Query 034648
Match_columns 88
No_of_seqs 16 out of 18
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 05:02:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034648.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034648hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03885 DUF327: Protein of un 52.7 7.4 0.00016 27.1 1.1 23 41-63 58-80 (147)
2 PF13679 Methyltransf_32: Meth 50.8 8.1 0.00018 25.6 1.0 11 69-79 126-136 (141)
3 PF14511 RE_EcoO109I: Type II 50.4 8.5 0.00018 29.4 1.1 14 65-78 140-153 (200)
4 PF00919 UPF0004: Uncharacteri 48.5 13 0.00029 24.3 1.7 23 59-81 60-82 (98)
5 PRK08178 acetolactate synthase 44.6 22 0.00047 24.4 2.3 45 25-75 29-83 (96)
6 COG3216 Uncharacterized protei 39.7 9.5 0.00021 29.4 -0.1 18 64-81 89-106 (184)
7 CHL00073 chlN photochlorophyll 38.9 25 0.00055 29.3 2.3 47 26-80 63-111 (457)
8 PF02107 FlgH: Flagellar L-rin 36.3 16 0.00035 26.4 0.7 14 61-74 24-37 (179)
9 smart00302 GED Dynamin GTPase 32.9 25 0.00053 22.6 1.1 29 40-68 60-89 (92)
10 PRK12698 flgH flagellar basal 32.3 23 0.00051 26.9 1.0 15 59-73 61-75 (224)
11 PF08439 Peptidase_M3_N: Oligo 30.3 19 0.00041 21.4 0.2 23 39-61 11-33 (70)
12 COG0828 RpsU Ribosomal protein 29.9 19 0.00041 23.6 0.2 9 45-53 13-21 (67)
13 PF05026 DCP2: Dcp2, box A dom 29.5 19 0.00041 23.9 0.1 11 45-55 75-85 (85)
14 PRK12697 flgH flagellar basal 29.3 26 0.00056 27.0 0.8 14 60-73 67-80 (226)
15 COG5328 Uncharacterized protei 29.2 28 0.0006 26.4 1.0 32 3-34 95-127 (160)
16 COG2063 FlgH Flagellar basal b 28.0 26 0.00056 27.4 0.6 13 60-72 70-82 (230)
17 PRK11152 ilvM acetolactate syn 27.3 21 0.00046 23.0 0.1 41 25-71 24-74 (76)
18 PF11239 DUF3040: Protein of u 26.7 22 0.00048 22.4 0.0 17 37-53 14-31 (82)
19 PRK12699 flgH flagellar basal 26.6 30 0.00066 26.9 0.8 15 59-73 85-99 (246)
20 PRK12696 flgH flagellar basal 25.2 41 0.0009 25.8 1.3 14 60-73 64-77 (236)
21 PF08374 Protocadherin: Protoc 25.2 37 0.0008 26.8 1.0 23 8-30 153-175 (221)
22 PRK12407 flgH flagellar basal 24.7 33 0.00073 26.1 0.7 14 60-73 63-76 (221)
23 TIGR00726 uncharacterized prot 24.5 62 0.0013 23.8 2.1 10 72-81 135-144 (221)
24 PRK00249 flgH flagellar basal 23.2 40 0.00087 25.5 0.9 15 59-73 61-75 (222)
25 PF02212 GED: Dynamin GTPase e 23.1 41 0.00089 21.2 0.8 30 39-68 59-89 (92)
26 PF06971 Put_DNA-bind_N: Putat 22.9 70 0.0015 19.3 1.7 22 45-66 5-26 (50)
27 PRK12788 flgH flagellar basal 21.9 44 0.00095 25.9 0.9 14 60-73 73-86 (234)
28 PF06161 DUF975: Protein of un 21.4 54 0.0012 23.2 1.2 22 41-62 172-193 (243)
29 PRK12701 flgH flagellar basal 21.2 43 0.00094 25.7 0.7 14 60-73 67-80 (230)
30 PF06732 Pescadillo_N: Pescadi 20.3 76 0.0016 25.5 1.9 28 37-64 63-90 (281)
No 1
>PF03885 DUF327: Protein of unknown function (DUF327); InterPro: IPR005585 The proteins in this family are around 140-170 residues in length. The proteins contain many conserved residues, with the most conserved motifs found in the central and C-terminal region. The function of these proteins is unknown. ; PDB: 2P61_A 2QUP_A.
Probab=52.74 E-value=7.4 Score=27.09 Aligned_cols=23 Identities=30% Similarity=0.430 Sum_probs=18.3
Q ss_pred ccccchhhhhhhhhhHHHHHHHH
Q 034648 41 LLADDPVLKRFKSHKKSVWRLKR 63 (88)
Q Consensus 41 LL~eD~aLKrFKS~K~sv~~l~r 63 (88)
-|++.|.+..++.||+.|++.-+
T Consensus 58 ~L~~~~t~~~l~~YK~~Vk~Fl~ 80 (147)
T PF03885_consen 58 RLAESPTLENLKRYKELVKQFLK 80 (147)
T ss_dssp HHHHH--HHHHHHHHHHHHHHHH
T ss_pred HHhhCCCHHHHHHHHHHHHHHHH
Confidence 57899999999999999998754
No 2
>PF13679 Methyltransf_32: Methyltransferase domain
Probab=50.75 E-value=8.1 Score=25.58 Aligned_cols=11 Identities=9% Similarity=-0.016 Sum_probs=8.7
Q ss_pred EEeeeecccee
Q 034648 69 TIVVVAGKTGD 79 (88)
Q Consensus 69 T~vVvagC~ye 79 (88)
..+++.||||-
T Consensus 126 ~~l~~vpCCyh 136 (141)
T PF13679_consen 126 RFLVLVPCCYH 136 (141)
T ss_pred CEEEEcCCccc
Confidence 56788999984
No 3
>PF14511 RE_EcoO109I: Type II restriction endonuclease EcoO109I; PDB: 1WTD_A 1WTE_A.
Probab=50.41 E-value=8.5 Score=29.38 Aligned_cols=14 Identities=21% Similarity=-0.031 Sum_probs=10.4
Q ss_pred cCeeEEeeeeccce
Q 034648 65 GDVLTIVVVAGKTG 78 (88)
Q Consensus 65 gdvLT~vVvagC~y 78 (88)
-++..+++|.||||
T Consensus 140 ~~~~~~~~v~G~~Y 153 (200)
T PF14511_consen 140 KSGQNIDAVNGCCY 153 (200)
T ss_dssp -GGG-SEEEEEESS
T ss_pred ccccccceeeEEEe
Confidence 56777888999998
No 4
>PF00919 UPF0004: Uncharacterized protein family UPF0004; InterPro: IPR013848 The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain (see PDOC50926 from PROSITEDOC). The core forms a radical SAM fold (or AdoMet radical), containing a cysteine motif CxxxCxxC that binds a [4Fe-4S] cluster [, , ]. A reducing equivalent from the [4Fe-4S]+ cluster is used to cleave S-adenosylmethionine (SAM) to generate methionine and a 5'-deoxyadenosyl radical. The latter is thought to produce a reactive substrate radical that is amenable to sulphur insertion [, ]. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition. The tertiary structure of the central radical SAM fold has six beta/alpha motifs resembling a three-quarter TIM barrel core (see PDOC00155 from PROSITEDOC) []. The N-terminal MTTase domain might form an additional [beta/alpha]2 TIM barrel unit []. ; GO: 0003824 catalytic activity, 0051539 4 iron, 4 sulfur cluster binding, 0009451 RNA modification
Probab=48.52 E-value=13 Score=24.33 Aligned_cols=23 Identities=22% Similarity=0.196 Sum_probs=14.3
Q ss_pred HHHHHhcCeeEEeeeeccceeee
Q 034648 59 WRLKRMGDVLTIVVVAGKTGDFG 81 (88)
Q Consensus 59 ~~l~r~gdvLT~vVvagC~yei~ 81 (88)
.++++..+-=..|||+||--+.+
T Consensus 60 ~~l~~~~~~~~~ivv~GC~aq~~ 82 (98)
T PF00919_consen 60 RKLKKLKKPGAKIVVTGCMAQRY 82 (98)
T ss_pred HHHHHhcCCCCEEEEEeCccccC
Confidence 33333333347899999986654
No 5
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=44.57 E-value=22 Score=24.43 Aligned_cols=45 Identities=22% Similarity=0.380 Sum_probs=31.7
Q ss_pred ccccccccc---cCcccccccccchhhhhh-------hhhhHHHHHHHHhcCeeEEeeeec
Q 034648 25 LSRRGYHVE---LGPREKALLADDPVLKRF-------KSHKKSVWRLKRMGDVLTIVVVAG 75 (88)
Q Consensus 25 ~~rRgfHvE---~gaReKALL~eD~aLKrF-------KS~K~sv~~l~r~gdvLT~vVvag 75 (88)
.+||||.|| -|+=| ||.+.|+ ..-.+-+|||.|.-||+-+..+..
T Consensus 29 FsRRgyNIeSLtvg~te------~~~iSRmtivv~~~~~i~Qi~kQL~KLidVikV~~l~~ 83 (96)
T PRK08178 29 FARRAFNVEGILCLPIQ------DGDKSRIWLLVNDDQRLEQMISQIEKLEDVLKVRRNQS 83 (96)
T ss_pred HhcCCcCeeeEEEeecC------CCCceEEEEEEcCchHHHHHHHHHhCCcCEEEEEECCC
Confidence 799999998 34433 3333332 356788999999999998876653
No 6
>COG3216 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.65 E-value=9.5 Score=29.36 Aligned_cols=18 Identities=28% Similarity=0.492 Sum_probs=16.3
Q ss_pred hcCeeEEeeeeccceeee
Q 034648 64 MGDVLTIVVVAGKTGDFG 81 (88)
Q Consensus 64 ~gdvLT~vVvagC~yei~ 81 (88)
+-|-||+.++.||+||++
T Consensus 89 l~NPlT~P~I~~~tyelG 106 (184)
T COG3216 89 LANPLTMPFIWGATYELG 106 (184)
T ss_pred hcCCcccceeeeeeHhhh
Confidence 459999999999999986
No 7
>CHL00073 chlN photochlorophyllide reductase subunit N
Probab=38.90 E-value=25 Score=29.25 Aligned_cols=47 Identities=21% Similarity=0.268 Sum_probs=35.5
Q ss_pred cccccccccCcccccccccchh--hhhhhhhhHHHHHHHHhcCeeEEeeeeccceee
Q 034648 26 SRRGYHVELGPREKALLADDPV--LKRFKSHKKSVWRLKRMGDVLTIVVVAGKTGDF 80 (88)
Q Consensus 26 ~rRgfHvE~gaReKALL~eD~a--LKrFKS~K~sv~~l~r~gdvLT~vVvagC~yei 80 (88)
+|-|| -++.. .|.+ +---|.-++.+.++.+-.|.=.++|+++|.-||
T Consensus 63 ~r~~~-tdl~E-------~Di~~~~g~~~~L~~~i~ei~~~~~p~~ifv~~TC~t~i 111 (457)
T CHL00073 63 PRYAM-AELEE-------GDISAQLNDYEELKRLCLQIKKDRNPSVIVWIGTCTTEI 111 (457)
T ss_pred cccee-cccCc-------hhhhhhcCCHHHHHHHHHHHHHhCCCCEEEEEccCcHHh
Confidence 66666 55543 3444 455566678999999999999999999999776
No 8
>PF02107 FlgH: Flagellar L-ring protein; InterPro: IPR000527 The flgH, flgI and fliF genes of Salmonella typhimurium encode the major proteins for the L, P and M rings of the flagellar basal body []. In fact, the basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament []. The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FlgH and FlgI, which are exported across the cell membrane to their destinations in the outer membrane and periplasmic space, have typical N-terminal cleaved signal-peptide sequences. FlgH is predicted to have an extensive beta-sheet structure, in keeping with other outer membrane proteins [].; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009427 bacterial-type flagellum basal body, distal rod, L ring
Probab=36.28 E-value=16 Score=26.35 Aligned_cols=14 Identities=43% Similarity=0.866 Sum_probs=11.7
Q ss_pred HHHhcCeeEEeeee
Q 034648 61 LKRMGDVLTIVVVA 74 (88)
Q Consensus 61 l~r~gdvLT~vVva 74 (88)
-.++||++||+|.-
T Consensus 24 A~~VGDiiTV~v~E 37 (179)
T PF02107_consen 24 ARRVGDIITVVVSE 37 (179)
T ss_pred ccCCCCEEEEEEEE
Confidence 45899999999864
No 9
>smart00302 GED Dynamin GTPase effector domain.
Probab=32.94 E-value=25 Score=22.63 Aligned_cols=29 Identities=31% Similarity=0.472 Sum_probs=22.7
Q ss_pred cccccchhhh-hhhhhhHHHHHHHHhcCee
Q 034648 40 ALLADDPVLK-RFKSHKKSVWRLKRMGDVL 68 (88)
Q Consensus 40 ALL~eD~aLK-rFKS~K~sv~~l~r~gdvL 68 (88)
.||+|||... +=+.-++.++.|+++.++|
T Consensus 60 ~LL~E~~~i~~kR~~~~~~l~~L~~A~~~l 89 (92)
T smart00302 60 ELLEEDPEIASKRKELKKRLELLKKARQII 89 (92)
T ss_pred HHHcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5899999863 4467788888888888776
No 10
>PRK12698 flgH flagellar basal body L-ring protein; Reviewed
Probab=32.30 E-value=23 Score=26.87 Aligned_cols=15 Identities=27% Similarity=0.687 Sum_probs=12.3
Q ss_pred HHHHHhcCeeEEeee
Q 034648 59 WRLKRMGDVLTIVVV 73 (88)
Q Consensus 59 ~~l~r~gdvLT~vVv 73 (88)
+|-.++||++||++.
T Consensus 61 ~rA~~VGDivTV~i~ 75 (224)
T PRK12698 61 IKAHKVGDIITVVLK 75 (224)
T ss_pred cccccCCCeEEEEEE
Confidence 345689999999985
No 11
>PF08439 Peptidase_M3_N: Oligopeptidase F; InterPro: IPR013647 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain is found towards the N terminus of metallopeptidases belonging to MEROPS peptidase subfamily M3B (oligopeptidase F, clan MA). An example protein is Lactococcus lactisPepF []. The function of this N-terminal domain is unknown.; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 2QR4_B 3CE2_A.
Probab=30.29 E-value=19 Score=21.43 Aligned_cols=23 Identities=26% Similarity=0.547 Sum_probs=14.4
Q ss_pred ccccccchhhhhhhhhhHHHHHH
Q 034648 39 KALLADDPVLKRFKSHKKSVWRL 61 (88)
Q Consensus 39 KALL~eD~aLKrFKS~K~sv~~l 61 (88)
++++++||.|+.|+-|=+.+++.
T Consensus 11 ~~~~~~~~~l~~y~~~l~~i~r~ 33 (70)
T PF08439_consen 11 ESLIKEDPELKEYRFYLEEIRRY 33 (70)
T ss_dssp HHHHHH-CCCGGGHHHHHHHHGG
T ss_pred HHHHhcCccHHHHHHHHHHHHHh
Confidence 35677888888777665555443
No 12
>COG0828 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]
Probab=29.94 E-value=19 Score=23.64 Aligned_cols=9 Identities=56% Similarity=0.947 Sum_probs=7.5
Q ss_pred chhhhhhhh
Q 034648 45 DPVLKRFKS 53 (88)
Q Consensus 45 D~aLKrFKS 53 (88)
|.||++||-
T Consensus 13 d~ALrrFKr 21 (67)
T COG0828 13 DKALRRFKR 21 (67)
T ss_pred HHHHHHHHH
Confidence 679999984
No 13
>PF05026 DCP2: Dcp2, box A domain; InterPro: IPR007722 This presumed domain is always found to the N-terminal side of the NUDIX hydrolase domain IPR000086 from INTERPRO. This domain appears to be specific to mRNA decapping protein 2 P53550 from SWISSPROT and its close homologues. This region has been termed Box A [].; GO: 0003723 RNA binding, 0016787 hydrolase activity, 0030145 manganese ion binding; PDB: 2QKM_H 2A6T_B 2QKL_B.
Probab=29.50 E-value=19 Score=23.92 Aligned_cols=11 Identities=55% Similarity=0.773 Sum_probs=8.2
Q ss_pred chhhhhhhhhh
Q 034648 45 DPVLKRFKSHK 55 (88)
Q Consensus 45 D~aLKrFKS~K 55 (88)
|.++++|++||
T Consensus 75 ~~~~~~f~~YK 85 (85)
T PF05026_consen 75 DEALKKFKKYK 85 (85)
T ss_dssp HHHHHHHHHHS
T ss_pred HHHHHHHHccC
Confidence 55778888886
No 14
>PRK12697 flgH flagellar basal body L-ring protein; Reviewed
Probab=29.31 E-value=26 Score=26.97 Aligned_cols=14 Identities=50% Similarity=0.916 Sum_probs=11.7
Q ss_pred HHHHhcCeeEEeee
Q 034648 60 RLKRMGDVLTIVVV 73 (88)
Q Consensus 60 ~l~r~gdvLT~vVv 73 (88)
|-.++||+|||++.
T Consensus 67 RA~~VGDiiTV~i~ 80 (226)
T PRK12697 67 RPRNVGDILTIVIA 80 (226)
T ss_pred ccccCCCEEEEEEE
Confidence 45689999999985
No 15
>COG5328 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.19 E-value=28 Score=26.40 Aligned_cols=32 Identities=31% Similarity=0.442 Sum_probs=23.8
Q ss_pred hhhhhhhhhhhccCCccccccc-cccccccccc
Q 034648 3 YLLKTSIASHLRSHTQEKREDA-LSRRGYHVEL 34 (88)
Q Consensus 3 fll~ssi~S~lRS~sq~~~~~~-~~rRgfHvE~ 34 (88)
|+.--|.-+-.||.+|++-+.. ..|||.|-|-
T Consensus 95 fmICeSYY~AIRsstPsqIEAiDMGRRGlHNeG 127 (160)
T COG5328 95 FMICESYYQAIRSSTPSQIEAIDMGRRGLHNEG 127 (160)
T ss_pred HHHHHHHHHHHHhCCHhhhhHhhhccccccccc
Confidence 3444666777888888876655 7899999874
No 16
>COG2063 FlgH Flagellar basal body L-ring protein [Cell motility and secretion]
Probab=27.99 E-value=26 Score=27.44 Aligned_cols=13 Identities=54% Similarity=0.945 Sum_probs=11.0
Q ss_pred HHHHhcCeeEEee
Q 034648 60 RLKRMGDVLTIVV 72 (88)
Q Consensus 60 ~l~r~gdvLT~vV 72 (88)
|-.++||+|||++
T Consensus 70 RA~~vGDilTV~i 82 (230)
T COG2063 70 RASNVGDILTIVI 82 (230)
T ss_pred ccccCCCEEEEEE
Confidence 4568999999986
No 17
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=27.25 E-value=21 Score=22.96 Aligned_cols=41 Identities=17% Similarity=0.252 Sum_probs=24.6
Q ss_pred ccccccccc---cCcccccccccchhhhhh-------hhhhHHHHHHHHhcCeeEEe
Q 034648 25 LSRRGYHVE---LGPREKALLADDPVLKRF-------KSHKKSVWRLKRMGDVLTIV 71 (88)
Q Consensus 25 ~~rRgfHvE---~gaReKALL~eD~aLKrF-------KS~K~sv~~l~r~gdvLT~v 71 (88)
.++|||+|+ .|+-| |+..-|- ..-..-++||.|.=||+-+=
T Consensus 24 f~rRGfnI~sl~v~~t~------~~~~sriti~v~~~~~i~ql~kQL~KL~dV~~V~ 74 (76)
T PRK11152 24 VRHRGFQVCSMNMTQNT------DAQNINIELTVASERPIDLLSSQLNKLVDVAHVE 74 (76)
T ss_pred HhcCCeeeeeEEeeecC------CCCEEEEEEEECCCchHHHHHHHHhcCcCeEEEE
Confidence 799999987 34332 2222221 12345678888888887653
No 18
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=26.69 E-value=22 Score=22.40 Aligned_cols=17 Identities=47% Similarity=0.708 Sum_probs=12.3
Q ss_pred ccccccccchhhh-hhhh
Q 034648 37 REKALLADDPVLK-RFKS 53 (88)
Q Consensus 37 ReKALL~eD~aLK-rFKS 53 (88)
=|++|.+|||.+. ++++
T Consensus 14 iEr~L~~~DP~fa~~l~~ 31 (82)
T PF11239_consen 14 IERQLRADDPRFAARLRS 31 (82)
T ss_pred HHHHHHhcCcHHHHHhcc
Confidence 3778999999874 3444
No 19
>PRK12699 flgH flagellar basal body L-ring protein; Reviewed
Probab=26.57 E-value=30 Score=26.89 Aligned_cols=15 Identities=20% Similarity=0.592 Sum_probs=12.1
Q ss_pred HHHHHhcCeeEEeee
Q 034648 59 WRLKRMGDVLTIVVV 73 (88)
Q Consensus 59 ~~l~r~gdvLT~vVv 73 (88)
+|-.++||++||++.
T Consensus 85 ~RA~~VGDiiTV~i~ 99 (246)
T PRK12699 85 RRARQIGDTIIVLLN 99 (246)
T ss_pred cccccCCCEEEEEEE
Confidence 345689999999985
No 20
>PRK12696 flgH flagellar basal body L-ring protein; Reviewed
Probab=25.20 E-value=41 Score=25.79 Aligned_cols=14 Identities=36% Similarity=0.840 Sum_probs=11.6
Q ss_pred HHHHhcCeeEEeee
Q 034648 60 RLKRMGDVLTIVVV 73 (88)
Q Consensus 60 ~l~r~gdvLT~vVv 73 (88)
|-.++||++||+|.
T Consensus 64 RA~~VGDivTV~i~ 77 (236)
T PRK12696 64 RARRVGDIVLVKIV 77 (236)
T ss_pred ccccCCCEEEEEEE
Confidence 44689999999985
No 21
>PF08374 Protocadherin: Protocadherin; InterPro: IPR013585 The structure of protocadherins is similar to that of classic cadherins (IPR002126 from INTERPRO), but they also have some unique features associated with the cytoplasmic domains. They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated [].
Probab=25.16 E-value=37 Score=26.75 Aligned_cols=23 Identities=13% Similarity=0.128 Sum_probs=17.1
Q ss_pred hhhhhhccCCccccccccccccc
Q 034648 8 SIASHLRSHTQEKREDALSRRGY 30 (88)
Q Consensus 8 si~S~lRS~sq~~~~~~~~rRgf 30 (88)
.|++|++|.||+|+-.+||--..
T Consensus 153 DLarHYkS~SPqPa~qlqP~tP~ 175 (221)
T PF08374_consen 153 DLARHYKSASPQPAFQLQPETPT 175 (221)
T ss_pred chhhhcccCCCCCceeccCCCCC
Confidence 58999999999986655554443
No 22
>PRK12407 flgH flagellar basal body L-ring protein; Reviewed
Probab=24.72 E-value=33 Score=26.11 Aligned_cols=14 Identities=43% Similarity=0.802 Sum_probs=11.7
Q ss_pred HHHHhcCeeEEeee
Q 034648 60 RLKRMGDVLTIVVV 73 (88)
Q Consensus 60 ~l~r~gdvLT~vVv 73 (88)
|-.++||+|||++.
T Consensus 63 rA~~VGDiiTV~i~ 76 (221)
T PRK12407 63 RAYRVGDILTVILD 76 (221)
T ss_pred cccCCCCEEEEEEE
Confidence 45689999999886
No 23
>TIGR00726 uncharacterized protein, YfiH family. PSI-BLAST converges on members of this family of uncharacterized bacterial proteins and shows no significant similarity to any characterized protein. No completed genome to date has two members. Members of the family have been crystallized but the function is unknown.
Probab=24.46 E-value=62 Score=23.80 Aligned_cols=10 Identities=10% Similarity=0.199 Sum_probs=8.0
Q ss_pred eeeccceeee
Q 034648 72 VVAGKTGDFG 81 (88)
Q Consensus 72 VvagC~yei~ 81 (88)
-+.+||||+.
T Consensus 135 ~I~~~cYEV~ 144 (221)
T TIGR00726 135 AIGGCCYEVD 144 (221)
T ss_pred ccCCcceeEC
Confidence 4678999984
No 24
>PRK00249 flgH flagellar basal body L-ring protein; Reviewed
Probab=23.17 E-value=40 Score=25.46 Aligned_cols=15 Identities=40% Similarity=0.760 Sum_probs=12.2
Q ss_pred HHHHHhcCeeEEeee
Q 034648 59 WRLKRMGDVLTIVVV 73 (88)
Q Consensus 59 ~~l~r~gdvLT~vVv 73 (88)
.|-.++||++||+|.
T Consensus 61 ~rA~~VGDivTV~i~ 75 (222)
T PRK00249 61 RRARNVGDILTVVLQ 75 (222)
T ss_pred cccccCCCeEEEEEE
Confidence 355789999999985
No 25
>PF02212 GED: Dynamin GTPase effector domain; InterPro: IPR003130 Dynamin GTPase effector domain found in proteins related to dynamin. Dynamin is a GTP-hydrolysing protein that is an essential participant in clathrin-mediated endocytosis by cells. It self-assembles into 'collars' in vivo at the necks of invaginated coated pits; the self-assembly of dynamin being coordinated by the GTPase domain. Mutation studies indicate that dynamin functions as a molecular regulator of receptor-mediated endocytosis [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 3ZYS_B 3SZR_A 3LJB_B 3T35_C 3T34_A 2X2F_D 2X2E_D 3SNH_A 3ZYC_D 3ZVR_A.
Probab=23.10 E-value=41 Score=21.24 Aligned_cols=30 Identities=33% Similarity=0.513 Sum_probs=19.2
Q ss_pred ccccccchhhhh-hhhhhHHHHHHHHhcCee
Q 034648 39 KALLADDPVLKR-FKSHKKSVWRLKRMGDVL 68 (88)
Q Consensus 39 KALL~eD~aLKr-FKS~K~sv~~l~r~gdvL 68 (88)
..||+|||.... =+.-++.+++|+++-++|
T Consensus 59 ~~Ll~Ed~~i~~kR~~l~~~~~~L~~A~~~L 89 (92)
T PF02212_consen 59 EELLQEDPEIAEKREELKKKLERLKKAQQIL 89 (92)
T ss_dssp CCCT--GHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 468999998753 355677777777766554
No 26
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=22.92 E-value=70 Score=19.35 Aligned_cols=22 Identities=18% Similarity=0.231 Sum_probs=19.1
Q ss_pred chhhhhhhhhhHHHHHHHHhcC
Q 034648 45 DPVLKRFKSHKKSVWRLKRMGD 66 (88)
Q Consensus 45 D~aLKrFKS~K~sv~~l~r~gd 66 (88)
+|.++|...|-+-+++|+..|-
T Consensus 5 ~~ti~RL~~Y~r~L~~l~~~G~ 26 (50)
T PF06971_consen 5 KATIRRLPLYLRYLEQLKEEGV 26 (50)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHHHHHHHHHcCC
Confidence 5789999999999999998774
No 27
>PRK12788 flgH flagellar basal body L-ring protein; Reviewed
Probab=21.87 E-value=44 Score=25.86 Aligned_cols=14 Identities=43% Similarity=0.774 Sum_probs=11.8
Q ss_pred HHHHhcCeeEEeee
Q 034648 60 RLKRMGDVLTIVVV 73 (88)
Q Consensus 60 ~l~r~gdvLT~vVv 73 (88)
|-.++||+||+++.
T Consensus 73 RA~~VGDIlTV~I~ 86 (234)
T PRK12788 73 RASRTGDLLTVTIS 86 (234)
T ss_pred ccccCCCeEEEEEE
Confidence 45689999999885
No 28
>PF06161 DUF975: Protein of unknown function (DUF975); InterPro: IPR010380 This is a family of uncharacterised bacterial proteins.
Probab=21.42 E-value=54 Score=23.22 Aligned_cols=22 Identities=41% Similarity=0.575 Sum_probs=18.9
Q ss_pred ccccchhhhhhhhhhHHHHHHH
Q 034648 41 LLADDPVLKRFKSHKKSVWRLK 62 (88)
Q Consensus 41 LL~eD~aLKrFKS~K~sv~~l~ 62 (88)
+|+|||.++.++.-|.|.+-++
T Consensus 172 il~d~~~~~~~~al~~S~~lmk 193 (243)
T PF06161_consen 172 ILADNPELGAFEALKRSRKLMK 193 (243)
T ss_pred HHHhCcCCCHHHHHHHHHHHHh
Confidence 6789999999999999987665
No 29
>PRK12701 flgH flagellar basal body L-ring protein; Reviewed
Probab=21.25 E-value=43 Score=25.66 Aligned_cols=14 Identities=36% Similarity=0.766 Sum_probs=11.6
Q ss_pred HHHHhcCeeEEeee
Q 034648 60 RLKRMGDVLTIVVV 73 (88)
Q Consensus 60 ~l~r~gdvLT~vVv 73 (88)
|-.++||++||++.
T Consensus 67 rA~~VGDiiTV~i~ 80 (230)
T PRK12701 67 RARHPGDILTVYLI 80 (230)
T ss_pred ccccCCCEEEEEEE
Confidence 45689999999875
No 30
>PF06732 Pescadillo_N: Pescadillo N-terminus; InterPro: IPR010613 Pescadillo protein localises to distinct substructures of the interphase nucleus including nucleoli, the site of ribosome biogenesis. During mitosis pescadillo closely associates with the periphery of metaphase chromosomes and by late anaphase is associated with nucleolus-derived foci and prenucleolar bodies. Blastomeres in mouse embryos lacking pescadillo arrest at morula stages of development, the nucleoli fail to differentiate and accumulation of ribosomes is inhibited. It has been proposed that in mammalian cells pescadillo is essential for ribosome biogenesis and nucleologenesis and that disruption to its function results in cell cycle arrest []. ; GO: 0042254 ribosome biogenesis, 0005730 nucleolus
Probab=20.32 E-value=76 Score=25.52 Aligned_cols=28 Identities=25% Similarity=0.604 Sum_probs=24.4
Q ss_pred ccccccccchhhhhhhhhhHHHHHHHHh
Q 034648 37 REKALLADDPVLKRFKSHKKSVWRLKRM 64 (88)
Q Consensus 37 ReKALL~eD~aLKrFKS~K~sv~~l~r~ 64 (88)
..-+-|..||-+..|+.||.-.++++|+
T Consensus 63 KDI~~L~hepil~kfRe~k~~~kK~~ka 90 (281)
T PF06732_consen 63 KDIKFLAHEPILQKFREIKAFLKKLRKA 90 (281)
T ss_pred HHHHHHhccHHHHHHHHHHHHHHHHHHH
Confidence 4556899999999999999999998875
Done!