Query psy6103
Match_columns 125
No_of_seqs 102 out of 150
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 17:40:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6103.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6103hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1420|consensus 100.0 1E-34 2.3E-39 249.9 1.4 112 14-125 422-533 (1103)
2 KOG3193|consensus 99.9 6.6E-25 1.4E-29 189.0 4.0 99 15-121 355-453 (1087)
3 PF03493 BK_channel_a: Calcium 99.6 2.3E-16 5E-21 109.6 3.9 44 80-123 3-46 (101)
4 PRK10537 voltage-gated potassi 98.6 1.5E-07 3.2E-12 79.0 9.0 98 9-120 282-384 (393)
5 PF02254 TrkA_N: TrkA-N domain 98.1 6.6E-06 1.4E-10 56.3 5.0 62 17-92 54-115 (116)
6 PF06241 DUF1012: Protein of u 97.4 0.0014 2.9E-08 50.6 8.7 88 26-121 1-90 (206)
7 PRK10669 putative cation:proto 97.3 0.00068 1.5E-08 58.7 6.4 84 17-114 473-556 (558)
8 PRK09496 trkA potassium transp 97.2 0.0016 3.6E-08 54.0 7.6 83 17-114 289-371 (453)
9 PRK03659 glutathione-regulated 96.5 0.0079 1.7E-07 52.9 6.8 72 17-102 456-527 (601)
10 PRK09496 trkA potassium transp 96.3 0.018 3.9E-07 47.8 7.6 86 17-113 57-144 (453)
11 PRK03562 glutathione-regulated 96.0 0.024 5.1E-07 50.2 7.0 75 18-106 457-531 (621)
12 COG0569 TrkA K+ transport syst 95.7 0.04 8.6E-07 42.8 6.4 85 17-115 58-142 (225)
13 COG1226 Kch Kef-type K+ transp 91.1 1.4 3E-05 31.2 7.0 80 17-110 77-157 (212)
14 KOG3193|consensus 71.4 0.66 1.4E-05 41.7 -1.8 101 16-118 775-902 (1087)
15 KOG1420|consensus 49.4 13 0.00029 33.9 2.3 109 11-121 795-955 (1103)
16 COG4333 Uncharacterized protei 37.4 81 0.0018 23.7 4.6 86 3-93 11-117 (167)
17 PF00919 UPF0004: Uncharacteri 33.6 1E+02 0.0022 20.9 4.3 45 24-70 35-79 (98)
18 PRK14337 (dimethylallyl)adenos 30.6 84 0.0018 26.7 4.2 43 23-65 37-79 (446)
19 PRK14325 (dimethylallyl)adenos 29.2 90 0.0019 26.4 4.2 42 23-65 38-80 (444)
20 TIGR00160 MGSA methylglyoxal s 26.9 71 0.0015 23.6 2.8 37 20-56 68-104 (143)
21 smart00174 RHO Rho (Ras homolo 23.3 1.7E+02 0.0036 20.3 4.1 53 18-72 62-114 (174)
22 PRK14333 (dimethylallyl)adenos 21.7 1.4E+02 0.0031 25.3 4.0 42 23-65 41-83 (448)
23 cd05294 LDH-like_MDH_nadp A la 21.7 2.2E+02 0.0047 23.0 4.9 48 22-70 69-123 (309)
24 PF02310 B12-binding: B12 bind 21.7 1.7E+02 0.0036 19.3 3.7 45 19-68 45-89 (121)
No 1
>KOG1420|consensus
Probab=100.00 E-value=1e-34 Score=249.92 Aligned_cols=112 Identities=88% Similarity=1.356 Sum_probs=110.1
Q ss_pred CcccccccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecccchHhhhhcCCCCCCCCCCeEeEh
Q psy6103 14 GNHQNSNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQYHNKAYLLNIPSWDWKQGDDVICL 93 (125)
Q Consensus 14 ~~~DL~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~e~k~~l~~a~~w~~~~ad~vIc~ 93 (125)
++.||.|+++++|+||+||||+|+.||++||+.||||+++||+|.|++|||+|+++.+||+|+.|+|+|+|+.+|.|||.
T Consensus 422 np~dl~rvki~~adaclvlankyc~dpdaedaanimrvisiknys~dirvi~qlmqyhnkayllnipswdwk~gddvicl 501 (1103)
T KOG1420|consen 422 NPHDLARVKIESADACLVLANKYCADPDAEDAANIMRVISIKNYSPDIRVITQLMQYHNKAYLLNIPSWDWKEGDDVICL 501 (1103)
T ss_pred ChhhhhheeccccceeeeecccccCCCChhhhhhheEEEEeccCCCchhHHHHHHHhhchheeecCCCcccccCCceEEe
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcccCChHHHHHHHHhhcccCC
Q psy6103 94 AELKLGFIAQSCLAPGFSTMMANLFAMRSFKT 125 (125)
Q Consensus 94 ~elk~~lLA~sc~~PG~sTli~NL~~~~s~~~ 125 (125)
.|+|++++||||+.||+||++.|||.++|+|+
T Consensus 502 aelklgfiaqsclapgfstmmanlfamrsfkt 533 (1103)
T KOG1420|consen 502 AELKLGFIAQSCLAPGFSTMMANLFAMRSFKT 533 (1103)
T ss_pred hhhhhhhhHHHhhcccHHHHHHHHHHHHhccC
Confidence 99999999999999999999999999999985
No 2
>KOG3193|consensus
Probab=99.90 E-value=6.6e-25 Score=188.96 Aligned_cols=99 Identities=23% Similarity=0.520 Sum_probs=94.7
Q ss_pred cccccccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecccchHhhhhcCCCCCCCCCCeEeEhH
Q psy6103 15 NHQNSNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQYHNKAYLLNIPSWDWKQGDDVICLA 94 (125)
Q Consensus 15 ~~DL~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~e~k~~l~~a~~w~~~~ad~vIc~~ 94 (125)
+.||.||++.+|+|||||+-++-.+..+.|.++|||.||||+|.|+++.||||.+||.|.|+ +.|..+||.+
T Consensus 355 d~dl~ra~~~~s~acfilsar~~~~k~a~dehtilrswaikdfapnv~qyvqifr~e~k~hi--------~~ae~~iced 426 (1087)
T KOG3193|consen 355 DEDLERANVATSKACFILSARHVNRKVATDEHTILRSWAIKDFAPNVKQYVQIFRAETKMHI--------EHAEVLICED 426 (1087)
T ss_pred cchhhhhhhcccchheeeehhhhccccccchhhHHHHHhhhhcCCchHHHhhhhchhhhhhh--------hhheeEEehh
Confidence 56999999999999999999999999999999999999999999999999999999999887 5689999999
Q ss_pred HHHHHHHHhhcccCChHHHHHHHHhhc
Q psy6103 95 ELKLGFIAQSCLAPGFSTMMANLFAMR 121 (125)
Q Consensus 95 elk~~lLA~sc~~PG~sTli~NL~~~~ 121 (125)
|||++|||++|.|||+|||++-|+++.
T Consensus 427 efkyallannc~cpg~st~itll~hts 453 (1087)
T KOG3193|consen 427 EFKYALLANNCICPGISTFITLLMHTS 453 (1087)
T ss_pred hHHHHHHhcCCcCCCHHHHHHHHhhhc
Confidence 999999999999999999999999864
No 3
>PF03493 BK_channel_a: Calcium-activated BK potassium channel alpha subunit; InterPro: IPR003929 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 alpha subunit of the BK channel was initially thought to share the characteristic 6TM organisation of the voltage-gated K+ channels. However, the molecule is now thought to possess an additional TM domain, with an extracellular N terminus and intracellular C terminus. This C-terminal region contains 4 predominantly hydrophobic domains, which are also thought to lie intracellularly. The extracellular N terminus and the first TM region are required for modulation by the beta subunit. The precise location of the Ca2+-binding site that modulates channel activation remains unknown, but it is thought to lie within the C-terminal hydrophobic domains.; GO: 0015269 calcium-activated potassium channel activity, 0006813 potassium ion transport, 0016020 membrane; PDB: 3NAF_A 3MT5_A 3U6N_E.
Probab=99.63 E-value=2.3e-16 Score=109.56 Aligned_cols=44 Identities=59% Similarity=1.123 Sum_probs=35.7
Q ss_pred CCCCCCCCCeEeEhHHHHHHHHHhhcccCChHHHHHHHHhhccc
Q psy6103 80 PSWDWKQGDDVICLAELKLGFIAQSCLAPGFSTMMANLFAMRSF 123 (125)
Q Consensus 80 ~~w~~~~ad~vIc~~elk~~lLA~sc~~PG~sTli~NL~~~~s~ 123 (125)
++|.++++|+|||.+|+|++|||+||+|||++|||+||+++.+.
T Consensus 3 ~~~~~~~~d~vIc~~elK~~lLA~sc~~PG~sTLi~NL~~s~~~ 46 (101)
T PF03493_consen 3 SKWHWKFADQVICIEELKLGLLAQSCLCPGFSTLITNLFHSSSG 46 (101)
T ss_dssp TT--TTTT-EEEEHHHHHHHHHHHHHHSTTHHHHHHHTTS----
T ss_pred cccccccCceEEEHHHHHHHHHHHHcCCCcHHHHHHHHHHhcCc
Confidence 56788999999999999999999999999999999999999764
No 4
>PRK10537 voltage-gated potassium channel; Provisional
Probab=98.65 E-value=1.5e-07 Score=78.98 Aligned_cols=98 Identities=18% Similarity=0.255 Sum_probs=84.1
Q ss_pred cccccCcc----cccccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecccchHhhhhcCCCCCC
Q psy6103 9 DDMQCGNH----QNSNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQYHNKAYLLNIPSWDW 84 (125)
Q Consensus 9 ~~~~~~~~----DL~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~e~k~~l~~a~~w~~ 84 (125)
-+...|+. +|+||++++|++++++.+ +|..|++.++++|.++|+++++++...+++..++..+
T Consensus 282 ~~vI~GD~td~e~L~~AgI~~A~aVI~~t~--------dD~~Nl~ivL~ar~l~p~~kIIa~v~~~~~~~~L~~~----- 348 (393)
T PRK10537 282 ADLIPGDSSDSAVLKKAGAARARAILALRD--------NDADNAFVVLAAKEMSSDVKTVAAVNDSKNLEKIKRV----- 348 (393)
T ss_pred CcEEEeCCCCHHHHHhcCcccCCEEEEcCC--------ChHHHHHHHHHHHHhCCCCcEEEEECCHHHHHHHHhc-----
Confidence 34556654 599999999999999886 3899999999999999999999999999999888665
Q ss_pred CCCCeEeEhHHHHHHHHHhhcccCCh-HHHHHHHHhh
Q psy6103 85 KQGDDVICLAELKLGFIAQSCLAPGF-STMMANLFAM 120 (125)
Q Consensus 85 ~~ad~vIc~~elk~~lLA~sc~~PG~-sTli~NL~~~ 120 (125)
|+|.||+..++-...|++...-|-+ ...|..++-+
T Consensus 349 -GaD~VIsp~~l~g~~la~~l~g~~I~~~~i~~~~~~ 384 (393)
T PRK10537 349 -HPDMIFSPQLLGSELLARTLNGEEIDNDMITSMLFN 384 (393)
T ss_pred -CCCEEECHHHHHHHHHHHHhcCCCCCHHHHHHHHcc
Confidence 4999999999999999999988887 6677766643
No 5
>PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 3L4B_E 1LSS_C 3LLV_A 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A 2AEJ_A 3RBZ_A ....
Probab=98.09 E-value=6.6e-06 Score=56.33 Aligned_cols=62 Identities=24% Similarity=0.408 Sum_probs=56.0
Q ss_pred cccccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecccchHhhhhcCCCCCCCCCCeEeE
Q psy6103 17 QNSNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQYHNKAYLLNIPSWDWKQGDDVIC 92 (125)
Q Consensus 17 DL~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~e~k~~l~~a~~w~~~~ad~vIc 92 (125)
.|.++++.+|++++++.+ .|..|++.++.+|.++|+.++++++..+++...+..++ +|.||.
T Consensus 54 ~l~~a~i~~a~~vv~~~~--------~d~~n~~~~~~~r~~~~~~~ii~~~~~~~~~~~l~~~g------~d~vi~ 115 (116)
T PF02254_consen 54 VLERAGIEKADAVVILTD--------DDEENLLIALLARELNPDIRIIARVNDPENAELLRQAG------ADHVIS 115 (116)
T ss_dssp HHHHTTGGCESEEEEESS--------SHHHHHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHTT-------SEEEE
T ss_pred HHhhcCccccCEEEEccC--------CHHHHHHHHHHHHHHCCCCeEEEEECCHHHHHHHHHCC------cCEEEC
Confidence 499999999999999998 49999999999999999999999999999998887754 898885
No 6
>PF06241 DUF1012: Protein of unknown function (DUF1012); InterPro: IPR010420 This entry represents the CASTOR/POLLUX/SYM8 family of ion channels, which are found in plants. They have been implicated in modulating the nuclear membrane envelope potential [].
Probab=97.42 E-value=0.0014 Score=50.59 Aligned_cols=88 Identities=19% Similarity=0.352 Sum_probs=74.8
Q ss_pred ccEEEEccCCCCCCchhHHHHHHHHHHhhhhcC--CCCcEEEEecccchHhhhhcCCCCCCCCCCeEeEhHHHHHHHHHh
Q psy6103 26 ADACLVLANKYCQDPDAEDAANIMRVISIKNYS--DDIRVIIQLMQYHNKAYLLNIPSWDWKQGDDVICLAELKLGFIAQ 103 (125)
Q Consensus 26 A~AvfILad~~~~d~~~~D~~tILr~laVK~~~--p~~~i~vqil~~e~k~~l~~a~~w~~~~ad~vIc~~elk~~lLA~ 103 (125)
|.|++||+.+ .|+.+.|++.++.+||....- -..+++||+-...+...+...+ +..|=-++.+-+.||-|
T Consensus 1 ARaIIiL~~k--~d~ye~Da~a~lsVLaL~~v~e~~~g~vIVE~S~~~t~~LlKsv~------G~~VetV~dv~skL~VQ 72 (206)
T PF06241_consen 1 ARAIIILAEK--EDRYESDADAFLSVLALQPVKEGLSGHVIVEVSDSDTEQLLKSVS------GLKVETVHDVISKLMVQ 72 (206)
T ss_pred CceEEEeCCC--CCcchhhHHHHHHHhhcccccccCcccEEEEecCCChHHHHHhhc------CceeeeHHHHHHHHHHH
Confidence 7899999984 488999999999999987755 4799999999998887776554 67776669999999999
Q ss_pred hcccCChHHHHHHHHhhc
Q psy6103 104 SCLAPGFSTMMANLFAMR 121 (125)
Q Consensus 104 sc~~PG~sTli~NL~~~~ 121 (125)
+...||+...+-.|+...
T Consensus 73 CsRQ~GL~~Iy~~iL~~~ 90 (206)
T PF06241_consen 73 CSRQPGLAQIYEDILGFE 90 (206)
T ss_pred hccCccHHHHHHHHhCCC
Confidence 999999999998887543
No 7
>PRK10669 putative cation:proton antiport protein; Provisional
Probab=97.27 E-value=0.00068 Score=58.68 Aligned_cols=84 Identities=13% Similarity=0.050 Sum_probs=69.2
Q ss_pred cccccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecccchHhhhhcCCCCCCCCCCeEeEhHHH
Q psy6103 17 QNSNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQYHNKAYLLNIPSWDWKQGDDVICLAEL 96 (125)
Q Consensus 17 DL~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~e~k~~l~~a~~w~~~~ad~vIc~~el 96 (125)
.|++|.+++|++++++.+. |..+..-+.++|..+|+.++++..-.+++...+.. .|+|.||..++.
T Consensus 473 ~L~~a~i~~a~~viv~~~~--------~~~~~~iv~~~~~~~~~~~iiar~~~~~~~~~l~~------~Gad~vv~p~~~ 538 (558)
T PRK10669 473 IMQLAHLDCARWLLLTIPN--------GYEAGEIVASAREKRPDIEIIARAHYDDEVAYITE------RGANQVVMGERE 538 (558)
T ss_pred HHHhcCccccCEEEEEcCC--------hHHHHHHHHHHHHHCCCCeEEEEECCHHHHHHHHH------cCCCEEEChHHH
Confidence 4899999999999998763 34444455567888999999999988888877755 459999999999
Q ss_pred HHHHHHhhcccCChHHHH
Q psy6103 97 KLGFIAQSCLAPGFSTMM 114 (125)
Q Consensus 97 k~~lLA~sc~~PG~sTli 114 (125)
-..-+++....||.+...
T Consensus 539 ~a~~i~~~l~~~~~~~~~ 556 (558)
T PRK10669 539 IARTMLELLETPPAGEVV 556 (558)
T ss_pred HHHHHHHHhcCCCccccc
Confidence 999999999999987654
No 8
>PRK09496 trkA potassium transporter peripheral membrane component; Reviewed
Probab=97.19 E-value=0.0016 Score=54.03 Aligned_cols=83 Identities=19% Similarity=0.165 Sum_probs=70.7
Q ss_pred cccccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecccchHhhhhcCCCCCCCCCCeEeEhHHH
Q psy6103 17 QNSNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQYHNKAYLLNIPSWDWKQGDDVICLAEL 96 (125)
Q Consensus 17 DL~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~e~k~~l~~a~~w~~~~ad~vIc~~el 96 (125)
.|.++.+.+|++++++++. |..|++.++..|.+++. +++++...+++...+..+ |+|.||..+++
T Consensus 289 ~L~~~~~~~a~~vi~~~~~--------~~~n~~~~~~~~~~~~~-~ii~~~~~~~~~~~~~~~------g~~~vi~p~~~ 353 (453)
T PRK09496 289 LLEEEGIDEADAFIALTND--------DEANILSSLLAKRLGAK-KVIALVNRPAYVDLVEGL------GIDIAISPRQA 353 (453)
T ss_pred HHHhcCCccCCEEEECCCC--------cHHHHHHHHHHHHhCCC-eEEEEECCcchHHHHHhc------CCCEEECHHHH
Confidence 4889999999999998873 57888888989998775 899999999988776554 48999999999
Q ss_pred HHHHHHhhcccCChHHHH
Q psy6103 97 KLGFIAQSCLAPGFSTMM 114 (125)
Q Consensus 97 k~~lLA~sc~~PG~sTli 114 (125)
-...+++....|++..+.
T Consensus 354 ~~~~~~~~~~~~~~~~~~ 371 (453)
T PRK09496 354 TASEILRHVRRGDIVAVH 371 (453)
T ss_pred HHHHHHHHhhccchhhhh
Confidence 999999999999986644
No 9
>PRK03659 glutathione-regulated potassium-efflux system protein KefB; Provisional
Probab=96.52 E-value=0.0079 Score=52.91 Aligned_cols=72 Identities=8% Similarity=-0.042 Sum_probs=58.5
Q ss_pred cccccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecccchHhhhhcCCCCCCCCCCeEeEhHHH
Q psy6103 17 QNSNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQYHNKAYLLNIPSWDWKQGDDVICLAEL 96 (125)
Q Consensus 17 DL~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~e~k~~l~~a~~w~~~~ad~vIc~~el 96 (125)
.|++|.+++|++++++.+. |..|+..+..+|.++|+.+|++-.-.+++...+..+ |+|.|+...--
T Consensus 456 ~L~~agi~~A~~vv~~~~d--------~~~n~~i~~~~r~~~p~~~IiaRa~~~~~~~~L~~~------Ga~~vv~e~~e 521 (601)
T PRK03659 456 LLRAAGAEKAEAIVITCNE--------PEDTMKIVELCQQHFPHLHILARARGRVEAHELLQA------GVTQFSRETFS 521 (601)
T ss_pred HHHhcCCccCCEEEEEeCC--------HHHHHHHHHHHHHHCCCCeEEEEeCCHHHHHHHHhC------CCCEEEccHHH
Confidence 3999999999999999873 778888888999999999999999999998888765 48988765433
Q ss_pred HHHHHH
Q psy6103 97 KLGFIA 102 (125)
Q Consensus 97 k~~lLA 102 (125)
-.-.|+
T Consensus 522 s~l~l~ 527 (601)
T PRK03659 522 SALELG 527 (601)
T ss_pred HHHHHH
Confidence 333333
No 10
>PRK09496 trkA potassium transporter peripheral membrane component; Reviewed
Probab=96.33 E-value=0.018 Score=47.84 Aligned_cols=86 Identities=16% Similarity=0.067 Sum_probs=68.5
Q ss_pred cccccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecccch--HhhhhcCCCCCCCCCCeEeEhH
Q psy6103 17 QNSNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQYHN--KAYLLNIPSWDWKQGDDVICLA 94 (125)
Q Consensus 17 DL~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~e~--k~~l~~a~~w~~~~ad~vIc~~ 94 (125)
.|.++.++.|++++++.+. |..|+..+..+|.++|..++++..-.+++ ...+.... ..|++.||+.+
T Consensus 57 ~l~~~~~~~a~~vi~~~~~--------~~~n~~~~~~~r~~~~~~~ii~~~~~~~~~~~~~l~~~~---~~G~~~vi~p~ 125 (453)
T PRK09496 57 VLREAGAEDADLLIAVTDS--------DETNMVACQIAKSLFGAPTTIARVRNPEYAEYDKLFSKE---ALGIDLLISPE 125 (453)
T ss_pred HHHHcCCCcCCEEEEecCC--------hHHHHHHHHHHHHhcCCCeEEEEECCccccchhhhhhhh---cCCccEEECHH
Confidence 5888999999999998863 67788888999999999999999877665 12221001 14699999999
Q ss_pred HHHHHHHHhhcccCChHHH
Q psy6103 95 ELKLGFIAQSCLAPGFSTM 113 (125)
Q Consensus 95 elk~~lLA~sc~~PG~sTl 113 (125)
++-...|+.....|+...+
T Consensus 126 ~~~a~~l~~~l~~~~~~~~ 144 (453)
T PRK09496 126 LLVAREIARLIEYPGALDV 144 (453)
T ss_pred HHHHHHHHHHhcCCCceEe
Confidence 9999999999999997554
No 11
>PRK03562 glutathione-regulated potassium-efflux system protein KefC; Provisional
Probab=96.00 E-value=0.024 Score=50.22 Aligned_cols=75 Identities=8% Similarity=-0.054 Sum_probs=60.4
Q ss_pred ccccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecccchHhhhhcCCCCCCCCCCeEeEhHHHH
Q psy6103 18 NSNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQYHNKAYLLNIPSWDWKQGDDVICLAELK 97 (125)
Q Consensus 18 L~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~e~k~~l~~a~~w~~~~ad~vIc~~elk 97 (125)
|.+|.+++|++++++.+. |..|+..+..+|+.+|++++++-.-.+++...+.++ |+|.|+-...-.
T Consensus 457 L~~agi~~A~~vvv~~~d--------~~~n~~i~~~ar~~~p~~~iiaRa~d~~~~~~L~~~------Gad~v~~e~~e~ 522 (621)
T PRK03562 457 LESAGAAKAEVLINAIDD--------PQTSLQLVELVKEHFPHLQIIARARDVDHYIRLRQA------GVEKPERETFEG 522 (621)
T ss_pred HHhcCCCcCCEEEEEeCC--------HHHHHHHHHHHHHhCCCCeEEEEECCHHHHHHHHHC------CCCEEehhhHhH
Confidence 788999999999999873 788999999999999999999998888887777654 489887665555
Q ss_pred HHHHHhhcc
Q psy6103 98 LGFIAQSCL 106 (125)
Q Consensus 98 ~~lLA~sc~ 106 (125)
.-.+++..+
T Consensus 523 sl~l~~~~L 531 (621)
T PRK03562 523 ALKSGRLVL 531 (621)
T ss_pred HHHHHHHHH
Confidence 555555544
No 12
>COG0569 TrkA K+ transport systems, NAD-binding component [Inorganic ion transport and metabolism]
Probab=95.68 E-value=0.04 Score=42.83 Aligned_cols=85 Identities=16% Similarity=0.307 Sum_probs=68.2
Q ss_pred cccccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecccchHhhhhcCCCCCCCCCCeEeEhHHH
Q psy6103 17 QNSNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQYHNKAYLLNIPSWDWKQGDDVICLAEL 96 (125)
Q Consensus 17 DL~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~e~k~~l~~a~~w~~~~ad~vIc~~el 96 (125)
-|.+|.+.+|++++...+. .....++..++.|.+. --++++-+-.++....+... +++.+|+.+..
T Consensus 58 ~L~~agi~~aD~vva~t~~-------d~~N~i~~~la~~~~g-v~~viar~~~~~~~~~~~~~------g~~~ii~Pe~~ 123 (225)
T COG0569 58 VLEEAGIDDADAVVAATGN-------DEVNSVLALLALKEFG-VPRVIARARNPEHEKVLEKL------GADVIISPEKL 123 (225)
T ss_pred HHHhcCCCcCCEEEEeeCC-------CHHHHHHHHHHHHhcC-CCcEEEEecCHHHHHHHHHc------CCcEEECHHHH
Confidence 3999999999999999875 2455666667777664 46788988888777666544 48999999999
Q ss_pred HHHHHHhhcccCChHHHHH
Q psy6103 97 KLGFIAQSCLAPGFSTMMA 115 (125)
Q Consensus 97 k~~lLA~sc~~PG~sTli~ 115 (125)
-...+++....||+..++.
T Consensus 124 ~~~~l~~~i~~p~~~~~~~ 142 (225)
T COG0569 124 AAKRLARLIVTPGALDVLE 142 (225)
T ss_pred HHHHHHHHhcCCChheEEe
Confidence 9999999999999876543
No 13
>COG1226 Kch Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]
Probab=91.08 E-value=1.4 Score=31.16 Aligned_cols=80 Identities=15% Similarity=0.140 Sum_probs=61.6
Q ss_pred cccccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecc-cchHhhhhcCCCCCCCCCCeEeEhHH
Q psy6103 17 QNSNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQ-YHNKAYLLNIPSWDWKQGDDVICLAE 95 (125)
Q Consensus 17 DL~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~-~e~k~~l~~a~~w~~~~ad~vIc~~e 95 (125)
.|.+|.+..|.++++..+. +..++.-+..++.++|++++++=.-. ..+..++.. .|++.+++...
T Consensus 77 ~l~~a~~~~a~~vi~~~~~--------~~~~~~~~~~~~~~~p~~~i~~~~~~~~~~~~~l~~------~G~~~vi~~~~ 142 (212)
T COG1226 77 VLEAAGIERARAVIVTLSD--------DATNVFIVLLARAINPELEILARARDLDEAVETLTT------VGADEVVPPTF 142 (212)
T ss_pred HHHhcChhheeEEEEecCC--------HHHHHHHHHHHHHHCCCCEEEEEeccchHHHHHHHH------cCCCeeecHHH
Confidence 4778999999999999873 66666666779999999997666666 444455544 45999999988
Q ss_pred HHHHHHHhhcccCCh
Q psy6103 96 LKLGFIAQSCLAPGF 110 (125)
Q Consensus 96 lk~~lLA~sc~~PG~ 110 (125)
.....++...+.+..
T Consensus 143 ~~~~~~~~~~~~~~~ 157 (212)
T COG1226 143 ESALLLARAALVGLG 157 (212)
T ss_pred HHHHHHHHHHhcccC
Confidence 888888777776655
No 14
>KOG3193|consensus
Probab=71.45 E-value=0.66 Score=41.75 Aligned_cols=101 Identities=15% Similarity=0.174 Sum_probs=67.3
Q ss_pred ccccccccCcccEEEEccCC-CCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecccchHhhhh-----------------
Q psy6103 16 HQNSNSKVHEADACLVLANK-YCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQYHNKAYLL----------------- 77 (125)
Q Consensus 16 ~DL~Ra~~~~A~AvfILad~-~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~e~k~~l~----------------- 77 (125)
.||.||.+..|+.|++.-.- ....+..+|-.+|..+--+.++.|.++-|.++-+..|-+.++
T Consensus 775 d~llragvs~ae~vvvvke~a~~aee~tadcntii~vq~~~r~fp~lr~itelt~atnmrf~qf~~h~~ysl~~sr~ekk 854 (1087)
T KOG3193|consen 775 DCLLRAGVSSAEHVVVVKETAVMAEEHTADCNTIITVQKIHRMFPRLRMITELTHATNMRFVQFNPHNAYSLAQSRFEKK 854 (1087)
T ss_pred HHHHHhcccccceEEEEehhhhhhhhhccccchhhhHHHHHHhchhHHHHHHHhhhccceEEeecCcchhHHHHHHHHHH
Confidence 35999999999999998331 223555677889999999999999998888776554433222
Q ss_pred ---------cCCCCCCCCCCeEeEhHHHHHHHHHhhcccCChHHHHHHHH
Q psy6103 78 ---------NIPSWDWKQGDDVICLAELKLGFIAQSCLAPGFSTMMANLF 118 (125)
Q Consensus 78 ---------~a~~w~~~~ad~vIc~~elk~~lLA~sc~~PG~sTli~NL~ 118 (125)
.+-|. ..|..-+-...+--.||-|..+-|=..+|+.-|+
T Consensus 855 er~rgsh~~~mfrl--pfa~g~vfsa~mld~llyqa~ik~~vv~~vrlll 902 (1087)
T KOG3193|consen 855 ERKRGSHMPFMFRL--PFAQGGVFSANMLDRLLYQAIIKPFVVDLVRLLL 902 (1087)
T ss_pred HhhccCCCceEEec--cccccceeeHHHHHHHHHHHHhhHHHHHHHHHHh
Confidence 00000 1233334444455567888888887788877665
No 15
>KOG1420|consensus
Probab=49.38 E-value=13 Score=33.93 Aligned_cols=109 Identities=16% Similarity=0.273 Sum_probs=74.8
Q ss_pred cccCcc----cccccccCcccEEEEccCC--CCCCchhHHHHHHHHHHhhhhcC----------------C---------
Q psy6103 11 MQCGNH----QNSNSKVHEADACLVLANK--YCQDPDAEDAANIMRVISIKNYS----------------D--------- 59 (125)
Q Consensus 11 ~~~~~~----DL~Ra~~~~A~AvfILad~--~~~d~~~~D~~tILr~laVK~~~----------------p--------- 59 (125)
.++|.+ ||+-+++.-.+.|.|++-+ +..|+.-+|.+.||..|-||... |
T Consensus 795 ilngsplsradlravninlcdmcvilsa~vpn~ddttladkeailaslnikamqfddtigvl~~r~q~fd~~ssp~gspi 874 (1103)
T KOG1420|consen 795 ILNGSPLSRADLRAVNINLCDMCVILSANVPNIDDTTLADKEAILASLNIKAMQFDDTIGVLQARSQGFDPPSSPDGSPI 874 (1103)
T ss_pred ecCCCCCchhhhhhccccccceeEEEecCCCCCCCcccccHHHHHhhccceeeeeccceeeeeccCCCCCCCCCCCCCCe
Confidence 345654 8999999999999999875 45588999999999999999642 1
Q ss_pred -----------CCcEEEEecccchHhhhhcCCCCCCCCCCeEe------EhH----HHHHHHHHhhcccCChHHHHHHHH
Q psy6103 60 -----------DIRVIIQLMQYHNKAYLLNIPSWDWKQGDDVI------CLA----ELKLGFIAQSCLAPGFSTMMANLF 118 (125)
Q Consensus 60 -----------~~~i~vqil~~e~k~~l~~a~~w~~~~ad~vI------c~~----elk~~lLA~sc~~PG~sTli~NL~ 118 (125)
++++|.++....|...+-.-. +..+-.+.. |-. ..--+||....+.-..-|||..|.
T Consensus 875 ~lq~~g~~~g~nvpmitelvndsnvqfldqdd--dddpdtelyltqpfacgtafavsvldslmsttyfndnaltlirtlv 952 (1103)
T KOG1420|consen 875 HLQQPGITTGVNVPMITELVNDSNVQFLDQDD--DDDPDTELYLTQPFACGTAFAVSVLDSLMSTTYFNDNALTLIRTLV 952 (1103)
T ss_pred EEecCCcccccCchhhhhhhccccceecccCC--CCCCCceeEecCccccchhhHHHHHHHHhhhceecchHHHHHHHHH
Confidence 678888888777765442100 001111221 222 223457888888889999999988
Q ss_pred hhc
Q psy6103 119 AMR 121 (125)
Q Consensus 119 ~~~ 121 (125)
+..
T Consensus 953 tgg 955 (1103)
T KOG1420|consen 953 TGG 955 (1103)
T ss_pred hCC
Confidence 753
No 16
>COG4333 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.37 E-value=81 Score=23.69 Aligned_cols=86 Identities=17% Similarity=0.159 Sum_probs=52.1
Q ss_pred cccccccccccCccc--cccc-ccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEE-----ecc-----
Q psy6103 3 EMKHESDDMQCGNHQ--NSNS-KVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQ-----LMQ----- 69 (125)
Q Consensus 3 ~~~~~~~~~~~~~~D--L~Ra-~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vq-----il~----- 69 (125)
+|+.|-.--.||-.- |.|. .-+++...||.-+++-.|.. .|-.||+|-++.-+--..--+|+- +-+
T Consensus 11 ti~~~AifS~cgkyRY~L~r~WDe~Kp~~~fi~lnPs~ada~-~Dd~Ti~rci~fA~swgyGgvy~~NLFa~~~T~~~~L 89 (167)
T COG4333 11 TMIKDAIFSPCGKYRYSLSRVWDESKPYTLFIGLNPSYADAE-KDDRTLSRCISFAKSWGYGGVYMANLFAFVHTQRHEL 89 (167)
T ss_pred heeeeeeeccchhhhhhhhhhhcccCCeeEEEEeccchhhhh-hcchHHHHHHHHHhhcccCcEEeeehhhhccCCHHHH
Confidence 455555555666552 4553 34677888999998775554 888999999887663322222222 222
Q ss_pred --------cchHhhhhcCCCCCCCCCCeEeEh
Q psy6103 70 --------YHNKAYLLNIPSWDWKQGDDVICL 93 (125)
Q Consensus 70 --------~e~k~~l~~a~~w~~~~ad~vIc~ 93 (125)
++|-.|+.++- .+++-|||.
T Consensus 90 ~~~~dPigkdnD~HL~~~~----s~a~~vI~A 117 (167)
T COG4333 90 MKASDPIGKDNDSHLIRLV----SGAGLVIAA 117 (167)
T ss_pred hcCCCCCCCCchHHHHHHH----hcCCeEEEE
Confidence 23445555543 568888885
No 17
>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification
Probab=33.60 E-value=1e+02 Score=20.85 Aligned_cols=45 Identities=11% Similarity=0.170 Sum_probs=27.1
Q ss_pred CcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEeccc
Q psy6103 24 HEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQY 70 (125)
Q Consensus 24 ~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~ 70 (125)
++||.++|-+---. ++.++....-++-+.=.+ .|+.+|+|==.-+
T Consensus 35 e~AD~iiiNTC~V~-~~Ae~k~~~~i~~l~~~~-~~~~~ivv~GC~a 79 (98)
T PF00919_consen 35 EEADVIIINTCTVR-ESAEQKSRNRIRKLKKLK-KPGAKIVVTGCMA 79 (98)
T ss_pred ccCCEEEEEcCCCC-cHHHHHHHHHHHHHHHhc-CCCCEEEEEeCcc
Confidence 78999999887655 444444444444333222 5998888754444
No 18
>PRK14337 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=30.56 E-value=84 Score=26.71 Aligned_cols=43 Identities=16% Similarity=0.165 Sum_probs=29.0
Q ss_pred cCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEE
Q psy6103 23 VHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVII 65 (125)
Q Consensus 23 ~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~v 65 (125)
-.+||.++|-+--...+..++=...|.+.-.+|..+|+.+|+|
T Consensus 37 ~~~ADiiiiNTC~v~~~A~~~~~~~i~~~~~~k~~~p~~~ivv 79 (446)
T PRK14337 37 EEEARVFIVNTCSVRDKPEQKVYSLLGRIRHATKKNPDVFVAV 79 (446)
T ss_pred cCCCCEEEEeccCeecHHHHHHHHHHHHHHHHHHhCCCCEEEE
Confidence 3679999998876553333333344555556788999988885
No 19
>PRK14325 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=29.17 E-value=90 Score=26.36 Aligned_cols=42 Identities=19% Similarity=0.169 Sum_probs=28.9
Q ss_pred cCcccEEEEccCCCCCCchhHHHHH-HHHHHhhhhcCCCCcEEE
Q psy6103 23 VHEADACLVLANKYCQDPDAEDAAN-IMRVISIKNYSDDIRVII 65 (125)
Q Consensus 23 ~~~A~AvfILad~~~~d~~~~D~~t-ILr~laVK~~~p~~~i~v 65 (125)
...||.++|-+.-.. .+.+++..+ |.++-.+|..+|+++|++
T Consensus 38 ~~~aDvviinTC~v~-~~a~~~~~~~i~~~~~~k~~~p~~~vvv 80 (444)
T PRK14325 38 PEEADLILLNTCSIR-EKAQEKVFSELGRWRKLKEKNPDLIIGV 80 (444)
T ss_pred cCCCCEEEEEcceee-ehHHHHHHHHHHHHHHHHHhCCCCEEEE
Confidence 467899999877544 444444444 444456799999998876
No 20
>TIGR00160 MGSA methylglyoxal synthase. Methylglyoxal synthase (MGS) generates methylglyoxal (MG), a toxic metabolite (that may also be a regulatory metabolite and) that is detoxified, prinicipally, through a pathway involving glutathione and glyoxylase I. Totemeyer, et al. (MUID:98149311) propose that, during a loss of control over carbon flux, with accumulation of phosphorylated sugars and depletion of phosphate, as might happen during a rapid shift to a richer medium, MGS aids the cell by converting some dihydroxyacetone phosphate (DHAP) to MG and phosphate. This is therefore an alternative to triosephosphate isomerase and the remainder of the glycolytic pathway for the disposal of DHAP during the stress of a sudden increase in available sugars.
Probab=26.92 E-value=71 Score=23.65 Aligned_cols=37 Identities=16% Similarity=0.257 Sum_probs=33.2
Q ss_pred ccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhh
Q psy6103 20 NSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKN 56 (125)
Q Consensus 20 Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~ 56 (125)
|+.-.+=++||.+-|+....|.+.|-+.++|.-.|.+
T Consensus 68 ~Ia~g~id~vIFf~DPl~~~phepDi~aLlRlc~v~n 104 (143)
T TIGR00160 68 LIAEGKIDAVIFFWDPLNAQPHEPDVKALLRLCTVWN 104 (143)
T ss_pred HHHhCCCCEEEEecCCCCCCCCCcCHHHHHHHHHhhC
Confidence 5556778999999999999999999999999999887
No 21
>smart00174 RHO Rho (Ras homology) subfamily of Ras-like small GTPases. Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms.
Probab=23.27 E-value=1.7e+02 Score=20.30 Aligned_cols=53 Identities=8% Similarity=0.033 Sum_probs=32.6
Q ss_pred ccccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEecccch
Q psy6103 18 NSNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLMQYHN 72 (125)
Q Consensus 18 L~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil~~e~ 72 (125)
+.+.....|++++++-|-....+-++-....+. .++.+.|+.++++-..+.+.
T Consensus 62 ~~~~~~~~~d~~ilv~d~~~~~s~~~~~~~~~~--~i~~~~~~~piilv~nK~Dl 114 (174)
T smart00174 62 LRPLSYPDTDVFLICFSVDSPASFENVKEKWYP--EVKHFCPNTPIILVGTKLDL 114 (174)
T ss_pred hchhhcCCCCEEEEEEECCCHHHHHHHHHHHHH--HHHhhCCCCCEEEEecChhh
Confidence 555667889999999885432222211122333 34567789999998877553
No 22
>PRK14333 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=21.72 E-value=1.4e+02 Score=25.32 Aligned_cols=42 Identities=17% Similarity=0.180 Sum_probs=27.6
Q ss_pred cCcccEEEEccCCCCCCchhHHH-HHHHHHHhhhhcCCCCcEEE
Q psy6103 23 VHEADACLVLANKYCQDPDAEDA-ANIMRVISIKNYSDDIRVII 65 (125)
Q Consensus 23 ~~~A~AvfILad~~~~d~~~~D~-~tILr~laVK~~~p~~~i~v 65 (125)
...||.++|=+---. +..+.+. ..|.+....|..+|+++|+|
T Consensus 41 ~~~ADiiiiNTC~v~-~~a~~~~~~~i~~~~~~k~~~p~~~vvv 83 (448)
T PRK14333 41 ELQADLVLYNTCTIR-DNAEQKVYSYLGRQAKRKHKNPDLTLVV 83 (448)
T ss_pred cccCCEEEEEeeeee-ehHHHHHHHHHHHHHHHHhcCCCCEEEE
Confidence 456899888877555 3444444 44445545588899988776
No 23
>cd05294 LDH-like_MDH_nadp A lactate dehydrogenases-like structure with malate dehydrogenase enzymatic activity. The LDH-like MDH proteins have a lactate dehyhydrogenase-like (LDH-like) structure and malate dehydrogenase (MDH) enzymatic activity. This subgroup is composed of some archaeal LDH-like MDHs that prefer NADP(H) rather than NAD(H) as a cofactor. One member, MJ0490 from Methanococcus jannaschii, has been observed to form dimers and tetramers during crystalization, although it is believed to exist primarilly as a tetramer in solution. In addition to its MDH activity, MJ0490 also possesses fructose-1,6-bisphosphate-activated LDH activity. Members of this subgroup have a higher sequence similarity to LDHs than to other MDHs. LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carbox
Probab=21.70 E-value=2.2e+02 Score=22.97 Aligned_cols=48 Identities=17% Similarity=0.252 Sum_probs=28.9
Q ss_pred ccCcccEEEEccCCCCC-CchhHHH----HHHHHH--HhhhhcCCCCcEEEEeccc
Q psy6103 22 KVHEADACLVLANKYCQ-DPDAEDA----ANIMRV--ISIKNYSDDIRVIIQLMQY 70 (125)
Q Consensus 22 ~~~~A~AvfILad~~~~-d~~~~D~----~tILr~--laVK~~~p~~~i~vqil~~ 70 (125)
.++.||.|||.+..... +....|. ..+++. -.++.++|+..++|-- .|
T Consensus 69 ~l~~aDiViitag~p~~~~~~r~dl~~~n~~i~~~~~~~i~~~~~~~~viv~~-np 123 (309)
T cd05294 69 DVAGSDIVIITAGVPRKEGMSRLDLAKKNAKIVKKYAKQIAEFAPDTKILVVT-NP 123 (309)
T ss_pred HhCCCCEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCeEEEEeC-Cc
Confidence 48999999999985332 2222333 133333 3467888987666543 44
No 24
>PF02310 B12-binding: B12 binding domain; InterPro: IPR006158 The cobalamin (vitamin B12) binding domain can bind two different forms of the cobalamin cofactor, with cobalt bonded either to a methyl group (methylcobalamin) or to 5'-deoxyadenosine (adenosylcobalamin). Cobalamin-binding domains are mainly found in two families of enzymes present in animals and prokaryotes, which perform distinct kinds of reactions at the cobalt-carbon bond. Enzymes that require methylcobalamin carry out methyl transfer reactions. Enzymes that require adenosylcobalamin catalyse reactions in which the first step is the cleavage of adenosylcobalamin to form cob(II)alamin and the 5'-deoxyadenosyl radical, and thus act as radical generators. In both types of enzymes the B12-binding domain uses a histidine to bind the cobalt atom of cobalamin cofactors. This histidine is embedded in a DXHXXG sequence, the most conserved primary sequence motif of the domain [, , ]. Proteins containing the cobalamin-binding domain include: Animal and prokaryotic methionine synthase (2.1.1.13 from EC), which catalyse the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Animal and prokaryotic methylmalonyl-CoA mutase (5.4.99.2 from EC), which are involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle. Prokaryotic lysine 5,6-aminomutase (5.4.3.4 from EC). Prokaryotic glutamate mutase (5.4.99.1 from EC) []. Prokaryotic methyleneglutarate mutase (5.4.99.4 from EC). Prokaryotic isobutyryl-CoA mutase (5.4.99.13 from EC). The core structure of the cobalamin-binding domain is characterised by a five-stranded alpha/beta (Rossmann) fold, which consists of 5 parallel beta-sheets surrounded by 4-5 alpha helices in three layers (alpha/beta/alpha) []. Upon binding cobalamin, important elements of the binding site appear to become structured, including an alpha-helix that forms on one side of the cleft accommodating the nucleotide 'tail' of the cofactor. In cobalamin, the cobalt atom can be either free (dmb-off) or bound to dimethylbenzimidazole (dmb-on) according to the pH. When bound to the cobalamin-binding domain, the dimethylbenzimidazole ligand is replaced by the active histidine (His-on) of the DXHXXG motif. The replacement of dimethylbenzimidazole by histidine allows switching between the catalytic and activation cycles []. In methionine synthase the cobalamin cofactor is sandwiched between the cobalamin-binding domain and an approximately 90 residues N-terminal domain forming a helical bundle comprising two pairs of antiparallel helices []. In methionine synthase, there is a second, adjacent domain involved in cobalamin binding that forms a 4-helical bundle cap (IPR003759 from INTERPRO); in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO) [].; GO: 0031419 cobalamin binding, 0046872 metal ion binding; PDB: 1Y80_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 3KP1_A 3KOW_A 3KOZ_A ....
Probab=21.68 E-value=1.7e+02 Score=19.32 Aligned_cols=45 Identities=16% Similarity=0.268 Sum_probs=32.3
Q ss_pred cccccCcccEEEEccCCCCCCchhHHHHHHHHHHhhhhcCCCCcEEEEec
Q psy6103 19 SNSKVHEADACLVLANKYCQDPDAEDAANIMRVISIKNYSDDIRVIIQLM 68 (125)
Q Consensus 19 ~Ra~~~~A~AvfILad~~~~d~~~~D~~tILr~laVK~~~p~~~i~vqil 68 (125)
.++.-.+.+.|.+.+.. .+.-.....+.+. +|..+|++++++==-
T Consensus 45 ~~~~~~~pd~V~iS~~~---~~~~~~~~~l~~~--~k~~~p~~~iv~GG~ 89 (121)
T PF02310_consen 45 EALRAERPDVVGISVSM---TPNLPEAKRLARA--IKERNPNIPIVVGGP 89 (121)
T ss_dssp HHHHHTTCSEEEEEESS---STHHHHHHHHHHH--HHTTCTTSEEEEEES
T ss_pred HHHhcCCCcEEEEEccC---cCcHHHHHHHHHH--HHhcCCCCEEEEECC
Confidence 44666788888886632 4555666777776 999999999988543
Done!