Query psy6694
Match_columns 136
No_of_seqs 130 out of 1183
Neff 5.6
Searched_HMMs 46136
Date Sat Aug 17 00:39:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6694.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6694hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00379 Chitin_bind_4: Insect 99.7 2.2E-16 4.7E-21 99.9 7.0 47 34-82 1-52 (52)
2 PF06004 DUF903: Bacterial pro 78.9 1.8 4E-05 27.3 2.1 37 37-73 3-40 (50)
3 KOG3317|consensus 67.5 61 0.0013 25.7 8.6 37 66-104 108-144 (188)
4 PRK05461 apaG CO2+/MG2+ efflux 58.4 48 0.001 24.5 6.2 21 52-72 93-113 (127)
5 COG5294 Uncharacterized protei 56.9 26 0.00056 25.8 4.4 46 29-77 26-75 (113)
6 PF13511 DUF4124: Domain of un 55.2 10 0.00022 23.5 2.0 17 58-77 14-30 (60)
7 COG3422 Uncharacterized conser 51.6 24 0.00051 23.1 3.2 20 24-43 5-24 (59)
8 PF07437 YfaZ: YfaZ precursor; 50.2 44 0.00095 26.0 5.1 10 1-10 1-10 (180)
9 COG4939 Major membrane immunog 43.1 69 0.0015 24.3 5.0 44 29-72 29-76 (147)
10 TIGR01655 yxeA_fam conserved h 42.6 37 0.00079 24.4 3.4 18 60-77 55-76 (114)
11 KOG1691|consensus 42.1 1.7E+02 0.0036 23.7 7.4 31 55-86 80-110 (210)
12 PF13956 Ibs_toxin: Toxin Ibs, 38.9 11 0.00023 19.2 0.1 8 1-8 1-8 (19)
13 TIGR01965 VCBS_repeat VCBS rep 37.4 58 0.0013 23.1 3.7 48 27-76 30-77 (99)
14 PF11131 PhrC_PhrF: Rap-phr ex 37.0 15 0.00032 21.9 0.5 11 2-12 3-13 (37)
15 cd07241 Glo_EDI_BRP_like_3 Thi 36.4 1.2E+02 0.0027 19.8 6.0 14 58-72 111-124 (125)
16 PF06286 Coleoptericin: Coleop 35.8 5 0.00011 30.2 -2.0 12 1-12 1-12 (143)
17 PF13127 DUF3955: Protein of u 33.4 24 0.00052 23.0 1.1 11 60-70 25-35 (63)
18 cd07252 BphC1-RGP6_N_like N-te 31.4 65 0.0014 21.8 3.1 20 58-77 100-119 (120)
19 cd08344 MhqB_like_N N-terminal 29.9 56 0.0012 21.8 2.6 18 59-76 93-110 (112)
20 PF10681 Rot1: Chaperone for p 29.7 74 0.0016 25.8 3.5 28 56-87 68-95 (212)
21 COG2967 ApaG Uncharacterized p 29.0 2.5E+02 0.0054 21.0 5.9 22 52-73 92-113 (126)
22 cd07240 ED_TypeI_classII_N N-t 28.9 82 0.0018 20.6 3.2 20 58-77 97-116 (117)
23 PHA02978 hypothetical protein; 26.3 64 0.0014 23.8 2.4 19 55-73 72-90 (135)
24 cd07244 FosA FosA, a Fosfomyci 25.6 78 0.0017 21.4 2.7 18 59-76 94-111 (121)
25 cd07266 HPCD_N_class_II N-term 25.4 95 0.002 20.7 3.1 17 59-75 102-118 (121)
26 cd09013 BphC-JF8_N_like N-term 24.9 96 0.0021 20.8 3.1 17 59-75 102-118 (121)
27 PF04170 NlpE: NlpE N-terminal 24.8 2.2E+02 0.0049 19.1 5.1 57 22-85 13-69 (87)
28 cd08352 Glo_EDI_BRP_like_1 Thi 24.2 2.1E+02 0.0045 18.5 5.2 14 59-72 110-123 (125)
29 TIGR03836 termin_org_HMW1 cyta 23.9 37 0.0008 23.3 0.8 20 63-84 28-47 (82)
30 cd07242 Glo_EDI_BRP_like_6 Thi 23.0 1.1E+02 0.0024 20.5 3.1 16 59-74 112-127 (128)
31 cd09012 Glo_EDI_BRP_like_24 Th 22.9 1.1E+02 0.0024 20.6 3.1 14 61-74 110-123 (124)
32 cd08361 PpCmtC_N N-terminal do 22.9 1.1E+02 0.0025 20.9 3.2 17 60-76 104-120 (124)
33 PF00659 POLO_box: POLO box du 22.8 2.1E+02 0.0045 18.0 5.3 38 33-70 4-45 (68)
34 PF09242 FCSD-flav_bind: Flavo 21.2 1.3E+02 0.0028 19.8 3.0 29 57-86 8-37 (71)
35 PRK06724 hypothetical protein; 21.0 1.1E+02 0.0024 21.7 2.8 21 57-77 103-125 (128)
36 cd08357 Glo_EDI_BRP_like_18 Th 20.9 1.3E+02 0.0028 19.9 3.0 15 60-74 110-124 (125)
37 PF06486 DUF1093: Protein of u 20.8 1.2E+02 0.0025 19.9 2.7 20 58-77 26-49 (78)
38 PTZ00459 mucin-associated surf 20.8 38 0.00083 28.2 0.4 9 3-11 8-16 (291)
39 PF04234 CopC: CopC domain; I 20.7 1.4E+02 0.003 20.3 3.2 8 55-62 87-94 (97)
40 cd08362 BphC5-RrK37_N_like N-t 20.1 1.4E+02 0.0031 19.6 3.1 17 59-75 101-117 (120)
41 COG0450 AhpC Peroxiredoxin [Po 20.0 1.9E+02 0.0042 23.1 4.2 29 53-83 121-149 (194)
No 1
>PF00379 Chitin_bind_4: Insect cuticle protein; InterPro: IPR000618 Insect cuticle is composed of proteins and chitin. The cuticular proteins seem to be specific to the type of cuticle (flexible or stiff) that occur at stages of the insect development. The proteins found in the flexible cuticle of larva and pupa of different insects share a conserved C-terminal section [] such a region is also found in the soft endocuticle of adults insects [] as well as in other cuticular proteins including in arachnids []. In addition, cuticular proteins share hydrophobic regions dominated by tetrapeptide repeats (A-A-P-A/V), which are presumed to be functionally important [, ]. Many insect cuticle proteins also include a 35-36 amino acid motif known as the R and R consensus. An extended form of this motif has been shown [] to bind chitin. It has no sequence similiarity to the cysteine-containing chitin-binding domain of chitinases and some peritrophic membrane proteins, suggesting that arthropods have two distinct classes of chitin-binding proteins, those with the chitin-binding domains found in lectins, chitinases and peritrophic membranes (cysCBD), and those with the type of chitin-binding domains found in cuticular proteins (non-cysCBD) []. The cuticle protein signature has been found in locust cuticle proteins 7 (LM-7), 8 (LM-8), 19 (LM-19) and endocuticle structural glycoprotein ABD-4; Hyalophora cecropia (Cecropia moth) cuticle proteins 12 and 66; Drosophila melanogaster (Fruit fly) larval cuticles proteins I, II, III and IV (LCP1 to LCP4); drosophila pupal cuticle proteins PCP, EDG-78E and EDG-84E; Manduca sexta (Tobacco hawkmoth) cuticle protein LCP-14; Tenebrio molitor (Yellow mealworm) cuticle proteins ACP-20, A1A, A2B and A3A; and Araneus diadematus (Spider) cuticle proteins ACP 11.9, ACP 12.4, ACP 12.6, ACP 15.5 and ACP 15.7.; GO: 0042302 structural constituent of cuticle
Probab=99.67 E-value=2.2e-16 Score=99.91 Aligned_cols=47 Identities=40% Similarity=0.916 Sum_probs=43.3
Q ss_pred eeEEEecCCCCEEEEee-----CCCCeEEEEEEEECCCCcEEEEEEEeeCCCCc
Q psy6694 34 YTFGYEAADGSFKIETR-----DVGGNVKGMFGFVDENGELKRISYSARNGTGF 82 (136)
Q Consensus 34 Y~f~yet~dG~~~~E~g-----~~~~~v~GsYsy~~pdG~~~~V~Y~AD~e~Gf 82 (136)
|+|+|+++|| .++|++ +..++|+|+|+|++|||+.++|+|+|| ++||
T Consensus 1 Y~f~Y~~~dg-~~~e~~~~~~~~~~~~v~GsY~y~~pdG~~~~V~Y~Ad-~~Gf 52 (52)
T PF00379_consen 1 YSFGYETSDG-SRQEEGRPETEDEGGVVRGSYSYIDPDGQTRTVTYVAD-ENGF 52 (52)
T ss_pred CeeEeEcCCC-CEEEEEEcccCCCCCEEEEEEEEECCCCCEEEEEEECC-CCCC
Confidence 7999999999 666666 488999999999999999999999999 9998
No 2
>PF06004 DUF903: Bacterial protein of unknown function (DUF903); InterPro: IPR010305 This family consists of several small bacterial proteins several of which are classified as putative lipoproteins. The function of this family is unknown.; PDB: 2RB6_B 3BDU_F 2RA2_F 2RD1_C 3FIF_H 2JN0_A 2K57_A.
Probab=78.93 E-value=1.8 Score=27.27 Aligned_cols=37 Identities=19% Similarity=0.380 Sum_probs=22.4
Q ss_pred EEecCCCCEEEEeeCCC-CeEEEEEEEECCCCcEEEEE
Q psy6694 37 GYEAADGSFKIETRDVG-GNVKGMFGFVDENGELKRIS 73 (136)
Q Consensus 37 ~yet~dG~~~~E~g~~~-~~v~GsYsy~~pdG~~~~V~ 73 (136)
--.+.||..-.-.|.+. ..-.|-|+|.|.+|+.+.|+
T Consensus 3 vi~t~dG~~i~t~gkP~~D~~tG~~~y~D~~G~~~qIn 40 (50)
T PF06004_consen 3 VITTNDGRTIVTDGKPKYDKDTGMYSYTDADGKEQQIN 40 (50)
T ss_dssp EEEETTSEEEEESSEEEEETTTTEEEEEBTTS-EEEEE
T ss_pred EEEeCCCcEEEeCCCccccCCCCcEEEECCCCCEEEEc
Confidence 34566774322222211 23469999999999998875
No 3
>KOG3317|consensus
Probab=67.49 E-value=61 Score=25.71 Aligned_cols=37 Identities=14% Similarity=0.202 Sum_probs=23.6
Q ss_pred CCcEEEEEEEeeCCCCccccCCCCCCCCCcccccccccc
Q psy6694 66 NGELKRISYSARNGTGFQASGTIATPVENARLNPSYTTV 104 (136)
Q Consensus 66 dG~~~~V~Y~AD~e~Gf~~~g~~lP~p~p~~v~~~l~~~ 104 (136)
+|...+|+|.++ |.| ..+....-+|.|..|...-++-
T Consensus 108 ~~t~atVty~~~-e~g-~~~~~~ts~~~~gyila~re~~ 144 (188)
T KOG3317|consen 108 NGTPATVTYRIP-EKG-ALQEAYTSPPGPGYILAQREPD 144 (188)
T ss_pred ccCceEEEEEcC-CCC-ceeEEeecCCCCcceeeecCcc
Confidence 355679999999 888 4433333455667776665433
No 4
>PRK05461 apaG CO2+/MG2+ efflux protein ApaG; Reviewed
Probab=58.39 E-value=48 Score=24.48 Aligned_cols=21 Identities=33% Similarity=0.665 Sum_probs=17.0
Q ss_pred CCCeEEEEEEEECCCCcEEEE
Q psy6694 52 VGGNVKGMFGFVDENGELKRI 72 (136)
Q Consensus 52 ~~~~v~GsYsy~~pdG~~~~V 72 (136)
+.|..+|+|.+++++|..+.|
T Consensus 93 p~G~M~G~y~~~~~~G~~F~v 113 (127)
T PRK05461 93 PSGTMQGHYQMVDEDGERFEV 113 (127)
T ss_pred CCEEEEEEEEEEeCCCCEEEE
Confidence 457899999999999986554
No 5
>COG5294 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.87 E-value=26 Score=25.76 Aligned_cols=46 Identities=22% Similarity=0.374 Sum_probs=29.5
Q ss_pred CCCCCeeEEEecCCCCEEEEeeCCCCeEEEEEEEE----CCCCcEEEEEEEee
Q psy6694 29 NDDGSYTFGYEAADGSFKIETRDVGGNVKGMFGFV----DENGELKRISYSAR 77 (136)
Q Consensus 29 ~~dGsY~f~yet~dG~~~~E~g~~~~~v~GsYsy~----~pdG~~~~V~Y~AD 77 (136)
+-|| |++=-...+.-.+.|+.+.++.. -|+|. +.+|+.-+|.|+|+
T Consensus 26 ~~d~-fnpyvk~~~~y~k~~~~t~~~~~--~y~y~i~ayn~~Gkkk~v~f~a~ 75 (113)
T COG5294 26 NYDR-FNPYVKITDSYAKVEEDTQDGSP--GYEYTITAYNKNGKKKEVKFTAT 75 (113)
T ss_pred ccCC-CCceEEEeccceecccccccCCc--cceeeehhhccCCcEEEEEEEec
Confidence 3443 55544554443566666556555 45554 67899999999998
No 6
>PF13511 DUF4124: Domain of unknown function (DUF4124)
Probab=55.20 E-value=10 Score=23.51 Aligned_cols=17 Identities=41% Similarity=0.804 Sum_probs=13.8
Q ss_pred EEEEEECCCCcEEEEEEEee
Q psy6694 58 GMFGFVDENGELKRISYSAR 77 (136)
Q Consensus 58 GsYsy~~pdG~~~~V~Y~AD 77 (136)
.-|.|+|.+|+ |+|+-.
T Consensus 14 ~vYk~~D~~G~---v~ysd~ 30 (60)
T PF13511_consen 14 EVYKWVDENGV---VHYSDT 30 (60)
T ss_pred cEEEEECCCCC---EEECcc
Confidence 57999999996 677765
No 7
>COG3422 Uncharacterized conserved protein [Function unknown]
Probab=51.58 E-value=24 Score=23.11 Aligned_cols=20 Identities=30% Similarity=0.428 Sum_probs=16.6
Q ss_pred EeeecCCCCCeeEEEecCCC
Q psy6694 24 QINRLNDDGSYTFGYEAADG 43 (136)
Q Consensus 24 ~~~~~~~dGsY~f~yet~dG 43 (136)
.+-..+.+|.|.|.+...||
T Consensus 5 fei~kdk~Ge~rfrlkA~N~ 24 (59)
T COG3422 5 FEIYKDKAGEYRFRLKAANG 24 (59)
T ss_pred EEEEEcCCCcEEEEEEccCc
Confidence 34456789999999999998
No 8
>PF07437 YfaZ: YfaZ precursor; InterPro: IPR009998 This family contains the precursor of the bacterial protein YfaZ (approximately 180 residues long). Many members of this family are hypothetical proteins.
Probab=50.16 E-value=44 Score=25.99 Aligned_cols=10 Identities=30% Similarity=0.517 Sum_probs=7.1
Q ss_pred ChhHHHHHhc
Q psy6694 1 MLRLLLVCTQ 10 (136)
Q Consensus 1 M~klvlvc~l 10 (136)
|-|+++.|++
T Consensus 1 m~k~~~a~~~ 10 (180)
T PF07437_consen 1 MKKFLLASAA 10 (180)
T ss_pred CchHHHHHHH
Confidence 7788877653
No 9
>COG4939 Major membrane immunogen, membrane-anchored lipoprotein [Function unknown]
Probab=43.10 E-value=69 Score=24.33 Aligned_cols=44 Identities=30% Similarity=0.422 Sum_probs=30.9
Q ss_pred CCCCCeeEEEecCCCC----EEEEeeCCCCeEEEEEEEECCCCcEEEE
Q psy6694 29 NDDGSYTFGYEAADGS----FKIETRDVGGNVKGMFGFVDENGELKRI 72 (136)
Q Consensus 29 ~~dGsY~f~yet~dG~----~~~E~g~~~~~v~GsYsy~~pdG~~~~V 72 (136)
-.||.|+-.|+.-|.. +-+=+-+.+..|+=.|-|.+.+|+...=
T Consensus 29 ~~dGtY~~~y~~fDd~gwk~f~~iti~dGKiv~~~ydy~~k~G~~Ks~ 76 (147)
T COG4939 29 FNDGTYQGHYESFDDHGWKAFVTITIQDGKIVACTYDYRDKKGNIKSD 76 (147)
T ss_pred ccCCceeeeeccccccCccceEEEEEeCCEEEEEEeeeecCCCCcccc
Confidence 3789999999987742 2222223456789999999999987543
No 10
>TIGR01655 yxeA_fam conserved hypothetical protein TIGR01655. This model represents a family of small (about 115 amino acids) uncharacterized proteins with N-terminal signal sequences, found exclusively in Gram-positive organisms. Most genomes that have any members of this family have at least two members.
Probab=42.58 E-value=37 Score=24.39 Aligned_cols=18 Identities=17% Similarity=0.571 Sum_probs=15.0
Q ss_pred EEEE----CCCCcEEEEEEEee
Q psy6694 60 FGFV----DENGELKRISYSAR 77 (136)
Q Consensus 60 Ysy~----~pdG~~~~V~Y~AD 77 (136)
|.|. |.+|+..+++++|+
T Consensus 55 y~Y~~~~yd~~G~~k~i~f~~~ 76 (114)
T TIGR01655 55 YEYKLDAYDSSGKKHKVKFMAG 76 (114)
T ss_pred EEEEEEEECCCCCEEEEEEEcC
Confidence 6554 88999999999886
No 11
>KOG1691|consensus
Probab=42.07 E-value=1.7e+02 Score=23.74 Aligned_cols=31 Identities=23% Similarity=0.412 Sum_probs=26.4
Q ss_pred eEEEEEEEECCCCcEEEEEEEeeCCCCccccC
Q psy6694 55 NVKGMFGFVDENGELKRISYSARNGTGFQASG 86 (136)
Q Consensus 55 ~v~GsYsy~~pdG~~~~V~Y~AD~e~Gf~~~g 86 (136)
+..|+|+|+..+-..+.+-++|| ..|.+|..
T Consensus 80 v~~gqFaFta~e~~~y~~Cf~~~-~~~~~p~~ 110 (210)
T KOG1691|consen 80 VTKGQFAFTAEESGMYEACFTAD-VPGHKPET 110 (210)
T ss_pred cccceEEEEeccCCcEEEEEecc-cCCCCCCc
Confidence 34999999999988999999998 77887744
No 12
>PF13956 Ibs_toxin: Toxin Ibs, type I toxin-antitoxin system
Probab=38.93 E-value=11 Score=19.25 Aligned_cols=8 Identities=25% Similarity=0.833 Sum_probs=6.2
Q ss_pred ChhHHHHH
Q psy6694 1 MLRLLLVC 8 (136)
Q Consensus 1 M~klvlvc 8 (136)
|||++++.
T Consensus 1 MMk~vIIl 8 (19)
T PF13956_consen 1 MMKLVIIL 8 (19)
T ss_pred CceehHHH
Confidence 89988763
No 13
>TIGR01965 VCBS_repeat VCBS repeat. This domain of about 100 residues is found multiple (up to 35) copies in long proteins from several species of Vibrio, Colwellia, Bradyrhizobium, and Shewanella (hence the name VCBS) and in smaller copy numbers in proteins from several other bacteria. The large protein size and repeat copy numbers, species distribution, and suggested activities of several member proteins suggests a role for this domain in adhesion.
Probab=37.37 E-value=58 Score=23.14 Aligned_cols=48 Identities=13% Similarity=0.349 Sum_probs=30.7
Q ss_pred ecCCCCCeeEEEecCCCCEEEEeeCCCCeEEEEEEEECCCCcEEEEEEEe
Q psy6694 27 RLNDDGSYTFGYEAADGSFKIETRDVGGNVKGMFGFVDENGELKRISYSA 76 (136)
Q Consensus 27 ~~~~dGsY~f~yet~dG~~~~E~g~~~~~v~GsYsy~~pdG~~~~V~Y~A 76 (136)
.++.+|+|.|....++. ..+.-+ .+..+.=+|.|...||....|.-+=
T Consensus 30 ti~~~G~wtYtl~n~~~-avq~L~-~Ge~~tdsFtvtv~DGtt~~vtItI 77 (99)
T TIGR01965 30 SIDADGQWTYQADNSQT-AVQALK-AGETLTDTFTVTSADGTSQTVTITI 77 (99)
T ss_pred EECCCCcEEEEeCCCcH-HHHhhc-CCCEEEEEEEEEEeCCCeEEEEEEE
Confidence 35778877666654442 222222 3456777899999999877776553
No 14
>PF11131 PhrC_PhrF: Rap-phr extracellular signalling
Probab=36.99 E-value=15 Score=21.87 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=8.5
Q ss_pred hhHHHHHhccc
Q psy6694 2 LRLLLVCTQEV 12 (136)
Q Consensus 2 ~klvlvc~la~ 12 (136)
.||+++|++++
T Consensus 3 sKl~l~CLA~a 13 (37)
T PF11131_consen 3 SKLFLICLAAA 13 (37)
T ss_pred hhHHHHHHHHH
Confidence 58999998654
No 15
>cd07241 Glo_EDI_BRP_like_3 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=36.36 E-value=1.2e+02 Score=19.81 Aligned_cols=14 Identities=21% Similarity=0.321 Sum_probs=10.5
Q ss_pred EEEEEECCCCcEEEE
Q psy6694 58 GMFGFVDENGELKRI 72 (136)
Q Consensus 58 GsYsy~~pdG~~~~V 72 (136)
..| +.||||...++
T Consensus 111 ~~~-~~DPdG~~iE~ 124 (125)
T cd07241 111 ESV-ILDPEGNRIEI 124 (125)
T ss_pred EEE-EECCCCCEEEe
Confidence 344 88999998775
No 16
>PF06286 Coleoptericin: Coleoptericin; InterPro: IPR009382 This family consists of several insect coleoptericin, acaloleptin, holotricin and rhinocerosin proteins which are all known to be antibacterial proteins []. These all appear to be short, glycine-rich molecules, inducible by infection.; GO: 0042742 defense response to bacterium, 0005576 extracellular region
Probab=35.77 E-value=5 Score=30.19 Aligned_cols=12 Identities=17% Similarity=0.379 Sum_probs=9.3
Q ss_pred ChhHHHHHhccc
Q psy6694 1 MLRLLLVCTQEV 12 (136)
Q Consensus 1 M~klvlvc~la~ 12 (136)
||||.+++||.+
T Consensus 1 mmkl~i~~~lia 12 (143)
T PF06286_consen 1 MMKLYIIFGLIA 12 (143)
T ss_pred CceEeeehhHHH
Confidence 999998876644
No 17
>PF13127 DUF3955: Protein of unknown function (DUF3955)
Probab=33.43 E-value=24 Score=23.02 Aligned_cols=11 Identities=45% Similarity=0.712 Sum_probs=7.9
Q ss_pred EEEECCCCcEE
Q psy6694 60 FGFVDENGELK 70 (136)
Q Consensus 60 Ysy~~pdG~~~ 70 (136)
+||+|+||..+
T Consensus 25 ~syVd~~G~L~ 35 (63)
T PF13127_consen 25 GSYVDEDGVLH 35 (63)
T ss_pred cceECCCCeEe
Confidence 46788888764
No 18
>cd07252 BphC1-RGP6_N_like N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC 1.13.11.39) 1 from Rhodococcus globerulus P6 (BphC1-RGP6) and similar proteins. This subfamily contains the N-terminal, non-catalytic, domain of BphC1-RGP6 and similar proteins. BphC catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). This subfamily of BphCs belongs to the type I extradiol dioxygenase family, which require a metal in the active site in its catalytic mechanism. Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of 2,3-dihydroxybiphenyl 1,2-dioxygenases. For example, three types of BphC enzymes have been found in Rhodococcus globerulus (BphC1-RGP6 - BphC3-RGP6), all three enzymes are type I extradiol dioxygenases. BphC1-RGP6 has an internal duplication, it is a two-domain dioxygenase which forms octamers, and has Fe(II) at the catalytic site. Its N-
Probab=31.37 E-value=65 Score=21.84 Aligned_cols=20 Identities=20% Similarity=0.612 Sum_probs=16.4
Q ss_pred EEEEEECCCCcEEEEEEEee
Q psy6694 58 GMFGFVDENGELKRISYSAR 77 (136)
Q Consensus 58 GsYsy~~pdG~~~~V~Y~AD 77 (136)
..+.+.||||...++.|.-+
T Consensus 100 ~~~~~~DPdG~~iE~~~~~~ 119 (120)
T cd07252 100 GLIRFADPDGNRHELFWGPK 119 (120)
T ss_pred EEEEEECCCCCEEEEEeccc
Confidence 46789999999999887654
No 19
>cd08344 MhqB_like_N N-terminal domain of MhqB, a type I extradiol dioxygenase, and similar proteins. This subfamily contains the N-terminal, non-catalytic, domain of Burkholderia sp. NF100 MhqB and similar proteins. MhqB is a type I extradiol dioxygenase involved in the catabolism of methylhydroquinone, an intermediate in the degradation of fenitrothion. The purified enzyme has shown extradiol ring cleavage activity toward 3-methylcatechol. Fe2+ was suggested as a cofactor, the same as most other enzymes in the family. Burkholderia sp. NF100 MhqB is encoded on the plasmid pNF1. The type I family of extradiol dioxygenases contains two structurally homologous barrel-shaped domains at the N- and C-terminal. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism.
Probab=29.91 E-value=56 Score=21.81 Aligned_cols=18 Identities=22% Similarity=0.337 Sum_probs=14.7
Q ss_pred EEEEECCCCcEEEEEEEe
Q psy6694 59 MFGFVDENGELKRISYSA 76 (136)
Q Consensus 59 sYsy~~pdG~~~~V~Y~A 76 (136)
++-+.||||...++.+-+
T Consensus 93 ~~~~~DP~Gn~iel~~~~ 110 (112)
T cd08344 93 GVWFRDPDGNLLQVKVAE 110 (112)
T ss_pred EEEEECCCCCEEEEecCC
Confidence 477999999999998643
No 20
>PF10681 Rot1: Chaperone for protein-folding within the ER, fungal; InterPro: IPR019623 This conserved fungal family is an essential molecular chaperone in the endoplasmic reticulum. Molecular chaperones transiently interact with unfolded proteins to inhibit their self-aggregation and to support their folding and/or assembly. Rot1 is a general chaperone with some substrate specificity, its substrates being the structurally unrelated Kre5 Kre6 Big1 Atg22, which are type I, type II, and polytopic membrane proteins. The dependencies of each for Rot1 do not share similarities. However, their folding does require BiP, and one of these proteins was simultaneously associated with both Rot1 and BiP. In addition, Rot1 may cooperate with BiP/Kar2 in the folding of Kre6 [].
Probab=29.68 E-value=74 Score=25.78 Aligned_cols=28 Identities=21% Similarity=0.382 Sum_probs=22.1
Q ss_pred EEEEEEEECCCCcEEEEEEEeeCCCCccccCC
Q psy6694 56 VKGMFGFVDENGELKRISYSARNGTGFQASGT 87 (136)
Q Consensus 56 v~GsYsy~~pdG~~~~V~Y~AD~e~Gf~~~g~ 87 (136)
.+|+|..- ++|...-.-+..| |.|-..+
T Consensus 68 QHGtY~l~-~nGsl~L~P~~~D---GrQl~sd 95 (212)
T PF10681_consen 68 QHGTYELN-SNGSLTLTPFAVD---GRQLVSD 95 (212)
T ss_pred ecceEEEC-CCCcEEEeecCCC---CceeccC
Confidence 58999877 7898888878776 8887664
No 21
>COG2967 ApaG Uncharacterized protein affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism]
Probab=29.00 E-value=2.5e+02 Score=21.00 Aligned_cols=22 Identities=27% Similarity=0.653 Sum_probs=17.9
Q ss_pred CCCeEEEEEEEECCCCcEEEEE
Q psy6694 52 VGGNVKGMFGFVDENGELKRIS 73 (136)
Q Consensus 52 ~~~~v~GsYsy~~pdG~~~~V~ 73 (136)
+.|..+|.|.-++.||..++|.
T Consensus 92 p~G~M~GhY~M~~e~G~~F~v~ 113 (126)
T COG2967 92 PSGTMQGHYEMIDEDGETFDVA 113 (126)
T ss_pred CcceEEEEEEEecCCCcEEEee
Confidence 4578899999999999977653
No 22
>cd07240 ED_TypeI_classII_N N-terminal domain of type I, class II extradiol dioxygenases; non-catalytic domain. This family contains the N-terminal, non-catalytic, domain of type I, class II extradiol dioxygenases. Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site; extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon, whereas intradiol enzymes cleave the aromatic ring between two hydroxyl groups. Extradiol dioxygenases are classified into type I and type II enzymes. Type I extradiol dioxygenases include class I and class II enzymes. These two classes of enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. The extradiol dioxygenases represented in this fa
Probab=28.91 E-value=82 Score=20.58 Aligned_cols=20 Identities=25% Similarity=0.316 Sum_probs=15.8
Q ss_pred EEEEEECCCCcEEEEEEEee
Q psy6694 58 GMFGFVDENGELKRISYSAR 77 (136)
Q Consensus 58 GsYsy~~pdG~~~~V~Y~AD 77 (136)
-++.+.||||...++.+..|
T Consensus 97 ~~~~~~DP~G~~ie~~~~~~ 116 (117)
T cd07240 97 RGLRFQDPDGHLLELFVEAD 116 (117)
T ss_pred eEEEEECCCCCEEEEEEccC
Confidence 35568999999999987654
No 23
>PHA02978 hypothetical protein; Provisional
Probab=26.27 E-value=64 Score=23.84 Aligned_cols=19 Identities=21% Similarity=0.399 Sum_probs=14.8
Q ss_pred eEEEEEEEECCCCcEEEEE
Q psy6694 55 NVKGMFGFVDENGELKRIS 73 (136)
Q Consensus 55 ~v~GsYsy~~pdG~~~~V~ 73 (136)
...=.+||.||||...+|+
T Consensus 72 ~iiiy~sy~~~~gisiqvs 90 (135)
T PHA02978 72 EIIIYFSYADPDGISIQVS 90 (135)
T ss_pred EEEEEEEecCCCceEEEEe
Confidence 3445677899999988886
No 24
>cd07244 FosA FosA, a Fosfomycin resistance protein, catalyzes the addition of glutathione to the antibiotic fosfomycin, making it inactive. This subfamily family contains FosA, a fosfomycin resistant protein. Fosfomycin inhibits the enzyme UDP-N-acetylglucosamine-3-enolpyruvyltransferase (MurA), which catalyzes the first committed step in bacterial cell wall biosynthesis. FosA, catalyzes the addition of glutathione to the antibiotic fosfomycin, (1R,2S)-epoxypropylphosphonic acid, making it inactive. FosA is a Mn(II) dependent enzyme. It is evolutionarily related to glyoxalase I and type I extradiol dioxygenases.
Probab=25.56 E-value=78 Score=21.39 Aligned_cols=18 Identities=22% Similarity=0.427 Sum_probs=14.5
Q ss_pred EEEEECCCCcEEEEEEEe
Q psy6694 59 MFGFVDENGELKRISYSA 76 (136)
Q Consensus 59 sYsy~~pdG~~~~V~Y~A 76 (136)
++-+.||||..+++.+.|
T Consensus 94 ~~~f~DPdG~~ie~~~~~ 111 (121)
T cd07244 94 SFYFLDPDGHKLELHVGS 111 (121)
T ss_pred EEEEECCCCCEEEEEeCC
Confidence 556899999999988654
No 25
>cd07266 HPCD_N_class_II N-terminal domain of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (HPCD); belongs to the type I class II family of extradiol dioxygenases. This subfamily contains the N-terminal, non-catalytic, domain of HPCD. HPCD catalyses the second step in the degradation of 4-hydroxyphenylacetate to succinate and pyruvate. The aromatic ring of 4-hydroxyphenylacetate is opened by this dioxygenase to yield the 3,4-diol product, 2-hydroxy-5-carboxymethylmuconate semialdehyde. HPCD is a homotetramer and each monomer contains two structurally homologous barrel-shaped domains at the N- and C-terminus. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism. Most extradiol dioxygenases contain Fe(II) in their active site, but HPCD can be activated by either Mn(II) or Fe(II). These enzymes belong to the type I class II family of extradiol dioxygenases. The class III 3,4-dihydroxyphenylacetate 2,3-dioxygenases belong to a differ
Probab=25.43 E-value=95 Score=20.66 Aligned_cols=17 Identities=12% Similarity=-0.085 Sum_probs=13.8
Q ss_pred EEEEECCCCcEEEEEEE
Q psy6694 59 MFGFVDENGELKRISYS 75 (136)
Q Consensus 59 sYsy~~pdG~~~~V~Y~ 75 (136)
++.+.||||..+++.|-
T Consensus 102 ~~~~~DPdG~~ve~~~~ 118 (121)
T cd07266 102 ALRVEDPLGFPIEFYAE 118 (121)
T ss_pred EEEEECCCCCEEEEEec
Confidence 56788999999888753
No 26
>cd09013 BphC-JF8_N_like N-terminal, non-catalytic, domain of BphC_JF8, (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Bacillus sp. JF8 and similar proteins. 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, a key step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). BphC belongs to the type I extradiol dioxygenase family, which requires a metal ion in the active site in its catalytic mechanism. Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of BphCs. This subfamily of BphC is represented by the enzyme purified from the thermophilic biphenyl and naphthalene degrader, Bacillus sp. JF8. The members in this family of BphC enzymes may use either Mn(II) or Fe(II) as cofactors. The enzyme purified from Bacillus sp. JF8 is Mn(II)-dependent, however, the enzyme from Rhodococcus jostii RHAI has Fe(II) bound to it. BphC_JF8 is thermostable and its optimum activity is at 85 degrees C
Probab=24.88 E-value=96 Score=20.81 Aligned_cols=17 Identities=12% Similarity=0.383 Sum_probs=14.1
Q ss_pred EEEEECCCCcEEEEEEE
Q psy6694 59 MFGFVDENGELKRISYS 75 (136)
Q Consensus 59 sYsy~~pdG~~~~V~Y~ 75 (136)
++.+.||||...++.|-
T Consensus 102 ~~~~~DPdG~~iEl~~~ 118 (121)
T cd09013 102 AYRFRSPDGHPMELYWE 118 (121)
T ss_pred eEEEECCCCCEEEEEEe
Confidence 56789999999988863
No 27
>PF04170 NlpE: NlpE N-terminal domain; InterPro: IPR007298 This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway []. This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. NlpE from Escherichia coli and Salmonella typhi is also known to confer copper tolerance in copper-sensitive strains of E. coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes [].; PDB: 3LHN_A 2Z4I_B 2Z4H_A.
Probab=24.78 E-value=2.2e+02 Score=19.09 Aligned_cols=57 Identities=19% Similarity=0.223 Sum_probs=28.8
Q ss_pred EEEeeecCCCCCeeEEEecCCCCEEEEeeCCCCeEEEEEEEECCCCcEEEEEEEeeCCCCcccc
Q psy6694 22 LRQINRLNDDGSYTFGYEAADGSFKIETRDVGGNVKGMFGFVDENGELKRISYSARNGTGFQAS 85 (136)
Q Consensus 22 ~~~~~~~~~dGsY~f~yet~dG~~~~E~g~~~~~v~GsYsy~~pdG~~~~V~Y~AD~e~Gf~~~ 85 (136)
++..-..+.||+|...-.--+. .+..-...|+|.|... |..+++.-.+++..=|++.
T Consensus 13 I~t~L~L~~D~ty~l~~~Yl~~------~~~~~~~~g~g~w~~~-~~~i~L~~~~~~~~~f~v~ 69 (87)
T PF04170_consen 13 IKTTLTLNADGTYTLTETYLGK------EDGPFTEKGSGTWNVD-GNIITLTDNNGDKRYFKVG 69 (87)
T ss_dssp EEEEEEE-TTSEEEEEEEEETT------TSCCCEEEEEEEEECT-SSEEEEEETTTTCEEEEEE
T ss_pred eEEEEEECCCCcEEEEEEECCC------CCCCceEEEEEEEEcc-CCEEEEecCCCCEEEEEEC
Confidence 4444556788876643221111 1123468899999854 5555664443322234443
No 28
>cd08352 Glo_EDI_BRP_like_1 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=24.25 E-value=2.1e+02 Score=18.55 Aligned_cols=14 Identities=21% Similarity=0.218 Sum_probs=10.0
Q ss_pred EEEEECCCCcEEEE
Q psy6694 59 MFGFVDENGELKRI 72 (136)
Q Consensus 59 sYsy~~pdG~~~~V 72 (136)
...+.||+|..+++
T Consensus 110 ~~~~~DP~G~~iEl 123 (125)
T cd08352 110 FTFFYDPDGLPLEL 123 (125)
T ss_pred EEEEECCCCCEEEe
Confidence 45567888887765
No 29
>TIGR03836 termin_org_HMW1 cytadherence high molecular weight protein 1 N-terminal region. This model describes the N-terminal region of the Mycoplasma cytadherence protein HMW1, up to but not including the first EAGR box domain. The apparent orthologs in different Mycoplasma species differ profoundly in archictecture C-terminally to the region described here.
Probab=23.91 E-value=37 Score=23.26 Aligned_cols=20 Identities=35% Similarity=0.780 Sum_probs=13.8
Q ss_pred ECCCCcEEEEEEEeeCCCCccc
Q psy6694 63 VDENGELKRISYSARNGTGFQA 84 (136)
Q Consensus 63 ~~pdG~~~~V~Y~AD~e~Gf~~ 84 (136)
+-.||. +.|-|-|| .|||-.
T Consensus 28 v~eDg~-ikvAyDaD-gNgYYI 47 (82)
T TIGR03836 28 VPEDGS-IKVAYDAD-GNGYYI 47 (82)
T ss_pred cCCCCc-EEEEEecC-CCEEEE
Confidence 334664 57888888 788765
No 30
>cd07242 Glo_EDI_BRP_like_6 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=22.98 E-value=1.1e+02 Score=20.46 Aligned_cols=16 Identities=19% Similarity=0.152 Sum_probs=12.4
Q ss_pred EEEEECCCCcEEEEEE
Q psy6694 59 MFGFVDENGELKRISY 74 (136)
Q Consensus 59 sYsy~~pdG~~~~V~Y 74 (136)
++.+.||||..+++.+
T Consensus 112 ~~~~~DpdG~~ie~~~ 127 (128)
T cd07242 112 ALFFEDPDGIRLELVA 127 (128)
T ss_pred EEEEECCCCcEEEEEe
Confidence 4566899999888865
No 31
>cd09012 Glo_EDI_BRP_like_24 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping.
Probab=22.93 E-value=1.1e+02 Score=20.56 Aligned_cols=14 Identities=29% Similarity=0.586 Sum_probs=12.2
Q ss_pred EEECCCCcEEEEEE
Q psy6694 61 GFVDENGELKRISY 74 (136)
Q Consensus 61 sy~~pdG~~~~V~Y 74 (136)
-+.||||...++.|
T Consensus 110 ~~~DPdG~~ie~~~ 123 (124)
T cd09012 110 SFADLDGHLWEVLW 123 (124)
T ss_pred EEECCCCCEEEEEE
Confidence 48899999999887
No 32
>cd08361 PpCmtC_N N-terminal domain of 2,3-dihydroxy-p-cumate-3,4-dioxygenase (PpCmtC). This subfamily contains the N-terminal, non-catalytic, domain of PpCmtC. 2,3-dihydroxy-p-cumate-3,4-dioxygenase (CmtC of Pseudomonas putida F1) is a dioxygenase involved in the eight-step catabolism pathway of p-cymene. CmtC acts upon the reaction intermediate 2,3-dihydroxy-p-cumate, yielding 2-hydroxy-3-carboxy-6-oxo-7-methylocta-2,4-dienoate. The CmtC belongs to the type I family of extradiol dioxygenases. Fe2+ was suggested as a cofactor, same as other enzymes in the family. The type I family of extradiol dioxygenases contains two structurally homologous barrel-shaped domains at the N- and C-terminal. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism.
Probab=22.89 E-value=1.1e+02 Score=20.88 Aligned_cols=17 Identities=18% Similarity=0.317 Sum_probs=13.6
Q ss_pred EEEECCCCcEEEEEEEe
Q psy6694 60 FGFVDENGELKRISYSA 76 (136)
Q Consensus 60 Ysy~~pdG~~~~V~Y~A 76 (136)
..+.||||...++.|.-
T Consensus 104 ~~f~DPdG~~iE~~~~~ 120 (124)
T cd08361 104 IAFRDPSGNSIELVVRP 120 (124)
T ss_pred EEEECcCCCEEEEEEee
Confidence 35899999999987653
No 33
>PF00659 POLO_box: POLO box duplicated region; InterPro: IPR000959 A subgroup of serine/threonine protein kinases, Polo or Polo-like kinases play multiple roles during the cell cycle. Polo kinases are required at several key points through mitosis, starting from control of the G2/M transition through phosphorylation of Cdc25C and mitotic cyclins. Polo kinases are characterised by an amino terminal catalytic domain, and a carboxy terminal non-catalytic domain consisting of three blocks of conserved sequences known as polo boxes which form one single functional domain []. The domain is named after its founding member encoded by the polo gene of Drosophila melanogaster []. This domain of around 70 amino acids has been found in species ranging from yeast to mammals. Polo boxes appear to mediate interaction with multiple proteins through protein:protein interactions; some but not all of these proteins are substrates for the kinase domain of the molecule []. The crystal structure of the polo domain of the murine protein, Sak, is dimeric, consisting of two alpha-helices and two six-stranded beta-sheets []. The topology of one polypeptide subunit of the dimer consists of, from its N- to C terminus, an extended strand segment, five beta-strands, one alpha-helix (A) and a C-terminal beta-strand. Beta-strands from one subunit form a contiguous antiparallel beta-sheet with beta-strands from the second subunit. The two beta-sheets pack with a crossing angle of 110 degrees, orienting the hydrophobic surfaces inward and the hydrophilic surfaces outward. Helix A, which is colinear with beta-strand 6 of the same polypeptide, buries a large portion of the non-overlapping hydrophobic beta-sheet surfaces. Interactions involving helices A comprise a majority of the hydrophobic core structure and also the dimer interface. Point mutations in the Polo box of the budding yeast Cdc5 protein abolish the ability of overexpressed Cdc5 to interact with the spindle poles and to organise cytokinetic structures [].; GO: 0005515 protein binding; PDB: 1MBY_B 3P37_A 3MHN_A 1Q4K_A 3HIK_A 3Q1I_A 3P35_A 3MHQ_A 1UMW_B 3MQ8_B ....
Probab=22.79 E-value=2.1e+02 Score=18.01 Aligned_cols=38 Identities=24% Similarity=0.559 Sum_probs=19.6
Q ss_pred CeeEEEecCCCCEEEEeeCCCCeE----EEEEEEECCCCcEE
Q psy6694 33 SYTFGYEAADGSFKIETRDVGGNV----KGMFGFVDENGELK 70 (136)
Q Consensus 33 sY~f~yet~dG~~~~E~g~~~~~v----~GsYsy~~pdG~~~ 70 (136)
.|.+.|..+||..+--=.|..-.| .....|++++|+..
T Consensus 4 k~gi~~~LSng~vqv~FnD~tkivl~~~~~~v~yi~~~~~~~ 45 (68)
T PF00659_consen 4 KYGIGYQLSNGTVQVNFNDHTKIVLSPDGRLVTYIDRDGERQ 45 (68)
T ss_dssp CSEEEEEETTSEEEEEETTS-EEEEETTCCEEEEE-TTS-EE
T ss_pred ceEEEEEEeCCCEEEEEeCCCEEEECCCCCEEEEECCCCcEE
Confidence 367888888885433322221111 13777888777643
No 34
>PF09242 FCSD-flav_bind: Flavocytochrome c sulphide dehydrogenase, flavin-binding; InterPro: IPR015323 This entry represents the flavin-binding domain of flavocytochrome c sulphide dehydrogenase (FCSD), enzymes found in sulphur-oxidising bacteria such as the purple phototrophic bacteria Chromatium vinosum [, ]. These enzymes are complexes of flavoprotein and a dihaem cytochrome that carry out hydrogen sulphide-dependent cytochrome C reduction. The dihaem cytochrome folds into two domains, each of which resembles mitochondrial cytochrome c, with the two haem groups bound to the interior of the subunit. The flavoprotein subunit has a glutathione reductase-like fold consisting of a beta(3,4)-alpha(3) core, and an alpha+beta sandwich. The active site of the flavoprotein subunit contains a catalytically important disulphide bridge located above the pyrimidine portion of the flavin ring []. Electrons are transferred from the flavin to one of the haem groups in the cytochrome. This entry represents a flavoprotein domain required for binding to flavin, and subsequent electron transfer. ; PDB: 1FCD_A.
Probab=21.17 E-value=1.3e+02 Score=19.80 Aligned_cols=29 Identities=7% Similarity=-0.010 Sum_probs=20.5
Q ss_pred EEEEEEECCC-CcEEEEEEEeeCCCCccccC
Q psy6694 57 KGMFGFVDEN-GELKRISYSARNGTGFQASG 86 (136)
Q Consensus 57 ~GsYsy~~pd-G~~~~V~Y~AD~e~Gf~~~g 86 (136)
-=.||+++|| |..+.-.|.-+ ++++....
T Consensus 8 NtCYSlv~p~~aIsVa~vy~~~-~~~i~~v~ 37 (71)
T PF09242_consen 8 NTCYSLVAPDYAISVAGVYRYD-DGKIVEVP 37 (71)
T ss_dssp EEEEEEEETTEEEEEEEEEEE--TTTEEE-T
T ss_pred eeEEEEeCCCceEEEEEEEEEC-CCeEEEeC
Confidence 3479999987 88888889998 66765433
No 35
>PRK06724 hypothetical protein; Provisional
Probab=20.98 E-value=1.1e+02 Score=21.68 Aligned_cols=21 Identities=29% Similarity=0.689 Sum_probs=15.3
Q ss_pred EEEEE--EECCCCcEEEEEEEee
Q psy6694 57 KGMFG--FVDENGELKRISYSAR 77 (136)
Q Consensus 57 ~GsYs--y~~pdG~~~~V~Y~AD 77 (136)
.|.|+ +.||||...++.|.++
T Consensus 103 ~g~~~~~f~DPdG~~iEl~~~~~ 125 (128)
T PRK06724 103 EGYYTIDFYDPNGFIIEVAYTPN 125 (128)
T ss_pred CCEEEEEEECCCCCEEEEEeCCC
Confidence 34444 6799999999987653
No 36
>cd08357 Glo_EDI_BRP_like_18 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=20.85 E-value=1.3e+02 Score=19.87 Aligned_cols=15 Identities=20% Similarity=0.239 Sum_probs=11.8
Q ss_pred EEEECCCCcEEEEEE
Q psy6694 60 FGFVDENGELKRISY 74 (136)
Q Consensus 60 Ysy~~pdG~~~~V~Y 74 (136)
+-+.||||...++..
T Consensus 110 ~~~~DPdG~~iE~~~ 124 (125)
T cd08357 110 FFLKDPSGNALEFKA 124 (125)
T ss_pred EEEECCCCCEEEEee
Confidence 458899999888763
No 37
>PF06486 DUF1093: Protein of unknown function (DUF1093); InterPro: IPR006542 These are a family of small (about 115 amino acids) uncharacterised proteins with N-terminal signal sequences, found exclusively in Gram-positive organisms. Most genomes that have any members of this family have at least two members.; PDB: 3NPP_B 2K5Q_A 2K5W_A.
Probab=20.85 E-value=1.2e+02 Score=19.85 Aligned_cols=20 Identities=25% Similarity=0.607 Sum_probs=14.8
Q ss_pred EEEEEE----CCCCcEEEEEEEee
Q psy6694 58 GMFGFV----DENGELKRISYSAR 77 (136)
Q Consensus 58 GsYsy~----~pdG~~~~V~Y~AD 77 (136)
+.|.|. |.+|+.+.|++.|+
T Consensus 26 ~~Y~Y~l~~yd~~G~~k~l~f~~~ 49 (78)
T PF06486_consen 26 KGYEYTLKGYDEDGKEKTLTFTAS 49 (78)
T ss_dssp CEEEEEEEEEETT--EEEEEEEES
T ss_pred ceEEEEEEEECCCCCEEEEEEEec
Confidence 666664 78999999999997
No 38
>PTZ00459 mucin-associated surface protein (MASP); Provisional
Probab=20.82 E-value=38 Score=28.23 Aligned_cols=9 Identities=56% Similarity=0.940 Sum_probs=6.4
Q ss_pred hHHHHHhcc
Q psy6694 3 RLLLVCTQE 11 (136)
Q Consensus 3 klvlvc~la 11 (136)
+.||||+|-
T Consensus 8 RVLLVCALC 16 (291)
T PTZ00459 8 RVLLVCALC 16 (291)
T ss_pred hHHHHHHHH
Confidence 578888753
No 39
>PF04234 CopC: CopC domain; InterPro: IPR007348 CopC is a bacterial blue copper protein that binds 1 atom of copper per protein molecule. Along with CopA, CopC mediates copper resistance by sequestration of copper in the periplasm [].; GO: 0005507 copper ion binding, 0046688 response to copper ion, 0042597 periplasmic space; PDB: 1IX2_B 1LYQ_A 2C9P_C 2C9R_A 2C9Q_A 1M42_A 1OT4_A 1NM4_A.
Probab=20.70 E-value=1.4e+02 Score=20.33 Aligned_cols=8 Identities=50% Similarity=0.924 Sum_probs=4.6
Q ss_pred eEEEEEEE
Q psy6694 55 NVKGMFGF 62 (136)
Q Consensus 55 ~v~GsYsy 62 (136)
.+.|+|+|
T Consensus 87 ~~~G~~~F 94 (97)
T PF04234_consen 87 PVSGSFSF 94 (97)
T ss_dssp EEEEEEEE
T ss_pred CcCCEEEE
Confidence 45566655
No 40
>cd08362 BphC5-RrK37_N_like N-terminal, non-catalytic, domain of BphC5 (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Rhodococcus rhodochrous K37, and similar proteins. 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). The enzyme contains a N-terminal and a C-terminal domain of similar structure fold, resulting from an ancient gene duplication. BphC belongs to the type I extradiol dioxygenase family, which requires a metal in the active site for its catalytic activity. Polychlorinated biphenyl degrading bacteria demonstrate multiplicity of BphCs. Bacterium Rhodococcus rhodochrous K37 has eight genes encoding BphC enzymes. This family includes the N-terminal domain of BphC5-RrK37. The crystal structure of the protein from Novosphingobium aromaticivorans has a Mn(II)in the active site, although most proteins of type I extradiol dioxyge
Probab=20.09 E-value=1.4e+02 Score=19.60 Aligned_cols=17 Identities=35% Similarity=0.526 Sum_probs=13.8
Q ss_pred EEEEECCCCcEEEEEEE
Q psy6694 59 MFGFVDENGELKRISYS 75 (136)
Q Consensus 59 sYsy~~pdG~~~~V~Y~ 75 (136)
.+.+.||||....+.+.
T Consensus 101 ~~~~~DP~G~~iel~~~ 117 (120)
T cd08362 101 GFRFFDPDGRLIEFSAD 117 (120)
T ss_pred EEEEECCCCCEEEEEec
Confidence 45689999999888764
No 41
>COG0450 AhpC Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=20.02 E-value=1.9e+02 Score=23.06 Aligned_cols=29 Identities=24% Similarity=0.494 Sum_probs=23.5
Q ss_pred CCeEEEEEEEECCCCcEEEEEEEeeCCCCcc
Q psy6694 53 GGNVKGMFGFVDENGELKRISYSARNGTGFQ 83 (136)
Q Consensus 53 ~~~v~GsYsy~~pdG~~~~V~Y~AD~e~Gf~ 83 (136)
+..+||.| -+||||+.+.+.|... ..|=.
T Consensus 121 g~a~R~~F-IIDp~g~ir~~~v~~~-~iGRn 149 (194)
T COG0450 121 GLALRGTF-IIDPDGVIRHILVNPL-TIGRN 149 (194)
T ss_pred CcceeEEE-EECCCCeEEEEEEecC-CCCcC
Confidence 33789998 7899999999999987 55643
Done!