Query 043289
Match_columns 695
No_of_seqs 208 out of 844
Neff 3.7
Searched_HMMs 29240
Date Mon Mar 25 05:21:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043289.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/043289hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1msz_A DNA-binding protein smu 99.1 8.4E-11 2.9E-15 102.7 6.0 64 432-495 16-80 (86)
2 1whr_A Hypothetical KIAA1002 p 98.6 3.7E-08 1.3E-12 90.9 6.8 63 435-499 34-97 (124)
3 2cpm_A Sperm-associated antige 98.5 3.5E-07 1.2E-11 80.8 8.3 60 436-495 15-76 (94)
4 3gku_A Probable RNA-binding pr 95.3 0.01 3.4E-07 59.8 3.9 59 436-494 152-211 (225)
5 1ug8_A Poly(A)-specific ribonu 79.2 2.3 7.8E-05 37.4 4.8 58 434-492 13-76 (87)
6 3lup_A DEGV family protein; PS 23.3 1.9E+02 0.0064 29.4 7.6 78 417-495 127-209 (285)
7 3d45_A Poly(A)-specific ribonu 15.7 32 0.0011 37.9 0.0 59 434-493 176-240 (507)
8 2a1r_A Poly(A)-specific ribonu 15.4 33 0.0011 37.0 0.0 59 434-493 181-245 (430)
9 3fdj_A DEGV family protein; GU 14.7 1.6E+02 0.0056 29.7 4.9 84 421-511 126-214 (278)
10 3zqp_A Terminase small subunit 13.1 1.7E+02 0.0057 28.2 4.1 59 416-474 71-142 (164)
No 1
>1msz_A DNA-binding protein smubp-2; R3H fold; NMR {Homo sapiens} SCOP: d.68.7.1
Probab=99.09 E-value=8.4e-11 Score=102.71 Aligned_cols=64 Identities=25% Similarity=0.474 Sum_probs=58.0
Q ss_pred CChHHHHHHHHHHHhcCCceeeeCC-CCccchHHHHHHHHHhCCcccccCCCcceEEEEEecCCC
Q 043289 432 VDLEDINSTLEQIVLEEVDMFSFQP-MHHRDCSQVRRLAAIYRLRSDSQGSGKKRFVTVTRTQHT 495 (695)
Q Consensus 432 ~dLedI~~EIe~FL~d~~dsLsFPP-MDk~~RK~VH~LA~~YnLKSkS~GkGkkRfpvL~KTkrT 495 (695)
....+|..+|+.|+.+..+.|.||| |+++.|++||.||..|+|+++|.|.|..|+++|+|...+
T Consensus 16 ~~~~~i~~~l~~F~~~~~~~l~FP~sLs~~eR~~IH~lA~~~GL~h~S~G~G~~R~l~V~k~~~~ 80 (86)
T 1msz_A 16 DGVDHFRAMIVEFMASKKMQLEFPPSLNSHDRLRVHQIAEEHGLRHDSSGEGKRRFITVSKRAGS 80 (86)
T ss_dssp -CCHHHHHHHHHHHHHTCSEEEECTTCCSHHHHHHHHHHHHTTEEEEEECSSSCCEEEEEECC--
T ss_pred hhHHHHHHHHHHHhcCCCcEEEcCCCCCHHHHHHHHHHHHHcCCCcceeeCCCCeEEEEEEeCCc
Confidence 4577899999999987799999999 899999999999999999999999999999999998654
No 2
>1whr_A Hypothetical KIAA1002 protein; R3H domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.68.7.1
Probab=98.63 E-value=3.7e-08 Score=90.88 Aligned_cols=63 Identities=16% Similarity=0.326 Sum_probs=57.2
Q ss_pred HHHHHHHHHHHhcC-CceeeeCCCCccchHHHHHHHHHhCCcccccCCCcceEEEEEecCCCCCCC
Q 043289 435 EDINSTLEQIVLEE-VDMFSFQPMHHRDCSQVRRLAAIYRLRSDSQGSGKKRFVTVTRTQHTCMPS 499 (695)
Q Consensus 435 edI~~EIe~FL~d~-~dsLsFPPMDk~~RK~VH~LA~~YnLKSkS~GkGkkRfpvL~KTkrT~~ps 499 (695)
..|..+|..||.++ .+.+.||||++..|..||+||..|+|.+..-|.| |+++|+||..|.+|.
T Consensus 34 l~lE~~i~~Fi~d~~~~~~ef~pmnSy~RllvHrvAe~ygL~h~~d~~~--r~VvV~Kt~~tr~P~ 97 (124)
T 1whr_A 34 LKLEQEILEFINDNNNQFKKFPQMTSYHRMLLHRVAAYFGMDHNVDQTG--KAVIINKTSNTRIPE 97 (124)
T ss_dssp HHHHHHHHHHHHCSSCCEEECCCCCHHHHHHHHHHHHHHTCCEEECSSC--SSEEEECCTTCCCCS
T ss_pred HHHHHHHHHHHhCCCccceECCCCCHHHHHHHHHHHHHhCcCccccCCC--CEEEEEeCCCCCCCh
Confidence 56778999999998 6779999999999999999999999999877765 889999999999885
No 3
>2cpm_A Sperm-associated antigen 7; R3H domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=98.47 E-value=3.5e-07 Score=80.81 Aligned_cols=60 Identities=18% Similarity=0.321 Sum_probs=53.0
Q ss_pred HHHHHHHHHHhcCCc-eeeeCCCCccchHHHHHHHHHhCCcccccCCCcc-eEEEEEecCCC
Q 043289 436 DINSTLEQIVLEEVD-MFSFQPMHHRDCSQVRRLAAIYRLRSDSQGSGKK-RFVTVTRTQHT 495 (695)
Q Consensus 436 dI~~EIe~FL~d~~d-sLsFPPMDk~~RK~VH~LA~~YnLKSkS~GkGkk-RfpvL~KTkrT 495 (695)
...+.|+.|+..... .+.|+||++..|++||.+|..|+|.|.|.|.+-. |+|||++...+
T Consensus 15 ~re~~L~~la~~~g~~~v~L~PM~~~eRriIH~~l~~~gl~S~S~Geep~~R~VvI~~~~~~ 76 (94)
T 2cpm_A 15 RMEKEVSDFIQDSGQIKKKFQPMNKIERSILHDVVEVAGLTSFSFGEDDDCRYVMIFKKEFA 76 (94)
T ss_dssp HHHHHHHHHHHCSSCCEEECCCCCSSHHHHHHHHHHHHTCEEEEECSSSSCCEEEEECSTTC
T ss_pred HHHHHHHHHHHhcCCCceEeCCCCHHHHHHHHHHHHHCCCEEEEecCCCCceEEEEEeCCCC
Confidence 345678888888766 5999999999999999999999999999999997 99999987654
No 4
>3gku_A Probable RNA-binding protein; APC21302, clostridium symbiosum ATCC 14 structural genomics, PSI-2, protein structure initiative; 2.95A {Clostridium symbiosum atcc 14940}
Probab=95.33 E-value=0.01 Score=59.80 Aligned_cols=59 Identities=14% Similarity=0.149 Sum_probs=48.3
Q ss_pred HHHHHHHHHHhcCCceeeeCCCCccchHHHHHHHHHh-CCcccccCCCcceEEEEEecCC
Q 043289 436 DINSTLEQIVLEEVDMFSFQPMHHRDCSQVRRLAAIY-RLRSDSQGSGKKRFVTVTRTQH 494 (695)
Q Consensus 436 dI~~EIe~FL~d~~dsLsFPPMDk~~RK~VH~LA~~Y-nLKSkS~GkGkkRfpvL~KTkr 494 (695)
++...+-.=|......+.|+||.+..|++||.....+ ++.+.|.|.|-.|++||+-.+.
T Consensus 152 ~lA~~~A~kV~~tg~~v~L~PM~~~ERriIH~al~~~~~V~T~SeGeep~R~VVI~~~~~ 211 (225)
T 3gku_A 152 TLAKNIAYKVKRTKRSVSLEPMNPYERRIIHAALQNDKYVVTRSDGEEPFRHVIISLKRE 211 (225)
T ss_dssp HHHHHHHHHHHHHCSCEECCCCCHHHHHHHHHHTTTCSSEEEEEESSTTSCEEEEEECCC
T ss_pred HHHHHHHHHHHHhCCEEEccCCCHHHHHHHHHHHccCCCcEEEEeecCCCeEEEEEEcCC
Confidence 3444444445566788999999999999999987776 8999999999999999987653
No 5
>1ug8_A Poly(A)-specific ribonuclease; R3H domain, poly(A)-specific 3'-exoribonuclease, PARN, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.68.7.1
Probab=79.16 E-value=2.3 Score=37.44 Aligned_cols=58 Identities=10% Similarity=0.233 Sum_probs=42.3
Q ss_pred hHHHHHHHHHHHhcCC-ceeeeCCCCccchHHHHHHHH-HhCCc----ccccCCCcceEEEEEec
Q 043289 434 LEDINSTLEQIVLEEV-DMFSFQPMHHRDCSQVRRLAA-IYRLR----SDSQGSGKKRFVTVTRT 492 (695)
Q Consensus 434 LedI~~EIe~FL~d~~-dsLsFPPMDk~~RK~VH~LA~-~YnLK----SkS~GkGkkRfpvL~KT 492 (695)
|++|.++|+.||.+.. +.|.+||...-.|+.|...+. .|.=+ +....+ +++++++.|-
T Consensus 13 id~i~~kIe~FL~s~~~~~l~l~pCN~f~RkLIYQ~~~~kfp~~i~vet~~~e~-~~~~ivv~~~ 76 (87)
T 1ug8_A 13 IDQVIEKIEDFLQSEEKRSLELDPCTGFQRKLIYQTLSWKYPKGIHVETLETDK-KERHIVISKV 76 (87)
T ss_dssp HHHHHHHHHHHHHCSSCCEEECCCCCSHHHHHHHHHHHHHSSSSEEEEEECCSS-SCSEEEEEEC
T ss_pred HHHHHHHHHHHHhCCCCCceecCCchHHHHHHHHHHHHHhcCCceEEEEEecCC-ceEEEEEEec
Confidence 7899999999999985 889999999999998876644 34322 333333 4566665544
No 6
>3lup_A DEGV family protein; PSI-2, MCSG, structural genomics, fatty acid binding, protei structure initiative; HET: ELA; 2.65A {Streptococcus agalactiae} SCOP: c.119.1.0
Probab=23.29 E-value=1.9e+02 Score=29.35 Aligned_cols=78 Identities=10% Similarity=0.156 Sum_probs=55.2
Q ss_pred HHHHHHHHhhhccCCCChHHHHHHHHHHHhcCCceeeeCCCCc---cc--hHHHHHHHHHhCCcccccCCCcceEEEEEe
Q 043289 417 EMIAVKRRERMLRRGVDLEDINSTLEQIVLEEVDMFSFQPMHH---RD--CSQVRRLAAIYRLRSDSQGSGKKRFVTVTR 491 (695)
Q Consensus 417 ~ere~kRaqgmL~rG~dLedI~~EIe~FL~d~~dsLsFPPMDk---~~--RK~VH~LA~~YnLKSkS~GkGkkRfpvL~K 491 (695)
+-..++++.+|+..|.++++|.+.|+.+......-+...-|+- -+ -+..--|++.+++|.--+=.-.-...++.|
T Consensus 127 ~g~~v~~A~~l~~~G~s~eeI~~~l~~~~~~~~~~f~v~~L~~L~kGGRis~~~a~ig~lL~IKPIl~~~~~G~l~~~~K 206 (285)
T 3lup_A 127 QGNLVRNALMCSREGMDFDVIVNKIQSQIEKIEGFIVVNDLNHLVKGGRLSNGSAIIGNLLSIKPVLHFNEEGKIVVYEK 206 (285)
T ss_dssp HHHHHHHHHHHHTTTCCHHHHHHHHHHHHTTCEEEEECSCTHHHHHHTCBTTHHHHHHHHTTSCCEEEECTTSCEEEEEC
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhcEEEEEECChHHHhhCCCccHHHHHHHHhhCcEEEEEEccCceEEEeee
Confidence 4456778888899999999999999998877666666555554 23 368888999999997654431223444555
Q ss_pred cCCC
Q 043289 492 TQHT 495 (695)
Q Consensus 492 TkrT 495 (695)
+ ||
T Consensus 207 v-Rg 209 (285)
T 3lup_A 207 V-RT 209 (285)
T ss_dssp C-SS
T ss_pred c-CC
Confidence 5 44
No 7
>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}
Probab=15.66 E-value=32 Score=37.86 Aligned_cols=59 Identities=10% Similarity=0.284 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHhcC-CceeeeCCCCccchHHHHHHHHH-h----CCcccccCCCcceEEEEEecC
Q 043289 434 LEDINSTLEQIVLEE-VDMFSFQPMHHRDCSQVRRLAAI-Y----RLRSDSQGSGKKRFVTVTRTQ 493 (695)
Q Consensus 434 LedI~~EIe~FL~d~-~dsLsFPPMDk~~RK~VH~LA~~-Y----nLKSkS~GkGkkRfpvL~KTk 493 (695)
++++..+|+.||... .+.|.+||+..+.|+.||.+... | .+.+ ..+.++.++++|.+..
T Consensus 176 ~~~~~~~I~~wl~~~~~~~l~i~~~n~~~r~Lv~q~l~~~fp~~v~~~~-~~~~~~~~~i~v~~~~ 240 (507)
T 3d45_A 176 IDQVIEKIEDFLQSEEKRSLELDPCTGFQRKLIYQTLSWKYPKGIHVET-LETDKKERHIVISKVD 240 (507)
T ss_dssp ------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHhcCCCCccccCCCcHHHHHHHHHHHHHhCCCceEeee-ccCCCcceeEEEEeCC
Confidence 567889999999877 56699999999999998876532 2 1222 2334556777765543
No 8
>2a1r_A Poly(A)-specific ribonuclease PARN; DEDD, nuclease domain, hydrolase-RNA complex; 2.60A {Homo sapiens} PDB: 2a1s_A
Probab=15.40 E-value=33 Score=37.04 Aligned_cols=59 Identities=10% Similarity=0.299 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHhcC-CceeeeCCCCccchHHHHHHHH-HhC----CcccccCCCcceEEEEEecC
Q 043289 434 LEDINSTLEQIVLEE-VDMFSFQPMHHRDCSQVRRLAA-IYR----LRSDSQGSGKKRFVTVTRTQ 493 (695)
Q Consensus 434 LedI~~EIe~FL~d~-~dsLsFPPMDk~~RK~VH~LA~-~Yn----LKSkS~GkGkkRfpvL~KTk 493 (695)
+++|.+.|+.||.+. ...|.+||...+.|+.||.+.. .|. +.+.... ++.++++|+|..
T Consensus 181 ~~~~~~~i~~~l~~~~~~~l~l~~~~~~qr~Lv~q~l~~~fp~~~~~~~~~~~-~~~~~v~v~k~~ 245 (430)
T 2a1r_A 181 IDQVVEKIEDLLQSEENKNLDLEPCTGFQRKLIYQTLSWKYPKGIHVETLETE-KKERYIVISKVD 245 (430)
T ss_dssp ------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHcCCCCCccccCCCcHHHHHHHHHHHHHhCCCceeeeeeeec-CCceEEEEEeCC
Confidence 567788889998876 5789999999999999998754 232 2222222 346777777764
No 9
>3fdj_A DEGV family protein; GUT microbiome, structural genomics, PSI-2, protein ST initiative, midwest center for structural genomics, MCSG; HET: MSE P6G PG4; 1.80A {Eubacterium eligens} SCOP: c.119.1.0
Probab=14.69 E-value=1.6e+02 Score=29.68 Aligned_cols=84 Identities=15% Similarity=0.276 Sum_probs=0.0
Q ss_pred HHHHhhhccCCCChHHHHHHHHHHHhcCCceeeeCCCCc-----cchHHHHHHHHHhCCcccccCCCcceEEEEEecCCC
Q 043289 421 VKRRERMLRRGVDLEDINSTLEQIVLEEVDMFSFQPMHH-----RDCSQVRRLAAIYRLRSDSQGSGKKRFVTVTRTQHT 495 (695)
Q Consensus 421 ~kRaqgmL~rG~dLedI~~EIe~FL~d~~dsLsFPPMDk-----~~RK~VH~LA~~YnLKSkS~GkGkkRfpvL~KTkrT 495 (695)
++++.+|+..|.++++|.+.|+.+......-+...-|+- |--+..--|++.+++|.--+-.-.-...++.|++..
T Consensus 126 v~~A~~~~~~G~s~~eI~~~l~~~~~~~~~~f~v~~L~~L~kGGRis~~~a~ig~lL~IKPIl~~~~~G~l~~~~KvRg~ 205 (278)
T 3fdj_A 126 LEQLQQMIEEGKKFEEIDGAIDAYMQKTRLFCSLKSLHNLAQNGRVSKVVASAAEVLGISVIGTASSHGTLEAIGKCRGD 205 (278)
T ss_dssp HHHHHHHHHTTCCHHHHHHHHHHHHTTEEEEEEESCCHHHHHTTSSCHHHHHGGGSTTEEEEEEECTTSSEEEEEEEESH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHhcceEEEEECChHHHHHCCcchHHHHHHHHhhCcEEEEEEccCCeEEEeeeecCH
Q ss_pred CCCCchhHHHHHHHHh
Q 043289 496 CMPSSADRLRLEKLIG 511 (695)
Q Consensus 496 ~~ps~~~~~rIekLL~ 511 (695)
+..+.+|+.
T Consensus 206 -------kka~~~l~~ 214 (278)
T 3fdj_A 206 -------KKLLVKLQA 214 (278)
T ss_dssp -------HHHHHHHHH
T ss_pred -------HHHHHHHHH
No 10
>3zqp_A Terminase small subunit; DNA-binding protein, DNA packaging; 3.00A {Bacillus phage SF6} PDB: 3zqq_A
Probab=13.07 E-value=1.7e+02 Score=28.25 Aligned_cols=59 Identities=10% Similarity=0.103 Sum_probs=0.0
Q ss_pred HHHHHHHHHhhhccCCCChHHHHHHHHHHHhcCC-------------ceeeeCCCCccchHHHHHHHHHhCC
Q 043289 416 KEMIAVKRRERMLRRGVDLEDINSTLEQIVLEEV-------------DMFSFQPMHHRDCSQVRRLAAIYRL 474 (695)
Q Consensus 416 K~ere~kRaqgmL~rG~dLedI~~EIe~FL~d~~-------------dsLsFPPMDk~~RK~VH~LA~~YnL 474 (695)
++.+++++++..-...++.++|.++|.+...... ..+..||=.+...|-+..|...|+|
T Consensus 71 ~~~I~el~~e~~~~~~~t~deVL~~Lt~Iarg~~~e~v~~~~~~G~~~~~~~~~~~~driKAlelLgK~~g~ 142 (164)
T 3zqp_A 71 RARIDARLKEINEKKILQANEVLEHLTRIALGQEKEQVLMGIGKGAETKTHVEVSAKDRIKALELLGKAHAV 142 (164)
T ss_dssp --------------CCCCHHHHHHHHHHHHTTCCEEEEEEEEETTEEEEEEEECCHHHHHHHHHHHHHHTTC
T ss_pred HHHHHHHHHHHHhhccCCHHHHHHHHHHHHcCCCceEEEeecCCCceeeeecCCCHHHHHHHHHHHHHHccc
Done!