Query 030903
Match_columns 169
No_of_seqs 57 out of 59
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 06:19:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030903.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030903hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11341 DUF3143: Protein of u 100.0 3.3E-36 7.2E-41 212.4 7.9 63 102-168 1-63 (63)
2 PF08519 RFC1: Replication fac 52.6 4.6 0.0001 32.2 0.0 27 139-165 100-126 (155)
3 PF07727 RVT_2: Reverse transc 52.4 5.2 0.00011 33.5 0.3 46 94-139 134-179 (246)
4 PF11895 DUF3415: Domain of un 50.1 4.3 9.3E-05 30.5 -0.5 16 150-165 41-56 (80)
5 PRK15360 pathogenicity island 42.1 1.1E+02 0.0025 24.9 6.4 51 93-143 2-58 (137)
6 PF03484 B5: tRNA synthetase B 41.3 21 0.00046 24.4 1.9 36 90-125 19-54 (70)
7 PF14076 DUF4258: Domain of un 39.6 23 0.0005 23.0 1.8 20 149-168 8-27 (73)
8 PF00536 SAM_1: SAM domain (St 38.0 24 0.00052 22.8 1.7 14 93-106 6-19 (64)
9 PF13331 DUF4093: Domain of un 33.5 28 0.00061 25.7 1.6 20 146-165 67-86 (87)
10 PF07647 SAM_2: SAM domain (St 32.4 42 0.0009 21.7 2.1 16 91-106 5-20 (66)
11 PF04255 DUF433: Protein of un 30.4 34 0.00073 22.7 1.4 19 147-166 36-54 (56)
12 PF13953 PapC_C: PapC C-termin 29.2 34 0.00073 23.2 1.3 25 128-158 41-65 (68)
13 smart00874 B5 tRNA synthetase 28.6 53 0.0012 21.7 2.2 36 93-128 22-58 (71)
14 PF10722 YbjN: Putative bacter 28.4 48 0.001 22.4 2.0 38 91-128 1-42 (127)
15 PF09695 YtfJ_HI0045: Bacteria 28.3 83 0.0018 26.2 3.7 40 110-165 115-154 (160)
16 COG2442 Uncharacterized conser 28.1 40 0.00088 24.6 1.6 16 151-166 50-66 (79)
17 COG2023 RPR2 RNase P subunit R 27.4 82 0.0018 24.7 3.3 43 112-163 61-103 (105)
18 COG3831 Uncharacterized conser 26.9 1.3E+02 0.0029 22.8 4.2 32 128-164 23-54 (85)
19 PRK14737 gmk guanylate kinase; 26.4 44 0.00094 26.6 1.7 17 152-168 78-94 (186)
20 smart00454 SAM Sterile alpha m 24.5 51 0.0011 20.4 1.5 16 91-106 5-20 (68)
21 COG5457 Uncharacterized conser 24.2 51 0.0011 23.6 1.5 12 155-166 47-58 (63)
22 COG5097 MED6 RNA polymerase II 24.1 1.4E+02 0.0031 25.9 4.5 56 68-123 8-92 (210)
23 PF03214 RGP: Reversibly glyco 23.2 20 0.00042 33.2 -0.9 30 135-168 135-164 (348)
24 KOG4497 Uncharacterized conser 22.9 67 0.0015 30.5 2.4 31 110-140 72-103 (447)
25 PRK13666 hypothetical protein; 22.3 42 0.00092 25.9 0.9 15 153-168 50-64 (92)
26 PF07408 DUF1507: Protein of u 22.2 26 0.00056 27.0 -0.3 14 154-168 49-62 (90)
27 COG5440 Uncharacterized conser 21.8 55 0.0012 27.5 1.5 29 94-122 9-41 (161)
28 cd00166 SAM Sterile alpha moti 21.5 76 0.0017 19.6 1.8 19 92-110 4-22 (63)
29 PF01265 Cyto_heme_lyase: Cyto 21.2 1.1E+02 0.0023 27.2 3.2 25 96-120 189-213 (259)
30 PF10061 DUF2299: Uncharacteri 20.1 63 0.0014 25.6 1.5 23 94-116 1-25 (138)
No 1
>PF11341 DUF3143: Protein of unknown function (DUF3143); InterPro: IPR021489 This family of proteins has no known function.
Probab=100.00 E-value=3.3e-36 Score=212.36 Aligned_cols=63 Identities=54% Similarity=1.030 Sum_probs=61.8
Q ss_pred cCCccCCCCCeeeEEecCCceEEEEeeeeeeEEEEeecCCCCCcCceeeecccCCCHHHHHHHHhcC
Q 030903 102 LGFHQSSDDRAVWLVEKHDWHAQLSLDMTDLYIRYLKNGPGNLEKDIERRFSYALSREDIENAILGG 168 (169)
Q Consensus 102 LG~~qd~~d~~~W~lerP~WsAeL~Ld~edL~Vry~~~G~~gle~diqRsF~YsLSReDVEaAIf~G 168 (169)
|||+||.+|+|||+|++|+|+|+|+||+|||+|+|.++|+ +++||+|||||||+|||||||+|
T Consensus 1 lG~~qd~~d~~~W~~~~p~W~Ael~Ld~e~L~V~y~~~g~----~~~~rsF~YsLSR~DvE~Ai~~G 63 (63)
T PF11341_consen 1 LGCQQDDEDPCCWRLERPDWSAELSLDQEDLVVRYLQSGP----QDIQRSFPYSLSREDVEAAIFSG 63 (63)
T ss_pred CCceeCCCCceEEEEeCCCCeEEEEEeeeEEEEEEccCCC----cccEEeccCcCCHHHHHHHHhcC
Confidence 7999999999999999999999999999999999999997 79999999999999999999998
No 2
>PF08519 RFC1: Replication factor RFC1 C terminal domain; InterPro: IPR013725 This is the C-terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo [, ]. ; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_A.
Probab=52.58 E-value=4.6 Score=32.18 Aligned_cols=27 Identities=30% Similarity=0.516 Sum_probs=0.0
Q ss_pred cCCCCCcCceeeecccCCCHHHHHHHH
Q 030903 139 NGPGNLEKDIERRFSYALSREDIENAI 165 (169)
Q Consensus 139 ~G~~gle~diqRsF~YsLSReDVEaAI 165 (169)
.|.+|.+..|+.--.|+|+|||+|+-+
T Consensus 100 ~~~~~v~~vi~~Md~Y~Ltred~d~i~ 126 (155)
T PF08519_consen 100 QGKDGVDEVIDLMDEYGLTREDWDNIM 126 (155)
T ss_dssp ---------------------------
T ss_pred cCcccHHHHHHHHHHhCCCHHHHHHHH
Confidence 455678888999999999999997643
No 3
>PF07727 RVT_2: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR013103 A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This entry includes reverse transcriptases not recognised by IPR000477 from INTERPRO [].
Probab=52.37 E-value=5.2 Score=33.51 Aligned_cols=46 Identities=22% Similarity=0.388 Sum_probs=38.4
Q ss_pred HHHHHHHHcCCccCCCCCeeeEEecCCceEEEEeeeeeeEEEEeec
Q 030903 94 CIEAWLRSLGFHQSSDDRAVWLVEKHDWHAQLSLDMTDLYIRYLKN 139 (169)
Q Consensus 94 ~IE~WL~~LG~~qd~~d~~~W~lerP~WsAeL~Ld~edL~Vry~~~ 139 (169)
.+-..|+++|++|+..|+|.+.-...+=..-|.+=+||+-|...+.
T Consensus 134 ~l~~~L~~~GF~~~~~D~clfi~~~~~~~~ii~vYVDDili~~~~~ 179 (246)
T PF07727_consen 134 TLDKFLKKLGFKQSKADPCLFIKKSGDGFIIILVYVDDILIAGPSE 179 (246)
T ss_pred hcccccchhhhhcccccccccccccccccccccccccccccccccc
Confidence 4567899999999999999999877654488999999998887443
No 4
>PF11895 DUF3415: Domain of unknown function (DUF3415); InterPro: IPR024589 Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Peroxidases are found in bacteria, fungi, plants and animals. Fungal ligninases are extracellular haem enzymes involved in the degradation of lignin. They include lignin peroxidases (LiPs), manganese-dependent peroxidases (MnPs) and versatile peroxidases, which combine the substrate-specificity characteristics of the other two []. In MnP, Mn2+ serves as the reducing substrate []. It is commonly thought that the plant polymer lignin is the second most abundant organic compound on Earth, exceeded only by cellulose. Higher plants synthesise vast quantities of insoluble macromolecules, including lignins. Lignin is an amorphous three-dimensional aromatic biopolymer composed of oxyphenylpropane units. Biodegradation of lignins is slow - it is probable that their decomposition is the rate-limiting step in the biospheric carbon-oxygen cycle, which is mediated almost entirely by the catabolic activities of microorganisms. The white-rot fungi are able extensively to decompose all the important structural components of wood, including both cellulose and lignin. Under the proper environmental conditions, white-rot fungi completely degrade all structural components of lignin, with ultimate formation of CO2 and H2O. The first step in lignin degradation is depolymerisation, catalysed by the LiPs (ligninases). LiPs are secreted, along with hydrogen peroxide (H2O2), by white-rot fungi under conditions of nutrient limitation. The enzymes are not only important in lignin biodegradation, but are also potentially valuable in chemical waste disposal because of their ability to degrade environmental pollutants []. To date, 3D structures have been determined for LiP [] and MnP [] from Phanerochaete chrysosporium (White-rot fungus), and for the fungal peroxidase from Arthromyces ramosus []. All these proteins share the same architecture and consist of 2 all-alpha domains, between which is embedded the haem group. The helical topography of LiPs is nearly identical to that of yeast cytochrome c peroxidase (CCP) [], despite the former having 4 disulphide bonds, which are absent in CCP (MnP has an additional disulphide bond at the C terminus). This uncharacterised C-terminal domain is found in fungal ligninases. It is about 80 amino acids in length and associated with Pfam:PF00141.; PDB: 1B85_B 1B82_A 1B80_A 1YYG_A 1YZP_A 1MNP_A 1MN1_A 1YZR_A 1MN2_A 3M8M_A ....
Probab=50.11 E-value=4.3 Score=30.48 Aligned_cols=16 Identities=38% Similarity=0.401 Sum_probs=10.3
Q ss_pred eecccCCCHHHHHHHH
Q 030903 150 RRFSYALSREDIENAI 165 (169)
Q Consensus 150 RsF~YsLSReDVEaAI 165 (169)
-.|+.|++++|||+|-
T Consensus 41 a~fPAg~~~~DieqaC 56 (80)
T PF11895_consen 41 AHFPAGKSPADIEQAC 56 (80)
T ss_dssp SEBGTT--GGGB--S-
T ss_pred cccCCCCCHHHHHhhc
Confidence 6899999999999985
No 5
>PRK15360 pathogenicity island 2 effector protein SseE; Provisional
Probab=42.15 E-value=1.1e+02 Score=24.86 Aligned_cols=51 Identities=12% Similarity=0.084 Sum_probs=42.3
Q ss_pred HHHHHHHHHcCCc------cCCCCCeeeEEecCCceEEEEeeeeeeEEEEeecCCCC
Q 030903 93 PCIEAWLRSLGFH------QSSDDRAVWLVEKHDWHAQLSLDMTDLYIRYLKNGPGN 143 (169)
Q Consensus 93 P~IE~WL~~LG~~------qd~~d~~~W~lerP~WsAeL~Ld~edL~Vry~~~G~~g 143 (169)
-.|++||.+.|+. +...=+=.|+++.+.+.---++|.+++.|+++..-..|
T Consensus 2 d~l~q~L~~~G~~v~P~yl~~S~i~lG~~~~~~g~~lvyRvE~~eliIc~lrR~~~~ 58 (137)
T PRK15360 2 QEIEQWLRRHQVFTEPAYLGETAILLGQQFILSPYLVIYRIEAKEMIICEFRRLTPG 58 (137)
T ss_pred chhHHHHHHCCCccccHHhcCCccceeEEEEEcCEEEEEEecCCEEEEEEEEeccCC
Confidence 3588999999986 45555667999999999999999999999998875534
No 6
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=41.28 E-value=21 Score=24.39 Aligned_cols=36 Identities=22% Similarity=0.187 Sum_probs=27.9
Q ss_pred CChHHHHHHHHHcCCccCCCCCeeeEEecCCceEEE
Q 030903 90 HSLPCIEAWLRSLGFHQSSDDRAVWLVEKHDWHAQL 125 (169)
Q Consensus 90 HsLP~IE~WL~~LG~~qd~~d~~~W~lerP~WsAeL 125 (169)
-+.-.+...|+.|||.-...+-..|.+.-|.|..-|
T Consensus 19 i~~~~i~~~L~~lg~~~~~~~~~~~~v~vP~~R~Di 54 (70)
T PF03484_consen 19 ISPEEIIKILKRLGFKVEKIDGDTLEVTVPSYRFDI 54 (70)
T ss_dssp --HHHHHHHHHHTT-EEEE-CTTEEEEEEETTSTT-
T ss_pred CCHHHHHHHHHHCCCEEEECCCCEEEEEcCCCcCCc
Confidence 355678999999999999999999999999998544
No 7
>PF14076 DUF4258: Domain of unknown function (DUF4258)
Probab=39.62 E-value=23 Score=22.99 Aligned_cols=20 Identities=45% Similarity=0.597 Sum_probs=15.6
Q ss_pred eeecccCCCHHHHHHHHhcC
Q 030903 149 ERRFSYALSREDIENAILGG 168 (169)
Q Consensus 149 qRsF~YsLSReDVEaAIf~G 168 (169)
+|...=++|.+||+.|+..|
T Consensus 8 ~rm~eR~Is~~~I~~~l~~g 27 (73)
T PF14076_consen 8 ERMQERGISEEDIEDALENG 27 (73)
T ss_pred HHHHhCCCCHHHHHHHHhcC
Confidence 34444579999999999887
No 8
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=37.96 E-value=24 Score=22.79 Aligned_cols=14 Identities=43% Similarity=0.914 Sum_probs=11.8
Q ss_pred HHHHHHHHHcCCcc
Q 030903 93 PCIEAWLRSLGFHQ 106 (169)
Q Consensus 93 P~IE~WL~~LG~~q 106 (169)
-.+.+||+++|+.+
T Consensus 6 ~~V~~WL~~~~l~~ 19 (64)
T PF00536_consen 6 EDVSEWLKSLGLEQ 19 (64)
T ss_dssp HHHHHHHHHTTGGG
T ss_pred HHHHHHHHHCCCHH
Confidence 46889999999865
No 9
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=33.46 E-value=28 Score=25.68 Aligned_cols=20 Identities=25% Similarity=0.519 Sum_probs=16.7
Q ss_pred CceeeecccCCCHHHHHHHH
Q 030903 146 KDIERRFSYALSREDIENAI 165 (169)
Q Consensus 146 ~diqRsF~YsLSReDVEaAI 165 (169)
|-.+|.=-|++||+|+++||
T Consensus 67 qllkrLN~f~it~~e~~~al 86 (87)
T PF13331_consen 67 QLLKRLNMFGITREEFEEAL 86 (87)
T ss_pred HHHHHHHHcCCCHHHHHHHh
Confidence 45666677999999999997
No 10
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=32.45 E-value=42 Score=21.72 Aligned_cols=16 Identities=44% Similarity=0.794 Sum_probs=12.6
Q ss_pred ChHHHHHHHHHcCCcc
Q 030903 91 SLPCIEAWLRSLGFHQ 106 (169)
Q Consensus 91 sLP~IE~WL~~LG~~q 106 (169)
+...+..||+++|+.+
T Consensus 5 ~~~~v~~WL~~~gl~~ 20 (66)
T PF07647_consen 5 SPEDVAEWLKSLGLEQ 20 (66)
T ss_dssp CHHHHHHHHHHTTCGG
T ss_pred CHHHHHHHHHHCCcHH
Confidence 3467899999999854
No 11
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=30.41 E-value=34 Score=22.75 Aligned_cols=19 Identities=32% Similarity=0.529 Sum_probs=11.2
Q ss_pred ceeeecccCCCHHHHHHHHh
Q 030903 147 DIERRFSYALSREDIENAIL 166 (169)
Q Consensus 147 diqRsF~YsLSReDVEaAIf 166 (169)
++..-|+. |+.+||++|+.
T Consensus 36 eI~~~yp~-Lt~~~i~aAl~ 54 (56)
T PF04255_consen 36 EIAEDYPS-LTLEDIRAALA 54 (56)
T ss_dssp HHHHHSTT---HHHHHHHHH
T ss_pred HHHHHCCC-CCHHHHHHHHH
Confidence 34444433 99999999973
No 12
>PF13953 PapC_C: PapC C-terminal domain; PDB: 3L48_E 2XET_A 3RFZ_E 2KT6_A.
Probab=29.24 E-value=34 Score=23.24 Aligned_cols=25 Identities=20% Similarity=0.489 Sum_probs=17.6
Q ss_pred eeeeeEEEEeecCCCCCcCceeeecccCCCH
Q 030903 128 DMTDLYIRYLKNGPGNLEKDIERRFSYALSR 158 (169)
Q Consensus 128 d~edL~Vry~~~G~~gle~diqRsF~YsLSR 158 (169)
+...|.|+| |.+ .+-+|.+.|.|.-
T Consensus 41 ~~~~L~V~w---~~~---~~~~C~~~~~~~~ 65 (68)
T PF13953_consen 41 PKGTLTVKW---GDG---ANQQCQIDYPLPE 65 (68)
T ss_dssp TCEEEEEES---TSC---TTSEEEEEEET-C
T ss_pred CCcEEEEEE---CCC---CCCeEEEEecCCC
Confidence 356799999 432 2679999998864
No 13
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=28.58 E-value=53 Score=21.74 Aligned_cols=36 Identities=19% Similarity=0.293 Sum_probs=27.1
Q ss_pred HHHHHHHHHcCCccCCCC-CeeeEEecCCceEEEEee
Q 030903 93 PCIEAWLRSLGFHQSSDD-RAVWLVEKHDWHAQLSLD 128 (169)
Q Consensus 93 P~IE~WL~~LG~~qd~~d-~~~W~lerP~WsAeL~Ld 128 (169)
-.+...|+.|||.-...+ -..|.++-|.|..-|.-+
T Consensus 22 ~ei~~~L~~lg~~~~~~~~~~~~~v~~P~~R~Di~~~ 58 (71)
T smart00874 22 EEIEEILKRLGFEVEVSGDDDTLEVTVPSYRFDILIE 58 (71)
T ss_pred HHHHHHHHHCCCeEEecCCCCeEEEECCCCccccCcc
Confidence 368999999999875433 467999999998655433
No 14
>PF10722 YbjN: Putative bacterial sensory transduction regulator; InterPro: IPR019660 YbjN is a putative sensory transduction regulator protein found in Proteobacteria. As it is a multi-copy suppressor of the coenzyme A-associated temperature sensitivity in temperature-sensitive mutant strains of Escherichia coli the suggestion is that it both helps CoA-A1 and possibly works as a general stabiliser for some other unstable proteins []. ; PDB: 2PLG_B.
Probab=28.44 E-value=48 Score=22.38 Aligned_cols=38 Identities=21% Similarity=0.318 Sum_probs=10.0
Q ss_pred ChHHHHHHHHHcCCc--cCCCCCee--eEEecCCceEEEEee
Q 030903 91 SLPCIEAWLRSLGFH--QSSDDRAV--WLVEKHDWHAQLSLD 128 (169)
Q Consensus 91 sLP~IE~WL~~LG~~--qd~~d~~~--W~lerP~WsAeL~Ld 128 (169)
++-.|++||++.|.. ...++-.. +.....+..-.|.+.
T Consensus 1 ~~d~l~~~l~~~g~~~~~~~d~~~~~~~~~~~~~~~~~i~~~ 42 (127)
T PF10722_consen 1 TLDRLEAFLEEAGYKYEVEEDEDGDVVLRFEFGGIRVFIRFD 42 (127)
T ss_dssp -------------------ETTEE--EEEEEETTEEEEEEE-
T ss_pred CccccccccccccccccccCCCCCeEEEEeccCCEEEEEEEE
Confidence 355799999999998 54444444 566555555544444
No 15
>PF09695 YtfJ_HI0045: Bacterial protein of unknown function (YtfJ_HI0045); InterPro: IPR006513 These are sequences from gammaproteobacteria that are related to the Escherichia coli protein, YtfJ.
Probab=28.27 E-value=83 Score=26.20 Aligned_cols=40 Identities=25% Similarity=0.542 Sum_probs=32.7
Q ss_pred CCeeeEEecCCceEEEEeeeeeeEEEEeecCCCCCcCceeeecccCCCHHHHHHHH
Q 030903 110 DRAVWLVEKHDWHAQLSLDMTDLYIRYLKNGPGNLEKDIERRFSYALSREDIENAI 165 (169)
Q Consensus 110 d~~~W~lerP~WsAeL~Ld~edL~Vry~~~G~~gle~diqRsF~YsLSReDVEaAI 165 (169)
-.+-|.+. ++=+|-|.||.+.. |.|.+.|+ ||-+||++.|
T Consensus 115 ~~~aW~L~-~~~SaiiVlDK~G~-V~F~k~G~--------------Ls~~Ev~qVi 154 (160)
T PF09695_consen 115 VRKAWQLQ-EESSAIIVLDKQGK-VQFVKEGA--------------LSPAEVQQVI 154 (160)
T ss_pred eeccccCC-CCCceEEEEcCCcc-EEEEECCC--------------CCHHHHHHHH
Confidence 35668876 46689999999987 99988886 8889998876
No 16
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=28.07 E-value=40 Score=24.64 Aligned_cols=16 Identities=38% Similarity=0.476 Sum_probs=12.5
Q ss_pred ecccC-CCHHHHHHHHh
Q 030903 151 RFSYA-LSREDIENAIL 166 (169)
Q Consensus 151 sF~Ys-LSReDVEaAIf 166 (169)
.--|- |+|+||.+|+.
T Consensus 50 l~dyp~Lt~~dI~aal~ 66 (79)
T COG2442 50 LADYPDLTLEDIRAALR 66 (79)
T ss_pred HHhCCCCCHHHHHHHHH
Confidence 34466 99999999984
No 17
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=27.35 E-value=82 Score=24.70 Aligned_cols=43 Identities=23% Similarity=0.339 Sum_probs=34.6
Q ss_pred eeeEEecCCceEEEEeeeeeeEEEEeecCCCCCcCceeeecccCCCHHHHHH
Q 030903 112 AVWLVEKHDWHAQLSLDMTDLYIRYLKNGPGNLEKDIERRFSYALSREDIEN 163 (169)
Q Consensus 112 ~~W~lerP~WsAeL~Ld~edL~Vry~~~G~~gle~diqRsF~YsLSReDVEa 163 (169)
.|=.+--|+=+|++.++...|.|.=+..|. .+.|+|+ |++.|.
T Consensus 61 kC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~-------~~R~p~~--r~~ker 103 (105)
T COG2023 61 KCYTPLVPGKNARVRLRKGRVVVTCLECGT-------IRRYPYG--REKKER 103 (105)
T ss_pred ccCcccccCcceEEEEcCCeEEEEecCCCc-------EEEeccc--cchhhc
Confidence 345566788999999999999888877764 7889998 888774
No 18
>COG3831 Uncharacterized conserved protein [Function unknown]
Probab=26.88 E-value=1.3e+02 Score=22.77 Aligned_cols=32 Identities=19% Similarity=0.243 Sum_probs=25.0
Q ss_pred eeeeeEEEEeecCCCCCcCceeeecccCCCHHHHHHH
Q 030903 128 DMTDLYIRYLKNGPGNLEKDIERRFSYALSREDIENA 164 (169)
Q Consensus 128 d~edL~Vry~~~G~~gle~diqRsF~YsLSReDVEaA 164 (169)
+..+|.|+|-.-|..| |.....|.= .+|.++|
T Consensus 23 ~g~~L~~~wGRiG~~G--q~~~k~F~~---~~~a~~~ 54 (85)
T COG3831 23 EGAELTRNWGRIGTKG--QSQIKSFDD---SADAEKA 54 (85)
T ss_pred ecceeEEeecccccCc--ceeeeeCCC---HHHHHHH
Confidence 3889999999999998 888888873 5555544
No 19
>PRK14737 gmk guanylate kinase; Provisional
Probab=26.42 E-value=44 Score=26.64 Aligned_cols=17 Identities=29% Similarity=0.345 Sum_probs=15.1
Q ss_pred cccCCCHHHHHHHHhcC
Q 030903 152 FSYALSREDIENAILGG 168 (169)
Q Consensus 152 F~YsLSReDVEaAIf~G 168 (169)
..||.||++|++++-.|
T Consensus 78 ~~YGt~~~~i~~~~~~g 94 (186)
T PRK14737 78 NYYGTPKAFIEDAFKEG 94 (186)
T ss_pred eeecCcHHHHHHHHHcC
Confidence 36999999999998877
No 20
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=24.49 E-value=51 Score=20.44 Aligned_cols=16 Identities=38% Similarity=0.783 Sum_probs=12.6
Q ss_pred ChHHHHHHHHHcCCcc
Q 030903 91 SLPCIEAWLRSLGFHQ 106 (169)
Q Consensus 91 sLP~IE~WL~~LG~~q 106 (169)
+...+..||+.+|+.+
T Consensus 5 ~~~~v~~wL~~~g~~~ 20 (68)
T smart00454 5 SPESVADWLESIGLEQ 20 (68)
T ss_pred CHHHHHHHHHHCChHH
Confidence 3457889999999876
No 21
>COG5457 Uncharacterized conserved small protein [Function unknown]
Probab=24.23 E-value=51 Score=23.56 Aligned_cols=12 Identities=42% Similarity=0.562 Sum_probs=9.9
Q ss_pred CCCHHHHHHHHh
Q 030903 155 ALSREDIENAIL 166 (169)
Q Consensus 155 sLSReDVEaAIf 166 (169)
||||.||++.+-
T Consensus 47 GisR~d~~~e~~ 58 (63)
T COG5457 47 GISRADIEAEAA 58 (63)
T ss_pred CCCHHHHHHHHH
Confidence 899999988753
No 22
>COG5097 MED6 RNA polymerase II transcriptional regulation mediator [Transcription]
Probab=24.11 E-value=1.4e+02 Score=25.95 Aligned_cols=56 Identities=25% Similarity=0.477 Sum_probs=44.6
Q ss_pred cCCCchhHHhhhCCC---------CCCCCCCCC----------------hHHHHHHHHHcCCcc----CCCCCeeeEEec
Q 030903 68 ELPSTEDEWLEKLPE---------KNKPLYSHS----------------LPCIEAWLRSLGFHQ----SSDDRAVWLVEK 118 (169)
Q Consensus 68 ~~~~~~~~w~~~LP~---------~~TPLYnHs----------------LP~IE~WL~~LG~~q----d~~d~~~W~ler 118 (169)
++.=...||||+++- +..|.|.|+ |++++.=|..||..+ +.-++-.|.+.+
T Consensus 8 siqw~~pew~qs~gLrteNVLeYFs~SPFydk~sNNeilKMQ~QF~~LdL~ql~~~l~~l~g~~~V~ss~rep~lwVIrK 87 (210)
T COG5097 8 SIQWVDPEWLQSKGLRTENVLEYFSGSPFYDKSSNNEILKMQTQFRGLDLGQLSKLLSMLGGFYEVESSNREPTLWVIRK 87 (210)
T ss_pred ceeecCHHHHhccCCcchhHHHHhcCCCccccccchHHHHHHHHhhccChHHHHHHHHhccCEEEEEecCCCCcEEEEeh
Confidence 455667899999985 356999986 889999999999765 567889999988
Q ss_pred CCceE
Q 030903 119 HDWHA 123 (169)
Q Consensus 119 P~WsA 123 (169)
..=+-
T Consensus 88 q~r~n 92 (210)
T COG5097 88 QYRHN 92 (210)
T ss_pred hhhcC
Confidence 65543
No 23
>PF03214 RGP: Reversibly glycosylated polypeptide; InterPro: IPR004901 Alpha-1,4-glucan-protein synthase catalyses the reaction: protein + UDP-D-glucose = alpha-D-glucosyl-protein + UDP The enzyme has a possible role in the synthesis of cell wall polysaccharides in plants []. It is found associated with the cell wall, with the highest concentrations in the plasmodesmata. It is also located in the Golgi apparatus.; GO: 0008466 glycogenin glucosyltransferase activity, 0016758 transferase activity, transferring hexosyl groups, 0007047 cellular cell wall organization, 0030244 cellulose biosynthetic process, 0005618 cell wall, 0030054 cell junction
Probab=23.21 E-value=20 Score=33.17 Aligned_cols=30 Identities=30% Similarity=0.560 Sum_probs=22.9
Q ss_pred EEeecCCCCCcCceeeecccCCCHHHHHHHHhcC
Q 030903 135 RYLKNGPGNLEKDIERRFSYALSREDIENAILGG 168 (169)
Q Consensus 135 ry~~~G~~gle~diqRsF~YsLSReDVEaAIf~G 168 (169)
-|....+++ +-.|-||||+ |+.|+-||-+|
T Consensus 135 Lyd~~~e~~---~f~RGyPfS~-Regv~~~~s~G 164 (348)
T PF03214_consen 135 LYDPYREGA---DFPRGYPFSL-REGVDTAASAG 164 (348)
T ss_pred hcccccccC---cccCCCCccc-ccCCceeeecc
Confidence 354444555 8999999996 99998888776
No 24
>KOG4497 consensus Uncharacterized conserved protein WDR8, contains WD repeats [General function prediction only]
Probab=22.88 E-value=67 Score=30.54 Aligned_cols=31 Identities=19% Similarity=0.508 Sum_probs=25.8
Q ss_pred CCeeeEEecCCceEEEEeeeeeeE-EEEeecC
Q 030903 110 DRAVWLVEKHDWHAQLSLDMTDLY-IRYLKNG 140 (169)
Q Consensus 110 d~~~W~lerP~WsAeL~Ld~edL~-Vry~~~G 140 (169)
-.-.|.+++|+|.+.|-=++..|. ++|..+|
T Consensus 72 ~vqvwsl~Qpew~ckIdeg~agls~~~WSPdg 103 (447)
T KOG4497|consen 72 KVQVWSLVQPEWYCKIDEGQAGLSSISWSPDG 103 (447)
T ss_pred eEEEEEeecceeEEEeccCCCcceeeeECCCc
Confidence 567899999999999998888875 7785555
No 25
>PRK13666 hypothetical protein; Provisional
Probab=22.27 E-value=42 Score=25.93 Aligned_cols=15 Identities=40% Similarity=0.598 Sum_probs=10.9
Q ss_pred ccCCCHHHHHHHHhcC
Q 030903 153 SYALSREDIENAILGG 168 (169)
Q Consensus 153 ~YsLSReDVEaAIf~G 168 (169)
=|||||| |+=||.-|
T Consensus 50 mfGlSre-VdFAvrlg 64 (92)
T PRK13666 50 MFGLSRE-VDFAVRLG 64 (92)
T ss_pred HhhhHHH-HHHHHHhc
Confidence 4889986 77777655
No 26
>PF07408 DUF1507: Protein of unknown function (DUF1507); InterPro: IPR009983 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; however they form alpha helical bundles and are thought to be involved in control of cell shape [].; PDB: 2ODM_B 2GBO_B.
Probab=22.23 E-value=26 Score=26.97 Aligned_cols=14 Identities=57% Similarity=0.759 Sum_probs=10.6
Q ss_pred cCCCHHHHHHHHhcC
Q 030903 154 YALSREDIENAILGG 168 (169)
Q Consensus 154 YsLSReDVEaAIf~G 168 (169)
|||||| |.=||.-|
T Consensus 49 yGlSre-IdFAVrlg 62 (90)
T PF07408_consen 49 YGLSRE-IDFAVRLG 62 (90)
T ss_dssp HHHHHH-HHHHHHTT
T ss_pred hchhHH-HHHHHHhC
Confidence 888886 77777765
No 27
>COG5440 Uncharacterized conserved protein [Function unknown]
Probab=21.84 E-value=55 Score=27.51 Aligned_cols=29 Identities=17% Similarity=0.180 Sum_probs=22.4
Q ss_pred HHHHHHHHcCCccC----CCCCeeeEEecCCce
Q 030903 94 CIEAWLRSLGFHQS----SDDRAVWLVEKHDWH 122 (169)
Q Consensus 94 ~IE~WL~~LG~~qd----~~d~~~W~lerP~Ws 122 (169)
.|++||+++|...+ .+.+--|.+.-|.=.
T Consensus 9 ~I~~WL~EeG~~~~kv~~~na~fH~~v~~P~~~ 41 (161)
T COG5440 9 MILDWLAEEGNVSVKVPDENAPFHFVVKPPTGG 41 (161)
T ss_pred HHHHHHHHhCceeeccCCCCCceeEEecCCCCC
Confidence 69999999999764 566667888777643
No 28
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=21.53 E-value=76 Score=19.57 Aligned_cols=19 Identities=37% Similarity=0.665 Sum_probs=13.7
Q ss_pred hHHHHHHHHHcCCccCCCC
Q 030903 92 LPCIEAWLRSLGFHQSSDD 110 (169)
Q Consensus 92 LP~IE~WL~~LG~~qd~~d 110 (169)
...+.+||+.+|+.+-.+.
T Consensus 4 ~~~V~~wL~~~~~~~y~~~ 22 (63)
T cd00166 4 PEDVAEWLESLGLGQYADN 22 (63)
T ss_pred HHHHHHHHHHcChHHHHHH
Confidence 4578899999998654433
No 29
>PF01265 Cyto_heme_lyase: Cytochrome c/c1 heme lyase; InterPro: IPR000511 Cytochrome c haem-lyase (CCHL) (4.4.1.17 from EC) and cytochrome Cc1 haem-lyase (CC1HL) [] are mitochondrial enzymes that catalyse the covalent attachment of a haem group on two cysteine residues of cytochrome c and c1. These two enzymes are functionally and evolutionary related. There are two conserved regions, the first is located in the central section and the second in the C-terminal section. Both patterns contain conserved histidine, tryptophan and acidic residues which could be important for the interaction of the enzymes with the apoproteins and/or the haem group.; GO: 0004408 holocytochrome-c synthase activity, 0005739 mitochondrion
Probab=21.17 E-value=1.1e+02 Score=27.21 Aligned_cols=25 Identities=32% Similarity=0.397 Sum_probs=20.7
Q ss_pred HHHHHHcCCccCCCCCeeeEEecCC
Q 030903 96 EAWLRSLGFHQSSDDRAVWLVEKHD 120 (169)
Q Consensus 96 E~WL~~LG~~qd~~d~~~W~lerP~ 120 (169)
.+|++.+--..-.=|+|.|.|.|.+
T Consensus 189 kAr~~~~lG~~~PFDRHDW~VdRcG 213 (259)
T PF01265_consen 189 KARIRSLLGYELPFDRHDWIVDRCG 213 (259)
T ss_pred HHHHHHHhCCCCCCCcccceEecCC
Confidence 5677776557788899999999998
No 30
>PF10061 DUF2299: Uncharacterized conserved protein (DUF2299); InterPro: IPR018747 Members of this family of hypothetical bacterial proteins have no known function. ; PDB: 3CXJ_D.
Probab=20.05 E-value=63 Score=25.57 Aligned_cols=23 Identities=30% Similarity=0.602 Sum_probs=14.7
Q ss_pred HHHHHHHHcCCccCC--CCCeeeEE
Q 030903 94 CIEAWLRSLGFHQSS--DDRAVWLV 116 (169)
Q Consensus 94 ~IE~WL~~LG~~qd~--~d~~~W~l 116 (169)
.|+.||+++|..... +...-|++
T Consensus 1 ~I~~WL~eeG~~~~~~~~~~~~fh~ 25 (138)
T PF10061_consen 1 EIENWLKEEGLKVEEPPDANAYFHI 25 (138)
T ss_dssp HHHHHHHHTT-EEEE---TTEEEEE
T ss_pred ChHHHHHhcCceEecCCCCCceEEE
Confidence 489999999987654 33445543
Done!