Conserved Domains in CDD Database Detected by RPS-BLAST and HHsearch
Conserved Domains in CDD Database Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
Original result of RPS-BLASTagainst CDD database part II
Identity Alignment graph Length
Definition
E-value
Target 64
hypothetical protein CLIBASIA_03130 [Candidatus Liberib
PRK11827 60
PRK11827, PRK11827, hypothetical protein; Provisional
1e-07
pfam03966 47
pfam03966, Trm112p, Trm112p-like protein
1e-05
COG2835 60
COG2835, COG2835, Uncharacterized conserved protein [Fu
1e-13
>gnl|CDD|183328 PRK11827, PRK11827, hypothetical protein; Provisional
Back Show alignment and domain information
Score = 50.0 bits (119), Expect = 1e-07
Identities = 23/51 (45%), Positives = 35/51 (68%)
Query: 8 IDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEAR 58
+D +LLEI+ CP+ G L E EL+ K +LA+P+R G+P++L +EAR
Sbjct: 1 MDHRLLEIIACPVCNGKLWYNQEKQELICKLDNLAFPLRDGIPVLLETEAR 51
>gnl|CDD|146547 pfam03966, Trm112p, Trm112p-like protein
Back Show alignment and domain information
Score = 43.1 bits (102), Expect = 1e-05
Identities = 23/47 (48%), Positives = 26/47 (55%), Gaps = 7/47 (14%)
Query: 9 DPQLLEILVCPLTKGNLTLIS-------EGTELLSKKASLAYPIRSG 48
D LLEIL CPL KG L L+ E EL+ + LAYPIR G
Sbjct: 1 DLLLLEILACPLCKGPLALVEVAGHYDIEEGELVCPECGLAYPIRDG 47
The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices. Length = 47
>gnl|CDD|32663 COG2835, COG2835, Uncharacterized conserved protein [Function unknown]
Back Show alignment and domain information
Score = 70.2 bits (172), Expect = 1e-13
Identities = 26/55 (47%), Positives = 36/55 (65%)
Query: 8 IDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDD 62
+D +LLEIL CP+ KG L E EL+ + LAYPIR G+P++L EAR + +
Sbjct: 1 MDYRLLEILACPVCKGPLVYDEEKQELICPRCKLAYPIRDGIPVLLPDEARDLSE 55
Conserved Domains in CDD Database Detected by HHsearch
Original result of HHsearch against CDD database
Identity Alignment graph Length
Definition
Probability
Target
64
hypothetical protein CLIBASIA_03130 [Candidatus Liberib
PRK11827 60
hypothetical protein; Provisional
99.9
COG2835 60
Uncharacterized conserved protein [Function unknown]
99.86
pfam03966 47
Trm112p Trm112p-like protein. The function of this fami
99.27
KOG1088 124
consensus
98.0
PRK05580
699
primosome assembly protein PriA; Validated
92.3
pfam08271 40
TF_Zn_Ribbon TFIIB zinc-binding. The transcription fact
91.39
PRK00423
310
tfb transcription initiation factor IIB; Reviewed
91.18
COG1645 131
Uncharacterized Zn-finger containing protein [General f
90.9
PRK10220 111
hypothetical protein; Provisional
90.47
>PRK11827 hypothetical protein; Provisional
Back Show alignment and domain information
Probab=99.90 E-value=4.6e-25 Score=154.19 Aligned_cols=56 Identities=41% Similarity=0.790 Sum_probs=54.7
Q ss_pred CCHHHHHHHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHHEECCCC
Q ss_conf 28688965116789873689567885775210812401176340587771304458
Q gi|254780739|r 8 IDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQ 63 (64)
Q Consensus 8 ~~~~LL~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l~~~ 63 (64)
T Consensus 1 mD~kLL~ILvCP~ckg~L~yd~~~~ELic~~~~LAyPIrdgIPVmL~~eAR~Ls~d 56 (60)
T PRK11827 1 MDHRLLEIIACPVCNGKLWYNQEKQELICKLDNLAFPLRDGIPVLLETEARVLTAD 56 (60)
T ss_pred CCHHHHHEEECCCCCCCCEECCCCCEEEECCCCEECCCCCCCEECCHHHHCCCCHH
T ss_conf 98677322557788990339876898860664742655389732179994628763
>COG2835 Uncharacterized conserved protein [Function unknown]
Back Show alignment and domain information
Probab=99.86 E-value=6.8e-23 Score=142.69 Aligned_cols=56 Identities=46% Similarity=0.863 Sum_probs=54.4
Q ss_pred CCHHHHHHHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHHEECCCC
Q ss_conf 28688965116789873689567885775210812401176340587771304458
Q gi|254780739|r 8 IDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQ 63 (64)
Q Consensus 8 ~~~~LL~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l~~~ 63 (64)
T Consensus 1 md~~LLeiLaCP~~kg~L~~~~~~~~L~c~~~~~aYpI~dGIPvlL~~eaR~~~~d 56 (60)
T COG2835 1 MDYRLLEILACPVCKGPLVYDEEKQELICPRCKLAYPIRDGIPVLLPDEARDLSED 56 (60)
T ss_pred CCHHHHEEEECCCCCCCCEEECCCCEEEECCCCCEEECCCCCCCCCCHHHCCCHHH
T ss_conf 96103114666675895068156898971534813133469544385465261022
>pfam03966 Trm112p Trm112p-like protein
Back Show alignment and domain information
Probab=99.27 E-value=9.1e-13 Score=89.08 Aligned_cols=40 Identities=55% Similarity=0.836 Sum_probs=37.4
Q ss_pred CHHHHHHHCCCCCCCEE-------EEECCCCEEECHHCCCCCCCCCC
Q ss_conf 86889651167898736-------89567885775210812401176
Q gi|254780739|r 9 DPQLLEILVCPLTKGNL-------TLISEGTELLSKKASLAYPIRSG 48 (64)
Q Consensus 9 ~~~LL~iL~CP~~k~~L-------~~~~~~~~Lvc~~~~~~YPI~dg 48 (64)
T Consensus 1 ~~~ll~iL~CP~~kgpL~l~~~~~~~~~~egeLvC~~~~~~yPI~dG 47 (47)
T pfam03966 1 DLLLLEILACPLCKGPLALVEVAGHYDIEEGELVCPECGLAYPIRDG 47 (47)
T ss_pred CCCHHEEEECCCCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCC
T ss_conf 90321077555757834224443444611277862355602404689
The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices.
>KOG1088 consensus
Back Show alignment and domain information
Probab=98.00 E-value=1.3e-06 Score=56.59 Aligned_cols=34 Identities=32% Similarity=0.528 Sum_probs=28.5
Q ss_pred EEEECCCCEEECHHCCCCCCCCCCEEECCHHHHE
Q ss_conf 6895678857752108124011763405877713
Q gi|254780739|r 25 LTLISEGTELLSKKASLAYPIRSGVPIMLVSEAR 58 (64)
Q Consensus 25 L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr 58 (64)
T Consensus 90 le~~v~EG~l~CpetG~vfpI~~GIPNMLL~e~E 123 (124)
T KOG1088 90 LEIDVIEGELVCPETGRVFPISDGIPNMLLSEDE 123 (124)
T ss_pred HHHHHCCCEEECCCCCCEEECCCCCCCCCCCCCC
T ss_conf 5310102468668887376523588421258343
>PRK05580 primosome assembly protein PriA; Validated
Back Show alignment and domain information
Probab=92.30 E-value=0.08 Score=31.13 Aligned_cols=35 Identities=29% Similarity=0.434 Sum_probs=29.7
Q ss_pred HHHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCC
Q ss_conf 65116789873689567885775210812401176
Q gi|254780739|r 14 EILVCPLTKGNLTLISEGTELLSKKASLAYPIRSG 48 (64)
Q Consensus 14 ~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dg 48 (64)
T Consensus 412 ~~~~C~~C~~~L~~h~~~~~l~Ch~Cg~~~~~~~~ 446 (699)
T PRK05580 412 WVARCPHCDGPLTLHRAGRRLRCHHCGYQEPIPRA 446 (699)
T ss_pred CEEECCCCCCEEEECCCCCCEECCCCCCCCCCCCC
T ss_conf 94565678986342068983322646883657554
>pfam08271 TF_Zn_Ribbon TFIIB zinc-binding
Back Show alignment and domain information
Probab=91.39 E-value=0.14 Score=29.93 Aligned_cols=27 Identities=19% Similarity=0.358 Sum_probs=23.1
Q ss_pred HCCCCCCCE-EEEECCCCEEECHHCCCC
Q ss_conf 116789873-689567885775210812
Q gi|254780739|r 16 LVCPLTKGN-LTLISEGTELLSKKASLA 42 (64)
Q Consensus 16 L~CP~~k~~-L~~~~~~~~Lvc~~~~~~ 42 (64)
T Consensus 1 ~~Cp~Cg~~~~~~D~~~Ge~vC~~CG~V 28 (40)
T pfam08271 1 MKCPNCGSTEIVFDYERGEYVCTECGLV 28 (40)
T ss_pred CCCCCCCCCCEEEECCCCCEECCCCCEE
T ss_conf 9388799970677277897870579719
The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure.
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Back Show alignment and domain information
Probab=91.18 E-value=0.14 Score=29.82 Aligned_cols=30 Identities=23% Similarity=0.314 Sum_probs=24.7
Q ss_pred HHHCCCCCCCE-EEEECCCCEEECHHCCCCC
Q ss_conf 65116789873-6895678857752108124
Q gi|254780739|r 14 EILVCPLTKGN-LTLISEGTELLSKKASLAY 43 (64)
Q Consensus 14 ~iL~CP~~k~~-L~~~~~~~~Lvc~~~~~~Y 43 (64)
T Consensus 10 ~~~kCp~Cg~~~ii~D~~~G~~vC~~CG~Vi 40 (310)
T PRK00423 10 EELRCPECGSDKLIYDYERGEIVCADCGYVI 40 (310)
T ss_pred CEEECCCCCCCCEEEECCCCCEECCCCCCEE
T ss_conf 7358989869853567899877530288761
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Back Show alignment and domain information
Probab=90.90 E-value=0.13 Score=30.02 Aligned_cols=31 Identities=16% Similarity=0.200 Sum_probs=23.6
Q ss_pred HHHHHHCCCCCCCEEEEECCCCEEECHHCCCCCC
Q ss_conf 8896511678987368956788577521081240
Q gi|254780739|r 11 QLLEILVCPLTKGNLTLISEGTELLSKKASLAYP 44 (64)
Q Consensus 11 ~LL~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YP 44 (64)
T Consensus 25 kML~~-hCp~Cg~PLF~--KdG~v~CPvC~~~~~ 55 (131)
T COG1645 25 KMLAK-HCPKCGTPLFR--KDGEVFCPVCGYREV 55 (131)
T ss_pred HHHHH-HCCCCCCCCEE--ECCEEECCCCCCEEE
T ss_conf 78874-48655883163--089587777776677
>PRK10220 hypothetical protein; Provisional
Back Show alignment and domain information
Probab=90.47 E-value=0.19 Score=29.10 Aligned_cols=29 Identities=10% Similarity=0.303 Sum_probs=25.2
Q ss_pred HHCCCCCCCEEEEECCCCEEECHHCCCCCC
Q ss_conf 511678987368956788577521081240
Q gi|254780739|r 15 ILVCPLTKGNLTLISEGTELLSKKASLAYP 44 (64)
Q Consensus 15 iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YP 44 (64)
T Consensus 3 lP~CP~C~seytY-edg~~~vCpeC~hEW~ 31 (111)
T PRK10220 3 LPHCPKCNSEYTY-EDNGMYICPECAHEWN 31 (111)
T ss_pred CCCCCCCCCCCEE-CCCCEEECCCCCCCCC
T ss_conf 8869989892438-2799789977647479
Homologous Domains in SCOP and MMDB Database Detected by RPS-BLAST and HHsearch
Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST
Original result of RPS-BLAST against SCOP70(version1.75) database
Identity Alignment graph Length
Definition
E-value
Target
64
hypothetical protein CLIBASIA_03130 [Candidatus Liberib
d2hf1a1 59
b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromob
4e-17
d2jnya1 59
b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg15
8e-17
d2pk7a1 59
b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pse
1e-15
>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]} Length = 59
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class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Hypothetical protein CV3345
species: Chromobacterium violaceum [TaxId: 536]
Score = 80.4 bits (199), Expect = 4e-17
Identities = 27/54 (50%), Positives = 35/54 (64%)
Query: 9 DPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDD 62
D + LEILVCPL KG L EL+ K LA+PI+ G+P+ML SEAR++
Sbjct: 1 DAKFLEILVCPLCKGPLVFDKSKDELICKGDRLAFPIKDGIPMMLESEARELAP 54
>d2jnya1 b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg1592 {Corynebacterium glutamicum [TaxId: 1718]} Length = 59
Back Show information, alignment and structure
class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein Cgl1405/cg1592
species: Corynebacterium glutamicum [TaxId: 1718]
Score = 79.3 bits (196), Expect = 8e-17
Identities = 22/56 (39%), Positives = 35/56 (62%)
Query: 8 IDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQ 63
+DPQLLE+L CP KG L + L++++ +LAY I G+P++L+ EA +
Sbjct: 3 LDPQLLEVLACPKDKGPLRYLESEQLLVNERLNLAYRIDDGIPVLLIDEATEWTPN 58
>d2pk7a1 b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pseudomonas fluorescens [TaxId: 294]} Length = 59
Back Show information, alignment and structure
class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein PFL1779
species: Pseudomonas fluorescens [TaxId: 294]
Score = 75.4 bits (186), Expect = 1e-15
Identities = 30/51 (58%), Positives = 38/51 (74%)
Query: 12 LLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDD 62
LL+IL CP+ KG L L ++ TEL+SK A LAYPIR G+P+ML SEAR +
Sbjct: 3 LLDILACPICKGPLKLSADKTELISKGAGLAYPIRDGIPVMLESEARTLTT 53
Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
Identity Alignment graph Length
Definition
Probability
Target 64
hypothetical protein CLIBASIA_03130 [Candidatus Liberib
d2jnya1 59
Uncharacterized protein Cgl1405/cg1592 {Corynebacterium
99.88
d2hf1a1 59
Hypothetical protein CV3345 {Chromobacterium violaceum
99.85
d2pk7a1 59
Uncharacterized protein PFL1779 {Pseudomonas fluorescen
99.85
d1p91a_
268
rRNA methyltransferase RlmA {Escherichia coli [TaxId: 5
95.36
d1dl6a_ 58
Transcription initiation factor TFIIB, N-terminal domai
91.92
d1pfta_ 50
Transcription initiation factor TFIIB, N-terminal domai
90.42
>d2jnya1 b.171.1.1 (A:1-59) Uncharacterized protein Cgl1405/cg1592 {Corynebacterium glutamicum [TaxId: 1718]}
Back Hide information, alignment and structure
class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein Cgl1405/cg1592
species: Corynebacterium glutamicum [TaxId: 1718]
Probab=99.88 E-value=3.2e-24 Score=147.32 Aligned_cols=59 Identities=37% Similarity=0.747 Sum_probs=56.9
Q ss_pred HHCCHHHHHHHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHHEECCCCC
Q ss_conf 00286889651167898736895678857752108124011763405877713044589
Q gi|254780739|r 6 FNIDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQG 64 (64)
Q Consensus 6 ~~~~~~LL~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l~~~~ 64 (64)
|+||++||+||+||.||++|+|++++++|+|++|+++|||+|||||||+||||+++.+.
T Consensus 1 M~~~~~LL~iL~CP~ck~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deA~~l~~~~ 59 (59)
T d2jnya1 1 MSLDPQLLEVLACPKDKGPLRYLESEQLLVNERLNLAYRIDDGIPVLLIDEATEWTPNN 59 (59)
T ss_dssp CCSCGGGTCCCBCTTTCCBCEEETTTTEEEETTTTEEEEEETTEECCCSSCCEECCCCC
T ss_pred CCCCHHHHHHHCCCCCCCEEEEECCCCEEECCCCCCCCCCCCCCCCCCHHHHCCCCCCC
T ss_conf 99797999871587999870796889989748648545252995021899930177899
>d2hf1a1 b.171.1.1 (A:2-60) Hypothetical protein CV3345 {Chromobacterium violaceum [TaxId: 536]}
Back Show information, alignment and structure
class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Hypothetical protein CV3345
species: Chromobacterium violaceum [TaxId: 536]
Probab=99.85 E-value=2.5e-23 Score=142.57 Aligned_cols=55 Identities=49% Similarity=0.861 Sum_probs=52.9
Q ss_pred CHHHHHHHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHHEECCCC
Q ss_conf 8688965116789873689567885775210812401176340587771304458
Q gi|254780739|r 9 DPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQ 63 (64)
Q Consensus 9 ~~~LL~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l~~~ 63 (64)
|++||+|||||+|||+|+|++++++|+|++|+++|||+|||||||+++||+++++
T Consensus 1 D~~LL~iL~CP~ck~~L~~~~~~~~Lvc~~~~l~YPI~dGIPvlL~~eAr~l~~~ 55 (59)
T d2hf1a1 1 DAKFLEILVCPLCKGPLVFDKSKDELICKGDRLAFPIKDGIPMMLESEARELAPE 55 (59)
T ss_dssp CCCCEEECBCTTTCCBCEEETTTTEEEETTTTEEEEEETTEECCCGGGCEECCHH
T ss_pred CHHHHHHHCCCCCCCEEEEECCCCEEECCCCCCCCCCCCCCCCCCHHHHCCCCHH
T ss_conf 9667664358798986369588998963876844544189231289994318654
>d2pk7a1 b.171.1.1 (A:3-61) Uncharacterized protein PFL1779 {Pseudomonas fluorescens [TaxId: 294]}
Back Show information, alignment and structure
class: All beta proteins
fold: Trm112p-like
superfamily: Trm112p-like
family: Trm112p-like
domain: Uncharacterized protein PFL1779
species: Pseudomonas fluorescens [TaxId: 294]
Probab=99.85 E-value=5.6e-23 Score=140.74 Aligned_cols=53 Identities=57% Similarity=0.967 Sum_probs=51.3
Q ss_pred HHHHHHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHHEECCCC
Q ss_conf 88965116789873689567885775210812401176340587771304458
Q gi|254780739|r 11 QLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQ 63 (64)
Q Consensus 11 ~LL~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l~~~ 63 (64)
+||+|||||+|||+|+|++++++|+|++|+++|||+|||||||++|||+++++
T Consensus 2 kLL~iL~CP~ck~~L~~~~~~~~Lvc~~~~laYPI~dGIPvlL~~eAr~l~~~ 54 (59)
T d2pk7a1 2 KLLDILACPICKGPLKLSADKTELISKGAGLAYPIRDGIPVMLESEARTLTTE 54 (59)
T ss_dssp CGGGTCCCTTTCCCCEECTTSSEEEETTTTEEEEEETTEECCCGGGCEECCHH
T ss_pred CHHHHEECCCCCCCCEEECCCCEEECCCCCCCCCCCCCCCCCCHHHHCCCCHH
T ss_conf 34761478798986569488998964875855424089010589995207745
>d1p91a_ c.66.1.33 (A:) rRNA methyltransferase RlmA {Escherichia coli [TaxId: 562]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: rRNA methyltransferase RlmA
domain: rRNA methyltransferase RlmA
species: Escherichia coli [TaxId: 562]
Probab=95.36 E-value=0.0053 Score=34.98 Aligned_cols=40 Identities=15% Similarity=0.214 Sum_probs=29.7
Q ss_pred HCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHH
Q ss_conf 116789873689567885775210812401176340587771
Q gi|254780739|r 16 LVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEA 57 (64)
Q Consensus 16 L~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deA 57 (64)
++||+|+++|.... +.|+|..|+.....++|+-.+++...
T Consensus 2 f~CP~C~~~L~~~~--~~l~C~~~h~fd~~~~Gy~~ll~~~~ 41 (268)
T d1p91a_ 2 FSCPLCHQPLSREK--NSYICPQRHQFDMAKEGYVNLLPVQH 41 (268)
T ss_dssp BBCTTTCCBCEEET--TEEECTTCCEEEBCTTSCEECSCSSS
T ss_pred CCCCCCCHHHHCCC--CEEECCCCCCCCCCCCCEEECCCCCC
T ss_conf 64989981220579--86988999850656684576365654
>d1dl6a_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}
Back Show information, alignment and structure
class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]
Probab=91.92 E-value=0.034 Score=30.73 Aligned_cols=31 Identities=16% Similarity=0.281 Sum_probs=26.2
Q ss_pred HHHHHCCCCCCCE-EEEECCCCEEECHHCCCC
Q ss_conf 8965116789873-689567885775210812
Q gi|254780739|r 12 LLEILVCPLTKGN-LTLISEGTELLSKKASLA 42 (64)
Q Consensus 12 LL~iL~CP~~k~~-L~~~~~~~~Lvc~~~~~~ 42 (64)
+++-+.||.|++. +.+|...++++|..|++.
T Consensus 8 ~~~~~~Cp~Cgs~~ii~D~~~Ge~vC~~CG~V 39 (58)
T d1dl6a_ 8 ALPRVTCPNHPDAILVEDYRAGDMICPECGLV 39 (58)
T ss_dssp CCSCCSBTTBSSSCCEECSSSCCEECTTTCCE
T ss_pred CCCCCCCCCCCCCCEEEECCCCCEECCCCCCE
T ss_conf 55666897997987778878882850359989
>d1pfta_ g.41.3.1 (A:) Transcription initiation factor TFIIB, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}
Back Show information, alignment and structure
class: Small proteins
fold: Rubredoxin-like
superfamily: Zinc beta-ribbon
family: Transcriptional factor domain
domain: Transcription initiation factor TFIIB, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]
Probab=90.42 E-value=0.084 Score=28.62 Aligned_cols=27 Identities=26% Similarity=0.431 Sum_probs=23.6
Q ss_pred HCCCCCCC-EEEEECCCCEEECHHCCCC
Q ss_conf 11678987-3689567885775210812
Q gi|254780739|r 16 LVCPLTKG-NLTLISEGTELLSKKASLA 42 (64)
Q Consensus 16 L~CP~~k~-~L~~~~~~~~Lvc~~~~~~ 42 (64)
..||.|++ .+..|.+.++++|..|++.
T Consensus 6 ~~Cp~Cgs~~iv~D~~~Ge~vC~~CG~V 33 (50)
T d1pfta_ 6 KVCPACESAELIYDPERGEIVCAKCGYV 33 (50)
T ss_dssp CSCTTTSCCCEEEETTTTEEEESSSCCB
T ss_pred CCCCCCCCCCEEEECCCCEEECCCCCCE
T ss_conf 3484887983788878790850049869
Homologous Domains in MMDB70 Database Detected by RPS-BLAST
Original result of RPS-BLAST against MMDB70 database
Identity Alignment graph Length
Definition
E-value
Target
64
hypothetical protein CLIBASIA_03130 [Candidatus Li
2pk7_A_ 69
(A:) Uncharacterized protein; NESG, PLR1, putative
2e-16
2js4_A_ 70
(A:) UPF0434 protein BB2007; NESG, northeast struc
2e-16
2hf1_A_ 68
(A:) Tetraacyldisaccharide-1-P 4-kinase; LPXK, lip
2e-16
2jr6_A_ 68
(A:) UPF0434 protein NMA0874; solution, structural
3e-16
2jny_A_ 67
(A:) Uncharacterized BCR; structure, CGR1, NESG, s
4e-16
2kpi_A_ 56
(A:) Uncharacterized protein SCO3027; zinc finger,
1e-15
2k5r_A_ 97
(A:) Uncharacterized protein XF2673; solution stru
5e-12
>2pk7_A (A:) Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4KFT4, structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens pf-5}Length = 69
Back Hide alignment and structure
Score = 79.4 bits (196), Expect = 2e-16
Identities = 30/54 (55%), Positives = 39/54 (72%)
Query: 9 DPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDD 62
D +LL+IL CP+ KG L L ++ TEL+SK A LAYPIR G+P+ L SEAR +
Sbjct: 2 DTKLLDILACPICKGPLKLSADKTELISKGAGLAYPIRDGIPVXLESEARTLTT 55
>2js4_A (A:) UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}Length = 70
Back Show alignment and structure
Score = 79.0 bits (195), Expect = 2e-16
Identities = 26/56 (46%), Positives = 37/56 (66%)
Query: 8 IDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQ 63
++ +LL+ILVCP+ KG L EL+ LA+P+R GVPIML +EAR +D +
Sbjct: 1 MESRLLDILVCPVCKGRLEFQRAQAELVCNADRLAFPVRDGVPIMLEAEARSLDAE 56
>2hf1_A (A:) Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthesis, NESG, structural genomics, PSI-2; 1.90A {Chromobacterium violaceum atcc 12472}Length = 68
Back Show alignment and structure
Score = 78.9 bits (195), Expect = 2e-16
Identities = 26/54 (48%), Positives = 33/54 (61%)
Query: 9 DPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDD 62
D + LEILVCPL KG L EL+ K LA+PI+ G+P L SEAR++
Sbjct: 2 DAKFLEILVCPLCKGPLVFDKSKDELICKGDRLAFPIKDGIPXXLESEARELAP 55
>2jr6_A (A:) UPF0434 protein NMA0874; solution, structural genomics, PSI, protein structure initiative, northeast structural genomics consortium; NMR {Neisseria meningitidis Z2491}Length = 68
Back Show alignment and structure
Score = 78.2 bits (193), Expect = 3e-16
Identities = 26/56 (46%), Positives = 40/56 (71%)
Query: 8 IDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQ 63
++ + L+ILVCP+TKG L + EL S++A LAYPI+ G+P ML +EAR + ++
Sbjct: 1 MEKKFLDILVCPVTKGRLEYHQDKQELWSRQAKLAYPIKDGIPYMLENEARPLSEE 56
>2jny_A (A:) Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum}Length = 67
Back Show alignment and structure
Score = 77.8 bits (192), Expect = 4e-16
Identities = 22/57 (38%), Positives = 36/57 (63%)
Query: 7 NIDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQ 63
++DPQLLE+L CP KG L + L++++ +LAY I G+P++L+ EA +
Sbjct: 2 SLDPQLLEVLACPKDKGPLRYLESEQLLVNERLNLAYRIDDGIPVLLIDEATEWTPN 58
>2kpi_A (A:) Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}Length = 56
Back Show alignment and structure
Score = 76.2 bits (188), Expect = 1e-15
Identities = 20/54 (37%), Positives = 29/54 (53%)
Query: 8 IDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVD 61
++ LLEIL CP L + LAYP+R G+P++LV EAR+ +
Sbjct: 3 LEAGLLEILACPACHAPLEERDAELICTGQDCGLAYPVRDGIPVLLVDEARRPE 56
>2k5r_A (A:) Uncharacterized protein XF2673; solution structure, structural genomics, PSI-2, protein structure initiative; NMR {Xylella fastidiosa TEMECULA1}Length = 97
Back Show alignment and structure
Score = 64.3 bits (156), Expect = 5e-12
Identities = 14/82 (17%), Positives = 27/82 (32%), Gaps = 27/82 (32%)
Query: 8 IDPQLLEILVCPLTKGNLTLISEGT---------------------------ELLSKKAS 40
+D +LL +L P T+ L+L+ L+++
Sbjct: 1 MDRKLLHLLCSPDTRQPLSLLESKGLEALNKAIVSGTVQRADGSIQNQSLHEALITRDRK 60
Query: 41 LAYPIRSGVPIMLVSEARQVDD 62
+ I +P++L EA
Sbjct: 61 QVFRIEDSIPVLLPEEAIATIQ 82
Homologous Domains in MMDB70 Database Detected by HHsearch
Original result of HHsearch against MMDB70 database
Identity Alignment graph Length
Definition
Probability
Target 64
hypothetical protein CLIBASIA_03130 [Candidatus Liberib
2jny_A_ 67
Uncharacterized BCR; structure, CGR1, NESG, struct
99.88
2pk7_A_ 69
Uncharacterized protein; NESG, PLR1, putative tetr
99.87
2js4_A_ 70
UPF0434 protein BB2007; NESG, northeast structural
99.86
2hf1_A_ 68
Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A
99.86
2kpi_A_ 56
Uncharacterized protein SCO3027; zinc finger, PSI-
99.86
2jr6_A_ 68
UPF0434 protein NMA0874; solution, structural geno
99.86
2k5r_A_ 97
Uncharacterized protein XF2673; solution structure
99.83
2j6a_A_ 141
Protein TRM112; translation termination, methyltra
98.05
1p91_A_
269
Ribosomal RNA large subunit methyltransferase A; R
95.8
3k1f_M_1-57 57
Transcription initiation factor IIB; RNA polymeras
95.09
1pft_A_ 50
TFIIB, PFTFIIBN; N-terminal domain, transcription
93.9
1dl6_A_ 58
Transcription factor II B (TFIIB); zinc ribbon; NM
93.74
>2jny_A (A:) Uncharacterized BCR; structure, CGR1, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Corynebacterium glutamicum}
Back Hide alignment and structure
Probab=99.88 E-value=5.9e-24 Score=147.99 Aligned_cols=58 Identities=38% Similarity=0.758 Sum_probs=56.5
Q ss_pred HHCCHHHHHHHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHHEECCCC
Q ss_conf 0028688965116789873689567885775210812401176340587771304458
Q gi|254780739|r 6 FNIDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQ 63 (64)
Q Consensus 6 ~~~~~~LL~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l~~~ 63 (64)
|+||++||+||+||.||++|+|+.+.++|+|+.|+++|||+|||||||+||||.++++
T Consensus 1 M~~d~~LL~iL~CP~ck~~L~~~~~~~~Lvc~~~~~~yPI~dGIPvlL~dear~~~~~ 58 (67)
T 2jny_A 1 MSLDPQLLEVLACPKDKGPLRYLESEQLLVNERLNLAYRIDDGIPVLLIDEATEWTPN 58 (67)
T ss_dssp CCSCGGGTCCCBCTTTCCBCEEETTTTEEEETTTTEEEEEETTEECCCSSCCEECCCC
T ss_pred CCCCHHHHHHHCCCCCCCCCEEECCCCEEECCCCCCCCCCCCCCCCCCHHHHCCCCHH
T ss_conf 9979799988268798984659488997988865844635389010089994519999
>2pk7_A (A:) Uncharacterized protein; NESG, PLR1, putative tetraacyldisaccharide-1-P 4-kinase, Q4KFT4, structural genomics, PSI-2; 2.20A {Pseudomonas fluorescens pf-5}
Back Show alignment and structure
Probab=99.87 E-value=2.5e-23 Score=144.63 Aligned_cols=56 Identities=54% Similarity=0.918 Sum_probs=53.5
Q ss_pred CCHHHHHHHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHHEECCCC
Q ss_conf 28688965116789873689567885775210812401176340587771304458
Q gi|254780739|r 8 IDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQ 63 (64)
Q Consensus 8 ~~~~LL~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l~~~ 63 (64)
.|++||+|||||+|||+|+|+.+.++|+|+.|+++|||+|||||||++|||+++++
T Consensus 1 ~D~~LLeiLaCP~ckg~L~~~~~~~~Lvc~~~~laYPI~dgIPvlL~deAr~l~~~ 56 (69)
T 2pk7_A 1 XDTKLLDILACPICKGPLKLSADKTELISKGAGLAYPIRDGIPVXLESEARTLTTE 56 (69)
T ss_dssp --CCGGGTCCCTTTCCCCEECTTSSEEEETTTTEEEEEETTEECCCGGGCEECCHH
T ss_pred CCHHHHHHEECCCCCCEEEEECCCCEEECCCCCCCCCCCCCCCCCCHHHHCCCCHH
T ss_conf 98688867068799987469688997974876825515188322089996107777
>2js4_A (A:) UPF0434 protein BB2007; NESG, northeast structural genomics consortium, beta, PSI-2, protein structure initiative; NMR {Bordetella bronchiseptica RB50}
Back Show alignment and structure
Probab=99.86 E-value=5.3e-23 Score=142.93 Aligned_cols=57 Identities=46% Similarity=0.867 Sum_probs=54.8
Q ss_pred CCHHHHHHHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHHEECCCCC
Q ss_conf 286889651167898736895678857752108124011763405877713044589
Q gi|254780739|r 8 IDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQG 64 (64)
Q Consensus 8 ~~~~LL~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l~~~~ 64 (64)
||++||+||+||.||++|.|+.++++|+|+.|+++|||+|||||||+++||+++++.
T Consensus 1 md~~LL~iL~CP~ck~~L~~~~~~~~Lvc~~c~~~YPI~dGIPvLL~~ear~l~~~e 57 (70)
T 2js4_A 1 MESRLLDILVCPVCKGRLEFQRAQAELVCNADRLAFPVRDGVPIMLEAEARSLDAEA 57 (70)
T ss_dssp CCCCCCCCCBCTTTCCBEEEETTTTEEEETTTTEEEEEETTEECCCGGGSEESSSCC
T ss_pred CCHHHHHHHCCCCCCCEEEEECCCCEEECCCCCCCCCCCCCCCCCCHHHHCCCCCCC
T ss_conf 986889881687999985595889989647538656250890230899942066467
>2hf1_A (A:) Tetraacyldisaccharide-1-P 4-kinase; LPXK, lipid A biosynthesis, NESG, structural genomics, PSI-2; 1.90A {Chromobacterium violaceum atcc 12472}
Back Show alignment and structure
Probab=99.86 E-value=3e-23 Score=144.23 Aligned_cols=56 Identities=46% Similarity=0.805 Sum_probs=53.6
Q ss_pred CCHHHHHHHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHHEECCCC
Q ss_conf 28688965116789873689567885775210812401176340587771304458
Q gi|254780739|r 8 IDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQ 63 (64)
Q Consensus 8 ~~~~LL~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l~~~ 63 (64)
.|++||+|||||+|||+|.|+++.++|||+.|+++|||+|||||||++|||+++++
T Consensus 1 ~D~~LLeiLaCP~ckg~L~~~~~~~~Lvc~~~~laYPI~dGIPvlL~~eAr~l~~~ 56 (68)
T 2hf1_A 1 XDAKFLEILVCPLCKGPLVFDKSKDELICKGDRLAFPIKDGIPXXLESEARELAPE 56 (68)
T ss_dssp -CCCCEEECBCTTTCCBCEEETTTTEEEETTTTEEEEEETTEECCCGGGCEECCHH
T ss_pred CCHHHHHHHCCCCCCCEEEEECCCCEEECCCCCCCCCCCCCCCCCCHHHHCCCCHH
T ss_conf 98699878368798987379488998963876865625289022189994639999
>2kpi_A (A:) Uncharacterized protein SCO3027; zinc finger, PSI-2, NESG, all beta, structural genomics, protein structure initiative; NMR {Streptomyces coelicolor}
Back Show alignment and structure
Probab=99.86 E-value=3.5e-23 Score=143.88 Aligned_cols=56 Identities=36% Similarity=0.667 Sum_probs=54.3
Q ss_pred HHCCHHHHHHHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHHEECC
Q ss_conf 00286889651167898736895678857752108124011763405877713044
Q gi|254780739|r 6 FNIDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVD 61 (64)
Q Consensus 6 ~~~~~~LL~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l~ 61 (64)
|+||++||+||+||+|||+|+|+.++++|+|++|+++|||+|||||||+||||+++
T Consensus 1 M~~d~~LL~iL~CP~ck~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvlL~dear~le 56 (56)
T 2kpi_A 1 MPLEAGLLEILACPACHAPLEERDAELICTGQDCGLAYPVRDGIPVLLVDEARRPE 56 (56)
T ss_dssp CCCCCSCTTSCCCSSSCSCEEEETTEEEECSSSCCCEEEEETTEECCCTTTCBCCC
T ss_pred CCCCHHHHHHHCCCCCCCCCEECCCCCEEECCCCCEECCCCCCCCCCCHHHHCCCC
T ss_conf 99797999883388999945072877889768777036452891030988822779
>2jr6_A (A:) UPF0434 protein NMA0874; solution, structural genomics, PSI, protein structure initiative, northeast structural genomics consortium; NMR {Neisseria meningitidis Z2491}
Back Show alignment and structure
Probab=99.86 E-value=4.7e-23 Score=143.18 Aligned_cols=56 Identities=46% Similarity=0.887 Sum_probs=54.0
Q ss_pred CCHHHHHHHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHHEECCCC
Q ss_conf 28688965116789873689567885775210812401176340587771304458
Q gi|254780739|r 8 IDPQLLEILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQVDDQ 63 (64)
Q Consensus 8 ~~~~LL~iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l~~~ 63 (64)
||++||+||+||+||++|.|+.++++|+|+.|+++|||+|||||||+++||+++++
T Consensus 1 md~~LL~iL~CP~ck~~L~~~~~~~~Lvc~~c~~~YPI~dGIPvlL~dear~l~~~ 56 (68)
T 2jr6_A 1 MEKKFLDILVCPVTKGRLEYHQDKQELWSRQAKLAYPIKDGIPYMLENEARPLSEE 56 (68)
T ss_dssp CCCSSSCCCBCSSSCCBCEEETTTTEEEETTTTEEEEEETTEECCCTTTCEECCHH
T ss_pred CCHHHHHHHCCCCCCCEEEEECCCCEEECCCCCCCCCCCCCCCCCCHHHHCCCCHH
T ss_conf 98699978179798998179688998962865865625289022289994509999
>2k5r_A (A:) Uncharacterized protein XF2673; solution structure, structural genomics, PSI-2, protein structure initiative; NMR {Xylella fastidiosa TEMECULA1}
Back Show alignment and structure
Probab=99.83 E-value=6.6e-22 Score=137.14 Aligned_cols=56 Identities=25% Similarity=0.464 Sum_probs=52.4
Q ss_pred CCHHHHHHHCCCCCCCEEEEECC---------------------------CCEEECHHCCCCCCCCCCEEECCHHHHEEC
Q ss_conf 28688965116789873689567---------------------------885775210812401176340587771304
Q gi|254780739|r 8 IDPQLLEILVCPLTKGNLTLISE---------------------------GTELLSKKASLAYPIRSGVPIMLVSEARQV 60 (64)
Q Consensus 8 ~~~~LL~iL~CP~~k~~L~~~~~---------------------------~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l 60 (64)
|+++||+|||||.|||+|+|.++ .++|+|+.|+++|||+|||||||+|+||.+
T Consensus 1 M~~~LLdiLaCP~ck~~L~l~~~~~~~~~~~~~~~g~~~~~~~~~~~ei~~g~L~C~~c~~~YPI~dGIPvLL~dear~~ 80 (97)
T 2k5r_A 1 MDRKLLHLLCSPDTRQPLSLLESKGLEALNKAIVSGTVQRADGSIQNQSLHEALITRDRKQVFRIEDSIPVLLPEEAIAT 80 (97)
T ss_dssp CCTTTCSSCCCCTTSSCCEECCHHHHHHHHHHHHHTCCBCTTSCBCCCCCSEEEECTTSCEEEEEETTEEECCGGGEEEG
T ss_pred CCHHHHHHHCCCCCCCCCEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCEEECCCCCEEEECCCCCCEECHHHHHHH
T ss_conf 98688757178798991356453220012333201100122333224402484875764856244389332579997135
Q ss_pred CCC
Q ss_conf 458
Q gi|254780739|r 61 DDQ 63 (64)
Q Consensus 61 ~~~ 63 (64)
++|
T Consensus 81 ~~d 83 (97)
T 2k5r_A 81 IQI 83 (97)
T ss_dssp GGC
T ss_pred HHH
T ss_conf 676
>2j6a_A (A:) Protein TRM112; translation termination, methyltransferase, transferase, ERF1, nuclear protein, protein methylation; 1.7A {Saccharomyces cerevisiae}
Back Show alignment and structure
Probab=98.05 E-value=5.8e-07 Score=58.02 Aligned_cols=29 Identities=21% Similarity=0.414 Sum_probs=24.6
Q ss_pred ECCCCEEECHHCCCCCCCCCCEEECCHHH
Q ss_conf 56788577521081240117634058777
Q gi|254780739|r 28 ISEGTELLSKKASLAYPIRSGVPIMLVSE 56 (64)
Q Consensus 28 ~~~~~~Lvc~~~~~~YPI~dgIPvLL~de 56 (64)
+..++.|+|+.|++.|||++|||.||..|
T Consensus 104 ~V~EG~LvCp~cgr~fpI~~GIPNMLL~e 132 (141)
T 2j6a_A 104 SIAEGEMKCRNCGHIYYIKNGIPNLLLPP 132 (141)
T ss_dssp EEEEEEEECTTTCCEEEEETTEESSCCCS
T ss_pred EEEECEEECCCCCCCCCCCCCCCCCCCCH
T ss_conf 75524688799998821326856546655
>1p91_A (A:) Ribosomal RNA large subunit methyltransferase A; RLMA, RRMA, 23S rRNA, NESG, structural genomics, PSI, protein structure initiative; HET: SAM; 2.80A {Escherichia coli}
Back Show alignment and structure
Probab=95.80 E-value=0.0067 Score=36.50 Aligned_cols=44 Identities=14% Similarity=0.224 Sum_probs=36.9
Q ss_pred HHCCCCCCCEEEEECCCCEEECHHCCCCCCCCCCEEECCHHHHEEC
Q ss_conf 5116789873689567885775210812401176340587771304
Q gi|254780739|r 15 ILVCPLTKGNLTLISEGTELLSKKASLAYPIRSGVPIMLVSEARQV 60 (64)
Q Consensus 15 iL~CP~~k~~L~~~~~~~~Lvc~~~~~~YPI~dgIPvLL~deAr~l 60 (64)
.|+||.|+++|...+ ..+.|..|+..++.++|+-.++.+..+..
T Consensus 2 ~~~Cp~c~~~l~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 45 (269)
T 1p91_A 2 SFSCPLCHQPLSREK--NSYICPQRHQFDXAKEGYVNLLPVQHKRS 45 (269)
T ss_dssp CBBCTTTCCBCEEET--TEEECTTCCEEEBCTTSCEECSCSSSSCS
T ss_pred CEECCCCCHHHHCCC--CEEEECCCCCCCCCCCCEEECCCCCCCCC
T ss_conf 524889980441679--87993899631655684253475544456
>3k1f_M (M:1-57) Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae}
Back Show alignment and structure
Probab=95.09 E-value=0.012 Score=35.17 Aligned_cols=35 Identities=20% Similarity=0.286 Sum_probs=28.9
Q ss_pred CCHHHHHHHCCCCCCC---EEEEECCCCEEECHHCCCC
Q ss_conf 2868896511678987---3689567885775210812
Q gi|254780739|r 8 IDPQLLEILVCPLTKG---NLTLISEGTELLSKKASLA 42 (64)
Q Consensus 8 ~~~~LL~iL~CP~~k~---~L~~~~~~~~Lvc~~~~~~ 42 (64)
..+.+-+.++||.|++ .|..|.+.+++||..|++.
T Consensus 14 ~~~~~~~~~~CPeC~s~~~~lv~D~~~Ge~VC~~CGlV 51 (57)
T 3k1f_M 14 RGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLV 51 (57)
T ss_dssp CSSCCCCCCCCTTTCCSSCCEEEEGGGTEEEETTTCBB
T ss_pred CCCCCEEEEECCCCCCCCCEEEEECCCCCEECCCCCEE
T ss_conf 79998644689899998988988798896797358919
>1pft_A (A:) TFIIB, PFTFIIBN; N-terminal domain, transcription initiation factor; NMR {Pyrococcus furiosus}
Back Show alignment and structure
Probab=93.90 E-value=0.041 Score=32.33 Aligned_cols=28 Identities=25% Similarity=0.393 Sum_probs=25.0
Q ss_pred HHCCCCCCC-EEEEECCCCEEECHHCCCC
Q ss_conf 511678987-3689567885775210812
Q gi|254780739|r 15 ILVCPLTKG-NLTLISEGTELLSKKASLA 42 (64)
Q Consensus 15 iL~CP~~k~-~L~~~~~~~~Lvc~~~~~~ 42 (64)
-..||.|++ .+.+|.+.+++||..|++.
T Consensus 5 ~~~Cp~Cg~~~iv~D~~~Ge~vC~~CG~V 33 (50)
T 1pft_A 5 QKVCPACESAELIYDPERGEIVCAKCGYV 33 (50)
T ss_dssp CCSCTTTSCCCEEEETTTTEEEESSSCCB
T ss_pred CCCCCCCCCCCEEEECCCCEEECCCCCCE
T ss_conf 55592987982788788791851269859
>1dl6_A (A:) Transcription factor II B (TFIIB); zinc ribbon; NMR {Homo sapiens}
Back Show alignment and structure
Probab=93.74 E-value=0.032 Score=32.89 Aligned_cols=33 Identities=15% Similarity=0.237 Sum_probs=27.6
Q ss_pred HHHHHHCCCCCCC-EEEEECCCCEEECHHCCCCC
Q ss_conf 8896511678987-36895678857752108124
Q gi|254780739|r 11 QLLEILVCPLTKG-NLTLISEGTELLSKKASLAY 43 (64)
Q Consensus 11 ~LL~iL~CP~~k~-~L~~~~~~~~Lvc~~~~~~Y 43 (64)
...+...||.|++ .+.+|.+.+++||..|++.-
T Consensus 7 ~~~~~~~Cp~Cg~~~iv~D~~~Ge~vC~~CG~Vl 40 (58)
T 1dl6_A 7 DALPRVTCPNHPDAILVEDYRAGDMICPECGLVV 40 (58)
T ss_dssp CCCSCCSBTTBSSSCCEECSSSCCEECTTTCCEE
T ss_pred CCCCCCCCCCCCCCCEEEECCCCEEECCCCCCEE
T ss_conf 3557559969979877788788818520299893