Query psy5734
Match_columns 205
No_of_seqs 51 out of 53
Neff 3.1
Searched_HMMs 46136
Date Fri Aug 16 16:39:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5734.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5734hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03185 CaKB: Calcium-activat 98.4 8E-08 1.7E-12 82.5 0.0 120 27-201 24-157 (201)
2 PF10399 UCR_Fe-S_N: Ubiquitin 50.1 30 0.00066 23.3 3.6 29 1-29 1-29 (41)
3 PRK13872 conjugal transfer pro 50.0 23 0.00051 30.3 3.9 28 12-39 38-65 (228)
4 PRK13887 conjugal transfer pro 48.3 25 0.00055 30.7 3.9 28 12-39 52-79 (250)
5 PF11952 DUF3469: Protein of u 45.2 6.3 0.00014 30.1 -0.3 16 157-172 40-57 (87)
6 PF10642 Tom5: Mitochondrial i 45.1 14 0.0003 26.0 1.5 16 27-42 28-43 (49)
7 COG2864 FdnI Cytochrome b subu 41.6 38 0.00081 30.3 3.9 34 3-36 5-38 (218)
8 PRK13865 type IV secretion sys 41.6 34 0.00075 30.1 3.7 29 12-40 37-65 (229)
9 PF04060 FeS: Putative Fe-S cl 40.5 19 0.00042 23.1 1.5 17 162-181 6-22 (35)
10 PF06783 UPF0239: Uncharacteri 40.5 32 0.0007 26.8 3.0 27 3-29 10-39 (85)
11 TIGR00964 secE_bact preprotein 39.0 54 0.0012 22.5 3.6 24 11-34 20-43 (55)
12 PF07234 DUF1426: Protein of u 38.1 39 0.00084 27.6 3.2 41 8-48 9-49 (117)
13 PF03904 DUF334: Domain of unk 37.4 37 0.0008 30.7 3.3 26 12-37 145-170 (230)
14 COG3736 VirB8 Type IV secretor 36.7 45 0.00097 30.1 3.7 29 12-40 40-68 (239)
15 PRK08455 fliL flagellar basal 34.2 21 0.00046 30.3 1.2 36 1-36 1-42 (182)
16 PF00287 Na_K-ATPase: Sodium / 32.0 37 0.0008 30.8 2.4 28 9-36 36-63 (289)
17 PRK07597 secE preprotein trans 31.4 84 0.0018 22.1 3.7 24 11-34 29-52 (64)
18 COG2864 FdnI Cytochrome b subu 30.1 64 0.0014 28.9 3.5 34 10-43 112-147 (218)
19 COG4038 Predicted membrane pro 26.4 47 0.001 25.9 1.8 34 13-50 5-38 (87)
20 PF14990 DUF4516: Domain of un 24.6 1.3E+02 0.0029 21.1 3.6 27 9-35 6-32 (47)
21 PRK13468 F0F1 ATP synthase sub 24.5 1.2E+02 0.0025 23.2 3.6 36 4-39 42-80 (82)
22 COG0690 SecE Preprotein transl 23.5 1.4E+02 0.003 21.9 3.8 24 11-34 39-62 (73)
23 PF07332 DUF1469: Protein of u 23.4 76 0.0016 24.0 2.5 32 7-38 24-57 (121)
24 PRK08764 ferredoxin; Provision 21.1 62 0.0013 25.7 1.6 17 162-181 19-35 (135)
25 KOG3970|consensus 21.0 1.1E+02 0.0024 28.4 3.4 26 7-37 246-271 (299)
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=98.35 E-value=8e-08 Score=82.54 Aligned_cols=120 Identities=27% Similarity=0.560 Sum_probs=0.0
Q ss_pred HHHHHHhhhhhceeecchhhhhhcccccccceeEEEeeeeccCCCCCcccccccccc-ccccCeeEEEEEeEeccCcccc
Q psy5734 27 IFSLFGFLFLVPFVIEPACTTIMREFDEVPATCETIQVENLRGASNCSWTSCREGCT-REIYECTQITVSYKVSVNTSVQ 105 (205)
Q Consensus 27 v~S~~AfLfLvp~vvdPA~~ti~~~f~~~Pv~C~Tt~~~~~~G~~NCsWsSCrEgCt-k~~~~C~QI~Vnyr~~~~~n~~ 105 (205)
++|+.+++.|--.++-|++...+ .++..|++.+.....-.-+|+- ||+--|- ...|.|-||+|||.....
T Consensus 24 ~~svlm~~vlGitiv~P~l~s~~----~~et~Ctvl~s~i~~~~v~Cs~-~cg~~c~~~s~yPCLqV~Vn~t~sg~---- 94 (201)
T PF03185_consen 24 ICSVLMLFVLGITIVKPYLKSLW----FEETNCTVLSSHIVGEWVDCSF-SCGSDCRGVSKYPCLQVFVNYTHSGQ---- 94 (201)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHhccchhhhhcc----cccceEEEEEEEeecccccccc-cCCCCCCCcCCCCceEEEEEecCCCc----
Confidence 45666777777788899987766 4789999998876332233331 3444443 467899999999965320
Q ss_pred chhhHHhHhhHHhhhhhccCCCCccCCcccCCCCCCCCCCCCCCCcccccccEEeecccCCCCCCccch-----------
Q psy5734 106 STITAQSLRLYNRFRRAVLGEDDVLLPSFEDNFLETPAIPEGNSSEWDFVGAKFFPNVKGCGYPPYLNC----------- 174 (205)
Q Consensus 106 ~~~~~~~~r~~~~~~r~~~d~~~~~~~~~~~~~~~~~~~l~~~~s~w~~~~a~L~vNvkGCGYPP~vnC----------- 174 (205)
+++. -.+ |..+..|-| |-|-| .|
T Consensus 95 ---------------~a~L------~~~----------------------E~~l~~n~k-CsY~P--~C~~d~~~~~~~V 128 (201)
T PF03185_consen 95 ---------------TALL------HHD----------------------EETLDSNPK-CSYIP--KCHRDRQDNRAEV 128 (201)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ---------------eEEE------EEc----------------------hHhhccCCc-ceecC--cccccHHHHHHHH
Confidence 1111 111 222233444 88866 23
Q ss_pred hHHHHhhccC-CCcceeeeecCC-CceEe
Q psy5734 175 SIFHKKYAVV-GKQYPCYYSTVE-PALVI 201 (205)
Q Consensus 175 s~F~k~Y~~~-G~~FpCyYSr~~-p~~Vi 201 (205)
.+|-+.|+.. |..|||||+-.+ |+-||
T Consensus 129 ~~~~~~~~~~~gq~f~Cfy~P~~~~~~Vi 157 (201)
T PF03185_consen 129 EDFQENFGQQNGQTFPCFYDPDNQPEDVI 157 (201)
T ss_dssp -----------------------------
T ss_pred HHHHHHhhhccCcceeeeecCCCCcceEE
Confidence 3677888888 999999999997 45555
No 2
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=50.07 E-value=30 Score=23.31 Aligned_cols=29 Identities=14% Similarity=0.153 Sum_probs=16.0
Q ss_pred CccccchhhHHHHHHHHHHHHHHHHHHHH
Q psy5734 1 MAEEAGKESSREKLLFYTTAFFILLAIFS 29 (205)
Q Consensus 1 m~~e~~~~t~rek~~FYtTa~~~l~av~S 29 (205)
|.++...+.-|.++|.++|+..+.+++.+
T Consensus 1 ms~~~~~~~~RRdFL~~at~~~gavG~~~ 29 (41)
T PF10399_consen 1 MSSNEPVDPTRRDFLTIATSAVGAVGAAA 29 (41)
T ss_dssp ---------HHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCCchHHHHHHHHHHHHHHHHHHH
Confidence 67777788889999999998877666553
No 3
>PRK13872 conjugal transfer protein TrbF; Provisional
Probab=50.04 E-value=23 Score=30.30 Aligned_cols=28 Identities=7% Similarity=-0.138 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhce
Q psy5734 12 EKLLFYTTAFFILLAIFSLFGFLFLVPF 39 (205)
Q Consensus 12 ek~~FYtTa~~~l~av~S~~AfLfLvp~ 39 (205)
+|++......+.++++++++|+++|.|+
T Consensus 38 ~~~w~~va~~~l~i~~~~v~av~~l~pl 65 (228)
T PRK13872 38 ARNWRLMAFGCLALSAGLAGGLVWQSAR 65 (228)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 3455556666777788888999999884
No 4
>PRK13887 conjugal transfer protein TrbF; Provisional
Probab=48.31 E-value=25 Score=30.71 Aligned_cols=28 Identities=11% Similarity=0.126 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhce
Q psy5734 12 EKLLFYTTAFFILLAIFSLFGFLFLVPF 39 (205)
Q Consensus 12 ek~~FYtTa~~~l~av~S~~AfLfLvp~ 39 (205)
.|.+........+++++|++|+++|.|+
T Consensus 52 ~~~w~v~a~~~~~ia~~~v~av~~l~pl 79 (250)
T PRK13887 52 RQTWQVVGILSLLIALAAVGGVIHIGSQ 79 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 3444444555577788899999999886
No 5
>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=45.22 E-value=6.3 Score=30.11 Aligned_cols=16 Identities=38% Similarity=1.090 Sum_probs=12.1
Q ss_pred cEEeeccc--CCCCCCcc
Q psy5734 157 AKFFPNVK--GCGYPPYL 172 (205)
Q Consensus 157 a~L~vNvk--GCGYPP~v 172 (205)
+.+++|++ ||+|||-|
T Consensus 40 s~v~~N~~fLGC~Yp~~~ 57 (87)
T PF11952_consen 40 SQVWANMEFLGCRYPPEV 57 (87)
T ss_pred HHHHHhHHHHhcCCCHHH
Confidence 45677876 99999854
No 6
>PF10642 Tom5: Mitochondrial import receptor subunit or translocase; InterPro: IPR019603 This entry represents a short family of yeast proteins. Tom5 is one of three very small translocases of the mitochondrial outer membrane. Tom5 links mitochondrial preprotein receptors to the general import pore []. Although Tom5 has allegedly been identified in vertebrates this could not be confirmed.
Probab=45.06 E-value=14 Score=25.98 Aligned_cols=16 Identities=31% Similarity=0.636 Sum_probs=12.4
Q ss_pred HHHHHHhhhhhceeec
Q psy5734 27 IFSLFGFLFLVPFVIE 42 (205)
Q Consensus 27 v~S~~AfLfLvp~vvd 42 (205)
.....++|||.||++|
T Consensus 28 a~~~a~~LylsP~~~~ 43 (49)
T PF10642_consen 28 AAAAAALLYLSPFAID 43 (49)
T ss_pred HHHHHHHHHHhHHHHH
Confidence 3445688999999886
No 7
>COG2864 FdnI Cytochrome b subunit of formate dehydrogenase [Energy production and conversion]
Probab=41.62 E-value=38 Score=30.30 Aligned_cols=34 Identities=15% Similarity=0.326 Sum_probs=31.1
Q ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy5734 3 EEAGKESSREKLLFYTTAFFILLAIFSLFGFLFL 36 (205)
Q Consensus 3 ~e~~~~t~rek~~FYtTa~~~l~av~S~~AfLfL 36 (205)
..+|+=|..||..-.++|++.++..+|++++.|.
T Consensus 5 ~~IeR~t~~eR~~Hw~~ai~f~il~lSG~~~~~~ 38 (218)
T COG2864 5 KKIERYTALERINHWIVAICFFILALSGLAFFFP 38 (218)
T ss_pred cEEeecchHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3467889999999999999999999999999987
No 8
>PRK13865 type IV secretion system protein VirB8; Provisional
Probab=41.56 E-value=34 Score=30.06 Aligned_cols=29 Identities=14% Similarity=0.231 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhcee
Q psy5734 12 EKLLFYTTAFFILLAIFSLFGFLFLVPFV 40 (205)
Q Consensus 12 ek~~FYtTa~~~l~av~S~~AfLfLvp~v 40 (205)
+|..+-...+..+++++|++|+..|+|+-
T Consensus 37 ~k~aw~va~~~~~~~~~~~~Av~~l~PLK 65 (229)
T PRK13865 37 SRVLAAVAGIAVAGNVAQAFAIATMVPLE 65 (229)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcccC
Confidence 34444455667888889999999999873
No 9
>PF04060 FeS: Putative Fe-S cluster; InterPro: IPR007202 These proteins contain a domain with four conserved cysteines that probably form an Fe-S redox cluster.; GO: 0051536 iron-sulfur cluster binding; PDB: 2YCL_A 4DJF_E 4DJD_C 4DJE_C.
Probab=40.53 E-value=19 Score=23.09 Aligned_cols=17 Identities=41% Similarity=1.058 Sum_probs=12.9
Q ss_pred cccCCCCCCccchhHHHHhh
Q psy5734 162 NVKGCGYPPYLNCSIFHKKY 181 (205)
Q Consensus 162 NvkGCGYPP~vnCs~F~k~Y 181 (205)
|=..|||| +|..|+++-
T Consensus 6 nCg~CG~~---~C~~fA~ai 22 (35)
T PF04060_consen 6 NCGACGYP---TCRAFAEAI 22 (35)
T ss_dssp ---TTSSS---SHHHHHHHH
T ss_pred cCCCCCCc---cHHHHHHHH
Confidence 66789999 999999875
No 10
>PF06783 UPF0239: Uncharacterised protein family (UPF0239); InterPro: IPR009621 This is a group of transmembrane proteins of unknown function.; GO: 0016021 integral to membrane
Probab=40.47 E-value=32 Score=26.84 Aligned_cols=27 Identities=37% Similarity=0.479 Sum_probs=20.6
Q ss_pred cccchhhHHHHHHHHH---HHHHHHHHHHH
Q psy5734 3 EEAGKESSREKLLFYT---TAFFILLAIFS 29 (205)
Q Consensus 3 ~e~~~~t~rek~~FYt---Ta~~~l~av~S 29 (205)
+|+-..||.|.++-|. .|+|||+-|++
T Consensus 10 ~ei~Eet~~e~llRYGLf~GAIFQliCilA 39 (85)
T PF06783_consen 10 PEIPEETFFENLLRYGLFVGAIFQLICILA 39 (85)
T ss_pred ccCCcchHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3555789999999886 47788877773
No 11
>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=38.98 E-value=54 Score=22.54 Aligned_cols=24 Identities=38% Similarity=0.668 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Q psy5734 11 REKLLFYTTAFFILLAIFSLFGFL 34 (205)
Q Consensus 11 rek~~FYtTa~~~l~av~S~~AfL 34 (205)
|+.+..+|.+++.+++++|++.++
T Consensus 20 ~~e~~~~t~~Vi~~~~~~~~~~~~ 43 (55)
T TIGR00964 20 RKELITYTIVVIVFVIFFSLFLFG 43 (55)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHH
Confidence 678888999999999998876654
No 12
>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=38.13 E-value=39 Score=27.60 Aligned_cols=41 Identities=24% Similarity=0.420 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeecchhhhh
Q psy5734 8 ESSREKLLFYTTAFFILLAIFSLFGFLFLVPFVIEPACTTI 48 (205)
Q Consensus 8 ~t~rek~~FYtTa~~~l~av~S~~AfLfLvp~vvdPA~~ti 48 (205)
.-+.|=++|+...|.+++.+--+.|+||=+|-+|---.+-+
T Consensus 9 KlfFEwFLF~~AIFiAItIlYILLalL~EvPkYIK~~VrYl 49 (117)
T PF07234_consen 9 KLFFEWFLFFGAIFIAITILYILLALLFEVPKYIKELVRYL 49 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 34678889999999999999999999999998876655544
No 13
>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=37.42 E-value=37 Score=30.71 Aligned_cols=26 Identities=15% Similarity=0.294 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy5734 12 EKLLFYTTAFFILLAIFSLFGFLFLV 37 (205)
Q Consensus 12 ek~~FYtTa~~~l~av~S~~AfLfLv 37 (205)
.+.+--++.+-+|++||++||+++++
T Consensus 145 k~~k~~~~gi~aml~Vf~LF~lvmt~ 170 (230)
T PF03904_consen 145 KRQKSMYKGIGAMLFVFMLFALVMTI 170 (230)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHh
Confidence 34444556788899999999998855
No 14
>COG3736 VirB8 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]
Probab=36.71 E-value=45 Score=30.10 Aligned_cols=29 Identities=24% Similarity=0.529 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhcee
Q psy5734 12 EKLLFYTTAFFILLAIFSLFGFLFLVPFV 40 (205)
Q Consensus 12 ek~~FYtTa~~~l~av~S~~AfLfLvp~v 40 (205)
.|+.|....++.++++++++++..|+|+-
T Consensus 40 r~~~~~va~~~~~l~v~~~~~Ia~llPLK 68 (239)
T COG3736 40 RRLAWRVAILFTLLAVAAVIAIAILLPLK 68 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 38888888999999999999999999973
No 15
>PRK08455 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=34.24 E-value=21 Score=30.27 Aligned_cols=36 Identities=31% Similarity=0.504 Sum_probs=21.0
Q ss_pred CccccchhhH-----HHHHHHHHH-HHHHHHHHHHHHHhhhh
Q psy5734 1 MAEEAGKESS-----REKLLFYTT-AFFILLAIFSLFGFLFL 36 (205)
Q Consensus 1 m~~e~~~~t~-----rek~~FYtT-a~~~l~av~S~~AfLfL 36 (205)
||||.+...- .-|++|-.- +++.++++.+++|++|+
T Consensus 1 MAee~~~~~~~~~k~~~~l~~iIi~~~llll~~~G~~~~~~~ 42 (182)
T PRK08455 1 MAEEQENEAQQKKKKSKALLIIIIGVVVLLLLIVGVIAMLLM 42 (182)
T ss_pred CCcchhhhhcccCCCCceeEEehHHHHHHHHHHHHHHHHHHh
Confidence 8988654321 013344333 56667777777777665
No 16
>PF00287 Na_K-ATPase: Sodium / potassium ATPase beta chain; InterPro: IPR000402 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 beta subunit found in the P-type cation exchange ATPases located in the plasma membranes of animal cells. These P-ATPases include both H+/K+-ATPases (3.6.3.10 from EC) and Na+/K+-ATPases (3.6.3.9 from EC), which belong to the IIC subfamily of ATPases [, ]. These ATPases catalyse the hydrolysis of ATP coupled with the exchange of cations, pumping one cation out of the cell (H+ or Na+) in exchange for K+. These ATPases contain an alpha subunit (IPR005775 from INTERPRO) that is the catalytic component, and a glycosylated beta subunit that regulates the number of sodium pumps transported to the plasma membrane through the assembly of alpha/beta heterodimers. The beta subunit has three highly conserved disulphide bonds within the extracellular domain that stabilise the alpha subunit, the alpha/beta interaction, and the catalytic activity of the alpha subunit []. Different beta isoforms exist, permitting greater regulatory control. An example of a H+/K+-ATPase is the gastric pump responsible for acid secretion in the stomach, transporting protons from the cytoplasm of parietal cells to create a large pH gradient in exchange for the internalisation of potassium ions, using ATP hydrolysis to drive the pump []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0005391 sodium:potassium-exchanging ATPase activity, 0006754 ATP biosynthetic process, 0006813 potassium ion transport, 0006814 sodium ion transport, 0016020 membrane; PDB: 2XZB_B 3A3Y_B 3N2F_D 3B8E_D 3KDP_D 3N23_D.
Probab=32.04 E-value=37 Score=30.83 Aligned_cols=28 Identities=36% Similarity=0.600 Sum_probs=18.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy5734 9 SSREKLLFYTTAFFILLAIFSLFGFLFL 36 (205)
Q Consensus 9 t~rek~~FYtTa~~~l~av~S~~AfLfL 36 (205)
+|-.=++||.-.-..|+|+|++...+||
T Consensus 36 sW~~I~lFYlifY~~La~lfa~~m~v~l 63 (289)
T PF00287_consen 36 SWGKILLFYLIFYAFLAALFAICMWVFL 63 (289)
T ss_dssp THHHHHHHHHTTHHHHHHHHHHHHHHHH
T ss_pred ccchhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 3444578888777777777766666665
No 17
>PRK07597 secE preprotein translocase subunit SecE; Reviewed
Probab=31.38 E-value=84 Score=22.05 Aligned_cols=24 Identities=33% Similarity=0.628 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Q psy5734 11 REKLLFYTTAFFILLAIFSLFGFL 34 (205)
Q Consensus 11 rek~~FYtTa~~~l~av~S~~AfL 34 (205)
|+.+.-+|..++.++.++|++.++
T Consensus 29 ~~e~~~~t~~Vi~~~~~~~~~i~~ 52 (64)
T PRK07597 29 RKELVRSTIVVLVFVAFFALFFYL 52 (64)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHH
Confidence 667888999999999888877654
No 18
>COG2864 FdnI Cytochrome b subunit of formate dehydrogenase [Energy production and conversion]
Probab=30.05 E-value=64 Score=28.89 Aligned_cols=34 Identities=26% Similarity=0.541 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh--hhhhceeecc
Q psy5734 10 SREKLLFYTTAFFILLAIFSLFGF--LFLVPFVIEP 43 (205)
Q Consensus 10 ~rek~~FYtTa~~~l~av~S~~Af--LfLvp~vvdP 43 (205)
.=||++|++-....++...|+.++ .|..|..-.|
T Consensus 112 ~GqKl~fw~~~l~~~~l~iTGivmw~~y~~~~~~i~ 147 (218)
T COG2864 112 AGQKLLFWTAILAIVLLLITGIVIWRPYFAPYFSIP 147 (218)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHhhhccccccHH
Confidence 349999999999998888888888 5555544333
No 19
>COG4038 Predicted membrane protein [Function unknown]
Probab=26.38 E-value=47 Score=25.91 Aligned_cols=34 Identities=24% Similarity=0.381 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhceeecchhhhhhc
Q psy5734 13 KLLFYTTAFFILLAIFSLFGFLFLVPFVIEPACTTIMR 50 (205)
Q Consensus 13 k~~FYtTa~~~l~av~S~~AfLfLvp~vvdPA~~ti~~ 50 (205)
.++||+.|++..++.++.++ -|.+-||-.+.+--
T Consensus 5 ~~~~y~ga~~ii~gs~~~~~----gp~~~dpiv~~LN~ 38 (87)
T COG4038 5 EAILYTGAFMIILGTLGAAI----GPARSDPVVKSLNL 38 (87)
T ss_pred hhhhhhccHHHHHhHHHhhc----CCcccCcHHHHhcc
Confidence 57999999999999887764 58888887776543
No 20
>PF14990 DUF4516: Domain of unknown function (DUF4516)
Probab=24.61 E-value=1.3e+02 Score=21.10 Aligned_cols=27 Identities=19% Similarity=0.113 Sum_probs=22.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy5734 9 SSREKLLFYTTAFFILLAIFSLFGFLF 35 (205)
Q Consensus 9 t~rek~~FYtTa~~~l~av~S~~AfLf 35 (205)
++++=++|.+++++.|+|-.+++=..|
T Consensus 6 ~~~~yl~~~~~s~~sM~aGA~vVH~~y 32 (47)
T PF14990_consen 6 SWPSYLKSLVASLLSMLAGASVVHNIY 32 (47)
T ss_pred cHHHHHHHHHHHHHHHHhhhHHHHHHh
Confidence 578889999999999999888876554
No 21
>PRK13468 F0F1 ATP synthase subunit C; Provisional
Probab=24.46 E-value=1.2e+02 Score=23.17 Aligned_cols=36 Identities=25% Similarity=0.444 Sum_probs=22.3
Q ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHHH---hhhhhce
Q psy5734 4 EAGKESSREKLLFYTTAFFILLAIFSLFG---FLFLVPF 39 (205)
Q Consensus 4 e~~~~t~rek~~FYtTa~~~l~av~S~~A---fLfLvp~ 39 (205)
..|...-.++..|...++.=.+++++++. ++|.-||
T Consensus 42 qPe~~g~l~~~m~ig~al~E~~ai~alviallllfa~p~ 80 (82)
T PRK13468 42 QPDAAGTISRTLFVGLAMIESMAIYCFVVAMILLFANPF 80 (82)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 34444455566777777777777777653 4555555
No 22
>COG0690 SecE Preprotein translocase subunit SecE [Intracellular trafficking and secretion]
Probab=23.51 E-value=1.4e+02 Score=21.94 Aligned_cols=24 Identities=33% Similarity=0.527 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Q psy5734 11 REKLLFYTTAFFILLAIFSLFGFL 34 (205)
Q Consensus 11 rek~~FYtTa~~~l~av~S~~AfL 34 (205)
|+.+.-||-+++.+++++|++.++
T Consensus 39 rke~~~~t~~Vl~~v~~~s~~~~~ 62 (73)
T COG0690 39 RKELIRSTLIVLVVVAFFSLFLYG 62 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 777888998999999888876554
No 23
>PF07332 DUF1469: Protein of unknown function (DUF1469); InterPro: IPR009937 This entry represents proteins found in hypothetical bacterial proteins where is is annotated as ycf49 or ycf49-like. The function is not known.
Probab=23.40 E-value=76 Score=24.03 Aligned_cols=32 Identities=34% Similarity=0.514 Sum_probs=17.4
Q ss_pred hhhHHHHHHHHHH--HHHHHHHHHHHHHhhhhhc
Q psy5734 7 KESSREKLLFYTT--AFFILLAIFSLFGFLFLVP 38 (205)
Q Consensus 7 ~~t~rek~~FYtT--a~~~l~av~S~~AfLfLvp 38 (205)
+.+++||..-..+ +.+.+.+++.+++++||..
T Consensus 24 ~~E~~~~~~~~~~~~~~~~~a~vl~~~~l~~l~~ 57 (121)
T PF07332_consen 24 KAELREKARRLGRGLALLVLAAVLALLALLFLLV 57 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5566666665554 3444555555555555443
No 24
>PRK08764 ferredoxin; Provisional
Probab=21.07 E-value=62 Score=25.70 Aligned_cols=17 Identities=18% Similarity=0.694 Sum_probs=14.3
Q ss_pred cccCCCCCCccchhHHHHhh
Q psy5734 162 NVKGCGYPPYLNCSIFHKKY 181 (205)
Q Consensus 162 NvkGCGYPP~vnCs~F~k~Y 181 (205)
|=.+|||| .|..|+.+-
T Consensus 19 ncg~cg~~---~c~~~a~~~ 35 (135)
T PRK08764 19 QCGQCGFD---GCRPYAQAM 35 (135)
T ss_pred CCccCCCc---CHHHHHHHH
Confidence 78899999 888888765
No 25
>KOG3970|consensus
Probab=20.99 E-value=1.1e+02 Score=28.40 Aligned_cols=26 Identities=19% Similarity=0.646 Sum_probs=18.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy5734 7 KESSREKLLFYTTAFFILLAIFSLFGFLFLV 37 (205)
Q Consensus 7 ~~t~rek~~FYtTa~~~l~av~S~~AfLfLv 37 (205)
+++..++++ |++++|++++++|++|.
T Consensus 246 P~~~~~ra~-----fli~lgvLafi~~i~lM 271 (299)
T KOG3970|consen 246 PQEAKKRAL-----FLIFLGVLAFITIIMLM 271 (299)
T ss_pred CHHHHHHHH-----HHHHHHHHHHHHHHHHH
Confidence 445556555 56778888888888774
Done!