYYLWMGLVLTLLWNIIACLA 154 (313)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4688999998888888877777766
No 28
>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []. This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.
Probab=28.40 E-value=29 Score=25.01 Aligned_cols=26 Identities=19% Similarity=0.579 Sum_probs=18.0
Q ss_pred hhhhHHHHhhhhhhhhhcccccccccc
Q psy5445 224 IPFIICVVCSIVLCVMHCECQCNDNIA 250 (315)
Q Consensus 224 VP~vlFvISvi~L~i~hc~C~C~~~~~ 250 (315)
|-.|+-+++.+++|++++-| |.|+.+
T Consensus 9 Iv~V~vg~~iiii~~~~YaC-cykk~~ 34 (38)
T PF02439_consen 9 IVAVVVGMAIIIICMFYYAC-CYKKHR 34 (38)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHcccc
Confidence 33566677788888888777 665544
No 29
>PF10166 DUF2368: Uncharacterised conserved protein (DUF2368); InterPro: IPR019319 This family is conserved from nematodes to humans. The function is not known.
Probab=28.10 E-value=78 Score=27.68 Aligned_cols=29 Identities=34% Similarity=0.673 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh------hhcccee
Q psy5445 60 KQKIWFYTTSFFAMTAVSTGSSL------LFLVPLY 89 (315)
Q Consensus 60 rek~~FYtT~~l~~~av~S~faf------LFLVPfv 89 (315)
||.++.| ..|.+++++++..++ ++|+|++
T Consensus 47 RE~~~w~-~~f~~l~~~~~~~~~~k~K~~~~l~Plv 81 (131)
T PF10166_consen 47 RELFKWF-ASFYALAAVGLIAGAIKRKNPLFLIPLV 81 (131)
T ss_pred HHHHHHH-HHHHHHHHHHHHHHHHhccCcchhhhHH
Confidence 4555543 334444444444333 4555554
No 30
>PF13253 DUF4044: Protein of unknown function (DUF4044)
Probab=26.96 E-value=1.4e+02 Score=21.15 Aligned_cols=26 Identities=15% Similarity=0.162 Sum_probs=18.1
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHH
Q psy5445 56 KRTCKQKIWFYTTSFFAMTAVSTGSS 81 (315)
Q Consensus 56 ~~t~rek~~FYtT~~l~~~av~S~fa 81 (315)
++|..||+.--....++++-++|+++
T Consensus 5 kKS~fekiT~v~v~lM~i~tvg~v~~ 30 (35)
T PF13253_consen 5 KKSTFEKITMVVVWLMLILTVGSVVA 30 (35)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35899998777666666666666554
No 31
>COG1459 PulF Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=26.24 E-value=58 Score=32.76 Aligned_cols=32 Identities=19% Similarity=0.373 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccceeec
Q psy5445 60 KQKIWFYTTSFFAMTAVSTGSSLLFLVPLYVD 91 (315)
Q Consensus 60 rek~~FYtT~~l~~~av~S~fafLFLVPfvVd 91 (315)
-.+++.|=...++++.+...|-+.|+||=..+
T Consensus 159 i~~Al~YP~vll~v~~~v~~~Ll~~VvP~f~~ 190 (397)
T COG1459 159 IKSALIYPLVLLVVALVVVLFLLIFVVPQFAE 190 (397)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHHhccHHH
Confidence 45789999999988888888888887775443
No 32
>TIGR00964 secE_bact preprotein translocase, SecE subunit, bacterial. This model represents exclusively the bacterial (and some organellar) SecE protein. SecE is part of the core heterotrimer, SecYEG, of the Sec preprotein translocase system. Other components are the ATPase SecA, a cytosolic chaperone SecB, and an accessory complex of SecDF and YajC.
Probab=25.50 E-value=2e+02 Score=20.97 Aligned_cols=28 Identities=7% Similarity=0.011 Sum_probs=22.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5445 57 RTCKQKIWFYTTSFFAMTAVSTGSSLLF 84 (315)
Q Consensus 57 ~t~rek~~FYtT~~l~~~av~S~fafLF 84 (315)
=.-|+.++.+|...+++++++|++.+++
T Consensus 17 WPt~~e~~~~t~~Vi~~~~~~~~~~~~~ 44 (55)
T TIGR00964 17 WPSRKELITYTIVVIVFVIFFSLFLFGV 44 (55)
T ss_pred CcCHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 3457778889999999999988887665
No 33
>PRK07597 secE preprotein translocase subunit SecE; Reviewed
Probab=24.18 E-value=1.3e+02 Score=22.54 Aligned_cols=27 Identities=11% Similarity=-0.007 Sum_probs=21.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5445 58 TCKQKIWFYTTSFFAMTAVSTGSSLLF 84 (315)
Q Consensus 58 t~rek~~FYtT~~l~~~av~S~fafLF 84 (315)
--|+..+-+|...++++.++|+|.+++
T Consensus 27 Ps~~e~~~~t~~Vi~~~~~~~~~i~~v 53 (64)
T PRK07597 27 PTRKELVRSTIVVLVFVAFFALFFYLV 53 (64)
T ss_pred cCHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 346678889999999999998887665
No 34
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain []. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins []. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.; GO: 0016192 vesicle-mediated transport, 0016021 integral to membrane; PDB: 3EGX_C 2NUP_C 3EGD_C 2NUT_C 1IOU_A 1H8M_A 3B5N_A 3ZYM_A 2NPS_A 1SFC_E ....
Probab=24.12 E-value=1e+02 Score=23.85 Aligned_cols=31 Identities=13% Similarity=0.314 Sum_probs=17.5
Q ss_pred hhHHHHHH-HHHHHHHHHHHHHHHHHhhhccc
Q psy5445 57 RTCKQKIW-FYTTSFFAMTAVSTGSSLLFLVP 87 (315)
Q Consensus 57 ~t~rek~~-FYtT~~l~~~av~S~fafLFLVP 87 (315)
+.++.|.+ -+.-..+++.+++.+++++..+|
T Consensus 55 ~~l~r~~~~~~~k~~~i~~~iv~~~~~~i~~~ 86 (89)
T PF00957_consen 55 KKLKRKMWWRNYKLYIIIIIIVIIIILIIIIV 86 (89)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHhHHhhhhhhhhHHHHH
Confidence 45666655 45555566666665555555444
No 35
>PF03904 DUF334: Domain of unknown function (DUF334); InterPro: IPR005602 This is a family of proteins found in Staphylococcus aureus plasmid with no characterised function.
Probab=23.77 E-value=2.5e+02 Score=27.16 Aligned_cols=24 Identities=17% Similarity=-0.111 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhc
Q psy5445 62 KIWFYTTSFFAMTAVSTGSSLLFL 85 (315)
Q Consensus 62 k~~FYtT~~l~~~av~S~fafLFL 85 (315)
..+-.++.+-++++||++|+++++
T Consensus 146 ~~k~~~~gi~aml~Vf~LF~lvmt 169 (230)
T PF03904_consen 146 RQKSMYKGIGAMLFVFMLFALVMT 169 (230)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHH
Confidence 334445567788888888888874
No 36
>COG3736 VirB8 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]
Probab=23.54 E-value=98 Score=29.68 Aligned_cols=27 Identities=22% Similarity=0.459 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccce
Q psy5445 62 KIWFYTTSFFAMTAVSTGSSLLFLVPL 88 (315)
Q Consensus 62 k~~FYtT~~l~~~av~S~fafLFLVPf 88 (315)
|..|.+..++.++++++++++.+|+|+
T Consensus 41 ~~~~~va~~~~~l~v~~~~~Ia~llPL 67 (239)
T COG3736 41 RLAWRVAILFTLLAVAAVIAIAILLPL 67 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 788899999999999999999999886
No 37
>COG5393 Predicted membrane protein [Function unknown]
Probab=22.39 E-value=1.6e+02 Score=26.30 Aligned_cols=43 Identities=26% Similarity=0.229 Sum_probs=22.5
Q ss_pred HHHHHhhcCcccchhHHHHHHH-HHHHHHHHHHHHHHHHhhhccceeechhhh
Q psy5445 44 LELAQNKNKKKVKRTCKQKIWF-YTTSFFAMTAVSTGSSLLFLVPLYVDPAIS 95 (315)
Q Consensus 44 ~ela~~k~~~~~~~t~rek~~F-YtT~~l~~~av~S~fafLFLVPfvVdPAis 95 (315)
.||+.+|. .+.+-++| =.|..|+.+|+.|+.+ ||-.++||+-.
T Consensus 38 vELeEeKa------nll~lllm~gLtl~fa~~~lmsL~v---Lvi~~f~~tyR 81 (131)
T COG5393 38 VELEEEKA------NLLQLLLMAGLTLLFAAFGLMSLMV---LVIWAFDPTYR 81 (131)
T ss_pred hhHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHcCcHHH
Confidence 46666665 33332222 2344555555555444 44477888754
No 38
>COG4038 Predicted membrane protein [Function unknown]
Probab=22.31 E-value=51 Score=27.25 Aligned_cols=33 Identities=21% Similarity=0.394 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccceeechhhhhhh
Q psy5445 62 KIWFYTTSFFAMTAVSTGSSLLFLVPLYVDPAISTLT 98 (315)
Q Consensus 62 k~~FYtT~~l~~~av~S~fafLFLVPfvVdPAisTi~ 98 (315)
.+|||+.++++++|.++-.+ -|-+-||-+..+-
T Consensus 5 ~~~~y~ga~~ii~gs~~~~~----gp~~~dpiv~~LN 37 (87)
T COG4038 5 EAILYTGAFMIILGTLGAAI----GPARSDPVVKSLN 37 (87)
T ss_pred hhhhhhccHHHHHhHHHhhc----CCcccCcHHHHhc
Confidence 58999999999999887653 4778888777664
No 39
>TIGR01195 oadG_fam sodium pump decarboxylases, gamma subunit. Most sequences scoring between the noise and trusted cutoffs are eukaryotic sodium channel proteins.
Probab=22.18 E-value=1e+02 Score=24.64 Aligned_cols=41 Identities=12% Similarity=0.139 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccceeechhhhhhhcCC-CCCC
Q psy5445 64 WFYTTSFFAMTAVSTGSSLLFLVPLYVDPAISTLTSDF-NPNP 105 (315)
Q Consensus 64 ~FYtT~~l~~~av~S~fafLFLVPfvVdPAisTi~adF-dp~P 105 (315)
+|...+-+.++|+.-+|.||.+.-++++. ++.++..| .|+|
T Consensus 3 ll~~~~~l~v~GM~~VF~fL~lLi~~i~~-~~~~~~~~~~~e~ 44 (82)
T TIGR01195 3 LLLEGATLTVLGMGIVFLFLSLLIYAVRG-MGKVVGRKKVPEP 44 (82)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhccCCCCc
Confidence 56667778888888888888888788775 56666677 4444
No 40
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=22.11 E-value=90 Score=22.96 Aligned_cols=18 Identities=28% Similarity=0.267 Sum_probs=7.9
Q ss_pred hcCCCcccccchHHHHHH
Q psy5445 23 MRGSSSELLLDPQQQLRK 40 (315)
Q Consensus 23 mr~~sselll~~~~~~r~ 40 (315)
+..+++.=|-+.|-+.|+
T Consensus 13 l~t~~~~GLs~~ev~~r~ 30 (69)
T PF00690_consen 13 LNTSSSQGLSSEEVEERR 30 (69)
T ss_dssp HTTBTSSBBTHHHHHHHH
T ss_pred HCcCCCCCCCHHHHHHHH
Confidence 333444445444544444
No 41
>PF14143 YrhC: YrhC-like protein
Probab=21.77 E-value=1.7e+02 Score=23.50 Aligned_cols=42 Identities=26% Similarity=0.136 Sum_probs=34.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhhccc-eeechhhhhhhc
Q psy5445 58 TCKQKIWFYTTSFFAMTAVSTGSSLLFLVP-LYVDPAISTLTS 99 (315)
Q Consensus 58 t~rek~~FYtT~~l~~~av~S~fafLFLVP-fvVdPAisTi~a 99 (315)
.+++|+-=|....++++|+.+-+-++.++| --.+++-..+.+
T Consensus 2 ~l~~Ki~DyKrf~~vLLAvs~FlYiG~viP~~~~~~~~~~~m~ 44 (72)
T PF14143_consen 2 ELKEKIEDYKRFAFVLLAVSTFLYIGTVIPIGAKETAQKYIMM 44 (72)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHhhCCccchhHHHHHHHH
Confidence 478888889999999999999999999999 667766665543
No 42
>COG5528 Predicted integral membrane protein [Function unknown]
Probab=21.00 E-value=3.5e+02 Score=24.63 Aligned_cols=49 Identities=22% Similarity=0.252 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHhhcCcccchhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5445 36 QQLRKRKLLELAQNKNKKKVKRTCKQKIWFYTTSFFAMTAVSTGSSLLF 84 (315)
Q Consensus 36 ~~~r~rk~~ela~~k~~~~~~~t~rek~~FYtT~~l~~~av~S~fafLF 84 (315)
.|.|-|.+-|-|...-.+-++++.|+=-..+.-.|.++.++++.+-+..
T Consensus 102 ~qmr~rrlAeaA~~AGepLp~~y~rlfrvwfv~gfpafaavlAi~wLMv 150 (155)
T COG5528 102 RQMRVRRLAEAAETAGEPLPEQYLRLFRVWFVMGFPAFAAVLAIAWLMV 150 (155)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 3466666777665555667789999866666667777777777665543
No 43
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=20.66 E-value=69 Score=25.61 Aligned_cols=22 Identities=32% Similarity=0.659 Sum_probs=15.7
Q ss_pred hhhhhhhhHHHHhhhhhh-hhhc
Q psy5445 220 HYFIIPFIICVVCSIVLC-VMHC 241 (315)
Q Consensus 220 ~a~~VP~vlFvISvi~L~-i~hc 241 (315)
..+++|+++|++-|..+- +.|+
T Consensus 4 ~fl~~Pliif~ifVap~wl~lHY 26 (75)
T TIGR02976 4 FFLAIPLIIFVIFVAPLWLILHY 26 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999987765544 3475
No 44
>PF01200 Ribosomal_S28e: Ribosomal protein S28e; InterPro: IPR000289 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities. Examples are: Mammalian S28 [] Plant S28 [] Fungi S33 [] Archaebacterial S28e. These proteins have from 64 to 78 amino acids and a highly conserved C-terminal region.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_Y 2XZN_1 2XZM_1 1NY4_A 1NE3_A 3U5C_c 3U5G_c 3O30_R 3O2Z_R 3IZB_Y.
Probab=20.42 E-value=1.5e+02 Score=23.75 Aligned_cols=29 Identities=24% Similarity=0.320 Sum_probs=21.0
Q ss_pred ccCCccceEEEEEeecCCCCCCCCCCCCcCceEeeccCC
Q psy5445 132 TSDMYKCFQIFVKYVDYNVTFSEEPLYVDNAILLVNIKG 170 (315)
Q Consensus 132 Tsd~y~C~QI~VnY~~~n~~~~e~~~~~~earLliNikG 170 (315)
|.....|+|++|.+-.. ..+..+.=|+||
T Consensus 20 tGs~G~~tQVrv~~l~~----------~~gR~i~RNVkG 48 (69)
T PF01200_consen 20 TGSRGQVTQVRVEFLDG----------DKGRSIIRNVKG 48 (69)
T ss_dssp CTSSSSEEEEEEEESSS----------SSS-EEEEEECS
T ss_pred ccCcccEEEEEEEEecC----------CcceEEeecccC
Confidence 56788999999999773 123567778887
No 45
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=20.27 E-value=1.4e+02 Score=24.88 Aligned_cols=38 Identities=8% Similarity=0.172 Sum_probs=30.9
Q ss_pred ceEEeecCHHHHHHHhhhhhhhhhhHHHHhhhhhhhhh
Q psy5445 203 TIVMDKYDEEEQMYIIIHYFIIPFIICVVCSIVLCVMH 240 (315)
Q Consensus 203 ~~VVaryd~d~t~~~Ll~a~~VP~vlFvISvi~L~i~h 240 (315)
|.|....+-..-++.-++..++|++.|+++.++.-.+.
T Consensus 56 D~V~v~i~~~~~~~aa~l~Y~lPll~li~g~~l~~~~~ 93 (135)
T PF04246_consen 56 DRVEVEIPESSLLKAAFLVYLLPLLALIAGAVLGSYLG 93 (135)
T ss_pred CEEEEEeccchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67888888877888888999999999998877665543
Done!