peg_816

peg_816

GeneID in NCBI database:Locus tag:
Protein GI in NCBI database:not defined in NCBI databaseProtein Accession:
Gene range:-(874850, 875143)Protein Length:97aa
Gene description:
COG prediction:none
KEGG prediction:not defined in KEGG
SEED prediction:DNA repair protein RadC
Pathway involved in KEGG:not defined
Subsystem involved in SEED:DNA repair, bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------
LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII
cccccccccccEEEEEEcccccEEEcHHHHHHHHHHccccEEEEEEEcccccccccHHHHHHHHHHHHHHHHcccEEEEEEEEccccEEEHHHcccc
ccccccHHHEEccEEEEEccccccccHHHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHccccEEEccEEEEccccEEEHHHcccc
lfldkhniliadevqsrgtidhvPVYIREIVQRCLELSATSIIlvhnhpsgnpnpsdadinMTQNIittlnplniivhdhiiigkdafvsfkglrii
LFLDKHNIliadevqsrgtidhvPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII
LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQniittlnplniiVHDHIIIGKDAFVSFKGLRII
LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII
LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII
LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII
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LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII
LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII
LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target97
315122683237 DNA repair protein RadC [Candidatus Liberibacter solana 1 4e-43
159184835280 DNA repair protein RadC [Agrobacterium tumefaciens str. 1 5e-35
325292997281 DNA repair protein RadC [Agrobacterium sp. H13-3] Lengt 1 1e-34
170744786247 DNA repair protein RadC [Methylobacterium sp. 4-46] Len 1 1e-34
222148674278 DNA repair protein RadC [Agrobacterium vitis S4] Length 1 2e-34
220927247242 DNA repair protein RadC [Methylobacterium nodulans ORS 1 5e-34
86357475274 DNA repair protein RadC [Rhizobium etli CFN 42] Length 1 8e-34
90419162257 DNA repair protein [Aurantimonas manganoxydans SI85-9A1 1 8e-34
218510678274 DNA repair protein RadC [Rhizobium etli Brasil 5] Lengt 1 9e-34
190891537274 DNA repair protein [Rhizobium etli CIAT 652] Length = 2 1 1e-33
>gi|315122683|ref|YP_004063172.1| DNA repair protein RadC [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 237 Back     alignment and organism information
 Score =  177 bits (449), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 84/97 (86%), Positives = 92/97 (94%)

Query: 1   LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADI 60
           LFL+KH++LIADE+QSRGTIDHVPVY+REIV RCLELSA+SIILVHNHPSGNPNPS+ADI
Sbjct: 141 LFLNKHDVLIADEIQSRGTIDHVPVYLREIVYRCLELSASSIILVHNHPSGNPNPSNADI 200

Query: 61  NMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII 97
            MTQNII+TL PLNI VHDHIIIGKD FVSFKGLRII
Sbjct: 201 GMTQNIISTLTPLNITVHDHIIIGKDEFVSFKGLRII 237


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|159184835|ref|NP_354601.2| DNA repair protein RadC [Agrobacterium tumefaciens str. C58] Length = 280 Back     alignment and organism information
>gi|325292997|ref|YP_004278861.1| DNA repair protein RadC [Agrobacterium sp. H13-3] Length = 281 Back     alignment and organism information
>gi|170744786|ref|YP_001773441.1| DNA repair protein RadC [Methylobacterium sp. 4-46] Length = 247 Back     alignment and organism information
>gi|222148674|ref|YP_002549631.1| DNA repair protein RadC [Agrobacterium vitis S4] Length = 278 Back     alignment and organism information
>gi|220927247|ref|YP_002502549.1| DNA repair protein RadC [Methylobacterium nodulans ORS 2060] Length = 242 Back     alignment and organism information
>gi|86357475|ref|YP_469367.1| DNA repair protein RadC [Rhizobium etli CFN 42] Length = 274 Back     alignment and organism information
>gi|90419162|ref|ZP_01227072.1| DNA repair protein [Aurantimonas manganoxydans SI85-9A1] Length = 257 Back     alignment and organism information
>gi|218510678|ref|ZP_03508556.1| DNA repair protein RadC [Rhizobium etli Brasil 5] Length = 274 Back     alignment and organism information
>gi|190891537|ref|YP_001978079.1| DNA repair protein [Rhizobium etli CIAT 652] Length = 274 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target97
PRK00024224 PRK00024, PRK00024, hypothetical protein; Reviewed 4e-38
pfam04002123 pfam04002, DUF2466, Protein of unknown function (DUF246 8e-31
TIGR00608218 TIGR00608, radc, DNA repair protein radc 6e-29
COG2003224 COG2003, RadC, DNA repair proteins [DNA replication, re 1e-28
cd08071113 cd08071, MPN_DUF2466, Mov34/MPN/PAD-1 family 2e-31
cd08059101 cd08059, MPN_prok_mb, Mpr1p, Pad1p N-terminal (MPN) dom 7e-04
>gnl|CDD|178801 PRK00024, PRK00024, hypothetical protein; Reviewed Back     alignment and domain information
>gnl|CDD|146570 pfam04002, DUF2466, Protein of unknown function (DUF2466) Back     alignment and domain information
>gnl|CDD|161955 TIGR00608, radc, DNA repair protein radc Back     alignment and domain information
>gnl|CDD|32186 COG2003, RadC, DNA repair proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|163702 cd08071, MPN_DUF2466, Mov34/MPN/PAD-1 family Back     alignment and domain information
>gnl|CDD|163690 cd08059, MPN_prok_mb, Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 97
TIGR00608223 radc DNA repair protein RadC; InterPro: IPR001405 RadC 100.0
PRK00024224 radC DNA repair protein RadC; Reviewed 100.0
pfam04002123 DUF2466 Protein of unknown function (DUF2466). This fam 100.0
COG2003224 RadC DNA repair proteins [DNA replication, recombinatio 100.0
COG1310134 Predicted metal-dependent protease of the PAD1/JAB1 sup 92.41
>TIGR00608 radc DNA repair protein RadC; InterPro: IPR001405 RadC is a DNA repair protein found in many bacteria Back     alignment and domain information
>PRK00024 radC DNA repair protein RadC; Reviewed Back     alignment and domain information
>pfam04002 DUF2466 Protein of unknown function (DUF2466) Back     alignment and domain information
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only] Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target97
2qlc_A126 The Crystal Structure Of Dna Repair Protein Radc Fr 1e-26
>gi|158430296|pdb|2QLC|A Chain A, The Crystal Structure Of Dna Repair Protein Radc From Chlorobium Tepidum Tls Length = 126 Back     alignment and structure
 Score =  122 bits (308), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 36/97 (37%), Positives = 57/97 (58%)

Query: 1   LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADI 60
           LFL   N ++  E  + GT+    ++ REI +  +  SA SIILVHNHPSG+  PS+AD 
Sbjct: 30  LFLSTKNQILRHETITIGTLTASLIHPREIFKAAIRESAHSIILVHNHPSGDVQPSNADK 89

Query: 61  NMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII 97
            +T  +    + L I + DH+I+G + + SF+   ++
Sbjct: 90  QVTSILKKAGDLLQIELLDHVIVGNNDWFSFRDHALL 126


Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target97
2qlc_A126 DNA repair protein RADC homolog; MCSG, structural genom 6e-23
>2qlc_A DNA repair protein RADC homolog; MCSG, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; HET: DNA; 2.30A {Chlorobium tepidum tls} Length = 126 Back     alignment and structure
 Score =  101 bits (252), Expect = 6e-23
 Identities = 36/97 (37%), Positives = 57/97 (58%)

Query: 1   LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADI 60
           LFL   N ++  E  + GT+    ++ REI +  +  SA SIILVHNHPSG+  PS+AD 
Sbjct: 30  LFLSTKNQILRHETITIGTLTASLIHPREIFKAAIRESAHSIILVHNHPSGDVQPSNADK 89

Query: 61  NMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII 97
            +T  +    + L I + DH+I+G + + SF+   ++
Sbjct: 90  QVTSILKKAGDLLQIELLDHVIVGNNDWFSFRDHALL 126


Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target97
2qlc_A126 DNA repair protein RADC homolog; MCSG, structural genom 100.0
2kks_A146 Uncharacterized protein; NESG, structural genomics, PSI 92.5
2kcq_A153 MOV34/MPN/PAD-1 family; NESG, structure, structural gen 92.46
1oi0_A124 AF2198, hypothetical protein AF2198; proteasome, deubiq 95.52
>2qlc_A DNA repair protein RADC homolog; MCSG, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; HET: DNA; 2.30A {Chlorobium tepidum tls} Back     alignment and structure
Probab=100.00  E-value=3.2e-39  Score=251.08  Aligned_cols=97  Identities=37%  Similarity=0.587  Sum_probs=95.9

Q ss_pred             CCCCCCCCEEEEEEEEECCCCEEEECHHHHHHHHHHHCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEE
Q ss_conf             95156887734899854046358932999999999731968999955689898814778999999999997649889979
Q 537021.9.peg.8    1 LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDH   80 (97)
Q Consensus         1 l~Ld~~~~li~~e~i~~Gt~~~~~v~~r~i~~~al~~~A~~vilaHNHPsG~~~PS~~Di~~T~~l~~a~~~l~i~llDH   80 (97)
                      +|||++|++|+++.+++||++++.++||+||++||..+|+++|++||||||+++||++|+++|++|+++|+.+||+|+||
T Consensus        30 l~Ld~~~~~i~~~~i~~Gt~~~~~v~pR~i~~~al~~~A~~vIlaHNHPSG~~~PS~~D~~~T~~l~~a~~~l~i~llDH  109 (126)
T 2qlc_A           30 LFLSTKNQILRHETITIGTLTASLIHPREIFKAAIRESAHSIILVHNHPSGDVQPSNADKQVTSILKKAGDLLQIELLDH  109 (126)
T ss_dssp             EEECTTCBEEEEEEEEESSCCGGGCCHHHHHHHHHHTTCSEEEEEEECSSSCCSCCHHHHHHHHHHHHHHHHHTCEEEEE
T ss_pred             EEECCCCCEEEEEEECCCCCCEEEECHHHHHHHHHHHCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             99869998997999775816688742999999999816875999986797989968899999999999998779779779


Q ss_pred             EEECCCCEEEHHHCCCC
Q ss_conf             99859959974525899
Q 537021.9.peg.8   81 IIIGKDAFVSFKGLRII   97 (97)
Q Consensus        81 iIv~~~~~~S~re~gll   97 (97)
                      +|||+++||||||+|+|
T Consensus       110 iIv~~~~~~S~re~gll  126 (126)
T 2qlc_A          110 VIVGNNDWFSFRDHALL  126 (126)
T ss_dssp             EEECSSCEEETTTTTCC
T ss_pred             EEEECCCEEEHHHCCCC
T ss_conf             99939919982314789



>2kks_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiative; NMR {Desulfitobacterium hafniense Y51} Back     alignment and structure
>2kcq_A MOV34/MPN/PAD-1 family; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Salinibacter ruber dsm 13855} Back     alignment and structure
>1oi0_A AF2198, hypothetical protein AF2198; proteasome, deubiquitination, archaea, hydrolase; 1.5A {Archaeoglobus fulgidus} SCOP: c.97.3.1 PDB: 1r5x_A Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

No hit with e-value below 0.005

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target97
d1oi0a_121 Hypothetical protein AF2198 {Archaeon Archaeoglobus ful 95.82
>d1oi0a_ c.97.3.1 (A:) Hypothetical protein AF2198 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: JAB1/MPN domain
family: JAB1/MPN domain
domain: Hypothetical protein AF2198
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]
Probab=95.82  E-value=0.0041  Score=37.07  Aligned_cols=51  Identities=24%  Similarity=0.425  Sum_probs=38.4

Q ss_pred             HHHCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEEEEC----CCCEEEHHHCC
Q ss_conf             97319689999556898988147789999999999976498899799985----99599745258
Q 537021.9.peg.8   35 LELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDHIIIG----KDAFVSFKGLR   95 (97)
Q Consensus        35 l~~~A~~vilaHNHPsG~~~PS~~Di~~T~~l~~a~~~l~i~llDHiIv~----~~~~~S~re~g   95 (97)
                      ...+-.-+-+.|-||+|.+.||+.|++.-       +..|+   =|+|++    .++|-.|+..|
T Consensus        59 ~~~~~~ivgi~HSHP~~~a~PS~~D~~~~-------~~~g~---~~~Ivs~p~~~~~~~~~~~~G  113 (121)
T d1oi0a_          59 LPIGMKVFGTVHSHPSPSCRPSEEDLSLF-------TRFGK---YHIIVCYPYDENSWKCYNRKG  113 (121)
T ss_dssp             --CCCEEEEEEEEESSSCCSCCHHHHHHH-------HHSCS---EEEEEETTCCTTCEEEEETTS
T ss_pred             HHCCCEEEEEEEECCCCCCCCCHHHHHHH-------HCCCC---EEEEEECCCCCCCEEEEECCC
T ss_conf             31587699999726899997698999742-------50698---899996788988899994898



Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 97
2qlc_A_126 (A:) DNA repair protein RADC homolog; MCSG, struct 5e-24
>2qlc_A (A:) DNA repair protein RADC homolog; MCSG, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; HET: DNA; 2.30A {Chlorobium tepidum tls}Length = 126 Back     alignment and structure
 Score =  104 bits (260), Expect = 5e-24
 Identities = 36/97 (37%), Positives = 57/97 (58%)

Query: 1   LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADI 60
           LFL   N ++  E  + GT+    ++ REI +  +  SA SIILVHNHPSG+  PS+AD 
Sbjct: 30  LFLSTKNQILRHETITIGTLTASLIHPREIFKAAIRESAHSIILVHNHPSGDVQPSNADK 89

Query: 61  NMTQNIITTLNPLNIIVHDHIIIGKDAFVSFKGLRII 97
            +T  +    + L I + DH+I+G + + SF+   ++
Sbjct: 90  QVTSILKKAGDLLQIELLDHVIVGNNDWFSFRDHALL 126


Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target97
2qlc_A_126 DNA repair protein RADC homolog; MCSG, structural 100.0
1oi0_A_124 AF2198, hypothetical protein AF2198; proteasome, d 93.24
>2qlc_A (A:) DNA repair protein RADC homolog; MCSG, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; HET: DNA; 2.30A {Chlorobium tepidum tls} Back     alignment and structure
Probab=100.00  E-value=6e-38  Score=244.46  Aligned_cols=97  Identities=37%  Similarity=0.587  Sum_probs=95.9

Q ss_pred             CCCCCCCCEEEEEEEEECCCCEEEECHHHHHHHHHHHCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEE
Q ss_conf             95156887734899854046358932999999999731968999955689898814778999999999997649889979
Q 537021.9.peg.8    1 LFLDKHNILIADEVQSRGTIDHVPVYIREIVQRCLELSATSIILVHNHPSGNPNPSDADINMTQNIITTLNPLNIIVHDH   80 (97)
Q Consensus         1 l~Ld~~~~li~~e~i~~Gt~~~~~v~~r~i~~~al~~~A~~vilaHNHPsG~~~PS~~Di~~T~~l~~a~~~l~i~llDH   80 (97)
                      +|||++|++++++.+++||++++.++||+||++||+.+|+++|++||||||+++||++|+++|++|+++|+.+||+|+||
T Consensus        30 l~Ld~~~~ii~~~~i~~Gt~~~~~v~~R~i~~~al~~~A~~vil~HNHPsG~~~PS~~D~~~T~~l~~a~~~l~I~llDH  109 (126)
T 2qlc_A           30 LFLSTKNQILRHETITIGTLTASLIHPREIFKAAIRESAHSIILVHNHPSGDVQPSNADKQVTSILKKAGDLLQIELLDH  109 (126)
T ss_dssp             EEECTTCBEEEEEEEEESSCCGGGCCHHHHHHHHHHTTCSEEEEEEECSSSCCSCCHHHHHHHHHHHHHHHHHTCEEEEE
T ss_pred             EEECCCCCEEEEEEECCCCCCEEEECHHHHHHHHHHCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             99879998878999715777457883999999999816975999987477889978667999999999997689889769


Q ss_pred             EEECCCCEEEHHHCCCC
Q ss_conf             99859959974525899
Q 537021.9.peg.8   81 IIIGKDAFVSFKGLRII   97 (97)
Q Consensus        81 iIv~~~~~~S~re~gll   97 (97)
                      +|||+++||||||+|+|
T Consensus       110 iIi~~~~~~S~~e~gll  126 (126)
T 2qlc_A          110 VIVGNNDWFSFRDHALL  126 (126)
T ss_dssp             EEECSSCEEETTTTTCC
T ss_pred             EEEECCEEEEHHHCCCC
T ss_conf             99929909986635789



>1oi0_A (A:) AF2198, hypothetical protein AF2198; proteasome, deubiquitination, archaea, hydrolase; 1.5A {Archaeoglobus fulgidus} Back     alignment and structure