Query 021577
Match_columns 310
No_of_seqs 12 out of 14
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 04:04:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021577.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021577hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13730 HTH_36: Helix-turn-he 53.6 30 0.00065 23.5 4.2 43 213-255 1-55 (55)
2 PLN03207 stomagen; Provisional 52.3 7.3 0.00016 33.3 1.1 26 21-46 84-110 (113)
3 PLN02971 tryptophan N-hydroxyl 46.7 24 0.00051 34.1 3.8 17 92-108 52-68 (543)
4 PHA03163 hypothetical protein; 38.2 35 0.00077 28.5 3.0 27 282-308 9-35 (92)
5 PF09538 FYDLN_acid: Protein o 36.7 22 0.00048 29.4 1.7 37 10-52 3-39 (108)
6 KOG0156 Cytochrome P450 CYP2 s 28.5 49 0.0011 33.0 2.8 14 96-109 25-38 (489)
7 PF06322 Phage_NinH: Phage Nin 26.1 56 0.0012 25.9 2.2 18 200-217 43-60 (64)
8 TIGR02300 FYDLN_acid conserved 25.2 44 0.00095 29.3 1.6 39 10-54 3-41 (129)
9 PF06624 RAMP4: Ribosome assoc 24.4 54 0.0012 25.2 1.8 42 82-137 19-60 (63)
10 PF06692 MNSV_P7B: Melon necro 23.5 84 0.0018 24.7 2.7 13 43-56 4-16 (61)
11 TIGR02378 nirD_assim_sml nitri 23.5 37 0.00081 26.0 0.8 12 37-48 65-76 (105)
12 PF04879 Molybdop_Fe4S4: Molyb 21.2 82 0.0018 21.8 2.1 24 192-215 7-32 (55)
13 PF00680 RdRP_1: RNA dependent 20.3 8E+02 0.017 23.8 9.2 88 210-297 246-334 (491)
14 cd04338 Rieske_RO_Alpha_Tic55 20.2 35 0.00075 28.0 0.0 13 35-47 74-86 (134)
15 cd03474 Rieske_T4moC Toluene-4 20.2 33 0.00072 26.3 -0.1 11 35-45 57-67 (108)
No 1
>PF13730 HTH_36: Helix-turn-helix domain
Probab=53.64 E-value=30 Score=23.53 Aligned_cols=43 Identities=19% Similarity=0.170 Sum_probs=31.9
Q ss_pred ccchhhHHHHHHHHHHHH------------HHHhhhccchhHHHHHHHHhhhcee
Q 021577 213 RGWSVTTSLVVGTLCLRI------------VRRLYEANKAKITAIMSLLESLSFI 255 (310)
Q Consensus 213 RGwS~Tt~~vv~~LC~Ri------------vCri~ge~~~~~~~ik~~lE~~swi 255 (310)
.++|.++++|...|++.. +++.+|-.++.+.-...-||..+||
T Consensus 1 ~~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 1 KNLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 368889999998888765 6677777766666666667777775
No 2
>PLN03207 stomagen; Provisional
Probab=52.31 E-value=7.3 Score=33.33 Aligned_cols=26 Identities=46% Similarity=0.712 Sum_probs=21.1
Q ss_pred eeeeecceeee-cccCCccCCcceecC
Q 021577 21 TFLKCVGWQTE-ETLDPINCPYHYYCD 46 (310)
Q Consensus 21 tf~KC~rWQ~E-eT~D~InCPYHYyCD 46 (310)
-=+||.-=|+. |--||||-.|||-|-
T Consensus 84 cr~kc~~eqvpv~~~dp~nsayhy~cv 110 (113)
T PLN03207 84 CRYKCRAEQVPVEGNDPINSAYHYKCV 110 (113)
T ss_pred ccccccceeccccCCCCCccccccccC
Confidence 34788887875 677999999999984
No 3
>PLN02971 tryptophan N-hydroxylase
Probab=46.73 E-value=24 Score=34.15 Aligned_cols=17 Identities=41% Similarity=0.794 Sum_probs=14.0
Q ss_pred ccceeeccCCCchHHHH
Q 021577 92 QSKRFLLPSGPFSLPII 108 (310)
Q Consensus 92 ~~rryllPSGP~sLPli 108 (310)
++|++-+|.||.++|+|
T Consensus 52 ~~r~~~lPPGP~~lPii 68 (543)
T PLN02971 52 NKKLHPLPPGPTGFPIV 68 (543)
T ss_pred cCCCCCCCcCCCCCCcc
Confidence 45667789999999987
No 4
>PHA03163 hypothetical protein; Provisional
Probab=38.16 E-value=35 Score=28.51 Aligned_cols=27 Identities=37% Similarity=0.737 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCCC
Q 021577 282 GVFVLICLHLLKKACNKVAQWSCPRPR 308 (310)
Q Consensus 282 ~v~~Li~L~vlkk~c~q~~~~~~~~~~ 308 (310)
+++.|||||++..+..-++|=++..|.
T Consensus 9 ~i~~li~lcl~~nv~~~~~~~n~t~p~ 35 (92)
T PHA03163 9 GIFLLICLCLLDNVSQVLCQNNSTTPH 35 (92)
T ss_pred hHHHHHHHHHhhhhHHHHHhcCCCCCC
Confidence 799999999999999888887766554
No 5
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=36.66 E-value=22 Score=29.43 Aligned_cols=37 Identities=30% Similarity=0.586 Sum_probs=24.8
Q ss_pred CCCCCchhhhheeeeecceeeecccCCccCCcceecCCCCCCC
Q 021577 10 VPEWNLEDVRTTFLKCVGWQTEETLDPINCPYHYYCDSTYPGN 52 (310)
Q Consensus 10 ~peW~~e~i~~tf~KC~rWQ~EeT~D~InCPYHYyCDs~YPgn 52 (310)
+|||+. +|+=.+|-.=-.-=.-|||.||| |-..||..
T Consensus 3 kpelGt---KR~Cp~CG~kFYDLnk~PivCP~---CG~~~~~~ 39 (108)
T PF09538_consen 3 KPELGT---KRTCPSCGAKFYDLNKDPIVCPK---CGTEFPPE 39 (108)
T ss_pred ccccCC---cccCCCCcchhccCCCCCccCCC---CCCccCcc
Confidence 578885 45555564433333349999996 99999877
No 6
>KOG0156 consensus Cytochrome P450 CYP2 subfamily [Secondary metabolites biosynthesis, transport and catabolism]
Probab=28.48 E-value=49 Score=32.98 Aligned_cols=14 Identities=57% Similarity=0.757 Sum_probs=12.2
Q ss_pred eeccCCCchHHHHH
Q 021577 96 FLLPSGPFSLPIIL 109 (310)
Q Consensus 96 yllPSGP~sLPlil 109 (310)
.=+|.||.+||+|=
T Consensus 25 ~~lPPGP~~lPiIG 38 (489)
T KOG0156|consen 25 RNLPPGPPPLPIIG 38 (489)
T ss_pred CCCCcCCCCCCccc
Confidence 55899999999983
No 7
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.07 E-value=56 Score=25.86 Aligned_cols=18 Identities=44% Similarity=0.741 Sum_probs=15.4
Q ss_pred cceeEEccEEEEEccchh
Q 021577 200 KEVLVVGGKLVTYRGWSV 217 (310)
Q Consensus 200 kE~LVVGG~lV~YRGwS~ 217 (310)
+.=.||-|.|+.+|||+.
T Consensus 43 ~~HaIvNgvLMvhrG~~~ 60 (64)
T PF06322_consen 43 KRHAIVNGVLMVHRGWSG 60 (64)
T ss_pred ceEEEEcCEEEEEeCCCC
Confidence 455789999999999985
No 8
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=25.24 E-value=44 Score=29.26 Aligned_cols=39 Identities=13% Similarity=0.195 Sum_probs=27.2
Q ss_pred CCCCCchhhhheeeeecceeeecccCCccCCcceecCCCCCCCCC
Q 021577 10 VPEWNLEDVRTTFLKCVGWQTEETLDPINCPYHYYCDSTYPGNYP 54 (310)
Q Consensus 10 ~peW~~e~i~~tf~KC~rWQ~EeT~D~InCPYHYyCDs~YPgny~ 54 (310)
+|||+. +|+=.+|-+=-..=.-+||.||| |-..||-.|.
T Consensus 3 k~elGt---Kr~Cp~cg~kFYDLnk~p~vcP~---cg~~~~~~~~ 41 (129)
T TIGR02300 3 KPDLGT---KRICPNTGSKFYDLNRRPAVSPY---TGEQFPPEEA 41 (129)
T ss_pred chhhCc---cccCCCcCccccccCCCCccCCC---cCCccCcchh
Confidence 578875 45666676544444559999996 8888887643
No 9
>PF06624 RAMP4: Ribosome associated membrane protein RAMP4; InterPro: IPR010580 This entry contains Serp1/Ramp4, which has been shown to interacts with target proteins during their translocation into the lumen of the endoplasmic reticulum. It has also been shown to protect unfolded target proteins against degradation during ER stress. It may facilitate glycosylation of target proteins after termination of ER stress and may modulate the use of N-glycosylation sites on target proteins [, ].
Probab=24.41 E-value=54 Score=25.23 Aligned_cols=42 Identities=26% Similarity=0.502 Sum_probs=27.7
Q ss_pred ccCCCCCcccccceeeccCCCchHHHHHHHHhcCCccceeeeccchhHHHHHHHHh
Q 021577 82 SSRGPASSFSQSKRFLLPSGPFSLPIILLMLAKGHRINSVFPLSCVGPAILQLVYI 137 (310)
Q Consensus 82 ~sr~~~~~~~~~rryllPSGP~sLPlilL~lAKG~riNtvFPls~~GPAiL~llq~ 137 (310)
..||.-+...+.+..=.|-||+.|-+++.+ -+|.||+|+++.
T Consensus 19 ~krG~v~~~~k~k~~k~pVgp~~L~l~iFV--------------V~Gs~ifqiir~ 60 (63)
T PF06624_consen 19 TKRGKVPKSLKKKEKKYPVGPWLLGLFIFV--------------VCGSAIFQIIRS 60 (63)
T ss_pred HhcCCCccccccccccCCcCHHHHhhhhee--------------eEcHHHHHHHHH
Confidence 445664333333435568899988776655 379999998864
No 10
>PF06692 MNSV_P7B: Melon necrotic spot virus P7B protein; InterPro: IPR009575 This family consists of several Melon necrotic spot virus (MNSV) P7B proteins. The function of this family is unknown.
Probab=23.48 E-value=84 Score=24.66 Aligned_cols=13 Identities=46% Similarity=1.025 Sum_probs=10.1
Q ss_pred eecCCCCCCCCChH
Q 021577 43 YYCDSTYPGNYPPA 56 (310)
Q Consensus 43 YyCDs~YPgny~p~ 56 (310)
|-|||. ||||.-.
T Consensus 4 ~rc~~~-p~d~~~~ 16 (61)
T PF06692_consen 4 CRCDSA-PGDYSGP 16 (61)
T ss_pred cccCCC-CccchhH
Confidence 679986 9999754
No 11
>TIGR02378 nirD_assim_sml nitrite reductase [NAD(P)H], small subunit. This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused.
Probab=23.46 E-value=37 Score=26.00 Aligned_cols=12 Identities=25% Similarity=0.451 Sum_probs=9.8
Q ss_pred ccCCcceecCCC
Q 021577 37 INCPYHYYCDST 48 (310)
Q Consensus 37 InCPYHYyCDs~ 48 (310)
|.||||.+.=+.
T Consensus 65 i~Cp~Hg~~Fdl 76 (105)
T TIGR02378 65 VACPLHKRNFRL 76 (105)
T ss_pred EECCcCCCEEEc
Confidence 999999887543
No 12
>PF04879 Molybdop_Fe4S4: Molybdopterin oxidoreductase Fe4S4 domain; InterPro: IPR006963 The molybdopterin oxidoreductase Fe4S4 domain is found in a number of reductase/dehydrogenase families, which include the periplasmic nitrate reductase precursor and the formate dehydrogenase alpha chain [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2VPZ_A 2VPY_A 2VPW_A 2VPX_A 2NYA_A 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 ....
Probab=21.22 E-value=82 Score=21.83 Aligned_cols=24 Identities=38% Similarity=0.656 Sum_probs=17.3
Q ss_pred cccce--eeecceeEEccEEEEEccc
Q 021577 192 ECVSC--VCRKEVLVVGGKLVTYRGW 215 (310)
Q Consensus 192 EC~sC--vCRkE~LVVGG~lV~YRGw 215 (310)
.|..| -|..++-|.+|++++.+|=
T Consensus 7 ~C~~C~~gC~i~~~v~~g~i~~v~g~ 32 (55)
T PF04879_consen 7 VCPYCSSGCGIDVYVKDGKIVKVEGD 32 (55)
T ss_dssp E-SSCTT--EEEEEEETTEEEEEEE-
T ss_pred ECcCCcCCCcEEEEEecCceEEEECC
Confidence 34544 5999999999999999884
No 13
>PF00680 RdRP_1: RNA dependent RNA polymerase; InterPro: IPR001205 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This entry represents RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses viruses. It is part of the genome polyprotein that contains other polypeptides such as coat proteins VP1 to VP4, core proteins P2A to P2C and P3A, genome-linked protein VPG and picornain 3C (3.4.22.28 from EC). Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases [, ].; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3SFU_C 3NAH_A 3UR0_C 3UPF_C 3SFG_A 3NAI_C 3QID_B 3UQS_A 3OLB_M 3OLA_M ....
Probab=20.29 E-value=8e+02 Score=23.79 Aligned_cols=88 Identities=15% Similarity=0.146 Sum_probs=61.7
Q ss_pred EEEccchhhHHHHHHHHHHHHHHHhhhccchhHHHHHHHHhhh-ceeEEecceeeeecCCChhhhHHHHHHHHHHHHHHH
Q 021577 210 VTYRGWSVTTSLVVGTLCLRIVRRLYEANKAKITAIMSLLESL-SFIFIIKDSLYLATNSPPEQYLLRAAAFGGVFVLIC 288 (310)
Q Consensus 210 V~YRGwS~Tt~~vv~~LC~RivCri~ge~~~~~~~ik~~lE~~-swi~i~~D~vYL~~~sp~E~~~l~vaafg~v~~Li~ 288 (310)
..|.+|..|.-.-+.-....|+.+.++.+.........+.+.+ .-+.+..|.+|.+...-|-|...-+..=+.+-.+.+
T Consensus 246 ~DyS~FD~s~~~~~~~~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~g~~y~~~~G~PSG~~~Tsi~NSi~N~i~~ 325 (491)
T PF00680_consen 246 GDYSNFDSSLSPQLIDAAFDILNRFYDDSEEFSRLRRNLIQSICNPIHLCGGKVYRVNGGNPSGSPLTSIINSIVNNIYI 325 (491)
T ss_dssp EEESSTHHHS-HHHHHHHHHHHHHTTHHHSSHHHHHHHHHHHHHEEEEEETTEEEEEESSS-TTSTTHHHHHHHHHHHHH
T ss_pred eehhhcCCcccHHHHHHHHHHhhhhhcccccchHHHHHHHHhcCCeeeecccceeeeccccccccccchhccccccceee
Confidence 5899999999999999999999999955433333333333333 356788999999999989888776666666666666
Q ss_pred HHHHHHHHH
Q 021577 289 LHLLKKACN 297 (310)
Q Consensus 289 L~vlkk~c~ 297 (310)
.++.++++.
T Consensus 326 ~~a~~~~~~ 334 (491)
T PF00680_consen 326 RYAWRKLYP 334 (491)
T ss_dssp HHHHHHHST
T ss_pred chhhhhccc
Confidence 666666543
No 14
>cd04338 Rieske_RO_Alpha_Tic55 Tic55 is a 55kDa LLS1-related non-heme iron oxygenase associated with protein transport through the plant inner chloroplast membrane. This domain represents the N-terminal Rieske domain of the Tic55 oxygenase alpha subunit. Tic55 is closely related to the oxygenase alpha subunits of a small subfamily of enzymes found in plants as well as oxygenic cyanobacterial photosynthesizers including LLS1 (lethal leaf spot 1, also known as PaO), Ptc52, and ACD1 (accelerated cell death 1). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis.
Probab=20.21 E-value=35 Score=28.01 Aligned_cols=13 Identities=23% Similarity=0.508 Sum_probs=10.0
Q ss_pred CCccCCcceecCC
Q 021577 35 DPINCPYHYYCDS 47 (310)
Q Consensus 35 D~InCPYHYyCDs 47 (310)
+.|.||||-.+=+
T Consensus 74 ~~i~CP~Hgw~Fd 86 (134)
T cd04338 74 GKLECLYHGWQFG 86 (134)
T ss_pred CEEEccCCCCEEC
Confidence 4799999986643
No 15
>cd03474 Rieske_T4moC Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). T4moC contains a Rieske domain and functions as an obligate electron carrier between T4moF and T4moH. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.
Probab=20.17 E-value=33 Score=26.31 Aligned_cols=11 Identities=18% Similarity=0.537 Sum_probs=9.2
Q ss_pred CCccCCcceec
Q 021577 35 DPINCPYHYYC 45 (310)
Q Consensus 35 D~InCPYHYyC 45 (310)
+.|.||||...
T Consensus 57 ~~i~CP~Hg~~ 67 (108)
T cd03474 57 GVLTCRAHLWQ 67 (108)
T ss_pred CEEEeCCcCCE
Confidence 57999999865
Done!