Query gi|254781203|ref|YP_003065616.1| hypothetical protein CLIBASIA_05550 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 478
No_of_seqs 6 out of 8
Neff 1.7
Searched_HMMs 39220
Date Mon May 30 06:35:44 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781203.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02955 TMAO_TorT TMAO reduc 70.3 0.38 9.6E-06 26.6 -2.6 68 187-254 16-94 (304)
2 pfam03518 consensus 64.2 11 0.00028 17.8 8.0 118 61-189 157-312 (349)
3 KOG1709 consensus 54.4 5.3 0.00014 19.7 0.9 61 116-193 53-113 (271)
4 PRK08211 hypothetical protein; 53.4 17 0.00042 16.6 3.9 135 151-303 237-382 (653)
5 PRK09867 hypothetical protein; 53.1 7.7 0.0002 18.7 1.6 48 197-244 153-205 (209)
6 PRK10037 cell division protein 50.0 11 0.00028 17.7 1.9 107 169-284 11-141 (250)
7 PRK05201 hslU ATP-dependent pr 42.5 5.1 0.00013 19.7 -0.7 21 31-54 58-79 (442)
8 pfam01542 HCV_core Hepatitis C 40.9 11 0.00027 17.8 0.7 48 98-151 5-53 (75)
9 KOG0759 consensus 40.4 27 0.00068 15.4 2.9 35 231-265 108-142 (286)
10 pfam04065 Not3 Not1 N-terminal 39.7 16 0.0004 16.8 1.4 12 464-475 202-213 (233)
11 PHA00451 protein kinase 38.7 28 0.00072 15.2 3.0 89 197-288 155-244 (364)
12 pfam05461 ApoL Apolipoprotein 37.4 30 0.00075 15.1 2.6 80 52-131 59-147 (313)
13 KOG2385 consensus 36.9 19 0.00049 16.2 1.5 26 143-168 218-243 (633)
14 KOG1019 consensus 36.1 21 0.00055 16.0 1.7 33 402-434 558-590 (837)
15 pfam12157 DUF3591 Protein of u 32.4 33 0.00084 14.8 2.1 14 89-102 115-128 (457)
16 PRK05342 clpX ATP-dependent pr 29.8 12 0.0003 17.6 -0.6 17 86-102 69-85 (411)
17 KOG2150 consensus 29.7 29 0.00074 15.1 1.5 65 356-420 418-491 (575)
18 TIGR00160 MGSA methylglyoxal s 29.6 18 0.00045 16.5 0.4 35 92-130 34-68 (143)
19 COG4294 Uve UV damage repair e 29.1 16 0.00041 16.7 0.1 130 199-341 146-294 (347)
20 COG1970 MscL Large-conductance 25.3 40 0.001 14.3 1.5 41 206-249 6-46 (130)
21 cd02016 TPP_E1_OGDC_like Thiam 24.7 20 0.0005 16.2 -0.1 132 176-313 30-183 (265)
22 TIGR01793 cit_synth_euk citrat 24.5 40 0.001 14.3 1.4 31 125-156 141-171 (430)
23 pfam10478 consensus 24.0 50 0.0013 13.7 1.9 24 108-131 119-142 (575)
24 TIGR00405 L26e_arch ribosomal 23.2 28 0.00071 15.3 0.4 34 359-392 76-112 (151)
25 COG0278 Glutaredoxin-related p 21.7 34 0.00086 14.8 0.6 16 3-18 51-66 (105)
26 COG5209 RCD1 Uncharacterized p 21.2 57 0.0015 13.3 4.1 10 45-54 93-102 (315)
27 TIGR00681 kdpC K+-transporting 21.0 58 0.0015 13.3 1.7 37 4-40 91-135 (193)
28 TIGR00154 ispE 4-diphosphocyti 20.2 59 0.0015 13.3 1.6 15 440-454 291-305 (322)
29 pfam10225 DUF2215 Uncharacteri 20.0 24 0.00062 15.6 -0.4 43 359-404 197-239 (247)
No 1
>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT; InterPro: IPR014301 Members of this entry are the periplasmic protein TorT that, together with the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase and shows homology to a periplasmic D-ribose binding protein..
Probab=70.26 E-value=0.38 Score=26.64 Aligned_cols=68 Identities=24% Similarity=0.408 Sum_probs=54.3
Q ss_pred HHHHHHHH----HHHHHHHHHHCCHHHHHHHHH------HHHHHHHHHHHHHHHHHHCCCHHHHH-CHHHHHHHHHHHH
Q ss_conf 34577775----214689988589799999887------63034677888888886112357652-2146667878887
Q gi|254781203|r 187 NVPFGMVE----RGWSSKVLEDHGYPDMAQHYR------IFDMESLITDGLIGAFFGGMHSKQVQ-NMSLRLVNDLKEG 254 (478)
Q Consensus 187 NiafGMaq----RG~sa~tLe~~GY~emA~QYr------V~D~QALatDgVLGaAFGGvh~~~~~-~~s~~~~~~~~~~ 254 (478)
-|-|||++ +|..=++||-|||.+..+|-+ -|+..||+.-.|=--||-..=....+ -|-.-|||+++.-
T Consensus 16 SiNYGM~e~Ak~~~v~L~VlEAGGY~~~~~Q~~Qi~~C~~wgadAILLG~V~~~~~~~~L~~~~~~~PVfalVN~l~~~ 94 (304)
T TIGR02955 16 SINYGMVEQAKKLGVELKVLEAGGYPNLDKQLAQIEQCVSWGADAILLGTVSPEALNQDLAQLTKSIPVFALVNQLDSN 94 (304)
T ss_pred HHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHCCCCHHHHCCCCCEEEECCCCCC
T ss_conf 3126589999970984799706887007899999998630798589961568566202304350884603221331465
No 2
>pfam03518 consensus
Probab=64.19 E-value=11 Score=17.76 Aligned_cols=118 Identities=17% Similarity=0.091 Sum_probs=61.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHC-CHHHHHHHHHH---------
Q ss_conf 65002456428875311467866652276767552388886415650688888886415-20378898763---------
Q gi|254781203|r 61 PNYYRGSRTDPHSVGTGAHLVEGLTSLAPYIAGAALAGKLLSFIPTPLTRLAGLALQSA-PLAAGALYAYL--------- 130 (478)
Q Consensus 61 p~ind~S~q~~~evrK~AeL~~~v~sLtPd~attGtAGqvL~~i~t~L~~lgG~Al~g~-P~ggaAlv~~l--------- 130 (478)
-+.++.+++|-.++||-.++|+. .|.+|++++.+-+ .--..+.+..|| -++.+++.-++
T Consensus 157 kd~ekKA~Ey~~~~rKAEe~nk~----------mgCvgKI~g~vlt-~VsvvAAv~TGGASLAlAaVGlAl~v~DeI~qa 225 (349)
T pfam03518 157 AEMEKKSAEFAAETRKAEELNRI----------MGCIGKILGALLT-IVSVVAAAFSGGASLALAAVGLALMVADAIVKA 225 (349)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHH-HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 88998899999999999999988----------8799999999999-999999996273589999999999999999998
Q ss_pred -CCCCH-----------------------HHHHHHHCCCCHHHHHHHHHHHHHHHHH----HHHCCHHHHHHHHHHHHHH
Q ss_conf -03201-----------------------2344442165611356778888788878----9861046654456787777
Q gi|254781203|r 131 -SHKAE-----------------------SSIHHQIEGVDKETADALAWREAIVHTS----ALLAPGAIASQSIAKTVAS 182 (478)
Q Consensus 131 -qgfSe-----------------------~e~kl~AeGVD~~TA~~lAl~egv~agl----G~llPggi~aesVA~~~A~ 182 (478)
-|.|= +..-|..=|||++||-..+---|-++++ +++.-.+..+++++.-++.
T Consensus 226 aTG~Sfm~~~m~pvMe~viqPLm~~is~~iTaiL~~~GVd~e~AE~iGsI~gaiaAaIvmia~~v~v~~~~k~~a~k~~~ 305 (349)
T pfam03518 226 ATGNSFIEQALNPIMEAVIEPLIELIGDAFTKALEGLGVDKKKAEMAGSILGAIAAAIALVAAIVLVATVGKGAAAKLAE 305 (349)
T ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 72202999887788999999999999999999999929888999999999999999999999999999987878999999
Q ss_pred HHHHHHH
Q ss_conf 6433345
Q gi|254781203|r 183 GAVLNVP 189 (478)
Q Consensus 183 Gag~Nia 189 (478)
..+-+++
T Consensus 306 ~~~K~~~ 312 (349)
T pfam03518 306 AIGKIIG 312 (349)
T ss_pred HHHHHHH
T ss_conf 9998999
No 3
>KOG1709 consensus
Probab=54.45 E-value=5.3 Score=19.65 Aligned_cols=61 Identities=31% Similarity=0.376 Sum_probs=33.3
Q ss_pred HHHCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 641520378898763032012344442165611356778888788878986104665445678777764333457777
Q gi|254781203|r 116 LQSAPLAAGALYAYLSHKAESSIHHQIEGVDKETADALAWREAIVHTSALLAPGAIASQSIAKTVASGAVLNVPFGMV 193 (478)
Q Consensus 116 l~g~P~ggaAlv~~lqgfSe~e~kl~AeGVD~~TA~~lAl~egv~aglG~llPggi~aesVA~~~A~Gag~NiafGMa 193 (478)
..++--.+.+++-+||.-.|. +++.+| -++-..|+.-+.+++..++- +-.|-.+||||||+
T Consensus 53 s~n~~~~a~~~qd~ls~~~D~--ll~~~~----k~VMm~WEtpiMha~A~ai~-----------tkggrvLnVGFGMg 113 (271)
T KOG1709 53 SPNADGNAPYLQDYLSTAEDT--LLDSLG----KGVMMRWETPIMHALAEAIS-----------TKGGRVLNVGFGMG 113 (271)
T ss_pred CCCCCCCCHHHHHHHHHHHHH--HHHHCC----CHHHHHHHHHHHHHHHHHHH-----------HCCCEEEEECCCHH
T ss_conf 866432246788777553567--776405----43556521489999999986-----------17964898423167
No 4
>PRK08211 hypothetical protein; Provisional
Probab=53.40 E-value=17 Score=16.63 Aligned_cols=135 Identities=17% Similarity=0.213 Sum_probs=79.3
Q ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 67788887888789861046654456---787777643334577775214689988589799999887630346778888
Q gi|254781203|r 151 DALAWREAIVHTSALLAPGAIASQSI---AKTVASGAVLNVPFGMVERGWSSKVLEDHGYPDMAQHYRIFDMESLITDGL 227 (478)
Q Consensus 151 ~~lAl~egv~aglG~llPggi~aesV---A~~~A~Gag~NiafGMaqRG~sa~tLe~~GY~emA~QYrV~D~QALatDgV 227 (478)
++.++.|-+.-++|+.|||.++.-+. -.++|+-+|- ..+.|+++|.... ||+.++|+----+
T Consensus 237 GTAsTmQvmaEALGLsLPgSAl~Pa~~~~~~~~Ar~sgr-av~~L~~~Git~R--------------DILT~kAFeNAi~ 301 (653)
T PRK08211 237 GTAGTSQVVAEALGLALPHSALAPSGQPIWREIARRSAR-AALELDQRGITTR--------------DILTDKAIENAMV 301 (653)
T ss_pred ECHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHH-HHHHHHHCCCCHH--------------HCCCHHHHHHHHH
T ss_conf 528889999999647788744589997799999999999-9999997599868--------------7348999998999
Q ss_pred HHHHHHCCCHHHHHCH------HHHH--HHHHHHHHHHCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 8888611235765221------4666--7878887763042011023458997678667676579999999875415687
Q gi|254781203|r 228 IGAFFGGMHSKQVQNM------SLRL--VNDLKEGITERLPYKHGVKSSSPGLHTSFDAYEAHTDTLAHGVDSLVRGEYP 299 (478)
Q Consensus 228 LGaAFGGvh~~~~~~~------s~~~--~~~~~~~iTER~~~~H~~~~ssPGL~~~~~a~~AH~D~L~~~v~~l~RGE~~ 299 (478)
+-+|+||--..-+.-+ -+.+ .+|.+ .|..+.|+---++-+.|-.+.+.+.|.| --...-+..|...-+-
T Consensus 302 V~aAiGGSTNavLHLpAIA~eAGI~lptldDFd-~Isr~vP~Ladl~PsG~~~~~~~d~~~A--GGVPaVmkeL~~~GLL 378 (653)
T PRK08211 302 VHAAFGGSTNLLLHIPAIAHAAGCTIPTVDDWT-RINRKVPRLVDVLPNGPVYHPTVRAFLA--GGVPEVMLHLRSLGLL 378 (653)
T ss_pred HHHHHCCHHHHHHHHHHHHHHCCCCCCCHHHHH-HHHCCCCEEEEECCCCCCCCCCCHHHHC--CCHHHHHHHHHHCCCC
T ss_conf 999843456699999999986299989989999-9860698168865899864021020531--8999999999977896
Q ss_pred CCCH
Q ss_conf 7578
Q gi|254781203|r 300 HFDQ 303 (478)
Q Consensus 300 ~~~~ 303 (478)
|-|.
T Consensus 379 h~D~ 382 (653)
T PRK08211 379 HEDA 382 (653)
T ss_pred CCCC
T ss_conf 7887
No 5
>PRK09867 hypothetical protein; Provisional
Probab=53.11 E-value=7.7 Score=18.67 Aligned_cols=48 Identities=19% Similarity=0.382 Sum_probs=37.0
Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH-----HHHCCCHHHHHCHH
Q ss_conf 4689988589799999887630346778888888-----86112357652214
Q gi|254781203|r 197 WSSKVLEDHGYPDMAQHYRIFDMESLITDGLIGA-----FFGGMHSKQVQNMS 244 (478)
Q Consensus 197 ~sa~tLe~~GY~emA~QYrV~D~QALatDgVLGa-----AFGGvh~~~~~~~s 244 (478)
|++..+.+.+-+=+..|=|+||.|.=..=+.+|+ .|...|.+|.+|..
T Consensus 153 ~~A~~~g~~a~afLGtQGDiWDaQkDM~~a~lGAi~al~l~~~~hdr~l~rl~ 205 (209)
T PRK09867 153 WAALAMGQGADDFLGTQGDQWDTQSDMFCALLGALTTVIFLARFHCRQLRRFG 205 (209)
T ss_pred HHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 99996263489861666560668999999999999999999898999999855
No 6
>PRK10037 cell division protein; Provisional
Probab=50.00 E-value=11 Score=17.75 Aligned_cols=107 Identities=19% Similarity=0.294 Sum_probs=67.2
Q ss_pred HHHHHHHHHHHHHHH----------------HHHHHHHHHH---HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 466544567877776----------------4333457777---521468998858979999988763034677888888
Q gi|254781203|r 169 GAIASQSIAKTVASG----------------AVLNVPFGMV---ERGWSSKVLEDHGYPDMAQHYRIFDMESLITDGLIG 229 (478)
Q Consensus 169 ggi~aesVA~~~A~G----------------ag~NiafGMa---qRG~sa~tLe~~GY~emA~QYrV~D~QALatDgVLG 229 (478)
||++.-+|+..+|++ --+..-|||- .+||+..+|+..-+.+.+-+| ++++.-
T Consensus 11 GGVGkTTltAnLA~aL~~~g~~VlaID~dpqN~Lrlhfg~~~~~~~Gwa~a~l~g~~W~~a~~~~---------~~gl~~ 81 (250)
T PRK10037 11 GGVGTTSITAALAWSLQMLGENVLVIDACPDNLLRLSFNVDFTHRQGWARALLDGQDWRDAGLRY---------TSQLDL 81 (250)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHCCCCCCCCCCHHHHHHCCCCHHHHHHHC---------CCCCEE
T ss_conf 88768999999999999779918999578256678754998544772999985699789998505---------699369
Q ss_pred HHHHCCCHHHHHCHHHHHHH--HHHHHH---HHCCCHHHCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 88611235765221466678--788877---63042011023458997678667676579
Q gi|254781203|r 230 AFFGGMHSKQVQNMSLRLVN--DLKEGI---TERLPYKHGVKSSSPGLHTSFDAYEAHTD 284 (478)
Q Consensus 230 aAFGGvh~~~~~~~s~~~~~--~~~~~i---TER~~~~H~~~~ssPGL~~~~~a~~AH~D 284 (478)
+-||-+...+..+..-++.. ++-..+ ....+|..-.+|+.||+-.-.+.+.+.-|
T Consensus 82 LPfG~l~~~~~~~~~~~~~~~~~l~~~l~~l~~~~~~~~vliD~P~g~s~~~~~~l~~AD 141 (250)
T PRK10037 82 LPFGQLSIEEQENPQHWQTTLGDICSALQQLKASGRYQWILLDLPRGASPLTRQLLSLCD 141 (250)
T ss_pred EECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHCC
T ss_conf 727879989986388776517999999862002578998999659998299999998578
No 7
>PRK05201 hslU ATP-dependent protease ATP-binding subunit; Provisional
Probab=42.54 E-value=5.1 Score=19.74 Aligned_cols=21 Identities=57% Similarity=0.816 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHH-HHHH
Q ss_conf 11136898613788898753-6789
Q gi|254781203|r 31 HTGLGKEVINMPARSLDKLV-APFR 54 (478)
Q Consensus 31 ytGLgS~Li~~Paq~LDKlV-sP~a 54 (478)
-||.|+-.|+ +-|+|++ +||.
T Consensus 58 PTGvGKTeIA---RrLAkl~~aPFv 79 (442)
T PRK05201 58 PTGVGKTEIA---RRLAKLANAPFI 79 (442)
T ss_pred CCCCCHHHHH---HHHHHHHCCCEE
T ss_conf 8886678999---999998489858
No 8
>pfam01542 HCV_core Hepatitis C virus core protein. The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression.
Probab=40.89 E-value=11 Score=17.83 Aligned_cols=48 Identities=25% Similarity=0.421 Sum_probs=27.5
Q ss_pred HHHHHHCCCHHHHHHHHH-HHHCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHH
Q ss_conf 888641565068888888-641520378898763032012344442165611356
Q gi|254781203|r 98 GKLLSFIPTPLTRLAGLA-LQSAPLAAGALYAYLSHKAESSIHHQIEGVDKETAD 151 (478)
Q Consensus 98 GqvL~~i~t~L~~lgG~A-l~g~P~ggaAlv~~lqgfSe~e~kl~AeGVD~~TA~ 151 (478)
|+|+.-+--.|+|+-|-. ++|+|+||-|- .+-+- ...--|||++-|-.
T Consensus 5 Gkvidtltcgfadlmgyiplvg~p~ggvar--alahg----Vr~leDgvN~Atgn 53 (75)
T pfam01542 5 GKVIDTLTCGFADLMGYIPLVGAPVGGVAR--ALAHG----VRVLEDGINYATGN 53 (75)
T ss_pred CCEECCCCCCHHHHHCCCCCCCCCCHHHHH--HHHHH----HHHHHCCCCCCCCC
T ss_conf 111011230367662545533563068999--99857----88761675301367
No 9
>KOG0759 consensus
Probab=40.43 E-value=27 Score=15.39 Aligned_cols=35 Identities=20% Similarity=0.254 Sum_probs=24.3
Q ss_pred HHHCCCHHHHHCHHHHHHHHHHHHHHHCCCHHHCC
Q ss_conf 86112357652214666787888776304201102
Q gi|254781203|r 231 FFGGMHSKQVQNMSLRLVNDLKEGITERLPYKHGV 265 (478)
Q Consensus 231 AFGGvh~~~~~~~s~~~~~~~~~~iTER~~~~H~~ 265 (478)
|+||+--.-..--..|..+|.+....+|-||+|..
T Consensus 108 a~Gg~vGtPadv~~VRMQ~D~~LP~~~RRNYknv~ 142 (286)
T KOG0759 108 AIGGVVGTPADVANVRMQADGRLPPEQRRNYKNVF 142 (286)
T ss_pred HHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf 75241178999899987605779877753246676
No 10
>pfam04065 Not3 Not1 N-terminal domain, CCR4-Not complex component.
Probab=39.73 E-value=16 Score=16.77 Aligned_cols=12 Identities=33% Similarity=0.670 Sum_probs=6.5
Q ss_pred HHHHHHHHHHCC
Q ss_conf 999988898516
Q gi|254781203|r 464 IKEAINCFLRTG 475 (478)
Q Consensus 464 ~~~~~~~~~~~~ 475 (478)
|++.|.+|+...
T Consensus 202 ikedieyYve~n 213 (233)
T pfam04065 202 IKEDIEYYVESN 213 (233)
T ss_pred HHHHHHHHHHCC
T ss_conf 888899998649
No 11
>PHA00451 protein kinase
Probab=38.72 E-value=28 Score=15.22 Aligned_cols=89 Identities=17% Similarity=0.197 Sum_probs=58.2
Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCHHHHHHHHHHHHHHHCCCHHHCCCCCCCC-CCCC
Q ss_conf 468998858979999988763034677888888886112357652214666787888776304201102345899-7678
Q gi|254781203|r 197 WSSKVLEDHGYPDMAQHYRIFDMESLITDGLIGAFFGGMHSKQVQNMSLRLVNDLKEGITERLPYKHGVKSSSPG-LHTS 275 (478)
Q Consensus 197 ~sa~tLe~~GY~emA~QYrV~D~QALatDgVLGaAFGGvh~~~~~~~s~~~~~~~~~~iTER~~~~H~~~~ssPG-L~~~ 275 (478)
++..+.+.+..+.-...+ +|..-|-|--.+--+|-|+-|-.|..-.+-..++-..-||.-....|-. .--|| .|.|
T Consensus 155 ~A~~~ie~~~~d~~~~~~--~~~~FIETCkmIRkFF~GIASFDmHSGNiMf~~~g~p~ITDPVSFS~Dr-~re~G~F~ld 231 (364)
T PHA00451 155 AAREIIECDCFDAAEEAP--ISDEFIETCKMIRKFFYGIASFDMHSGNIMFDKMGVPYITDPVSFSADR-KREPGEFPLD 231 (364)
T ss_pred HHHHHHHCCCCCHHHHCC--CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEECCCCCEEECCCCCCCCCC-CCCCCCCCCC
T ss_conf 999998456873665267--7624899999999998433101235784346789974552785555422-3479978889
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 6676765799999
Q gi|254781203|r 276 FDAYEAHTDTLAH 288 (478)
Q Consensus 276 ~~a~~AH~D~L~~ 288 (478)
|+..||.-.++++
T Consensus 232 Pd~LiaEvEaia~ 244 (364)
T PHA00451 232 PDELIAEVEAIAN 244 (364)
T ss_pred HHHHHHHHHHHHH
T ss_conf 8999999999988
No 12
>pfam05461 ApoL Apolipoprotein L. Apo L belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular processes such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. There are six apo L genes located in close proximity to each other on chromosome 22q12 in humans. 22q12 is a confirmed high-susceptibility locus for schizophrenia and close to the region associated with velocardiofacial syndrome that includes symptoms of schizophrenia.
Probab=37.42 E-value=30 Score=15.10 Aligned_cols=80 Identities=13% Similarity=0.059 Sum_probs=56.9
Q ss_pred HHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCC----CCCCCCCHHHHHHHHCCCHHHHHHHH-----HHHHCCHH
Q ss_conf 7898606686500245642887531146786665227----67675523888864156506888888-----86415203
Q gi|254781203|r 52 PFREETHDQPNYYRGSRTDPHSVGTGAHLVEGLTSLA----PYIAGAALAGKLLSFIPTPLTRLAGL-----ALQSAPLA 122 (478)
Q Consensus 52 P~a~e~~dqp~ind~S~q~~~evrK~AeL~~~v~sLt----Pd~attGtAGqvL~~i~t~L~~lgG~-----Al~g~P~g 122 (478)
--.+|..+-|-+-+--.++|...+-.|.-++.+..-. --.+++|.++-||+.+|..|.|.-+- ...|--+|
T Consensus 59 ~~e~FL~eFP~lK~eLe~~I~kL~aLAD~vDkvHk~cTIsnvVa~St~~vSGvlsilGLaLAPvT~G~SL~Lsa~G~GLG 138 (313)
T pfam05461 59 DRERFLKEFPRLKAELEEHIRKLRALADQVDKVHRGCTISNVVASSTSAASGVLTILGLALAPFTAGGSLVLSATGLGLG 138 (313)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf 89999998675689999999999998888888740562135554328988547998735643403763199999857589
Q ss_pred HHHHHHHHC
Q ss_conf 788987630
Q gi|254781203|r 123 AGALYAYLS 131 (478)
Q Consensus 123 gaAlv~~lq 131 (478)
.+|.|++.+
T Consensus 139 ~Aa~VT~i~ 147 (313)
T pfam05461 139 AAAAVTSIS 147 (313)
T ss_pred HHHHHHHHH
T ss_conf 999999998
No 13
>KOG2385 consensus
Probab=36.90 E-value=19 Score=16.25 Aligned_cols=26 Identities=19% Similarity=-0.035 Sum_probs=16.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 16561135677888878887898610
Q gi|254781203|r 143 EGVDKETADALAWREAIVHTSALLAP 168 (478)
Q Consensus 143 eGVD~~TA~~lAl~egv~aglG~llP 168 (478)
+-+-+++...+-|.-++.-|++.+.-
T Consensus 218 e~~m~~~~~~~k~Kr~~~~GlAg~~G 243 (633)
T KOG2385 218 EDVMYPRRRWKKRKRYIIMGLAGLGG 243 (633)
T ss_pred HHHHCHHHHHHHHHHHHHHHHHHCCC
T ss_conf 44513114477887765542321256
No 14
>KOG1019 consensus
Probab=36.06 E-value=21 Score=15.96 Aligned_cols=33 Identities=30% Similarity=0.476 Sum_probs=29.6
Q ss_pred CCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 456752112102344315443488888788666
Q gi|254781203|r 402 FTDAPHAKFDATTFTESLPHVDEQTMHRFSELK 434 (478)
Q Consensus 402 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 434 (478)
..+-||..|----||++|+||.-+.|-++++++
T Consensus 558 ~~~~~~l~~~k~~~Td~L~~v~lg~~p~~s~V~ 590 (837)
T KOG1019 558 YSANPHLGFLKMEFTDYLNHVRLGGTPRLSAVE 590 (837)
T ss_pred HHCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf 525741347776545553033456652044541
No 15
>pfam12157 DUF3591 Protein of unknown function (DUF3591). This domain is found in eukaryotes and is typically between 445 to 462 amino acids in length. Most members are annotated as being transcription initiation factor TFIID subunit 1, and this region is the conserved central portion of these proteins.
Probab=32.36 E-value=33 Score=14.82 Aligned_cols=14 Identities=14% Similarity=0.534 Sum_probs=7.0
Q ss_pred CCCCCCCHHHHHHH
Q ss_conf 67675523888864
Q gi|254781203|r 89 PYIAGAALAGKLLS 102 (478)
Q Consensus 89 Pd~attGtAGqvL~ 102 (478)
|-..--|||..|.|
T Consensus 115 ~llsn~GM~skiin 128 (457)
T pfam12157 115 PVLSNFGMGSKIIN 128 (457)
T ss_pred HHHCCCCHHHHHHH
T ss_conf 35435534666665
No 16
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=29.79 E-value=12 Score=17.57 Aligned_cols=17 Identities=41% Similarity=0.591 Sum_probs=8.3
Q ss_pred HCCCCCCCCCHHHHHHH
Q ss_conf 22767675523888864
Q gi|254781203|r 86 SLAPYIAGAALAGKLLS 102 (478)
Q Consensus 86 sLtPd~attGtAGqvL~ 102 (478)
.|--|.-+|--|-++|+
T Consensus 69 ~LD~yVIGQ~~AKk~ls 85 (411)
T PRK05342 69 HLDQYVIGQERAKKVLS 85 (411)
T ss_pred HHHHHHCCCHHHHHHHH
T ss_conf 86214028488889999
No 17
>KOG2150 consensus
Probab=29.72 E-value=29 Score=15.13 Aligned_cols=65 Identities=25% Similarity=0.222 Sum_probs=34.5
Q ss_pred HHHHHHHHH---CHHHHHHHHHHHHCCCCCC--CCCCCCCCCCCCCCCCCC----CCCCCCCCCCHHHHHHHCC
Q ss_conf 998888631---2012345766541489887--866653225436333665----4567521121023443154
Q gi|254781203|r 356 VERELSEIE---GAKKESSARKFFDEGSPDH--SPFKGERNQKLDPMRGAD----FTDAPHAKFDATTFTESLP 420 (478)
Q Consensus 356 ~~~~~~~~~---~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~ 420 (478)
+++.++... +--+++--+..--+-+-++ -|---|+-|+..|---++ |-..|---+|.+.+++-|-
T Consensus 418 ~~~~~~p~g~~~~~~~e~i~~~~~~e~a~~~~~~psdsE~pq~y~pk~p~~tp~~~~q~~~~~~ds~~~~~rl~ 491 (575)
T KOG2150 418 FELGLSPLGVQSEITNEQIRFLYALEAACKLVPIPSDSEKPQGYLPKTPLPTPSYFPQTPPSLTDSTEITERLD 491 (575)
T ss_pred HHHCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCC
T ss_conf 33203644554665201200178887664237787432146677899988787657777875202566776326
No 18
>TIGR00160 MGSA methylglyoxal synthase; InterPro: IPR004363 Methylglyoxal synthase (MGS) catalyzes the conversion of dihydroxyacetone phosphate to methylglyoxal and phosphate: Glycerone phosphate = methylglyoxal + phosphate It provides bacteria with an alternative to triosephosphate isomerase for metabolizing dihydroxyacetone phosphate. MGS is a small protein of about 13 to 17 kDa. An aspartate residue is involved in the catalytic mechanism. Methylglyoxal synthase contains a domain shared by other enzymes. Other proteins containing this domain include purine biosynthesis protein PurH and carbamoyl phosphate synthetase.; GO: 0008929 methylglyoxal synthase activity, 0019242 methylglyoxal biosynthetic process, 0005737 cytoplasm.
Probab=29.64 E-value=18 Score=16.45 Aligned_cols=35 Identities=26% Similarity=0.268 Sum_probs=27.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf 755238888641565068888888641520378898763
Q gi|254781203|r 92 AGAALAGKLLSFIPTPLTRLAGLALQSAPLAAGALYAYL 130 (478)
Q Consensus 92 attGtAGqvL~~i~t~L~~lgG~Al~g~P~ggaAlv~~l 130 (478)
--|||-|.+++ -=+.|.=+++.|||+||--=+|++
T Consensus 34 yATGTTG~~i~----~~TGL~i~~~~SGPmGGDqQiGa~ 68 (143)
T TIGR00160 34 YATGTTGELIE----RATGLAIEKLLSGPMGGDQQIGAL 68 (143)
T ss_pred EEECCCHHHHH----HHCCCCEECCCCCCCCHHHHHHHH
T ss_conf 53166627766----520770110056899624678999
No 19
>COG4294 Uve UV damage repair endonuclease [DNA replication, recombination, and repair]
Probab=29.10 E-value=16 Score=16.70 Aligned_cols=130 Identities=28% Similarity=0.354 Sum_probs=77.0
Q ss_pred HHHHHHCCHHHHHHHHHHHHHHHHHHHHHH----HHHHHCCCHHHH--HCHHHHHHHHHHHHHHHCCCHHHCCCCCCC--
Q ss_conf 899885897999998876303467788888----888611235765--221466678788877630420110234589--
Q gi|254781203|r 199 SKVLEDHGYPDMAQHYRIFDMESLITDGLI----GAFFGGMHSKQV--QNMSLRLVNDLKEGITERLPYKHGVKSSSP-- 270 (478)
Q Consensus 199 a~tLe~~GY~emA~QYrV~D~QALatDgVL----GaAFGGvh~~~~--~~~s~~~~~~~~~~iTER~~~~H~~~~ssP-- 270 (478)
++...++---+||.|||++|+--|+-+.++ |-.|||..-..- ..-.-+|-+.|| +||--..-+++-++
T Consensus 146 ~~eV~~ssir~layH~r~l~~mgl~~Rs~~~lhlgg~~gGK~~~~eqf~kni~~LP~~vk----sRl~LENDd~sYs~ee 221 (347)
T COG4294 146 REEVVDSSIRDLAYHYRILDGMGLAERSVWNLHLGGTHGGKKERLEQFIKNIQRLPDSVK----SRLTLENDDKSYSTEE 221 (347)
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCHHHH----HHHEEECCCCCCCHHH
T ss_conf 568899899999999999864389867726997145447700379999998863388899----7653306654366999
Q ss_pred --------CCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCC-HHHHHHHHHCCCCCCCC--CCCCCCCCCCCCHHHHHHCC
Q ss_conf --------97678667676579999999875415687757-89987753022237565--88899988673012100001
Q gi|254781203|r 271 --------GLHTSFDAYEAHTDTLAHGVDSLVRGEYPHFD-QEKLQTIADNTLEDPHF--KPHLPEPEPLPQYKEHSDRQ 339 (478)
Q Consensus 271 --------GL~~~~~a~~AH~D~L~~~v~~l~RGE~~~~~-~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~ 339 (478)
+.|.-||+ -|.+.. +.+-| |-|-+ ++-+++| -.|.++|-. |-||.+|.--++-..|||+-
T Consensus 222 lL~lCek~~iPlVfD~--HHh~v~----~~l~~--~~~~sl~~~~~r~-r~TW~~~~lq~kvHlSs~~~~~~dr~H~~~i 292 (347)
T COG4294 222 LLPLCEKLNIPLVFDA--HHHNVH----PGLDR--EDSPSLMELIPRI-RETWTRPGLQQKVHLSSPASGTADRRHSDYI 292 (347)
T ss_pred HHHHHHHHCCCEEEEC--HHHHCC----CCCCC--CCCHHHHHHHHHH-HHHCCCCCCCEEEEECCCCCCCCCCHHHHHH
T ss_conf 9999887389879850--123306----88865--5781499999999-9742587876147756888754440266652
Q ss_pred CC
Q ss_conf 43
Q gi|254781203|r 340 KP 341 (478)
Q Consensus 340 ~~ 341 (478)
.-
T Consensus 293 ~a 294 (347)
T COG4294 293 HA 294 (347)
T ss_pred CC
T ss_conf 01
No 20
>COG1970 MscL Large-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=25.26 E-value=40 Score=14.29 Aligned_cols=41 Identities=24% Similarity=0.460 Sum_probs=28.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHCHHHHHHH
Q ss_conf 97999998876303467788888888611235765221466678
Q gi|254781203|r 206 GYPDMAQHYRIFDMESLITDGLIGAFFGGMHSKQVQNMSLRLVN 249 (478)
Q Consensus 206 GY~emA~QYrV~D~QALatDgVLGaAFGGvh~~~~~~~s~~~~~ 249 (478)
++-+-+..+.|.| ||+--|+|+|||.+-+|-|.+--.-+..
T Consensus 6 eFkeF~~RGNVvD---LAVgVIIGaAFg~IV~SlV~diImPlIg 46 (130)
T COG1970 6 EFKEFALRGNVVD---LAVGVIIGAAFGKIVTSLVNDIIMPLIG 46 (130)
T ss_pred HHHHHHHHCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999997057166---7788885898988999999988876366
No 21
>cd02016 TPP_E1_OGDC_like Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA and carbon dioxide, a key reaction of the tricarboxylic acid cycle.
Probab=24.73 E-value=20 Score=16.17 Aligned_cols=132 Identities=20% Similarity=0.207 Sum_probs=59.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHHHH---------HHH----HH--H-CCCH
Q ss_conf 6787777643334577775214689988589--799999887630346778888---------888----86--1-1235
Q gi|254781203|r 176 IAKTVASGAVLNVPFGMVERGWSSKVLEDHG--YPDMAQHYRIFDMESLITDGL---------IGA----FF--G-GMHS 237 (478)
Q Consensus 176 VA~~~A~Gag~NiafGMaqRG~sa~tLe~~G--Y~emA~QYrV~D~QALatDgV---------LGa----AF--G-Gvh~ 237 (478)
+....+....-+|-+||+|||-+.-+-.--| |.++-+.. +...-..+.. ||. -+ | -+|-
T Consensus 30 li~~a~~~gv~~iviGMaHRGRLNvL~nvl~Kp~~~iF~eF---~g~~~~~~~~~~sGDVKYHlG~s~~~~~~~gk~v~l 106 (265)
T cd02016 30 LIDRAAELGVEEVVIGMAHRGRLNVLANVLGKPLEQIFSEF---EGKSEFPEDDEGSGDVKYHLGYSSDRKTPSGKKVHL 106 (265)
T ss_pred HHHHHHHCCCCEEEECCCCCCHHHHHHHHHCCCHHHHHHHH---CCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCEEEE
T ss_conf 99999876986799825666518899998641799999852---799889632466677163784245786269988999
Q ss_pred HHHHCHH-HHHHHHHHHHHHHCCCHHHCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHH-HHHHHHCC
Q ss_conf 7652214-66678788877630420110234589976--78667676579999999875415687757899-87753022
Q gi|254781203|r 238 KQVQNMS-LRLVNDLKEGITERLPYKHGVKSSSPGLH--TSFDAYEAHTDTLAHGVDSLVRGEYPHFDQEK-LQTIADNT 313 (478)
Q Consensus 238 ~~~~~~s-~~~~~~~~~~iTER~~~~H~~~~ssPGL~--~~~~a~~AH~D~L~~~v~~l~RGE~~~~~~~~-~~~~~~~~ 313 (478)
+-+-||| |..||-|-.|.+--.-...++.+...-|| .-=||+.+-|--. -|.++--..|+|.--- +.-|..|-
T Consensus 107 sL~~NPSHLEaVnPVv~G~~RAkQ~~~~~~~~~kvlpiliHGDAAfaGQGvv---~Etl~ls~l~gy~~GGtiHiivNNQ 183 (265)
T cd02016 107 SLAPNPSHLEAVNPVVMGKTRAKQDYRGDGERDKVLPILIHGDAAFAGQGVV---YETLNLSNLPGYTTGGTIHIVVNNQ 183 (265)
T ss_pred EECCCCCCCEEECCEECCHHHHHHHHHCCCCCCEEEEEEEECCCCCCCCCHH---HHHHHHHCCCCCCCCCEEEEEEECC
T ss_conf 9758976416777774440565677644877663789999666111456589---9876663389985476699998074
No 22
>TIGR01793 cit_synth_euk citrate (Si)-synthase, eukaryotic; InterPro: IPR010109 Citrate synthase 2.3.3.1 from EC is a member of a small family of enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors. It catalyses the first reaction in the Krebs' cycle, namely the conversion of oxaloacetate and acetyl-coenzyme A into citrate and coenzyme A. This reaction is important for energy generation and for carbon assimilation. The reaction proceeds via a non-covalently bound citryl-coenzyme A intermediate in a 2-step process (aldol-Claisen condensation followed by the hydrolysis of citryl-CoA). Citrate synthase enzymes are found in two distinct structural types: type I enzymes (found in eukaryotes, Gram-positive bacteria and archaea) form homodimers and have shorter sequences than type II enzymes, which are found in Gram-negative bacteria and are hexameric in structure. In both types, the monomer is composed of two domains: a large alpha-helical domain consisting of two structural repeats, where the second repeat is interrupted by a small alpha-helical domain. The cleft between these domains forms the active site, where both citrate and acetyl-coenzyme A bind. The enzyme undergoes a conformational change upon binding of the oxaloacetate ligand, whereby the active site cleft closes over in order to form the acetyl-CoA binding site . The energy required for domain closure comes from the interaction of the enzyme with the substrate. Type II enzymes possess an extra N-terminal beta-sheet domain, and some type II enzymes are allosterically inhibited by NADH . This entry includes both mitochondrial and peroxisomal forms of citrate synthase. Peroxisomal forms of the enzyme, recognized by the C-terminal targeting motif SKL, act in the glyoxylate cycle. Eukaryotic homologs include a Tetrahymena thermophila citrate synthase that doubles as a filament protein, a putative citrate synthase from Plasmodium falciparum (no TCA cycle), and a methylcitrate synthase from Aspergillus nidulans (Emericella nidulans).; GO: 0004108 citrate (Si)-synthase activity, 0044262 cellular carbohydrate metabolic process.
Probab=24.49 E-value=40 Score=14.28 Aligned_cols=31 Identities=16% Similarity=0.144 Sum_probs=14.6
Q ss_pred HHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 89876303201234444216561135677888
Q gi|254781203|r 125 ALYAYLSHKAESSIHHQIEGVDKETADALAWR 156 (478)
Q Consensus 125 Alv~~lqgfSe~e~kl~AeGVD~~TA~~lAl~ 156 (478)
+.|.+|+.+|+|+ |-.++||+|..==+-+.+
T Consensus 141 ~av~AL~~eS~Fa-kAyakGi~K~~YWeytyE 171 (430)
T TIGR01793 141 LAVAALEVESEFA-KAYAKGIAKKKYWEYTYE 171 (430)
T ss_pred HHHHHHHHHHHHH-HHHHHCCCCCCCCCCCHH
T ss_conf 9999887410453-367725541124573044
No 23
>pfam10478 consensus
Probab=24.00 E-value=50 Score=13.69 Aligned_cols=24 Identities=25% Similarity=0.293 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHC
Q ss_conf 688888886415203788987630
Q gi|254781203|r 108 LTRLAGLALQSAPLAAGALYAYLS 131 (478)
Q Consensus 108 L~~lgG~Al~g~P~ggaAlv~~lq 131 (478)
|-++|..-+.+--|+=..+..+++
T Consensus 119 LlRlg~~Ka~sv~~~l~tl~s~l~ 142 (575)
T pfam10478 119 LQRLGQDKAQSVGWSLSTIFTRLK 142 (575)
T ss_pred HHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 998146631279889999999975
No 24
>TIGR00405 L26e_arch ribosomal protein L24; InterPro: IPR011590 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 of 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 protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons..
Probab=23.23 E-value=28 Score=15.26 Aligned_cols=34 Identities=29% Similarity=0.433 Sum_probs=16.0
Q ss_pred HHHHHHCHHHHHHHHHHHHCCCC---CCCCCCCCCCC
Q ss_conf 88863120123457665414898---87866653225
Q gi|254781203|r 359 ELSEIEGAKKESSARKFFDEGSP---DHSPFKGERNQ 392 (478)
Q Consensus 359 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~ 392 (478)
.++||+---+-..+-.-..+|+- =-.||||||-.
T Consensus 76 ~feEie~fL~Pkkiie~I~kGd~VEiisGPFKGErAk 112 (151)
T TIGR00405 76 DFEEIERFLTPKKIIESIKKGDVVEIISGPFKGERAK 112 (151)
T ss_pred EHHHHHHHCCCCHHHHCCCCCCEEEEEECCCCCCEEE
T ss_conf 4756020058421453134788889953899764468
No 25
>COG0278 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=21.66 E-value=34 Score=14.76 Aligned_cols=16 Identities=31% Similarity=0.729 Sum_probs=6.3
Q ss_pred CCCCCHHHHHHHHHHH
Q ss_conf 3458878998999999
Q gi|254781203|r 3 FNAVSDEDIRDNIKEW 18 (478)
Q Consensus 3 ~~~~~~~~i~~~i~~~ 18 (478)
+|-|.+.+||++||+.
T Consensus 51 vnVL~d~eiR~~lk~~ 66 (105)
T COG0278 51 VDVLQDPEIRQGLKEY 66 (105)
T ss_pred EEECCCHHHHHCCHHH
T ss_conf 6421699898524644
No 26
>COG5209 RCD1 Uncharacterized protein involved in cell differentiation/sexual development [General function prediction only]
Probab=21.20 E-value=57 Score=13.35 Aligned_cols=10 Identities=10% Similarity=0.448 Sum_probs=3.7
Q ss_pred HHHHHHHHHH
Q ss_conf 8987536789
Q gi|254781203|r 45 SLDKLVAPFR 54 (478)
Q Consensus 45 ~LDKlVsP~a 54 (478)
.|..++++|-
T Consensus 93 LLqEiisvYp 102 (315)
T COG5209 93 LLQEIISVYP 102 (315)
T ss_pred HHHHHHHHHH
T ss_conf 9998876632
No 27
>TIGR00681 kdpC K+-transporting ATPase, C subunit; InterPro: IPR003820 Kdp, the high affinity ATP-driven K+-transport system of Escherichia coli, is a complex of the membrane-bound subunits KdpA, KdpB, KdpC and the small peptide KdpF. KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilize the Kdp complex . It has been suggested that KdpC could be one of the connecting links between the energy providing subunit KdpB and the K+- transporting subunit KdpA . The K+ transport system actively transports K+ ions via ATP hydrolysis.; GO: 0008556 potassium-transporting ATPase activity, 0006813 potassium ion transport, 0016020 membrane.
Probab=20.96 E-value=58 Score=13.32 Aligned_cols=37 Identities=22% Similarity=0.057 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHHHH--HHHCCCCCCCCCH------HHHHHHHHHH
Q ss_conf 45887899899999--9857655788412------1113689861
Q gi|254781203|r 4 NAVSDEDIRDNIKE--WAQRPRVSPDIKW------HTGLGKEVIN 40 (478)
Q Consensus 4 ~~~~~~~i~~~i~~--~~q~p~~s~D~~w------ytGLgS~Li~ 40 (478)
-|++-++.-..|.+ .++|-+|.+|.+- -++++|||=+
T Consensus 91 LapsNp~Ll~~iaaRV~A~R~enn~~a~~~vpvdlvt~SgSGLDp 135 (193)
T TIGR00681 91 LAPSNPELLKLIAARVEALRKENNLDAAVSVPVDLVTASGSGLDP 135 (193)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHCCCCCCCCC
T ss_conf 567888899999999999866357886554613321012125673
No 28
>TIGR00154 ispE 4-diphosphocytidyl-2C-methyl-D-erythritol kinase; InterPro: IPR004424 4-diphosphocytidyl-2C-methyl-D-erythritol kinase is a member of the family of GHMP kinases that were previously designated as conserved hypothetical protein YchB or as isopentenyl monophosphate kinase. In Lycopersicon esculentum (tomato) and Escherichia coli the protein has been indentified as 4-diphosphocytidyl-2C-methyl-D-erythritol kinase, an enzyme of the deoxyxylulose phosphate pathway of terpenoid biosynthesis.; GO: 0050515 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity, 0016114 terpenoid biosynthetic process.
Probab=20.23 E-value=59 Score=13.28 Aligned_cols=15 Identities=60% Similarity=0.773 Sum_probs=5.4
Q ss_pred CHHHHHHHHHHHHHH
Q ss_conf 089999989996301
Q gi|254781203|r 440 EAREVLEGLQEKLQG 454 (478)
Q Consensus 440 ~~~~~~~~~~~~~~~ 454 (478)
||+.|++--.|+|.|
T Consensus 291 ea~~v~~~a~E~L~g 305 (322)
T TIGR00154 291 EAEQVLEQAPEKLNG 305 (322)
T ss_pred HHHHHHHHCCHHHCC
T ss_conf 789998734400058
No 29
>pfam10225 DUF2215 Uncharacterized conserved protein (DUF2215). This entry is the central 200 residues of a family of proteins conserved from worms to humans. The function is unknown.
Probab=20.02 E-value=24 Score=15.60 Aligned_cols=43 Identities=33% Similarity=0.356 Sum_probs=27.2
Q ss_pred HHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 8886312012345766541489887866653225436333665456
Q gi|254781203|r 359 ELSEIEGAKKESSARKFFDEGSPDHSPFKGERNQKLDPMRGADFTD 404 (478)
Q Consensus 359 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 404 (478)
|-.++|-.|--..-|++- .|||.++.+--.+ .-||+|-|||-.
T Consensus 197 ~Qg~~eT~kaL~elR~yc--~SP~~~~w~~vs~-l~~P~rfA~f~~ 239 (247)
T pfam10225 197 EQGEGETVSSLQELREYC--NSPDCSVWKTFSR-LQSPRRFADFVE 239 (247)
T ss_pred HHCHHCCHHHHHHHHHHH--CCCCCCHHHHHHC-CCCHHHHHHHHC
T ss_conf 301010147899999985--7999857788615-678689998846
Done!