Query psy16212
Match_columns 233
No_of_seqs 8 out of 10
Neff 1.6
Searched_HMMs 46136
Date Fri Aug 16 23:41:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16212.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16212hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07586 HXXSHH: Protein of un 68.9 7.1 0.00015 33.7 3.9 28 125-152 181-208 (302)
2 COG3360 Uncharacterized conser 44.8 3.5 7.7E-05 31.6 -1.7 36 127-162 27-67 (71)
3 PF11662 DUF3263: Protein of u 23.4 26 0.00055 26.8 -0.1 24 196-219 18-41 (77)
4 PF10134 RPA: Replication init 20.6 87 0.0019 26.9 2.5 25 135-159 90-114 (229)
5 KOG0216|consensus 19.2 41 0.00089 36.0 0.3 66 146-219 86-153 (1111)
6 PF10458 Val_tRNA-synt_C: Valy 19.1 1.5E+02 0.0032 20.7 3.0 25 124-148 42-66 (66)
7 cd02067 B12-binding B12 bindin 14.1 1.3E+02 0.0028 21.9 1.8 28 158-185 26-53 (119)
8 PF05890 Ebp2: Eukaryotic rRNA 13.1 82 0.0018 28.2 0.6 63 147-220 47-112 (271)
9 PF06519 TolA: TolA C-terminal 13.0 1.1E+02 0.0025 23.3 1.3 31 170-201 20-50 (96)
10 smart00524 DWB Domain B in dwa 11.4 1.1E+02 0.0023 26.2 0.7 16 181-197 132-147 (171)
No 1
>PF07586 HXXSHH: Protein of unknown function (DUF1552); InterPro: IPR011447 This is a family of proteins identified in Rhodopirellula baltica.
Probab=68.86 E-value=7.1 Score=33.70 Aligned_cols=28 Identities=21% Similarity=0.376 Sum_probs=24.6
Q ss_pred HHHhHHHhhhhHHHHHHHHHhhcccccc
Q psy16212 125 VTQTRLESYLSALEFIEAQLDRMKHTSY 152 (233)
Q Consensus 125 v~q~r~e~~~~~~~~~~~~~~~~~~~~~ 152 (233)
..|.|||.||.++.-||.+|+.+....-
T Consensus 181 ~Dr~kLd~yl~sireiE~rl~~~~~~~~ 208 (302)
T PF07586_consen 181 EDRQKLDQYLDSIREIEKRLQQAEAWAD 208 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhccc
Confidence 4599999999999999999998887663
No 2
>COG3360 Uncharacterized conserved protein [Function unknown]
Probab=44.83 E-value=3.5 Score=31.62 Aligned_cols=36 Identities=31% Similarity=0.438 Sum_probs=25.3
Q ss_pred HhHHHhhhhHHHHHHHHHhhc-----ccccceeeeeeccee
Q psy16212 127 QTRLESYLSALEFIEAQLDRM-----KHTSYRTTLEVGFES 162 (233)
Q Consensus 127 q~r~e~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~ 162 (233)
-+|++.-|..|++.|-+-.|| +-..|++||+|||+-
T Consensus 27 i~RA~~t~~~l~wfeV~~~rg~v~~g~v~hyqv~lkVgFrl 67 (71)
T COG3360 27 IARAADTLDNLDWFEVVETRGHVVDGAVAHYQVTLKVGFRL 67 (71)
T ss_pred HHHHHhhhhcceEEEEEeecccEeecceEEEEEEEEEEEEe
Confidence 357777778887766544344 334499999999974
No 3
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=23.39 E-value=26 Score=26.83 Aligned_cols=24 Identities=33% Similarity=0.772 Sum_probs=21.4
Q ss_pred ccccCcccchhhhhhccCCccccc
Q psy16212 196 MKSSGLKEKKLVETYGIRPSGYYL 219 (233)
Q Consensus 196 ~~~~~~~~~~~~~~~~~~~~~~~~ 219 (233)
.+..|-||.-+-+.+||.|.-||.
T Consensus 18 w~~~GaKe~aIre~fGls~~rYyq 41 (77)
T PF11662_consen 18 WRHGGAKEEAIREEFGLSPTRYYQ 41 (77)
T ss_pred CcCCCCcHHHHHHHHCCCHHHHHH
Confidence 357799999999999999999984
No 4
>PF10134 RPA: Replication initiator protein A; InterPro: IPR018777 Members of this family of bacterial proteins are single-stranded DNA binding proteins that are involved in DNA replication, repair and recombination.
Probab=20.55 E-value=87 Score=26.91 Aligned_cols=25 Identities=28% Similarity=0.452 Sum_probs=20.6
Q ss_pred hHHHHHHHHHhhcccccceeeeeec
Q psy16212 135 SALEFIEAQLDRMKHTSYRTTLEVG 159 (233)
Q Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (233)
...+-|++-|+|++.|.|.|.+.-+
T Consensus 90 ~~Y~~L~~aL~RL~~T~i~t~~~~~ 114 (229)
T PF10134_consen 90 RYYERLREALDRLQGTTIETNIRTG 114 (229)
T ss_pred HHHHHHHHHHHHhcCCEEEEEEccC
Confidence 3567789999999999998887744
No 5
>KOG0216|consensus
Probab=19.19 E-value=41 Score=36.00 Aligned_cols=66 Identities=24% Similarity=0.412 Sum_probs=50.3
Q ss_pred hcccccceeeeeecceeeccCCCcchhHHHhhhhhhhhhhhhccceeeecccccCcccchhhh--hhccCCccccc
Q psy16212 146 RMKHTSYRTTLEVGFESIHSGQSLVPESIQKSLMDIKYDVEKKLCSIRMSMKSSGLKEKKLVE--TYGIRPSGYYL 219 (233)
Q Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~ 219 (233)
|-.+++|+-+|-|.+.--+.|-..++ |...|=.+-.-|-.|+|.++ |++.++||+ .--..-.|||+
T Consensus 86 RqR~~TY~Gkl~v~v~wsVNg~~~~~--e~~dlG~vPIMlrSklChL~------g~sp~eLV~hkEe~~EmGGYFI 153 (1111)
T KOG0216|consen 86 RQRGLTYKGKLVVRVSWSVNGGHVVI--EKRDLGHVPIMLRSKLCHLN------GASPKELVKHKEESSEMGGYFI 153 (1111)
T ss_pred hhccceecceEEEEEEEEECCeeeee--eeeecCccceEEeccccccC------CCChHHHhhccCchhhcCcEEE
Confidence 55789999999999999999998888 44455555556788999886 788888887 33344457764
No 6
>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.
Probab=19.14 E-value=1.5e+02 Score=20.74 Aligned_cols=25 Identities=32% Similarity=0.478 Sum_probs=18.7
Q ss_pred hHHHhHHHhhhhHHHHHHHHHhhcc
Q psy16212 124 EVTQTRLESYLSALEFIEAQLDRMK 148 (233)
Q Consensus 124 ev~q~r~e~~~~~~~~~~~~~~~~~ 148 (233)
+.++.+++.+..-++-|+++|..|+
T Consensus 42 e~er~kl~~~~~~~~~l~~~l~~Lk 66 (66)
T PF10458_consen 42 EKEREKLEELEEELEKLEEALEQLK 66 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4567788888888888888888775
No 7
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=14.12 E-value=1.3e+02 Score=21.88 Aligned_cols=28 Identities=32% Similarity=0.488 Sum_probs=23.8
Q ss_pred ecceeeccCCCcchhHHHhhhhhhhhhh
Q psy16212 158 VGFESIHSGQSLVPESIQKSLMDIKYDV 185 (233)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 185 (233)
-||+.+..|..+-|+.+.+.+.+.+.|+
T Consensus 26 ~G~~V~~lg~~~~~~~l~~~~~~~~pdv 53 (119)
T cd02067 26 AGFEVIDLGVDVPPEEIVEAAKEEDADA 53 (119)
T ss_pred CCCEEEECCCCCCHHHHHHHHHHcCCCE
Confidence 5899999999988899998888777775
No 8
>PF05890 Ebp2: Eukaryotic rRNA processing protein EBP2; InterPro: IPR008610 This family consists of several eukaryotic rRNA processing protein EBP2 sequences. Ebp2p is required for the maturation of 25S rRNA and 60S subunit assembly. Ebp2p may be one of the target proteins of Rrs1p for executing the signal to regulate ribosome biogenesis [].
Probab=13.12 E-value=82 Score=28.23 Aligned_cols=63 Identities=22% Similarity=0.474 Sum_probs=41.9
Q ss_pred cccccceeeeeecceeeccCCCcchhHHHhhhhhhhhhhhhccceeeecccccCcccchhhhhhcc---CCcccccc
Q psy16212 147 MKHTSYRTTLEVGFESIHSGQSLVPESIQKSLMDIKYDVEKKLCSIRMSMKSSGLKEKKLVETYGI---RPSGYYLP 220 (233)
Q Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~ 220 (233)
++...|--||.|- .|+.+...+-|+.-|...-+.-++..+.+- +.-..++...|| ||+.||-.
T Consensus 47 ~~~~pWiE~L~vt----------s~~~~~~~~~d~~dD~~RE~aFy~qAl~av-~~a~~~L~~~gip~~RP~DYfAE 112 (271)
T PF05890_consen 47 PKKLPWIETLDVT----------SPEPTDEQIKDVNDDLKRELAFYKQALEAV-KEARPRLKKLGIPFKRPDDYFAE 112 (271)
T ss_pred cCCCCCeeEEeee----------cCccchhhhccccccHHHHHHHHHHHHHHH-HHHHHHHHHcCCCccCCCcchHH
Confidence 6667888888775 345556667777788777777666666532 333445566676 89999854
No 9
>PF06519 TolA: TolA C-terminal; InterPro: IPR014161 TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cut-offs are based largely on conserved operon structure. The Tol-Pal complex is required for maintaining outer membrane integrity, and is also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins OmpC, PhoE and LamB.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2X9A_D 3QDP_A 3QDR_A 1TOL_A 1S62_A.
Probab=13.01 E-value=1.1e+02 Score=23.31 Aligned_cols=31 Identities=29% Similarity=0.584 Sum_probs=20.0
Q ss_pred chhHHHhhhhhhhhhhhhccceeeecccccCc
Q psy16212 170 VPESIQKSLMDIKYDVEKKLCSIRMSMKSSGL 201 (233)
Q Consensus 170 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 (233)
+-..||.-|.|-.. .--|-|.++|.|-..|+
T Consensus 20 I~~~Iq~~l~~~~~-y~GK~C~v~i~l~~dG~ 50 (96)
T PF06519_consen 20 IKQAIQRNLYDDES-YKGKECRVRIRLAPDGL 50 (96)
T ss_dssp HHHHHHTTTTTGGG-GTT--EEEEEEEETTSE
T ss_pred HHHHHHHhcCCccc-cCCCEEEEEEEECCCCc
Confidence 44556665555432 34589999999999997
No 10
>smart00524 DWB Domain B in dwarfin family proteins.
Probab=11.36 E-value=1.1e+02 Score=26.18 Aligned_cols=16 Identities=38% Similarity=0.831 Sum_probs=12.9
Q ss_pred hhhhhhhccceeeeccc
Q psy16212 181 IKYDVEKKLCSIRMSMK 197 (233)
Q Consensus 181 ~~~~~~~~~~~~~~~~~ 197 (233)
-.||..+ +|+||||.-
T Consensus 132 ~~~~l~~-~c~iriSFv 147 (171)
T smart00524 132 GVYDLAR-MCTIRISFV 147 (171)
T ss_pred cccchhh-heeEEEEEe
Confidence 4678777 999999963
Done!