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 122
30S ribosomal protein S13 [Candidatus Liberibacter asia
PRK05179 122
PRK05179, rpsM, 30S ribosomal protein S13; Validated
7e-52
TIGR03631 113
TIGR03631, bact_S13, 30S ribosomal protein S13
4e-46
CHL00137 122
CHL00137, rps13, ribosomal protein S13; Validated
7e-36
pfam00416 106
pfam00416, Ribosomal_S13, Ribosomal protein S13/S18
8e-29
PRK04053 149
PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed
9e-16
TIGR03629 144
TIGR03629, arch_S13P, archaeal ribosomal protein S13P
2e-15
KOG3311 152
KOG3311, KOG3311, KOG3311, Ribosomal protein S18 [Trans
1e-11
PTZ00134 154
PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisio
2e-06
COG0099 121
COG0099, RpsM, Ribosomal protein S13 [Translation, ribo
4e-38
>gnl|CDD|179955 PRK05179, rpsM, 30S ribosomal protein S13; Validated
Back Show alignment and domain information
Score = 197 bits (503), Expect = 7e-52
Identities = 74/111 (66%), Positives = 90/111 (81%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
MARIAGV+IPR KRVV AL YI+GIG +++I I P+ RV L + E+ +IR+ I
Sbjct: 1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEI 60
Query: 61 EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRK 111
+++Y+VEGDLRR V+MNIKRLMD+GCYRGLRHRRGLPVRGQRT TNARTRK
Sbjct: 61 DKNYKVEGDLRREVSMNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRK 111
>gnl|CDD|163364 TIGR03631, bact_S13, 30S ribosomal protein S13
Back Show alignment and domain information
Score = 178 bits (453), Expect = 4e-46
Identities = 72/109 (66%), Positives = 84/109 (77%)
Query: 3 RIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62
RIAGV+IP KRV AL YI+GIG ++ I K I P++RV L E E+ IR+ IE
Sbjct: 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEA 60
Query: 63 DYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRK 111
Y+VEGDLRR V++NIKRLMD+GCYRGLRHRRGLPVRGQRT TNARTRK
Sbjct: 61 KYKVEGDLRREVSLNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRK 109
This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type. Length = 113
>gnl|CDD|177059 CHL00137, rps13, ribosomal protein S13; Validated
Back Show alignment and domain information
Score = 144 bits (364), Expect = 7e-36
Identities = 66/122 (54%), Positives = 88/122 (72%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
M RIAGV++PR KR+ AL YI+GIG S+++I K I P+ R L + ++ +R+ I
Sbjct: 1 MVRIAGVDLPRNKRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREII 60
Query: 61 EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVAR 120
E++YQVEGDLRR ++NIKRLM++ CYRG RHR GLPVRGQRT TNARTR+ K +
Sbjct: 61 EENYQVEGDLRRFESLNIKRLMEINCYRGRRHRLGLPVRGQRTRTNARTRRGAKKTVAGK 120
Query: 121 KR 122
K+
Sbjct: 121 KK 122
>gnl|CDD|144128 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18
Back Show alignment and domain information
Score = 120 bits (304), Expect = 8e-29
Identities = 53/107 (49%), Positives = 68/107 (63%), Gaps = 1/107 (0%)
Query: 3 RIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62
RI N+ K++ AL YI GIG + + I K + ++RV +L E E+ +IR I
Sbjct: 1 RILNTNLDGNKKIEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRIRDIISN 60
Query: 63 DYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNART 109
Y VE DLRR + +I+RL + CYRGLRH RGLPVRGQRT TNART
Sbjct: 61 -YVVENDLRRKIRNDIERLKKIRCYRGLRHIRGLPVRGQRTKTNART 106
This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes. Length = 106
>gnl|CDD|179731 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed
Back Show alignment and domain information
Score = 77.2 bits (191), Expect = 9e-16
Identities = 47/142 (33%), Positives = 70/142 (49%), Gaps = 25/142 (17%)
Query: 3 RIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62
RIAG ++ K V AL I GIG ++++ I KL + P ++ L + E+ +I +A+E
Sbjct: 11 RIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALED 70
Query: 63 DYQ----------------------VEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRG 100
+ + DL TV +I R+ + YRG+RH GL VRG
Sbjct: 71 PAEEGIPSWMLNRRKDYETGEDLHLIGSDLILTVREDINRMKKIRSYRGIRHELGLKVRG 130
Query: 101 QRTHTNARTRKKFGKGGVARKR 122
QRT + RT G GV+RK+
Sbjct: 131 QRTRSTGRTG---GTVGVSRKK 149
>gnl|CDD|132668 TIGR03629, arch_S13P, archaeal ribosomal protein S13P
Back Show alignment and domain information
Score = 76.5 bits (189), Expect = 2e-15
Identities = 45/143 (31%), Positives = 70/143 (48%), Gaps = 24/143 (16%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
+ RIA ++ K V AL I GIG + ++ I KL + P ++ L + E+ ++ +A+
Sbjct: 5 IVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAV 64
Query: 61 E--------------QDYQ-------VEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVR 99
E +DY+ + DL TV +I R+ + YRG+RH GL VR
Sbjct: 65 ENYEYGIPSWLLNRRKDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVR 124
Query: 100 GQRTHTNARTRKKFGKGGVARKR 122
GQRT + R GV+RK+
Sbjct: 125 GQRTKSTGRRG---RTVGVSRKK 144
This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13. Length = 144
>gnl|CDD|38521 KOG3311, KOG3311, KOG3311, Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Back Show alignment and domain information
Score = 63.7 bits (155), Expect = 1e-11
Identities = 44/144 (30%), Positives = 69/144 (47%), Gaps = 25/144 (17%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
+ RI N+ ++V AL I GIG + ++ +C K + +R +L E ++++I Q +
Sbjct: 12 ILRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQIL 71
Query: 61 E--------------QDYQVEGD--------LRRTVAMNIKRLMDLGCYRGLRHRRGLPV 98
Q ++G L + +I+RL + C+RGLRH GL V
Sbjct: 72 NDPRQYKIPDWFLNRQKDIIDGKVNHLLGNGLDTRLRADIERLKKIRCHRGLRHFWGLRV 131
Query: 99 RGQRTHTNARTRKKFGKGGVARKR 122
RGQRT TN R K GV+ K+
Sbjct: 132 RGQRTKTNGRRGKTV---GVSGKK 152
>gnl|CDD|185469 PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisional
Back Show alignment and domain information
Score = 46.6 bits (111), Expect = 2e-06
Identities = 39/144 (27%), Positives = 63/144 (43%), Gaps = 25/144 (17%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
+ RI N+ ++V AL I GIG + + +C K I +R +L E+ +I + I
Sbjct: 14 ILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEII 73
Query: 61 E---------------------QDYQV-EGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPV 98
++ + L + +++RL + +RGLRH GL V
Sbjct: 74 ANPLQFKIPDWFLNRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLHRGLRHHWGLRV 133
Query: 99 RGQRTHTNARTRKKFGKGGVARKR 122
RGQ T T R + GV+RK+
Sbjct: 134 RGQHTKTTGRRGRTV---GVSRKK 154
>gnl|CDD|30448 COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Back Show alignment and domain information
Score = 151 bits (384), Expect = 4e-38
Identities = 76/121 (62%), Positives = 93/121 (76%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
MARIAGV+IP KRVV AL YI+GIG + +++IC K I P++RV +L E E+ ++R AI
Sbjct: 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAI 60
Query: 61 EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVAR 120
+ Y VEGDLRR V M+IKRLM +GCYRG+RHRRGLPVRGQRT TNARTRK KG +
Sbjct: 61 QNKYLVEGDLRREVRMDIKRLMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKGVAKK 120
Query: 121 K 121
K
Sbjct: 121 K 121
Conserved Domains in CDD Database Detected by HHsearch
Original result of HHsearch against CDD database
Identity Alignment graph Length
Definition
Probability
Target
122
30S ribosomal protein S13 [Candidatus Liberibacter asia
CHL00137 122
rps13 ribosomal protein S13; Validated
100.0
PRK05179 122
rpsM 30S ribosomal protein S13; Validated
100.0
COG0099 121
RpsM Ribosomal protein S13 [Translation, ribosomal stru
100.0
PRK04053 149
rps13p 30S ribosomal protein S13P; Reviewed
100.0
PTZ00134 154
40S ribosomal protein S18; Provisional
100.0
TIGR03629 144
arch_S13P archaeal ribosomal protein S13P. This model d
100.0
TIGR03631 113
bact_S13 30S ribosomal protein S13. This model describe
100.0
pfam00416 106
Ribosomal_S13 Ribosomal protein S13/S18. This family in
100.0
KOG3311 152
consensus
99.96
PRK13945 283
formamidopyrimidine-DNA glycosylase; Provisional
96.8
pfam06831 93
H2TH Formamidopyrimidine-DNA glycosylase H2TH domain. F
96.42
PRK01103 273
formamidopyrimidine-DNA glycosylase; Validated
96.37
PRK10445 263
endonuclease VIII; Provisional
96.13
TIGR00577 292
fpg formamidopyrimidine-DNA glycosylase; InterPro: IPR0
95.35
PRK04184
533
DNA topoisomerase VI subunit B; Validated
94.91
COG0266 273
Nei Formamidopyrimidine-DNA glycosylase [DNA replicatio
94.13
pfam05833
447
FbpA Fibronectin-binding protein A N-terminus (FbpA). T
93.04
>CHL00137 rps13 ribosomal protein S13; Validated
Back Show alignment and domain information
Probab=100.00 E-value=0 Score=316.88 Aligned_cols=122 Identities=57% Similarity=0.919 Sum_probs=119.5
Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf 94551675899857666431200717689999999808882120022798999999986124564333788999999999
Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKR 80 (122)
Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~r 80 (122)
T Consensus 1 MvrI~g~~i~~~K~v~~aLt~I~GIG~~~A~~Ic~~lgi~~~~k~~~Ls~~qi~~i~~~i~~~~~ie~dLr~~~~~dI~r 80 (122)
T CHL00137 1 MVRIAGVDLPRNKRIEIALTYIYGIGLTSAKKILEKANIDPDTRTKDLTDEQIVSIRQIIEENYQVEGDLRRFESMNIKR 80 (122)
T ss_pred CCEECCCCCCCCCEEEEHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHCCEECHHHHHHHHHHHHH
T ss_conf 96484767999977313111000618999999999849898855262999999999999984765222789999998999
Q ss_pred HHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 973031001233179878770778776577776655423469
Q gi|254780239|r 81 LMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122 (122)
Q Consensus 81 l~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk 122 (122)
T Consensus 81 l~~I~sYRG~RH~~GLPvRGQRT~tNarT~kg~~~~v~~kKk 122 (122)
T CHL00137 81 LMEINCYRGKRHRLGLPVRGQRTRTNARTRRGAKKTVAGKKK 122 (122)
T ss_pred HHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 988560147665059987877887787678898776777889
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Back Show alignment and domain information
Probab=100.00 E-value=0 Score=318.42 Aligned_cols=122 Identities=61% Similarity=0.975 Sum_probs=118.6
Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf 94551675899857666431200717689999999808882120022798999999986124564333788999999999
Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKR 80 (122)
Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~r 80 (122)
T Consensus 1 M~RI~g~dl~~~K~v~~ALt~I~GIG~~~A~~Ic~~lgId~~~k~g~Ls~~qi~~I~~~I~~~~~ve~dLr~~v~~dIkr 80 (122)
T PRK05179 1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKLREEIDKNYKVEGDLRREVSMNIKR 80 (122)
T ss_pred CCEECCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf 97472734899978684773002758999999999829997668876569999999999981574507899999999999
Q ss_pred HHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 973031001233179878770778776577776655423469
Q gi|254780239|r 81 LMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122 (122)
Q Consensus 81 l~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk 122 (122)
T Consensus 81 l~~i~syRG~RH~~gLpvRGQrT~tn~rt~kg~~~~v~~kkk 122 (122)
T PRK05179 81 LMDIGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKTIAGKKK 122 (122)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 999999999998749987876677775356898675777789
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Back Show alignment and domain information
Probab=100.00 E-value=0 Score=308.74 Aligned_cols=121 Identities=64% Similarity=1.047 Sum_probs=117.6
Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf 94551675899857666431200717689999999808882120022798999999986124564333788999999999
Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKR 80 (122)
Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~r 80 (122)
T Consensus 1 maRIagvdip~~K~v~iALt~IyGIG~~~a~~I~~~~gi~~~~r~~~Lteeei~~ir~~i~~~~~vegDLr~~v~~dIkR 80 (121)
T COG0099 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAIQNKYLVEGDLRREVRMDIKR 80 (121)
T ss_pred CCEECCCCCCCCCEEEEHHHHHCCCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHHHCCEEHHHHHHHHHHHHHH
T ss_conf 93263667999825765046303536999999999919886676452999999999999986274013899999997999
Q ss_pred HHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 973031001233179878770778776577776655423469
Q gi|254780239|r 81 LMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122 (122)
Q Consensus 81 l~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk 122 (122)
T Consensus 81 l~~i~~YRGiRH~~GLpVRGQrTktnaRtrkG~~~~-v~~KK 121 (121)
T COG0099 81 LMKIGCYRGIRHRRGLPVRGQRTKTNARTRKGPRKG-VAKKK 121 (121)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC-CCCCC
T ss_conf 987520222554069987785267665265888665-55679
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Back Show alignment and domain information
Probab=100.00 E-value=0 Score=307.88 Aligned_cols=119 Identities=38% Similarity=0.600 Sum_probs=115.2
Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCC----------------
Q ss_conf 9455167589985766643120071768999999980888212002279899999998612456----------------
Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDY---------------- 64 (122)
Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~---------------- 64 (122)
T Consensus 9 mvRI~gvdIp~~K~i~~ALt~IyGIG~~~A~~Ic~~lgId~~~k~~~Lte~qi~~l~~~i~~~~~~~iP~wl~Nr~kd~~ 88 (149)
T PRK04053 9 IVRIANTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPHAKLGYLSDEEIEKIEEALENPAEEGIPSWMLNRRKDYE 88 (149)
T ss_pred HHHHCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHCCCCCCC
T ss_conf 58650867899968644411114848999999999918998773074999999999999974643156467650446555
Q ss_pred ------CCCHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf ------4333788999999999973031001233179878770778776577776655423469
Q gi|254780239|r 65 ------QVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122 (122)
Q Consensus 65 ------~i~~~L~~~~~~~i~rl~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk 122 (122)
T Consensus 89 tG~~~hli~~dL~~~~~~~I~rl~~i~syRG~RH~~gLpVRGQRTrtN~Rtg~tv---gv~~kk 149 (149)
T PRK04053 89 TGEDLHLIGSDLVLTVREDINRMKKIRSYRGIRHELGLKVRGQRTRSTGRTGSTV---GVKRKK 149 (149)
T ss_pred CCCCEEEEHHHHHHHHHHHHHHHHHHCHHEHHHHCCCCCCCCCCCCCCCCCCCEE---EEECCC
T ss_conf 6851021248899999999998865221110034079976787787777788700---002579
>PTZ00134 40S ribosomal protein S18; Provisional
Back Show alignment and domain information
Probab=100.00 E-value=2.8e-45 Score=302.00 Aligned_cols=119 Identities=31% Similarity=0.506 Sum_probs=115.1
Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCC-----------------
Q ss_conf 945516758998576664312007176899999998088821200227989999999861245-----------------
Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQD----------------- 63 (122)
Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~----------------- 63 (122)
T Consensus 14 ivRI~gtdi~g~K~v~~aLt~I~GIG~~~A~~Ic~~~gid~~~r~g~Lteeei~~i~~~I~~~~~~~iP~w~~Nr~kD~~ 93 (154)
T PTZ00134 14 ILRILNTNVDGREKVTIALTAIKGIGRRFATVVCKQAGVDVTKRAGELTQEEINKIVAIISSPAQFKIPDWFLNRQKDVK 93 (154)
T ss_pred HHHHCCCCCCCCCEEEEEEEEECCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHH
T ss_conf 15403875899958899853220648999999999809894542164999999999999727210156488765577765
Q ss_pred -----CCCCHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf -----64333788999999999973031001233179878770778776577776655423469
Q gi|254780239|r 64 -----YQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122 (122)
Q Consensus 64 -----~~i~~~L~~~~~~~i~rl~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk 122 (122)
T Consensus 94 ~G~~~hlv~~dL~~~~~~dIkRlk~I~~yRG~RH~~GLpVRGQRTktn~R~G~tv---GV~rKK 154 (154)
T PTZ00134 94 EGKNLHNTSNQLDSCLREDLERLKKIRLHRGLRHHWGLRVRGQHTKTTGRHGRTV---GVAKKK 154 (154)
T ss_pred HCCEEEEECCHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCE---EEECCC
T ss_conf 0631245301288999988999987552102222379976787588888887500---111479
>TIGR03629 arch_S13P archaeal ribosomal protein S13P
Back Show alignment and domain information
Probab=100.00 E-value=5.6e-45 Score=301.01 Aligned_cols=119 Identities=36% Similarity=0.580 Sum_probs=114.6
Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC------------------
Q ss_conf 94551675899857666431200717689999999808882120022798999999986124------------------
Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ------------------ 62 (122)
Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~------------------ 62 (122)
T Consensus 5 mvRI~g~di~~~K~v~~aLt~I~GIG~~~A~~Ic~~~gid~~~k~~~Lt~~ei~~i~~~i~~~~~~iP~w~~Nr~kd~~t 84 (144)
T TIGR03629 5 IVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVENYEYGIPSWLLNRRKDYET 84 (144)
T ss_pred EEEEECCCCCCCCEEEEEEEEECCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCC
T ss_conf 20120754899968988722123728999999999909993536041999999999999985343486788726566456
Q ss_pred ---CCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf ---564333788999999999973031001233179878770778776577776655423469
Q gi|254780239|r 63 ---DYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122 (122)
Q Consensus 63 ---~~~i~~~L~~~~~~~i~rl~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk 122 (122)
T Consensus 85 G~~~hlv~~dL~~~~~~dI~rl~~I~~yRG~RH~~gLpVRGQrT~tNaR~g~~~---gv~~kK 144 (144)
T TIGR03629 85 GEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQRTKSTGRRGRTV---GVSRKK 144 (144)
T ss_pred CCCCEEECHHHHHHHHHHHHHHHHHCHHHHHHHHCCCCCCCCCCCCCCCCCCCC---CCCCCC
T ss_conf 751134107899999986999987430302134059976877787787888734---330579
This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
>TIGR03631 bact_S13 30S ribosomal protein S13
Back Show alignment and domain information
Probab=100.00 E-value=1.5e-44 Score=297.86 Aligned_cols=112 Identities=64% Similarity=1.002 Sum_probs=110.0
Q ss_pred EEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 55167589985766643120071768999999980888212002279899999998612456433378899999999997
Q gi|254780239|r 3 RIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLM 82 (122)
Q Consensus 3 rI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~rl~ 82 (122)
T Consensus 1 RI~g~di~~~K~v~~ALt~I~GIG~~~A~~Ic~~lgId~~~k~g~Ls~~qi~~I~~~I~~~~~i~~dL~~~~~~dI~rl~ 80 (113)
T TIGR03631 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEAKYKVEGDLRREVSLNIKRLM 80 (113)
T ss_pred CCCCCCCCCCCCHHHHHHCEECCCHHHHHHHHHHCCCCCCCCHHHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf 96786499996746065200275899999999992999877864499999999999998257440689999999999998
Q ss_pred HCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 30310012331798787707787765777766
Q gi|254780239|r 83 DLGCYRGLRHRRGLPVRGQRTHTNARTRKKFG 114 (122)
Q Consensus 83 ~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~ 114 (122)
T Consensus 81 ~i~syRG~RH~~gLpVRGQrT~tn~rt~kg~~ 112 (113)
T TIGR03631 81 DIGCYRGLRHRRGLPVRGQRTKTNARTRKGPR 112 (113)
T ss_pred HHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 84521122221699878877877753468999
This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
>pfam00416 Ribosomal_S13 Ribosomal protein S13/S18
Back Show alignment and domain information
Probab=100.00 E-value=2.5e-42 Score=284.25 Aligned_cols=106 Identities=50% Similarity=0.817 Sum_probs=104.6
Q ss_pred EEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 55167589985766643120071768999999980888212002279899999998612456433378899999999997
Q gi|254780239|r 3 RIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLM 82 (122)
Q Consensus 3 rI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~rl~ 82 (122)
T Consensus 1 RI~gtdi~~~K~v~~ALt~I~GIG~~~A~~Ic~~lgi~~~~k~~~Lt~~qi~~l~~~i~-~~~i~~dL~~~~~~~I~rl~ 79 (106)
T pfam00416 1 RILNTNLDGNKKIEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRIRDIIS-NYVVENDLRRKIRNDIERLK 79 (106)
T ss_pred CCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHH
T ss_conf 96787799996864441121052899999999991959775715499999999999997-52004789999999899998
Q ss_pred HCCCCCCHHHHCCCCCCCCCCCCCCCC
Q ss_conf 303100123317987877077877657
Q gi|254780239|r 83 DLGCYRGLRHRRGLPVRGQRTHTNART 109 (122)
Q Consensus 83 ~i~syrG~RH~~gLpvRGQRT~tn~rt 109 (122)
T Consensus 80 ~i~syrG~RH~~gLpvRGQrT~tn~rT 106 (106)
T pfam00416 80 KIRCYRGLRHIRGLPVRGQRTKTNART 106 (106)
T ss_pred HHCHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 744030126637997688768888898
This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.
>KOG3311 consensus
Back Show alignment and domain information
Probab=99.96 E-value=1.9e-30 Score=210.45 Aligned_cols=119 Identities=35% Similarity=0.582 Sum_probs=112.0
Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC------------------
Q ss_conf 94551675899857666431200717689999999808882120022798999999986124------------------
Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ------------------ 62 (122)
Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~------------------ 62 (122)
T Consensus 12 i~~il~~~~dg~~~V~fAl~~i~Gig~~~A~~ic~K~~~~~~~r~gelt~~qi~~i~~i~~d~~~~~~~~~~l~rq~~~~ 91 (152)
T KOG3311 12 ILRILNTNVDGKRKVTFALTSIKGIGRRYAEIVCKKADLDLTKRAGELTEEQILRILQILNDPRQYKIPDWFLNRQKDII 91 (152)
T ss_pred HHHHHCCCCCCCCEEEEEEEEEEEECHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCHHHHCCCHHHHHHHCCCC
T ss_conf 99997268789800689888886511224444442037405554131249999999998619877418218877423200
Q ss_pred ----CCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf ----564333788999999999973031001233179878770778776577776655423469
Q gi|254780239|r 63 ----DYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122 (122)
Q Consensus 63 ----~~~i~~~L~~~~~~~i~rl~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk 122 (122)
T Consensus 92 dG~~~~l~~~~ld~r~r~~ieRlkki~~~RG~rh~~gl~vRGQ~Tkt~~~~gk~v---~Vs~Kk 152 (152)
T KOG3311 92 DGKVNHLLGNGLDTRLRADIERLKKIRCHRGLRHFWGLRVRGQRTKTNGRRGKTV---GVSGKK 152 (152)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCCCCCCCCCCCEE---EECCCC
T ss_conf 4730222010256678999998764010334011148842486453445455254---410369
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Back Show alignment and domain information
Probab=96.80 E-value=0.0023 Score=42.40 Aligned_cols=50 Identities=24% Similarity=0.356 Sum_probs=43.5
Q ss_pred CCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 85766643---120071768999999980888212002279899999998612
Q gi|254780239|r 12 AKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 12 ~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
T Consensus 165 ~~~IK~~LlDQ~~iaGIGNiyadEiLf~a~I~P~~~~~~Ls~~e~~~L~~~i~ 217 (283)
T PRK13945 165 TRSIKTALLDQSIVAGIGNIYADESLFKAGIRPTTEAGTLKKNQLERLREAIV 217 (283)
T ss_pred CCCCCEEEECCCEECCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 75435177518852345499999999985999778603089999999999999
>pfam06831 H2TH Formamidopyrimidine-DNA glycosylase H2TH domain
Back Show alignment and domain information
Probab=96.42 E-value=0.0042 Score=40.79 Aligned_cols=49 Identities=24% Similarity=0.378 Sum_probs=41.3
Q ss_pred CEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 5766643---120071768999999980888212002279899999998612
Q gi|254780239|r 13 KRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 13 K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
T Consensus 24 ~~Ik~~LlDQ~~iaGiGNiy~dEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~ 75 (93)
T pfam06831 24 RPIKTALLDQRVVAGIGNIYADEVLFRAGIHPERPASSLSKKECEALHTVIK 75 (93)
T ss_pred CHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 5199998667742565399999999991899678706199999999999999
Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain.
>PRK01103 formamidopyrimidine-DNA glycosylase; Validated
Back Show alignment and domain information
Probab=96.37 E-value=0.0047 Score=40.48 Aligned_cols=49 Identities=22% Similarity=0.330 Sum_probs=41.8
Q ss_pred CEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 5766643---120071768999999980888212002279899999998612
Q gi|254780239|r 13 KRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 13 K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
T Consensus 155 ~~Ik~~LlDQ~~iaGiGNiyadEiLf~a~IhP~~~~~~Ls~~e~~~L~~~~~ 206 (273)
T PRK01103 155 TAIKPALLDQTIVVGVGNIYADEALFRAGIHPERPAGSLSKARAERLVEAIK 206 (273)
T ss_pred CHHHHHHCCCCEEECCCHHHHHHHHHHCCCCCCCHHCCCCHHHHHHHHHHHH
T ss_conf 4266762258846035398999999876487135001179999999999999
>PRK10445 endonuclease VIII; Provisional
Back Show alignment and domain information
Probab=96.13 E-value=0.0076 Score=39.20 Aligned_cols=50 Identities=12% Similarity=0.274 Sum_probs=43.0
Q ss_pred CCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 85766643---120071768999999980888212002279899999998612
Q gi|254780239|r 12 AKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 12 ~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
T Consensus 151 ~~~IK~~LLDQ~vvaGIGNIYa~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~ 203 (263)
T PRK10445 151 NRQFSGLLLDQAFLAGLGNYLRVEILWQVGLTGQHKAKDLNAAQLDALAHALL 203 (263)
T ss_pred CCHHHHHHHCCCEEEECCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 75076651168867511388998999982899788702099999999999999
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase; InterPro: IPR000191 Formamidopyrimidine-DNA glycosylase (3
Back Show alignment and domain information
Probab=95.35 E-value=0.013 Score=37.79 Aligned_cols=52 Identities=25% Similarity=0.404 Sum_probs=45.2
Q ss_pred CCCCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 9985766643---120071768999999980888212002279899999998612
Q gi|254780239|r 10 PRAKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 10 ~~~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
T Consensus 165 ~~~r~~K~~LLDQ~~V~G~GNIYADE~LF~A~ihP~~~A~~L~~~~~~~L~~~i~ 219 (292)
T TIGR00577 165 KSKRKIKTALLDQRLVAGLGNIYADEVLFRAGIHPERLANQLSKEECELLHKAIK 219 (292)
T ss_pred HCCCHHHHHHHCCCEEEEEHHHHHHHHHHHHCCCCCHHHHCCCHHHHHHHHHHHH
T ss_conf 4040345686548757651010666899873688101000158889999999999
2.2.23 from EC) (Fapy-DNA glycosylase) (gene fpg) is a bacterial enzyme involved in DNA repair and which excise oxidized purine bases to release 2,6-diamino-4-hydroxy-5N-methylformamido- pyrimidine (Fapy) and 7,8-dihydro-8-oxoguanine (8-OxoG) residues. In addition to its glycosylase activity, FPG can also nick DNA at apurinic/apyrimidinic sites (AP sites). FPG is a monomeric protein of about 32 Kd which binds and require zinc for its activity. The C-terminal region is the zinc binding site in the enzyme where four conserved and essential cysteines are located ..
>PRK04184 DNA topoisomerase VI subunit B; Validated
Back Show alignment and domain information
Probab=94.91 E-value=0.032 Score=35.33 Aligned_cols=43 Identities=16% Similarity=0.332 Sum_probs=40.1
Q ss_pred EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 1200717689999999808882120022798999999986124
Q gi|254780239|r 20 CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122)
T Consensus 262 ~eFsrVg~~~A~ei~~~agl~~~~~p~~l~~~e~~~L~~a~~~ 304 (533)
T PRK04184 262 SEFSRVGEKTAKEILEYAGLDPNKKPKELTWEEAERLVEAMKK 304 (533)
T ss_pred HHCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 5435569899999999728999999001899999999999984
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Back Show alignment and domain information
Probab=94.13 E-value=0.068 Score=33.28 Aligned_cols=51 Identities=24% Similarity=0.393 Sum_probs=42.8
Q ss_pred CCCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 985766643---120071768999999980888212002279899999998612
Q gi|254780239|r 11 RAKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 11 ~~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
T Consensus 154 ~~~~IK~~LLDQ~vvaGvGNIYa~E~Lf~agI~P~~~a~~l~~~~~~~l~~~i~ 207 (273)
T COG0266 154 KKRRIKTALLDQKVVAGVGNIYADEILFRAGIHPARPAGDLSLAQLALLHEAIK 207 (273)
T ss_pred CCCCHHHHHHCCCCEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 764167776407703034178888899873798546703027899999999999
>pfam05833 FbpA Fibronectin-binding protein A N-terminus (FbpA)
Back Show alignment and domain information
Probab=93.04 E-value=0.099 Score=32.28 Aligned_cols=42 Identities=12% Similarity=0.309 Sum_probs=37.1
Q ss_pred EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 120071768999999980888212002279899999998612
Q gi|254780239|r 20 CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
T Consensus 193 ~~~~G~sp~la~El~~rag~~~~~~~~~l~~~~~~~L~~~~~ 234 (447)
T pfam05833 193 QAFQGLSPLLAEELCYRAGLDKNTPVEELSDEDWERLYEAFK 234 (447)
T ss_pred HHHCCCCHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHH
T ss_conf 982699889999999982898677711249899999999999
This family consists of the N-terminal region of the prokaryotic fibronectin-binding protein. Fibronectin binding is considered to be an important virulence factor in streptococcal infections. Fibronectin is a dimeric glycoprotein that is present in a soluble form in plasma and extracellular fluids; it is also present in a fibrillar form on cell surfaces. Both the soluble and cellular forms of fibronectin may be incorporated into the extracellular tissue matrix. While fibronectin has critical roles in eukaryotic cellular processes, such as adhesion, migration and differentiation, it is also a substrate for the attachment of bacteria. The binding of pathogenic Streptococcus pyogenes and Staphylococcus aureus to epithelial cells via fibronectin facilitates their internalisation and systemic spread within the host.
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
122
30S ribosomal protein S13 [Candidatus Liberibacter asia
d2uubm1 125
a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus ther
2e-33
d2gy9m1 114
a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia
5e-33
>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]} Length = 125
Back Hide information, alignment and structure
class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Ribosomal protein S13
domain: Ribosomal protein S13
species: Thermus thermophilus [TaxId: 274]
Score = 134 bits (339), Expect = 2e-33
Identities = 71/121 (58%), Positives = 88/121 (72%)
Query: 2 ARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61
ARIAGV IPR KRV AL YI+GIG +++ K I P RV L E+EV+++R+ +E
Sbjct: 1 ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVE 60
Query: 62 QDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARK 121
+++EG+LR VA NIKRLMD+GCYRGLRHRRGLPVRGQRT TNARTRK K +K
Sbjct: 61 NTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKK 120
Query: 122 R 122
+
Sbjct: 121 K 121
>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]} Length = 114
Back Show information, alignment and structure
class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Ribosomal protein S13
domain: Ribosomal protein S13
species: Escherichia coli [TaxId: 562]
Score = 133 bits (336), Expect = 5e-33
Identities = 62/111 (55%), Positives = 78/111 (70%), Gaps = 1/111 (0%)
Query: 2 ARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61
ARIAG+NIP K V AL I+G+G S+ I I + ++ +L E ++ +R +
Sbjct: 1 ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA 60
Query: 62 QDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKK 112
+ VEGDLRR ++M+IKRLMDLGCYRGLRHRRGLPVRGQRT TNARTRK
Sbjct: 61 KFV-VEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKG 110
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 122
30S ribosomal protein S13 [Candidatus Liberibacter asia
d2uubm1 125
Ribosomal protein S13 {Thermus thermophilus [TaxId: 274
100.0
d2gy9m1 114
Ribosomal protein S13 {Escherichia coli [TaxId: 562]}
100.0
d2hkja1 78
Topoisomerase VI-B subunit middle domain {Archaeon Sulf
97.14
d1k82a1 88
DNA repair protein MutM (Fpg) {Escherichia coli [TaxId:
96.7
d1r2za1 94
DNA repair protein MutM (Fpg) {Bacillus stearothermophi
96.68
d1tdza1 88
DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxI
96.64
d1ee8a1 89
DNA repair protein MutM (Fpg) {Thermus thermophilus [Ta
96.61
d1k3xa1 89
Endonuclease VIII {Escherichia coli [TaxId: 562]}
96.57
d1tdha1 115
Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapiens)
90.69
>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]}
Back Hide information, alignment and structure
class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Ribosomal protein S13
domain: Ribosomal protein S13
species: Thermus thermophilus [TaxId: 274]
Probab=100.00 E-value=0 Score=304.10 Aligned_cols=121 Identities=59% Similarity=0.915 Sum_probs=115.9
Q ss_pred CEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 45516758998576664312007176899999998088821200227989999999861245643337889999999999
Q gi|254780239|r 2 ARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRL 81 (122)
Q Consensus 2 vrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~rl 81 (122)
+||+|+|||++|+|.+|||+|||||+++|.+||+.+||||++++++||++|+++|+++|+++|.+|+||++.+.+||+||
T Consensus 1 aRI~g~di~~~K~v~~ALt~I~GIG~~~A~~Ic~~lgId~~~k~~~Lt~~qi~~I~~~i~~~~~i~~~L~~~~~~dIkrl 80 (125)
T d2uubm1 1 ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRL 80 (125)
T ss_dssp CCCSTTCCCCSSBHHHHHTTSTTCCHHHHHHHHHTTTCCTTSBGGGCCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHH
T ss_pred CCCCCCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 92268669999788876320558189999999998299833333525699999999998411164778999999989999
Q ss_pred HHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 73031001233179878770778776577776655423469
Q gi|254780239|r 82 MDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122 (122)
Q Consensus 82 ~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk 122 (122)
++|+||||+||.+|||||||||||||||+|+..+++.++||
T Consensus 81 ~~i~~yRG~RH~~gLpvRGQRT~tN~rt~kg~~~~v~~kk~ 121 (125)
T d2uubm1 81 MDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKK 121 (125)
T ss_dssp HHTTCHHHHHHHHTCCSSSCCCSSCCHHHHCSCCCCCCCSS
T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 87610333432279987777787775466888542555667
>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]}
Back Show information, alignment and structure
class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Ribosomal protein S13
domain: Ribosomal protein S13
species: Escherichia coli [TaxId: 562]
Probab=100.00 E-value=7.1e-44 Score=290.99 Aligned_cols=114 Identities=55% Similarity=0.862 Sum_probs=110.6
Q ss_pred CEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 45516758998576664312007176899999998088821200227989999999861245643337889999999999
Q gi|254780239|r 2 ARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRL 81 (122)
Q Consensus 2 vrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~rl 81 (122)
+||+|+|||++|+|.+|||+|||||+++|.+||..+||||++++++||++|++.|+++|+ +|.+|+||++.+++||+||
T Consensus 1 aRI~g~dip~~K~v~~ALt~I~GIG~~~A~~Ic~~lgid~~~kv~~Lt~~qi~~l~~~i~-~~~i~~~L~~~~~~dI~rl 79 (114)
T d2gy9m1 1 ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA-KFVVEGDLRREISMSIKRL 79 (114)
T ss_dssp CCCSSSCCCCSSBHHHHHTTSSSCCHHHHHHHHHHHTCCTTSBTTSCCHHHHHHHHHHHH-SSCCSHHHHHHHHHHHHHT
T ss_pred CCCCCCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH-HCCCHHHHHHHHHHHHHHH
T ss_conf 912586689997888872315684899999999981989531357456999999999987-1055889999999989999
Q ss_pred HHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 73031001233179878770778776577776655
Q gi|254780239|r 82 MDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKG 116 (122)
Q Consensus 82 ~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~ 116 (122)
++|+||||+||.+|||||||||||||||+|+.+|+
T Consensus 80 ~~I~~yrG~RH~~gLpvRGQrT~tNart~k~~~k~ 114 (114)
T d2gy9m1 80 MDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKP 114 (114)
T ss_dssp TTTTCHHHHHHHCCSCCCCCCSSSSCHHHHCSCCC
T ss_pred HHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 87500102210479987877787776366899998
>d2hkja1 a.156.1.3 (A:229-306) Topoisomerase VI-B subunit middle domain {Archaeon Sulfolobus shibatae [TaxId: 2286]}
Back Show information, alignment and structure
class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Topoisomerase VI-B subunit middle domain
domain: Topoisomerase VI-B subunit middle domain
species: Archaeon Sulfolobus shibatae [TaxId: 2286]
Probab=97.14 E-value=0.00018 Score=46.40 Aligned_cols=49 Identities=18% Similarity=0.398 Sum_probs=42.0
Q ss_pred EEEEEEEE-EECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 76664312-00717689999999808882120022798999999986124
Q gi|254780239|r 14 RVVRALCY-IHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122)
Q Consensus 14 ~i~~aLt~-I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122)
++...|+. +-|||..+|..||..+||+|++++++|+++|+..|-+.|.+
T Consensus 25 k~~l~lq~~f~GvGn~~a~Eil~~agi~P~~~~~~L~~~e~~~L~~air~ 74 (78)
T d2hkja1 25 TIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK 74 (78)
T ss_dssp BHHHHHHHHSSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 59999888855668999999999807775660241999999999999860
>d1k82a1 a.156.1.2 (A:129-216) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]}
Back Show information, alignment and structure
class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Middle domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Escherichia coli [TaxId: 562]
Probab=96.70 E-value=0.00093 Score=42.02 Aligned_cols=51 Identities=18% Similarity=0.193 Sum_probs=42.7
Q ss_pred CCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 85766643---1200717689999999808882120022798999999986124
Q gi|254780239|r 12 AKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122)
Q Consensus 12 ~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122)
+.+|.-+| ..|-|||...+..||..++|+|+.++.+|+++|+..|-+.+..
T Consensus 22 ~~~ik~~LlDQ~~iaGiGN~y~~EiLf~a~I~P~~~~~~L~~~~~~~L~~~i~~ 75 (88)
T d1k82a1 22 KTAIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIKA 75 (88)
T ss_dssp CSBHHHHHTCTTTCSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred CCHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHCCHHHHHHHHHHHHH
T ss_conf 851899997053335521189999999977885681877899999999999999
>d1r2za1 a.156.1.2 (A:135-228) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]}
Back Show information, alignment and structure
class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Middle domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Bacillus stearothermophilus [TaxId: 1422]
Probab=96.68 E-value=0.00098 Score=41.88 Aligned_cols=51 Identities=18% Similarity=0.251 Sum_probs=43.6
Q ss_pred CCCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 985766643---120071768999999980888212002279899999998612
Q gi|254780239|r 11 RAKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 11 ~~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
.+.+|.-+| +.+-|||...+..||..++|+|..++++|+++|+..|-+.+.
T Consensus 21 ~~~~ik~~LlDQ~~~aGiGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~L~~~~~ 74 (94)
T d1r2za1 21 TKRSVKALLLDQTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMV 74 (94)
T ss_dssp CCSBHHHHHHCTTTSSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 886289999836545786508999999999726641497866779999999999
>d1tdza1 a.156.1.2 (A:132-219) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]}
Back Show information, alignment and structure
class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Middle domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Lactococcus lactis [TaxId: 1358]
Probab=96.64 E-value=0.001 Score=41.73 Aligned_cols=49 Identities=24% Similarity=0.382 Sum_probs=41.5
Q ss_pred CEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 5766643---120071768999999980888212002279899999998612
Q gi|254780239|r 13 KRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 13 K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
++|.-+| +.|-|||...|..||..++|+|+.++.+|+++|+..|-+.+.
T Consensus 23 ~~ik~~LldQ~~iaGIGNiy~~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~ 74 (88)
T d1tdza1 23 KKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSII 74 (88)
T ss_dssp SBHHHHHHTSSSSSCCCHHHHHHHHHHTTCCTTCBGGGCCHHHHHHHHHHHH
T ss_pred CCHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHHCCHHHHHHHHHHHH
T ss_conf 5089999855434785768999999999758256465769999999999999
>d1ee8a1 a.156.1.2 (A:122-210) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]}
Back Show information, alignment and structure
class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Middle domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Thermus thermophilus [TaxId: 274]
Probab=96.61 E-value=0.0011 Score=41.67 Aligned_cols=42 Identities=19% Similarity=0.286 Sum_probs=38.8
Q ss_pred EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 120071768999999980888212002279899999998612
Q gi|254780239|r 20 CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
..|-|||...+..||..++|+|..++++|+++|+..|-+.+.
T Consensus 33 ~~iaGiGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~L~~~i~ 74 (89)
T d1ee8a1 33 RLAAGVGNIYADEALFRARLSPFRPARSLTEEEARRLYRALR 74 (89)
T ss_dssp SSSTTCCHHHHHHHHHHTTCCSSSBGGGCCHHHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHCCCCCHHHHCCHHHHHHHHHHHH
T ss_conf 444777758999999999767135453599999999999999
>d1k3xa1 a.156.1.2 (A:125-213) Endonuclease VIII {Escherichia coli [TaxId: 562]}
Back Show information, alignment and structure
class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Middle domain of MutM-like DNA repair proteins
domain: Endonuclease VIII
species: Escherichia coli [TaxId: 562]
Probab=96.57 E-value=0.0012 Score=41.40 Aligned_cols=51 Identities=14% Similarity=0.302 Sum_probs=43.6
Q ss_pred CCCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 985766643---120071768999999980888212002279899999998612
Q gi|254780239|r 11 RAKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 11 ~~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
.+++|.-+| +.+-|||...+..||..++|+|+.++++|+++|+..|-+.+-
T Consensus 25 ~~~~Ik~~LlDQ~~~aGIGN~~~~EiL~~a~i~P~~~~~~L~~~~~~~L~~~~~ 78 (89)
T d1k3xa1 25 RNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALL 78 (89)
T ss_dssp TTSCHHHHTTCTTTSBTCCHHHHHHHHHHHTCCSSCCGGGSCHHHHHHHHHHHH
T ss_pred CCCHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHH
T ss_conf 555299998468630354758999999996666047130199999999999999
>d1tdha1 a.156.1.2 (A:132-246) Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapiens) [TaxId: 9606]}
Back Show information, alignment and structure
class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Middle domain of MutM-like DNA repair proteins
domain: Endonuclease VIII-like 1 (NEIL1)
species: Human (Homo sapiens) [TaxId: 9606]
Probab=90.69 E-value=0.02 Score=33.71 Aligned_cols=49 Identities=22% Similarity=0.363 Sum_probs=40.3
Q ss_pred CCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHH
Q ss_conf 85766643---12007176899999998088821200227989999999861
Q gi|254780239|r 12 AKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60 (122)
Q Consensus 12 ~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I 60 (122)
+++|.-+| ..|-|||...+..||..++|+|..++.+|++++...+....
T Consensus 27 ~~~i~~~LldQ~~~aGiGN~~~~EiLf~a~i~P~~~~~~l~~~~~~~l~~~~ 78 (115)
T d1tdha1 27 DRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPE 78 (115)
T ss_dssp GSBHHHHTTCTTTSTTCCHHHHHHHHHHHTCCTTSBHHHHHGGGC-----CC
T ss_pred CCCHHHHHHCCCHHCCCCHHHHHHHHHHCCCCCCCCHHHCCHHHHHHHHHHH
T ss_conf 8849999854643125138999999998489977704043899996777667
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
122
30S ribosomal protein S13 [Candidatus Liberibacter
3bbn_M_ 145
(M:) Ribosomal protein S13; small ribosomal subuni
1e-27
2zkq_m_1-88 88
(m:1-88) 40S ribosomal protein S18E; protein-RNA c
4e-19
2vqe_M_1-64 64
(M:1-64) 30S ribosomal protein S13, 30S ribosomal
2e-17
3i1m_M_1-63 63
(M:1-63) 30S ribosomal protein S13; ribosome struc
3e-16
2zbk_B_229-310 82
(B:229-310) Type 2 DNA topoisomerase 6 subunit B;
3e-15
>3bbn_M (M:) Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa}Length = 145
Back Hide alignment and structure
Score = 116 bits (292), Expect = 1e-27
Identities = 48/111 (43%), Positives = 60/111 (54%), Gaps = 12/111 (10%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
RI GV IP KRV +L YIHGIG S+ I L + L E EVI +R+
Sbjct: 46 CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDN-KVTKDLSEEEVIILRK-- 102
Query: 61 EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRK 111
+R + I+RL ++ CYRG+RH+ GLPVRGQRT N RT K
Sbjct: 103 ---------EKRFNRVAIERLKEIRCYRGIRHKLGLPVRGQRTKNNCRTLK 144
>2zkq_m (m:1-88) 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_MLength = 88
Back Show alignment and structure
Score = 87.8 bits (218), Expect = 4e-19
Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
+ R+ NI +++ A+ I G+G + + + K I +R +L E EV ++ +
Sbjct: 12 ILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIM 71
Query: 61 EQDYQVEGD---LRR 72
+ Q + L R
Sbjct: 72 QNPRQYKIPDWFLNR 86
>2vqe_M (M:1-64) 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}Length = 64
Back Show alignment and structure
Score = 82.3 bits (204), Expect = 2e-17
Identities = 31/64 (48%), Positives = 42/64 (65%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
MARIAGV IPR KRV AL YI+GIG +++ K I P RV L E+EV+++R+ +
Sbjct: 1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV 60
Query: 61 EQDY 64
E +
Sbjct: 61 ENTW 64
>3i1m_M (M:1-63) 30S ribosomal protein S13; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F 1vs5_M 3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M ...Length = 63
Back Show alignment and structure
Score = 78.1 bits (193), Expect = 3e-16
Identities = 22/62 (35%), Positives = 35/62 (56%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
MARIAG+NIP K V AL I+G+G S+ I I + ++ +L E ++ +R +
Sbjct: 1 MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEV 60
Query: 61 EQ 62
+
Sbjct: 61 AK 62
>2zbk_B (B:229-310) Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae}Length = 82
Back Show alignment and structure
Score = 75.5 bits (186), Expect = 3e-15
Identities = 10/72 (13%), Positives = 25/72 (34%), Gaps = 4/72 (5%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
+ + + IG ++ I + P ++V L E E+ ++ +
Sbjct: 13 IKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVET- 71
Query: 61 EQDYQVEGDLRR 72
++ + D R
Sbjct: 72 ---FKKDEDFRS 80
Homologous Domains in MMDB70 Database Detected by HHsearch
Original result of HHsearch against MMDB70 database
>3bbn_M (M:) Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa}
Back Hide alignment and structure
Probab=100.00 E-value=6.2e-37 Score=250.33 Aligned_cols=100 Identities=48% Similarity=0.735 Sum_probs=93.6
Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf 94551675899857666431200717689999999808882120022798999999986124564333788999999999
Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKR 80 (122)
Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~r 80 (122)
||||+|+|||++|+|.+|||+|||||+++|.+||+++||||+. +++|+++|+..|.+.. +.+++||+|
T Consensus 46 mvrI~gt~i~~~K~i~~ALt~IyGIG~~~A~~Ic~~lGi~~~k-~~~Lt~~qi~~l~~L~-----------r~v~~dI~R 113 (145)
T 3bbn_M 46 CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDNKV-TKDLSEEEVIILRKEK-----------RFNRVAIER 113 (145)
T ss_dssp -CCCSSSCCCCSSBTTTGGGGSTTCCSSTTTGGGTTTTCCSCB-TTSCCSSTTHHHHSSC-----------CCCSTTTHH
T ss_pred EEEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHH-HHHCCHHHHHHHHHHH-----------HHHHHHHHH
T ss_conf 8999586379997889986537550899999999986985454-6543588999989999-----------988999999
Q ss_pred HHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf 97303100123317987877077877657777
Q gi|254780239|r 81 LMDLGCYRGLRHRRGLPVRGQRTHTNARTRKK 112 (122)
Q Consensus 81 l~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~ 112 (122)
|++|+||||+||.+|||||||||||||||+|+
T Consensus 114 l~~I~sYRG~RH~~GLPVRGQRTrTNart~kg 145 (145)
T 3bbn_M 114 LKEIRCYRGIRHKLGLPVRGQRTKNNCRTLKG 145 (145)
T ss_dssp HHCCCCSCCTTTTTTCCSSSCCTTTCCCSSCC
T ss_pred HHHHCCEEEHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf 87523101013306998787778777546788
>2zkq_m (m:1-88) 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M
Back Show alignment and structure
Probab=99.81 E-value=3e-21 Score=153.03 Aligned_cols=73 Identities=23% Similarity=0.342 Sum_probs=70.1
Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHH---HHHH
Q ss_conf 945516758998576664312007176899999998088821200227989999999861245643337---8899
Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGD---LRRT 73 (122)
Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~---L~~~ 73 (122)
||||+|+|||++|+|.+|||+|||||+++|.+||+++||||++++++||++|+++|+++|+++|.+|+| |+|.
T Consensus 12 mvrI~g~~l~~~K~i~~ALt~I~GIG~~~A~~Ic~~lgi~~~~k~~~Lt~~qi~~l~~~i~~~~~~e~p~w~l~R~ 87 (88)
T 2zkq_m 12 ILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIMQNPRQYKIPDWFLNRQ 87 (88)
T ss_dssp -CCCSTTCCCCSSBHHHHGGGSTTCCHHHHHHHHHHHTCCTTSBTTTSCHHHHHHHHHHHHTTCSCCSCCCSSCSS
T ss_pred HHHCCCCCCCCCCEEEEEHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCHHHHHCC
T ss_conf 2421384189996873603024662899999999982999543336399999999999984000203637776151
>2vqe_M (M:1-64) 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}
Back Show alignment and structure
Probab=99.78 E-value=4e-20 Score=146.06 Aligned_cols=64 Identities=48% Similarity=0.756 Sum_probs=63.1
Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCC
Q ss_conf 9455167589985766643120071768999999980888212002279899999998612456
Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDY 64 (122)
Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~ 64 (122)
||||+|+|||++|++.+|||+|||||+++|.+||+++||||++++++||++|+++|+++|+++|
T Consensus 1 MvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgi~~~~k~~~Lt~~qi~~i~~~i~~~y 64 (64)
T 2vqe_M 1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTW 64 (64)
T ss_dssp -CCCSTTCCCCSSBHHHHHTTSSSCCSHHHHHHTTTTTCCTTSBGGGCCHHHHHHHHHHHHTTS
T ss_pred CCEECCCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf 9716375589996888873306581899999999982998332215135999999999873165
>3i1m_M (M:1-63) 30S ribosomal protein S13; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F 1vs5_M 3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M ...
Back Show alignment and structure
Probab=99.74 E-value=3e-19 Score=140.55 Aligned_cols=62 Identities=35% Similarity=0.553 Sum_probs=61.0
Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 94551675899857666431200717689999999808882120022798999999986124
Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122)
Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122)
||||+|+|||++|+|.+|||+|||||+++|.+||+++||||++++++||++|+++|+++|++
T Consensus 1 MvrI~g~~i~~~K~v~~aLt~i~GIG~~~A~~Ic~~~gi~~~~k~~~Lt~~qi~~l~~~i~~ 62 (63)
T 3i1m_M 1 MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAK 62 (63)
T ss_dssp -CCCSSSCCCCSSCHHHHGGGSTTCCHHHHHHHHTTTTCCSSCCSTTCCHHHHHHHHTTSSS
T ss_pred CCEECCCCCCCCCEEEEEEECEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 97364632799968888753445738999999999919896423463569999999988752
>2zbk_B (B:229-310) Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae}
Back Show alignment and structure
Probab=99.52 E-value=5.8e-16 Score=120.21 Aligned_cols=68 Identities=15% Similarity=0.221 Sum_probs=62.4
Q ss_pred CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHH
Q ss_conf 945516758998576664312007176899999998088821200227989999999861245643337889
Q gi|254780239|r 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRR 72 (122)
Q Consensus 1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~ 72 (122)
|+||+++|++++|++.+||++|||||+++|.+||+.+||||++++++||++|+++|.+.+. +|+||++
T Consensus 13 ~~ri~~~~~~~~k~i~~aLt~i~GIG~~~A~~I~~~~gi~~~~~~~~Lt~~qi~~L~~~~~----~e~~lrr 80 (82)
T 2zbk_B 13 IKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFK----KDEDFRS 80 (82)
T ss_dssp HHHHHTTCSSCCBHHHHHHTTSTTCCHHHHHHHHHHTTCCSSCBSSCCCHHHHHHHHHHHH----HCCCCCC
T ss_pred HHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHCCCC----CEEEECC
T ss_conf 7887750232101334551576467608777666552366334723336788876411010----1111023
>1mu5_A (A:230-311) Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae}
Back Show alignment and structure
Probab=97.03 E-value=0.00055 Score=45.84 Aligned_cols=43 Identities=19% Similarity=0.404 Sum_probs=39.5
Q ss_pred EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 1200717689999999808882120022798999999986124
Q gi|254780239|r 20 CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122)
Q Consensus 20 t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122)
+.+-|||..+|..||..+||+|++++++|+++|+..|-+.+.+
T Consensus 32 ~~~~GiGn~~a~EiL~~agi~P~~~~~~Ls~~e~~~L~~~~~~ 74 (82)
T 1mu5_A 32 NEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK 74 (82)
T ss_dssp TSSSSCCHHHHHHHHHHTTCCTTSBGGGCCTTHHHHHHHHHHH
T ss_pred HHHCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 6515557689999999718996667565999999999999986
>1k82_A (A:129-225) Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli}
Back Show alignment and structure
Probab=96.79 E-value=0.0018 Score=42.72 Aligned_cols=51 Identities=18% Similarity=0.224 Sum_probs=42.9
Q ss_pred CCCEEEEEEE---EEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 9857666431---20071768999999980888212002279899999998612
Q gi|254780239|r 11 RAKRVVRALC---YIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 11 ~~K~i~~aLt---~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
.+++|.-+|- .|-|||...|..||..++|+|+.++++||++|+..|-..+.
T Consensus 21 ~~~~ik~~LlDQ~~iaGiGNiyadEiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~ 74 (97)
T 1k82_A 21 KKTAIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIK 74 (97)
T ss_dssp CCSBHHHHHTCTTTCSSCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHH
T ss_pred CCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCCHHHCCHHHHHHHHHHHH
T ss_conf 555541378517612667588999999873789778120199999999999999
>1tdz_A (A:137-272) Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis}
Back Show alignment and structure
Probab=96.57 E-value=0.003 Score=41.28 Aligned_cols=49 Identities=24% Similarity=0.382 Sum_probs=41.7
Q ss_pred CEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 5766643---120071768999999980888212002279899999998612
Q gi|254780239|r 13 KRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 13 K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
.+|.-+| +.|-|||...+..||..++|+|..++++|+++|+..|-+.+-
T Consensus 19 ~~Ik~~LlDQ~~iaGIGNiy~~EiLf~A~IhP~~~~~~Ls~~~~~~L~~~~~ 70 (136)
T 1tdz_A 19 KKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSII 70 (136)
T ss_dssp SBHHHHHHTSSSSSCCCHHHHHHHHHHTTCCTTCBGGGCCHHHHHHHHHHHH
T ss_pred CCCEEEEEECCEECCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 1100167505255056767255576564432533222020100466787763
>3a46_A (A:144-289) Formamidopyrimidine-DNA glycosylase; helix two turns helix, zinc-LESS finger, hydrolase, THF, glycosidase, lyase, multifunctional enzyme; HET: DNA 3DR; 2.20A {Acanthamoeba polyphaga mimivirus} PDB: 3a45_A* 3a42_A
Back Show alignment and structure
Probab=96.33 E-value=0.0053 Score=39.78 Aligned_cols=50 Identities=22% Similarity=0.284 Sum_probs=42.1
Q ss_pred CCEEEEEE--EE-E-ECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 85766643--12-0-071768999999980888212002279899999998612
Q gi|254780239|r 12 AKRVVRAL--CY-I-HGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 12 ~K~i~~aL--t~-I-~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
+.+|.-+| +. | -|||.-.+..||..++|+|..++.+|+++|+..|-+.+.
T Consensus 11 ~~~Ik~~LlDQ~~i~AGIGNiy~dEiLf~A~IhP~~~~~~Ls~~~~~~L~~~i~ 64 (146)
T 3a46_A 11 KQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIK 64 (146)
T ss_dssp CSBHHHHHHCSSSSCBCCCHHHHHHHHHHTTBCTTCBGGGCCHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCEECCCCHHHHHHHHHHHHCCCCCHHCCCCHHHHHHHHHHHH
T ss_conf 022346644367366485389999999975048334011099999999999999
>3gpu_A (A:133-256) DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 2f5n_A 2f5o_A 2f5p_A 3gp1_A* 3gq4_A* 3gpy_A* 3gq5_A* 3gpp_A* 2f5q_A* 2f5s_A* 1l1z_A* 1l1t_A* 1l2b_A* 1l2c_A* 1l2d_A* 1r2z_A* 1r2y_A* 3jr5_A* ...
Back Show alignment and structure
Probab=96.32 E-value=0.0051 Score=39.84 Aligned_cols=51 Identities=18% Similarity=0.251 Sum_probs=42.6
Q ss_pred CCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 85766643---1200717689999999808882120022798999999986124
Q gi|254780239|r 12 AKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122)
Q Consensus 12 ~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122)
+++|.-+| +-|-|||.-.|..||..++|+|..++.+|+++|+..|-+.+.+
T Consensus 23 ~~~Ik~~LlDQ~~iaGiGNiya~EiLf~a~ihP~~~~~~Ls~~~~~~L~~~i~~ 76 (124)
T 3gpu_A 23 KRSVKALLLDCTVVAGFGNIYVDESLFRAGILPGRPAASLSSKEIERLHEEMVA 76 (124)
T ss_dssp CSBHHHHHHCTTTSTTCCHHHHHHHHHHHTCCTTSBGGGCCHHHHHHHHHHHHH
T ss_pred CCCHHHHEECCCEEEECCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 755678501075263034125788998816884775655546667678999999
>1ee8_A (A:121-219) MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8}
Back Show alignment and structure
Probab=96.24 E-value=0.0059 Score=39.49 Aligned_cols=51 Identities=20% Similarity=0.277 Sum_probs=42.7
Q ss_pred CCCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 985766643---120071768999999980888212002279899999998612
Q gi|254780239|r 11 RAKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 11 ~~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
.+.+|.-+| +-|-|||.-+|..||..++|+|..++.+|+++|+..|-+.+.
T Consensus 22 ~~~~Ik~~LlDQ~viaGiGNiya~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~i~ 75 (99)
T 1ee8_A 22 SARPLKALLLDQRLAAGVGNIYADEALFRARLSPFRPARSLTEEEARRLYRALR 75 (99)
T ss_dssp CCSBHHHHHHHSSSSTTCCHHHHHHHHHHTTCCSSSBGGGCCHHHHHHHHHHHH
T ss_pred CCCCHHHHHHCCCEECCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 875288986158813156698999999974899778822189999999999999
>1k3x_A (A:125-262) Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli}
Back Show alignment and structure
Probab=96.19 E-value=0.0065 Score=39.20 Aligned_cols=52 Identities=13% Similarity=0.307 Sum_probs=44.9
Q ss_pred CCCEEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 985766643---1200717689999999808882120022798999999986124
Q gi|254780239|r 11 RAKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122)
Q Consensus 11 ~~K~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122)
.+.+|.-+| +-|-|||.-.|..|+..++|+|..++.+||++|+..|-+.+..
T Consensus 25 ~~~~ik~~LlDQ~~iaGiGNiy~dEiLf~a~ihP~~~~~~Ls~~~~~~L~~~i~~ 79 (138)
T 1k3x_A 25 RNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLE 79 (138)
T ss_dssp TTSCHHHHTTCTTTSBTCCHHHHHHHHHHHTCCSSCCGGGSCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCEEHEHHHHHHHHHHHHHHH
T ss_conf 0268999984277434656899999998600487661010027789999999999
>1tdh_A (A:156-364) NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens}
Back Show alignment and structure
Probab=94.99 E-value=0.004 Score=40.51 Aligned_cols=49 Identities=22% Similarity=0.328 Sum_probs=41.3
Q ss_pred EEEEEE---EEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCC
Q ss_conf 766643---1200717689999999808882120022798999999986124
Q gi|254780239|r 14 RVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 (122)
Q Consensus 14 ~i~~aL---t~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~ 62 (122)
+|.-+| +.|-|||...+..||..++|+|..++.+|+++|+..|-..|..
T Consensus 5 pIk~~LLDQ~~iaGIGN~~~dEILf~A~IhP~~~~~~L~~~~~~~L~~~i~~ 56 (209)
T 1tdh_A 5 PICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELT 56 (209)
T ss_dssp BHHHHTTCTTTSTTCCHHHHHHHHHHHTCCTTSBHHHHHGGGC-----CCSC
T ss_pred CHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCCCCH
T ss_conf 2889984477015664348999999828996663123457664134421000
>2i0z_A (A:302-368) NAD(FAD)-utilizing dehydrogenases; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; HET: FAD; 1.84A {Bacillus cereus}
Back Show alignment and structure
Probab=91.75 E-value=0.28 Score=29.10 Aligned_cols=49 Identities=10% Similarity=0.022 Sum_probs=39.0
Q ss_pred CCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHC
Q ss_conf 985766643120071768999999980888212002279899999998612
Q gi|254780239|r 11 RAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61 (122)
Q Consensus 11 ~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~ 61 (122)
++|.+.-+|. ..+-.+.+..+|..+|||+++++++||..++..|...+.
T Consensus 18 ~~k~i~n~l~--~~lP~rL~~~ll~~~gI~~~~~~~~ls~~~~~~L~~~lK 66 (67)
T 2i0z_A 18 PKKGIKNVLK--GYVPERYFLFLLEKNEIDGSEQAGQVSHEKIRALVKDFK 66 (67)
T ss_dssp TTSBHHHHTT--TSSCHHHHHHHHHHTTCCTTSBGGGSCHHHHHHHHHHHH
T ss_pred CCHHHHHHHH--HHHHHHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHHHH
T ss_conf 1001222221--000245689998750332011231078999999999875