Query psy1250
Match_columns 111
No_of_seqs 112 out of 636
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 20:53:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1250.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1250hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3589|consensus 99.8 3.9E-20 8.5E-25 138.5 8.5 85 6-90 117-205 (221)
2 smart00315 RGS Regulator of G 99.8 2.4E-18 5.2E-23 114.4 7.4 79 6-84 38-118 (118)
3 PF00615 RGS: Regulator of G p 99.7 1E-16 2.2E-21 105.5 7.4 79 6-84 38-118 (118)
4 KOG3590|consensus 99.0 3.6E-10 7.9E-15 92.2 3.1 70 17-86 235-308 (602)
5 KOG3590|consensus 98.9 3.7E-09 8.1E-14 86.4 6.5 94 4-97 359-455 (602)
6 PF09128 RGS-like: Regulator o 97.2 0.001 2.2E-08 49.4 5.8 62 7-68 44-110 (188)
7 KOG0986|consensus 93.8 0.21 4.6E-06 42.3 6.3 80 9-88 93-175 (591)
8 PF02184 HAT: HAT (Half-A-TPR) 57.2 8.8 0.00019 20.6 1.6 14 16-29 4-17 (32)
9 PF11946 DUF3463: Domain of un 47.4 24 0.00052 25.1 2.9 27 61-88 29-55 (138)
10 COG1381 RecO Recombinational D 28.7 1.6E+02 0.0034 22.4 5.1 46 50-95 110-155 (251)
11 PRK13740 conjugal transfer pro 27.7 1.6E+02 0.0035 18.5 4.1 53 33-87 15-67 (70)
12 PF10384 Scm3: Centromere prot 27.2 21 0.00046 21.6 0.0 31 6-36 6-39 (58)
13 PF10537 WAC_Acf1_DNA_bd: ATP- 27.1 1.3E+02 0.0028 20.0 3.9 38 36-73 61-98 (102)
14 PF07425 Pardaxin: Pardaxin; 26.8 8.8 0.00019 20.3 -1.5 24 72-95 6-29 (33)
15 PF08594 UPF0300: Uncharacteri 24.5 41 0.00089 25.6 1.2 29 60-88 25-53 (215)
16 PF12645 HTH_16: Helix-turn-he 24.2 1.5E+02 0.0032 18.0 3.5 32 17-48 17-57 (65)
17 PF01706 FliG_C: FliG C-termin 21.3 2.4E+02 0.0052 18.4 4.3 34 35-68 63-99 (110)
No 1
>KOG3589|consensus
Probab=99.82 E-value=3.9e-20 Score=138.48 Aligned_cols=85 Identities=35% Similarity=0.603 Sum_probs=79.4
Q ss_pred ccCCCh--hhHHHHHHHhHHHHhCCCCCccccCCHHHHHHHHHHhcCCC--hHHHHHHHHHHHHHHhhCccccccccHHH
Q psy1250 6 KRAGRR--GNVQSSKRRAARPYINTKQSFKVSLDSRVREIVNRNMVSPS--NHTFDEAQLQIYTLMHRDSYPRFINSTVY 81 (111)
Q Consensus 6 kk~~~~--~~l~~~A~~Iy~~yi~~~a~~eVNI~~~~r~~i~~~l~~p~--~~~Fd~AQ~~I~~lMe~D~yprFl~S~~Y 81 (111)
|+...+ ..+...|+.||++||.++||.+||||..+|..+.++|..|+ +++||.||.+||.||+.|+|||||+|+.|
T Consensus 117 k~~~~~~~~~~~~~a~~i~~~f~~~~ap~~vn~d~~tre~~~~~l~~p~~~~~~f~~Aq~~i~~lm~~dsy~RFl~s~~y 196 (221)
T KOG3589|consen 117 KKRRSEKSTKMSEKAKEIYEEFSAPAAPKEVNLDSKTRELTNRNLSEPSGQRTCFDEAQKHVYTLMEKDSYPRFLRSPLY 196 (221)
T ss_pred HhCcCchhhhhhHHHHHHHHHHhccCCCCCCCCchHHHHHHHHHhcCCCCCCCcHHHHHHHHHHhcccCCCccccCCHHH
Confidence 555555 77999999999999999999999999999999999999998 99999999999999999999999999999
Q ss_pred HHHHHhcCC
Q psy1250 82 KQLAQLDSS 90 (111)
Q Consensus 82 ~~~l~~~~~ 90 (111)
++++...+.
T Consensus 197 ~~l~~~~~~ 205 (221)
T KOG3589|consen 197 LDLLKQPKK 205 (221)
T ss_pred HHHHHHhhc
Confidence 999997765
No 2
>smart00315 RGS Regulator of G protein signalling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
Probab=99.76 E-value=2.4e-18 Score=114.38 Aligned_cols=79 Identities=33% Similarity=0.585 Sum_probs=73.0
Q ss_pred ccCCChhhHHHHHHHhHHHHhCCCCCccccCCHHHHHHHHHHhcC--CChHHHHHHHHHHHHHHhhCccccccccHHHHH
Q psy1250 6 KRAGRRGNVQSSKRRAARPYINTKQSFKVSLDSRVREIVNRNMVS--PSNHTFDEAQLQIYTLMHRDSYPRFINSTVYKQ 83 (111)
Q Consensus 6 kk~~~~~~l~~~A~~Iy~~yi~~~a~~eVNI~~~~r~~i~~~l~~--p~~~~Fd~AQ~~I~~lMe~D~yprFl~S~~Y~~ 83 (111)
|+.....++...|+.||++||.++|+.+|||+..+|+.|...+.. +++++|+.||.+|+.+|+.|.||+|++|+.|.+
T Consensus 38 ~~~~~~~~~~~~a~~I~~~yi~~~s~~~~ni~~~~~~~i~~~~~~~~~~~~~F~~~~~~v~~~l~~~~~~~F~~S~~y~~ 117 (118)
T smart00315 38 KKAEDDEERIAKAREIYDKFLSPNAPKEVNLDSDLREKIEENLESEEPPPDLFDEAQEEVYELLEKDSFPRFLESDYYLR 117 (118)
T ss_pred HhcCCHHHHHHHHHHHHHHHhCCCCCCceeCCHHHHHHHHHHHhcCCCChHHHHHHHHHHHHHHhcCchHHHhCCHhhcc
Confidence 555566789999999999999999999999999999999999975 899999999999999999999999999999976
Q ss_pred H
Q psy1250 84 L 84 (111)
Q Consensus 84 ~ 84 (111)
+
T Consensus 118 ~ 118 (118)
T smart00315 118 F 118 (118)
T ss_pred C
Confidence 3
No 3
>PF00615 RGS: Regulator of G protein signaling domain; InterPro: IPR000342 RGS (Regulator of G Protein Signalling) proteins are multi-functional, GTPase-accelerating proteins that promote GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways []. Upon activation by GPCRs, heterotrimeric G proteins exchange GDP for GTP, are released from the receptor, and dissociate into free, active GTP-bound alpha subunit and beta-gamma dimer, both of which activate downstream effectors. The response is terminated upon GTP hydrolysis by the alpha subunit (IPR001019 from INTERPRO), which can then bind the beta-gamma dimer (IPR001632 from INTERPRO, IPR001770 from INTERPRO) and the receptor. RGS proteins markedly reduce the lifespan of GTP-bound alpha subunits by stabilising the G protein transition state. All RGS proteins contain an 'RGS-box' (or RGS domain), which is required for activity. Some small RGS proteins such as RGS1 and RGS4 are comprised of little more than an RGS domain, while others also contain additional domains that confer further functionality []. RGS domains can be found in conjunction with a variety of domains, including: DEP for membrane targeting (IPR000591 from INTERPRO), PDZ for binding to GPCRs (IPR001478 from INTERPRO), PTB for phosphotyrosine-binding (IPR006020 from INTERPRO), RBD for Ras-binding (IPR003116 from INTERPRO), GoLoco for guanine nucleotide inhibitor activity (IPR003109 from INTERPRO), PX for phosphatidylinositol-binding (IPR001683 from INTERPRO), PXA that is associated with PX (IPR003114 from INTERPRO), PH for stimulating guanine nucleotide exchange (IPR001849 from INTERPRO), and GGL (G protein gamma subunit-like) for binding G protein beta subunits (IPR001770 from INTERPRO) []. Those RGS proteins that contain GGL domains can interact with G protein beta subunits to form novel dimers that prevent G protein gamma subunit binding and G protein alpha subunit association, thereby preventing heterotrimer formation.; GO: 0004871 signal transducer activity; PDB: 2BCJ_A 3PSC_A 3PVU_A 1YM7_B 3PVW_A 1OMW_A 2EBZ_A 2BV1_B 2GTP_D 1CMZ_A ....
Probab=99.69 E-value=1e-16 Score=105.50 Aligned_cols=79 Identities=25% Similarity=0.494 Sum_probs=73.8
Q ss_pred ccCCChhhHHHHHHHhHHHHhCCCCCccccCCHHHHHHHHHHhcC--CChHHHHHHHHHHHHHHhhCccccccccHHHHH
Q psy1250 6 KRAGRRGNVQSSKRRAARPYINTKQSFKVSLDSRVREIVNRNMVS--PSNHTFDEAQLQIYTLMHRDSYPRFINSTVYKQ 83 (111)
Q Consensus 6 kk~~~~~~l~~~A~~Iy~~yi~~~a~~eVNI~~~~r~~i~~~l~~--p~~~~Fd~AQ~~I~~lMe~D~yprFl~S~~Y~~ 83 (111)
++..+...+...|..||++||.++|+.+|||+..+++.+...+.. +.+++|+.||.+|+..|+.+.||+|++|+.|.+
T Consensus 38 ~~~~~~~~~~~~a~~I~~~fi~~~s~~~l~i~~~~~~~~~~~~~~~~~~~~~f~~a~~~v~~~L~~~~~~~F~~S~~y~~ 117 (118)
T PF00615_consen 38 KSSESEEQRKKLAQQIYNKFISPGSPNELNIPSKIRKEVQDALENAPPSPDLFDEAQEEVYEMLEEDWFPKFLKSEEYKQ 117 (118)
T ss_dssp HTSCSHHHHHHHHHHHHHHHTSTTSTTCCSSTHHHHHHHHHHHTSTSTTTTTTHHHHHHHHHHHHHTHHHHHHTSHHHHH
T ss_pred HhhcchhhHHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhhchHHhHccCHhhhc
Confidence 445567788899999999999999999999999999999999986 899999999999999999999999999999997
Q ss_pred H
Q psy1250 84 L 84 (111)
Q Consensus 84 ~ 84 (111)
+
T Consensus 118 ~ 118 (118)
T PF00615_consen 118 F 118 (118)
T ss_dssp H
T ss_pred C
Confidence 5
No 4
>KOG3590|consensus
Probab=98.96 E-value=3.6e-10 Score=92.20 Aligned_cols=70 Identities=17% Similarity=0.336 Sum_probs=64.9
Q ss_pred HHHHhHHHHhCCCCCccccCCHHHHHHHHHHhc----CCChHHHHHHHHHHHHHHhhCccccccccHHHHHHHH
Q psy1250 17 SKRRAARPYINTKQSFKVSLDSRVREIVNRNMV----SPSNHTFDEAQLQIYTLMHRDSYPRFINSTVYKQLAQ 86 (111)
Q Consensus 17 ~A~~Iy~~yi~~~a~~eVNI~~~~r~~i~~~l~----~p~~~~Fd~AQ~~I~~lMe~D~yprFl~S~~Y~~~l~ 86 (111)
.|..||.+||.++|..+|-|+..+|..|...|+ ..++.|||+||..|+..||.|+|..||+|..|-.|.-
T Consensus 235 dai~~~~ky~~~~a~~~i~~~~~~~~~i~~~~cg~d~~i~~~CFDEAq~~v~~~~e~Dhf~~fl~s~h~~~y~L 308 (602)
T KOG3590|consen 235 DAVNTFTKYISPDAAKPIPITEAMRNDIIARICGEDGQVDPNCFDEAQSIVFSAMEQDHFSEFLRSHHFCKYQL 308 (602)
T ss_pred hhhhhhhhhcccccccCccchHHHHhhHHHHHhccCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhccccceee
Confidence 599999999999999999999999999999997 3589999999999999999999999999999876543
No 5
>KOG3590|consensus
Probab=98.89 E-value=3.7e-09 Score=86.38 Aligned_cols=94 Identities=16% Similarity=0.203 Sum_probs=82.5
Q ss_pred ccccCCChhhHHHHHHHhHHHHhCCCCCccccCCHHHHHHHHHHhc---CCChHHHHHHHHHHHHHHhhCccccccccHH
Q psy1250 4 CTKRAGRRGNVQSSKRRAARPYINTKQSFKVSLDSRVREIVNRNMV---SPSNHTFDEAQLQIYTLMHRDSYPRFINSTV 80 (111)
Q Consensus 4 ~~kk~~~~~~l~~~A~~Iy~~yi~~~a~~eVNI~~~~r~~i~~~l~---~p~~~~Fd~AQ~~I~~lMe~D~yprFl~S~~ 80 (111)
|.-..-++++-+..|..||++|++-.|.+.+.++..+|-+|+.+|+ .|.+..|+.|...-+..|+..+++.||+|.+
T Consensus 359 ~~E~~~d~~eAq~DAMilYdKYFSlQat~~l~~~~~~RlevEs~IC~e~gp~~~AF~tAl~~~~~~Le~KYl~DFLKs~~ 438 (602)
T KOG3590|consen 359 AKEGQYDGQEAQNDAMILYDKYFSLQATHPLGFDDVVRLEIESNICREGGPLPNAFTTALRQAWTTLEKKYLPDFLKSNL 438 (602)
T ss_pred hcccccchhhhhcchhHHHHHHhhhhccCccchhHHHHHHHHHHhccCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4433456778888999999999999999999999999999999998 4678999999999999999999999999999
Q ss_pred HHHHHHhcCCCCCCCCC
Q psy1250 81 YKQLAQLDSSPGDTGGN 97 (111)
Q Consensus 81 Y~~~l~~~~~~~~~~~~ 97 (111)
|.+|+...+...++.++
T Consensus 439 y~NYlnEL~~~~~~~~f 455 (602)
T KOG3590|consen 439 YYNYLNELIHSVRGDEF 455 (602)
T ss_pred HHHHHHHHHhhccCCcc
Confidence 99999977665555444
No 6
>PF09128 RGS-like: Regulator of G protein signalling-like domain; InterPro: IPR015212 This entry represents a domain consisting of twelve helices that fold into a compact structure that contains the overall structural scaffold observed in other regulator of G protein signalling (RGS) proteins and three additional helical elements that pack closely to it. Helices 1-9 comprise the RGS fold, in which helices 4-7 form a classic antiparallel bundle adjacent to the other helices. Like other RGS structures, helices 7 and 8 span the length of the folded domain and form essentially one continuous helix with a kink in the middle. Helices 10-12 form an apparently stable C-terminal extension of the structural domain, and although other RGS proteins lack this structure, these elements are intimately associated with the rest of the structural framework by hydrophobic interactions. This domain binds to active G-alpha proteins, promoting GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways []. ; GO: 0005089 Rho guanyl-nucleotide exchange factor activity, 0005737 cytoplasm; PDB: 3CX6_B 3CX8_B 3CX7_B 1HTJ_F 1SHZ_C 3AB3_D 1IAP_A.
Probab=97.20 E-value=0.001 Score=49.39 Aligned_cols=62 Identities=13% Similarity=0.266 Sum_probs=43.1
Q ss_pred cCCChhhHHHHHHHhHHHHhCCCCCccccCCHHHHHHHHHH----hc-CCChHHHHHHHHHHHHHHh
Q psy1250 7 RAGRRGNVQSSKRRAARPYINTKQSFKVSLDSRVREIVNRN----MV-SPSNHTFDEAQLQIYTLMH 68 (111)
Q Consensus 7 k~~~~~~l~~~A~~Iy~~yi~~~a~~eVNI~~~~r~~i~~~----l~-~p~~~~Fd~AQ~~I~~lMe 68 (111)
+..+.++++..|.+||.+||.++||..|++|..+...|... +. ..-..+|..||+.+..-+.
T Consensus 44 k~~~~Ke~rk~~~ei~stFL~~~ApL~v~v~~~v~~ei~~~~~~~~~~e~~r~~f~~~~~~a~~eI~ 110 (188)
T PF09128_consen 44 KQGNAKEMRKWAYEIHSTFLDPGAPLRVNVPESVASEIDRTRPELIKEEILRQIFQEAQQRALPEIQ 110 (188)
T ss_dssp TTS-TTCHHHHHHHHHHHHTSTT-TT-----HHHHHHHTT-HHHHCTTHCHHHHHHHHHHHHHHHHH
T ss_pred hccCHHHHHHHHHHHHHHHcCCCCCceecCCHHHHHhHHhhccccCcHHHHHHHHHHHHHHHHHHHH
Confidence 34777889999999999999999999999999999999422 11 2456889988888776664
No 7
>KOG0986|consensus
Probab=93.77 E-value=0.21 Score=42.26 Aligned_cols=80 Identities=13% Similarity=0.270 Sum_probs=61.9
Q ss_pred CChhhHHHHHHHhHHHHhCCCCCcc-ccCC-HHHHHHHHHHhc-CCChHHHHHHHHHHHHHHhhCccccccccHHHHHHH
Q psy1250 9 GRRGNVQSSKRRAARPYINTKQSFK-VSLD-SRVREIVNRNMV-SPSNHTFDEAQLQIYTLMHRDSYPRFINSTVYKQLA 85 (111)
Q Consensus 9 ~~~~~l~~~A~~Iy~~yi~~~a~~e-VNI~-~~~r~~i~~~l~-~p~~~~Fd~AQ~~I~~lMe~D~yprFl~S~~Y~~~l 85 (111)
.+.++....++.|++.||....+-. -+.+ ..+...+...+. .|.+++|..--+.+-..|..+.|..|+.|..|..++
T Consensus 93 ~~~~~r~~~~~~i~~~~l~~~~~~~~~~~s~~~~v~~~~~~l~~~~~~~lf~~~~~~~~~~L~~~pF~~f~~S~yf~rFl 172 (591)
T KOG0986|consen 93 ADDDERKDKARQILDAYLMKELLACLPQFSSKDLVTHVQEHLLEKPPKDLFQPLARAICAYLRGDPFQEFLESDYFTRFL 172 (591)
T ss_pred CCcccchhhHHHHHHHHhhccccccCCCcchhhhhHHHhhhccccCchhhhHHHHHHHHHHhccchHhHhHHHHHHHHHH
Confidence 3455677899999999998665322 2233 455556666664 579999999999999999999999999999999998
Q ss_pred Hhc
Q psy1250 86 QLD 88 (111)
Q Consensus 86 ~~~ 88 (111)
++.
T Consensus 173 QWK 175 (591)
T KOG0986|consen 173 QWK 175 (591)
T ss_pred HHH
Confidence 854
No 8
>PF02184 HAT: HAT (Half-A-TPR) repeat; InterPro: IPR003107 The HAT (Half A TPR) repeat has a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs (tetratricopeptide repeats), though they lack the highly conserved alanine and glycine residues found in TPRs. The number of HAT repeats found in different proteins varies between 9 and 12. HAT-repeat-containing proteins appear to be components of macromolecular complexes that are required for RNA processing []. The repeats may be involved in protein-protein interactions. The HAT motif has striking structural similarities to HEAT repeats (IPR000357 from INTERPRO), being of a similar length and consisting of two short helices connected by a loop domain, as in HEAT repeats.; GO: 0006396 RNA processing, 0005622 intracellular
Probab=57.16 E-value=8.8 Score=20.62 Aligned_cols=14 Identities=7% Similarity=0.161 Sum_probs=11.4
Q ss_pred HHHHHhHHHHhCCC
Q psy1250 16 SSKRRAARPYINTK 29 (111)
Q Consensus 16 ~~A~~Iy~~yi~~~ 29 (111)
.+|+.||+.||.-.
T Consensus 4 dRAR~IyeR~v~~h 17 (32)
T PF02184_consen 4 DRARSIYERFVLVH 17 (32)
T ss_pred HHHHHHHHHHHHhC
Confidence 47999999998643
No 9
>PF11946 DUF3463: Domain of unknown function (DUF3463); InterPro: IPR022563 This functionally uncharacterised domain is found in bacteria and archaea, which is about 140 amino acids in length and is found C-terminal to PF04055 from PFAM. It contains two conserved sequence motifs: CTPWG and PCYL. This domain is associated with hopanoid biosynthesis associated radical SAM proteins.
Probab=47.41 E-value=24 Score=25.09 Aligned_cols=27 Identities=15% Similarity=0.310 Sum_probs=20.5
Q ss_pred HHHHHHHhhCccccccccHHHHHHHHhc
Q psy1250 61 LQIYTLMHRDSYPRFINSTVYKQLAQLD 88 (111)
Q Consensus 61 ~~I~~lMe~D~yprFl~S~~Y~~~l~~~ 88 (111)
+.|+..+....|+ |..|++|.++|...
T Consensus 29 r~i~~~~~~k~w~-f~~SplyLdfL~G~ 55 (138)
T PF11946_consen 29 RKIFAKGKKKKWR-FNHSPLYLDFLAGN 55 (138)
T ss_pred HHHHHhcccCCcc-ccCCHHHHHHHcCC
Confidence 3455456667787 99999999999753
No 10
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=28.72 E-value=1.6e+02 Score=22.39 Aligned_cols=46 Identities=11% Similarity=0.050 Sum_probs=38.1
Q ss_pred CCChHHHHHHHHHHHHHHhhCccccccccHHHHHHHHhcCCCCCCC
Q psy1250 50 SPSNHTFDEAQLQIYTLMHRDSYPRFINSTVYKQLAQLDSSPGDTG 95 (111)
Q Consensus 50 ~p~~~~Fd~AQ~~I~~lMe~D~yprFl~S~~Y~~~l~~~~~~~~~~ 95 (111)
+++|.+|...+..+..++....-|.++-.-+..++|...|...+..
T Consensus 110 ~~~p~Lf~~~~~~L~~l~~~~~~~~~~l~~fel~lL~~~G~~~~l~ 155 (251)
T COG1381 110 DPNPELFELYLETLEYLLSDGNDPELLLRRFELKLLGELGIGPNLT 155 (251)
T ss_pred CCChHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHcCCccchH
Confidence 5899999999999999998888888888888889998888654443
No 11
>PRK13740 conjugal transfer protein TraY; Provisional
Probab=27.66 E-value=1.6e+02 Score=18.53 Aligned_cols=53 Identities=17% Similarity=0.375 Sum_probs=33.7
Q ss_pred cccCCHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhhCccccccccHHHHHHHHh
Q psy1250 33 KVSLDSRVREIVNRNMVSPSNHTFDEAQLQIYTLMHRDSYPRFINSTVYKQLAQL 87 (111)
Q Consensus 33 eVNI~~~~r~~i~~~l~~p~~~~Fd~AQ~~I~~lMe~D~yprFl~S~~Y~~~l~~ 87 (111)
-+-+|..+-+.+.+....-...-=.+|+-.+-..| ..||.|-+|+++.+-.+.
T Consensus 15 ~~~Ld~etn~lL~~A~~RSGRSK~~EA~lRL~DHL--~rFpDfy~sei~~e~~~e 67 (70)
T PRK13740 15 SLKLDEDTNNKLIEAKERSGRSKTNEVQIRLRDHL--KRFPDFYNSEIFREVAEE 67 (70)
T ss_pred EEEeCHHHHHHHHHHHHHcCCcccHHHHHHHHHHH--HhCccccchHHhhHhhhc
Confidence 44577777777766654222222345555566556 349999999998876553
No 12
>PF10384 Scm3: Centromere protein Scm3; InterPro: IPR018465 The centromere protein Scm3 is a non-histone component of centromeric chromatin that binds to CenH3-H4 histones, which are required for kinetochore assembly. Scm3 is required for Cse4 localisation and is required for its centromeric association [, ]. The histone H3 variant Cse4 replaces conventional histone H3 in centromeric chromatin and helps direct the assembly of the kinetochore. In addition, Scm3 has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for G2/M progression []. Scm3 is required to maintain kinetochore function throughout the cell cycle. Scm3 contains a nuclear export signal (NES). The N-terminal region of Scm3 is well conserved and functions as the CenH3-interacting domain, while the C-terminal region is variable in size and sometimes consists of DNA binding motifs [].; GO: 0005634 nucleus; PDB: 3R45_C 2YFV_C 2L5A_A.
Probab=27.20 E-value=21 Score=21.56 Aligned_cols=31 Identities=13% Similarity=0.101 Sum_probs=21.4
Q ss_pred ccCCChhhHHHHHHHhHHHHhCC--CCC-ccccC
Q psy1250 6 KRAGRRGNVQSSKRRAARPYINT--KQS-FKVSL 36 (111)
Q Consensus 6 kk~~~~~~l~~~A~~Iy~~yi~~--~a~-~eVNI 36 (111)
++..+...++..+..||++|=.+ ..+ =+|.|
T Consensus 6 ~~~~s~~r~k~~~e~I~~KY~~~d~~~~~DeIDL 39 (58)
T PF10384_consen 6 LRKQSDQRFKSRWESIIEKYGQPDFEDQGDEIDL 39 (58)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCSG-TCCSSEBCTT
T ss_pred HHHHHHHHHHHHHHHHHHHhcCcccCCccceeec
Confidence 34445667899999999999774 322 45555
No 13
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=27.11 E-value=1.3e+02 Score=20.01 Aligned_cols=38 Identities=13% Similarity=0.255 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhhCccc
Q psy1250 36 LDSRVREIVNRNMVSPSNHTFDEAQLQIYTLMHRDSYP 73 (111)
Q Consensus 36 I~~~~r~~i~~~l~~p~~~~Fd~AQ~~I~~lMe~D~yp 73 (111)
+|..++..|...+.-....-+|+--..||..++.+.|+
T Consensus 61 fP~~l~~piL~~v~~s~~~rld~Lv~~v~~~~k~~ff~ 98 (102)
T PF10537_consen 61 FPEELREPILRLVQFSTRSRLDDLVDDVYDFFKDRFFV 98 (102)
T ss_pred CCHHHHHHHHHHHHccccccHHHHHHHHHHHHHHcCcC
Confidence 67788888888876444556888899999999988876
No 14
>PF07425 Pardaxin: Pardaxin; InterPro: IPR009990 This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin []. Pardaxin has also been found to have a shark repellent action [].; GO: 0005576 extracellular region; PDB: 1XC0_A 2KNS_A.
Probab=26.79 E-value=8.8 Score=20.27 Aligned_cols=24 Identities=25% Similarity=0.386 Sum_probs=18.6
Q ss_pred cccccccHHHHHHHHhcCCCCCCC
Q psy1250 72 YPRFINSTVYKQLAQLDSSPGDTG 95 (111)
Q Consensus 72 yprFl~S~~Y~~~l~~~~~~~~~~ 95 (111)
.|..+.|++|+.++..++....++
T Consensus 6 ipkiissplfktllsavgsalsss 29 (33)
T PF07425_consen 6 IPKIISSPLFKTLLSAVGSALSSS 29 (33)
T ss_dssp HHHHCCTTTCHHHHHHHHHHCTTT
T ss_pred hhHHHccHHHHHHHHHHHHHHhcc
Confidence 467789999999999888655433
No 15
>PF08594 UPF0300: Uncharacterised protein family (UPF0300); InterPro: IPR013903 This entry of proteins appear to be specific to Schizosaccharomyces pombe (Fission yeast).
Probab=24.54 E-value=41 Score=25.62 Aligned_cols=29 Identities=28% Similarity=0.526 Sum_probs=23.3
Q ss_pred HHHHHHHHhhCccccccccHHHHHHHHhc
Q psy1250 60 QLQIYTLMHRDSYPRFINSTVYKQLAQLD 88 (111)
Q Consensus 60 Q~~I~~lMe~D~yprFl~S~~Y~~~l~~~ 88 (111)
|--|-++|-.|.||.|++..++.-...-.
T Consensus 25 ~VLiHHvMLYd~Yp~~lq~aLW~AV~~yv 53 (215)
T PF08594_consen 25 QVLIHHVMLYDYYPEFLQEALWKAVEHYV 53 (215)
T ss_pred HHHHHHHHHHHhCcHHHHHHHHHHHHHHH
Confidence 44577999999999999999998655533
No 16
>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein. Some proteins with this domain are annotated as conjugative transposon proteins.
Probab=24.16 E-value=1.5e+02 Score=17.97 Aligned_cols=32 Identities=13% Similarity=0.219 Sum_probs=24.6
Q ss_pred HHHHhHHHHhC---------CCCCccccCCHHHHHHHHHHh
Q psy1250 17 SKRRAARPYIN---------TKQSFKVSLDSRVREIVNRNM 48 (111)
Q Consensus 17 ~A~~Iy~~yi~---------~~a~~eVNI~~~~r~~i~~~l 48 (111)
..-+.|+-||. +.+..-.-+|..+++.+...|
T Consensus 17 ~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kL 57 (65)
T PF12645_consen 17 EILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKL 57 (65)
T ss_pred HHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHH
Confidence 45667888888 666667778888888887765
No 17
>PF01706 FliG_C: FliG C-terminal domain; InterPro: IPR023087 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour []. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour []. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN []. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important []. Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins []. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [, ]. FliG is present in about 25 copies per flagellum. This entry represents the C-terminal domain of FliG, the structure of which is known. This domain functions specifically in motor rotation [].; PDB: 3USY_B 3USW_A 3HJL_A 3AJC_A 1LKV_X 1QC7_B.
Probab=21.32 E-value=2.4e+02 Score=18.39 Aligned_cols=34 Identities=21% Similarity=0.347 Sum_probs=23.6
Q ss_pred cCCHHHHHHHHHHhc---CCChHHHHHHHHHHHHHHh
Q psy1250 35 SLDSRVREIVNRNMV---SPSNHTFDEAQLQIYTLMH 68 (111)
Q Consensus 35 NI~~~~r~~i~~~l~---~p~~~~Fd~AQ~~I~~lMe 68 (111)
|++...++.+.+.+. ..+..-=+.||+.|...++
T Consensus 63 nms~r~a~~l~~e~~~~g~v~~~di~~Aq~~iv~~~r 99 (110)
T PF01706_consen 63 NMSKRAAEMLREEMEALGPVRLSDIEEAQREIVEIVR 99 (110)
T ss_dssp TS-HHHHHHHHHHHHHH-S--HHHHHHHHHHHHHHHH
T ss_pred HcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence 677778877777765 3466777889999887764
Done!