Query psy176
Match_columns 101
No_of_seqs 46 out of 48
Neff 2.8
Searched_HMMs 46136
Date Fri Aug 16 18:12:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy176.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/176hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0163|consensus 99.8 2.8E-21 6E-26 173.8 5.2 64 38-101 1-64 (1259)
2 PF02736 Myosin_N: Myosin N-te 99.3 2.2E-12 4.7E-17 77.1 5.3 42 41-84 1-42 (42)
3 PTZ00014 myosin-A; Provisional 97.8 4.4E-05 9.5E-10 68.5 5.6 62 40-101 32-103 (821)
4 KOG0161|consensus 97.1 0.0008 1.7E-08 65.7 5.1 63 36-99 25-87 (1930)
5 PF09378 HAS-barrel: HAS barre 83.9 2.5 5.3E-05 26.7 4.1 47 18-64 1-49 (91)
6 PF08141 SspH: Small acid-solu 81.8 2.6 5.6E-05 27.3 3.6 35 40-84 21-55 (58)
7 cd04508 TUDOR Tudor domains ar 78.0 8.6 0.00019 21.7 4.6 45 41-86 1-47 (48)
8 cd01734 YlxS_C YxlS is a Bacil 76.9 12 0.00026 24.4 5.6 35 54-88 42-77 (83)
9 TIGR02861 SASP_H small acid-so 74.6 4.8 0.0001 26.1 3.2 23 40-62 21-43 (58)
10 PF02576 DUF150: Uncharacteris 70.9 12 0.00026 26.4 4.8 47 41-87 89-138 (141)
11 PF03242 LEA_3: Late embryogen 67.7 2.3 4.9E-05 29.7 0.6 15 40-54 59-73 (93)
12 PF00567 TUDOR: Tudor domain; 67.0 23 0.00051 22.0 5.1 46 44-90 59-105 (121)
13 PRK14639 hypothetical protein; 64.5 24 0.00051 25.6 5.4 47 41-88 88-134 (140)
14 PRK03174 sspH acid-soluble spo 64.0 11 0.00023 24.7 3.1 23 40-62 21-43 (59)
15 PRK01625 sspH acid-soluble spo 60.7 13 0.00029 24.3 3.2 24 40-63 21-44 (59)
16 PRK00092 ribosome maturation p 60.0 26 0.00057 25.3 4.9 37 51-88 112-148 (154)
17 PF06856 DUF1251: Protein of u 57.5 53 0.0011 24.1 6.2 66 27-96 8-74 (120)
18 PF07039 DUF1325: SGF29 tudor- 56.6 49 0.0011 23.8 5.8 43 47-89 13-59 (130)
19 PRK14637 hypothetical protein; 53.9 41 0.00089 24.8 5.2 45 41-88 98-143 (151)
20 PF02237 BPL_C: Biotin protein 52.9 46 0.001 19.6 5.0 43 41-85 3-45 (48)
21 PRK14636 hypothetical protein; 50.2 54 0.0012 24.8 5.4 44 43-88 102-147 (176)
22 cd05841 BS69_related The PWWP 48.2 64 0.0014 22.0 5.1 52 40-91 9-60 (83)
23 PRK14638 hypothetical protein; 46.3 55 0.0012 24.0 4.8 45 41-88 100-144 (150)
24 PF10369 ALS_ss_C: Small subun 46.1 20 0.00043 23.3 2.2 18 56-73 28-45 (75)
25 smart00333 TUDOR Tudor domain. 42.9 66 0.0014 18.5 5.6 50 39-89 4-54 (57)
26 cd06080 MUM1_like Mutated mela 40.5 80 0.0017 21.3 4.6 52 40-91 3-56 (80)
27 PRK02001 hypothetical protein; 40.3 99 0.0021 23.0 5.4 47 41-87 90-147 (152)
28 cd07246 Glo_EDI_BRP_like_8 Thi 39.9 37 0.0008 21.0 2.7 17 38-55 101-117 (122)
29 PF00855 PWWP: PWWP domain; I 39.1 95 0.0021 19.2 5.5 49 40-89 3-59 (86)
30 PF04385 FAINT: Domain of unkn 38.7 75 0.0016 18.0 4.9 39 33-71 34-73 (78)
31 PF02874 ATP-synt_ab_N: ATP sy 37.1 82 0.0018 19.0 3.9 23 51-73 33-55 (69)
32 PRK14641 hypothetical protein; 36.9 1.2E+02 0.0025 23.1 5.4 48 41-88 104-167 (173)
33 COG0779 Uncharacterized protei 36.0 1.2E+02 0.0026 22.8 5.3 43 44-89 104-148 (153)
34 PF07076 DUF1344: Protein of u 35.7 72 0.0016 21.1 3.6 31 54-86 5-35 (61)
35 PF13122 DUF3977: Protein of u 34.2 17 0.00037 25.2 0.5 31 21-55 31-61 (77)
36 PF03055 RPE65: Retinal pigmen 33.7 1.2E+02 0.0026 25.2 5.5 46 29-74 409-459 (486)
37 PHA02580 8 baseplate wedge sub 33.3 66 0.0014 27.4 3.9 47 5-59 222-272 (331)
38 PRK04012 translation initiatio 33.2 1.5E+02 0.0033 20.7 5.2 39 41-81 10-49 (100)
39 PF06312 Neurexophilin: Neurex 33.0 60 0.0013 25.8 3.5 22 47-69 79-100 (219)
40 PF15057 DUF4537: Domain of un 32.8 1.2E+02 0.0026 21.4 4.7 52 35-88 53-112 (124)
41 cd05791 S1_CSL4 S1_CSL4: CSL4, 31.6 74 0.0016 21.2 3.3 38 53-90 9-46 (92)
42 PRK14644 hypothetical protein; 31.1 88 0.0019 22.7 3.8 35 51-85 99-134 (136)
43 PRK14647 hypothetical protein; 31.1 83 0.0018 23.1 3.7 34 53-88 120-153 (159)
44 COG1097 RRP4 RNA-binding prote 30.9 1.9E+02 0.0041 23.6 6.0 50 18-73 37-86 (239)
45 PRK11713 16S ribosomal RNA met 30.3 1.3E+02 0.0029 22.7 4.8 35 38-72 30-64 (234)
46 TIGR00119 acolac_sm acetolacta 30.3 34 0.00073 25.5 1.6 19 55-73 108-126 (157)
47 TIGR00046 RNA methyltransferas 29.7 1.4E+02 0.003 22.8 4.8 34 38-71 32-65 (240)
48 PF11160 DUF2945: Protein of u 29.0 1.6E+02 0.0034 19.1 4.4 36 42-84 3-38 (62)
49 PRK14645 hypothetical protein; 29.0 1.5E+02 0.0032 22.0 4.7 42 41-86 102-143 (154)
50 cd05834 HDGF_related The PWWP 27.9 1.5E+02 0.0031 19.6 4.2 50 40-92 5-61 (83)
51 PF04452 Methyltrans_RNA: RNA 27.4 1.2E+02 0.0025 22.8 4.1 34 38-71 17-50 (225)
52 PRK14634 hypothetical protein; 26.8 96 0.0021 22.8 3.5 34 52-88 115-148 (155)
53 COG1047 SlpA FKBP-type peptidy 26.8 1.2E+02 0.0026 23.4 4.1 36 37-73 90-128 (174)
54 TIGR00739 yajC preprotein tran 26.3 84 0.0018 21.1 2.8 19 52-70 48-66 (84)
55 CHL00100 ilvH acetohydroxyacid 25.9 42 0.00091 25.4 1.5 43 28-73 85-127 (174)
56 PRK11895 ilvH acetolactate syn 25.6 43 0.00093 25.0 1.4 44 27-73 84-127 (161)
57 PRK06764 hypothetical protein; 25.5 55 0.0012 23.8 1.9 39 48-87 49-100 (105)
58 PF06620 DUF1150: Protein of u 25.4 73 0.0016 21.5 2.4 32 28-59 25-56 (76)
59 PRK04163 exosome complex RNA-b 25.2 3.1E+02 0.0067 21.1 6.1 64 17-87 35-98 (235)
60 PF06605 Prophage_tail: Propha 24.9 1E+02 0.0022 23.9 3.4 47 14-63 243-290 (327)
61 PF01330 RuvA_N: RuvA N termin 24.9 1.1E+02 0.0023 18.8 2.9 30 52-82 3-32 (61)
62 PF05239 PRC: PRC-barrel domai 24.8 1.7E+02 0.0037 17.7 4.7 47 41-90 11-67 (79)
63 PF04717 Phage_base_V: Phage-r 24.6 89 0.0019 19.7 2.6 27 33-59 39-69 (79)
64 KOG1719|consensus 24.3 51 0.0011 26.1 1.6 24 3-29 18-41 (183)
65 PRK14646 hypothetical protein; 24.1 2.4E+02 0.0052 20.7 5.1 35 52-89 115-149 (155)
66 PF05971 Methyltransf_10: Prot 24.1 50 0.0011 27.1 1.7 13 5-17 246-258 (299)
67 smart00743 Agenet Tudor-like d 24.0 1.7E+02 0.0036 17.3 5.4 51 40-90 5-58 (61)
68 TIGR00523 eIF-1A eukaryotic/ar 23.8 2.6E+02 0.0056 19.5 5.8 39 42-82 9-48 (99)
69 PRK10424 ilvG operon leader pe 23.4 73 0.0016 18.9 1.8 12 12-23 7-18 (32)
70 PRK02118 V-type ATP synthase s 23.2 4.4E+02 0.0096 22.9 7.2 55 10-73 3-57 (436)
71 PRK08472 fliI flagellum-specif 22.2 4.3E+02 0.0093 22.8 6.9 35 39-73 38-73 (434)
72 PRK14643 hypothetical protein; 21.5 1.5E+02 0.0032 22.2 3.6 35 54-88 121-158 (164)
73 PRK09521 exosome complex RNA-b 20.8 3.5E+02 0.0076 19.9 5.6 25 47-71 60-85 (189)
74 PRK07196 fliI flagellum-specif 20.6 2.1E+02 0.0045 24.7 4.7 35 38-73 36-71 (434)
75 PF08661 Rep_fac-A_3: Replicat 20.4 2.3E+02 0.0049 19.1 4.1 29 54-84 23-53 (109)
No 1
>KOG0163|consensus
Probab=99.83 E-value=2.8e-21 Score=173.82 Aligned_cols=64 Identities=41% Similarity=0.741 Sum_probs=62.8
Q ss_pred ccCCcEEEecCCCCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecCcCCCCCCcCCCCC
Q psy176 38 LMENQKVWVPDPADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTAEEHDSKDVDDNYS 101 (101)
Q Consensus 38 md~gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPAeED~~KDVDDNCs 101 (101)
|++||+||+||++|||++|||+|||.+++|+.|+|.++++++|.|+||+|+|||..|||||||+
T Consensus 1 ~e~gr~VWi~d~tdGf~~~rI~di~~~~ftl~~~d~k~~t~~~~~edv~a~eeD~~k~veDNC~ 64 (1259)
T KOG0163|consen 1 LEDGRLVWIRDATDGFIAGRITDIGAKGFTLTPLDRKGPTVTRHFEDVHACEEDSPKDVEDNCE 64 (1259)
T ss_pred CCCCceEeecccccchhheeeeeecCCceEEeecccCCcceeehhhhccccccccccccccccc
Confidence 6899999999999999999999999999999999999999999999999999999999999996
No 2
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=99.35 E-value=2.2e-12 Score=77.11 Aligned_cols=42 Identities=40% Similarity=0.696 Sum_probs=38.2
Q ss_pred CcEEEecCCCCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCc
Q psy176 41 NQKVWVPDPADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDR 84 (101)
Q Consensus 41 gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~ydd 84 (101)
++.||+|||++||++|+|+++.++.+||++.+ +++++++.||
T Consensus 1 K~~vWvpD~~egfv~g~I~~~~g~~vtV~~~~--G~~~tv~~dd 42 (42)
T PF02736_consen 1 KKWVWVPDPKEGFVKGEIIEEEGDKVTVKTED--GKEVTVKKDD 42 (42)
T ss_dssp TTEEEEEESSSSEEEEEEEEEESSEEEEEETT--TEEEEEEGGG
T ss_pred CCEEEEeCCcccEEEEEEEEEcCCEEEEEECC--CCEEEeCCCC
Confidence 47899999999999999999999999999997 5788888775
No 3
>PTZ00014 myosin-A; Provisional
Probab=97.76 E-value=4.4e-05 Score=68.52 Aligned_cols=62 Identities=16% Similarity=0.215 Sum_probs=52.6
Q ss_pred CCcEEEe-------cCCCCCeEEEEEE-EccCCeEEEEEcC-CCCCeEEecCCceecCcCCC-CCCcCCCCC
Q psy176 40 ENQKVWV-------PDPADGFVLGRIL-DLGMDEVTVQPLD-SKKPKAAFSLDRVYTAEEHD-SKDVDDNYS 101 (101)
Q Consensus 40 ~gq~VWa-------pDp~eGFiLgrIv-DIG~d~~TVqPld-~k~~~~~~~yddVFPAeED~-~KDVDDNCs 101 (101)
.|-.||. +||++||++|+|+ +...+.++|+.++ .++++++++.+++|++.... ...+||.|.
T Consensus 32 ~g~~vw~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~n~~~~~~~~~Dl~~ 103 (821)
T PTZ00014 32 KGFYVWTDKAPAVKEDPDLMFAKCLVLPGSTGEKLTLKQIDPPTNSTFEVKPEHAFNANSQIDPMTYGDIGL 103 (821)
T ss_pred cCCeEEeeCCCCCCCCchhheeeEEEEEecCCCEEEEEEecCCCCcEEEeeHHHhhhcCCCCCcCCcchhhh
Confidence 5788997 7899999999999 9999999999875 46899999999999998742 235788773
No 4
>KOG0161|consensus
Probab=97.06 E-value=0.0008 Score=65.70 Aligned_cols=63 Identities=27% Similarity=0.374 Sum_probs=50.4
Q ss_pred ccccCCcEEEecCCCCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecCcCCCCCCcCCC
Q psy176 36 PYLMENQKVWVPDPADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTAEEHDSKDVDDN 99 (101)
Q Consensus 36 ~~md~gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPAeED~~KDVDDN 99 (101)
+|.+..+.||+||+++||+.|.|..=..++++|.-.++ +......=++|+|...---..|||=
T Consensus 25 ~~~d~kk~vWvpd~~e~fv~~~i~~~~~~~v~v~~~~~-~~~~~v~~~~v~~~NPPkfdk~eDM 87 (1930)
T KOG0161|consen 25 RPFDSKKWVWVPDPKEGFVKAEIKSEEGEKVTVETEEG-GTLTQVKEDDVQKMNPPKFDKVEDM 87 (1930)
T ss_pred cchhhcceeeecCCCCCeeeeeeeccCCCceEEEEcCC-ceeEEecHHHcCcCCCCCccccccH
Confidence 78899999999999999999999988777899986655 3444488999999986433355553
No 5
>PF09378 HAS-barrel: HAS barrel domain; InterPro: IPR018538 The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family []. ; PDB: 3OAA_I.
Probab=83.87 E-value=2.5 Score=26.73 Aligned_cols=47 Identities=17% Similarity=0.232 Sum_probs=29.0
Q ss_pred EEEEEeeeecceeeeeeec--cccCCcEEEecCCCCCeEEEEEEEccCC
Q psy176 18 ISVVVGAVDFESVVYKFKP--YLMENQKVWVPDPADGFVLGRILDLGMD 64 (101)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~--~md~gq~VWapDp~eGFiLgrIvDIG~d 64 (101)
|..|+|...-....+...+ ++.-|.-|=+++...+.+||+|++|...
T Consensus 1 IG~ViG~~s~~~~~f~~~~~~~v~~GeyV~i~~~~~~~vlG~V~~i~~~ 49 (91)
T PF09378_consen 1 IGYVIGETSSNEFEFIVEPSKDVRVGEYVVIEYDDGEKVLGMVTSISRG 49 (91)
T ss_dssp -----EEEEEETTEEEEEE-TT-BTTEEEEES----TTEEEEEEEEES-
T ss_pred CCcccCceeEeeEEEEEeCCCCCCcCeEEEEEEechhhhhhhhheeEEc
Confidence 4566776665555555566 7888999999999999999999999984
No 6
>PF08141 SspH: Small acid-soluble spore protein H family; InterPro: IPR012610 This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties [].; GO: 0030436 asexual sporulation, 0042601 endospore-forming forespore
Probab=81.81 E-value=2.6 Score=27.32 Aligned_cols=35 Identities=17% Similarity=0.424 Sum_probs=24.4
Q ss_pred CCcEEEecCCCCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCc
Q psy176 40 ENQKVWVPDPADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDR 84 (101)
Q Consensus 40 ~gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~ydd 84 (101)
.|++||+-+-.+ ..++.+|.|+++..+...+|..+
T Consensus 21 ~G~pV~Ie~vde----------~~~tA~V~~l~~p~~~~~Vpv~~ 55 (58)
T PF08141_consen 21 NGVPVWIEHVDE----------ENGTARVHPLDNPEEEQEVPVND 55 (58)
T ss_pred CCEEEEEEEEcC----------CCCeEEEEECCCCCcEEEEEHHH
Confidence 589999988655 45666677776666666666544
No 7
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=78.03 E-value=8.6 Score=21.71 Aligned_cols=45 Identities=11% Similarity=0.043 Sum_probs=32.6
Q ss_pred CcEEEecCCC-CCeEEEEEEEcc-CCeEEEEEcCCCCCeEEecCCcee
Q psy176 41 NQKVWVPDPA-DGFVLGRILDLG-MDEVTVQPLDSKKPKAAFSLDRVY 86 (101)
Q Consensus 41 gq~VWapDp~-eGFiLgrIvDIG-~d~~TVqPld~k~~~~~~~yddVF 86 (101)
|+.+-|+.+. .-|--|+|+.+. .+.++|.-+|- +..-..+.+++.
T Consensus 1 G~~c~a~~~~d~~wyra~V~~~~~~~~~~V~f~Dy-G~~~~v~~~~l~ 47 (48)
T cd04508 1 GDLCLAKYSDDGKWYRAKITSILSDGKVEVFFVDY-GNTEVVPLSDLR 47 (48)
T ss_pred CCEEEEEECCCCeEEEEEEEEECCCCcEEEEEEcC-CCcEEEeHHHcC
Confidence 4667777776 668889999998 88899999984 333334555543
No 8
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=76.86 E-value=12 Score=24.44 Aligned_cols=35 Identities=23% Similarity=0.314 Sum_probs=26.8
Q ss_pred EEEEEEEccCCeEEEEEcC-CCCCeEEecCCceecC
Q psy176 54 VLGRILDLGMDEVTVQPLD-SKKPKAAFSLDRVYTA 88 (101)
Q Consensus 54 iLgrIvDIG~d~~TVqPld-~k~~~~~~~yddVFPA 88 (101)
..|+|.++..+++++.+-. +.+++++.||++|=-|
T Consensus 42 ~~G~L~~~~~~~v~l~~~~~~~~~~~~i~~~~I~ka 77 (83)
T cd01734 42 FEGTLLGVDDDTVTLEVDIKTRGKTVEIPLDKIAKA 77 (83)
T ss_pred EEEEEEeEeCCEEEEEEecCCCCeEEEEEhHHeeEE
Confidence 4799999999999998642 1256889999987533
No 9
>TIGR02861 SASP_H small acid-soluble spore protein, H-type. This model is derived from pfam08141 but has been expanded to include in the seed corresponding proteins from three species of Clostridium. Members of this family should occur only in endospore-forming bacteria, typically with two members per genome, but may be absent from the genomes of some endospore-forming bacteria. SspH (previously designated YfjU) was shown to be expressed specifically in spores of Bacillus subtilis.
Probab=74.62 E-value=4.8 Score=26.09 Aligned_cols=23 Identities=13% Similarity=0.221 Sum_probs=17.1
Q ss_pred CCcEEEecCCCCCeEEEEEEEcc
Q psy176 40 ENQKVWVPDPADGFVLGRILDLG 62 (101)
Q Consensus 40 ~gq~VWapDp~eGFiLgrIvDIG 62 (101)
.|+.||+-+-.|+=-.|||..++
T Consensus 21 ~G~pV~Ie~vde~~~tA~V~~l~ 43 (58)
T TIGR02861 21 KGVPVYIEHVDEQSGTARVYSLD 43 (58)
T ss_pred CCEEEEEEEEcCCCCeEEEEECC
Confidence 58999999987776666665555
No 10
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=70.89 E-value=12 Score=26.45 Aligned_cols=47 Identities=21% Similarity=0.381 Sum_probs=30.9
Q ss_pred CcEEEecCCCCC--eEEEEEEEccCCeEEEEEcCCC-CCeEEecCCceec
Q psy176 41 NQKVWVPDPADG--FVLGRILDLGMDEVTVQPLDSK-KPKAAFSLDRVYT 87 (101)
Q Consensus 41 gq~VWapDp~eG--FiLgrIvDIG~d~~TVqPld~k-~~~~~~~yddVFP 87 (101)
.=.||...+.+| -+.|++.+...++++++.-+.+ .++++.||++|=-
T Consensus 89 ~v~v~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~~I~k 138 (141)
T PF02576_consen 89 KVKVKLKQPVNGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFSDIKK 138 (141)
T ss_dssp EEEEE-SS-SSS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS--SS
T ss_pred eEEEEEeccCCCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHHHCce
Confidence 346777677776 5789999999999999755431 2488999998743
No 11
>PF03242 LEA_3: Late embryogenesis abundant protein; InterPro: IPR004926 Late-embryogenesis abundant (LEA) genes encode a diverse group of proteins that accumulate to high levels during the maturation phase of seed development []. This group includes LEA-5 [], whose expression is induced by salt, drought and heat stress [], and related proteins. ; GO: 0006950 response to stress
Probab=67.70 E-value=2.3 Score=29.74 Aligned_cols=15 Identities=33% Similarity=1.090 Sum_probs=12.3
Q ss_pred CCcEEEecCCCCCeE
Q psy176 40 ENQKVWVPDPADGFV 54 (101)
Q Consensus 40 ~gq~VWapDp~eGFi 54 (101)
..+.-|+|||.-||=
T Consensus 59 ~~~~~W~pDPvTGyy 73 (93)
T PF03242_consen 59 KEKSSWMPDPVTGYY 73 (93)
T ss_pred ccccccccCCCCccc
Confidence 346789999999984
No 12
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=67.02 E-value=23 Score=22.03 Aligned_cols=46 Identities=13% Similarity=0.113 Sum_probs=36.6
Q ss_pred EEecCCCCCeEEEEE-EEccCCeEEEEEcCCCCCeEEecCCceecCcC
Q psy176 44 VWVPDPADGFVLGRI-LDLGMDEVTVQPLDSKKPKAAFSLDRVYTAEE 90 (101)
Q Consensus 44 VWapDp~eGFiLgrI-vDIG~d~~TVqPld~k~~~~~~~yddVFPAeE 90 (101)
+=+.....+|-=|+| .+.+.+.+.|+-+|- |.+..++.+++++..+
T Consensus 59 ~~~~~~~~~w~Ra~I~~~~~~~~~~V~~iD~-G~~~~v~~~~l~~l~~ 105 (121)
T PF00567_consen 59 LCVVSEDGRWYRAVITVDIDENQYKVFLIDY-GNTEKVSASDLRPLPP 105 (121)
T ss_dssp EEEETTTSEEEEEEEEEEECTTEEEEEETTT-TEEEEEEGGGEEE--H
T ss_pred EEEEecCCceeeEEEEEecccceeEEEEEec-CceEEEcHHHhhhhCH
Confidence 334455668888999 999999999999999 8888899999997653
No 13
>PRK14639 hypothetical protein; Provisional
Probab=64.52 E-value=24 Score=25.65 Aligned_cols=47 Identities=17% Similarity=0.328 Sum_probs=33.5
Q ss_pred CcEEEecCCCCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecC
Q psy176 41 NQKVWVPDPADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTA 88 (101)
Q Consensus 41 gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPA 88 (101)
|++|=+.-.......|+|.++..++++++.+. ++++++.||++|=.|
T Consensus 88 G~~v~v~l~~~~~~~G~L~~~~~~~i~l~~~~-~~~~~~i~~~~I~ka 134 (140)
T PRK14639 88 GELVKITTNEKEKFEGKIVSVDDENITLENLE-NKEKTTINFNDIKKA 134 (140)
T ss_pred CCEEEEEECCCcEEEEEEEEEeCCEEEEEEcc-CCcEEEEEhHHeeeE
Confidence 34444433345678899999999999997653 246788999988543
No 14
>PRK03174 sspH acid-soluble spore protein H; Provisional
Probab=64.01 E-value=11 Score=24.72 Aligned_cols=23 Identities=13% Similarity=0.180 Sum_probs=18.1
Q ss_pred CCcEEEecCCCCCeEEEEEEEcc
Q psy176 40 ENQKVWVPDPADGFVLGRILDLG 62 (101)
Q Consensus 40 ~gq~VWapDp~eGFiLgrIvDIG 62 (101)
.|..||+-+-.++=-.|||..++
T Consensus 21 ~G~pV~Ie~vde~~~tA~I~~l~ 43 (59)
T PRK03174 21 NGVPIYIQHVDEQNGTARIHPLD 43 (59)
T ss_pred CCEEEEEEEEcCCCCeEEEEECC
Confidence 58999999988877777776665
No 15
>PRK01625 sspH acid-soluble spore protein H; Provisional
Probab=60.68 E-value=13 Score=24.26 Aligned_cols=24 Identities=17% Similarity=0.368 Sum_probs=17.9
Q ss_pred CCcEEEecCCCCCeEEEEEEEccC
Q psy176 40 ENQKVWVPDPADGFVLGRILDLGM 63 (101)
Q Consensus 40 ~gq~VWapDp~eGFiLgrIvDIG~ 63 (101)
.|+.||+-+-.++=-.|||..++.
T Consensus 21 ~G~pV~Iq~vde~~~tA~V~~~~~ 44 (59)
T PRK01625 21 EGVPVWIESCDEQSGVAQVYDVSN 44 (59)
T ss_pred CCEEEEEEEEcCCCCeEEEEecCC
Confidence 589999999877766666666543
No 16
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=59.96 E-value=26 Score=25.30 Aligned_cols=37 Identities=19% Similarity=0.238 Sum_probs=28.0
Q ss_pred CCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecC
Q psy176 51 DGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTA 88 (101)
Q Consensus 51 eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPA 88 (101)
.-...|+|.++..+++++++-..+ ++++.+|++|=.|
T Consensus 112 ~~~~~G~L~~~~~~~i~l~~~~~~-~~~~i~~~~I~~a 148 (154)
T PRK00092 112 RKKFQGILLAVDGETVTLEVEGKE-KEVEIPLDNIAKA 148 (154)
T ss_pred ceEEEEEEEEeeCCEEEEEECCCe-EEEEEEHHHcceE
Confidence 345679999999999999865322 4889999987543
No 17
>PF06856 DUF1251: Protein of unknown function (DUF1251); InterPro: IPR009661 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf17; it is a family of uncharacterised viral proteins.
Probab=57.47 E-value=53 Score=24.13 Aligned_cols=66 Identities=14% Similarity=0.228 Sum_probs=44.6
Q ss_pred cceeeeeeeccccCCcEEEecCC-CCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecCcCCCCCCc
Q psy176 27 FESVVYKFKPYLMENQKVWVPDP-ADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTAEEHDSKDV 96 (101)
Q Consensus 27 ~~~~~~~~~~~md~gq~VWapDp-~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPAeED~~KDV 96 (101)
=.+++|||..+....+..=-=++ ...|++|....- .+.++| ++.+.++..+-||- ||.+||..+.+
T Consensus 8 ~~~~~~ky~i~~~~~kv~V~v~s~~~~~iQatF~~~-~~~v~i--VNa~~~~~~i~FDG-F~d~~DE~~T~ 74 (120)
T PF06856_consen 8 CKSPFYKYRIPSSCAKVRVRVDSFDNKYIQATFCCG-HKHVCI--VNARDKQRPIVFDG-FPDEDDEGKTV 74 (120)
T ss_pred CCcEEEEEEccCCCcEEEEEEccCCCceEEEEEEeC-CceEEE--EeccCCCCceEECC-CCCcccccccc
Confidence 35788999887754333333355 899999999875 777888 66445666667766 55777766654
No 18
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=56.58 E-value=49 Score=23.78 Aligned_cols=43 Identities=14% Similarity=0.285 Sum_probs=34.2
Q ss_pred cCCCCCeEEEEEEEccCCe--EEEEEcCCC--CCeEEecCCceecCc
Q psy176 47 PDPADGFVLGRILDLGMDE--VTVQPLDSK--KPKAAFSLDRVYTAE 89 (101)
Q Consensus 47 pDp~eGFiLgrIvDIG~d~--~TVqPld~k--~~~~~~~yddVFPAe 89 (101)
.+..+.+|||+|+..-+++ ++|+=.+.. .+.+.++..+|-|--
T Consensus 13 ~~~~~~WIla~Vv~~~~~~~rYeV~D~d~~~~~~~~~~~~~~iIPLP 59 (130)
T PF07039_consen 13 GNEEEEWILAEVVKYNSDGNRYEVEDPDPEEEKKRYKLSRKQIIPLP 59 (130)
T ss_dssp TTTTCEEEEEEEEEEETTTTEEEEEETTTCTTTEEEEEEGGGEEEE-
T ss_pred CCCCCCEEEEEEEEEeCCCCEEEEecCCCCCCCceEEeCHHHEEECC
Confidence 3567889999999999987 999887775 357788888887643
No 19
>PRK14637 hypothetical protein; Provisional
Probab=53.94 E-value=41 Score=24.80 Aligned_cols=45 Identities=11% Similarity=0.113 Sum_probs=32.8
Q ss_pred CcEEEec-CCCCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecC
Q psy176 41 NQKVWVP-DPADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTA 88 (101)
Q Consensus 41 gq~VWap-Dp~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPA 88 (101)
|++|=+. +....|+.|+|.++-.++++++. +++++..||++|=.|
T Consensus 98 G~~V~V~l~~~~~~~~G~L~~~~d~~v~l~~---~~~~~~i~~~~I~ka 143 (151)
T PRK14637 98 GETVKVWFECTGQWQVGTIAEADETCLVLTS---DGVPVTIPYVQITKA 143 (151)
T ss_pred CCEEEEEECCCCcEEEEEEEEEeCCEEEEEE---CCEEEEEEHHHeeeE
Confidence 4555443 23456778999999999999983 356788899987544
No 20
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=52.93 E-value=46 Score=19.65 Aligned_cols=43 Identities=21% Similarity=0.183 Sum_probs=30.6
Q ss_pred CcEEEecCCCCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCce
Q psy176 41 NQKVWVPDPADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRV 85 (101)
Q Consensus 41 gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddV 85 (101)
||.|++.. .++=+.|++.+|..++.-+.-.+. +..+...--+|
T Consensus 3 G~~V~v~~-~~~~~~G~~~gId~~G~L~v~~~~-g~~~~i~sGdv 45 (48)
T PF02237_consen 3 GQEVRVET-GDGEIEGIAEGIDDDGALLVRTED-GSIRTISSGDV 45 (48)
T ss_dssp TSEEEEEE-TSCEEEEEEEEEETTSEEEEEETT-EEEEEESSSEE
T ss_pred CCEEEEEE-CCeEEEEEEEEECCCCEEEEEECC-CCEEEEEEEEE
Confidence 78999999 667779999999999988855544 33444343333
No 21
>PRK14636 hypothetical protein; Provisional
Probab=50.16 E-value=54 Score=24.82 Aligned_cols=44 Identities=20% Similarity=0.354 Sum_probs=32.3
Q ss_pred EEEecCCCCC--eEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecC
Q psy176 43 KVWVPDPADG--FVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTA 88 (101)
Q Consensus 43 ~VWapDp~eG--FiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPA 88 (101)
+|....|.+| ...|+|.+...+.+++..- ++.+++.||++|=.|
T Consensus 102 ~V~l~~~~~g~k~~~G~L~~v~~~~v~l~~~--~~~~~~i~~~~I~kA 147 (176)
T PRK14636 102 RIALSEPLDGRKQFRGELKGIDGDTVTIADN--KAGEVILPFAAIESA 147 (176)
T ss_pred EEEEecccCCeEEEEEEEEEEeCCEEEEEEc--CCcEEEEEhHHcceE
Confidence 3444455555 6789999999999998743 246788899988655
No 22
>cd05841 BS69_related The PWWP domain is part of BS69 protein, a nuclear protein that specifically binds adenoviral E1A and Epstein-Barr viral EBNA2 proteins, suppressing their transactivation functions. BS69 is a multi-domain protein, containing bromo, PHD, PWWP, and MYND domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=48.19 E-value=64 Score=21.98 Aligned_cols=52 Identities=10% Similarity=0.201 Sum_probs=44.6
Q ss_pred CCcEEEecCCCCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecCcCC
Q psy176 40 ENQKVWVPDPADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTAEEH 91 (101)
Q Consensus 40 ~gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPAeED 91 (101)
-+.+|||--.---+==|||.+.....+.|+=..+.....-.+.++++|-++.
T Consensus 9 p~dLVwAK~kGyp~WPAkV~~~~~~~~~V~FFG~t~~~a~v~~~~i~~~~~~ 60 (83)
T cd05841 9 PHELVWAKLKGFPYWPAKVMRVEDNQVDVRFFGGQHDRAWIPSNNIQPISTE 60 (83)
T ss_pred CCCEEEEeCCCCCCCCEEEeecCCCeEEEEEcCCCCCeEEEehHHeeehhhh
Confidence 4689999987777778999999999999998875688889999999988764
No 23
>PRK14638 hypothetical protein; Provisional
Probab=46.34 E-value=55 Score=24.00 Aligned_cols=45 Identities=20% Similarity=0.231 Sum_probs=32.6
Q ss_pred CcEEEecCCCCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecC
Q psy176 41 NQKVWVPDPADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTA 88 (101)
Q Consensus 41 gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPA 88 (101)
|++|=+.--..--..|+|.++..+++++.. +++++..||++|=.|
T Consensus 100 G~~v~V~~~~~k~~~G~L~~~~~~~i~l~~---~~~~~~i~~~~I~~a 144 (150)
T PRK14638 100 GKLAKIVTKDGKTFIGRIESFVDGTITISD---EKEKYEINIDDVKRA 144 (150)
T ss_pred CCEEEEEECCCcEEEEEEEEEeCCEEEEEE---CCcEEEEEhHHcceE
Confidence 455555433345568999999999999973 457889999988644
No 24
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=46.13 E-value=20 Score=23.26 Aligned_cols=18 Identities=22% Similarity=0.477 Sum_probs=14.6
Q ss_pred EEEEEccCCeEEEEEcCC
Q psy176 56 GRILDLGMDEVTVQPLDS 73 (101)
Q Consensus 56 grIvDIG~d~~TVqPld~ 73 (101)
|+|+|++.+.+++|-.+.
T Consensus 28 a~ivd~~~~~~iie~tG~ 45 (75)
T PF10369_consen 28 ARIVDVSPDSIIIELTGT 45 (75)
T ss_dssp -EEEEEETTEEEEEEEE-
T ss_pred CEEEEECCCEEEEEEcCC
Confidence 799999999999997644
No 25
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=42.85 E-value=66 Score=18.53 Aligned_cols=50 Identities=12% Similarity=0.005 Sum_probs=36.9
Q ss_pred cCCcEEEecCCCCCeEEEEEEEccC-CeEEEEEcCCCCCeEEecCCceecCc
Q psy176 39 MENQKVWVPDPADGFVLGRILDLGM-DEVTVQPLDSKKPKAAFSLDRVYTAE 89 (101)
Q Consensus 39 d~gq~VWapDp~eGFiLgrIvDIG~-d~~TVqPld~k~~~~~~~yddVFPAe 89 (101)
.-|+.|=|+....-|--|+|+.+-. +.+.|.-+|- |.....+.+++.|-.
T Consensus 4 ~~G~~~~a~~~d~~wyra~I~~~~~~~~~~V~f~D~-G~~~~v~~~~l~~l~ 54 (57)
T smart00333 4 KVGDKVAARWEDGEWYRARIIKVDGEQLYEVFFIDY-GNEEVVPPSDLRPLP 54 (57)
T ss_pred CCCCEEEEEeCCCCEEEEEEEEECCCCEEEEEEECC-CccEEEeHHHeecCC
Confidence 3456666666344578899999999 8999999985 445567788887643
No 26
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=40.45 E-value=80 Score=21.32 Aligned_cols=52 Identities=13% Similarity=0.121 Sum_probs=36.9
Q ss_pred CCcEEEecCCCCCeEEEEEEEcc--CCeEEEEEcCCCCCeEEecCCceecCcCC
Q psy176 40 ENQKVWVPDPADGFVLGRILDLG--MDEVTVQPLDSKKPKAAFSLDRVYTAEEH 91 (101)
Q Consensus 40 ~gq~VWapDp~eGFiLgrIvDIG--~d~~TVqPld~k~~~~~~~yddVFPAeED 91 (101)
-|.+|||--..-=+==|+|.++. ...+.|.=+.+......+.+++++|-++.
T Consensus 3 ~gdlVWaK~~g~P~WPa~I~~~~~~~~k~~V~FfG~~~~~a~~~~~~l~p~~~~ 56 (80)
T cd06080 3 KNDLVWAKIQGYPWWPAVIKSISRKKQKARVNFIGDNMQSEKKGIRVVKRWLKH 56 (80)
T ss_pred CCCEEEEeCCCCCCCCEEEeeecCCCCEEEEEEeCCCCceeccchhhccccccc
Confidence 46788887655555567888884 46788887776545666788888887763
No 27
>PRK02001 hypothetical protein; Validated
Probab=40.29 E-value=99 Score=22.96 Aligned_cols=47 Identities=9% Similarity=0.165 Sum_probs=32.3
Q ss_pred CcEEEecCCCCCeEEEEEEEccCCeEEEEEcCCC-----------CCeEEecCCceec
Q psy176 41 NQKVWVPDPADGFVLGRILDLGMDEVTVQPLDSK-----------KPKAAFSLDRVYT 87 (101)
Q Consensus 41 gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~k-----------~~~~~~~yddVFP 87 (101)
|++|=+.-....-..|+|.++..+++++.+-... ++.++.+|++|=.
T Consensus 90 G~~v~V~l~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~k~~~~~~~~~~i~~~~I~k 147 (152)
T PRK02001 90 GRELEVLTKNGKKIEGELKSADENDITLEVKAREPKEGGKGKVTVEKEETITYDDIKE 147 (152)
T ss_pred CCEEEEEECCCCEEEEEEEEEeCCEEEEEEcccccccccccccccceeEEEEhHheee
Confidence 4444444334456779999999999999876421 2458888888754
No 28
>cd07246 Glo_EDI_BRP_like_8 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=39.94 E-value=37 Score=20.98 Aligned_cols=17 Identities=24% Similarity=0.171 Sum_probs=10.7
Q ss_pred ccCCcEEEecCCCCCeEE
Q psy176 38 LMENQKVWVPDPADGFVL 55 (101)
Q Consensus 38 md~gq~VWapDp~eGFiL 55 (101)
.++.+.+|+.|| +|...
T Consensus 101 ~~g~~~~~~~DP-~G~~~ 117 (122)
T cd07246 101 FWGDRYGGVRDP-FGHRW 117 (122)
T ss_pred cccceEEEEECC-CCCEE
Confidence 345567777777 66554
No 29
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=39.13 E-value=95 Score=19.24 Aligned_cols=49 Identities=14% Similarity=0.091 Sum_probs=34.7
Q ss_pred CCcEEEecCCCCCeEEEEEEEcc--------CCeEEEEEcCCCCCeEEecCCceecCc
Q psy176 40 ENQKVWVPDPADGFVLGRILDLG--------MDEVTVQPLDSKKPKAAFSLDRVYTAE 89 (101)
Q Consensus 40 ~gq~VWapDp~eGFiLgrIvDIG--------~d~~TVqPld~k~~~~~~~yddVFPAe 89 (101)
-|++|||.-..-.+==|+|++.. .+.+.|.-+++. .---++.+++.|=+
T Consensus 3 ~GdlVWaK~~g~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg~~-~~~wv~~~~i~~f~ 59 (86)
T PF00855_consen 3 PGDLVWAKLKGYPWWPARVCDPDEKSKKKRKDGHVLVRFFGDN-DYAWVKPSNIKPFS 59 (86)
T ss_dssp TTEEEEEEETTSEEEEEEEEECCHCTSCSSSSTEEEEEETTTT-EEEEEEGGGEEECC
T ss_pred CCCEEEEEeCCCCCCceEEeecccccccCCCCCEEEEEecCCC-CEEEECHHHhhChh
Confidence 47899998755555669999984 577888888764 44456666666544
No 30
>PF04385 FAINT: Domain of unknown function, DUF529; InterPro: IPR007480 This entry represents a repeated region found in several Theileria parva proteins.The repeat is normally about 70 residues long and contains a conserved aromatic residue in the middle.
Probab=38.73 E-value=75 Score=17.98 Aligned_cols=39 Identities=10% Similarity=0.141 Sum_probs=29.8
Q ss_pred eeeccccCCcEEEecCCCCCeEEEEEEEccCCe-EEEEEc
Q psy176 33 KFKPYLMENQKVWVPDPADGFVLGRILDLGMDE-VTVQPL 71 (101)
Q Consensus 33 ~~~~~md~gq~VWapDp~eGFiLgrIvDIG~d~-~TVqPl 71 (101)
+|..=+++++.||=....+.+....+.-.+... ..|...
T Consensus 34 ~~~~V~~~~~~iW~~~~~~~~~~~~~~~~~~~~~~~i~l~ 73 (78)
T PF04385_consen 34 KCTKVKYGDKTIWKSKSDEEYSKKVIYYSKNGKIKLILLL 73 (78)
T ss_pred EEEEEEECCEEEEecCCCCCccEEEEEEcCCCccEEEEEE
Confidence 344445789999999999999999998888876 444433
No 31
>PF02874 ATP-synt_ab_N: ATP synthase alpha/beta family, beta-barrel domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR004100 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the N-terminal domain, which forms a closed beta-barrel with Greek-key topology. ; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015992 proton transport, 0046034 ATP metabolic process, 0016469 proton-transporting two-sector ATPase complex; PDB: 1W0K_A 1H8H_B 2WSS_A 1EFR_A 2JIZ_H 1E1Q_A 2V7Q_B 1E79_B 1E1R_C 2XND_C ....
Probab=37.08 E-value=82 Score=18.97 Aligned_cols=23 Identities=39% Similarity=0.512 Sum_probs=21.4
Q ss_pred CCeEEEEEEEccCCeEEEEEcCC
Q psy176 51 DGFVLGRILDLGMDEVTVQPLDS 73 (101)
Q Consensus 51 eGFiLgrIvDIG~d~~TVqPld~ 73 (101)
...++|.+..+..+.+.+||+.+
T Consensus 33 ~~~~~~~Vv~~~~~~v~~~~~~~ 55 (69)
T PF02874_consen 33 GNGVLGEVVGLDEDEVRLQVFGS 55 (69)
T ss_dssp TTEEEEEEEEEETTEEEEEESSS
T ss_pred eeeeeeeecccCccEEEEEEecC
Confidence 67899999999999999999966
No 32
>PRK14641 hypothetical protein; Provisional
Probab=36.86 E-value=1.2e+02 Score=23.11 Aligned_cols=48 Identities=21% Similarity=0.320 Sum_probs=33.1
Q ss_pred CcEEEe--cCCCCC--eEEEEEEEcc-----CCeEEEEEcCCC-------CCeEEecCCceecC
Q psy176 41 NQKVWV--PDPADG--FVLGRILDLG-----MDEVTVQPLDSK-------KPKAAFSLDRVYTA 88 (101)
Q Consensus 41 gq~VWa--pDp~eG--FiLgrIvDIG-----~d~~TVqPld~k-------~~~~~~~yddVFPA 88 (101)
|++|=+ .+|.+| -..|+|.++. .+.++++|...+ .++++.++++|=.|
T Consensus 104 G~~V~V~l~~~~~~~~~~~G~L~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~~v~~A 167 (173)
T PRK14641 104 GRLLRVTYRDEEGSEHEVTGHLQEVSLTEGEGASIVLKPEQKKKKGKQEETENITLELDAVIRA 167 (173)
T ss_pred CCEEEEEEecccCCeEEEEEEEEeeecccCCCCcEEEEeccccccccCCCCceEEEEhHHccce
Confidence 455544 345555 4679999986 789999988643 24578888888655
No 33
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.05 E-value=1.2e+02 Score=22.80 Aligned_cols=43 Identities=21% Similarity=0.366 Sum_probs=31.1
Q ss_pred EEecCCCCC--eEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecCc
Q psy176 44 VWVPDPADG--FVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTAE 89 (101)
Q Consensus 44 VWapDp~eG--FiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPAe 89 (101)
||-..|.+| .-.|+|..+-.+.+++. .++ +.++.||+.|=.|.
T Consensus 104 v~l~~~~~~~k~~~G~i~~~d~~~v~~~-~~~--k~v~Ip~~~i~kAr 148 (153)
T COG0779 104 VKLRLPIEGRKKFEGKIVAVDGETVTLE-VDG--KEVEIPFSDIAKAR 148 (153)
T ss_pred EEEecccCCceEEEEEEEEEcCCeEEEE-ECC--EEEEEEcccchhhe
Confidence 344334333 44799999999999997 544 66999999886654
No 34
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=35.73 E-value=72 Score=21.07 Aligned_cols=31 Identities=16% Similarity=0.181 Sum_probs=23.8
Q ss_pred EEEEEEEccCCeEEEEEcCCCCCeEEecCCcee
Q psy176 54 VLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVY 86 (101)
Q Consensus 54 iLgrIvDIG~d~~TVqPld~k~~~~~~~yddVF 86 (101)
+-|.|..|-.++.||+.-|+ +..++|-+==|
T Consensus 5 veG~I~~id~~~~titLdDG--ksy~lp~ef~~ 35 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDG--KSYKLPEEFDF 35 (61)
T ss_pred ceEEEEEEcCCceEEEecCC--CEEECCCcccc
Confidence 46899999999999996654 77777765433
No 35
>PF13122 DUF3977: Protein of unknown function (DUF3977)
Probab=34.17 E-value=17 Score=25.21 Aligned_cols=31 Identities=19% Similarity=0.447 Sum_probs=25.0
Q ss_pred EEeeeecceeeeeeeccccCCcEEEecCCCCCeEE
Q psy176 21 VVGAVDFESVVYKFKPYLMENQKVWVPDPADGFVL 55 (101)
Q Consensus 21 ~~~~~~~~~~~~~~~~~md~gq~VWapDp~eGFiL 55 (101)
+++++-|||+--+ ++-.+.+|+-|..|||..
T Consensus 31 ii~pi~feS~Y~R----iWfrktc~I~D~KEGFKk 61 (77)
T PF13122_consen 31 IIKPIYFESLYLR----IWFRKTCFIFDTKEGFKK 61 (77)
T ss_pred cccccchheeeee----eeeccEEEEEEcHHHHHH
Confidence 5688899997543 677789999999999963
No 36
>PF03055 RPE65: Retinal pigment epithelial membrane protein; InterPro: IPR004294 Carotenoids such as beta-carotene, lycopene, lutein and beta-cryptoxanthine are produced in plants and certain bacteria, algae and fungi, where they function as accessory photosynthetic pigments and as scavengers of oxygen radicals for photoprotection. They are also essential dietary nutrients in animals. Carotenoid oxygenases cleave a variety of carotenoids into a range of biologically important products, including apocarotenoids in plants that function as hormones, pigments, flavours, floral scents and defence compounds, and retinoids in animals that function as vitamins, visual pigments and signalling molecules []. Examples of carotenoid oxygenases include: Beta-carotene-15,15'-monooxygenase (BCDO1; 1.14.99.36 from EC) from animals, which cleaves beta-carotene symmetrically at the central double bond to yield two molecules of retinal []. Beta-carotene-9',10'-dioxygenase (BCDO2) from animals, which cleaves beta-carotene asymmetrically to apo-10'-beta-carotenal and beta-ionone, the latter being converted to retinoic acid. Lycopene is also oxidatively cleaved []. 9-cis-epoxycarotenoid dioxygenase from plants, which cleaves 9-cis xanthophylls to xanthoxin, a precursor of the hormone abscisic acid []. Apocarotenoid-15,15'-oxygenase from bacteria and cyanobacteria, which converts beta-apocarotenals rather than beta-carotene into retinal. This protein has a seven-bladed beta-propeller structure with four hisitidines that hold the iron active centre []. Retinal pigment RPE65 from animals, which in its soluble form binds all-trans retinol, and in its membrane-bound form binds all-trans retinyl esters. RPE65 is important for the production of 11-cis retinal during visual pigment regeneration []. ; PDB: 3NPE_A 2BIX_B 2BIW_A 3KVC_B 3FSN_B.
Probab=33.72 E-value=1.2e+02 Score=25.19 Aligned_cols=46 Identities=28% Similarity=0.543 Sum_probs=30.0
Q ss_pred eeeeeeeccccCCcEEEecCCC-----CCeEEEEEEEccCCeEEEEEcCCC
Q psy176 29 SVVYKFKPYLMENQKVWVPDPA-----DGFVLGRILDLGMDEVTVQPLDSK 74 (101)
Q Consensus 29 ~~~~~~~~~md~gq~VWapDp~-----eGFiLgrIvDIG~d~~TVqPld~k 74 (101)
...|.|.+-.--+-.|.||.|. |||+|+-+.|-....=.+.=+|.+
T Consensus 409 ~~~~~~~~~~~~~EpvFVPr~~~~~EdDG~Ll~~v~~~~~~~s~l~VlDA~ 459 (486)
T PF03055_consen 409 VQRWSFGPGCFPGEPVFVPRPGGAEEDDGYLLSVVYDSDTNRSELLVLDAK 459 (486)
T ss_dssp EEEEE-TTTEEE--EEEEE-TTS-STT-EEEEEEEEETTTTCEEEEEEETT
T ss_pred ceEEECCCCceecceEeccCCCCCCCCceEEEEEEEECCCCccEEEEEeCC
Confidence 3566666545567899999984 999999999998655555547774
No 37
>PHA02580 8 baseplate wedge subunit; Provisional
Probab=33.25 E-value=66 Score=27.44 Aligned_cols=47 Identities=34% Similarity=0.619 Sum_probs=32.5
Q ss_pred hhcceeeEEeeeEEEEEEeeeecceeeeeeeccccCCcEEEecCC----CCCeEEEEEE
Q psy176 5 MENNLTWYTSLISISVVVGAVDFESVVYKFKPYLMENQKVWVPDP----ADGFVLGRIL 59 (101)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~md~gq~VWapDp----~eGFiLgrIv 59 (101)
.+||++||.--.-+.--++++ ..+|+++|| -+..|+. +.||.+-.|+
T Consensus 222 y~n~i~w~~~~~~liyr~k~~-----tlRFrAyld---s~~Fp~~~lpGNkGfRQiSii 272 (331)
T PHA02580 222 YENNITWYPDDYDLIYRVKAN-----TLRFRAYLD---SVYFPEASLPGNKGFRQISII 272 (331)
T ss_pred cccceeeccCCcceEEEEeee-----EEeeeeecc---cccccccccCCCCCceEEEEe
Confidence 589999997655555555554 458999994 4555554 5799886664
No 38
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=33.25 E-value=1.5e+02 Score=20.70 Aligned_cols=39 Identities=26% Similarity=0.414 Sum_probs=29.0
Q ss_pred CcEEEecCCCCCeEEEEEEEc-cCCeEEEEEcCCCCCeEEec
Q psy176 41 NQKVWVPDPADGFVLGRILDL-GMDEVTVQPLDSKKPKAAFS 81 (101)
Q Consensus 41 gq~VWapDp~eGFiLgrIvDI-G~d~~TVqPld~k~~~~~~~ 81 (101)
...+=.|-|.+|-+.|+|+.. |.+-++|+-.| +.++.|.
T Consensus 10 ~~~~~~~~p~e~e~~g~V~~~lG~~~~~V~~~d--G~~~la~ 49 (100)
T PRK04012 10 VTRVRLPMPEEGEVFGVVEQMLGANRVRVRCMD--GVERMGR 49 (100)
T ss_pred ceeEEccCCCCCEEEEEEEEEcCCCEEEEEeCC--CCEEEEE
Confidence 345567889999999999987 66778887554 4666654
No 39
>PF06312 Neurexophilin: Neurexophilin
Probab=33.03 E-value=60 Score=25.80 Aligned_cols=22 Identities=32% Similarity=0.515 Sum_probs=17.3
Q ss_pred cCCCCCeEEEEEEEccCCeEEEE
Q psy176 47 PDPADGFVLGRILDLGMDEVTVQ 69 (101)
Q Consensus 47 pDp~eGFiLgrIvDIG~d~~TVq 69 (101)
+.-+.| +.|+|+|-|.+++||.
T Consensus 79 ~~l~ag-~~G~V~Dh~NGTYtv~ 100 (219)
T PF06312_consen 79 PKLKAG-AAGKVTDHGNGTYTVS 100 (219)
T ss_pred CCcccc-ceEEEEECCCCeEEEE
Confidence 344556 7899999999998875
No 40
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=32.77 E-value=1.2e+02 Score=21.43 Aligned_cols=52 Identities=21% Similarity=0.185 Sum_probs=40.7
Q ss_pred eccccCCcEEEecCCCCC--eEEEEEE------EccCCeEEEEEcCCCCCeEEecCCceecC
Q psy176 35 KPYLMENQKVWVPDPADG--FVLGRIL------DLGMDEVTVQPLDSKKPKAAFSLDRVYTA 88 (101)
Q Consensus 35 ~~~md~gq~VWapDp~eG--FiLgrIv------DIG~d~~TVqPld~k~~~~~~~yddVFPA 88 (101)
.+++.-|..|=||++..+ |.=|+|+ .-....+||+--|+ ++..+|-+.++.-
T Consensus 53 ~~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~ng--~~~~vp~~~~~~I 112 (124)
T PF15057_consen 53 RHSLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFYNG--KTAKVPRGEVIWI 112 (124)
T ss_pred cCcCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEECC--CCCccchhhEEEC
Confidence 678888999999987444 7778999 56889999998866 4666787777643
No 41
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=31.60 E-value=74 Score=21.16 Aligned_cols=38 Identities=18% Similarity=0.127 Sum_probs=27.1
Q ss_pred eEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecCcC
Q psy176 53 FVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTAEE 90 (101)
Q Consensus 53 FiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPAeE 90 (101)
.++|||+++......+.=+.-+......+|.-+.+..+
T Consensus 9 iVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~d 46 (92)
T cd05791 9 IVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKED 46 (92)
T ss_pred EEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHH
Confidence 68999999999999887544444555666666666444
No 42
>PRK14644 hypothetical protein; Provisional
Probab=31.12 E-value=88 Score=22.72 Aligned_cols=35 Identities=14% Similarity=0.314 Sum_probs=24.6
Q ss_pred CCeEEEEEEEccCCeEEEEE-cCCCCCeEEecCCce
Q psy176 51 DGFVLGRILDLGMDEVTVQP-LDSKKPKAAFSLDRV 85 (101)
Q Consensus 51 eGFiLgrIvDIG~d~~TVqP-ld~k~~~~~~~yddV 85 (101)
...+.|++.++..++++++- ..++.++++.++++|
T Consensus 99 ~~~~~G~L~~v~~~~i~l~~~~k~~~~~i~~~~~~i 134 (136)
T PRK14644 99 TDFITGELLENNPETITLKWNCKGQFRKVEINKENI 134 (136)
T ss_pred eEEEEEEEEEEeCCEEEEEEecCCcEEEEEECHHHh
Confidence 35778999999999999972 333335566666654
No 43
>PRK14647 hypothetical protein; Provisional
Probab=31.12 E-value=83 Score=23.12 Aligned_cols=34 Identities=26% Similarity=0.320 Sum_probs=26.7
Q ss_pred eEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecC
Q psy176 53 FVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTA 88 (101)
Q Consensus 53 FiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPA 88 (101)
-..|+|.++..+.+++.+- ++++++.||++|=.|
T Consensus 120 ~~~G~L~~~~~~~v~l~~~--~~~~~~i~~~~I~ka 153 (159)
T PRK14647 120 TFLGELEGLADGVVTIALK--EGQQARIPLDKIAKA 153 (159)
T ss_pred EEEEEEEeecCCEEEEEEc--CCcEEEEEHHHCCEE
Confidence 4579999999999999764 246788899988544
No 44
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=30.85 E-value=1.9e+02 Score=23.57 Aligned_cols=50 Identities=28% Similarity=0.522 Sum_probs=34.0
Q ss_pred EEEEEeeeecceeeeeeeccccCCcEEEecCCCCCeEEEEEEEccCCeEEEEEcCC
Q psy176 18 ISVVVGAVDFESVVYKFKPYLMENQKVWVPDPADGFVLGRILDLGMDEVTVQPLDS 73 (101)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~md~gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~ 73 (101)
-|.++|-++...-.-.+ -|+ +--.+|...| ++.|+|++++.+.-.|- +.+
T Consensus 37 yssv~G~~~~~~~~v~V-Ipl---~g~YiP~~gD-~VIG~I~~v~~~~W~VD-I~s 86 (239)
T COG1097 37 YSSVVGLLDVKGKLVRV-IPL---EGRYIPEVGD-VVIGKIIEVGPSGWKVD-IGS 86 (239)
T ss_pred EEEEEeEEEEeCCEEEE-EeC---CCcccCCCCC-EEEEEEEEEcccceEEE-cCC
Confidence 36678888876544332 233 2256777665 99999999999999885 444
No 45
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=30.33 E-value=1.3e+02 Score=22.74 Aligned_cols=35 Identities=29% Similarity=0.427 Sum_probs=30.1
Q ss_pred ccCCcEEEecCCCCCeEEEEEEEccCCeEEEEEcC
Q psy176 38 LMENQKVWVPDPADGFVLGRILDLGMDEVTVQPLD 72 (101)
Q Consensus 38 md~gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld 72 (101)
+..|..+.+-+...++-.|+|++++.+.++++.+.
T Consensus 30 ~~~Gd~i~v~~g~g~~~~~~i~~i~~~~~~~~i~~ 64 (234)
T PRK11713 30 LKEGDELRLFDGDGGEYLAEITEIGKKEVELEILE 64 (234)
T ss_pred CCCCCEEEEEeCCCCEEEEEEEEecCcEEEEEEEe
Confidence 56789999999988889999999999998877553
No 46
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=30.28 E-value=34 Score=25.47 Aligned_cols=19 Identities=37% Similarity=0.497 Sum_probs=16.6
Q ss_pred EEEEEEccCCeEEEEEcCC
Q psy176 55 LGRILDLGMDEVTVQPLDS 73 (101)
Q Consensus 55 LgrIvDIG~d~~TVqPld~ 73 (101)
-|+|+|++.+++++|-...
T Consensus 108 ~a~ivdv~~~~~~ie~tG~ 126 (157)
T TIGR00119 108 RGRIVDVSPDSYTVEVTGD 126 (157)
T ss_pred CCEEEEecCCEEEEEEcCC
Confidence 4899999999999997754
No 47
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=29.69 E-value=1.4e+02 Score=22.83 Aligned_cols=34 Identities=18% Similarity=0.080 Sum_probs=29.1
Q ss_pred ccCCcEEEecCCCCCeEEEEEEEccCCeEEEEEc
Q psy176 38 LMENQKVWVPDPADGFVLGRILDLGMDEVTVQPL 71 (101)
Q Consensus 38 md~gq~VWapDp~eGFiLgrIvDIG~d~~TVqPl 71 (101)
+..|..+.+-|...+.-.|+|++++.+.+++.-.
T Consensus 32 ~~~Gd~v~v~~g~g~~~~a~i~~~~~~~~~~~i~ 65 (240)
T TIGR00046 32 LKKGDKLKLLDGDGFIYHCEIKKISKKFVKCELL 65 (240)
T ss_pred CCCCCEEEEEeCCCCEEEEEEEEEcCCeEEEEEE
Confidence 4678999999998888999999999998876544
No 48
>PF11160 DUF2945: Protein of unknown function (DUF2945); InterPro: IPR021331 This family of proteins has no known function.
Probab=28.99 E-value=1.6e+02 Score=19.15 Aligned_cols=36 Identities=17% Similarity=0.385 Sum_probs=27.5
Q ss_pred cEEEecCCCCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCc
Q psy176 42 QKVWVPDPADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDR 84 (101)
Q Consensus 42 q~VWapDp~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~ydd 84 (101)
+.-| +..-|-.-|+|+++-.+.+++ ++.++.++-|+
T Consensus 3 ~V~W--~s~~g~~~G~V~~~~t~~~~~-----~G~~v~AS~dd 38 (62)
T PF11160_consen 3 KVRW--NSGQGTTTGTVVEVHTEPTEI-----KGRTVNASKDD 38 (62)
T ss_pred EEEE--cCCCCeEEEEEEEEEecceeE-----CCEEecCCCCC
Confidence 4457 778899999999998888876 56777666554
No 49
>PRK14645 hypothetical protein; Provisional
Probab=28.98 E-value=1.5e+02 Score=22.02 Aligned_cols=42 Identities=19% Similarity=0.163 Sum_probs=32.1
Q ss_pred CcEEEecCCCCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCcee
Q psy176 41 NQKVWVPDPADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVY 86 (101)
Q Consensus 41 gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVF 86 (101)
|++|=+.. ...-..|+|.++-.+.+++.. +++++..||++|=
T Consensus 102 G~~v~v~~-~~k~~~G~L~~~~d~~i~l~~---~~~~~~i~~~~I~ 143 (154)
T PRK14645 102 GLKAKVRG-PGENFTGRIKAVSGDQVTFDV---GGEDRTLRIGTFQ 143 (154)
T ss_pred CCEEEEEc-CCeEEEEEEEEEeCCEEEEEE---CCeEEEEEHHHhh
Confidence 56666654 345567999999999999974 4578899999983
No 50
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=27.85 E-value=1.5e+02 Score=19.65 Aligned_cols=50 Identities=12% Similarity=0.175 Sum_probs=38.5
Q ss_pred CCcEEEecCCCCCeE--EEEEEEcc-----CCeEEEEEcCCCCCeEEecCCceecCcCCC
Q psy176 40 ENQKVWVPDPADGFV--LGRILDLG-----MDEVTVQPLDSKKPKAAFSLDRVYTAEEHD 92 (101)
Q Consensus 40 ~gq~VWapDp~eGFi--LgrIvDIG-----~d~~TVqPld~k~~~~~~~yddVFPAeED~ 92 (101)
-|.+|||.= .||- =|+|.+.. ...+.|+=..+ ++..-++.++++|=++..
T Consensus 5 ~GdlVwaK~--kGyp~WPa~I~~~~~~~~~~~~~~V~FfGt-~~~a~v~~~~l~pf~~~~ 61 (83)
T cd05834 5 AGDLVFAKV--KGYPAWPARVDEPEDWKPPGKKYPVYFFGT-HETAFLKPEDLFPYTENK 61 (83)
T ss_pred CCCEEEEec--CCCCCCCEEEecccccCCCCCEEEEEEeCC-CCEeEECHHHceecccch
Confidence 478999987 5665 68888887 46788887765 566778999999887753
No 51
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=27.41 E-value=1.2e+02 Score=22.78 Aligned_cols=34 Identities=24% Similarity=0.241 Sum_probs=28.4
Q ss_pred ccCCcEEEecCCCCCeEEEEEEEccCCeEEEEEc
Q psy176 38 LMENQKVWVPDPADGFVLGRILDLGMDEVTVQPL 71 (101)
Q Consensus 38 md~gq~VWapDp~eGFiLgrIvDIG~d~~TVqPl 71 (101)
+..|..+.+-|...+.-.|+|++++.+.++++.+
T Consensus 17 ~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~ 50 (225)
T PF04452_consen 17 LKEGDSIEVFDGDGGEYRAEITEISKKSATLRIL 50 (225)
T ss_dssp --TT-EEEEEESSSEEEEEEEEEEESSEEEEEEE
T ss_pred CCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEe
Confidence 4578999999999999999999999999988766
No 52
>PRK14634 hypothetical protein; Provisional
Probab=26.83 E-value=96 Score=22.84 Aligned_cols=34 Identities=15% Similarity=0.184 Sum_probs=27.4
Q ss_pred CeEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecC
Q psy176 52 GFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTA 88 (101)
Q Consensus 52 GFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPA 88 (101)
--+.|+|.+...+.+++.. +++.+..||++|=-|
T Consensus 115 k~~~G~L~~~~~~~v~l~~---~~~~~~i~~~~I~ka 148 (155)
T PRK14634 115 QRLEGLLLERNEDHLQINI---RGRIKRIPRDSVISV 148 (155)
T ss_pred EEEEEEEEEEeCCEEEEEE---CCEEEEEEHHHeeeE
Confidence 3678999999999999974 356788999988654
No 53
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=26.75 E-value=1.2e+02 Score=23.39 Aligned_cols=36 Identities=28% Similarity=0.309 Sum_probs=31.0
Q ss_pred cccCCcEEEecCCCCCeEEEEEEEccCCeEEEE---EcCC
Q psy176 37 YLMENQKVWVPDPADGFVLGRILDLGMDEVTVQ---PLDS 73 (101)
Q Consensus 37 ~md~gq~VWapDp~eGFiLgrIvDIG~d~~TVq---Pld~ 73 (101)
+..-|..+=+..+. |=+.|+|++++.+.++|- ||.+
T Consensus 90 ~~~vGm~~~~~~~~-~~~~~~V~~V~~~~V~VDfNHpLAG 128 (174)
T COG1047 90 ELEVGMEVEAEGGD-GEIPGVVTEVSGDRVTVDFNHPLAG 128 (174)
T ss_pred CCCCCcEEEEcCCC-ceeeEEEEEEcCCEEEEeCCCcCCC
Confidence 56778899999888 999999999999999994 5544
No 54
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=26.34 E-value=84 Score=21.05 Aligned_cols=19 Identities=11% Similarity=0.440 Sum_probs=16.2
Q ss_pred CeEEEEEEEccCCeEEEEE
Q psy176 52 GFVLGRILDLGMDEVTVQP 70 (101)
Q Consensus 52 GFiLgrIvDIG~d~~TVqP 70 (101)
|=+.|+|++++.+.++++-
T Consensus 48 gGi~G~V~~i~d~~v~vei 66 (84)
T TIGR00739 48 GGIIGTVTKIAENTIVIEL 66 (84)
T ss_pred CCeEEEEEEEeCCEEEEEE
Confidence 4578999999999998873
No 55
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=25.92 E-value=42 Score=25.44 Aligned_cols=43 Identities=14% Similarity=0.183 Sum_probs=26.0
Q ss_pred ceeeeeeeccccCCcEEEecCCCCCeEEEEEEEccCCeEEEEEcCC
Q psy176 28 ESVVYKFKPYLMENQKVWVPDPADGFVLGRILDLGMDEVTVQPLDS 73 (101)
Q Consensus 28 ~~~~~~~~~~md~gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~ 73 (101)
|=+.+|.+.+..... =+-.-.+-| -|||+|++.+.+++|-...
T Consensus 85 El~LiKv~~~~~~r~--ei~~~~~~f-~a~ivdv~~~~~~ie~tG~ 127 (174)
T CHL00100 85 ELMLIKINVNSQTRP--EILEIAQIF-RAKVVDLSEESLILEVTGD 127 (174)
T ss_pred EEEEEEEecCCcCHH--HHHHHHHHh-CCEEEEecCCEEEEEEcCC
Confidence 445566665442211 112223445 3899999999999997654
No 56
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=25.62 E-value=43 Score=25.05 Aligned_cols=44 Identities=18% Similarity=0.179 Sum_probs=26.4
Q ss_pred cceeeeeeeccccCCcEEEecCCCCCeEEEEEEEccCCeEEEEEcCC
Q psy176 27 FESVVYKFKPYLMENQKVWVPDPADGFVLGRILDLGMDEVTVQPLDS 73 (101)
Q Consensus 27 ~~~~~~~~~~~md~gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~ 73 (101)
=|-+.+|.+.+-. ++-=+-.-.+=| -|+|+|++.++++++-...
T Consensus 84 rEl~LiKv~~~~~--~r~~i~~i~~~f-~a~ivdv~~~~~~iE~tG~ 127 (161)
T PRK11895 84 RELALVKVRASGE--NRAEILRLADIF-RAKIVDVTPESLTIEVTGD 127 (161)
T ss_pred eEEEEEEEECCcc--cHHHHHHHHHHh-CCEEEEecCCEEEEEEeCC
Confidence 3455666655431 111122223445 4899999999999997654
No 57
>PRK06764 hypothetical protein; Provisional
Probab=25.52 E-value=55 Score=23.77 Aligned_cols=39 Identities=23% Similarity=0.315 Sum_probs=24.8
Q ss_pred CCCCCeEE-EEEEEccCCe--------EEEEEcCCCCCeE----EecCCceec
Q psy176 48 DPADGFVL-GRILDLGMDE--------VTVQPLDSKKPKA----AFSLDRVYT 87 (101)
Q Consensus 48 Dp~eGFiL-grIvDIG~d~--------~TVqPld~k~~~~----~~~yddVFP 87 (101)
.-.|+|+| ||=+||-+.. +|++--.+ ++-+ -|.|+|||.
T Consensus 49 n~~e~y~lsgrsidilsgdkeaiqlnkyti~f~kp-g~yvirvngciy~dvyt 100 (105)
T PRK06764 49 NINELYVLSGRSIDVLSGDKEAIQLNKYTIRFSKP-GKYVIRVNGCIYNDVYT 100 (105)
T ss_pred eccceEEEcCceeeeecCChhheEeeeeEEEecCC-ccEEEEEccEEeeeeEE
Confidence 45789987 7888886654 45542222 3222 588999984
No 58
>PF06620 DUF1150: Protein of unknown function (DUF1150); InterPro: IPR009531 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=25.44 E-value=73 Score=21.50 Aligned_cols=32 Identities=19% Similarity=0.329 Sum_probs=24.3
Q ss_pred ceeeeeeeccccCCcEEEecCCCCCeEEEEEE
Q psy176 28 ESVVYKFKPYLMENQKVWVPDPADGFVLGRIL 59 (101)
Q Consensus 28 ~~~~~~~~~~md~gq~VWapDp~eGFiLgrIv 59 (101)
+.+--.|.+.+.+++..|+=|..+|-.++=.-
T Consensus 25 ~dl~~~~~~~~~~~~~l~Avh~AdG~~lal~~ 56 (76)
T PF06620_consen 25 DDLPEEFPPQIDPGETLYAVHAADGTPLALVD 56 (76)
T ss_pred HHhhhhcccccCCCceEEEEecCCCCEEEEEC
Confidence 33333455678999999999999999887543
No 59
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=25.17 E-value=3.1e+02 Score=21.15 Aligned_cols=64 Identities=28% Similarity=0.445 Sum_probs=41.7
Q ss_pred EEEEEEeeeecceeeeeeeccccCCcEEEecCCCCCeEEEEEEEccCCeEEEEEcCCCCCeEEecCCceec
Q psy176 17 SISVVVGAVDFESVVYKFKPYLMENQKVWVPDPADGFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYT 87 (101)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~md~gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFP 87 (101)
-.|-+.|.+.....++..++.. ++ ..|...| .+.|+|+++..+.+.|. +.+ .-.-..+..++..
T Consensus 35 i~As~~G~~~~~~~~i~V~p~~---~~-y~P~vGD-iViG~V~~i~~~~~~vd-I~~-~~~g~L~~s~i~~ 98 (235)
T PRK04163 35 IYSTVVGLVDIKDDKVRVIPLE---GK-YIPKVGD-LVIGKVTDVTFSGWEVD-INS-PYKAYLPVSEVLG 98 (235)
T ss_pred EEEEEeEEEEEECCEEEEEECC---Cc-ccCCCCC-EEEEEEEEEeCceEEEE-eCC-CceeEEEHHHcCC
Confidence 3466778888766555555543 23 5554433 89999999999999886 443 2234566666654
No 60
>PF06605 Prophage_tail: Prophage endopeptidase tail; InterPro: IPR010572 This entry is represented by the Bacteriophage 53, Orf003. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 3GS9_A.
Probab=24.91 E-value=1e+02 Score=23.92 Aligned_cols=47 Identities=26% Similarity=0.251 Sum_probs=24.9
Q ss_pred eeeEEEEEEeeeecceeeeeeeccccCCcEEEecCCCCC-eEEEEEEEccC
Q psy176 14 SLISISVVVGAVDFESVVYKFKPYLMENQKVWVPDPADG-FVLGRILDLGM 63 (101)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~md~gq~VWapDp~eG-FiLgrIvDIG~ 63 (101)
+-..+|.-|-.+|+.. |.. .-..-|..|++.|+.-| .+-+||+.+--
T Consensus 243 ~~P~~s~~v~~~dL~~--~~~-~~~~lGD~V~v~~~~~gi~~~~RIv~~~~ 290 (327)
T PF06605_consen 243 DQPKVSYTVDFVDLSK--YDL-EKVNLGDTVTVIDEDLGIDVKARIVKITY 290 (327)
T ss_dssp -S-EEEEEE-----------------TT-EEEEEETTTTEEEEEEEEEEEE
T ss_pred CCceEEEEEEEEEecc--ccc-CCCCCCCEEEEEECCCCEEEEEEEEEEEE
Confidence 5566777777888877 333 34567999999999999 67889987654
No 61
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=24.88 E-value=1.1e+02 Score=18.77 Aligned_cols=30 Identities=10% Similarity=0.262 Sum_probs=20.4
Q ss_pred CeEEEEEEEccCCeEEEEEcCCCCCeEEecC
Q psy176 52 GFVLGRILDLGMDEVTVQPLDSKKPKAAFSL 82 (101)
Q Consensus 52 GFiLgrIvDIG~d~~TVqPld~k~~~~~~~y 82 (101)
+|+-|+|++++.+.+.|. .++=+=.+.+|-
T Consensus 3 ~~l~G~v~~~~~~~vvi~-~~GvGy~v~v~~ 32 (61)
T PF01330_consen 3 AYLKGKVVEKNPDYVVID-VNGVGYEVFVPS 32 (61)
T ss_dssp EEEEEEEEEEESSEEEEE-ETTEEEEEEE-H
T ss_pred cEEEEEEEEEcCCEEEEE-ECCEEEEEEeCC
Confidence 588999999999998885 444333444443
No 62
>PF05239 PRC: PRC-barrel domain; InterPro: IPR007903 The PRC-barrel is an all beta barrel domain found in photosynthetic reaction centre subunit H of the purple bacteria. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the C terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain [].; PDB: 2QGG_A 3H9N_A 2WJN_H 2PRC_H 5PRC_H 2X5V_H 1DXR_H 1R2C_H 3G7F_H 1PRC_H ....
Probab=24.82 E-value=1.7e+02 Score=17.70 Aligned_cols=47 Identities=17% Similarity=0.217 Sum_probs=26.2
Q ss_pred CcEEEecCCCCCeEEEEEEEcc----CCe---EEEEEcCC---CCCeEEecCCceecCcC
Q psy176 41 NQKVWVPDPADGFVLGRILDLG----MDE---VTVQPLDS---KKPKAAFSLDRVYTAEE 90 (101)
Q Consensus 41 gq~VWapDp~eGFiLgrIvDIG----~d~---~TVqPld~---k~~~~~~~yddVFPAeE 90 (101)
|+.|.-++ |-.+|+|.||- ... +.+..-.. ..+.+..|++.+...+.
T Consensus 11 g~~V~~~~---G~~iG~V~di~id~~~~~i~~i~v~~~~~~~~~~~~~~iP~~~~v~~~~ 67 (79)
T PF05239_consen 11 GKEVIDRD---GEKIGKVKDIVIDPKTGKIVGIVVSSGGFFGIGGKKVLIPWDQIVDIGG 67 (79)
T ss_dssp TSEEEETT---SCEEEEEEEEEEETTTTEEEEEEEEETTSTCSSSEEEEEEGGEEEEECT
T ss_pred CCEEEcCC---CCEEEEEEEEEEeCCCCCEEEEEEcCCCccCcCCcEEEEcCeEeEEecC
Confidence 44555443 88899988882 222 23322211 23777888885554444
No 63
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=24.59 E-value=89 Score=19.65 Aligned_cols=27 Identities=30% Similarity=0.294 Sum_probs=11.6
Q ss_pred eeeccccCCcEEEe----cCCCCCeEEEEEE
Q psy176 33 KFKPYLMENQKVWV----PDPADGFVLGRIL 59 (101)
Q Consensus 33 ~~~~~md~gq~VWa----pDp~eGFiLgrIv 59 (101)
++-.|+.-|..||+ -|+..|||+|.+-
T Consensus 39 g~~~~P~iGeqV~v~~~~Gd~~~~~vlg~l~ 69 (79)
T PF04717_consen 39 GFWFPPEIGEQVLVLFPGGDPERPVVLGSLY 69 (79)
T ss_dssp B------TT-EEEEEEGGCTTTSEEEEEEE-
T ss_pred eeEccCCCCcEEEEEccCCcCCCCEEEEEEC
Confidence 33445556666665 2556677777653
No 64
>KOG1719|consensus
Probab=24.28 E-value=51 Score=26.11 Aligned_cols=24 Identities=42% Similarity=0.775 Sum_probs=19.7
Q ss_pred hhhhcceeeEEeeeEEEEEEeeeecce
Q psy176 3 EKMENNLTWYTSLISISVVVGAVDFES 29 (101)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 29 (101)
+| +....|| -|+--|++|+++|+|
T Consensus 18 ~k-~s~~~wy--~~~~~v~~~~~~FrS 41 (183)
T KOG1719|consen 18 EK-ASAFRWY--RIDEFVILGAMPFRS 41 (183)
T ss_pred HH-Hhhhcee--eecceEEEeeccccc
Confidence 45 6677899 567789999999999
No 65
>PRK14646 hypothetical protein; Provisional
Probab=24.08 E-value=2.4e+02 Score=20.74 Aligned_cols=35 Identities=14% Similarity=0.287 Sum_probs=28.2
Q ss_pred CeEEEEEEEccCCeEEEEEcCCCCCeEEecCCceecCc
Q psy176 52 GFVLGRILDLGMDEVTVQPLDSKKPKAAFSLDRVYTAE 89 (101)
Q Consensus 52 GFiLgrIvDIG~d~~TVqPld~k~~~~~~~yddVFPAe 89 (101)
....|+|.+...+.+++. + +++++..||++|=.|-
T Consensus 115 ~~~~G~L~~~~~~~v~l~-~--~g~~~~i~~~~I~ka~ 149 (155)
T PRK14646 115 KFLNGLLYEKSKDYLAIN-I--KGKIKKIPFNEVLKIS 149 (155)
T ss_pred EEEEEEEEEEeCCEEEEE-E--CCEEEEEEHHHeeeEE
Confidence 477899999999999996 3 3567888999886553
No 66
>PF05971 Methyltransf_10: Protein of unknown function (DUF890); InterPro: IPR010286 This family consists of several conserved hypothetical proteins from both eukaryotes and prokaryotes. The function of members of this family are unknown but are predicted to be SAM-dependent methyltransferases.; GO: 0008168 methyltransferase activity; PDB: 2H00_A.
Probab=24.05 E-value=50 Score=27.14 Aligned_cols=13 Identities=23% Similarity=0.994 Sum_probs=10.5
Q ss_pred hhcceeeEEeeeE
Q psy176 5 MENNLTWYTSLIS 17 (101)
Q Consensus 5 ~~~~~~~~~~~~~ 17 (101)
...+..|||||+|
T Consensus 246 ~~~~v~WfTsmvg 258 (299)
T PF05971_consen 246 LKDQVRWFTSMVG 258 (299)
T ss_dssp HGGGEEEEEEEES
T ss_pred hCCCcEEEeeccc
Confidence 3567899999976
No 67
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=24.02 E-value=1.7e+02 Score=17.34 Aligned_cols=51 Identities=12% Similarity=0.050 Sum_probs=36.0
Q ss_pred CCcEEEecC-CCCCeEEEEEEEccC-CeEEEEEcCC-CCCeEEecCCceecCcC
Q psy176 40 ENQKVWVPD-PADGFVLGRILDLGM-DEVTVQPLDS-KKPKAAFSLDRVYTAEE 90 (101)
Q Consensus 40 ~gq~VWapD-p~eGFiLgrIvDIG~-d~~TVqPld~-k~~~~~~~yddVFPAeE 90 (101)
-|..|-|.. ...++--|+|+.+.. +.+.|.-.+. .+..-+++..++=|..+
T Consensus 5 ~G~~Ve~~~~~~~~W~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~~ 58 (61)
T smart00743 5 KGDRVEVFSKEEDSWWEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHPP 58 (61)
T ss_pred CCCEEEEEECCCCEEEEEEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCCC
Confidence 355665553 378899999999988 7788887761 24566777777776543
No 68
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=23.83 E-value=2.6e+02 Score=19.47 Aligned_cols=39 Identities=28% Similarity=0.407 Sum_probs=28.9
Q ss_pred cEEEecCCCCCeEEEEEEEc-cCCeEEEEEcCCCCCeEEecC
Q psy176 42 QKVWVPDPADGFVLGRILDL-GMDEVTVQPLDSKKPKAAFSL 82 (101)
Q Consensus 42 q~VWapDp~eGFiLgrIvDI-G~d~~TVqPld~k~~~~~~~y 82 (101)
..+=.|++.||=+.|+|+.+ |.+-++|+-.| +.++.|..
T Consensus 9 ~~~~~p~~~e~e~~g~V~~~lG~~~~~V~~~d--G~~~la~i 48 (99)
T TIGR00523 9 IRVRLPRKEEGEILGVIEQMLGAGRVKVRCLD--GKTRLGRI 48 (99)
T ss_pred ceeeCCCCCCCEEEEEEEEEcCCCEEEEEeCC--CCEEEEEE
Confidence 45556888899999999987 67778887654 46666643
No 69
>PRK10424 ilvG operon leader peptide; Provisional
Probab=23.43 E-value=73 Score=18.91 Aligned_cols=12 Identities=58% Similarity=0.515 Sum_probs=8.5
Q ss_pred EEeeeEEEEEEe
Q psy176 12 YTSLISISVVVG 23 (101)
Q Consensus 12 ~~~~~~~~~~~~ 23 (101)
-.||+.|||||=
T Consensus 7 vislvvisvvvi 18 (32)
T PRK10424 7 VISLVVISVVVI 18 (32)
T ss_pred eeeEeEEEEEEE
Confidence 357888888763
No 70
>PRK02118 V-type ATP synthase subunit B; Provisional
Probab=23.19 E-value=4.4e+02 Score=22.91 Aligned_cols=55 Identities=27% Similarity=0.276 Sum_probs=37.2
Q ss_pred eeEEeeeEEEEEEeeeecceeeeeeeccccCCcEEEecCCCCCeEEEEEEEccCCeEEEEEcCC
Q psy176 10 TWYTSLISISVVVGAVDFESVVYKFKPYLMENQKVWVPDPADGFVLGRILDLGMDEVTVQPLDS 73 (101)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~md~gq~VWapDp~eGFiLgrIvDIG~d~~TVqPld~ 73 (101)
.+|..+.+|.-.+=.|.|. ...-+..+.+..+ +|-++|.|+.++.+.+.++|+.+
T Consensus 3 ~~~g~v~~i~G~~v~v~~~--------~~~~ge~~~i~~~-~~~~~geVi~~~~~~v~~~~~~~ 57 (436)
T PRK02118 3 KIYTKITDITGNVITVEAE--------GVGYGELATVERK-DGSSLAQVIRLDGDKVTLQVFGG 57 (436)
T ss_pred ceeEEEEEEECcEEEEEeC--------CCCCCCEEEEEcC-CCCEEEEEEEEcCCEEEEEEecC
Confidence 4566666665444334432 2335678888432 45589999999999999999965
No 71
>PRK08472 fliI flagellum-specific ATP synthase; Validated
Probab=22.24 E-value=4.3e+02 Score=22.80 Aligned_cols=35 Identities=11% Similarity=0.189 Sum_probs=27.7
Q ss_pred cCCcEEEecCCC-CCeEEEEEEEccCCeEEEEEcCC
Q psy176 39 MENQKVWVPDPA-DGFVLGRILDLGMDEVTVQPLDS 73 (101)
Q Consensus 39 d~gq~VWapDp~-eGFiLgrIvDIG~d~~TVqPld~ 73 (101)
.-|..|++.... .+=++|.|+.+..+.+.++|+++
T Consensus 38 ~~ge~~~i~~~~~~~~~~~eVv~~~~~~~~l~~~~~ 73 (434)
T PRK08472 38 SVGDIVKIESSDNGKECLGMVVVIEKEQFGISPFSF 73 (434)
T ss_pred CCCCEEEEecCCCCCceEEEEEEEeCCeEEEEEccC
Confidence 458999995432 12389999999999999999976
No 72
>PRK14643 hypothetical protein; Provisional
Probab=21.52 E-value=1.5e+02 Score=22.22 Aligned_cols=35 Identities=11% Similarity=0.178 Sum_probs=26.0
Q ss_pred EEEEEEEccCCeEEEEE---cCCCCCeEEecCCceecC
Q psy176 54 VLGRILDLGMDEVTVQP---LDSKKPKAAFSLDRVYTA 88 (101)
Q Consensus 54 iLgrIvDIG~d~~TVqP---ld~k~~~~~~~yddVFPA 88 (101)
..|.+.+...+.+++.. ++..+++++.||++|=-|
T Consensus 121 ~~G~L~~~~~~~~~l~l~~~~~~~~~~~~ip~~~I~ka 158 (164)
T PRK14643 121 FEGYVTKYNVNTNTFRFTFFIKGQKKKLDVKYEQIKFI 158 (164)
T ss_pred EEEEEEEEeCCcEEEEEEeeccCcCcEEEEeHHHhhhe
Confidence 46999999988888864 333467888999987543
No 73
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=20.78 E-value=3.5e+02 Score=19.88 Aligned_cols=25 Identities=28% Similarity=0.484 Sum_probs=21.1
Q ss_pred cCCCCC-eEEEEEEEccCCeEEEEEc
Q psy176 47 PDPADG-FVLGRILDLGMDEVTVQPL 71 (101)
Q Consensus 47 pDp~eG-FiLgrIvDIG~d~~TVqPl 71 (101)
..|+.| .+.|+|++|....+.|.-.
T Consensus 60 ~~~~~GdiV~GkV~~i~~~g~~V~I~ 85 (189)
T PRK09521 60 PLLKKGDIVYGRVVDVKEQRALVRIV 85 (189)
T ss_pred CCCCCCCEEEEEEEEEcCCeEEEEEE
Confidence 566777 8899999999999998853
No 74
>PRK07196 fliI flagellum-specific ATP synthase; Validated
Probab=20.62 E-value=2.1e+02 Score=24.69 Aligned_cols=35 Identities=17% Similarity=0.358 Sum_probs=28.2
Q ss_pred ccCCcEEEecCCCCC-eEEEEEEEccCCeEEEEEcCC
Q psy176 38 LMENQKVWVPDPADG-FVLGRILDLGMDEVTVQPLDS 73 (101)
Q Consensus 38 md~gq~VWapDp~eG-FiLgrIvDIG~d~~TVqPld~ 73 (101)
.--|..++++. .+| -++|+|+.+..+...++|+++
T Consensus 36 ~~~ge~~~i~~-~~~~~~~~eVv~~~~~~~~l~~~~~ 71 (434)
T PRK07196 36 LAIGQRCRIES-VDETFIEAQVVGFDRDITYLMPFKH 71 (434)
T ss_pred CCcCCEEEEEe-CCCceEEEEEEEecCCEEEEEECCC
Confidence 44589999943 244 399999999999999999966
No 75
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=20.37 E-value=2.3e+02 Score=19.07 Aligned_cols=29 Identities=17% Similarity=0.342 Sum_probs=20.3
Q ss_pred EEEEEEEcc--CCeEEEEEcCCCCCeEEecCCc
Q psy176 54 VLGRILDLG--MDEVTVQPLDSKKPKAAFSLDR 84 (101)
Q Consensus 54 iLgrIvDIG--~d~~TVqPld~k~~~~~~~ydd 84 (101)
+.||+..+. ++.++++..|+ ..+++....
T Consensus 23 ivGkv~~~~~~g~~~~l~~~d~--~~V~v~l~~ 53 (109)
T PF08661_consen 23 IVGKVESVDPDGGSATLSTSDG--GQVTVSLNP 53 (109)
T ss_dssp EEEEEEEE-TTSSEEEEE-TTS---EEEEEESS
T ss_pred EEEEEeeEcCCCCEEEEEcCCC--CEEEEEeCC
Confidence 689999999 99999988766 466665543
Done!