Query 028724
Match_columns 205
No_of_seqs 44 out of 46
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 16:00:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028724.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028724hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08744 NOZZLE: Plant transcr 99.1 1.3E-11 2.8E-16 110.5 1.9 40 20-59 42-81 (314)
2 PF15442 DUF4629: Domain of un 24.5 58 0.0013 27.7 2.2 27 32-66 122-148 (150)
3 PF03521 Kv2channel: Kv2 volta 12.4 2.5E+02 0.0053 26.3 3.4 41 9-50 19-73 (288)
4 KOG0303 Actin-binding protein 12.1 93 0.002 30.7 0.7 21 35-55 308-339 (472)
5 KOG2929 Transcription factor, 10.2 1.8E+02 0.004 27.8 1.9 30 24-53 287-316 (348)
6 KOG0493 Transcription factor E 10.1 2.3E+02 0.0049 26.9 2.4 33 19-51 228-262 (342)
7 PF15054 DUF4535: Domain of un 9.8 1.1E+02 0.0023 21.3 0.2 14 144-157 12-25 (46)
8 PF10243 MIP-T3: Microtubule-b 8.8 1.1E+02 0.0025 29.2 0.0 41 36-83 426-466 (539)
9 PF15050 SCIMP: SCIMP protein 7.4 3.3E+02 0.0072 23.0 2.1 54 25-89 36-90 (133)
10 PF07593 UnbV_ASPIC: ASPIC and 7.2 2E+02 0.0043 20.2 0.6 24 112-144 32-55 (71)
No 1
>PF08744 NOZZLE: Plant transcription factor NOZZLE; InterPro: IPR014855 NOZZLE is a transcription factor that plays a role in patterning the proximal-distal and adaxial-abaxial axes [, ].
Probab=99.14 E-value=1.3e-11 Score=110.50 Aligned_cols=40 Identities=38% Similarity=0.555 Sum_probs=33.5
Q ss_pred CCCCcccCCCCCCCCCCCCCCCcchhhhhhhhhccccccc
Q 028724 20 SSSSSRKGKKSNSDKPKQPQRGLGVAQLEKIRLHGQMACN 59 (205)
Q Consensus 20 ~~~s~r~~kk~~~~k~kqpqRGlGVAqLEkiRl~~~~~~~ 59 (205)
+.|+++..||.+..+||+|||||||||||+||||||++..
T Consensus 42 sr~Rkp~sk~~q~~QKk~~qRGmGVAQLErlRieE~~K~~ 81 (314)
T PF08744_consen 42 SRGRKPGSKKCQQKQKKPPQRGMGVAQLERLRIEEEKKKI 81 (314)
T ss_pred ccccCCccccchhcccCCccccccHHHHHHHHHHHHHhhh
Confidence 3455666666677899999999999999999999998765
No 2
>PF15442 DUF4629: Domain of unknown function (DUF4629)
Probab=24.49 E-value=58 Score=27.70 Aligned_cols=27 Identities=30% Similarity=0.648 Sum_probs=20.2
Q ss_pred CCCCCCCCCCcchhhhhhhhhcccccccccCCCCC
Q 028724 32 SDKPKQPQRGLGVAQLEKIRLHGQMACNNYHPITN 66 (205)
Q Consensus 32 ~~k~kqpqRGlGVAqLEkiRl~~~~~~~~~~Pl~~ 66 (205)
++-=|.|.-.||+-.||..- -|||||.
T Consensus 122 Qe~FKkPRs~LgMHMLeSVQ--------VFH~LGK 148 (150)
T PF15442_consen 122 QESFKKPRSCLGMHMLESVQ--------VFHPLGK 148 (150)
T ss_pred cccccCcccccchHHHHhHH--------hhhhccc
Confidence 34446688899999999864 4899875
No 3
>PF03521 Kv2channel: Kv2 voltage-gated K+ channel; InterPro: IPR003973 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. The Kv family can be divided into several subfamilies on the basis of sequence similarity and function. Four of these subfamilies, Kv1 (Shaker), Kv2 (Shab), Kv3 (Shaw) and Kv4 (Shal), consist of pore-forming alpha subunits that associate with different types of beta subunit. Each alpha subunit comprises six hydrophobic TM domains with a P-domain between the fifth and sixth, which partially resides in the membrane. The fourth TM domain has positively charged residues at every third residue and acts as a voltage sensor, which triggers the conformational change that opens the channel pore in response to a displacement in membrane potential []. More recently, 4 new electrically-silent alpha subunits have been cloned: Kv5 (KCNF), Kv6 (KCNG), Kv8 and Kv9 (KCNS). These subunits do not themselves possess any functional activity, but appear to form heteromeric channels with Kv2 subunits, and thus modulate Shab channel activity []. When highly expressed, they inhibit channel activity, but at lower levels show more specific modulatory actions. The Kv2 voltage-dependent potassium channels (also known as the Shab family) are responsible for much of the delayed rectifier current in Drosophila melanogaster (Fruit fly) nervous system and muscle. However, in vertebrates, Kv2 channels have been shwon to be involved in the delayed rectifier currents of the heart and skeletal muscles. They are also thought to be important in determining intrinsic neuronal excitability in both mammals and non-mammals []. Kv2 channels can be further divided into 2 subtypes, designated Kv2.1 and Kv2.2. This entry represents the voltage-dependent Kv2 potassium channels.; GO: 0005249 voltage-gated potassium channel activity, 0006813 potassium ion transport, 0008076 voltage-gated potassium channel complex
Probab=12.38 E-value=2.5e+02 Score=26.35 Aligned_cols=41 Identities=24% Similarity=0.400 Sum_probs=26.8
Q ss_pred CC-CCCCCCCCCCCCCcccCCCCCCCCC-------------CCCCCCcchhhhhhh
Q 028724 9 PN-LGNERGSSSSSSSSRKGKKSNSDKP-------------KQPQRGLGVAQLEKI 50 (205)
Q Consensus 9 ~~-~gn~~~~~s~~~s~r~~kk~~~~k~-------------kqpqRGlGVAqLEki 50 (205)
|+ ||...|..|.+++.|.=.++.+.-+ --||+ |-|-+||.+
T Consensus 19 PsRWk~~kr~~SetSs~KSfd~k~~~s~~~~s~~~~~~~~ssSPQH-LnaQkLEeM 73 (288)
T PF03521_consen 19 PSRWKWSKRALSETSSNKSFDTKYQESPQKSSHEQVNARSSSSPQH-LNAQKLEEM 73 (288)
T ss_pred cccCCCccccccccccCCCccccCCCCccccccccccccCCCCccc-ccHHHHHHH
Confidence 44 8888887777776666654433222 23554 899999974
No 4
>KOG0303 consensus Actin-binding protein Coronin, contains WD40 repeats [Cytoskeleton]
Probab=12.10 E-value=93 Score=30.73 Aligned_cols=21 Identities=52% Similarity=0.903 Sum_probs=12.2
Q ss_pred CCCCCCCcc--------hhhhhhhh---hccc
Q 028724 35 PKQPQRGLG--------VAQLEKIR---LHGQ 55 (205)
Q Consensus 35 ~kqpqRGlG--------VAqLEkiR---l~~~ 55 (205)
-|.||||+| |..-|..| |++.
T Consensus 308 S~epQRG~g~mPKRGl~Vs~cEI~rfyKl~~~ 339 (472)
T KOG0303|consen 308 SKEPQRGMGFMPKRGLDVSKCEIARFYKLHER 339 (472)
T ss_pred cCCccccccccccccccchHHHHHHHHHhhcc
Confidence 456666666 55666655 4555
No 5
>KOG2929 consensus Transcription factor, component of CCR4 transcriptional complex [Transcription]
Probab=10.20 E-value=1.8e+02 Score=27.80 Aligned_cols=30 Identities=33% Similarity=0.545 Sum_probs=23.7
Q ss_pred cccCCCCCCCCCCCCCCCcchhhhhhhhhc
Q 028724 24 SRKGKKSNSDKPKQPQRGLGVAQLEKIRLH 53 (205)
Q Consensus 24 ~r~~kk~~~~k~kqpqRGlGVAqLEkiRl~ 53 (205)
+++|+|-+.--.-+--||||+-+||+++.|
T Consensus 287 ~~~g~kvG~~~~~~g~~glgllr~e~~~~~ 316 (348)
T KOG2929|consen 287 KKKGRKVGRVISGEGLRGLGLLRLEKFKAQ 316 (348)
T ss_pred cccCceeeeeeccCcceeeeeeehhhhhcc
Confidence 566666655556677899999999999988
No 6
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=10.13 E-value=2.3e+02 Score=26.92 Aligned_cols=33 Identities=33% Similarity=0.541 Sum_probs=23.9
Q ss_pred CCCCCcccCCCCC--CCCCCCCCCCcchhhhhhhh
Q 028724 19 SSSSSSRKGKKSN--SDKPKQPQRGLGVAQLEKIR 51 (205)
Q Consensus 19 s~~~s~r~~kk~~--~~k~kqpqRGlGVAqLEkiR 51 (205)
|++-+.||.||++ .+..|.|.--+--.||.+|.
T Consensus 228 SsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK 262 (342)
T KOG0493|consen 228 SSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLK 262 (342)
T ss_pred CCCcccccccccCCccchhcCccccccHHHHHHHH
Confidence 3455677777654 56678888899999998554
No 7
>PF15054 DUF4535: Domain of unknown function (DUF4535)
Probab=9.79 E-value=1.1e+02 Score=21.33 Aligned_cols=14 Identities=43% Similarity=0.722 Sum_probs=12.7
Q ss_pred CccccccccCCCcc
Q 028724 144 TGISETQHFTQPNM 157 (205)
Q Consensus 144 ~~I~~~~h~~~pn~ 157 (205)
.|||-||+|.-||+
T Consensus 12 ~GiY~AQNY~VPnv 25 (46)
T PF15054_consen 12 TGIYVAQNYEVPNV 25 (46)
T ss_pred EEEEeeecccCCch
Confidence 48999999999998
No 8
>PF10243 MIP-T3: Microtubule-binding protein MIP-T3; InterPro: IPR018799 This entry represents a protein which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), and is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved []. ; PDB: 2EQO_A.
Probab=8.80 E-value=1.1e+02 Score=29.15 Aligned_cols=41 Identities=24% Similarity=0.408 Sum_probs=0.0
Q ss_pred CCCCCCcchhhhhhhhhcccccccccCCCCCCCCCCCCCCCCcccccc
Q 028724 36 KQPQRGLGVAQLEKIRLHGQMACNNYHPITNSFHTPYPTTNFNQEDMR 83 (205)
Q Consensus 36 kqpqRGlGVAqLEkiRl~~~~~~~~~~Pl~~p~~~~~pt~~~n~eD~r 83 (205)
..-.|.+.+.++++||-.=|.-|..-+|||.-+ .|-|||+-
T Consensus 426 ~~~~~~~~~~ei~~lr~~iQ~l~~s~~PLgk~~-------d~iqEDid 466 (539)
T PF10243_consen 426 SKKERESVEKEIEKLRESIQTLCRSANPLGKLM-------DYIQEDID 466 (539)
T ss_dssp ------------------------------------------------
T ss_pred hhccchhHHHHHHHHHHHHHHHHHhcchHHHHH-------HHHHhHHH
Confidence 355688999999999999999998889999853 55588854
No 9
>PF15050 SCIMP: SCIMP protein
Probab=7.39 E-value=3.3e+02 Score=22.97 Aligned_cols=54 Identities=31% Similarity=0.247 Sum_probs=25.3
Q ss_pred ccCCCCCCCCC-CCCCCCcchhhhhhhhhcccccccccCCCCCCCCCCCCCCCCccccccccCCCC
Q 028724 25 RKGKKSNSDKP-KQPQRGLGVAQLEKIRLHGQMACNNYHPITNSFHTPYPTTNFNQEDMRVQTPYS 89 (205)
Q Consensus 25 r~~kk~~~~k~-kqpqRGlGVAqLEkiRl~~~~~~~~~~Pl~~p~~~~~pt~~~n~eD~r~q~~~s 89 (205)
|+|||-+-.|+ ||.|| =+|+|-++-.+----++|.-+|-+.+-+||.--|..++
T Consensus 36 RqGkkweiakp~k~~~r-----------deEkmYENv~n~~~~~LPpLPPRg~~s~~~~spqetPs 90 (133)
T PF15050_consen 36 RQGKKWEIAKPLKQKQR-----------DEEKMYENVLNQSPVQLPPLPPRGSPSPEDSSPQETPS 90 (133)
T ss_pred Hccccceeccchhhhcc-----------cHHHHHHHhhcCCcCCCCCCCCCCCCCccccCcccCCC
Confidence 67777755544 44443 34445443222111122222344455577765554444
No 10
>PF07593 UnbV_ASPIC: ASPIC and UnbV; InterPro: IPR011519 This conserved sequence is found associated with IPR001440 from INTERPRO in several paralogous proteins in Rhodopirellula baltica. It is also found associated with IPR000413 from INTERPRO in several eukaryotic integrin-like proteins (e.g. human ASPIC Q9NQ78 from SWISSPROT) and in several other bacterial proteins (e.g. Q84HN1 from SWISSPROT) [].
Probab=7.22 E-value=2e+02 Score=20.19 Aligned_cols=24 Identities=25% Similarity=0.559 Sum_probs=15.3
Q ss_pred CCccccCCcccccceeeCCCCCCccccccCCCC
Q 028724 112 PSITMGLGDYERSTIIYGDSQPTTTATSWNPVT 144 (205)
Q Consensus 112 P~~~mg~~~Y~rtnIryGd~qp~~~~~sw~~s~ 144 (205)
|-++||+|.-. ....+.+.||.+.
T Consensus 32 ~~lhFGLG~~~---------~v~~v~V~WP~G~ 55 (71)
T PF07593_consen 32 PRLHFGLGDAT---------SVDSVEVRWPDGK 55 (71)
T ss_pred CCEEEECCCCC---------CEEEEEEECCCCC
Confidence 56788998722 2244566998644
Done!