Query gi|254780786|ref|YP_003065199.1| ribosome-binding factor A [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 128
No_of_seqs 102 out of 1288
Neff 6.6
Searched_HMMs 33803
Date Wed Jun 1 13:51:32 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780786.hhm -d /home/congqian_1/database/mmdb/mmdb70.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 >1jos_A RBFA, ribosome-binding 100.0 4.9E-31 1.4E-35 195.2 10.9 118 5-126 1-121 (128)
2 >2e7g_A Putative ribosome-bind 100.0 8E-32 2.4E-36 199.7 0.9 122 1-124 4-126 (129)
3 >1pa4_A Probable ribosome-bind 100.0 1.5E-30 4.3E-35 192.5 0.9 114 7-124 1-114 (116)
4 >2dyj_A Ribosome-binding facto 99.9 5.3E-25 1.6E-29 161.1 10.5 94 9-109 2-95 (95)
5 >1w63_A Adapter-related protei 44.7 4.3 0.00013 20.5 -0.5 37 69-105 8-46 (57)
6 >2vgl_A Adaptor protein comple 38.0 4.8 0.00014 20.2 -1.1 39 69-107 8-48 (72)
7 >1d0n_A Horse plasma gelsolin; 19.9 45 0.0013 14.8 1.2 42 56-100 149-190 (204)
8 >1aoy_A Arginine repressor; DN 17.0 15 0.00043 17.5 -1.8 42 5-55 4-52 (78)
9 >1jmx_B Amine dehydrogenase; o 15.0 83 0.0025 13.3 2.1 14 46-59 5-18 (43)
10 >1kmj_A Selenocysteine lyase; 11.0 58 0.0017 14.2 -0.1 81 38-120 28-115 (120)
No 1
>>1jos_A RBFA, ribosome-binding factor A; RNA binding protein, structure 2 function project, S2F, structural genomics; 1.70A {Haemophilus influenzae} (A:)
Probab=99.97 E-value=4.9e-31 Score=195.22 Aligned_cols=118 Identities=25% Similarity=0.446 Sum_probs=106.4
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCH---HHHHHHHHHHHHH
Q ss_conf 8777738999999999999999951413420126516898888985875655999982798647---7899999985689
Q gi|254780786|r 5 NPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSP---DRVISALNCNIKF 81 (128)
Q Consensus 5 ~~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~---~~~~~~L~~~~~~ 81 (128)
|+++|.|+.|++++|+++||++|.+ ++.||++. +||||+|++|+|+++|+||||++|+.++ +.++++|++++|+
T Consensus 1 M~~~s~R~~rv~~~i~~~is~il~~-ei~d~~~~--~vtIt~V~vs~Dl~~akVy~s~~~~~~~~~~~~~~~~L~~~~g~ 77 (128)
T 1jos_A 1 MAREFKRSDRVAQEIQKEIAVILQR-EVKDPRIG--MVTVSDVEVSSDLSYAKIFVTFLFDHDEMAIEQGMKGLEKASPY 77 (128)
T ss_dssp ------CHHHHHHHHHHHHHHHHHH-HCCCTTTC--CEEEEEEEECTTSCEEEEEEEESCCSCHHHHHHHHHHHHHTHHH
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHH-HCCCCCCC--CEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHH
T ss_conf 9898717899999999999999997-56576668--15897999768855179999956871056799999999998999
Q ss_pred HHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHHHHHHH
Q ss_conf 999999987521457858999738688899999985576777764
Q gi|254780786|r 82 IRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPVAL 126 (128)
Q Consensus 82 ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~v~~d~ 126 (128)
||+.||+++ .||++|+|+|++|++++++.+|++||++.+.+...
T Consensus 78 iR~~l~~~l-~lr~~P~L~F~~D~~~~~~~~i~~ll~~~~~~~~~ 121 (128)
T 1jos_A 78 IRSLLGKAM-RLRIVPEIRFIYDQSLVEGMRMSNLVTNVVREDEK 121 (128)
T ss_dssp HHHHHHHHH-CCSSCCEEEEEECCCCCCCC---------------
T ss_pred HHHHHHHHC-CCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999667-88079878999789778999999999998887663
No 2
>>2e7g_A Putative ribosome-binding factor A; RBFA, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} (A:)
Probab=99.96 E-value=8e-32 Score=199.65 Aligned_cols=122 Identities=16% Similarity=0.202 Sum_probs=111.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCC-CHHHHHHHHHHHH
Q ss_conf 998887777389999999999999999514134201265168988889858756559999827986-4778999999856
Q gi|254780786|r 1 MKNKNPKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDV-SPDRVISALNCNI 79 (128)
Q Consensus 1 mk~~~~~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~-~~~~~~~~L~~~~ 79 (128)
|+..+..++.|+.|++++|+++|+++|.++++.||.++ ++||||+|++|+|+++|+||||++++. +.+.++++|++++
T Consensus 4 ~~~~~~~~~~R~~rv~~~i~~~i~~il~~~~~~d~~~~-~~vtIt~V~vS~Dl~~a~Vy~s~~~~~~~~~~~~~~L~~a~ 82 (129)
T 2e7g_A 4 GSSGRKEDHARLRALNGLLYKALTDLLCTPEVSQELYD-LNVELSKVSLTPDFSACRAYWKTTLSAEQNAHMEAVLQRSA 82 (129)
T ss_dssp CSCCSSHHHHHHHHHHHHHHHHHHHHTTCTTTCHHHHH-HTCCEEEEEECTTSCCEEEEECCCSCHHHHHHHHHHHHHTH
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCC-CEEEEEEEEECCCCCEEEEEEEECCCHHHHHHHHHHHHHHH
T ss_conf 87888854478999999999999999985676766558-65999799987998868999985685345788999999999
Q ss_pred HHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHHHHH
Q ss_conf 899999999875214578589997386888999999855767777
Q gi|254780786|r 80 KFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPV 124 (128)
Q Consensus 80 ~~ir~~l~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~v~~ 124 (128)
|+||+.||+++ +||+||+|+|++|++++++.+|++||++...++
T Consensus 83 g~iR~~L~~~l-~~r~~P~L~F~~D~~~~~~~~i~~ll~~~~~~~ 126 (129)
T 2e7g_A 83 AHMRHLLMSQQ-TLRNVPPIVFVQDKGNAALAELDQLLAVADSGP 126 (129)
T ss_dssp HHHHHHHHTCT-TCSCCCCEEEEETTCCCCCCCCCCCSCCCCCCC
T ss_pred HHHHHHHHHHC-CCCCCCEEEEEECCCHHHHHHHHHHHHHCCCCC
T ss_conf 99999999773-886188589996797789999999997457998
No 3
>>1pa4_A Probable ribosome-binding factor A; structural genomics, distant homology, BSGC structure funded by NIH, protein structure initiative, PSI; NMR {Mycoplasma pneumoniae} (A:)
Probab=99.96 E-value=1.5e-30 Score=192.52 Aligned_cols=114 Identities=18% Similarity=0.230 Sum_probs=106.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 77738999999999999999951413420126516898888985875655999982798647789999998568999999
Q gi|254780786|r 7 KNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRI 86 (128)
Q Consensus 7 ~~s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~L~~~~~~ir~~l 86 (128)
++|.|+.|++++|+++||++|.+ ++.||++. +||||+|++|+|+++|+|||+++|+.+.+.++++|++++|+||+.|
T Consensus 1 M~s~R~~r~~~~i~~~is~il~~-~i~d~~~~--~itIt~V~vs~D~~~a~Vy~s~~~~~~~~~~~~~L~~~~~~iR~~l 77 (116)
T 1pa4_A 1 MASYKKERLENDIIRLINRTVIH-EIYNETVK--TGHVTHVKLSDDLLHVTVYLDCYNREQIDRVVGAFNQAKGVFSRVL 77 (116)
T ss_dssp -----CCHHHHHHHHHHHHHHTT-CSSSSCHH--HHCCSCCEEETTTTEEEECCCCSSSSSHHHHHHHHHHTHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHH-HCCCCCCC--CEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 98578999999999999999997-56486768--3588799989997668999984672037999999999899999999
Q ss_pred HHHHHHCCCCCEEEEEECCCHHHHHHHHHHHCCHHHHH
Q ss_conf 99875214578589997386888999999855767777
Q gi|254780786|r 87 GRSLRNLRYVPELRFRYDTSLQSYWKLNALMCLPKIPV 124 (128)
Q Consensus 87 ~~~l~~lr~~P~L~F~~D~s~e~~~~I~~LL~~~~v~~ 124 (128)
|+++ .||++|+|+|++|++++++.+|++||++.+.++
T Consensus 78 ~~~l-~lr~~P~L~F~~D~~~e~~~~i~~lL~~~~~~~ 114 (116)
T 1pa4_A 78 AHNL-YLAKAVQIHFVKDKAIDNAMRIESIINSLKKSK 114 (116)
T ss_dssp HTTC-CCGGGCCCEECSSSTTSSCC-------------
T ss_pred HHHC-CCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCC
T ss_conf 9676-884498789997897789999999999987458
No 4
>>2dyj_A Ribosome-binding factor A; 16S rRNA processing, 17S RNA, KH domain, structural genomics, NPPSFA; 1.84A {Thermus thermophilus HB8} (A:)
Probab=99.92 E-value=5.3e-25 Score=161.13 Aligned_cols=94 Identities=18% Similarity=0.246 Sum_probs=86.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 73899999999999999995141342012651689888898587565599998279864778999999856899999999
Q gi|254780786|r 9 SRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSPDRVISALNCNIKFIRGRIGR 88 (128)
Q Consensus 9 s~R~~rv~~~i~~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~AkVyvs~~~~~~~~~~~~~L~~~~~~ir~~l~~ 88 (128)
|.|+.|++++|+++|+++|. +++||++. +||||+|++|+|+++|+|||++++ ++++++++|++++|+||+.||+
T Consensus 2 s~r~~r~~~~i~~~is~il~--~~~d~~~~--~vtIt~V~lS~D~~~a~Vy~s~~~--~~~~~~~~L~~~~~~iR~~l~~ 75 (95)
T 2dyj_A 2 AYGKAHLEAQLKRALAEEIQ--ALEDPRLF--LLTVEAVRLSKDGSVLSVYVEAFR--EEEGALRALSRAERRLVAALAR 75 (95)
T ss_dssp --CHHHHHHHHHHHHHHHHH--TCCCGGGT--TCEEEEEEECTTSSEEEEEEECSS--CHHHHHHHHHHTHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHHHHHHH--HHCCCCCC--CEEEEEEEECCCCCEEEEEEEECC--CCHHHHHHHHHHHHHHHHHHHH
T ss_conf 74589999999999999999--80686669--469979998899775999999744--4179999999989999999986
Q ss_pred HHHHCCCCCEEEEEECCCHHH
Q ss_conf 875214578589997386888
Q gi|254780786|r 89 SLRNLRYVPELRFRYDTSLQS 109 (128)
Q Consensus 89 ~l~~lr~~P~L~F~~D~s~e~ 109 (128)
++ .||++|+|+|++|+++|.
T Consensus 76 ~l-~lr~~P~L~F~~D~~~e~ 95 (95)
T 2dyj_A 76 RV-RMRRLPRLEFLPWRASPA 95 (95)
T ss_dssp TS-CCSSCCEEEEEEGGGCC-
T ss_pred HC-CCCCCCEEEEEECCCCCC
T ss_conf 67-980798689985599889
No 5
>>1w63_A Adapter-related protein complex 1 gamma 1 subunit; endocytosis, clathrin adaptor, transport, coated PITS; 4.0A {Mus musculus} (A:381-437)
Probab=44.72 E-value=4.3 Score=20.54 Aligned_cols=37 Identities=16% Similarity=0.265 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHC--CCCCEEEEEECC
Q ss_conf 7899999985689999999987521--457858999738
Q gi|254780786|r 69 DRVISALNCNIKFIRGRIGRSLRNL--RYVPELRFRYDT 105 (128)
Q Consensus 69 ~~~~~~L~~~~~~ir~~l~~~l~~l--r~~P~L~F~~D~ 105 (128)
++.+..|..+-..||.++..++-.+ ||.|.-+++.|.
T Consensus 8 ~eLL~yL~~~D~~fk~el~~kI~~laek~ap~~~W~idt 46 (57)
T 1w63_A 8 KELLYFLDSCEPEFKADCASGIFLAAEKYAPSKRWHIDT 46 (57)
T ss_dssp HHHHHHHHHCCHHHHHHHHHHHHHHHHSSCCCHHHHHHH
T ss_pred HHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 999999885508899999999999998277518779999
No 6
>>2vgl_A Adaptor protein complex AP-2, alpha 2 subunit; cytoplasmic vesicle, alternative splicing, endocytosis, lipid-binding, golgi apparatus, adaptor, membrane, transport; HET: IHP; 2.59A {Rattus norvegicus} PDB: 2jkr_A 2jkt_A (A:400-471)
Probab=37.98 E-value=4.8 Score=20.25 Aligned_cols=39 Identities=26% Similarity=0.263 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHC--CCCCEEEEEECCCH
Q ss_conf 7899999985689999999987521--45785899973868
Q gi|254780786|r 69 DRVISALNCNIKFIRGRIGRSLRNL--RYVPELRFRYDTSL 107 (128)
Q Consensus 69 ~~~~~~L~~~~~~ir~~l~~~l~~l--r~~P~L~F~~D~s~ 107 (128)
++.+..|..+-..||.++..++-.+ ||.|.-+++.|..+
T Consensus 8 ~eLL~yL~~~D~~~k~el~~kI~~laek~ap~~~W~idt~l 48 (72)
T 2vgl_A 8 AEMLSYLETADYSIREEIVLKVAILAEKYAVDYTWYVDTIL 48 (72)
T ss_dssp HHHHHHHHHCCHHHHHHHHHHHHHHHHHHCSSTHHHHHHHH
T ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 99997223578178999999999999757881899999999
No 7
>>1d0n_A Horse plasma gelsolin; mixed alpha-beta structure, actin-binding protein, protein domain packing, contractIle protein; 2.50A {Equus caballus} (A:389-482,A:598-707)
Probab=19.90 E-value=45 Score=14.79 Aligned_cols=42 Identities=17% Similarity=0.240 Sum_probs=31.0
Q ss_pred EEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf 599998279864778999999856899999999875214578589
Q gi|254780786|r 56 ATVYISLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELR 100 (128)
Q Consensus 56 AkVyvs~~~~~~~~~~~~~L~~~~~~ir~~l~~~l~~lr~~P~L~ 100 (128)
-.||+++..+...++-.++|..++.+|..--+++ . |++|--.
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~-~~~~~~~ 190 (204)
T 1d0n_A 149 DQVFVWVGKDSQDEEKTEALTSAKRYIDTDPAHR--D-RRTPITV 190 (204)
T ss_dssp SCEEEEECTTSCHHHHSSHHHHHHHHHHHCTTCC--C-TTCCEEE
T ss_pred CEEEEEECCCCCHHHHHHHHHHHHHHHHHCHHCC--C-CCCCEEE
T ss_conf 9899997899899999999999999997474129--9-8997499
No 8
>>1aoy_A Arginine repressor; DNA-binding protein, expression regulation, DNA organization, winged helix; NMR {Escherichia coli} (A:)
Probab=17.01 E-value=15 Score=17.52 Aligned_cols=42 Identities=10% Similarity=0.056 Sum_probs=28.3
Q ss_pred CCCCCHHHHHHHHHHH-------HHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCE
Q ss_conf 8777738999999999-------99999995141342012651689888898587565
Q gi|254780786|r 5 NPKNSRRALRVGEEVR-------SALMWVILNNEFQDRLISRDVISISEVCMSVDLRV 55 (128)
Q Consensus 5 ~~~~s~R~~rv~~~i~-------~~is~il~~~~~~d~~~~~~~vtIt~V~vS~Dl~~ 55 (128)
+.+.+.|+..+.++|+ ++|.+.|... ++.+||..-+|+||+-
T Consensus 4 m~~K~~R~~~I~~lI~~~~i~tQ~eL~~~L~~~---------G~~~vTQaTiSRDL~e 52 (78)
T 1aoy_A 4 SAKQEELVKAFKALLKEEKFSSQGEIVAALQEQ---------GFDNINQSKVSRMLTK 52 (78)
T ss_dssp CCCSTTHHHHHHHHHHTCCCCSHHHHHHHHHHH---------TCSSCCHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC---------CCCCHHHHHHHHHHHH
T ss_conf 688999999999999808978999999999983---------9851109889999999
No 9
>>1jmx_B Amine dehydrogenase; oxidoreductase; HET: TRQ HEC; 1.90A {Pseudomonas putida} (B:43-85)
Probab=14.98 E-value=83 Score=13.27 Aligned_cols=14 Identities=36% Similarity=0.311 Sum_probs=11.2
Q ss_pred EEEECCCCCEEEEE
Q ss_conf 88985875655999
Q gi|254780786|r 46 EVCMSVDLRVATVY 59 (128)
Q Consensus 46 ~V~vS~Dl~~AkVy 59 (128)
.+.+|||-++|.|.
T Consensus 5 t~~~spD~k~AyVL 18 (43)
T 1jmx_B 5 TAMMAPDNRTAYVL 18 (43)
T ss_dssp EEEECTTSSEEEEE
T ss_pred EEEECCCCCEEEEE
T ss_conf 79998898999999
No 10
>>1kmj_A Selenocysteine lyase; persulfide perselenide NIFS pyridoxal phosphate, structural genomics, PSI, protein structure initiative; HET: PLP; 2.00A {Escherichia coli} (A:1-33,A:320-406)
Probab=11.02 E-value=58 Score=14.16 Aligned_cols=81 Identities=7% Similarity=-0.091 Sum_probs=55.5
Q ss_pred CCCEEEEEEEEECCCCCE-EEEEEEECCCCCHHHHHHHHHHHHHHH------HHHHHHHHHHCCCCCEEEEEECCCHHHH
Q ss_conf 651689888898587565-599998279864778999999856899------9999998752145785899973868889
Q gi|254780786|r 38 SRDVISISEVCMSVDLRV-ATVYISLPLDVSPDRVISALNCNIKFI------RGRIGRSLRNLRYVPELRFRYDTSLQSY 110 (128)
Q Consensus 38 ~~~~vtIt~V~vS~Dl~~-AkVyvs~~~~~~~~~~~~~L~~~~~~i------r~~l~~~l~~lr~~P~L~F~~D~s~e~~ 110 (128)
.|.--+|.+|.+-.+-.. ..|=|++ .+.+.+.+...|....=.+ -..+...+ ....+=.+.|.+.++.++.
T Consensus 28 ~~~~~~IpgV~i~g~~~r~~ivsf~v-~gi~~~~i~~~L~~~gI~vsaG~~cas~vl~al-g~~g~VRiS~~~ynT~eEI 105 (120)
T 1kmj_A 28 DSAASAVPDLTLYGPQNRLGVIAFNL-GKHHAYDVGSFLDNYGIAVRTGHHXAMPLMAYY-NVPAMCRASLAMYNTHEEV 105 (120)
T ss_dssp CTTTCCSTTEEEESCTTCCSEEEEEE-TTCCHHHHHHHHHHTTEECEEECTTCHHHHHHT-TCSCEEEEECCTTCCHHHH
T ss_pred ECCCCCCCCEEECCCCCCCCEEEEEC-CCCCHHHHHHHHHHCCCEEECCCHHHHHHHHHH-CCCCEEEEECCCCCCHHHH
T ss_conf 38200689635258866675799973-898999999999778959975603225678861-8997899978898999999
Q ss_pred HHHHHHHCCH
Q ss_conf 9999985576
Q gi|254780786|r 111 WKLNALMCLP 120 (128)
Q Consensus 111 ~~I~~LL~~~ 120 (128)
++.-+.|++.
T Consensus 106 D~li~aL~~i 115 (120)
T 1kmj_A 106 DRLVTGLQRI 115 (120)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
T ss_conf 9999999999
Done!