Query 043741
Match_columns 79
No_of_seqs 102 out of 221
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 07:55:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043741.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043741hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01568 A_thal_3678 uncharac 100.0 2.7E-40 5.9E-45 207.3 8.1 65 1-65 1-66 (66)
2 PF04844 Ovate: Transcriptiona 100.0 4.8E-38 1E-42 193.3 7.5 59 7-65 1-59 (59)
3 smart00544 MA3 Domain in DAP-5 86.7 1.7 3.6E-05 27.5 4.3 46 14-61 1-46 (113)
4 PF02847 MA3: MA3 domain; Int 65.0 13 0.00028 23.2 3.7 43 14-58 1-43 (113)
5 PF02979 NHase_alpha: Nitrile 64.4 17 0.00037 27.0 4.6 48 12-59 6-54 (188)
6 PF10273 WGG: Pre-rRNA-process 63.8 17 0.00036 23.0 4.0 36 7-42 29-64 (82)
7 PRK10072 putative transcriptio 60.5 18 0.0004 23.6 3.9 31 7-37 3-42 (96)
8 PF08887 GAD-like: GAD-like do 57.1 3.2 7E-05 27.8 -0.2 33 28-60 56-92 (109)
9 PHA03132 thymidine kinase; Pro 55.4 12 0.00027 31.7 2.9 62 12-73 489-561 (580)
10 PF09808 SNAPc_SNAP43: Small n 54.1 20 0.00044 25.3 3.5 28 31-63 4-31 (194)
11 PF09388 SpoOE-like: Spo0E lik 51.9 40 0.00087 18.7 3.9 31 13-43 8-44 (45)
12 TIGR01323 nitrile_alph nitrile 49.5 40 0.00087 25.1 4.5 44 16-59 4-48 (185)
13 PF02211 NHase_beta: Nitrile h 43.6 1E+02 0.0022 23.0 6.0 38 11-48 69-106 (222)
14 PF14551 MCM_N: MCM N-terminal 43.5 64 0.0014 20.0 4.3 52 14-65 18-75 (121)
15 PF04692 PDGF_N: Platelet-deri 43.4 32 0.0007 22.1 2.9 25 14-38 5-29 (78)
16 PF06761 IcmF-related: Intrace 41.9 1.4E+02 0.003 22.3 6.5 41 28-68 70-112 (312)
17 PF09164 VitD-bind_III: Vitami 41.1 76 0.0016 20.2 4.2 35 5-39 5-40 (68)
18 PF10415 FumaraseC_C: Fumarase 38.5 34 0.00073 20.1 2.2 25 16-40 26-50 (55)
19 PF09832 DUF2059: Uncharacteri 37.1 37 0.0008 19.6 2.3 28 13-42 4-31 (64)
20 KOG4746 Small nuclear RNA acti 35.6 49 0.0011 27.4 3.4 31 28-63 14-44 (423)
21 PF04858 TH1: TH1 protein; In 34.5 93 0.002 26.5 5.0 56 11-67 283-339 (584)
22 PF13427 DUF4111: Domain of un 34.3 38 0.00083 22.1 2.2 18 7-24 6-23 (106)
23 cd00982 gltB_C gltb_C. This do 34.1 28 0.0006 26.7 1.7 52 9-60 187-242 (251)
24 PF10995 DUF2819: Protein of u 33.7 59 0.0013 25.7 3.5 61 4-67 164-226 (316)
25 PF08684 ocr: DNA mimic ocr; 33.2 1.2E+02 0.0027 20.5 4.5 51 7-57 2-56 (101)
26 PF08293 MRP-S33: Mitochondria 33.1 53 0.0011 20.9 2.7 22 8-29 63-84 (87)
27 TIGR02908 CoxD_Bacillus cytoch 32.9 53 0.0012 22.4 2.8 27 37-63 72-98 (110)
28 COG4479 Uncharacterized protei 32.6 64 0.0014 20.8 2.9 29 35-65 42-70 (74)
29 COG3552 CoxE Protein containin 30.1 1.4E+02 0.003 24.6 5.1 42 17-59 36-77 (395)
30 PF14253 AbiH: Bacteriophage a 29.4 1.2E+02 0.0026 21.5 4.3 18 26-43 49-66 (270)
31 PRK11104 hemG protoporphyrinog 29.0 1.2E+02 0.0026 21.1 4.1 33 14-46 133-176 (177)
32 cd00171 Sec7 Sec7 domain; Doma 28.8 67 0.0015 22.7 2.8 39 30-68 82-120 (185)
33 KOG1406 Peroxisomal 3-ketoacyl 28.4 50 0.0011 26.8 2.3 66 8-76 187-264 (408)
34 PF05400 FliT: Flagellar prote 28.3 58 0.0013 19.0 2.1 23 21-43 1-23 (84)
35 PF08465 Herpes_TK_C: Thymidin 27.6 41 0.00089 18.6 1.2 26 48-73 2-27 (33)
36 COG4472 Uncharacterized protei 27.3 54 0.0012 21.7 2.0 17 31-47 71-87 (88)
37 PRK10548 flagellar biosynthesi 26.5 1.3E+02 0.0027 20.5 3.7 56 10-65 10-73 (121)
38 PF13524 Glyco_trans_1_2: Glyc 26.4 95 0.0021 18.3 2.9 32 28-60 47-78 (92)
39 COG2980 RlpB Rare lipoprotein 26.1 51 0.0011 24.3 1.9 25 4-28 37-61 (178)
40 PF04716 ETC_C1_NDUFA5: ETC co 26.1 81 0.0017 18.8 2.5 27 13-39 26-57 (57)
41 PF04727 ELMO_CED12: ELMO/CED- 25.7 38 0.00082 23.1 1.1 11 6-16 52-62 (170)
42 PF04994 TfoX_C: TfoX C-termin 25.4 81 0.0018 19.7 2.5 31 16-46 13-45 (81)
43 smart00684 DM15 Tandem repeat 24.7 1.4E+02 0.003 16.7 3.5 30 8-40 4-33 (39)
44 PF02337 Gag_p10: Retroviral G 23.9 1.8E+02 0.0039 19.0 4.0 30 12-41 8-38 (90)
45 smart00222 Sec7 Sec7 domain. D 23.6 81 0.0018 22.2 2.5 40 30-69 83-122 (187)
46 cd06207 CyPoR_like NADPH cytoc 23.4 50 0.0011 25.5 1.5 29 30-59 80-108 (382)
47 PF08916 Phe_ZIP: Phenylalanin 23.1 1.1E+02 0.0023 18.8 2.6 33 32-65 17-54 (59)
48 COG3643 Glutamate formiminotra 22.7 1.5E+02 0.0033 23.5 4.0 32 28-59 268-299 (302)
49 COG5631 Predicted transcriptio 22.4 2.9E+02 0.0062 20.7 5.2 50 10-65 61-110 (199)
50 PRK05473 hypothetical protein; 21.8 74 0.0016 21.0 1.8 14 31-44 71-84 (86)
51 PF10723 RepB-RCR_reg: Replica 21.2 1.9E+02 0.0042 18.4 3.7 30 13-42 51-80 (84)
52 PF11176 DUF2962: Protein of u 21.2 1.8E+02 0.0039 20.3 3.8 45 8-52 44-90 (155)
53 PF08636 Pkr1: ER protein Pkr1 21.1 68 0.0015 20.5 1.5 16 54-69 3-18 (75)
54 PRK12539 RNA polymerase sigma 20.7 2.7E+02 0.0059 18.6 6.2 47 18-64 8-68 (184)
55 PF01761 DHQ_synthase: 3-dehyd 20.5 1.5E+02 0.0032 22.4 3.4 48 7-54 105-156 (260)
No 1
>TIGR01568 A_thal_3678 uncharacterized plant-specific domain TIGR01568. This model describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence.
Probab=100.00 E-value=2.7e-40 Score=207.25 Aligned_cols=65 Identities=49% Similarity=0.835 Sum_probs=62.9
Q ss_pred CeeeccccChHHHHHHHHHHHHHhcCCC-CHHHHHHHHHHHHhcCCCCchHhHHHHHHHHHHHhhc
Q 043741 1 IAVVKDSNDPYEDFRRSMLQMIMEKEIY-SNDDLKELLNCFLQLNSPSNHDVIVQAFTGVWNEAVS 65 (79)
Q Consensus 1 vAVvk~S~DPy~DFR~SM~EMI~e~~i~-~~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl~~~l~~ 65 (79)
|||+|+|.|||+|||+||+|||+++|+. +|++|||||+|||+||+++||++|++||+|||.+|++
T Consensus 1 vAv~k~S~DPy~DFr~SM~EMI~~~~i~~~w~~LeeLL~cYL~LN~~~~H~~Iv~AF~dl~~~L~~ 66 (66)
T TIGR01568 1 VAVAKESDDPYEDFRRSMEEMIEERELEADWKELEELLACYLDLNPKKSHRFIVRAFVDILSALLS 66 (66)
T ss_pred CeeeeCCCChHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCchhhhHHHHHHHHHHHHHhC
Confidence 7999999999999999999999999995 7999999999999999999999999999999999985
No 2
>PF04844 Ovate: Transcriptional repressor, ovate; InterPro: IPR006458 This group of sequences contain an uncharacterised domain of about 70 residues found exclusively in plants, generally toward the C terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana (Mouse-ear cress). Other regions of these proteins tend to consist largely of low-complexity sequence. Function is not known.
Probab=100.00 E-value=4.8e-38 Score=193.31 Aligned_cols=59 Identities=59% Similarity=0.980 Sum_probs=57.8
Q ss_pred ccChHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhcCCCCchHhHHHHHHHHHHHhhc
Q 043741 7 SNDPYEDFRRSMLQMIMEKEIYSNDDLKELLNCFLQLNSPSNHDVIVQAFTGVWNEAVS 65 (79)
Q Consensus 7 S~DPy~DFR~SM~EMI~e~~i~~~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl~~~l~~ 65 (79)
|.|||+|||+||+|||+++|+.+|++|||||+|||+||+|+||++|++||+|||.++++
T Consensus 1 S~DP~~DFr~SM~EMI~~~~i~~~~~LeeLL~cYL~LN~~~~H~~Iv~aF~dv~~~l~s 59 (59)
T PF04844_consen 1 SSDPYEDFRESMVEMIEENGIRDWDDLEELLACYLSLNSPEHHKFIVEAFVDVWVELFS 59 (59)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCChhhhhHHHHHHHHHHHHHhC
Confidence 78999999999999999999999999999999999999999999999999999999985
No 3
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=86.67 E-value=1.7 Score=27.54 Aligned_cols=46 Identities=24% Similarity=0.471 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHHhcCCCCchHhHHHHHHHHHH
Q 043741 14 FRRSMLQMIMEKEIYSNDDLKELLNCFLQLNSPSNHDVIVQAFTGVWN 61 (79)
Q Consensus 14 FR~SM~EMI~e~~i~~~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl~~ 61 (79)
||+++...|.+- .+..|.+|...|...||.|.+|+.+++.....+.
T Consensus 1 ~~k~i~~~l~ey--~~~~D~~ea~~~l~~L~~~~~~~~vv~~~i~~~l 46 (113)
T smart00544 1 LKKKIFLIIEEY--LSSGDTDEAVHCLLELKLPEQHHEVVKVLLTCAL 46 (113)
T ss_pred ChhHHHHHHHHH--HHcCCHHHHHHHHHHhCCCcchHHHHHHHHHHHH
Confidence 466666666542 1225788889999999988777777766555443
No 4
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=64.98 E-value=13 Score=23.21 Aligned_cols=43 Identities=28% Similarity=0.648 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHHhcCCCCchHhHHHHHHH
Q 043741 14 FRRSMLQMIMEKEIYSNDDLKELLNCFLQLNSPSNHDVIVQAFTG 58 (79)
Q Consensus 14 FR~SM~EMI~e~~i~~~~dLeeLL~cYL~LN~~~~H~~I~~aF~d 58 (79)
||+++-..|.|- .+-.|.+|...|-..||.|.+|..++.....
T Consensus 1 ~rk~i~~~l~ey--~~~~d~~ea~~~l~el~~~~~~~~vv~~~l~ 43 (113)
T PF02847_consen 1 LRKKIFSILMEY--FSSGDVDEAVECLKELKLPSQHHEVVKVILE 43 (113)
T ss_dssp HHHHHHHHHHHH--HHHT-HHHHHHHHHHTT-GGGHHHHHHHHHH
T ss_pred ChHHHHHHHHHH--hcCCCHHHHHHHHHHhCCCccHHHHHHHHHH
Confidence 566666655542 1124667777777777777666666554443
No 5
>PF02979 NHase_alpha: Nitrile hydratase, alpha chain; InterPro: IPR004232 Nitrile hydratases (4.2.1.84 from EC) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, alpha(2)beta(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site [, ]. The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide [, ]. Fe- and cobalt-containing enzymes also display different inhibition patterns with nitrophenols. Thiocyanate hydrolase (SCNase) is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia []. The two enzymes, nitrile hydratase and SCNase, are homologous over regions corresponding to almost the entire coding regions of the genes: the beta and alpha subunits of thiocyanate hydrolase were homologous to the amino- and carboxyl-terminal halves of the beta subunit of nitrile hydratase, and the gamma subunit of thiocyanate hydrolase was homologous to the alpha subunit of nitrile hydratase []. This entry represents the structural domain of the alpha subunit of both iron- and cobalt-containing nitrile hydratases; the alpha subunit is a duplication of two structural repeats, each consisting of 4 layers, alpha/beta/beta/alpha []. This structure is also found in the related protein, the gamma subunit of thiocyanate hydrolase (SCNase).; GO: 0003824 catalytic activity, 0046914 transition metal ion binding, 0006807 nitrogen compound metabolic process; PDB: 2DPP_A 3HHT_A 1V29_A 2ZZD_I 2DXC_F 2DXB_F 2DD5_C 2DD4_C 2ZPH_A 2CYZ_A ....
Probab=64.36 E-value=17 Score=27.01 Aligned_cols=48 Identities=13% Similarity=0.305 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhc-CCCCchHhHHHHHHHH
Q 043741 12 EDFRRSMLQMIMEKEIYSNDDLKELLNCFLQL-NSPSNHDVIVQAFTGV 59 (79)
Q Consensus 12 ~DFR~SM~EMI~e~~i~~~~dLeeLL~cYL~L-N~~~~H~~I~~aF~dl 59 (79)
..--+.+++...|+|+.+.+++..++..|-+. ++..--++|-+|.+|=
T Consensus 6 ~~~~~al~~ll~ekg~~~~~~~~~~~~~~~~~~~P~~GarvVArAW~Dp 54 (188)
T PF02979_consen 6 AARVRALESLLIEKGLITPAEVDRIIETYESRVGPRNGARVVARAWTDP 54 (188)
T ss_dssp HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTSSHHHHHHHHHHHHH-H
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhccCccccceeehhhhCCH
Confidence 34456788899999999999999999999998 7777778888888774
No 6
>PF10273 WGG: Pre-rRNA-processing protein TSR2; InterPro: IPR019398 The pre-rRNA-processing protein TSR2 is required for 20S pre-rRNA processing []. This family contains a distinctive WGG motif.
Probab=63.77 E-value=17 Score=22.97 Aligned_cols=36 Identities=17% Similarity=0.282 Sum_probs=28.3
Q ss_pred ccChHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHh
Q 043741 7 SNDPYEDFRRSMLQMIMEKEIYSNDDLKELLNCFLQ 42 (79)
Q Consensus 7 S~DPy~DFR~SM~EMI~e~~i~~~~dLeeLL~cYL~ 42 (79)
|.+-...|...+.+++..+.-.+.++||++|.-||.
T Consensus 29 s~~K~~~l~~~i~~~f~~~~~~~~~~le~~L~~~m~ 64 (82)
T PF10273_consen 29 SQEKADWLAEVIVDWFTENKDPDADDLEDFLEDIMD 64 (82)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence 556667777888888888776779999999988873
No 7
>PRK10072 putative transcriptional regulator; Provisional
Probab=60.46 E-value=18 Score=23.58 Aligned_cols=31 Identities=23% Similarity=0.354 Sum_probs=24.0
Q ss_pred ccChHHHHHHHHHHHHHhcCC-----C----CHHHHHHHH
Q 043741 7 SNDPYEDFRRSMLQMIMEKEI-----Y----SNDDLKELL 37 (79)
Q Consensus 7 S~DPy~DFR~SM~EMI~e~~i-----~----~~~dLeeLL 37 (79)
-.||-.|..+||.||+.++|- . ...++++|.
T Consensus 3 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~eik~LR 42 (96)
T PRK10072 3 YKDPMFELLSSLEQIVFKDETQKITLTQKTTSFTEFEQLR 42 (96)
T ss_pred cCCHHHHHHHHHHHHHHhcCCccceeecccCChHHHHHHH
Confidence 369999999999999997661 1 556777763
No 8
>PF08887 GAD-like: GAD-like domain; InterPro: IPR014983 This domain is functionally uncharacterised, but it appears to be distantly related to the GAD domain IPR004115 from INTERPRO.
Probab=57.11 E-value=3.2 Score=27.77 Aligned_cols=33 Identities=18% Similarity=0.394 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHHh----cCCCCchHhHHHHHHHHH
Q 043741 28 YSNDDLKELLNCFLQ----LNSPSNHDVIVQAFTGVW 60 (79)
Q Consensus 28 ~~~~dLeeLL~cYL~----LN~~~~H~~I~~aF~dl~ 60 (79)
.++++-+++|..++. .+...+|.+...||.||+
T Consensus 56 vnP~dy~~vl~~~~~~~~~~~~~~~~~ia~tAFGdl~ 92 (109)
T PF08887_consen 56 VNPDDYEDVLDEWLGGTPLFDPDNYIPIARTAFGDLY 92 (109)
T ss_pred ECHHHHHHHHHHHhcCCccccCceEEEEEEcccccEE
Confidence 568999999999996 788999999999999984
No 9
>PHA03132 thymidine kinase; Provisional
Probab=55.45 E-value=12 Score=31.65 Aligned_cols=62 Identities=11% Similarity=0.197 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHHhc--CCCCHHHHHHHHHHH---------HhcCCCCchHhHHHHHHHHHHHhhcCCCCCCCC
Q 043741 12 EDFRRSMLQMIMEK--EIYSNDDLKELLNCF---------LQLNSPSNHDVIVQAFTGVWNEAVSKSPKKPCD 73 (79)
Q Consensus 12 ~DFR~SM~EMI~e~--~i~~~~dLeeLL~cY---------L~LN~~~~H~~I~~aF~dl~~~l~~~~~~~~~~ 73 (79)
.=|++||--|+.+. ..+.---|-|++.++ +-+|..++++.|-.+.++|..++..++..+|+.
T Consensus 489 ~l~~~S~f~~l~dvi~~~~~~~tl~e~c~~f~~eL~klqf~vvd~s~f~~Dv~G~Wt~iy~q~l~n~~IKt~~ 561 (580)
T PHA03132 489 KLWKNSIFNTLRDVIQPFRHDCTLLEVCLTFCKELSKLQFVVVDASEFQDDVPGLWTEIYTQILKNPAIKTRF 561 (580)
T ss_pred HHHHhhHHHHHHHHhhcccCCCcHHHHHHHHHHHhhhceEEEEehhhcCCCCcchHHHHHHHHhhccccccee
Confidence 34789998888774 455445566666553 678999999999999999999999999998874
No 10
>PF09808 SNAPc_SNAP43: Small nuclear RNA activating complex (SNAPc), subunit SNAP43; InterPro: IPR019188 Members of this family are part of the SNAPc complex required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. They bind to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Furthermore, they also recruit TBP and BRF2 to the U6 snRNA TATA box. SNAPc consists of at least four stably associated subunits, SNAP43, SNAP45, SNAP50, and SNAP190. None of the three small subunits can bind to the PSE on their own [].
Probab=54.14 E-value=20 Score=25.34 Aligned_cols=28 Identities=36% Similarity=0.624 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHhcCCCCchHhHHHHHHHHHHHh
Q 043741 31 DDLKELLNCFLQLNSPSNHDVIVQAFTGVWNEA 63 (79)
Q Consensus 31 ~dLeeLL~cYL~LN~~~~H~~I~~aF~dl~~~l 63 (79)
+|+++||.-|.+.|+-++ +.|.++|.+.
T Consensus 4 ~D~~~Ll~~F~~~~~~~F-----~~F~~~W~~~ 31 (194)
T PF09808_consen 4 EDIDELLQRFQQAESVRF-----EDFKRLWREM 31 (194)
T ss_pred HHHHHHHHHHHHcCCCCH-----HHHHHHHHHC
Confidence 689999999999988775 6788888754
No 11
>PF09388 SpoOE-like: Spo0E like sporulation regulatory protein; InterPro: IPR018540 Spore formation is an extreme response to starvation and can also be a component of disease transmission. Sporulation is controlled by an expanded two-component system where starvation signals result in sensor kinase activation and phosphorylation of the master sporulation response regulator Spo0A. Phosphatases such as Spo0E dephosphorylate Spo0A thereby inhibiting sporulation. This is a family of Spo0E-like phosphatases. The structure of a Bacillus anthracis member of this family has revealed an anti-parallel alpha-helical structure []. ; PDB: 2BZB_B 2C0S_A.
Probab=51.92 E-value=40 Score=18.72 Aligned_cols=31 Identities=19% Similarity=0.459 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHhcCCCCH------HHHHHHHHHHHhc
Q 043741 13 DFRRSMLQMIMEKEIYSN------DDLKELLNCFLQL 43 (79)
Q Consensus 13 DFR~SM~EMI~e~~i~~~------~dLeeLL~cYL~L 43 (79)
.-|+-|.+++..+|+.++ ..|-+|+..|..+
T Consensus 8 ~~R~~L~~~~~~~~l~~~~vl~~Sq~LD~lI~~y~~~ 44 (45)
T PF09388_consen 8 ELRQELNELAEKKGLTDPEVLELSQELDKLINEYQKL 44 (45)
T ss_dssp HHHHHHHHHHHHCCTTCHHHHHHHHHHHHHHHHHHCH
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhhh
Confidence 468889999999999887 5667788777643
No 12
>TIGR01323 nitrile_alph nitrile hydratase, alpha subunit. This model describes both iron- and cobalt-containing nitrile hydratase alpha chains. It excludes the thiocyanate hydrolase gamma subunit of Thiobacillus thioparus, a sequence that appears to have evolved from within the family of nitrile hydratase alpha subunits but which differs by several indels and a more rapid accumulation of point mutations.
Probab=49.46 E-value=40 Score=25.07 Aligned_cols=44 Identities=11% Similarity=0.285 Sum_probs=35.9
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHHh-cCCCCchHhHHHHHHHH
Q 043741 16 RSMLQMIMEKEIYSNDDLKELLNCFLQ-LNSPSNHDVIVQAFTGV 59 (79)
Q Consensus 16 ~SM~EMI~e~~i~~~~dLeeLL~cYL~-LN~~~~H~~I~~aF~dl 59 (79)
+-++++..++|+.+.++++.++..|-+ ..+..=-+++-+|++|=
T Consensus 4 ~Ale~ll~eKGli~~~~id~~i~~~~~~~gP~nGA~vVArAW~Dp 48 (185)
T TIGR01323 4 KALEQVLKSKGLIPEGAVDQLTSLYENEWGPENGAKVVAKAWVDP 48 (185)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHhccCCcchhhhhhHHhcCH
Confidence 457788899999999999999999999 46666667777877664
No 13
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=43.65 E-value=1e+02 Score=22.99 Aligned_cols=38 Identities=16% Similarity=0.403 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhcCCCCc
Q 043741 11 YEDFRRSMLQMIMEKEIYSNDDLKELLNCFLQLNSPSN 48 (79)
Q Consensus 11 y~DFR~SM~EMI~e~~i~~~~dLeeLL~cYL~LN~~~~ 48 (79)
|+-...+++.|++++|+.+.++|++...-....=.+..
T Consensus 69 Ye~Wl~ale~lLvekG~it~~EL~ar~~~~~~~~~~~~ 106 (222)
T PF02211_consen 69 YERWLAALEKLLVEKGVITAEELDARAGEWARPAAPTP 106 (222)
T ss_dssp HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHH-TT---S
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHhhhhcccCCCC
Confidence 67788999999999999999999998444444433333
No 14
>PF14551 MCM_N: MCM N-terminal domain; PDB: 2VL6_C 3F9V_A 1LTL_E.
Probab=43.51 E-value=64 Score=20.01 Aligned_cols=52 Identities=23% Similarity=0.208 Sum_probs=39.0
Q ss_pred HHHHHHHHHHhcC---CCCHHHHHH---HHHHHHhcCCCCchHhHHHHHHHHHHHhhc
Q 043741 14 FRRSMLQMIMEKE---IYSNDDLKE---LLNCFLQLNSPSNHDVIVQAFTGVWNEAVS 65 (79)
Q Consensus 14 FR~SM~EMI~e~~---i~~~~dLee---LL~cYL~LN~~~~H~~I~~aF~dl~~~l~~ 65 (79)
.++.+.+|+..+. ..++++|.+ =|+-.|.-|+.++..++-+|..+++..+..
T Consensus 18 Y~~~l~~~~~~~~~~l~Vd~~dL~~f~~~L~~~l~~~P~~~l~~~~~a~~~~~~~~~~ 75 (121)
T PF14551_consen 18 YMDQLREMIQRNKKSLYVDLDDLREFDPDLAEALIENPYRYLPLFEEALKEVVKELFP 75 (121)
T ss_dssp CHHHHHHHHHHT-SCEEEEHHHHHHH-HHHHHHHHHCCCCCHHHHHHHHHHCHHTT--
T ss_pred HHHHHHHHHHcCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3556677776543 256777765 788899999999999999999999987653
No 15
>PF04692 PDGF_N: Platelet-derived growth factor, N terminal region; InterPro: IPR006782 Platelet-derived growth factor (PDGF) [, ] is a potent mitogen for cells of mesenchymal origin, including smooth muscle cells and glial cells. In both mouse and human, the PDGF signalling network consists of four ligands, PDGFA-D, and two receptors, PDGFRalpha and PDGFRbeta. All PDGFs function as secreted, disulphide-linked homodimers, but only PDGFA and B can form functional heterodimers. PDGFRs also function as homo- and heterodimers. All known PDGFs have characteristic `PDGF domains', which include eight conserved cysteines that are involved in inter- and intramolecular bonds. Alternate splicing of the A chain transcript can give rise to two different forms that differ only in their C-terminal extremity. The transforming protein of Woolly monkey sarcoma virus (WMSV) (Simian sarcoma virus), encoded by the v-sis oncogene, is derived from the B chain of PDGF. PDGFs are mitogenic during early developmental stages, driving the proliferation of undifferentiated mesenchyme and some progenitor populations. During later maturation stages, PDGF signalling has been implicated in tissue remodelling and cellular differentiation, and in inductive events involved in patterning and morphogenesis. In addition to driving mesenchymal proliferation, PDGFs have been shown to direct the migration, differentiation and function of a variety of specialised mesenchymal and migratory cell types, both during development and in the adult animal []. PDGF is structurally related to a number of other growth factors which also form disulphide-linked homo- or heterodimers. This domain consists of the N-terminal regions of PGDF A and B.; GO: 0008083 growth factor activity, 0016020 membrane; PDB: 3MJK_Y 3MJG_A 1PDG_B.
Probab=43.37 E-value=32 Score=22.14 Aligned_cols=25 Identities=28% Similarity=0.453 Sum_probs=18.6
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHH
Q 043741 14 FRRSMLQMIMEKEIYSNDDLKELLN 38 (79)
Q Consensus 14 FR~SM~EMI~e~~i~~~~dLeeLL~ 38 (79)
|-+.|+||+....|.+-.||+-||.
T Consensus 5 iP~eliErLs~S~I~SIsDLQrLL~ 29 (78)
T PF04692_consen 5 IPEELIERLSNSEIRSISDLQRLLE 29 (78)
T ss_dssp S-HHHHHHHHTS---SHHHHHHHHT
T ss_pred ccHHHHHHHhcCCcccHHHHHHHHh
Confidence 3467899999999999999999996
No 16
>PF06761 IcmF-related: Intracellular multiplication and human macrophage-killing; InterPro: IPR009612 This entry represents a conserved region within several bacterial proteins that resemble ImcF, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation, resulting in increased adherence to epithelial cells and increased conjugation frequency. Note that many entry members are hypothetical proteins.
Probab=41.94 E-value=1.4e+02 Score=22.31 Aligned_cols=41 Identities=27% Similarity=0.477 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCch--HhHHHHHHHHHHHhhcCCC
Q 043741 28 YSNDDLKELLNCFLQLNSPSNH--DVIVQAFTGVWNEAVSKSP 68 (79)
Q Consensus 28 ~~~~dLeeLL~cYL~LN~~~~H--~~I~~aF~dl~~~l~~~~~ 68 (79)
.+.+.+-+.|..||-|..|++- ..+..-|...|...++..+
T Consensus 70 ~~~~~~y~aLk~YLML~~~~~~d~~~l~~w~~~~w~~~~~~~~ 112 (312)
T PF06761_consen 70 DDPDALYEALKAYLMLTDPEHRDADFLKAWLAQDWQEQYPGQP 112 (312)
T ss_pred ccHHHHHHHHHHHHhcCCCccCCHHHHHHHHHHHHHHhCCCCc
Confidence 8899999999999999988754 5677888888888887653
No 17
>PF09164 VitD-bind_III: Vitamin D binding protein, domain III; InterPro: IPR015247 This domain is predominantly found in Vitamin D binding proteins, and adopts a multihelical structure. It is required for formation of an actin 'clamp', allowing the protein to bind to actin []. ; PDB: 1MA9_A 1KW2_A 1KXP_D 1J7E_A 1J78_A 1LOT_A.
Probab=41.13 E-value=76 Score=20.17 Aligned_cols=35 Identities=17% Similarity=0.346 Sum_probs=27.3
Q ss_pred ccccChHHHHHHHHHHHHHhcC-CCCHHHHHHHHHH
Q 043741 5 KDSNDPYEDFRRSMLQMIMEKE-IYSNDDLKELLNC 39 (79)
Q Consensus 5 k~S~DPy~DFR~SM~EMI~e~~-i~~~~dLeeLL~c 39 (79)
-+|.+++.+|++-..|-+.++- -..+.+|++|..-
T Consensus 5 dYse~tFtEyKKrL~e~l~~k~P~at~~~l~~lve~ 40 (68)
T PF09164_consen 5 DYSENTFTEYKKRLAERLRAKLPDATPTELKELVEK 40 (68)
T ss_dssp TTTTS-HHHHHHHHHHHHHHH-TTS-HHHHHHHHHH
T ss_pred hhhhccHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 3799999999999999998875 4568999999863
No 18
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=38.46 E-value=34 Score=20.15 Aligned_cols=25 Identities=28% Similarity=0.553 Sum_probs=19.1
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHH
Q 043741 16 RSMLQMIMEKEIYSNDDLKELLNCF 40 (79)
Q Consensus 16 ~SM~EMI~e~~i~~~~dLeeLL~cY 40 (79)
+|..|-+.+.|+-+.++++++|.-.
T Consensus 26 ~svre~v~~~g~lt~ee~d~ll~p~ 50 (55)
T PF10415_consen 26 RSVREVVLEEGLLTEEELDELLDPE 50 (55)
T ss_dssp --HHHHHHHTTSS-HHHHHHHTSHH
T ss_pred CCHHHHHHHcCCCCHHHHHHHcCHH
Confidence 5788899999999999999998643
No 19
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=37.09 E-value=37 Score=19.58 Aligned_cols=28 Identities=14% Similarity=0.366 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHHHh
Q 043741 13 DFRRSMLQMIMEKEIYSNDDLKELLNCFLQ 42 (79)
Q Consensus 13 DFR~SM~EMI~e~~i~~~~dLeeLL~cYL~ 42 (79)
+|+.-|.+... ...+.++|++++..|=+
T Consensus 4 ~~~~~~~~~y~--~~ft~~El~~i~~FY~S 31 (64)
T PF09832_consen 4 KMIDQMAPIYA--EHFTEEELDAILAFYES 31 (64)
T ss_dssp HHHHHHHHHHH--HHS-HHHHHHHHHHHHS
T ss_pred HHHHHHHHHHH--HHCCHHHHHHHHHHHCC
Confidence 34444444433 35688999999999954
No 20
>KOG4746 consensus Small nuclear RNA activating complex (SNAPc), subunit SNAP43 [RNA processing and modification]
Probab=35.59 E-value=49 Score=27.43 Aligned_cols=31 Identities=26% Similarity=0.424 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCchHhHHHHHHHHHHHh
Q 043741 28 YSNDDLKELLNCFLQLNSPSNHDVIVQAFTGVWNEA 63 (79)
Q Consensus 28 ~~~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl~~~l 63 (79)
+=|+||+.||..||+.|+-++- .|.++|..+
T Consensus 14 Glr~Dl~~llr~fl~~~S~RF~-----df~~~fr~m 44 (423)
T KOG4746|consen 14 GLREDLDRLLRAFLDFESVRFE-----DFKRLFRNM 44 (423)
T ss_pred cHHHHHHHHHHHHhhccceehH-----HHHHHHHhc
Confidence 3489999999999999998874 466777643
No 21
>PF04858 TH1: TH1 protein; InterPro: IPR006942 TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans []. TH1 binds specifically to A-Raf kinase [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=34.47 E-value=93 Score=26.47 Aligned_cols=56 Identities=11% Similarity=0.249 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhcCCCCchHhHHHHHHHH-HHHhhcCC
Q 043741 11 YEDFRRSMLQMIMEKEIYSNDDLKELLNCFLQLNSPSNHDVIVQAFTGV-WNEAVSKS 67 (79)
Q Consensus 11 y~DFR~SM~EMI~e~~i~~~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl-~~~l~~~~ 67 (79)
|......+..|+..+.+ ++.|+..|..+|.+-|+|-.--+=.-.|.++ ..+||.++
T Consensus 283 ~p~a~~ai~smLs~~~l-~paDI~~Ly~~Y~~~~pPPV~lLR~P~~l~lLld~LF~pg 339 (584)
T PF04858_consen 283 YPEACQAIASMLSSNAL-NPADITKLYRMYSSPDPPPVELLRHPQFLDLLLDALFKPG 339 (584)
T ss_pred CchHHHHHHHHHhcCCC-CHHHHHHHHHHhccCCCCCchhhcCHHHHHHHHHHHcCCC
Confidence 34778899999987555 8899999999999999886543333444454 45677543
No 22
>PF13427 DUF4111: Domain of unknown function (DUF4111)
Probab=34.34 E-value=38 Score=22.11 Aligned_cols=18 Identities=28% Similarity=0.436 Sum_probs=15.1
Q ss_pred ccChHHHHHHHHHHHHHh
Q 043741 7 SNDPYEDFRRSMLQMIME 24 (79)
Q Consensus 7 S~DPy~DFR~SM~EMI~e 24 (79)
..=|..||++||...+.+
T Consensus 6 ~~Vp~~~~~~ai~~~l~~ 23 (106)
T PF13427_consen 6 PPVPREDYRDAIRDDLPE 23 (106)
T ss_pred CCCCHHHHHHHHHHHHHH
Confidence 345899999999999974
No 23
>cd00982 gltB_C gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the transfer of ammonia and electrons among three distinct active centers that carry out L-Gln hydrolysis, conversion of 2-oxoglutarate into L-Glu, and electron uptake from a donor. These catalytic sites appear to occur in other domains within the protein, and not the domain in this CD. This particular domain has no known function, but it likely has a structural role as it interacts with the amidotransferase and FMN-binding domains of gltS.
Probab=34.06 E-value=28 Score=26.67 Aligned_cols=52 Identities=17% Similarity=0.309 Sum_probs=37.5
Q ss_pred ChHHHHHHH-HHHHHHhcCCC---CHHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 043741 9 DPYEDFRRS-MLQMIMEKEIY---SNDDLKELLNCFLQLNSPSNHDVIVQAFTGVW 60 (79)
Q Consensus 9 DPy~DFR~S-M~EMI~e~~i~---~~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl~ 60 (79)
+|-.+|.+. -.+||.-..+. +++.|++||..|+..-.....+.|+.-|.+..
T Consensus 187 ~~~~~~~~~~n~~~V~~~~l~~~~d~~~l~~ll~~h~~~t~s~~a~~iL~~~~~~~ 242 (251)
T cd00982 187 DEDGDFEKKVNHEMVDLERLEDAEDEEQLKELIEEHVEYTGSEKAKEILANWEAYL 242 (251)
T ss_pred CCcCChhhhcCHhhEeeccCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHHh
Confidence 566667532 23555544444 67889999999999999888888888776543
No 24
>PF10995 DUF2819: Protein of unknown function (DUF2819); InterPro: IPR017745 This protein, called BcsE (bacterial cellulose synthase E) or YhjS, is required for cellulose biosynthesis in Salmonella enteritidis. Its role is this process across multiple bacterial species is implied by the partial phylogenetic profiling algorithm []. The protein is encoded in the vicinity of other cellulose biosynthesis genes and has been [] suggested to act as a protease.
Probab=33.68 E-value=59 Score=25.67 Aligned_cols=61 Identities=16% Similarity=0.250 Sum_probs=46.1
Q ss_pred eccccChHHHHHHHHHHHHHhcCCCC--HHHHHHHHHHHHhcCCCCchHhHHHHHHHHHHHhhcCC
Q 043741 4 VKDSNDPYEDFRRSMLQMIMEKEIYS--NDDLKELLNCFLQLNSPSNHDVIVQAFTGVWNEAVSKS 67 (79)
Q Consensus 4 vk~S~DPy~DFR~SM~EMI~e~~i~~--~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl~~~l~~~~ 67 (79)
+.-+.-|+..|. +|+|+|..-.... +++++.||..++.+-.+.|-. ..+|.+.+..+...+
T Consensus 164 Ivp~~~p~sR~l-t~ieslQGQ~f~R~vP~d~~~lL~~~~p~~~kGYl~--~~~F~~~v~~~~~~s 226 (316)
T PF10995_consen 164 IVPFNAPLSRFL-TLIESLQGQVFTRPVPADIEALLKALQPLQLKGYLP--PAAFCEYVRDLLDNS 226 (316)
T ss_pred EeecCCCHHHHH-HHHHHHhCCeecCCCCcCHHHHHHhcCCcCccCCCC--HHHHHHHHHHHHhcc
Confidence 334556777774 6778876443322 599999999999999999988 678999998888655
No 25
>PF08684 ocr: DNA mimic ocr; InterPro: IPR014798 The structure of an Ocr protein from bacteriophage T7 has shown that this protein mimics the size and shape of a bent DNA molecule []. Ocr has also been shown to be an inhibitor of the complex type I DNA restriction enzymes []. ; PDB: 1S7Z_A 2Y7C_E.
Probab=33.25 E-value=1.2e+02 Score=20.48 Aligned_cols=51 Identities=16% Similarity=0.289 Sum_probs=31.6
Q ss_pred ccChHHHHHHHHHHHHHh----cCCCCHHHHHHHHHHHHhcCCCCchHhHHHHHH
Q 043741 7 SNDPYEDFRRSMLQMIME----KEIYSNDDLKELLNCFLQLNSPSNHDVIVQAFT 57 (79)
Q Consensus 7 S~DPy~DFR~SM~EMI~e----~~i~~~~dLeeLL~cYL~LN~~~~H~~I~~aF~ 57 (79)
|.+.|.+.-.+-.||..| ..+++-+|+.+-|.-=-.-|-|.+-+-|..+|+
T Consensus 2 ~~~ty~~l~a~a~e~~~e~Iryd~i~~~DD~~DaiHe~~d~~VPhyy~diFtVmA 56 (101)
T PF08684_consen 2 NANTYYELYAAAVEALNERIRYDDITETDDYSDAIHEVADSNVPHYYHDIFTVMA 56 (101)
T ss_dssp ----HHHHHHHHHHHHHHHHHHTT---GGG-HHHHHHHHHHHS--SHHHHHHHHT
T ss_pred CcchHHHHHHHHHHHHHHHhhhhcccccchHHHHHHHHhccCCchhhHHHHHHhh
Confidence 556777777777777766 478888999888888888888888777766664
No 26
>PF08293 MRP-S33: Mitochondrial ribosomal subunit S27; InterPro: IPR013219 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a mitochondrial ribosomal subunit annotated as S27 in yeast and S33 in humans [, ]. It is a small 106 residue protein. The evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, reveals an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome [].
Probab=33.14 E-value=53 Score=20.91 Aligned_cols=22 Identities=27% Similarity=0.400 Sum_probs=18.3
Q ss_pred cChHHHHHHHHHHHHHhcCCCC
Q 043741 8 NDPYEDFRRSMLQMIMEKEIYS 29 (79)
Q Consensus 8 ~DPy~DFR~SM~EMI~e~~i~~ 29 (79)
.|+.+|||..|+++-..+|-+.
T Consensus 63 ~De~e~~R~e~~~~rk~RGKg~ 84 (87)
T PF08293_consen 63 RDEHEDFREEMVELRKRRGKGP 84 (87)
T ss_pred CChhHHHHHHHHHHHHhCCCCC
Confidence 5899999999999988777543
No 27
>TIGR02908 CoxD_Bacillus cytochrome c oxidase, subunit IVB. This model represents a small clade of cytochrome oxidase subunit IV's found in the Bacilli.
Probab=32.89 E-value=53 Score=22.40 Aligned_cols=27 Identities=15% Similarity=0.283 Sum_probs=21.5
Q ss_pred HHHHHhcCCCCchHhHHHHHHHHHHHh
Q 043741 37 LNCFLQLNSPSNHDVIVQAFTGVWNEA 63 (79)
Q Consensus 37 L~cYL~LN~~~~H~~I~~aF~dl~~~l 63 (79)
|.|||.+|.+.+...++-.|.-+...+
T Consensus 72 L~yFLHm~~k~~~~~~~~if~gi~va~ 98 (110)
T TIGR02908 72 LYYFMHMKDKGHEVPAQFIYGGVFVTM 98 (110)
T ss_pred HHHheeeCCCccchHHHHHHHHHHHHH
Confidence 679999999988888877777766543
No 28
>COG4479 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.65 E-value=64 Score=20.79 Aligned_cols=29 Identities=17% Similarity=0.436 Sum_probs=23.8
Q ss_pred HHHHHHHhcCCCCchHhHHHHHHHHHHHhhc
Q 043741 35 ELLNCFLQLNSPSNHDVIVQAFTGVWNEAVS 65 (79)
Q Consensus 35 eLL~cYL~LN~~~~H~~I~~aF~dl~~~l~~ 65 (79)
+.+.-||..|++-.+. +..|-+||.+...
T Consensus 42 ~~is~YLE~~a~f~~~--m~~FDeiwe~Yle 70 (74)
T COG4479 42 HEISDYLETNADFLFN--MSVFDEIWEEYLE 70 (74)
T ss_pred HHHHHHHHhcCCcccc--hhhHHHHHHHHHH
Confidence 3467899999999987 4789999998754
No 29
>COG3552 CoxE Protein containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=30.10 E-value=1.4e+02 Score=24.60 Aligned_cols=42 Identities=24% Similarity=0.388 Sum_probs=34.0
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 043741 17 SMLQMIMEKEIYSNDDLKELLNCFLQLNSPSNHDVIVQAFTGV 59 (79)
Q Consensus 17 SM~EMI~e~~i~~~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl 59 (79)
+|++-+...|+++.++|.+=|+|=| +-.|++|+.--.+|..+
T Consensus 36 da~~a~~~~g~g~r~~lr~al~a~l-v~rpd~~~~FDaaF~~l 77 (395)
T COG3552 36 DAIEALATLGIGDREDLREALRAAL-VKRPDHHGTFDAAFRLL 77 (395)
T ss_pred hHHHHHHHcCCCCHHHHHHHHHHHh-cCCchhhhHHHHHHHHH
Confidence 4566666678999999999999976 56788999888888754
No 30
>PF14253 AbiH: Bacteriophage abortive infection AbiH
Probab=29.44 E-value=1.2e+02 Score=21.48 Aligned_cols=18 Identities=11% Similarity=-0.036 Sum_probs=13.4
Q ss_pred CCCCHHHHHHHHHHHHhc
Q 043741 26 EIYSNDDLKELLNCFLQL 43 (79)
Q Consensus 26 ~i~~~~dLeeLL~cYL~L 43 (79)
.-..|.|+|+-|.-++.-
T Consensus 49 ~~~~W~d~E~~l~~~~~~ 66 (270)
T PF14253_consen 49 NNENWSDFENALGEIDKE 66 (270)
T ss_pred ccCCHHHHHHHHHHHHHH
Confidence 356788888888877764
No 31
>PRK11104 hemG protoporphyrinogen oxidase; Provisional
Probab=28.96 E-value=1.2e+02 Score=21.06 Aligned_cols=33 Identities=27% Similarity=0.431 Sum_probs=23.3
Q ss_pred HHHHHHHHHHh-----------cCCCCHHHHHHHHHHHHhcCCC
Q 043741 14 FRRSMLQMIME-----------KEIYSNDDLKELLNCFLQLNSP 46 (79)
Q Consensus 14 FR~SM~EMI~e-----------~~i~~~~dLeeLL~cYL~LN~~ 46 (79)
|-+.|+.||.. ...+||+.+++.-.-...||.+
T Consensus 133 ~~r~~~~~i~k~~~~~~~~~~~~~~~dw~~v~~fa~~~~~~~~~ 176 (177)
T PRK11104 133 FDRFMIKLIMKMTGGETDTSKEVEYTDWEQVANFAREFAQLTDK 176 (177)
T ss_pred HHHHHHHHHHHHcCCCCCCCCceeeCCHHHHHHHHHHHHhhccc
Confidence 34578887663 2257899998888887777654
No 32
>cd00171 Sec7 Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity.
Probab=28.76 E-value=67 Score=22.70 Aligned_cols=39 Identities=15% Similarity=0.276 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHhcCCCCchHhHHHHHHHHHHHhhcCCC
Q 043741 30 NDDLKELLNCFLQLNSPSNHDVIVQAFTGVWNEAVSKSP 68 (79)
Q Consensus 30 ~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl~~~l~~~~~ 68 (79)
.+.|+.+|..+.--.....-+-|+++|++-|..--++..
T Consensus 82 ~~ALR~~l~~f~lpgE~Q~Idrile~Fs~~y~~~Np~~~ 120 (185)
T cd00171 82 DEALRKFLQSFRLPGEAQKIDRLLEKFSERYCECNPGIF 120 (185)
T ss_pred HHHHHHHHHhccCCchHHHHHHHHHHHHHHHHHHCCCCC
Confidence 477888888877777888889999999999988766543
No 33
>KOG1406 consensus Peroxisomal 3-ketoacyl-CoA-thiolase P-44/SCP2 [Lipid transport and metabolism]
Probab=28.36 E-value=50 Score=26.76 Aligned_cols=66 Identities=20% Similarity=0.390 Sum_probs=37.8
Q ss_pred cChHHHHHH--HHHHHHHhcCCCCHHHHHHHHHHHHhcCCCCchHhHHHHHH----------HHHHHhhcCCCCCCCCCc
Q 043741 8 NDPYEDFRR--SMLQMIMEKEIYSNDDLKELLNCFLQLNSPSNHDVIVQAFT----------GVWNEAVSKSPKKPCDDQ 75 (79)
Q Consensus 8 ~DPy~DFR~--SM~EMI~e~~i~~~~dLeeLL~cYL~LN~~~~H~~I~~aF~----------dl~~~l~~~~~~~~~~~~ 75 (79)
.|||..||+ |..|.|...++.| .--+|+|-=.-....---+..+||+ +|.-.-...++++++++.
T Consensus 187 nnpysqf~deysldqvm~s~~v~d---flt~lqccptsdgaaaailaseafv~k~gl~~qaveivg~em~td~ps~faek 263 (408)
T KOG1406|consen 187 NNPYSQFRDEYSLDQVMKSPQVVD---FLTKLQCCPTSDGAAAAILASEAFVRKHGLEKQAVEIVGMEMATDPPSTFAEK 263 (408)
T ss_pred CChhHhhhhhccHHHHhcchHHHH---HHHHhhcCCCCCchHHHHHhHHHHHHhcccHHHHHHHHHHHhccCCchhhhhh
Confidence 689999997 7788888887766 3456666322221111122234554 333333445566677665
Q ss_pred c
Q 043741 76 S 76 (79)
Q Consensus 76 ~ 76 (79)
|
T Consensus 264 s 264 (408)
T KOG1406|consen 264 S 264 (408)
T ss_pred h
Confidence 4
No 34
>PF05400 FliT: Flagellar protein FliT; InterPro: IPR008622 This entry represents the bacterial flagellar FliT family of dual-function proteins. Together with FlgN, FliT has been proposed to act as a substrate-specific export chaperone, facilitating the incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum []. FliT has also been shown to act as a transcriptional regulator in Salmonella typhimurium [].; GO: 0019861 flagellum; PDB: 3A7M_A 3H3M_B 3NKZ_C 2G42_A 2FZT_B.
Probab=28.29 E-value=58 Score=18.98 Aligned_cols=23 Identities=30% Similarity=0.330 Sum_probs=15.5
Q ss_pred HHHhcCCCCHHHHHHHHHHHHhc
Q 043741 21 MIMEKEIYSNDDLKELLNCFLQL 43 (79)
Q Consensus 21 MI~e~~i~~~~dLeeLL~cYL~L 43 (79)
|+..-.-.+|+.+.+|+..+-.+
T Consensus 1 ml~aa~~~dWe~l~~l~~~R~~l 23 (84)
T PF05400_consen 1 MLEAAEAGDWEELEELLDERQEL 23 (84)
T ss_dssp HHHHHHCT-HHHHHHHHHHHHHH
T ss_pred ChHHHhhCcHHHHHHHHHHHHHH
Confidence 34444478899999999887553
No 35
>PF08465 Herpes_TK_C: Thymidine kinase from Herpesvirus C-terminal; InterPro: IPR013672 This domain is found towards the C terminus in Herpesvirus Thymidine kinases. ; GO: 0004797 thymidine kinase activity, 0005524 ATP binding
Probab=27.63 E-value=41 Score=18.59 Aligned_cols=26 Identities=12% Similarity=0.141 Sum_probs=21.9
Q ss_pred chHhHHHHHHHHHHHhhcCCCCCCCC
Q 043741 48 NHDVIVQAFTGVWNEAVSKSPKKPCD 73 (79)
Q Consensus 48 ~H~~I~~aF~dl~~~l~~~~~~~~~~ 73 (79)
+++.|-.+.++|..++...+..+||.
T Consensus 2 f~dDvpGlW~~IY~qi~kn~aIKt~~ 27 (33)
T PF08465_consen 2 FQDDVPGLWTEIYTQILKNPAIKTRF 27 (33)
T ss_pred CCCccccHHHHHHHHHHhCcccccee
Confidence 55667788999999999999888875
No 36
>COG4472 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.28 E-value=54 Score=21.74 Aligned_cols=17 Identities=24% Similarity=0.430 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHhcCCCC
Q 043741 31 DDLKELLNCFLQLNSPS 47 (79)
Q Consensus 31 ~dLeeLL~cYL~LN~~~ 47 (79)
+=+|||+..||.-|...
T Consensus 71 eIvEElvk~YLk~~~~~ 87 (88)
T COG4472 71 EIVEELVKYYLKGNGKD 87 (88)
T ss_pred HHHHHHHHHHHhhcCCC
Confidence 66899999999988653
No 37
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=26.45 E-value=1.3e+02 Score=20.45 Aligned_cols=56 Identities=13% Similarity=0.127 Sum_probs=40.7
Q ss_pred hHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhc------C--CCCchHhHHHHHHHHHHHhhc
Q 043741 10 PYEDFRRSMLQMIMEKEIYSNDDLKELLNCFLQL------N--SPSNHDVIVQAFTGVWNEAVS 65 (79)
Q Consensus 10 Py~DFR~SM~EMI~e~~i~~~~dLeeLL~cYL~L------N--~~~~H~~I~~aF~dl~~~l~~ 65 (79)
=|..--..-.+|++.-.-++|+.|=+|-..|+.+ + ++.....+-+.+.++...+..
T Consensus 10 ~Yq~I~~lS~~ML~aA~~g~Wd~Li~lE~~y~~~Ve~l~~~~~~~~l~~~~q~~~~~lL~~IL~ 73 (121)
T PRK10548 10 AWQQILTLSQSMLRLATEGQWDELIEQEVAYVQAVEEIAHLTIPPDISTVMQEQLRPMLRQILD 73 (121)
T ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHH
Confidence 3666667778999998899999999999999865 1 233455566666666665543
No 38
>PF13524 Glyco_trans_1_2: Glycosyl transferases group 1
Probab=26.37 E-value=95 Score=18.29 Aligned_cols=32 Identities=19% Similarity=0.275 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCchHhHHHHHHHHH
Q 043741 28 YSNDDLKELLNCFLQLNSPSNHDVIVQAFTGVW 60 (79)
Q Consensus 28 ~~~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl~ 60 (79)
.+.+++.+.+..||+ |+....+..-++...+.
T Consensus 47 ~~~~el~~~i~~ll~-~~~~~~~ia~~a~~~v~ 78 (92)
T PF13524_consen 47 NDPEELAEKIEYLLE-NPEERRRIAKNARERVL 78 (92)
T ss_pred CCHHHHHHHHHHHHC-CHHHHHHHHHHHHHHHH
Confidence 589999999999998 77766666666666554
No 39
>COG2980 RlpB Rare lipoprotein B [Cell envelope biogenesis, outer membrane]
Probab=26.09 E-value=51 Score=24.31 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=21.9
Q ss_pred eccccChHHHHHHHHHHHHHhcCCC
Q 043741 4 VKDSNDPYEDFRRSMLQMIMEKEIY 28 (79)
Q Consensus 4 vk~S~DPy~DFR~SM~EMI~e~~i~ 28 (79)
..+|+|||..|-+.+.+-...+|+.
T Consensus 37 ~l~s~d~y~~l~r~vrr~L~~n~v~ 61 (178)
T COG2980 37 SLESSDPYGPLTRAVRRQLRLNGVD 61 (178)
T ss_pred eeeccCCCChHHHHHHHHHHHcCce
Confidence 4579999999999999999988864
No 40
>PF04716 ETC_C1_NDUFA5: ETC complex I subunit conserved region; InterPro: IPR006806 This is a family of eukaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC) (1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 29.9 kDa protein. The conserved region is found at the N terminus of the member proteins [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022904 respiratory electron transport chain, 0005743 mitochondrial inner membrane
Probab=26.07 E-value=81 Score=18.83 Aligned_cols=27 Identities=11% Similarity=0.322 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHhc-----CCCCHHHHHHHHHH
Q 043741 13 DFRRSMLQMIMEK-----EIYSNDDLKELLNC 39 (79)
Q Consensus 13 DFR~SM~EMI~e~-----~i~~~~dLeeLL~c 39 (79)
.+|++.++++..+ .-.|++.+|+-+.|
T Consensus 26 ~YR~~tE~it~~Rl~iv~~~~d~~~iE~~i~c 57 (57)
T PF04716_consen 26 AYRQYTEAITKHRLKIVEEEEDIEKIEKKIGC 57 (57)
T ss_pred HHHHHHHHHHHHHHHHHHccccHHHHHHHhCc
Confidence 5788888888754 36788899988876
No 41
>PF04727 ELMO_CED12: ELMO/CED-12 family; InterPro: IPR006816 This entry represents the ELMO (EnguLfment and Cell MOtility) domain, which is found in a number of eukaryotic proteins involved in the cytoskeletal rearrangements required for phagocytosis of apoptotic cells and cell motility, including CED-12, ELMO-1 and ELMO-2. ELMO-1 and ELMO-2 are components of signalling pathways that regulate phagocytosis and cell migration and are mammalian orthologues of the Caenorhabditis elegans gene, ced-12 that is required for the engulfment of dying cells and cell migration. ELMO-1/2 act in association with DOCK1 and CRK. ELMO-1/2 interact with the SH3-domain of DOCK1 via an SH3-binding site to enhance the guanine nucleotide exchange factor (GEF) activity of DOCK1. ELMO-1/2 could be part of a complex with DOCK1 and Rac1 that could be required to activate Rac Rho small GTPases. Regulatory GTPases in the Ras superfamily employ a cycle of alternating GTP binding and hydrolysis, controlled by guanine nucleotide exchange factors and GTPase-activating proteins (GAPs), as essential features of their actions in cells. Within the Ras superfamily, the Arf family is composed of 30 members, including 22 Arf-like (Arl) proteins. The ELMO domain has been proposed to be a GAP domain for ARL2 and other members of the Arf family [].; GO: 0006909 phagocytosis, 0005856 cytoskeleton
Probab=25.70 E-value=38 Score=23.06 Aligned_cols=11 Identities=45% Similarity=0.836 Sum_probs=9.5
Q ss_pred cccChHHHHHH
Q 043741 6 DSNDPYEDFRR 16 (79)
Q Consensus 6 ~S~DPy~DFR~ 16 (79)
.+.||..|||.
T Consensus 52 Q~~dP~tDFR~ 62 (170)
T PF04727_consen 52 QGEDPATDFRG 62 (170)
T ss_pred CCCCcHHHHhh
Confidence 37899999997
No 42
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=25.36 E-value=81 Score=19.75 Aligned_cols=31 Identities=26% Similarity=0.479 Sum_probs=23.5
Q ss_pred HHHHHHHHhcCCCCHHHHHHH--HHHHHhcCCC
Q 043741 16 RSMLQMIMEKEIYSNDDLKEL--LNCFLQLNSP 46 (79)
Q Consensus 16 ~SM~EMI~e~~i~~~~dLeeL--L~cYL~LN~~ 46 (79)
.-++.|..+-||.+.++|+++ -.||+.|-..
T Consensus 13 ~~~e~~L~~vGI~t~~~L~~~Ga~~a~~~Lk~~ 45 (81)
T PF04994_consen 13 PKSERMLAKVGIHTVEDLRELGAVEAYLRLKAS 45 (81)
T ss_dssp HHHHHHHHHTT--SHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHhCHHHHHHHHHHH
Confidence 457889999999999999998 5678877644
No 43
>smart00684 DM15 Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function.
Probab=24.67 E-value=1.4e+02 Score=16.67 Aligned_cols=30 Identities=23% Similarity=0.336 Sum_probs=22.2
Q ss_pred cChHHHHHHHHHHHHHhcCCCCHHHHHHHHHHH
Q 043741 8 NDPYEDFRRSMLQMIMEKEIYSNDDLKELLNCF 40 (79)
Q Consensus 8 ~DPy~DFR~SM~EMI~e~~i~~~~dLeeLL~cY 40 (79)
..+|.+||+-=.|=....+ ..+|+-|..-|
T Consensus 4 ~~~Y~eFr~laled~~~~~---~~gm~~LfRFw 33 (39)
T smart00684 4 QNMYEEFRQLCLEDRKSLG---RYELNCLYRFW 33 (39)
T ss_pred hhHHHHHHHHHHHHHHHcC---ChhHHHHHHHH
Confidence 4689999998877666556 67787777655
No 44
>PF02337 Gag_p10: Retroviral GAG p10 protein; InterPro: IPR003322 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from beta-retroviruses such as Mason-Pfizer monkey virus (MPMV) (Simian Mason-Pfizer virus) and Mouse mammary tumor virus (MMTV) [, ]. This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 2F77_X 2F76_X.
Probab=23.91 E-value=1.8e+02 Score=18.99 Aligned_cols=30 Identities=20% Similarity=0.340 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHhcCC-CCHHHHHHHHHHHH
Q 043741 12 EDFRRSMLQMIMEKEI-YSNDDLKELLNCFL 41 (79)
Q Consensus 12 ~DFR~SM~EMI~e~~i-~~~~dLeeLL~cYL 41 (79)
.=|...|..++.++|+ ..+++|.+++.-=-
T Consensus 8 ~~fv~~Lk~lLk~rGi~v~~~~L~~f~~~i~ 38 (90)
T PF02337_consen 8 QPFVSILKHLLKERGIRVKKKDLINFLSFID 38 (90)
T ss_dssp HHHHHHHHHHHHCCT----HHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHcCeeecHHHHHHHHHHHH
Confidence 4588899999999997 46777777665433
No 45
>smart00222 Sec7 Sec7 domain. Domain named after the S. cerevisiae SEC7 gene product, which is required for proper protein transport through the Golgi. The domain facilitates guanine nucleotide exchange on the small GTPases, ARFs (ADP ribosylation factors).
Probab=23.62 E-value=81 Score=22.22 Aligned_cols=40 Identities=20% Similarity=0.326 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhcCCCCchHhHHHHHHHHHHHhhcCCCC
Q 043741 30 NDDLKELLNCFLQLNSPSNHDVIVQAFTGVWNEAVSKSPK 69 (79)
Q Consensus 30 ~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl~~~l~~~~~~ 69 (79)
.+.|+.+|.++.--.....-+-|+++|++-|..-.+....
T Consensus 83 ~~ALR~~l~~f~lpgE~q~Idrile~Fs~~y~~~N~~~~~ 122 (187)
T smart00222 83 DQALREFLESFRLPGEAQKIDRLLEAFSSRYCECNPSVFS 122 (187)
T ss_pred HHHHHHHHHhCcCCchHHHHHHHHHHHHHHHHHHCCCccC
Confidence 4677777777777777777888999999998887765443
No 46
>cd06207 CyPoR_like NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced fe
Probab=23.39 E-value=50 Score=25.47 Aligned_cols=29 Identities=14% Similarity=0.297 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 043741 30 NDDLKELLNCFLQLNSPSNHDVIVQAFTGV 59 (79)
Q Consensus 30 ~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl 59 (79)
+--+++||..|+.||++- ++-+++++++.
T Consensus 80 ~~t~~~ll~~~~dl~~~p-~~~~l~~La~~ 108 (382)
T cd06207 80 PISVRQLLKKFLDIFGKP-TKKFLKLLSQL 108 (382)
T ss_pred CccHHHHHHhhEEeCCCC-CHHHHHHHHHH
Confidence 458999999999999865 44566666654
No 47
>PF08916 Phe_ZIP: Phenylalanine zipper; InterPro: IPR015012 The phenylalanine zipper consists of aromatic side chains from ten phenylalanine residues that are stacked within a hydrophobic core. This zipper mediates dimerisation of various proteins, such as APS, SH2-B and Lnk []. ; GO: 0004871 signal transducer activity, 0035556 intracellular signal transduction; PDB: 1Q2H_B.
Probab=23.07 E-value=1.1e+02 Score=18.78 Aligned_cols=33 Identities=21% Similarity=0.476 Sum_probs=20.8
Q ss_pred HHHHHHHHHHhcCCCCc-----hHhHHHHHHHHHHHhhc
Q 043741 32 DLKELLNCFLQLNSPSN-----HDVIVQAFTGVWNEAVS 65 (79)
Q Consensus 32 dLeeLL~cYL~LN~~~~-----H~~I~~aF~dl~~~l~~ 65 (79)
|+-.=-.-|++.| |.+ |....+=|+|...+.|.
T Consensus 17 dfAk~~~~f~~~n-P~~a~~~~~~~F~~kF~d~F~~hF~ 54 (59)
T PF08916_consen 17 DFAKAFRRFINEN-PQYARPLSHRSFSRKFADLFQEHFE 54 (59)
T ss_dssp HHHHHHHHHHHH--GGG-STTHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcC-ccccCCCCHHHHHHHHHHHHHHHHH
Confidence 3333345688888 444 77777788888777663
No 48
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=22.68 E-value=1.5e+02 Score=23.47 Aligned_cols=32 Identities=16% Similarity=0.266 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCchHhHHHHHHHH
Q 043741 28 YSNDDLKELLNCFLQLNSPSNHDVIVQAFTGV 59 (79)
Q Consensus 28 ~~~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl 59 (79)
.-...|-+-+.+||++|.-..|.+|.+--.++
T Consensus 268 ~P~~aL~d~~~yYL~~~g~d~~~~~~~k~~~~ 299 (302)
T COG3643 268 VPEQALIDVAKYYLQLDGFDADKFIEDKILEL 299 (302)
T ss_pred chHHHHHHHHHHHHhccccchhHHHHHHHHHH
Confidence 34588999999999999999999998755443
No 49
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=22.45 E-value=2.9e+02 Score=20.72 Aligned_cols=50 Identities=14% Similarity=0.220 Sum_probs=41.1
Q ss_pred hHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhcCCCCchHhHHHHHHHHHHHhhc
Q 043741 10 PYEDFRRSMLQMIMEKEIYSNDDLKELLNCFLQLNSPSNHDVIVQAFTGVWNEAVS 65 (79)
Q Consensus 10 Py~DFR~SM~EMI~e~~i~~~~dLeeLL~cYL~LN~~~~H~~I~~aF~dl~~~l~~ 65 (79)
.|.-|-+-|++-+++-|.++...+|-||---++.|++. +-.+|||..+--
T Consensus 61 ay~Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrdR~------K~laDic~~ln~ 110 (199)
T COG5631 61 AYEAFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRDRP------KSLADICQMLNR 110 (199)
T ss_pred HHHHHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcCch------hhHHHHHHHhcc
Confidence 48889999999999999999999999999888887664 455677766543
No 50
>PRK05473 hypothetical protein; Provisional
Probab=21.77 E-value=74 Score=20.98 Aligned_cols=14 Identities=36% Similarity=0.581 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHhcC
Q 043741 31 DDLKELLNCFLQLN 44 (79)
Q Consensus 31 ~dLeeLL~cYL~LN 44 (79)
+=||||+..||.-+
T Consensus 71 EilEeLv~~Yl~~~ 84 (86)
T PRK05473 71 EILEELVKSYLKGN 84 (86)
T ss_pred HHHHHHHHHHHHhc
Confidence 66899999999643
No 51
>PF10723 RepB-RCR_reg: Replication regulatory protein RepB; InterPro: IPR019661 This family of proteins regulates the replication of rolling circle replication (RCR) plasmids that have a double-strand replication origin (dso). Regulation of the replication of the RCR plasmids occurs mainly at the initiation of leading strand synthesis at the dso, such that concentration of Rep protein controls plasmid replication []. ; PDB: 2KEL_B.
Probab=21.22 E-value=1.9e+02 Score=18.35 Aligned_cols=30 Identities=13% Similarity=0.327 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHHHh
Q 043741 13 DFRRSMLQMIMEKEIYSNDDLKELLNCFLQ 42 (79)
Q Consensus 13 DFR~SM~EMI~e~~i~~~~dLeeLL~cYL~ 42 (79)
+.++-+.+|-.+.|+.-.+-+|.|+..|+.
T Consensus 51 ~~K~~L~~lc~~~GlTQae~IE~LI~~~~~ 80 (84)
T PF10723_consen 51 ELKERLEELCKEQGLTQAEMIERLIKSELQ 80 (84)
T ss_dssp HHHHHHHHHHHHS---HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence 567788899999999999999999998874
No 52
>PF11176 DUF2962: Protein of unknown function (DUF2962); InterPro: IPR021346 This eukaryotic family of proteins has no known function. ; PDB: 2KKM_A.
Probab=21.18 E-value=1.8e+02 Score=20.34 Aligned_cols=45 Identities=16% Similarity=0.253 Sum_probs=30.6
Q ss_pred cChHHHHHHHHHHHHHh--cCCCCHHHHHHHHHHHHhcCCCCchHhH
Q 043741 8 NDPYEDFRRSMLQMIME--KEIYSNDDLKELLNCFLQLNSPSNHDVI 52 (79)
Q Consensus 8 ~DPy~DFR~SM~EMI~e--~~i~~~~dLeeLL~cYL~LN~~~~H~~I 52 (79)
.+|..+.-.-.++.|.+ ....+.+++.+|..-||.=|+.+.-.+-
T Consensus 44 ~~~~~~r~~wFq~~i~~~~~~~~t~~e~~~lI~~yl~R~DeEleql~ 90 (155)
T PF11176_consen 44 KNPELERLKWFQEAIDEKDKKPFTLEEIHELIERYLHRFDEELEQLK 90 (155)
T ss_dssp -HHHHHHHHHHHHHHHSTT-----HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHHHHHHHccccCCCCCCHHHHHHHHHHHHhcCHHHHHHHH
Confidence 35677777777788877 5678999999999999998876655443
No 53
>PF08636 Pkr1: ER protein Pkr1; InterPro: IPR013945 Pkr1 has been identified as an ER protein of unknown function.
Probab=21.09 E-value=68 Score=20.49 Aligned_cols=16 Identities=13% Similarity=0.457 Sum_probs=13.5
Q ss_pred HHHHHHHHHhhcCCCC
Q 043741 54 QAFTGVWNEAVSKSPK 69 (79)
Q Consensus 54 ~aF~dl~~~l~~~~~~ 69 (79)
..|.++|..+|-++++
T Consensus 3 sf~~~l~esIftPG~t 18 (75)
T PF08636_consen 3 SFFEELWESIFTPGTT 18 (75)
T ss_pred hHHHHHHHHccCCCCC
Confidence 4689999999988774
No 54
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.69 E-value=2.7e+02 Score=18.60 Aligned_cols=47 Identities=9% Similarity=0.129 Sum_probs=30.8
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHHh--------------cCCCCchHhHHHHHHHHHHHhh
Q 043741 18 MLQMIMEKEIYSNDDLKELLNCFLQ--------------LNSPSNHDVIVQAFTGVWNEAV 64 (79)
Q Consensus 18 M~EMI~e~~i~~~~dLeeLL~cYL~--------------LN~~~~H~~I~~aF~dl~~~l~ 64 (79)
..++|....-++.+.+++|+..|-. .|...-=+++-++|..+|..+-
T Consensus 8 ~~~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~ 68 (184)
T PRK12539 8 LKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRH 68 (184)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHh
Confidence 3455555455666666666554433 4677777888889999988664
No 55
>PF01761 DHQ_synthase: 3-dehydroquinate synthase; PDB: 3OKF_A 1NVA_B 1NUA_A 1NVE_D 1NVB_B 1SG6_A 1NR5_A 1NRX_B 1NVD_A 1NVF_C ....
Probab=20.50 E-value=1.5e+02 Score=22.38 Aligned_cols=48 Identities=15% Similarity=0.180 Sum_probs=29.9
Q ss_pred ccChHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhc----CCCCchHhHHH
Q 043741 7 SNDPYEDFRRSMLQMIMEKEIYSNDDLKELLNCFLQL----NSPSNHDVIVQ 54 (79)
Q Consensus 7 S~DPy~DFR~SM~EMI~e~~i~~~~dLeeLL~cYL~L----N~~~~H~~I~~ 54 (79)
..=|.++||.-|.|||.-.=+.|.+.++.|....-.+ +.+....+|.+
T Consensus 105 ~tL~~~e~~~G~aEiiK~a~i~d~~lf~~l~~~~~~~~~~~~~~~l~~~i~~ 156 (260)
T PF01761_consen 105 KTLPPREIRSGLAEIIKYALIADPELFELLEDHAKDLLEERDPDALEEIIKR 156 (260)
T ss_dssp GGS-HHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHHHHHTTTHCHHHHHHHH
T ss_pred hhccHHHHHhCHHHHHHHHHHCCHHHHHHHHhhHHHHhcccCHHHHHHHHHH
Confidence 3558899999999999876677765555444444333 44444444444
Done!