Query 039633
Match_columns 31
No_of_seqs 103 out of 155
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 11:36:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039633.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039633hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2230 Cfa Cyclopropane fatty 94.1 0.0069 1.5E-07 38.4 -1.3 31 1-31 201-232 (283)
2 PF02353 CMAS: Mycolic acid cy 93.9 0.006 1.3E-07 37.4 -1.9 30 1-31 195-226 (273)
3 PRK11705 cyclopropane fatty ac 76.7 0.66 1.4E-05 29.6 -0.4 31 1-31 291-321 (383)
4 PF15345 TMEM51: Transmembrane 72.1 0.74 1.6E-05 29.1 -1.0 9 23-31 3-11 (233)
5 COG0588 GpmA Phosphoglycerate 55.7 1.6 3.4E-05 27.7 -1.7 19 10-28 73-91 (230)
6 PF09478 CBM49: Carbohydrate b 55.6 13 0.00028 18.8 2.0 15 15-29 6-20 (80)
7 PF06674 DUF1176: Protein of u 52.8 8 0.00017 24.5 1.1 15 16-30 302-316 (340)
8 PHA03052 Hypothetical protein; 52.4 8.2 0.00018 20.6 0.9 10 19-28 33-42 (69)
9 PF11379 DUF3182: Protein of u 47.5 9.9 0.00021 25.5 0.9 11 15-25 288-298 (355)
10 PF07366 SnoaL: SnoaL-like pol 46.2 18 0.00038 18.5 1.6 14 15-28 70-83 (126)
11 PF01927 Mut7-C: Mut7-C RNAse 44.7 6.2 0.00014 22.1 -0.3 9 21-29 134-142 (147)
12 PHA02325 hypothetical protein 41.8 13 0.00029 20.0 0.8 8 21-28 13-20 (72)
13 PF01006 HCV_NS4a: Hepatitis C 41.3 19 0.00042 18.5 1.3 14 12-25 21-34 (56)
14 PTZ00450 macrophage migration 37.5 5.1 0.00011 22.0 -1.3 21 1-25 91-111 (113)
15 PRK01253 preprotein translocas 34.0 18 0.00038 18.1 0.4 14 1-14 11-24 (54)
16 PF15631 Imm-NTF2-2: NTF2 fold 33.4 20 0.00044 18.7 0.6 17 9-25 19-38 (66)
17 PHA00008 J DNA packaging prote 33.1 30 0.00065 15.5 1.1 11 17-27 15-25 (26)
18 KOG4457 Uncharacterized conser 30.4 48 0.001 20.8 2.0 16 10-25 108-123 (202)
19 PRK15286 putative minor fimbri 28.7 24 0.00051 21.2 0.4 17 10-30 54-70 (170)
20 cd07224 Pat_like Patatin-like 28.3 36 0.00078 20.2 1.1 22 3-24 132-155 (233)
21 PF01873 eIF-5_eIF-2B: Domain 27.6 9.7 0.00021 21.5 -1.3 24 5-28 50-79 (125)
22 KOG2805 tRNA (5-methylaminomet 27.5 27 0.00059 23.7 0.6 11 20-31 124-134 (377)
23 PF10184 DUF2358: Uncharacteri 27.2 58 0.0013 17.3 1.8 11 15-25 75-85 (113)
24 PF06832 BiPBP_C: Penicillin-B 26.7 60 0.0013 16.3 1.7 13 17-29 44-56 (89)
25 PF15643 Tox-PL-2: Papain fold 26.5 28 0.00061 19.6 0.4 12 17-28 62-73 (100)
26 PF12293 DUF3625: Protein of u 26.1 54 0.0012 20.4 1.7 14 17-30 183-196 (241)
27 PF02770 Acyl-CoA_dh_M: Acyl-C 25.4 26 0.00055 16.3 0.1 8 18-25 25-32 (52)
28 PHA02770 hypothetical protein; 24.9 55 0.0012 17.8 1.4 22 7-28 33-54 (81)
29 PF06868 DUF1257: Protein of u 24.1 41 0.00088 18.4 0.8 11 19-29 40-51 (105)
30 cd01043 DPS DPS protein, ferri 24.1 21 0.00046 19.0 -0.3 11 18-28 20-30 (139)
31 COG1898 RfbC dTDP-4-dehydrorha 23.5 47 0.001 19.9 1.0 22 9-30 44-65 (173)
32 PF15600 Imm39: Immunity prote 23.3 67 0.0015 19.9 1.7 15 11-25 166-181 (187)
33 COG3092 Uncharacterized protei 23.0 24 0.00051 21.3 -0.3 8 23-30 15-22 (149)
34 PF04726 Microvir_J: Microviru 21.9 27 0.00058 15.4 -0.2 10 18-27 15-24 (24)
35 PRK10718 RpoE-regulated lipopr 21.8 32 0.0007 21.3 0.1 7 1-7 173-179 (191)
36 PHA02779 E6 protein; Provision 21.3 81 0.0017 18.3 1.7 21 5-28 42-62 (150)
37 TIGR01221 rmlC dTDP-4-dehydror 20.2 50 0.0011 19.5 0.7 21 9-29 43-63 (176)
No 1
>COG2230 Cfa Cyclopropane fatty acid synthase and related methyltransferases [Cell envelope biogenesis, outer membrane]
Probab=94.13 E-value=0.0069 Score=38.39 Aligned_cols=31 Identities=19% Similarity=0.083 Sum_probs=27.0
Q ss_pred CCCCChhhh-hcCceeeEEEeeEcCeeccccC
Q 039633 1 MPSANLPLY-FQDDVSVIDHWLLNGMHFANKV 31 (31)
Q Consensus 1 MPS~dlll~-Fq~~l~v~~~W~~nG~HY~rTa 31 (31)
+||.+.+.. +++..-.+..|...|.||+||+
T Consensus 201 lPs~~~i~~~~~~~~~~v~~~~~~~~hYa~Tl 232 (283)
T COG2230 201 LPSISEILELASEAGFVVLDVESLRPHYARTL 232 (283)
T ss_pred CCCHHHHHHHHHhcCcEEehHhhhcHHHHHHH
Confidence 588777777 8888888999999999999984
No 2
>PF02353 CMAS: Mycolic acid cyclopropane synthetase; InterPro: IPR003333 This entry represents mycolic acid cyclopropane synthases and related enzymes, including CmaA1, CmaA2 (cyclopropane mycolic acid synthase A1 and A2) and MmaA1-4 (methoxymycolic acid synthase A1-4). All are thought to be S-adenosyl-L-methionine (SAM) utilising methyltransferases []. Mycolic acid cyclopropane synthase or cyclopropane-fatty-acyl-phospholipid synthase (CFA synthase) 2.1.1.79 from EC catalyses the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid -> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid. The major mycolic acid produced by Mycobacterium tuberculosis contains two cis-cyclopropanes in the meromycolate chain. Cyclopropanation may contribute to the structural integrity of the cell wall complex [].; GO: 0008610 lipid biosynthetic process; PDB: 3HA5_A 2FK8_A 3HA7_A 3HA3_A 2FK7_A 1KPG_D 1KP9_B 1KPH_D 3VC2_E 3VC1_D ....
Probab=93.90 E-value=0.006 Score=37.39 Aligned_cols=30 Identities=23% Similarity=0.231 Sum_probs=19.4
Q ss_pred CCCCChhhh-hc-CceeeEEEeeEcCeeccccC
Q 039633 1 MPSANLPLY-FQ-DDVSVIDHWLLNGMHFANKV 31 (31)
Q Consensus 1 MPS~dlll~-Fq-~~l~v~~~W~~nG~HY~rTa 31 (31)
|||.+.+.. ++ ..|.|+ +|.-.|.||+||+
T Consensus 195 lps~~~~~~~~~~~~l~v~-~~~~~~~hY~~Tl 226 (273)
T PF02353_consen 195 LPSLSEILRAAEDAGLEVE-DVENLGRHYARTL 226 (273)
T ss_dssp --BHHHHHHHHHHTT-EEE-EEEE-HHHHHHHH
T ss_pred CCCHHHHHHHHhcCCEEEE-EEEEcCcCHHHHH
Confidence 577776666 44 457765 7788899999994
No 3
>PRK11705 cyclopropane fatty acyl phospholipid synthase; Provisional
Probab=76.68 E-value=0.66 Score=29.62 Aligned_cols=31 Identities=16% Similarity=0.368 Sum_probs=20.4
Q ss_pred CCCCChhhhhcCceeeEEEeeEcCeeccccC
Q 039633 1 MPSANLPLYFQDDVSVIDHWLLNGMHFANKV 31 (31)
Q Consensus 1 MPS~dlll~Fq~~l~v~~~W~~nG~HY~rTa 31 (31)
+||.+.+..+.+..-...+|.--|.||++|+
T Consensus 291 lps~~~i~~~~~~~~~v~d~~~~~~hy~~TL 321 (383)
T PRK11705 291 LPSVRQIAQASEGLFVMEDWHNFGADYDRTL 321 (383)
T ss_pred CCCHHHHHHHHHCCcEEEEEecChhhHHHHH
Confidence 3554444444444444678899999999984
No 4
>PF15345 TMEM51: Transmembrane protein 51
Probab=72.15 E-value=0.74 Score=29.12 Aligned_cols=9 Identities=33% Similarity=0.623 Sum_probs=8.1
Q ss_pred cCeeccccC
Q 039633 23 NGMHFANKV 31 (31)
Q Consensus 23 nG~HY~rTa 31 (31)
||.||+.||
T Consensus 3 ~GshYAL~A 11 (233)
T PF15345_consen 3 SGSHYALTA 11 (233)
T ss_pred CchhHHHHH
Confidence 899999886
No 5
>COG0588 GpmA Phosphoglycerate mutase 1 [Carbohydrate transport and metabolism]
Probab=55.71 E-value=1.6 Score=27.68 Aligned_cols=19 Identities=37% Similarity=0.511 Sum_probs=16.5
Q ss_pred hcCceeeEEEeeEcCeecc
Q 039633 10 FQDDVSVIDHWLLNGMHFA 28 (31)
Q Consensus 10 Fq~~l~v~~~W~~nG~HY~ 28 (31)
.|..+.+.++|++|-+||.
T Consensus 73 d~~~ipv~kswrLNERhYG 91 (230)
T COG0588 73 DQLWIPVIKSWRLNERHYG 91 (230)
T ss_pred cccCcchhhHHHhhhhhhh
Confidence 4667888999999999996
No 6
>PF09478 CBM49: Carbohydrate binding domain CBM49; InterPro: IPR019028 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This domain is found at the C-terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose []. ; GO: 0030246 carbohydrate binding, 0005576 extracellular region
Probab=55.56 E-value=13 Score=18.84 Aligned_cols=15 Identities=20% Similarity=0.756 Sum_probs=12.8
Q ss_pred eeEEEeeEcCeeccc
Q 039633 15 SVIDHWLLNGMHFAN 29 (31)
Q Consensus 15 ~v~~~W~~nG~HY~r 29 (31)
.++++|.-||.+|.+
T Consensus 6 ~~~~sW~~~g~~y~q 20 (80)
T PF09478_consen 6 TLVNSWTENGQTYTQ 20 (80)
T ss_pred EEEeEEEeCCEEEEE
Confidence 578999999998864
No 7
>PF06674 DUF1176: Protein of unknown function (DUF1176); InterPro: IPR009560 This family consists of several hypothetical bacterial proteins of around 340 residues in length. Members of this family contain six highly conserved cysteine residues. The function of this family is unknown.
Probab=52.76 E-value=8 Score=24.53 Aligned_cols=15 Identities=20% Similarity=0.556 Sum_probs=12.0
Q ss_pred eEEEeeEcCeecccc
Q 039633 16 VIDHWLLNGMHFANK 30 (31)
Q Consensus 16 v~~~W~~nG~HY~rT 30 (31)
.-++|+|||+.|..+
T Consensus 302 ~~~~w~wdG~~F~L~ 316 (340)
T PF06674_consen 302 SSARWVWDGKRFVLS 316 (340)
T ss_pred CceEEEEeCcceEEe
Confidence 357899999998754
No 8
>PHA03052 Hypothetical protein; Provisional
Probab=52.41 E-value=8.2 Score=20.62 Aligned_cols=10 Identities=40% Similarity=1.079 Sum_probs=8.5
Q ss_pred EeeEcCeecc
Q 039633 19 HWLLNGMHFA 28 (31)
Q Consensus 19 ~W~~nG~HY~ 28 (31)
=|..||++|+
T Consensus 33 ~W~~N~~~~e 42 (69)
T PHA03052 33 FWISNGMYYE 42 (69)
T ss_pred EEEeCCcEEe
Confidence 4999999994
No 9
>PF11379 DUF3182: Protein of unknown function (DUF3182); InterPro: IPR021519 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=47.45 E-value=9.9 Score=25.46 Aligned_cols=11 Identities=18% Similarity=0.573 Sum_probs=9.1
Q ss_pred eeEEEeeEcCe
Q 039633 15 SVIDHWLLNGM 25 (31)
Q Consensus 15 ~v~~~W~~nG~ 25 (31)
.+||.||+.|-
T Consensus 288 VLEQSWRvGGA 298 (355)
T PF11379_consen 288 VLEQSWRVGGA 298 (355)
T ss_pred eeeeeeccCCC
Confidence 37999999983
No 10
>PF07366 SnoaL: SnoaL-like polyketide cyclase; InterPro: IPR009959 This domain is found in SnoaL [] a polyketide cyclase involved in nogalamycin biosynthesis. This domain was formerly known as DUF1486. It adopts a distorted alpha-beta barrel fold []. Structural data together with site-directed mutagenesis experiments have shown that SnoaL has a different mechanism to that of the classical aldolase for catalysing intramolecular aldol condensation [].; PDB: 2GEY_C 3F9S_A 2GEX_A 3EHC_B 2F99_D 2F98_D 1SJW_A 3K0Z_B.
Probab=46.24 E-value=18 Score=18.54 Aligned_cols=14 Identities=29% Similarity=0.615 Sum_probs=11.2
Q ss_pred eeEEEeeEcCeecc
Q 039633 15 SVIDHWLLNGMHFA 28 (31)
Q Consensus 15 ~v~~~W~~nG~HY~ 28 (31)
.+.-+|++.|+|-.
T Consensus 70 ~v~~~~~~~Gth~g 83 (126)
T PF07366_consen 70 RVAVRWTFTGTHTG 83 (126)
T ss_dssp EEEEEEEEEEEESS
T ss_pred EEEEEEEEEEeecC
Confidence 56779999999953
No 11
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=44.71 E-value=6.2 Score=22.07 Aligned_cols=9 Identities=22% Similarity=0.545 Sum_probs=7.1
Q ss_pred eEcCeeccc
Q 039633 21 LLNGMHFAN 29 (31)
Q Consensus 21 ~~nG~HY~r 29 (31)
.|.|+||.|
T Consensus 134 yW~GsH~~~ 142 (147)
T PF01927_consen 134 YWEGSHWRR 142 (147)
T ss_pred ecccccHHH
Confidence 588999875
No 12
>PHA02325 hypothetical protein
Probab=41.81 E-value=13 Score=19.99 Aligned_cols=8 Identities=38% Similarity=0.775 Sum_probs=5.8
Q ss_pred eEcCeecc
Q 039633 21 LLNGMHFA 28 (31)
Q Consensus 21 ~~nG~HY~ 28 (31)
+++|+||=
T Consensus 13 WldgqhYW 20 (72)
T PHA02325 13 WLDGQHYW 20 (72)
T ss_pred eEcceeee
Confidence 47888883
No 13
>PF01006 HCV_NS4a: Hepatitis C virus non-structural protein NS4a; InterPro: IPR000745 NS4a (non-structural protein) forms an integral part of the NS3 serine protease in Hepatitis C virus, as it is required in a number of cases as a cofactor of cleavage [, ]. It has also been reported that NS4a interacts with NS4b and NS3 to form a multi-subunit replicase complex [].; GO: 0016032 viral reproduction, 0044423 virion part; PDB: 3M5M_C 2FM2_D 3KNX_D 2A4R_B 2F9V_B 2OBQ_B 2O8M_C 3KEE_F 3KF2_C 1NS3_D ....
Probab=41.30 E-value=19 Score=18.53 Aligned_cols=14 Identities=36% Similarity=0.788 Sum_probs=10.7
Q ss_pred CceeeEEEeeEcCe
Q 039633 12 DDVSVIDHWLLNGM 25 (31)
Q Consensus 12 ~~l~v~~~W~~nG~ 25 (31)
.-+.|..+|.+||+
T Consensus 21 Gs~vvv~~~~v~g~ 34 (56)
T PF01006_consen 21 GSVVVVGRWSVNGK 34 (56)
T ss_dssp -EBEEEEEEETTS-
T ss_pred CcEEEEEEEEECCC
Confidence 45788999999996
No 14
>PTZ00450 macrophage migration inhibitory factor-like protein; Provisional
Probab=37.51 E-value=5.1 Score=22.05 Aligned_cols=21 Identities=19% Similarity=0.512 Sum_probs=16.0
Q ss_pred CCCCChhhhhcCceeeEEEeeEcCe
Q 039633 1 MPSANLPLYFQDDVSVIDHWLLNGM 25 (31)
Q Consensus 1 MPS~dlll~Fq~~l~v~~~W~~nG~ 25 (31)
.|.+....-|.|- ..|-|||+
T Consensus 91 Ip~dRiYI~f~d~----~~~G~nG~ 111 (113)
T PTZ00450 91 IPAERIYVFYYST----KHCGWNGT 111 (113)
T ss_pred CCcccEEEEEEcH----HHcccCcE
Confidence 3677777788872 56999997
No 15
>PRK01253 preprotein translocase subunit SecG; Reviewed
Probab=34.03 E-value=18 Score=18.11 Aligned_cols=14 Identities=43% Similarity=0.733 Sum_probs=11.4
Q ss_pred CCCCChhhhhcCce
Q 039633 1 MPSANLPLYFQDDV 14 (31)
Q Consensus 1 MPS~dlll~Fq~~l 14 (31)
|-|+.|+.||-||-
T Consensus 11 ~ssAGL~ryy~ed~ 24 (54)
T PRK01253 11 MSSAGLIRYFEEET 24 (54)
T ss_pred cccchhhhhhhccc
Confidence 56888999998874
No 16
>PF15631 Imm-NTF2-2: NTF2 fold immunity protein
Probab=33.40 E-value=20 Score=18.66 Aligned_cols=17 Identities=24% Similarity=0.446 Sum_probs=12.4
Q ss_pred hhcCceee---EEEeeEcCe
Q 039633 9 YFQDDVSV---IDHWLLNGM 25 (31)
Q Consensus 9 ~Fq~~l~v---~~~W~~nG~ 25 (31)
+.|..+.+ .+.|.|+|+
T Consensus 19 ~~ekP~~v~~~~~~WiV~Gt 38 (66)
T PF15631_consen 19 EEEKPYRVTLDGDSWIVEGT 38 (66)
T ss_pred hhcCCeEEecCCCeEEEEee
Confidence 45666665 467999998
No 17
>PHA00008 J DNA packaging protein
Probab=33.13 E-value=30 Score=15.47 Aligned_cols=11 Identities=27% Similarity=0.836 Sum_probs=8.7
Q ss_pred EEEeeEcCeec
Q 039633 17 IDHWLLNGMHF 27 (31)
Q Consensus 17 ~~~W~~nG~HY 27 (31)
.+-|.|.|+.|
T Consensus 15 ARLWYVGGtQf 25 (26)
T PHA00008 15 ARLWYVGGTQF 25 (26)
T ss_pred eEEEEeccEEc
Confidence 35699999876
No 18
>KOG4457 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.35 E-value=48 Score=20.82 Aligned_cols=16 Identities=25% Similarity=0.517 Sum_probs=13.7
Q ss_pred hcCceeeEEEeeEcCe
Q 039633 10 FQDDVSVIDHWLLNGM 25 (31)
Q Consensus 10 Fq~~l~v~~~W~~nG~ 25 (31)
-||+-.|.-+|||-|-
T Consensus 108 h~d~~Tvr~RWRv~gv 123 (202)
T KOG4457|consen 108 HIDEGTVRCRWRVKGV 123 (202)
T ss_pred cCCCceEEEEEEEecc
Confidence 3788899999999985
No 19
>PRK15286 putative minor fimbrial subunit StfE; Provisional
Probab=28.74 E-value=24 Score=21.16 Aligned_cols=17 Identities=18% Similarity=0.542 Sum_probs=11.9
Q ss_pred hcCceeeEEEeeEcCeecccc
Q 039633 10 FQDDVSVIDHWLLNGMHFANK 30 (31)
Q Consensus 10 Fq~~l~v~~~W~~nG~HY~rT 30 (31)
|.| +-+.+ |||..|.|+
T Consensus 54 FGd-V~~~~---IDG~nY~q~ 70 (170)
T PRK15286 54 FGN-VLTTK---VDGVNYRQA 70 (170)
T ss_pred CCc-ccccc---ccCeeeeEe
Confidence 555 54443 999999875
No 20
>cd07224 Pat_like Patatin-like phospholipase. Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of lipid acyl hydrolase, catalysing the cleavage of fatty acids from membrane lipids. Members of this family have been found also in vertebrates.
Probab=28.27 E-value=36 Score=20.16 Aligned_cols=22 Identities=23% Similarity=0.403 Sum_probs=17.9
Q ss_pred CCChhhhhcC--ceeeEEEeeEcC
Q 039633 3 SANLPLYFQD--DVSVIDHWLLNG 24 (31)
Q Consensus 3 S~dlll~Fq~--~l~v~~~W~~nG 24 (31)
|..++.+|+- -+.+..++.|+|
T Consensus 132 S~~iP~~~~p~~~v~~~G~~~vDG 155 (233)
T cd07224 132 SCNIPGYLAPWPATMFRGKLCVDG 155 (233)
T ss_pred hccCCcccCCCCCeeECCEEEEeC
Confidence 6678888885 478889999988
No 21
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=27.58 E-value=9.7 Score=21.50 Aligned_cols=24 Identities=17% Similarity=0.396 Sum_probs=16.2
Q ss_pred ChhhhhcCceeeE------EEeeEcCeecc
Q 039633 5 NLPLYFQDDVSVI------DHWLLNGMHFA 28 (31)
Q Consensus 5 dlll~Fq~~l~v~------~~W~~nG~HY~ 28 (31)
.+..||+..|... ++..+||.|=+
T Consensus 50 ~~~ky~~~ELgt~~~id~~~~lii~G~~~~ 79 (125)
T PF01873_consen 50 HVLKYFGKELGTQGSIDGKGRLIINGRFSS 79 (125)
T ss_dssp HHHHHHHHHSSSEEEEETTTEEEEESSSSC
T ss_pred HHHHHHHHHHCCceEECCCCEEEEEEecCH
Confidence 4566777665432 68999998744
No 22
>KOG2805 consensus tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=27.47 E-value=27 Score=23.70 Aligned_cols=11 Identities=55% Similarity=1.198 Sum_probs=8.6
Q ss_pred eeEcCeeccccC
Q 039633 20 WLLNGMHFANKV 31 (31)
Q Consensus 20 W~~nG~HY~rTa 31 (31)
|...| ||+||.
T Consensus 124 ~latG-HYAr~~ 134 (377)
T KOG2805|consen 124 WLATG-HYARVV 134 (377)
T ss_pred eEEee-eeeeee
Confidence 77776 999974
No 23
>PF10184 DUF2358: Uncharacterized conserved protein (DUF2358); InterPro: IPR018790 This entry represents a family of conserved proteins. The function is unknown.
Probab=27.16 E-value=58 Score=17.30 Aligned_cols=11 Identities=27% Similarity=0.818 Sum_probs=9.2
Q ss_pred eeEEEeeEcCe
Q 039633 15 SVIDHWLLNGM 25 (31)
Q Consensus 15 ~v~~~W~~nG~ 25 (31)
.|+-+|++.|.
T Consensus 75 ~I~~rW~~~g~ 85 (113)
T PF10184_consen 75 TIRARWRLRGV 85 (113)
T ss_pred EEEEEEEEEEE
Confidence 78889999874
No 24
>PF06832 BiPBP_C: Penicillin-Binding Protein C-terminus Family; InterPro: IPR009647 This conserved region of approximately 90 residues is found in a sub-group of bacterial Penicillin-Binding Proteins (PBPs). A variable length loop region separates this region from the transpeptidase unit (IPR001460 from INTERPRO). It is predicted to be a beta fold.
Probab=26.68 E-value=60 Score=16.26 Aligned_cols=13 Identities=15% Similarity=0.488 Sum_probs=9.8
Q ss_pred EEEeeEcCeeccc
Q 039633 17 IDHWLLNGMHFAN 29 (31)
Q Consensus 17 ~~~W~~nG~HY~r 29 (31)
.=.|.|||+--+.
T Consensus 44 ~~~W~vdg~~~g~ 56 (89)
T PF06832_consen 44 PVYWFVDGEPLGT 56 (89)
T ss_pred cEEEEECCEEccc
Confidence 4579999987644
No 25
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=26.45 E-value=28 Score=19.63 Aligned_cols=12 Identities=25% Similarity=0.459 Sum_probs=8.5
Q ss_pred EEEeeEcCeecc
Q 039633 17 IDHWLLNGMHFA 28 (31)
Q Consensus 17 ~~~W~~nG~HY~ 28 (31)
++.=.-||.||.
T Consensus 62 ~~sIt~NG~H~g 73 (100)
T PF15643_consen 62 QESITTNGRHYG 73 (100)
T ss_pred CcceeeCCEEEE
Confidence 344567999995
No 26
>PF12293 DUF3625: Protein of unknown function (DUF3625); InterPro: IPR022073 This family of proteins is found in bacteria. Proteins in this family are typically between 327 and 360 amino acids in length.
Probab=26.05 E-value=54 Score=20.41 Aligned_cols=14 Identities=7% Similarity=0.406 Sum_probs=12.6
Q ss_pred EEEeeEcCeecccc
Q 039633 17 IDHWLLNGMHFANK 30 (31)
Q Consensus 17 ~~~W~~nG~HY~rT 30 (31)
.+-|+.+|..|=||
T Consensus 183 ~~AW~~g~~lyvRT 196 (241)
T PF12293_consen 183 VQAWQYGDDLYVRT 196 (241)
T ss_pred eEEEEECCeEEEEe
Confidence 57899999999998
No 27
>PF02770 Acyl-CoA_dh_M: Acyl-CoA dehydrogenase, middle domain; InterPro: IPR006091 Acyl-CoA dehydrogenases (1.3.99.3 from EC) are a family of flavoproteins that catalyse the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with the concomitant reduction of enzyme-bound FAD. Different family members share a high sequence identity, catalytic mechanisms, and structural properties, but differ in the position of their catalytic bases and in their substrate binding specificity. Butyryl-CoA dehydrogenase [] prefers short chain substrates, medium chain- and long-chain acyl-CoA dehydrogenases prefer medium and long chain substrates, respectively, and Isovaleryl-CoA dehydrogenase [] prefers branched-chain substrates. The monomeric enzyme is folded into three domains of approximately equal size, where the N-terminal domain is all-alpha, the middle domain is an open (5,8) barrel, and the C-terminal domain is a four-helical bundle. The constituent families differ in the numbers of C-terminal domains. This entry represents the middle beta-barrel domain found in medium chain acyl-CoA dehydrogenases, as well as in the related peroxisomal acyl-CoA oxidase-II enzymes. Acyl-CoA oxidase (ACO; 1.3.3.6 from EC) catalyzes the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids [].; GO: 0003995 acyl-CoA dehydrogenase activity, 0055114 oxidation-reduction process; PDB: 3MDD_B 1UDY_C 3MDE_B 2UXW_A 3B96_A 1SIQ_A 1SIR_A 2R0N_A 2R0M_A 2D29_B ....
Probab=25.42 E-value=26 Score=16.30 Aligned_cols=8 Identities=50% Similarity=0.900 Sum_probs=5.3
Q ss_pred EEeeEcCe
Q 039633 18 DHWLLNGM 25 (31)
Q Consensus 18 ~~W~~nG~ 25 (31)
+.|++||.
T Consensus 25 ~~~~L~G~ 32 (52)
T PF02770_consen 25 DGYVLNGE 32 (52)
T ss_dssp TEEEEEEE
T ss_pred ceEEEeeE
Confidence 45777775
No 28
>PHA02770 hypothetical protein; Provisional
Probab=24.94 E-value=55 Score=17.81 Aligned_cols=22 Identities=18% Similarity=0.341 Sum_probs=15.5
Q ss_pred hhhhcCceeeEEEeeEcCeecc
Q 039633 7 PLYFQDDVSVIDHWLLNGMHFA 28 (31)
Q Consensus 7 ll~Fq~~l~v~~~W~~nG~HY~ 28 (31)
+.|-...-+|..--.+||+||.
T Consensus 33 lfyakkrnri~gylei~~~hyr 54 (81)
T PHA02770 33 LFYAKKRNRITGYLEVNGRHYR 54 (81)
T ss_pred eEeeeccCeEEEEEEEcCceEE
Confidence 3444455677777789999995
No 29
>PF06868 DUF1257: Protein of unknown function (DUF1257); InterPro: IPR009666 This family represents Ycf35, which is encoded in algal chloroplast and in cyanobacteria. The function of these proteins are unknown. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=24.08 E-value=41 Score=18.36 Aligned_cols=11 Identities=18% Similarity=0.226 Sum_probs=8.8
Q ss_pred EeeEcCee-ccc
Q 039633 19 HWLLNGMH-FAN 29 (31)
Q Consensus 19 ~W~~nG~H-Y~r 29 (31)
-|+|||.. |+-
T Consensus 40 GF~wn~~~sYeL 51 (105)
T PF06868_consen 40 GFRWNGDGSYEL 51 (105)
T ss_pred EEEECCCccEEE
Confidence 48999998 864
No 30
>cd01043 DPS DPS protein, ferritin-like diiron-binding domain. DPS (DNA Protecting protein under Starved conditions) domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide. These proteins assemble into dodecameric structures, some form DPS-DNA co-crystalline complexes, and possess iron and H2O2 detoxification capabilities. Expression of DPS is induced by oxidative or nutritional stress, including metal ion starvation. Members of the DPS family are homopolymers formed by 12 four-helix bundle subunits that assemble with 23 symmetry into a hollow shell. The DPS ferroxidase site is unusual in that it is not located in a four-helix bundle as in ferritin, but is shared by 2-fold symmetry-related subunits providing the iron ligands. Many DPS sequences (e.g., E. coli) disp
Probab=24.08 E-value=21 Score=19.02 Aligned_cols=11 Identities=36% Similarity=0.821 Sum_probs=9.1
Q ss_pred EEeeEcCeecc
Q 039633 18 DHWLLNGMHFA 28 (31)
Q Consensus 18 ~~W~~nG~HY~ 28 (31)
-||.|.|.++.
T Consensus 20 ~HW~v~G~~f~ 30 (139)
T cd01043 20 YHWNVKGPNFF 30 (139)
T ss_pred CCcCccCcCHH
Confidence 58999999874
No 31
>COG1898 RfbC dTDP-4-dehydrorhamnose 3,5-epimerase and related enzymes [Cell envelope biogenesis, outer membrane]
Probab=23.46 E-value=47 Score=19.87 Aligned_cols=22 Identities=32% Similarity=0.549 Sum_probs=16.9
Q ss_pred hhcCceeeEEEeeEcCeecccc
Q 039633 9 YFQDDVSVIDHWLLNGMHFANK 30 (31)
Q Consensus 9 ~Fq~~l~v~~~W~~nG~HY~rT 30 (31)
.=|+.+++-..=.+.|.||++.
T Consensus 44 ~~Q~n~S~S~~GvlRGlHyq~~ 65 (173)
T COG1898 44 FVQDNHSFSYPGVLRGLHYQHK 65 (173)
T ss_pred cccceEEEecCCeeEEEEcccC
Confidence 4477778777668999999874
No 32
>PF15600 Imm39: Immunity protein 39
Probab=23.35 E-value=67 Score=19.93 Aligned_cols=15 Identities=20% Similarity=0.756 Sum_probs=12.0
Q ss_pred cCceeeE-EEeeEcCe
Q 039633 11 QDDVSVI-DHWLLNGM 25 (31)
Q Consensus 11 q~~l~v~-~~W~~nG~ 25 (31)
-+++.|. .+|.++|-
T Consensus 166 n~~~~V~~~~W~IDGl 181 (187)
T PF15600_consen 166 NGSFHVYKNNWHIDGL 181 (187)
T ss_pred CCceEEEEeeeeecCc
Confidence 4678886 99999993
No 33
>COG3092 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.02 E-value=24 Score=21.28 Aligned_cols=8 Identities=25% Similarity=0.717 Sum_probs=6.7
Q ss_pred cCeecccc
Q 039633 23 NGMHFANK 30 (31)
Q Consensus 23 nG~HY~rT 30 (31)
.|.||.+|
T Consensus 15 ~GQhY~kt 22 (149)
T COG3092 15 RGQHYMKT 22 (149)
T ss_pred cccHHHhc
Confidence 49999887
No 34
>PF04726 Microvir_J: Microvirus J protein; InterPro: IPR006815 This small protein is involved in DNA packaging, interacting with DNA via its hydrophobic C terminus. In bacteriophage phi-X174, J is present in 60 copies, and forms an S-shaped polypeptide chain without any secondary structure. It is thought to interact with DNA through simple charge interactions [].; GO: 0003677 DNA binding, 0019073 viral DNA genome packaging, 0019028 viral capsid; PDB: 1M06_J 1GFF_3 1RB8_J 2BPA_3.
Probab=21.93 E-value=27 Score=15.37 Aligned_cols=10 Identities=30% Similarity=0.946 Sum_probs=2.6
Q ss_pred EEeeEcCeec
Q 039633 18 DHWLLNGMHF 27 (31)
Q Consensus 18 ~~W~~nG~HY 27 (31)
+-|.|.|+.|
T Consensus 15 rlwyvgg~qf 24 (24)
T PF04726_consen 15 RLWYVGGTQF 24 (24)
T ss_dssp ----SSS---
T ss_pred EEEEecceeC
Confidence 4588888764
No 35
>PRK10718 RpoE-regulated lipoprotein; Provisional
Probab=21.83 E-value=32 Score=21.26 Aligned_cols=7 Identities=43% Similarity=0.591 Sum_probs=5.9
Q ss_pred CCCCChh
Q 039633 1 MPSANLP 7 (31)
Q Consensus 1 MPS~dll 7 (31)
|||+|.|
T Consensus 173 mPpdd~L 179 (191)
T PRK10718 173 MPSDDTL 179 (191)
T ss_pred CCcHHHH
Confidence 8888887
No 36
>PHA02779 E6 protein; Provisional
Probab=21.30 E-value=81 Score=18.27 Aligned_cols=21 Identities=19% Similarity=0.487 Sum_probs=14.6
Q ss_pred ChhhhhcCceeeEEEeeEcCeecc
Q 039633 5 NLPLYFQDDVSVIDHWLLNGMHFA 28 (31)
Q Consensus 5 dlll~Fq~~l~v~~~W~~nG~HY~ 28 (31)
|+..+=..+|+|+ |+ +|.-|+
T Consensus 42 E~~~F~~k~L~lV--wR-~g~pyg 62 (150)
T PHA02779 42 EVYSFAYKELYVV--WR-GDFPFA 62 (150)
T ss_pred HHHHHHhCCcEEE--EE-CCEeeE
Confidence 4556667788888 87 676654
No 37
>TIGR01221 rmlC dTDP-4-dehydrorhamnose 3,5-epimerase. This enzyme participates in the biosynthesis of dTDP-L-rhamnose, often as a precursor to LPS O-antigen
Probab=20.16 E-value=50 Score=19.45 Aligned_cols=21 Identities=29% Similarity=0.509 Sum_probs=17.7
Q ss_pred hhcCceeeEEEeeEcCeeccc
Q 039633 9 YFQDDVSVIDHWLLNGMHFAN 29 (31)
Q Consensus 9 ~Fq~~l~v~~~W~~nG~HY~r 29 (31)
.-|+.+++-..=.+-|.||+.
T Consensus 43 ~~Q~n~S~S~~gvlRGlH~q~ 63 (176)
T TIGR01221 43 FVQDNHSKSYKGVLRGLHYQR 63 (176)
T ss_pred cceeEEEEecCCEEEEEEECC
Confidence 457888998889999999974
Done!