Query 025164
Match_columns 257
No_of_seqs 96 out of 105
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 03:16:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025164.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025164hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06485 DUF1092: Protein of u 100.0 7.1E-74 1.5E-78 520.2 15.7 152 101-253 1-152 (270)
2 PF00665 rve: Integrase core d 97.1 0.0026 5.6E-08 48.0 7.6 92 99-192 7-100 (120)
3 COG3607 Predicted lactoylgluta 72.7 2.2 4.8E-05 36.7 1.7 31 89-127 100-130 (133)
4 PHA02517 putative transposase 58.7 48 0.001 29.3 7.4 86 98-192 110-202 (277)
5 PF07058 Myosin_HC-like: Myosi 42.6 14 0.0003 36.1 1.6 55 148-203 45-117 (351)
6 COG0191 Fba Fructose/tagatose 34.2 89 0.0019 29.9 5.4 47 139-188 24-79 (286)
7 PF06363 Picorna_P3A: Picornav 30.5 32 0.0007 28.4 1.6 36 143-182 14-49 (100)
8 cd08494 PBP2_NikA_DppA_OppA_li 29.9 99 0.0021 28.7 4.9 50 152-203 305-360 (448)
9 PRK14031 glutamate dehydrogena 27.1 1.3E+02 0.0029 30.2 5.5 108 107-214 60-189 (444)
10 cd00995 PBP2_NikA_DppA_OppA_li 25.1 1.4E+02 0.003 27.5 5.0 43 152-194 310-361 (466)
11 PRK04191 rps3p 30S ribosomal p 24.2 1.1E+02 0.0024 27.4 4.0 51 137-195 86-138 (207)
12 PF09026 CENP-B_dimeris: Centr 23.1 28 0.0006 28.9 0.0 6 50-55 3-8 (101)
13 PF11332 DUF3134: Protein of u 22.8 52 0.0011 25.7 1.5 21 183-203 11-31 (73)
14 PTZ00084 40S ribosomal protein 22.8 1.3E+02 0.0029 27.6 4.3 50 137-194 92-143 (220)
15 PRK09409 IS2 transposase TnpB; 22.1 5.9E+02 0.013 23.6 8.4 91 99-192 127-224 (301)
16 TIGR02423 protocat_alph protoc 21.7 1.6E+02 0.0034 26.3 4.5 43 98-140 59-109 (193)
17 TIGR01008 rpsC_E_A ribosomal p 21.6 1.5E+02 0.0033 26.6 4.4 51 137-195 84-136 (195)
18 PHA02696 hypothetical protein; 20.7 70 0.0015 25.3 1.8 21 190-214 17-37 (79)
19 CHL00048 rps3 ribosomal protei 20.6 1.5E+02 0.0032 26.9 4.1 54 134-195 111-166 (214)
20 PRK11608 pspF phage shock prot 20.3 1.2E+02 0.0025 28.4 3.5 21 176-202 302-322 (326)
21 PF12513 SUV3_C: Mitochondrial 20.1 44 0.00095 23.3 0.5 19 192-210 9-27 (49)
No 1
>PF06485 DUF1092: Protein of unknown function (DUF1092); InterPro: IPR009472 This family consists of several hypothetical proteins of unknown function all from photosynthetic organisms including plants and cyanobacteria.
Probab=100.00 E-value=7.1e-74 Score=520.23 Aligned_cols=152 Identities=54% Similarity=0.944 Sum_probs=149.1
Q ss_pred ccccccccccccCCCceeEEEEEeeCCCceEEEecCCCCCCCHHHHHHHHHHHHhhcCCCCCCeeeeeHHHHHHHHHHHH
Q 025164 101 WELDFCSRPILDIRGKKIWELVVCDGSLSLQYTKYFPNNVINSITLKEAIVAICDDLGVPIPEKIRFFRSQMQTIITKAC 180 (257)
Q Consensus 101 WELDFYSRPilD~~GKKlWELLICDs~~~F~y~~~CP~s~VNS~WL~~AL~~Ai~~~~~~~P~~IRfFR~QM~nmI~kAc 180 (257)
||||||||||+|++|||+|||||||++++|+|+++||||+|||+||++||++|+++ |+.+|++|||||+||+|||++||
T Consensus 1 WElDFYsRPi~d~~gkk~WELLIcd~~~~f~~~~~cP~~~vNS~wL~~al~~a~~~-~~~~P~~Ir~FR~qm~~mI~~A~ 79 (270)
T PF06485_consen 1 WELDFYSRPILDENGKKLWELLICDSPGSFRYAKFCPNSEVNSIWLRQALEEAIDQ-GGEKPDRIRFFRSQMLNMITKAC 79 (270)
T ss_pred CccccccCcccCCCCCeeEEEEEEcCCCCEEEEEeCCCCccCHHHHHHHHHHHHHh-cCCCCcEEEEEhHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999996 77999999999999999999999
Q ss_pred hhCCCccccccchHHHHHHHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCCCcccCCCeeEEeeecCCceee
Q 025164 181 KELDIKPIPSKRCLSLLLWLEERYETVYTRHPGFQKGSKPLLALDNPFPMELPDNLFGDKWAFVQLPFSGEGL 253 (257)
Q Consensus 181 ~eLgI~v~PSRRT~AL~~WLeERy~~vYp~~pGy~~~~~~p~~ld~p~P~PLPDaL~GEkWaFvsLpa~~l~~ 253 (257)
++|||+++||||||||++||+||+++|||+|+||++++++++++++++|+|||||||||+|+||+||+++|.-
T Consensus 80 ~~lgI~~~pSRRt~aL~~wL~eR~~~vYp~~~gy~~~~~~~~~~~~~~P~pLPdaL~Ge~W~FvsLp~~~l~e 152 (270)
T PF06485_consen 80 EELGIPVEPSRRTYALKQWLEEREEEVYPQEPGYQPGAPPPVALDPPPPQPLPDALRGEKWAFVSLPAGDLRE 152 (270)
T ss_pred HHCCCceeecccHHHHHHHHHHHHHHhCcCCCCCCCCCCCccccCCCCCCCCChhhCCCceEEEEccHHHHHh
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999864
No 2
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=97.13 E-value=0.0026 Score=47.95 Aligned_cols=92 Identities=24% Similarity=0.321 Sum_probs=72.0
Q ss_pred ccccccccccccccCCCceeEEEEEeeCCCceEEEecCCCCCCCHHHHHHHHHHHHhhcCCCCCCeeeeeHHHHHH--HH
Q 025164 99 TEWELDFCSRPILDIRGKKIWELVVCDGSLSLQYTKYFPNNVINSITLKEAIVAICDDLGVPIPEKIRFFRSQMQT--II 176 (257)
Q Consensus 99 ~iWELDFYSRPilD~~GKKlWELLICDs~~~F~y~~~CP~s~VNS~WL~~AL~~Ai~~~~~~~P~~IRfFR~QM~n--mI 176 (257)
..|++||+.-++.+.+| +.|=+++.|.-+.+.+...++.. -++..+...|..++...|+..|..|+.=+..-+. .+
T Consensus 7 ~~~~~D~~~~~~~~~~~-~~~~~~~iD~~S~~~~~~~~~~~-~~~~~~~~~l~~~~~~~~~~~p~~i~tD~g~~f~~~~~ 84 (120)
T PF00665_consen 7 ERWQIDFTPMPIPDKGG-RVYLLVFIDDYSRFIYAFPVSSK-ETAEAALRALKRAIEKRGGRPPRVIRTDNGSEFTSHAF 84 (120)
T ss_dssp TEEEEEEEEETGGCTT--CEEEEEEEETTTTEEEEEEESSS-SHHHHHHHHHHHHHHHHS-SE-SEEEEESCHHHHSHHH
T ss_pred CEEEEeeEEEecCCCCc-cEEEEEEEECCCCcEEEEEeecc-cccccccccccccccccccccceecccccccccccchh
Confidence 58999999444444444 79999999999999999999988 6777888999999988765449999987766555 88
Q ss_pred HHHHhhCCCccccccc
Q 025164 177 TKACKELDIKPIPSKR 192 (257)
Q Consensus 177 ~kAc~eLgI~v~PSRR 192 (257)
+..|+++||.+..++.
T Consensus 85 ~~~~~~~~i~~~~~~~ 100 (120)
T PF00665_consen 85 EAWCKHLGIKHVFTPP 100 (120)
T ss_dssp HHHHHHHT-EEEESST
T ss_pred hhHHHHcCceEeeCCC
Confidence 9999999999988774
No 3
>COG3607 Predicted lactoylglutathione lyase [General function prediction only]
Probab=72.72 E-value=2.2 Score=36.68 Aligned_cols=31 Identities=26% Similarity=0.476 Sum_probs=25.2
Q ss_pred cCCCCCccccccccccccccccccCCCceeEEEEEeeCC
Q 025164 89 LDEETDPESITEWELDFCSRPILDIRGKKIWELVVCDGS 127 (257)
Q Consensus 89 ~~~~~~~~~m~iWELDFYSRPilD~~GKKlWELLICDs~ 127 (257)
.+|..|-.. +|+|-.+|.+|. +||++.||..
T Consensus 100 ~~~~~d~gf-------MYg~~fqDpDGh-~wE~l~m~~~ 130 (133)
T COG3607 100 ANEPQDEGF-------MYGRSFQDPDGH-VWEFLWMDPE 130 (133)
T ss_pred CCCcccccc-------ccceeeeCCCCC-eEEEEEeCHH
Confidence 455556554 799999999999 9999999964
No 4
>PHA02517 putative transposase OrfB; Reviewed
Probab=58.69 E-value=48 Score=29.30 Aligned_cols=86 Identities=16% Similarity=0.137 Sum_probs=54.0
Q ss_pred cccccccccccccccCCCceeEEEEEeeCCCceEEEecCCCCCCCHHHHHHHHHHHHhhcCCCCCCe--ee-----eeHH
Q 025164 98 ITEWELDFCSRPILDIRGKKIWELVVCDGSLSLQYTKYFPNNVINSITLKEAIVAICDDLGVPIPEK--IR-----FFRS 170 (257)
Q Consensus 98 m~iWELDFYSRPilD~~GKKlWELLICDs~~~F~y~~~CP~s~VNS~WL~~AL~~Ai~~~~~~~P~~--IR-----fFR~ 170 (257)
..+|+.||-.=++ .+| +.+=..|-|.-+.+... +.-....|+.+..++|+.|+...|. |.. |+ -|.+
T Consensus 110 n~~w~~D~t~~~~--~~g-~~yl~~iiD~~sr~i~~-~~~~~~~~~~~~~~~l~~a~~~~~~--~~~~i~~sD~G~~y~s 183 (277)
T PHA02517 110 NQLWVADFTYVST--WQG-WVYVAFIIDVFARRIVG-WRVSSSMDTDFVLDALEQALWARGR--PGGLIHHSDKGSQYVS 183 (277)
T ss_pred CCeEEeceeEEEe--CCC-CEEEEEecccCCCeeee-cccCCCCChHHHHHHHHHHHHhcCC--CcCcEeecccccccch
Confidence 3689999865332 234 46655555644333332 2234457888999999999987543 432 22 2333
Q ss_pred HHHHHHHHHHhhCCCccccccc
Q 025164 171 QMQTIITKACKELDIKPIPSKR 192 (257)
Q Consensus 171 QM~nmI~kAc~eLgI~v~PSRR 192 (257)
.-++.+|+++||....++.
T Consensus 184 ---~~~~~~~~~~gi~~~~~~~ 202 (277)
T PHA02517 184 ---LAYTQRLKEAGIRASTGSR 202 (277)
T ss_pred ---HHHHHHHHHcCcccccCCC
Confidence 3577899999999887765
No 5
>PF07058 Myosin_HC-like: Myosin II heavy chain-like; InterPro: IPR009768 This family represents a conserved region within a number of myosin II heavy chain-like proteins that seem to be specific to Arabidopsis thaliana.
Probab=42.63 E-value=14 Score=36.10 Aligned_cols=55 Identities=18% Similarity=0.284 Sum_probs=36.3
Q ss_pred HHHHHHHhhcCCCCCCeeeeeHHHHHHHHHHH----HhhCCCcccccc--------------chHHHHHHHHHH
Q 025164 148 EAIVAICDDLGVPIPEKIRFFRSQMQTIITKA----CKELDIKPIPSK--------------RCLSLLLWLEER 203 (257)
Q Consensus 148 ~AL~~Ai~~~~~~~P~~IRfFR~QM~nmI~kA----c~eLgI~v~PSR--------------RT~AL~~WLeER 203 (257)
..|++||- +||..-..+|+|++|..-|-..- .+=...+|...| ..--.+|||+||
T Consensus 45 ~ELEEaiL-agGaaaNavrdYqrq~~elneEkrtLeRELARaKV~aNRVA~vvANEWKD~nDkvMPVKqWLEER 117 (351)
T PF07058_consen 45 RELEEAIL-AGGAAANAVRDYQRQVQELNEEKRTLERELARAKVSANRVATVVANEWKDENDKVMPVKQWLEER 117 (351)
T ss_pred HHHHHHHH-hcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhcccccccCCccccHHHHHHHH
Confidence 45677776 56678899999999998875421 111223444443 344578999988
No 6
>COG0191 Fba Fructose/tagatose bisphosphate aldolase [Carbohydrate transport and metabolism]
Probab=34.19 E-value=89 Score=29.95 Aligned_cols=47 Identities=17% Similarity=0.260 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCCeeeeeHH---------HHHHHHHHHHhhCCCccc
Q 025164 139 NVINSITLKEAIVAICDDLGVPIPEKIRFFRS---------QMQTIITKACKELDIKPI 188 (257)
Q Consensus 139 s~VNS~WL~~AL~~Ai~~~~~~~P~~IRfFR~---------QM~nmI~kAc~eLgI~v~ 188 (257)
|-.|+.|++..|+.|-+. .+|-.|++=+. ....||...+++.+|+|.
T Consensus 24 N~~nlE~~~AileaA~e~---~sPvIiq~S~g~~~y~gg~~~~~~~v~~~a~~~~vPV~ 79 (286)
T COG0191 24 NINNLETLQAILEAAEEE---KSPVIIQFSEGAAKYAGGADSLAHMVKALAEKYGVPVA 79 (286)
T ss_pred eecCHHHHHHHHHHHHHh---CCCEEEEecccHHHHhchHHHHHHHHHHHHHHCCCCEE
Confidence 567999999999977775 67999988543 445688999999999985
No 7
>PF06363 Picorna_P3A: Picornaviridae P3A protein; InterPro: IPR009419 The viral polyprotein of parechoviruses contains: coat protein VP0 (P1AB); coat protein VP3 (P1C); coat protein VP1 (P1D); picornain 2A (3.4.22.29 from EC, core protein P2A); core protein P2B; core protein P2C; core protein P3A; genome-linked protein VPg (P3B); picornain 3C (3.4.22.28 from EC, MEROPS peptidase subfamily 3CF: parechovirus picornain 3C (P3C))[]. This entry consists of the parechovirus P3A protein. P3A has been identified as a genome-linked protein (VPg), which is involved in replication [].; GO: 0019012 virion
Probab=30.46 E-value=32 Score=28.40 Aligned_cols=36 Identities=33% Similarity=0.510 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhhcCCCCCCeeeeeHHHHHHHHHHHHhh
Q 025164 143 SITLKEAIVAICDDLGVPIPEKIRFFRSQMQTIITKACKE 182 (257)
Q Consensus 143 S~WL~~AL~~Ai~~~~~~~P~~IRfFR~QM~nmI~kAc~e 182 (257)
-..|++|++..|+ +.|....||-....+.+.+||++
T Consensus 14 ~s~LIEqiE~~i~----P~~S~F~CFa~~~~~~~~~a~~k 49 (100)
T PF06363_consen 14 MSELIEQIEAFIE----PRPSVFKCFASKVPTKIKTACDK 49 (100)
T ss_pred HHHHHHHHHHHHC----CCCChHHHHHhcccchhHHHHHH
Confidence 4578899998888 56999999998888888888876
No 8
>cd08494 PBP2_NikA_DppA_OppA_like_6 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=29.88 E-value=99 Score=28.68 Aligned_cols=50 Identities=14% Similarity=0.220 Sum_probs=33.4
Q ss_pred HHHhhcCCCCCCeeee------eHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHH
Q 025164 152 AICDDLGVPIPEKIRF------FRSQMQTIITKACKELDIKPIPSKRCLSLLLWLEER 203 (257)
Q Consensus 152 ~Ai~~~~~~~P~~IRf------FR~QM~nmI~kAc~eLgI~v~PSRRT~AL~~WLeER 203 (257)
+.++++|+..+..|.+ ++.+|..+|+..++++||++.---.. -..|+...
T Consensus 305 ~lL~~aG~~~g~~l~l~~~~~~~~~~~a~~i~~~l~~~GI~v~i~~~~--~~~~~~~~ 360 (448)
T cd08494 305 QLLAEAGAAYGLTLTLTLPPLPYARRIGEIIASQLAEVGITVKIEVVE--PATWLQRV 360 (448)
T ss_pred HHHHHcCCCCCeEEEEEecCCcchhHHHHHHHHHHHhcCcEEEEEEee--HHHHHHHh
Confidence 3455566654445554 57889999999999999998763333 33455443
No 9
>PRK14031 glutamate dehydrogenase; Provisional
Probab=27.10 E-value=1.3e+02 Score=30.18 Aligned_cols=108 Identities=11% Similarity=0.125 Sum_probs=74.2
Q ss_pred ccccccCCCc----eeEEEEEeeCC----CceEEEecCCCCCCCHHHHHHHHHHHHhh--cCCCC------C------Ce
Q 025164 107 SRPILDIRGK----KIWELVVCDGS----LSLQYTKYFPNNVINSITLKEAIVAICDD--LGVPI------P------EK 164 (257)
Q Consensus 107 SRPilD~~GK----KlWELLICDs~----~~F~y~~~CP~s~VNS~WL~~AL~~Ai~~--~~~~~------P------~~ 164 (257)
+-|+.+++|+ +-|.+.=++.- +.+||...+-..+|-..=+---++-|+.. .||.+ | +.
T Consensus 60 ~~p~~~d~g~~~~~~gyRvqhn~~lGP~kGGiR~~p~v~~~~v~aLa~~MT~K~Al~~lP~GGgKggi~~dP~~~s~~El 139 (444)
T PRK14031 60 RVTWVDDKGNVQTNMGYRVQHNNAIGPYKGGIRFHASVNLGILKFLAFEQTFKNSLTTLPMGGGKGGSDFSPRGKSNAEV 139 (444)
T ss_pred EEEEEECCCCEEEEeeEEEEecCCCcCCCCCeeecCCCCHHHHHHHHHHHHHHHHHcCCCCCCceeeeeCCCCCCCHHHH
Confidence 5588889997 88998877766 78999774333333222222233334432 22222 4 34
Q ss_pred eeeeHHHHHHHHHHHHhhCCCccccccchHHHHHHHHHHhhhhccCCCCC
Q 025164 165 IRFFRSQMQTIITKACKELDIKPIPSKRCLSLLLWLEERYETVYTRHPGF 214 (257)
Q Consensus 165 IRfFR~QM~nmI~kAc~eLgI~v~PSRRT~AL~~WLeERy~~vYp~~pGy 214 (257)
-|++|+-|..|-..-+-+.+|++.=.-=...-+.|+.+-|..+.++.+|.
T Consensus 140 er~~r~f~~~L~~~iGp~~dipApDvgt~~~~M~~i~d~y~~~~~~~~g~ 189 (444)
T PRK14031 140 MRFCQAFMLELWRHIGPETDVPAGDIGVGGREVGFMFGMYKKLSHEFTGT 189 (444)
T ss_pred HHHHHHHHHHHHhccCCCCccCccccCCCHHHHHHHHHHHHhhcCCcceE
Confidence 89999999999988788888988877777889999999988776665543
No 10
>cd00995 PBP2_NikA_DppA_OppA_like The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is inv
Probab=25.09 E-value=1.4e+02 Score=27.46 Aligned_cols=43 Identities=16% Similarity=0.146 Sum_probs=30.8
Q ss_pred HHHhhcCCCC--CCeeee-------eHHHHHHHHHHHHhhCCCccccccchH
Q 025164 152 AICDDLGVPI--PEKIRF-------FRSQMQTIITKACKELDIKPIPSKRCL 194 (257)
Q Consensus 152 ~Ai~~~~~~~--P~~IRf-------FR~QM~nmI~kAc~eLgI~v~PSRRT~ 194 (257)
+.++++|+.. |-.|++ -+.+|..+|+..++++||++.-.....
T Consensus 310 ~lL~~ag~~~~~~~~l~l~~~~~~~~~~~~a~~i~~~l~~~Gi~v~~~~~~~ 361 (466)
T cd00995 310 ELLAEAGYKDGKGLELTLLYNSDGPTRKEIAEAIQAQLKEIGIKVEIEPLDF 361 (466)
T ss_pred HHHHHhCCCCCCceEEEEEeCCCCCcHHHHHHHHHHHHHHcCceEEEEEech
Confidence 3445566644 556665 467889999999999999998755543
No 11
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=24.15 E-value=1.1e+02 Score=27.39 Aligned_cols=51 Identities=16% Similarity=0.195 Sum_probs=37.9
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCeeeeeHHHHHHHHHHHHhh--CCCccccccchHH
Q 025164 137 PNNVINSITLKEAIVAICDDLGVPIPEKIRFFRSQMQTIITKACKE--LDIKPIPSKRCLS 195 (257)
Q Consensus 137 P~s~VNS~WL~~AL~~Ai~~~~~~~P~~IRfFR~QM~nmI~kAc~e--LgI~v~PSRRT~A 195 (257)
.+...|..=+.+-|...++. ++ .||+.|+..|++|-+. .||+++-|-|=-.
T Consensus 86 ~~p~~~a~~vA~~ia~qLe~-------r~-~fRra~k~~i~~~~~agakGiki~iSGrL~G 138 (207)
T PRK04191 86 ENPELNARVVAFRLANALER-------GW-HFRRAAHSAIRRIMEAGALGVEIIISGKLTG 138 (207)
T ss_pred eCCCcCHHHHHHHHHHHHHc-------cc-hHHHHHHHHHHHHHHcCCeeEEEEEccccch
Confidence 33455666677777766664 23 4999999999998765 8999999998655
No 12
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=23.08 E-value=28 Score=28.91 Aligned_cols=6 Identities=33% Similarity=0.429 Sum_probs=0.0
Q ss_pred eeeccC
Q 025164 50 QHFRPR 55 (257)
Q Consensus 50 ~~~~~~ 55 (257)
+||.-.
T Consensus 3 ~~~~eg 8 (101)
T PF09026_consen 3 LHFLEG 8 (101)
T ss_dssp ------
T ss_pred eeeccc
Confidence 466543
No 13
>PF11332 DUF3134: Protein of unknown function (DUF3134); InterPro: IPR021481 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=22.84 E-value=52 Score=25.66 Aligned_cols=21 Identities=43% Similarity=0.502 Sum_probs=18.3
Q ss_pred CCCccccccchHHHHHHHHHH
Q 025164 183 LDIKPIPSKRCLSLLLWLEER 203 (257)
Q Consensus 183 LgI~v~PSRRT~AL~~WLeER 203 (257)
-...|+|.|+-.+|..||+.-
T Consensus 11 q~a~VIpl~~e~SlLdWLe~t 31 (73)
T PF11332_consen 11 QPAPVIPLKQESSLLDWLEST 31 (73)
T ss_pred CCCCeecCCCccHHHHHHHHc
Confidence 346799999999999999986
No 14
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=22.82 E-value=1.3e+02 Score=27.58 Aligned_cols=50 Identities=12% Similarity=0.088 Sum_probs=37.3
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCeeeeeHHHHHHHHHHHHhh--CCCccccccchH
Q 025164 137 PNNVINSITLKEAIVAICDDLGVPIPEKIRFFRSQMQTIITKACKE--LDIKPIPSKRCL 194 (257)
Q Consensus 137 P~s~VNS~WL~~AL~~Ai~~~~~~~P~~IRfFR~QM~nmI~kAc~e--LgI~v~PSRRT~ 194 (257)
.+.+.|..=+++-|...++. ++ .||+.|...|++|-+. .||+++-|-|=-
T Consensus 92 ~~P~l~A~lvA~~IA~qLe~-rv-------~FRRa~k~ai~~~m~aGakGikI~iSGRL~ 143 (220)
T PTZ00084 92 ENRGLCAMAQAESLRYKLLE-GL-------PVRRAAYGVLRHVMESGAKGCEVIVSGKLR 143 (220)
T ss_pred cCCCcCHHHHHHHHHHHHHh-cC-------cHHHHHHHHHHHHHHcCCceEEEEEccchh
Confidence 44556666666666666663 22 4999999999998776 899999999865
No 15
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=22.14 E-value=5.9e+02 Score=23.62 Aligned_cols=91 Identities=12% Similarity=0.075 Sum_probs=56.3
Q ss_pred ccccccccccccccCCCceeEEEEEeeCCCceEEEecCCCCC-CCHHHHHHHHHHHHhhc-CC---CCCCeeeeeHH-HH
Q 025164 99 TEWELDFCSRPILDIRGKKIWELVVCDGSLSLQYTKYFPNNV-INSITLKEAIVAICDDL-GV---PIPEKIRFFRS-QM 172 (257)
Q Consensus 99 ~iWELDFYSRPilD~~GKKlWELLICDs~~~F~y~~~CP~s~-VNS~WL~~AL~~Ai~~~-~~---~~P~~IRfFR~-QM 172 (257)
..|-.||---+ -.+|+++.=.+|-|-=+.... .+..+.. .++.-..++|+.|+... |. ..|-.|.-=|. |.
T Consensus 127 ~~W~tDiT~~~--~~~g~~~Yl~~ViD~~sR~iv-g~~~s~~~~~~~~v~~~l~~a~~~~~~~~~~~~~~iihSDrGsqy 203 (301)
T PRK09409 127 QRWCSDGFEFC--CDNGERLRVTFALDCCDREAL-HWAVTTGGFNSETVQDVMLGAVERRFGNDLPSSPVEWLTDNGSCY 203 (301)
T ss_pred CEEEeeeEEEE--eCCCCEEEEEEEeecccceEE-EEEeccCCCCHHHHHHHHHHHHHHHhccCCCCCCcEEecCCCccc
Confidence 69999975533 347888888888886543332 2233333 45656678888888764 21 23445554443 22
Q ss_pred -HHHHHHHHhhCCCccccccc
Q 025164 173 -QTIITKACKELDIKPIPSKR 192 (257)
Q Consensus 173 -~nmI~kAc~eLgI~v~PSRR 192 (257)
..-....|+++||...-||+
T Consensus 204 ~s~~~~~~l~~~gI~~Smsr~ 224 (301)
T PRK09409 204 RANETRQFARMLGLEPKNTAV 224 (301)
T ss_pred ccHHHHHHHHHcCCeEeeCCC
Confidence 22467888999999888875
No 16
>TIGR02423 protocat_alph protocatechuate 3,4-dioxygenase, alpha subunit. This model represents the alpha chain of protocatechuate 3,4-dioxygenase. The most closely related family outside this family is that of the beta chain (TIGR02422), typically encoded in an adjacent locus. This enzyme acts in the degradation of aromatic compounds by way of p-hydroxybenzoate to succinate and acetyl-CoA.
Probab=21.66 E-value=1.6e+02 Score=26.30 Aligned_cols=43 Identities=23% Similarity=0.336 Sum_probs=33.5
Q ss_pred ccccccc---cccccc-----ccCCCceeEEEEEeeCCCceEEEecCCCCC
Q 025164 98 ITEWELD---FCSRPI-----LDIRGKKIWELVVCDGSLSLQYTKYFPNNV 140 (257)
Q Consensus 98 m~iWELD---FYSRPi-----lD~~GKKlWELLICDs~~~F~y~~~CP~s~ 140 (257)
+.+||.| .|+..- .+..+-..|--+++|..+.|+|....|..-
T Consensus 59 VeiWqad~~G~Y~~~~~~~~~~~~~~f~grGr~~Td~~G~y~f~TI~Pg~Y 109 (193)
T TIGR02423 59 IEIWQADAAGRYNSPADLRAPATDPGFRGWGRTGTDESGEFTFETVKPGAV 109 (193)
T ss_pred EEEEccCCCCccCCccCCcccccCCCCCCeEEEEECCCCCEEEEEEcCCCc
Confidence 6899998 788642 123355678889999999999999999843
No 17
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=21.56 E-value=1.5e+02 Score=26.63 Aligned_cols=51 Identities=16% Similarity=0.171 Sum_probs=38.9
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCeeeeeHHHHHHHHHHHHhh--CCCccccccchHH
Q 025164 137 PNNVINSITLKEAIVAICDDLGVPIPEKIRFFRSQMQTIITKACKE--LDIKPIPSKRCLS 195 (257)
Q Consensus 137 P~s~VNS~WL~~AL~~Ai~~~~~~~P~~IRfFR~QM~nmI~kAc~e--LgI~v~PSRRT~A 195 (257)
.+.+.|..=+++.|...++. ++ .||+.|...|++|-+. .||+++-|-|=-.
T Consensus 84 ~~p~l~A~lvA~~Ia~qLe~-------rv-~fRra~k~ai~~~m~aGakGikI~iSGRL~G 136 (195)
T TIGR01008 84 ENPELNAQVQAERIARSLER-------GL-HFRRAAYTAVRRIMEAGAKGVEVTISGKLTG 136 (195)
T ss_pred eCCCcCHHHHHHHHHHHHHc-------cc-cHHHHHHHHHHHHHHcCCceEEEEEcccccc
Confidence 34566666677777777774 22 5999999999988765 8999999998655
No 18
>PHA02696 hypothetical protein; Provisional
Probab=20.74 E-value=70 Score=25.32 Aligned_cols=21 Identities=38% Similarity=0.909 Sum_probs=17.0
Q ss_pred ccchHHHHHHHHHHhhhhccCCCCC
Q 025164 190 SKRCLSLLLWLEERYETVYTRHPGF 214 (257)
Q Consensus 190 SRRT~AL~~WLeERy~~vYp~~pGy 214 (257)
-||.-.|-.||.+| ...+|||
T Consensus 17 aRRVr~Lc~~lRrr----v~r~~gY 37 (79)
T PHA02696 17 ARRVRRLCIWLRRR----VGREPGY 37 (79)
T ss_pred HHHHHHHHHHHHHH----hcCCCce
Confidence 48899999999999 3556777
No 19
>CHL00048 rps3 ribosomal protein S3
Probab=20.64 E-value=1.5e+02 Score=26.90 Aligned_cols=54 Identities=26% Similarity=0.130 Sum_probs=42.0
Q ss_pred ecCCCCCCCHHHHHHHHHHHHhhcCCCCCCeeeeeHHHHHHHHHHHHhh--CCCccccccchHH
Q 025164 134 KYFPNNVINSITLKEAIVAICDDLGVPIPEKIRFFRSQMQTIITKACKE--LDIKPIPSKRCLS 195 (257)
Q Consensus 134 ~~CP~s~VNS~WL~~AL~~Ai~~~~~~~P~~IRfFR~QM~nmI~kAc~e--LgI~v~PSRRT~A 195 (257)
.--.+...|+.-+.+-|...++. +. .||+.|..+|+++-+. .||+++-|-|=-.
T Consensus 111 ~ev~~p~~~A~~iA~~ia~~Le~-r~-------~fRra~~~~i~~~~~~ga~GikI~iSGRL~G 166 (214)
T CHL00048 111 TEVKKPYGEPNILAEYIAGQLEN-RV-------SFRKAMKKAIELAEKADIKGIKIQISGRLNG 166 (214)
T ss_pred EEecCCCcCHHHHHHHHHHHHhc-Ch-------hHHHHHHHHHHHHHHhCCcEEEEEEecccCc
Confidence 34455688999999999988885 22 3999999999876554 8899999988543
No 20
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=20.33 E-value=1.2e+02 Score=28.35 Aligned_cols=21 Identities=19% Similarity=0.208 Sum_probs=17.2
Q ss_pred HHHHHhhCCCccccccchHHHHHHHHH
Q 025164 176 ITKACKELDIKPIPSKRCLSLLLWLEE 202 (257)
Q Consensus 176 I~kAc~eLgI~v~PSRRT~AL~~WLeE 202 (257)
+++|++.||| ||.| |+++|++
T Consensus 302 ~~~aA~~LGI----sR~t--Lyrklk~ 322 (326)
T PRK11608 302 QKRAAELLGL----TYHQ--LRALLKK 322 (326)
T ss_pred HHHHHHHhCC----CHHH--HHHHHHH
Confidence 7899999999 7777 7777764
No 21
>PF12513 SUV3_C: Mitochondrial degradasome RNA helicase subunit C terminal; InterPro: IPR022192 This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with PF00271 from PFAM. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 3RC8_A 3RC3_A.
Probab=20.07 E-value=44 Score=23.28 Aligned_cols=19 Identities=37% Similarity=0.850 Sum_probs=15.0
Q ss_pred chHHHHHHHHHHhhhhccC
Q 025164 192 RCLSLLLWLEERYETVYTR 210 (257)
Q Consensus 192 RT~AL~~WLeERy~~vYp~ 210 (257)
+...|+-||..|++++|+.
T Consensus 9 k~l~lYlWLs~Rfp~~F~d 27 (49)
T PF12513_consen 9 KVLDLYLWLSYRFPDVFPD 27 (49)
T ss_dssp HHHHHHHHHHCC-TTTSTT
T ss_pred HHHHHHHHHHHHcccccCC
Confidence 4678999999999888865
Done!