Query gi|254781077|ref|YP_003065490.1| hypothetical protein CLIBASIA_04895 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 111
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Mon May 30 04:05:12 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781077.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3661 AguA Alpha-glucuronida 63.9 2.5 6.3E-05 23.2 0.5 44 11-57 54-97 (684)
2 cd08033 LARP_6 La RNA-binding 36.0 7.7 0.0002 20.3 -0.6 40 55-109 11-50 (77)
3 KOG1817 consensus 30.6 43 0.0011 16.0 2.5 51 47-106 5-56 (533)
4 cd08029 LA_like_fungal La-moti 30.3 12 0.0003 19.3 -0.5 39 55-108 11-49 (76)
5 cd08032 LARP_7 La RNA-binding 26.8 15 0.00039 18.6 -0.4 41 54-109 15-55 (82)
6 pfam07807 RED_C RED-like prote 25.7 35 0.0009 16.5 1.3 17 90-106 87-103 (118)
7 pfam04153 NOT2_3_5 NOT2 / NOT3 23.9 43 0.0011 16.0 1.5 27 14-40 18-61 (130)
8 pfam05383 La La domain. This p 22.5 20 0.0005 18.0 -0.5 40 54-108 7-46 (60)
9 cd08030 LA_like_plant La-motif 21.3 24 0.00061 17.5 -0.3 41 53-108 10-50 (90)
10 TIGR02533 type_II_gspE general 18.2 71 0.0018 14.7 1.6 25 37-61 271-295 (495)
No 1
>COG3661 AguA Alpha-glucuronidase [Carbohydrate transport and metabolism]
Probab=63.95 E-value=2.5 Score=23.19 Aligned_cols=44 Identities=32% Similarity=0.428 Sum_probs=37.5
Q ss_pred HHCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEEEEEEEECCCCC
Q ss_conf 73276666774478876543000021000004355400331220456
Q gi|254781077|r 11 SSMGINYNIPACYPDPLEDSSLFYHFHSTLNLMTLHLPLRLQEEGIS 57 (111)
Q Consensus 11 ssmginynipacypdpledsslfyhfhstlnlmtlhlplrlqeegis 57 (111)
++.|| -|+|+..+++|.+....--.++....+.||++|.|||.-
T Consensus 54 ~lvGi---tP~~~sa~~~~~~~l~~s~a~~a~~~~~l~~~LgEEGy~ 97 (684)
T COG3661 54 GLVGI---TPASASAGARDGVILLASGATPAITGLGLPLKLGEEGYL 97 (684)
T ss_pred HHCCC---CHHHHCCCCCCCEEEEECCCCHHHCCCCCCCCCCCCCEE
T ss_conf 33077---814413565562289842676776055666223675259
No 2
>cd08033 LARP_6 La RNA-binding domain of La-related protein 6. This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=36.04 E-value=7.7 Score=20.34 Aligned_cols=40 Identities=28% Similarity=0.336 Sum_probs=29.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHEECC
Q ss_conf 4561005410013354007789987410000045556667686543223210004
Q gi|254781077|r 55 GISQSNLRTDHNVKQHVAITPILQMLDLTNCRHSRVNQWRQISNIIGYKKIKRIN 109 (111)
Q Consensus 55 gisqsnlrtdhnvkqhvaitpilqmldltncrhsrvnqwrqisniigykkikrin 109 (111)
-.|.+||+.|.-.++++.-. -+.|-.|+.|.+++|+|...
T Consensus 11 YFSd~NL~~D~fL~~~~~~~---------------~~G~V~i~~i~~F~rmk~lt 50 (77)
T cd08033 11 YFSDENLLKDAFLLKHVRRN---------------KEGYVPIKLIASFKKVKALT 50 (77)
T ss_pred HCCHHHCCCCHHHHHHHCCC---------------CCCCEEHHHHHCCHHHHHHC
T ss_conf 82661115489999984457---------------89989639975362699875
No 3
>KOG1817 consensus
Probab=30.62 E-value=43 Score=16.02 Aligned_cols=51 Identities=29% Similarity=0.551 Sum_probs=32.5
Q ss_pred EEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH-HHHHHHHHHHHE
Q ss_conf 003312204561005410013354007789987410000045556667-686543223210
Q gi|254781077|r 47 LPLRLQEEGISQSNLRTDHNVKQHVAITPILQMLDLTNCRHSRVNQWR-QISNIIGYKKIK 106 (111)
Q Consensus 47 lplrlqeegisqsnlrtdhnvkqhvaitpilqmldltncrhsrvnqwr-qisniigykkik 106 (111)
+.+++..+|.-...+|.| |-||+..+|.+ |.|-|.+|-- .....|||+--.
T Consensus 5 ~~~~~~~~gf~~tg~~~d--v~~h~~m~~~~-------~~hir~~~~l~~~e~~i~y~f~~ 56 (533)
T KOG1817 5 VTVELSSQGFWKTGIRSD--VCQHAMMLPVL-------THHIRYHQSLDHLEELIGYTFQD 56 (533)
T ss_pred EEEEECCCHHHHHCCCHH--HHHHHHHHHHH-------HHHHHHHHHHHHHHHHHCEEECC
T ss_conf 058504430877176469--99888989998-------61366887699999984713121
No 4
>cd08029 LA_like_fungal La-motif domain of fungal proteins similar to the La autoantigen. This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=30.29 E-value=12 Score=19.30 Aligned_cols=39 Identities=31% Similarity=0.418 Sum_probs=26.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHEEC
Q ss_conf 456100541001335400778998741000004555666768654322321000
Q gi|254781077|r 55 GISQSNLRTDHNVKQHVAITPILQMLDLTNCRHSRVNQWRQISNIIGYKKIKRI 108 (111)
Q Consensus 55 gisqsnlrtdhnvkqhvaitpilqmldltncrhsrvnqwrqisniigykkikri 108 (111)
-.|.+||++|.-.++++.- .-+.|-.|+.|.+++|+|.+
T Consensus 11 YFSD~NL~~D~fL~~~~~~---------------~~dG~V~i~~i~~F~rmk~l 49 (76)
T cd08029 11 YFSDSNLPTDKFLWTLTGG---------------SNNGWVPIKTIASFKRMRRF 49 (76)
T ss_pred HCCHHHCCCCHHHHHHHCC---------------CCCCCEEHHHHHCCHHHHHC
T ss_conf 2663102418899998666---------------88998966997536178867
No 5
>cd08032 LARP_7 La RNA-binding domain of La-related protein 7. LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.
Probab=26.85 E-value=15 Score=18.59 Aligned_cols=41 Identities=17% Similarity=0.376 Sum_probs=28.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHEECC
Q ss_conf 04561005410013354007789987410000045556667686543223210004
Q gi|254781077|r 54 EGISQSNLRTDHNVKQHVAITPILQMLDLTNCRHSRVNQWRQISNIIGYKKIKRIN 109 (111)
Q Consensus 54 egisqsnlrtdhnvkqhvaitpilqmldltncrhsrvnqwrqisniigykkikrin 109 (111)
--.|.+||+.|.-.++++.-. -+.|-.|+-|.+++++|...
T Consensus 15 fYFSD~NL~~D~fL~~~~~~~---------------~dG~V~i~~i~sF~rmk~Lt 55 (82)
T cd08032 15 FWFGDVNLHKDRFLREQIEKS---------------RDGYIDISLLVSFNKMKKLT 55 (82)
T ss_pred HHCCCCCCCCCHHHHHHHHCC---------------CCCCEEHHHHHHHHHHHHHC
T ss_conf 636530023179999997158---------------89979679987216999874
No 6
>pfam07807 RED_C RED-like protein C-terminal region. This family contains sequences that are similar to the C-terminal region of Red protein. This and related proteins are thought to be localized to the nucleus, and contain a RED repeat which consists of a number of RE and RD sequence elements. The region in question has several conserved NLS sequences. The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated or that the protein self-aggregates extremely efficiently.
Probab=25.68 E-value=35 Score=16.49 Aligned_cols=17 Identities=18% Similarity=0.431 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHE
Q ss_conf 56667686543223210
Q gi|254781077|r 90 VNQWRQISNIIGYKKIK 106 (111)
Q Consensus 90 vnqwrqisniigykkik 106 (111)
-++|++|++||--+|..
T Consensus 87 dre~~kI~~Il~krK~~ 103 (118)
T pfam07807 87 DRELQKINKILAKRKME 103 (118)
T ss_pred HHHHHHHHHHHHHHHCC
T ss_conf 79999999999974144
No 7
>pfam04153 NOT2_3_5 NOT2 / NOT3 / NOT5 family. NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This family includes NOT2, NOT3 and NOT5.
Probab=23.87 E-value=43 Score=15.98 Aligned_cols=27 Identities=33% Similarity=0.654 Sum_probs=18.0
Q ss_pred CCCCCCCCCCC------C-----------CCCCCCEEEEEEEEE
Q ss_conf 76666774478------8-----------765430000210000
Q gi|254781077|r 14 GINYNIPACYP------D-----------PLEDSSLFYHFHSTL 40 (111)
Q Consensus 14 ginynipacyp------d-----------pledsslfyhfhstl 40 (111)
-..|.+|.||. + .+++..|||.|-+--
T Consensus 18 ~~~y~iP~~y~~~~~~~~~p~~~~~~~~~~~~~~tLFyiFY~~~ 61 (130)
T pfam04153 18 PPQYKIPECYLNTSSYPQQPPPLSPSKFQKFDLETLFYIFYYMP 61 (130)
T ss_pred CCCCCCCCHHCCCCCCCCCCCCCCHHHHHCCCCCCEEEEECCCC
T ss_conf 98878961001455556678873578884168742477852589
No 8
>pfam05383 La La domain. This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain.
Probab=22.51 E-value=20 Score=17.99 Aligned_cols=40 Identities=25% Similarity=0.403 Sum_probs=28.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHEEC
Q ss_conf 0456100541001335400778998741000004555666768654322321000
Q gi|254781077|r 54 EGISQSNLRTDHNVKQHVAITPILQMLDLTNCRHSRVNQWRQISNIIGYKKIKRI 108 (111)
Q Consensus 54 egisqsnlrtdhnvkqhvaitpilqmldltncrhsrvnqwrqisniigykkikri 108 (111)
-=.|.+||++|.-.++++.-. -+.|-.|+-|.+++|+|..
T Consensus 7 fYFSd~NL~~D~fL~~~~~~~---------------~dg~V~i~~i~~F~r~k~l 46 (60)
T pfam05383 7 YYFSDENLPRDKFLRKQMDKD---------------PDGYVPISTIASFKRIKKL 46 (60)
T ss_pred HHCCHHHCCCCHHHHHHHCCC---------------CCCCEEHHHHHCCCHHHHH
T ss_conf 005775405388999986278---------------8981851998447039887
No 9
>cd08030 LA_like_plant La-motif domain of plant proteins similar to the La autoantigen. This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=21.29 E-value=24 Score=17.47 Aligned_cols=41 Identities=20% Similarity=0.243 Sum_probs=26.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHEEC
Q ss_conf 20456100541001335400778998741000004555666768654322321000
Q gi|254781077|r 53 EEGISQSNLRTDHNVKQHVAITPILQMLDLTNCRHSRVNQWRQISNIIGYKKIKRI 108 (111)
Q Consensus 53 eegisqsnlrtdhnvkqhvaitpilqmldltncrhsrvnqwrqisniigykkikri 108 (111)
|--.|.+||.+|.-.++++.-. -+.|-.|+-|..++|+|.+
T Consensus 10 EfYFsD~NL~~D~fL~~~i~~~---------------~dG~V~i~~i~sF~rmk~l 50 (90)
T cd08030 10 EFYFSDSNLPRDDFLLEEVEED---------------PDGMVSLALICSFSRMRSL 50 (90)
T ss_pred HHHCCCCCCCCCHHHHHHHCCC---------------CCCCEEHHHHHCCHHHHHH
T ss_conf 7004644344089999984468---------------9998846998615699998
No 10
>TIGR02533 type_II_gspE general secretory pathway protein E; InterPro: IPR013369 GspE, the E protein of the type II secretion system, is also referred to as the main terminal branch of the general secretion pathway. ; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=18.18 E-value=71 Score=14.73 Aligned_cols=25 Identities=32% Similarity=0.477 Sum_probs=21.4
Q ss_pred EEEEEEEEEEEEEEEECCCCCCCCC
Q ss_conf 0000043554003312204561005
Q gi|254781077|r 37 HSTLNLMTLHLPLRLQEEGISQSNL 61 (111)
Q Consensus 37 hstlnlmtlhlplrlqeegisqsnl 61 (111)
.++.|.+|.-=|.-.|=+||+|--.
T Consensus 271 ~~~~NIlTvEDPVEY~i~GIgQ~Qv 295 (495)
T TIGR02533 271 TPERNILTVEDPVEYQIEGIGQIQV 295 (495)
T ss_pred CCCCCEEEEECCEEEEECCCCEEEE
T ss_conf 8997156865782476248763651
Done!