Query psy4528
Match_columns 87
No_of_seqs 52 out of 54
Neff 2.7
Searched_HMMs 46136
Date Fri Aug 16 19:27:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4528.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4528hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3836|consensus 98.5 1E-07 2.2E-12 81.7 4.0 81 3-83 163-283 (605)
2 KOG3836|consensus 97.9 3.9E-06 8.5E-11 72.2 1.7 71 2-80 418-488 (605)
3 PF00010 HLH: Helix-loop-helix 96.6 0.0029 6.2E-08 37.1 3.4 38 8-45 16-54 (55)
4 smart00353 HLH helix loop heli 96.2 0.01 2.2E-07 34.0 3.7 40 8-48 11-50 (53)
5 cd00083 HLH Helix-loop-helix d 94.5 0.077 1.7E-06 30.6 3.7 39 8-47 19-57 (60)
6 KOG0561|consensus 93.3 0.087 1.9E-06 43.8 3.2 39 7-47 74-112 (373)
7 KOG4029|consensus 89.9 0.26 5.7E-06 36.4 2.4 43 7-49 123-165 (228)
8 PF08013 Tagatose_6_P_K: Tagat 69.8 4.2 9.1E-05 34.5 2.7 23 23-45 133-155 (424)
9 PRK15458 tagatose 6-phosphate 61.3 7.8 0.00017 32.9 2.7 22 22-43 132-153 (426)
10 TIGR02810 agaZ_gatZ D-tagatose 57.9 9.3 0.0002 32.4 2.6 22 22-43 128-149 (420)
11 PRK15052 D-tagatose-1,6-bispho 57.3 9.7 0.00021 32.3 2.6 22 22-43 129-150 (421)
12 KOG4447|consensus 55.7 4.6 0.0001 30.8 0.4 41 10-52 95-135 (173)
13 KOG1318|consensus 41.6 22 0.00048 30.0 2.4 40 8-47 248-287 (411)
14 KOG1319|consensus 39.5 33 0.00071 27.2 2.9 39 8-46 77-118 (229)
15 cd08030 LA_like_plant La-motif 36.5 32 0.0007 23.3 2.2 34 10-47 42-75 (90)
16 KOG3960|consensus 36.0 34 0.00073 28.0 2.5 20 26-45 149-168 (284)
17 PF14561 TPR_20: Tetratricopep 34.8 37 0.0008 22.0 2.2 28 9-36 39-66 (90)
18 PF11278 DUF3079: Protein of u 34.4 23 0.0005 22.5 1.1 14 16-29 2-15 (52)
19 PF01858 RB_A: Retinoblastoma- 26.5 30 0.00065 25.6 0.7 37 11-47 9-56 (194)
20 PF08168 NUC205: NUC205 domain 24.6 37 0.00081 20.9 0.8 11 18-28 32-42 (44)
21 COG0587 DnaE DNA polymerase II 22.7 1.1E+02 0.0024 29.0 3.7 39 13-51 456-506 (1139)
22 KOG0595|consensus 20.3 52 0.0011 28.2 1.1 9 9-17 158-166 (429)
No 1
>KOG3836|consensus
Probab=98.49 E-value=1e-07 Score=81.73 Aligned_cols=81 Identities=23% Similarity=0.193 Sum_probs=68.3
Q ss_pred CCCCcchhhhhhhhhccCCCCCCCCCchH-----HHHHHhHHhHHHHHhCCCCCCCCC-C-------------------C
Q psy4528 3 LNEPTIDYGFQRLQKLIPRHPGDPEKLPK-----EIILKRAADLAEALYSMPRNNQLP-L-------------------P 57 (87)
Q Consensus 3 lneptIdygfqrl~K~~pr~pGdpErlpK-----eiiLkRaadl~ealy~~p~n~q~~-l-------------------~ 57 (87)
|++++|||+++|.++.+++|+++||...+ |++++||+|+.++.+++++.+++. + .
T Consensus 163 l~~rlID~~~~~~~it~~~q~knpel~~~l~~tse~~~sR~~d~s~s~~~rn~~~sd~vi~~rff~~F~ls~~~sclk~a 242 (605)
T KOG3836|consen 163 LNVRLIDSGVTKQQITYLGQDKNPELSRSLLCTSESLCSRASDLSKSCRRRNEPNSDSVIKPRFFLAFFLSCLQSCLKNA 242 (605)
T ss_pred ccccccccccccccccccccCCChhhhhhhcccchhhhhhhhhhhHHhhcCCCCCccccchhhhhhhhHhhhchhhhccC
Confidence 78999999999999999999999999999 999999999999999999999993 2 1
Q ss_pred CCCCCC---------------CCCCccccccccccccCCCC
Q psy4528 58 APPRSP---------------HHFNSYTGQLNVTVQENGNG 83 (87)
Q Consensus 58 ~~p~sp---------------~g~nSy~~ql~vsv~e~~~~ 83 (87)
+.||-. +|.|.+..+|+.++.|.+.+
T Consensus 243 gvprd~~~~Q~~i~~~~~v~~~g~n~~~~als~~~~~~s~~ 283 (605)
T KOG3836|consen 243 GVPRDMRRFQVLINGGVEVTLLGANFKDIALSTQCSEESTM 283 (605)
T ss_pred CCccccccccccccccceecccccchhhhhhcccccccccc
Confidence 233322 66777788888888877653
No 2
>KOG3836|consensus
Probab=97.93 E-value=3.9e-06 Score=72.22 Aligned_cols=71 Identities=23% Similarity=0.162 Sum_probs=58.5
Q ss_pred CCCCCcchhhhhhhhhccCCCCCCCCCchHHHHHHhHHhHHHHHhCCCCCCCCCCCCCCCCCCCCCccccccccccccC
Q psy4528 2 SLNEPTIDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSMPRNNQLPLPAPPRSPHHFNSYTGQLNVTVQEN 80 (87)
Q Consensus 2 ~lneptIdygfqrl~K~~pr~pGdpErlpKeiiLkRaadl~ealy~~p~n~q~~l~~~p~sp~g~nSy~~ql~vsv~e~ 80 (87)
++++|.||+.||++++.+|++||||+++.+...+|||+++.+..+-+++.-- |-...+++.+|+.....++
T Consensus 418 ~~~~~~~~d~f~~~p~~~~~~sgdp~~~~~~~~~~~~~~~~~~~~~~~r~~~--------s~~~~~~~~~~~~~~~t~~ 488 (605)
T KOG3836|consen 418 KGAHPNDDDKFGFTPLHIPQISGDPRIIQLLLNCKVAISLKSVNGMIARQVF--------SNYETSLEDGQLTRLLTDT 488 (605)
T ss_pred ccCccchhcccccccccccCCCCCHHHhhhhhhhhhhhhccccccccccccc--------cccccccccchhhhhhccc
Confidence 3689999999999999999999999999999999999999999887754421 3345677777777766653
No 3
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt).; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
Probab=96.64 E-value=0.0029 Score=37.12 Aligned_cols=38 Identities=37% Similarity=0.608 Sum_probs=33.5
Q ss_pred chhhhhhhhhccCCC-CCCCCCchHHHHHHhHHhHHHHH
Q psy4528 8 IDYGFQRLQKLIPRH-PGDPEKLPKEIILKRAADLAEAL 45 (87)
Q Consensus 8 Idygfqrl~K~~pr~-pGdpErlpKeiiLkRaadl~eal 45 (87)
|.=+|+.|..++|.. .+...++.|-.||+.|.++++.|
T Consensus 16 i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~L 54 (55)
T PF00010_consen 16 INDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQL 54 (55)
T ss_dssp HHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHh
Confidence 455899999999996 47779999999999999999876
No 4
>smart00353 HLH helix loop helix domain.
Probab=96.16 E-value=0.01 Score=33.99 Aligned_cols=40 Identities=33% Similarity=0.527 Sum_probs=35.3
Q ss_pred chhhhhhhhhccCCCCCCCCCchHHHHHHhHHhHHHHHhCC
Q psy4528 8 IDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSM 48 (87)
Q Consensus 8 Idygfqrl~K~~pr~pGdpErlpKeiiLkRaadl~ealy~~ 48 (87)
|.-+|..|..++|-.. ...++.|..||..|.++++.|...
T Consensus 11 ~n~~~~~L~~lip~~~-~~~k~~k~~iL~~ai~yi~~L~~~ 50 (53)
T smart00353 11 INEAFDELRSLLPTLP-NNKKLSKAEILRLAIEYIKSLQEE 50 (53)
T ss_pred HHHHHHHHHHHCCCCC-CCCCCCHHHHHHHHHHHHHHHHHH
Confidence 5568999999999776 789999999999999999988753
No 5
>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and
Probab=94.49 E-value=0.077 Score=30.58 Aligned_cols=39 Identities=36% Similarity=0.610 Sum_probs=34.2
Q ss_pred chhhhhhhhhccCCCCCCCCCchHHHHHHhHHhHHHHHhC
Q psy4528 8 IDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYS 47 (87)
Q Consensus 8 Idygfqrl~K~~pr~pGdpErlpKeiiLkRaadl~ealy~ 47 (87)
|.-+|..|..++|-.. ...++.|-.||..|.++++.|..
T Consensus 19 ~n~~~~~L~~llp~~~-~~~k~~k~~iL~~a~~yI~~L~~ 57 (60)
T cd00083 19 INDAFDELRSLLPTLP-PSKKLSKAEILRKAVDYIKSLQE 57 (60)
T ss_pred HHHHHHHHHHHCCCCC-CCCCCCHHHHHHHHHHHHHHHHH
Confidence 4568999999999887 67899999999999999998864
No 6
>KOG0561|consensus
Probab=93.27 E-value=0.087 Score=43.78 Aligned_cols=39 Identities=46% Similarity=0.734 Sum_probs=36.3
Q ss_pred cchhhhhhhhhccCCCCCCCCCchHHHHHHhHHhHHHHHhC
Q psy4528 7 TIDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYS 47 (87)
Q Consensus 7 tIdygfqrl~K~~pr~pGdpErlpKeiiLkRaadl~ealy~ 47 (87)
.|.-|||-|.-++|||-| |+|-|--||++-+|++-.|-+
T Consensus 74 SINAGFqsLr~LlPr~eG--EKLSKAAILQQTa~yI~~Le~ 112 (373)
T KOG0561|consen 74 SINAGFQSLRALLPRKEG--EKLSKAAILQQTADYIHQLEG 112 (373)
T ss_pred hhhHHHHHHHHhcCcccc--hhhHHHHHHHHHHHHHHHHHh
Confidence 478899999999999977 899999999999999999987
No 7
>KOG4029|consensus
Probab=89.91 E-value=0.26 Score=36.44 Aligned_cols=43 Identities=26% Similarity=0.424 Sum_probs=38.8
Q ss_pred cchhhhhhhhhccCCCCCCCCCchHHHHHHhHHhHHHHHhCCC
Q psy4528 7 TIDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSMP 49 (87)
Q Consensus 7 tIdygfqrl~K~~pr~pGdpErlpKeiiLkRaadl~ealy~~p 49 (87)
.+.+||++|.+.+|-+|.-.-+|.|.=+|+=|-.|+.-|..+-
T Consensus 123 ~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL 165 (228)
T KOG4029|consen 123 SVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLL 165 (228)
T ss_pred chhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHh
Confidence 4789999999999999997789999999999999999997643
No 8
>PF08013 Tagatose_6_P_K: Tagatose 6 phosphate kinase; InterPro: IPR012062 Escherichia coli and other enteric bacteria contain two closely related D-tagatose 1,6-bisphosphate (TagBP)-specific aldolases involved in catabolism of galactitol (genes gatY gatZ) and of N-acetyl-galactosamine and D-galactosamine (genes kbaY, kbaZ, also called agaY, agaZ). The catalytic subunits GatY/KbaY alone are sufficient to show aldolase activity and contain most or all of the residues that have been identified as essential in substrate/product recognition and catalysis for class II aldolases [, ]. However, these aldolases differ from other Class II aldolases (which are homodimeric enzymes) in that they require subunits GatZ/KbaZ for full activity and for good in vivo and in vitro stability. The Z subunits alone do not show any aldolase activity []. It should be noted that the previous suggestion of a tagatose 6P-kinase function for AgaZ [] and other members of this family turned out to be erroneous [, ].; GO: 0019402 galactitol metabolic process; PDB: 2FIQ_A 3TXV_A.
Probab=69.79 E-value=4.2 Score=34.46 Aligned_cols=23 Identities=48% Similarity=0.785 Sum_probs=18.4
Q ss_pred CCCCCCchHHHHHHhHHhHHHHH
Q psy4528 23 PGDPEKLPKEIILKRAADLAEAL 45 (87)
Q Consensus 23 pGdpErlpKeiiLkRaadl~eal 45 (87)
.|||..|+-+++.+|||.||+.-
T Consensus 133 a~d~~~L~d~~vA~Raa~L~~~a 155 (424)
T PF08013_consen 133 AGDPKPLPDETVAERAARLCEVA 155 (424)
T ss_dssp CTS-SC--HHHHHHHHHHHHHHH
T ss_pred CCCCCCCChHHHHHHHHHHHHHH
Confidence 79999999999999999999864
No 9
>PRK15458 tagatose 6-phosphate aldolase subunit KbaZ; Provisional
Probab=61.31 E-value=7.8 Score=32.87 Aligned_cols=22 Identities=45% Similarity=0.610 Sum_probs=21.1
Q ss_pred CCCCCCCchHHHHHHhHHhHHH
Q psy4528 22 HPGDPEKLPKEIILKRAADLAE 43 (87)
Q Consensus 22 ~pGdpErlpKeiiLkRaadl~e 43 (87)
-.|||..|+.+++..|||.|++
T Consensus 132 cagdp~pL~d~~vA~Raa~L~~ 153 (426)
T PRK15458 132 CADDPIPLTDEIVAERAARLAK 153 (426)
T ss_pred CCCCCCCCChHHHHHHHHHHHH
Confidence 7899999999999999999988
No 10
>TIGR02810 agaZ_gatZ D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit. Aldolases specific for D-tagatose-bisphosphate occur in distinct pathways in Escherichia coli and other bacteria, one for the degradation of galactitol (formerly dulcitol) and one for degradation of N-acetyl-galactosamine and D-galactosamine. This family represents a protein of both systems that behaves as a non-catalytic subunit of D-tagatose-bisphosphate aldolase, required both for full activity and for good stability of the aldolase. Note that members of this protein family appear in public databases annotated as putative tagatose 6-phosphate kinases, possibly in error.
Probab=57.87 E-value=9.3 Score=32.41 Aligned_cols=22 Identities=36% Similarity=0.566 Sum_probs=20.5
Q ss_pred CCCCCCCchHHHHHHhHHhHHH
Q psy4528 22 HPGDPEKLPKEIILKRAADLAE 43 (87)
Q Consensus 22 ~pGdpErlpKeiiLkRaadl~e 43 (87)
-.|||..|+-++|..||+.|++
T Consensus 128 ca~d~~~L~d~~vAeRaa~L~~ 149 (420)
T TIGR02810 128 CAGDPAPLDDATVAERAARLCA 149 (420)
T ss_pred ccCCCccCCHHHHHHHHHHHHH
Confidence 5699999999999999999988
No 11
>PRK15052 D-tagatose-1,6-bisphosphate aldolase subunit GatZ; Provisional
Probab=57.27 E-value=9.7 Score=32.33 Aligned_cols=22 Identities=36% Similarity=0.466 Sum_probs=20.5
Q ss_pred CCCCCCCchHHHHHHhHHhHHH
Q psy4528 22 HPGDPEKLPKEIILKRAADLAE 43 (87)
Q Consensus 22 ~pGdpErlpKeiiLkRaadl~e 43 (87)
-.|||..|+-++|..||+.|++
T Consensus 129 ca~d~~~L~d~~vA~Raa~L~~ 150 (421)
T PRK15052 129 CADDPIPLAPETVAERAAVLCQ 150 (421)
T ss_pred ccCCCccCCHHHHHHHHHHHHH
Confidence 5699999999999999999988
No 12
>KOG4447|consensus
Probab=55.70 E-value=4.6 Score=30.84 Aligned_cols=41 Identities=39% Similarity=0.556 Sum_probs=36.8
Q ss_pred hhhhhhhhccCCCCCCCCCchHHHHHHhHHhHHHHHhCCCCCC
Q psy4528 10 YGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYSMPRNN 52 (87)
Q Consensus 10 ygfqrl~K~~pr~pGdpErlpKeiiLkRaadl~ealy~~p~n~ 52 (87)
=+|.=|+|+||--|.| +|-|+--||-|+-++.+||.++.+.
T Consensus 95 ~AF~~lr~iiptlPsd--klSkiqtLklA~ryidfl~~vl~s~ 135 (173)
T KOG4447|consen 95 EAFAALRKIIPTLPSD--KLSKIQTLKLAARYIDFLYQVLQSD 135 (173)
T ss_pred HHHHHHHhhcCCCCcc--ccccccchhhcccCCchhhhccccc
Confidence 4799999999999976 7888889999999999999998775
No 13
>KOG1318|consensus
Probab=41.58 E-value=22 Score=30.02 Aligned_cols=40 Identities=30% Similarity=0.395 Sum_probs=34.4
Q ss_pred chhhhhhhhhccCCCCCCCCCchHHHHHHhHHhHHHHHhC
Q psy4528 8 IDYGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYS 47 (87)
Q Consensus 8 Idygfqrl~K~~pr~pGdpErlpKeiiLkRaadl~ealy~ 47 (87)
|.....-|-+|||.---+--+|-|.=|||++.|++.-|-.
T Consensus 248 IN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq 287 (411)
T KOG1318|consen 248 INDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQ 287 (411)
T ss_pred HHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHH
Confidence 5667778999999988888899999999999999988743
No 14
>KOG1319|consensus
Probab=39.53 E-value=33 Score=27.24 Aligned_cols=39 Identities=38% Similarity=0.620 Sum_probs=31.7
Q ss_pred chhhhhhhhhccCCC-CCCC--CCchHHHHHHhHHhHHHHHh
Q psy4528 8 IDYGFQRLQKLIPRH-PGDP--EKLPKEIILKRAADLAEALY 46 (87)
Q Consensus 8 Idygfqrl~K~~pr~-pGdp--ErlpKeiiLkRaadl~ealy 46 (87)
|.=|..-|+.+|||- |.|- -+|-|-+||+|+-|++..|-
T Consensus 77 Ik~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~ 118 (229)
T KOG1319|consen 77 IKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLH 118 (229)
T ss_pred HHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 556778899999996 4442 38999999999999998774
No 15
>cd08030 LA_like_plant La-motif domain of plant proteins similar to the La autoantigen. This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=36.52 E-value=32 Score=23.25 Aligned_cols=34 Identities=32% Similarity=0.586 Sum_probs=25.6
Q ss_pred hhhhhhhhccCCCCCCCCCchHHHHHHhHHhHHHHHhC
Q psy4528 10 YGFQRLQKLIPRHPGDPEKLPKEIILKRAADLAEALYS 47 (87)
Q Consensus 10 ygfqrl~K~~pr~pGdpErlpKeiiLkRaadl~ealy~ 47 (87)
-.|+|+.++.-.|.++++.+|.+. ...+++||-+
T Consensus 42 ~~F~rmk~l~~~~~~~~~~~~~~~----~~~I~~ALk~ 75 (90)
T cd08030 42 CSFSRMRSLLGLGGGKPEDVPEDT----LKAVAEALRT 75 (90)
T ss_pred hcChHHHHHhhcccccccccchhH----HHHHHHHHcc
Confidence 369999999999999998887654 2455666654
No 16
>KOG3960|consensus
Probab=36.04 E-value=34 Score=27.99 Aligned_cols=20 Identities=40% Similarity=0.529 Sum_probs=18.7
Q ss_pred CCCchHHHHHHhHHhHHHHH
Q psy4528 26 PEKLPKEIILKRAADLAEAL 45 (87)
Q Consensus 26 pErlpKeiiLkRaadl~eal 45 (87)
+.||||-=||+-|-+++|.|
T Consensus 149 NQRLPKVEILRsAI~YIE~L 168 (284)
T KOG3960|consen 149 NQRLPKVEILRSAIRYIERL 168 (284)
T ss_pred cccccHHHHHHHHHHHHHHH
Confidence 48999999999999999988
No 17
>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B.
Probab=34.83 E-value=37 Score=22.01 Aligned_cols=28 Identities=14% Similarity=0.321 Sum_probs=23.3
Q ss_pred hhhhhhhhhccCCCCCCCCCchHHHHHH
Q psy4528 9 DYGFQRLQKLIPRHPGDPEKLPKEIILK 36 (87)
Q Consensus 9 dygfqrl~K~~pr~pGdpErlpKeiiLk 36 (87)
+=++.+|.++|-|++++-+.-.|..||+
T Consensus 39 e~Al~~Ll~~v~~dr~~~~~~ar~~ll~ 66 (90)
T PF14561_consen 39 EEALDQLLELVRRDRDYEDDAARKRLLD 66 (90)
T ss_dssp HHHHHHHHHHHCC-TTCCCCHHHHHHHH
T ss_pred HHHHHHHHHHHHhCccccccHHHHHHHH
Confidence 3478899999999999999999888875
No 18
>PF11278 DUF3079: Protein of unknown function (DUF3079); InterPro: IPR021430 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=34.42 E-value=23 Score=22.54 Aligned_cols=14 Identities=43% Similarity=0.878 Sum_probs=12.3
Q ss_pred hhccCCCCCCCCCc
Q psy4528 16 QKLIPRHPGDPEKL 29 (87)
Q Consensus 16 ~K~~pr~pGdpErl 29 (87)
.|-||-||-.|||+
T Consensus 2 aKkFPlhP~hPERi 15 (52)
T PF11278_consen 2 AKKFPLHPKHPERI 15 (52)
T ss_pred CCcCCCCCCCccce
Confidence 58899999999985
No 19
>PF01858 RB_A: Retinoblastoma-associated protein A domain; InterPro: IPR002720 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and Simian virus 40 (SV40) large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion appears to be required for the stable folding of the B box (see IPR002719 from INTERPRO). Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the A-box is on N-terminal side of the B-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1O9K_A 3POM_A 1GH6_B 1N4M_A 4ELL_B 1AD6_A 1GUX_A 2R7G_C 4ELJ_A.
Probab=26.50 E-value=30 Score=25.55 Aligned_cols=37 Identities=38% Similarity=0.568 Sum_probs=25.8
Q ss_pred hhhhhhhccCCCCCCC-CCc----------hHHHHHHhHHhHHHHHhC
Q psy4528 11 GFQRLQKLIPRHPGDP-EKL----------PKEIILKRAADLAEALYS 47 (87)
Q Consensus 11 gfqrl~K~~pr~pGdp-Erl----------pKeiiLkRaadl~ealy~ 47 (87)
.-+||++++..++..| +.| |.+-|++|+.++.|.++.
T Consensus 9 ~~~~L~~~l~~~~~~PS~~L~~~~~~c~~~p~~~i~~rv~~l~~~~~~ 56 (194)
T PF01858_consen 9 SVSWLQALLSGLSDEPSEELLRIFKSCSRDPTESILKRVKQLLEKFCQ 56 (194)
T ss_dssp HHHHHHHHHHHS-SS--HHHHHHHHTSSS--HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHhcCCCcHHHHHHHHHHHHHHHHH
Confidence 3468888888777777 444 445599999999998864
No 20
>PF08168 NUC205: NUC205 domain; InterPro: IPR012584 This domain is found in a novel family of nucleolar proteins [].; GO: 0005634 nucleus
Probab=24.55 E-value=37 Score=20.87 Aligned_cols=11 Identities=64% Similarity=1.108 Sum_probs=9.5
Q ss_pred ccCCCCCCCCC
Q psy4528 18 LIPRHPGDPEK 28 (87)
Q Consensus 18 ~~pr~pGdpEr 28 (87)
+||-||+|||.
T Consensus 32 lip~~~~d~ee 42 (44)
T PF08168_consen 32 LIPISPKDPEE 42 (44)
T ss_pred eccccCCCccc
Confidence 68999999974
No 21
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=22.66 E-value=1.1e+02 Score=28.96 Aligned_cols=39 Identities=41% Similarity=0.592 Sum_probs=29.0
Q ss_pred hhhhhccCCCCC-C------CCCchH-----HHHHHhHHhHHHHHhCCCCC
Q psy4528 13 QRLQKLIPRHPG-D------PEKLPK-----EIILKRAADLAEALYSMPRN 51 (87)
Q Consensus 13 qrl~K~~pr~pG-d------pErlpK-----eiiLkRaadl~ealy~~p~n 51 (87)
.+|.|+||.-+| . .+.--+ .-..++.-|+|..|-|.||+
T Consensus 456 d~lsK~Ip~~~~~~l~~a~~~~~~l~~~~~~d~~~~~~~e~A~kLeGlpRh 506 (1139)
T COG0587 456 DKLAKLIPFWPGLTLAVAYEEEPELKELLDSDPEVKRLIELARKLEGLPRH 506 (1139)
T ss_pred HHHHhcCCCccccchhhhhcccHHHHhhccccHHHHHHHHHHHHhcCCCCC
Confidence 689999999999 1 111111 23578999999999999987
No 22
>KOG0595|consensus
Probab=20.29 E-value=52 Score=28.22 Aligned_cols=9 Identities=44% Similarity=1.102 Sum_probs=7.6
Q ss_pred hhhhhhhhh
Q psy4528 9 DYGFQRLQK 17 (87)
Q Consensus 9 dygfqrl~K 17 (87)
||||.|-.+
T Consensus 158 DFGfAR~L~ 166 (429)
T KOG0595|consen 158 DFGFARFLQ 166 (429)
T ss_pred ccchhhhCC
Confidence 899999765
Done!