Query 038085
Match_columns 85
No_of_seqs 62 out of 64
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 07:25:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038085.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038085hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01569 A_tha_TIGR01569 plan 99.3 4.5E-12 9.9E-17 90.0 5.5 65 15-79 76-154 (154)
2 PF04535 DUF588: Domain of unk 99.0 5.6E-10 1.2E-14 77.3 3.7 65 3-67 65-149 (149)
3 PF01284 MARVEL: Membrane-asso 79.1 4.6 9.9E-05 26.1 4.1 60 11-73 70-143 (144)
4 KOG4016 Synaptic vesicle prote 21.7 1.2E+02 0.0026 24.0 3.3 25 51-75 142-166 (233)
5 PF10966 DUF2768: Protein of u 19.1 1.5E+02 0.0033 18.7 2.8 49 18-77 3-52 (58)
6 PRK09500 potC spermidine/putre 16.9 3.7E+02 0.008 19.4 4.7 44 38-81 43-86 (256)
7 PF04403 PqiA: Paraquat-induci 16.2 84 0.0018 21.9 1.2 31 51-81 119-149 (160)
8 PF02060 ISK_Channel: Slow vol 15.3 1.4E+02 0.0031 21.7 2.2 25 54-81 45-69 (129)
9 PF07275 ArdA: Antirestriction 14.8 61 0.0013 22.2 0.2 14 10-23 134-147 (169)
10 PF11804 DUF3325: Protein of u 14.5 1.7E+02 0.0036 19.9 2.3 16 56-71 3-18 (106)
No 1
>TIGR01569 A_tha_TIGR01569 plant integral membrane protein TIGR01569. This model describes a region of ~160 residues found exclusively in plant proteins, generally as the near complete length of the protein. At least 24 different members are found in Arabidopsis thaliana. Members have four predicted transmembrane regions, the last of which is preceded by an invariant CXXXXX[FY]C motif. The family is not functionally characterized.
Probab=99.29 E-value=4.5e-12 Score=90.03 Aligned_cols=65 Identities=26% Similarity=0.175 Sum_probs=56.3
Q ss_pred hhhhhhhcchh----hhhhhhccccccc---------hhhhh-hccCCchhhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 038085 15 LKLLFDVADID----LSSSICIVFGCCP---------DDWQS-NWGEDEFPDMAKASVALSFLAFVALGFSSLISGYAL 79 (85)
Q Consensus 15 ~~~~fDf~~DQ----LLmSAsSaA~~r~---------~~w~s-~~~~d~Ft~~a~aSIsmsFlAF~alAlSsLiSgy~L 79 (85)
.+.|++|.+|| |++|+.++|.+.. ..|+. |-.-|+||+++.+|++++|+||+++++++++|+|++
T Consensus 76 ~~~~~~f~~D~v~~~Ll~sa~sAA~av~~l~~~G~~~~~W~~iC~~~~~FC~~~~~sl~~s~~a~v~~~llsv~Sa~~~ 154 (154)
T TIGR01569 76 FKLIALFFLDLVMLALLSSGTSAAAAVAYVGKLGNKEAGWLKICGVFGKFCDRIAGSLALSLFAVILLVLLSILSAISL 154 (154)
T ss_pred hHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 46899999999 9999999998743 24553 445789999999999999999999999999999985
No 2
>PF04535 DUF588: Domain of unknown function (DUF588); InterPro: IPR006702 This family of plant proteins contains a domain that may have a catalytic activity. It has a conserved arginine and aspartate that could form an active site. These proteins are predicted to contain 3 or 4 transmembrane helices.
Probab=98.96 E-value=5.6e-10 Score=77.30 Aligned_cols=65 Identities=38% Similarity=0.291 Sum_probs=55.4
Q ss_pred HHHHHHHh------hhhhhhhhhhhcchh----hhhhhhccccccchhhhh----------hccCCchhhHHHHHHHHHH
Q 038085 3 LQLLLLLY------LGEKLKLLFDVADID----LSSSICIVFGCCPDDWQS----------NWGEDEFPDMAKASVALSF 62 (85)
Q Consensus 3 ~~~~~~~~------~~ek~~~~fDf~~DQ----LLmSAsSaA~~r~~~w~s----------~~~~d~Ft~~a~aSIsmsF 62 (85)
+|+....+ .++|...|++|.+|| |++|+.++|++..+.+.+ |..-++||+++.+|++++|
T Consensus 65 ~~~~~~~~~~~~~~~~~~~~~~~~f~~Dqv~~~ll~sa~~Aa~~~~~~~~~g~~~~~W~~vC~~~~~FC~~~~~sv~lsf 144 (149)
T PF04535_consen 65 LQLVLSIYSLSRGKLRSKLLAWFLFILDQVLAYLLFSAASAAAAVAYLGKKGNSHVQWSKVCSQFGKFCNRAAASVALSF 144 (149)
T ss_pred HHHHHHHHHHHccCCcccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhccccccchhhccchhhHHHHHHHHHHHHH
Confidence 45555544 678999999999999 999999999998887764 4678999999999999999
Q ss_pred HHHHH
Q 038085 63 LAFVA 67 (85)
Q Consensus 63 lAF~a 67 (85)
+||++
T Consensus 145 ~a~~~ 149 (149)
T PF04535_consen 145 LAFVA 149 (149)
T ss_pred HHHHC
Confidence 99974
No 3
>PF01284 MARVEL: Membrane-associating domain; InterPro: IPR021128 This entry represents the ~130-residue MARVEL (MAL and related proteins for vesicle trafficking and membrane link) domain. The MARVEL domain is a module with a four transmembrane-helix architecture that has been identified in proteins of the myelin and lymphocyte (MAL), physins, gyrins and occludin families. All described MARVEL domain-containing proteins are consistent with the M-shaped topology: four transmembrane-helix region architecture with cytoplasmic N- and C-terminal regions. Their function could be related to cholesterol-rich membrane apposition events in a variety of cellular processes, such as biogenesis of vesicular transport carriers or tight junction regulation [].
Probab=79.06 E-value=4.6 Score=26.10 Aligned_cols=60 Identities=15% Similarity=0.020 Sum_probs=39.2
Q ss_pred hhhhhhhhhhhcchh----hhhhhhccccccchhhhh--h--------ccCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 038085 11 LGEKLKLLFDVADID----LSSSICIVFGCCPDDWQS--N--------WGEDEFPDMAKASVALSFLAFVALGFSSL 73 (85)
Q Consensus 11 ~~ek~~~~fDf~~DQ----LLmSAsSaA~~r~~~w~s--~--------~~~d~Ft~~a~aSIsmsFlAF~alAlSsL 73 (85)
.+.....+.|+..|. +-+.+...-+ ..+.+ | ...+.-++...|+++++|++++.+..+..
T Consensus 70 ~~~~~~~~~~~~~~~v~~il~l~a~~~~a---~~~~~~~~~~~~~~~~~~~~~~~~~~~Aa~~f~~~~~~l~~~s~~ 143 (144)
T PF01284_consen 70 RPRIPWPLVEFIFDAVFAILWLAAFIALA---AYLSDHSCSNTGNDYSYSGCSRCGAWKAAAAFGFLNWLLFIVSAV 143 (144)
T ss_pred ccccccchhHHHHHHHHHHHHHHHHHHHH---HHhcCcccccCCCCcCCCCCCcchhHHHHHHHHHHHHHHHHHHHH
Confidence 466788899999999 2222222111 12222 1 12334578999999999999999988764
No 4
>KOG4016 consensus Synaptic vesicle protein Synaptogyrin involved in regulation of Ca2+-dependent exocytosis [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.72 E-value=1.2e+02 Score=24.03 Aligned_cols=25 Identities=24% Similarity=0.521 Sum_probs=21.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhh
Q 038085 51 PDMAKASVALSFLAFVALGFSSLIS 75 (85)
Q Consensus 51 t~~a~aSIsmsFlAF~alAlSsLiS 75 (85)
+..++++|+.+|+.++.-+..+.+.
T Consensus 142 a~saraaIafsffSilsW~~~A~lA 166 (233)
T KOG4016|consen 142 AGSARAAIAFSFFSILSWGGQAVLA 166 (233)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHH
Confidence 4589999999999999999888764
No 5
>PF10966 DUF2768: Protein of unknown function (DUF2768); InterPro: IPR020076 This entry contains proteins with no known function.
Probab=19.14 E-value=1.5e+02 Score=18.71 Aligned_cols=49 Identities=18% Similarity=0.250 Sum_probs=29.5
Q ss_pred hhhhcchh-hhhhhhccccccchhhhhhccCCchhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 038085 18 LFDVADID-LSSSICIVFGCCPDDWQSNWGEDEFPDMAKASVALSFLAFVALGFSSLISGY 77 (85)
Q Consensus 18 ~fDf~~DQ-LLmSAsSaA~~r~~~w~s~~~~d~Ft~~a~aSIsmsFlAF~alAlSsLiSgy 77 (85)
|++|++-+ +.+|...--.+ |..-+|.|- ...++++||+++-++.+|=-|
T Consensus 3 WiS~~~iglMfisv~~i~~s------R~Klk~~~l-----k~i~~~vAy~lli~~gli~~~ 52 (58)
T PF10966_consen 3 WISFGAIGLMFISVILIYFS------RYKLKGKFL-----KFIVSLVAYILLIVSGLIMFF 52 (58)
T ss_pred chHHHHHHHHHHHHHHHHHH------HHHHhChHH-----HHHHHHHHHHHHHHHHHheEE
Confidence 66777776 44444443332 223344333 356889999999888877443
No 6
>PRK09500 potC spermidine/putrescine ABC transporter membrane protein; Reviewed
Probab=16.90 E-value=3.7e+02 Score=19.43 Aligned_cols=44 Identities=14% Similarity=0.232 Sum_probs=30.0
Q ss_pred chhhhhhccCCchhhHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 038085 38 PDDWQSNWGEDEFPDMAKASVALSFLAFVALGFSSLISGYALYN 81 (85)
Q Consensus 38 ~~~w~s~~~~d~Ft~~a~aSIsmsFlAF~alAlSsLiSgy~L~~ 81 (85)
.+++.+-+.++.+-+...-++.+++++.+.-..=++.-||-+.+
T Consensus 43 ~~~~~~~~~~~~~~~~~~~Tl~~~~~~~~i~~~lg~~~a~~~~~ 86 (256)
T PRK09500 43 TKWYELLFNNDSLLQAAQHSLTMAVFSATFATLIGSLTAVALYR 86 (256)
T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45566667778888888888888888765444444444776654
No 7
>PF04403 PqiA: Paraquat-inducible protein A; InterPro: IPR007498 Paraquat is a superoxide radical-generating agent. The promoter for the pqiA gene is also inducible by other known superoxide generators []. This is predicted to be a family of integral membrane proteins, possibly located in the inner membrane. This family is related to NADH dehydrogenase subunit 2 (IPR001750 from INTERPRO).
Probab=16.21 E-value=84 Score=21.93 Aligned_cols=31 Identities=23% Similarity=0.320 Sum_probs=25.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 038085 51 PDMAKASVALSFLAFVALGFSSLISGYALYN 81 (85)
Q Consensus 51 t~~a~aSIsmsFlAF~alAlSsLiSgy~L~~ 81 (85)
.+++.+....+|.+|+++.+.++..+..+.+
T Consensus 119 ~~~a~v~~g~g~~~f~~~~ll~~~~~~~~d~ 149 (160)
T PF04403_consen 119 SGLADVEPGPGFYAFAALVLLSMLASSSFDP 149 (160)
T ss_pred HHheeeeecHHHHHHHHHHHHHHHHHHhCCH
Confidence 4577788889999999999998888776543
No 8
>PF02060 ISK_Channel: Slow voltage-gated potassium channel; InterPro: IPR000369 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. Two types of beta subunit (KCNE and KCNAB) are presently known to associate with voltage-gated alpha subunits (Kv, KCNQ and eag-like). However, not all combinations of alpha and beta subunits are possible. The KCNE family of K+ channel subunits are membrane glycoproteins that possess a single transmembrane (TM) domain. They share no structural relationship with the alpha subunit proteins, which possess pore forming domains. The subunits appear to have a regulatory function, modulating the kinetics and voltage dependence of the alpha subunits of voltage-dependent K+ channels. KCNE subunits are formed from short polypeptides of ~130 amino acids, and are divided into five subfamilies: KCNE1 (MinK/IsK), KCNE2 (MiRP1), KCNE3 (MiRP2), KCNE4 (MiRP3) and KCNE1L (AMMECR2). ; GO: 0005249 voltage-gated potassium channel activity, 0006811 ion transport, 0016020 membrane; PDB: 2K21_A.
Probab=15.32 E-value=1.4e+02 Score=21.68 Aligned_cols=25 Identities=20% Similarity=0.434 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 038085 54 AKASVALSFLAFVALGFSSLISGYALYN 81 (85)
Q Consensus 54 a~aSIsmsFlAF~alAlSsLiSgy~L~~ 81 (85)
.=.-+.|+|++|..+++ +=||.-++
T Consensus 45 lYIL~vmgfFgff~~gI---mlsyvRSK 69 (129)
T PF02060_consen 45 LYILVVMGFFGFFTVGI---MLSYVRSK 69 (129)
T ss_dssp -HHHHHHHHHHHHHHHH---HHHHHHHH
T ss_pred ehHHHHHHHHHHHHHHH---HHHHHHHh
Confidence 44568899999887654 44454433
No 9
>PF07275 ArdA: Antirestriction protein (ArdA); InterPro: IPR009899 This family consists of several bacterial antirestriction (ArdA) proteins. ArdA functions in bacterial conjugation to allow an unmodified plasmid to evade restriction in the recipient bacterium and yet acquire cognate modification [].; PDB: 2W82_C.
Probab=14.77 E-value=61 Score=22.25 Aligned_cols=14 Identities=36% Similarity=0.441 Sum_probs=8.7
Q ss_pred hhhhhhhhhhhhcc
Q 038085 10 YLGEKLKLLFDVAD 23 (85)
Q Consensus 10 ~~~ek~~~~fDf~~ 23 (85)
-+||.++.||||-.
T Consensus 134 ~ipe~l~~YfDye~ 147 (169)
T PF07275_consen 134 DIPEELKRYFDYEA 147 (169)
T ss_dssp ---TGGGCGB-HHH
T ss_pred cCCHHHHhccCHHH
Confidence 37899999999854
No 10
>PF11804 DUF3325: Protein of unknown function (DUF3325); InterPro: IPR021762 This family of short proteins are functionally uncharacterised. This family is restricted to Alpha-, Beta- and Gamma-proteobacteria.
Probab=14.45 E-value=1.7e+02 Score=19.89 Aligned_cols=16 Identities=31% Similarity=0.584 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHH
Q 038085 56 ASVALSFLAFVALGFS 71 (85)
Q Consensus 56 aSIsmsFlAF~alAlS 71 (85)
++..++|.+|.++|++
T Consensus 3 ~a~~L~~~gf~~LALa 18 (106)
T PF11804_consen 3 LAFALCYAGFAALALA 18 (106)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 4567899999999885
Done!