Conserved Domains and Related Protein Families
Conserved Domains Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
ID Alignment Graph Length
Definition
E-value Query 72
smart00475 259
smart00475, 53EXOc, 5'-3' exonuclease
5e-15 cd09859 174
cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuc
5e-14 PRK05755 880
PRK05755, PRK05755, DNA polymerase I; Provisional
5e-12 PRK14976 281
PRK14976, PRK14976, 5'-3' exonuclease; Provisional
1e-08 pfam02739 169
pfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-term
2e-08 TIGR00593 887
TIGR00593, pola, DNA polymerase I
4e-07 PRK09482 256
PRK09482, PRK09482, flap endonuclease-like protein
8e-06 COG0258 310
COG0258, Exo, 5'-3' exonuclease (including N-termi
3e-04
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease
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Score = 66.1 bits (162), Expect = 5e-15
Identities = 27/95 (28%), Positives = 43/95 (45%), Gaps = 24/95 (25%)
Query: 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE------------------ 42
FRH LYP YK NRP TPD +++ + +K + A+ I V+E
Sbjct: 61 KTFRHELYPEYKANRPKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAE 120
Query: 43 -----IQVVSPNKDS-QILSHSLCLLRIAPRGFEL 71
+++VS +KD Q++S + +L E
Sbjct: 121 AEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEF 155
>gnl|CDD|189029 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs
Back Show alignment and domain information
Score = 62.1 bits (152), Expect = 5e-14
Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 24/91 (26%)
Query: 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEIQ----------------- 44
FRH LYP YK NRPP P+ + L +K ++A+ I V+E++
Sbjct: 61 TFRHELYPEYKANRPPMPEELRPQLPLIKELLEALGIPVLEVEGYEADDVIGTLAKKAEE 120
Query: 45 ------VVSPNKDS-QILSHSLCLLRIAPRG 68
+VS +KD Q++S ++ +L
Sbjct: 121 EGYEVVIVSGDKDLLQLVSENVRVLDPKKGS 151
The 5'-3' exonuclease (53EXO) PIN (PilT N terminus) domain of multi-domain DNA polymerase I and single domain protein homologs are included in this family. Taq contains a polymerase domain for synthesizing a new DNA strand and a 53EXO PIN domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO PIN domain recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO PIN domain cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 16 residues in 53EXO PIN domains) and a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included here) and the helical arch/clamp region are involved in DNA/RNA binding. The active site includes a set of conserved acidic residues that are essential for binding divalent metal ions required for nuclease activity. Length = 174
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional
Back Show alignment and domain information
Score = 58.6 bits (143), Expect = 5e-12
Identities = 16/42 (38%), Positives = 28/42 (66%)
Query: 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEI 43
FRH LYP YK NRPP P+ + + + ++ ++A+ I ++E+
Sbjct: 64 TFRHELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLLEL 105
>gnl|CDD|237877 PRK14976, PRK14976, 5'-3' exonuclease; Provisional
Back Show alignment and domain information
Score = 48.8 bits (117), Expect = 1e-08
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEIQ 44
FRH LY YK R TP++++ + LK +K IK E
Sbjct: 68 TFRHQLYDEYKQGRKKTPESLISQIPLLKKILKLAGIKWEEQP 110
>gnl|CDD|145734 pfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-terminal resolvase-like domain
Back Show alignment and domain information
Score = 47.6 bits (114), Expect = 2e-08
Identities = 17/41 (41%), Positives = 23/41 (56%)
Query: 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE 42
FRH LY YK NR TPD + + +K + A+ I V+E
Sbjct: 64 TFRHELYEEYKANRAKTPDELPPQIPLIKELLDALGIPVLE 104
>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I
Back Show alignment and domain information
Score = 44.6 bits (106), Expect = 4e-07
Identities = 15/41 (36%), Positives = 25/41 (60%)
Query: 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE 42
FRH Y YK NR PTP+ +++ + +K + A+ I ++E
Sbjct: 62 TFRHEAYAEYKANRAPTPEELIEQIPLIKELLDALGIPILE 102
All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 887
>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional
Back Show alignment and domain information
Score = 41.1 bits (97), Expect = 8e-06
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 4 RHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE 42
RH L P YK R P P+ + QGL ++A+ + + I
Sbjct: 64 RHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELGIDSWH 102
>gnl|CDD|223336 COG0258, Exo, 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Back Show alignment and domain information
Score = 36.5 bits (85), Expect = 3e-04
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 2 NFRHTLYPSYKNNRPP-TPDTMVQGLQYLKASIKAMSIKVIEI 43
FRH L YK NR PD + + L + A+ I ++E+
Sbjct: 73 TFRHELLEEYKANREKEMPDELAPQIPILTELLVALGIPLLEL 115
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
ID Alignment Graph Length
Definition
Probability Query
72
PF02739 169
5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv
99.92 PRK09482 256
flap endonuclease-like protein; Provisional
99.91 smart00475 259
53EXOc 5'-3' exonuclease.
99.9 PRK14976 281
5'-3' exonuclease; Provisional
99.89 cd00008 240
53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas
99.87 PHA02567 304
rnh RnaseH; Provisional
99.87 TIGR00593 887
pola DNA polymerase I. This family is based on the
99.85 PRK05755 880
DNA polymerase I; Provisional
99.82 PHA00439 286
exonuclease
99.82 COG0258 310
Exo 5'-3' exonuclease (including N-terminal domain
99.72 PRK03980 292
flap endonuclease-1; Provisional
98.85 PTZ00217 393
flap endonuclease-1; Provisional
98.66 TIGR03674 338
fen_arch flap structure-specific endonuclease. End
98.57 cd00128 316
XPG Xeroderma pigmentosum G N- and I-regions (XPGN
98.27 TIGR00288 160
conserved hypothetical protein TIGR00288. This fam
87.58 TIGR00264 116
alpha-NAC-related protein. This hypothetical prote
84.69 PF01936 146
NYN: NYN domain; InterPro: IPR021139 This highly c
82.36 PLN02320 502
seryl-tRNA synthetase
81.87
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities
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Probab=99.92 E-value=1.2e-26 Score=156.46 Aligned_cols=67 Identities=37% Similarity=0.718 Sum_probs=60.8
Q ss_pred CcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccCC
Q 035140 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILSH 57 (72)
Q Consensus 2 t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~~ 57 (72)
|||+++||+|||||+++|++|..|++.++++++++|+++++ |+|+|+|||| |||++
T Consensus 64 ~fR~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~ 143 (169)
T PF02739_consen 64 TFRKELYPEYKANRKPMPEELIPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDE 143 (169)
T ss_dssp HHHHHCCTTTTHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS
T ss_pred chHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCC
Confidence 79999999999999999999999999999999999999998 9999999999 99999
Q ss_pred --CEEEEEecCCc
Q 035140 58 --SLCLLRIAPRG 68 (72)
Q Consensus 58 --~v~v~~~~k~~ 68 (72)
+|.++++....
T Consensus 144 ~~~V~~~~~~~~~ 156 (169)
T PF02739_consen 144 NVNVYLLDPGKKK 156 (169)
T ss_dssp -TSEEEEETTTTC
T ss_pred CceEEEeecCCCC
Confidence 77777764333
The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
>PRK09482 flap endonuclease-like protein; Provisional
Back Show alignment and domain information
Probab=99.91 E-value=4.1e-25 Score=157.79 Aligned_cols=65 Identities=31% Similarity=0.564 Sum_probs=62.1
Q ss_pred CcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccCC
Q 035140 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILSH 57 (72)
Q Consensus 2 t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~~ 57 (72)
+|||++||+|||||++||++|..|++.|+++++++|+++++ |+|+|+|||+ |||++
T Consensus 62 ~fR~~l~p~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~ 141 (256)
T PRK09482 62 GWRHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSP 141 (256)
T ss_pred ccHHHHhHHHhcCCCCCcHHHHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCC
Confidence 39999999999999999999999999999999999999988 9999999999 99999
Q ss_pred CEEEEEecC
Q 035140 58 SLCLLRIAP 66 (72)
Q Consensus 58 ~v~v~~~~k 66 (72)
+|++|++.+
T Consensus 142 ~v~~~~~~~ 150 (256)
T PRK09482 142 TIQIRDYFQ 150 (256)
T ss_pred CeEEEeccc
Confidence 999998653
>smart00475 53EXOc 5'-3' exonuclease
Back Show alignment and domain information
Probab=99.90 E-value=6.8e-24 Score=150.99 Aligned_cols=66 Identities=39% Similarity=0.735 Sum_probs=63.3
Q ss_pred CCcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccC
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~ 56 (72)
++|||++||+|||||++||++|..|++.+++++++||+++++ ++|+|+|||| ||++
T Consensus 61 ~~~R~~l~p~YKa~R~~~pe~L~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~ 140 (259)
T smart00475 61 KTFRHELYPEYKANRPKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVS 140 (259)
T ss_pred CccccchhHHHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCC
Confidence 489999999999999999999999999999999999999998 8899999999 9999
Q ss_pred CCEEEEEecC
Q 035140 57 HSLCLLRIAP 66 (72)
Q Consensus 57 ~~v~v~~~~k 66 (72)
++|.+|++.+
T Consensus 141 ~~v~~~~~~~ 150 (259)
T smart00475 141 DKVSVLDPTK 150 (259)
T ss_pred CCEEEEeccC
Confidence 9999998865
>PRK14976 5'-3' exonuclease; Provisional
Back Show alignment and domain information
Probab=99.89 E-value=1.2e-23 Score=151.06 Aligned_cols=67 Identities=31% Similarity=0.495 Sum_probs=63.7
Q ss_pred CCcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccC
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~ 56 (72)
.+|||++||+||+||++||++|..|++.++++++++|+|+++ |+|+|+|||| ||++
T Consensus 67 ~~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~ 146 (281)
T PRK14976 67 KTFRHQLYDEYKQGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVN 146 (281)
T ss_pred CcccccccHHHhcCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCC
Confidence 489999999999999999999999999999999999999998 8999999999 9999
Q ss_pred CCEEEEEecCC
Q 035140 57 HSLCLLRIAPR 67 (72)
Q Consensus 57 ~~v~v~~~~k~ 67 (72)
++|+++++.++
T Consensus 147 ~~v~~~~~~~~ 157 (281)
T PRK14976 147 ENTDVLLKKKG 157 (281)
T ss_pred CCeEEEEecCC
Confidence 99999987654
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes
Back Show alignment and domain information
Probab=99.87 E-value=1.9e-22 Score=141.54 Aligned_cols=65 Identities=34% Similarity=0.622 Sum_probs=62.4
Q ss_pred CCcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccC
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~ 56 (72)
++|||++||+||+||+++|++|..|++.+++++++||+++++ ++|+|+|||| ||++
T Consensus 62 ~~~R~~l~p~YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~ 141 (240)
T cd00008 62 KTFRHELYPEYKANRKKMPEELREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVS 141 (240)
T ss_pred CcccccccHHHHcCCCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCC
Confidence 489999999999999999999999999999999999999998 7999999999 9999
Q ss_pred CCEEEEEec
Q 035140 57 HSLCLLRIA 65 (72)
Q Consensus 57 ~~v~v~~~~ 65 (72)
++|+++++.
T Consensus 142 ~~v~~~~~~ 150 (240)
T cd00008 142 DNVKVVSPM 150 (240)
T ss_pred CCEEEEeCC
Confidence 999999875
They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
>PHA02567 rnh RnaseH; Provisional
Back Show alignment and domain information
Probab=99.87 E-value=2.4e-22 Score=146.70 Aligned_cols=66 Identities=18% Similarity=0.184 Sum_probs=60.6
Q ss_pred CCcccccCccccCCCCCCchhHHHhH--------HHHHHHHHHcCCccEE-----------------------EEEecCC
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGL--------QYLKASIKAMSIKVIE-----------------------IQVVSPN 49 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql--------~~i~~~l~~lgi~~~~-----------------------v~IvS~D 49 (72)
++|||++||+|||||++||++|..|+ +.+++++++||+++++ |+|+|+|
T Consensus 76 ~tfR~elyp~YKAnR~~~Peel~~q~~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~VvIvS~D 155 (304)
T PHA02567 76 GYWRRDIAWYYKKNRKKDREESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSD 155 (304)
T ss_pred CCchhhhhhHhhcCCCCCChHHHHHHHHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEEEEeCC
Confidence 37999999999999999999988887 7889999999999998 9999999
Q ss_pred CCc-cccC-CCEEEEEecC
Q 035140 50 KDS-QILS-HSLCLLRIAP 66 (72)
Q Consensus 50 KD~-QLv~-~~v~v~~~~k 66 (72)
||| ||++ ++|.+|++.+
T Consensus 156 KDl~QLv~~~~v~~~~~~~ 174 (304)
T PHA02567 156 GDFTQLHKYPGVKQWSPMQ 174 (304)
T ss_pred CChhhccCCCCeEEeecCC
Confidence 999 9995 8999998764
>TIGR00593 pola DNA polymerase I
Back Show alignment and domain information
Probab=99.85 E-value=8.6e-22 Score=158.25 Aligned_cols=66 Identities=32% Similarity=0.634 Sum_probs=63.2
Q ss_pred CCcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccC
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~ 56 (72)
+||||++||+|||||++||++|..|++.+++++++||||+++ |+|+|+|||+ ||++
T Consensus 61 ~tfR~~~~~~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~ 140 (887)
T TIGR00593 61 PTFRHEAYAEYKANRAPTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVS 140 (887)
T ss_pred CcchHHHHHHHHhCCCCChHHHHHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCC
Confidence 489999999999999999999999999999999999999998 8999999999 9999
Q ss_pred CCEEEEEecC
Q 035140 57 HSLCLLRIAP 66 (72)
Q Consensus 57 ~~v~v~~~~k 66 (72)
++|+++++.+
T Consensus 141 ~~v~~~~~~~ 150 (887)
T TIGR00593 141 DNVKVLIPKG 150 (887)
T ss_pred CCEEEEeccC
Confidence 9999998754
This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
>PRK05755 DNA polymerase I; Provisional
Back Show alignment and domain information
Probab=99.82 E-value=2e-20 Score=149.37 Aligned_cols=65 Identities=34% Similarity=0.735 Sum_probs=62.6
Q ss_pred CCcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-cccC
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv~ 56 (72)
+||||++||+|||||+++|++|..|++.++++++++|+++++ ++|+|+|||| ||++
T Consensus 63 ~~~R~~~~~~YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~ 142 (880)
T PRK05755 63 KTFRHELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVD 142 (880)
T ss_pred CccccccCHHHhCCCCCCcHHHHHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCC
Confidence 489999999999999999999999999999999999999998 8999999999 9999
Q ss_pred CCEEEEEec
Q 035140 57 HSLCLLRIA 65 (72)
Q Consensus 57 ~~v~v~~~~ 65 (72)
++|++|++.
T Consensus 143 ~~v~~~~~~ 151 (880)
T PRK05755 143 DNVTLLDTM 151 (880)
T ss_pred CCEEEeecc
Confidence 999999875
>PHA00439 exonuclease
Back Show alignment and domain information
Probab=99.82 E-value=1.7e-20 Score=136.07 Aligned_cols=62 Identities=27% Similarity=0.304 Sum_probs=55.9
Q ss_pred CCcccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCccEE------------------------EEEecCCCCc-ccc
Q 035140 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIE------------------------IQVVSPNKDS-QIL 55 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~~Pe~L~~Ql~~i~~~l~~lgi~~~~------------------------v~IvS~DKD~-QLv 55 (72)
+||||++||+|||||++||++ ..|++.++++++++|+++++ |+|+|+|||| ||+
T Consensus 75 ~tfR~elyp~YKanR~~~p~~-~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QLv 153 (286)
T PHA00439 75 VNWRKEVVPTYKANRKAKRKP-VGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIP 153 (286)
T ss_pred CChHhhhhhHhcCCCCCCCCc-hhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhcC
Confidence 489999999999999999999 88999999999999999988 6999999999 999
Q ss_pred CCCEEEEEe
Q 035140 56 SHSLCLLRI 64 (72)
Q Consensus 56 ~~~v~v~~~ 64 (72)
+. +.+|.+
T Consensus 154 ~~-~~~~~~ 161 (286)
T PHA00439 154 NC-DFLWCT 161 (286)
T ss_pred cc-eEEEcc
Confidence 76 444443
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Back Show alignment and domain information
Probab=99.72 E-value=4.3e-18 Score=122.62 Aligned_cols=68 Identities=28% Similarity=0.474 Sum_probs=64.7
Q ss_pred CCcccccCccccCCCCC-CchhHHHhHHHHHHHHHHcCCccEE-----------------------EEEecCCCCc-ccc
Q 035140 1 MNFRHTLYPSYKNNRPP-TPDTMVQGLQYLKASIKAMSIKVIE-----------------------IQVVSPNKDS-QIL 55 (72)
Q Consensus 1 ~t~R~~~~p~YKanR~~-~Pe~L~~Ql~~i~~~l~~lgi~~~~-----------------------v~IvS~DKD~-QLv 55 (72)
++||+++|++||++|++ ||++|..|++.+.+.+.++|++.++ +.|+|+|||+ ||+
T Consensus 72 ~tfR~~~~~~yK~~R~~~~p~~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~~~g~~~~I~S~DkD~lql~ 151 (310)
T COG0258 72 PTFRHELLEEYKANREKEMPDELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAYKKGDVVLIISGDKDLLQLV 151 (310)
T ss_pred CcchHHHHHHHHhCCCccCHHHHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHHhcCCeEEEEeCCcchhhhc
Confidence 48999999999999999 9999999999999999999999988 9999999999 999
Q ss_pred CCCEEEEEecCCc
Q 035140 56 SHSLCLLRIAPRG 68 (72)
Q Consensus 56 ~~~v~v~~~~k~~ 68 (72)
++++.++++.++.
T Consensus 152 ~~~~~~~~~~~~~ 164 (310)
T COG0258 152 SPNVLVINGKKGE 164 (310)
T ss_pred CCCcEEEeccCCC
Confidence 9999999987764
>PRK03980 flap endonuclease-1; Provisional
Back Show alignment and domain information
Probab=98.85 E-value=8.4e-10 Score=80.06 Aligned_cols=58 Identities=16% Similarity=0.125 Sum_probs=53.8
Q ss_pred CcccccCccccCCCCCCchhHHH-----------------------hHHHHHHHHHHcCCccEE----------------
Q 035140 2 NFRHTLYPSYKNNRPPTPDTMVQ-----------------------GLQYLKASIKAMSIKVIE---------------- 42 (72)
Q Consensus 2 t~R~~~~p~YKanR~~~Pe~L~~-----------------------Ql~~i~~~l~~lgi~~~~---------------- 42 (72)
++|++.+++||++|.++|+++.. |++.++++|++||||++.
T Consensus 38 ~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~vt~~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~~g 117 (292)
T PRK03980 38 ELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKG 117 (292)
T ss_pred hHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccCCHHHHHHHHHHHHHCCCCEEecCchHHHHHHHHHHCC
Confidence 57999999999999999999877 999999999999999999
Q ss_pred --EEEecCCCCc-cccCCCE
Q 035140 43 --IQVVSPNKDS-QILSHSL 59 (72)
Q Consensus 43 --v~IvS~DKD~-QLv~~~v 59 (72)
..|+|+|+|+ |+.+++|
T Consensus 118 ~vd~V~S~D~D~l~fg~~~v 137 (292)
T PRK03980 118 DAWAVGSQDYDSLLFGAPRL 137 (292)
T ss_pred CeEEEecCCcCeeeecCCEE
Confidence 4789999999 9999875
>PTZ00217 flap endonuclease-1; Provisional
Back Show alignment and domain information
Probab=98.66 E-value=9.3e-09 Score=77.26 Aligned_cols=62 Identities=16% Similarity=0.216 Sum_probs=54.2
Q ss_pred CcccccCccccCCCCCCchhH-----------------------HHhHHHHHHHHHHcCCccEE----------------
Q 035140 2 NFRHTLYPSYKNNRPPTPDTM-----------------------VQGLQYLKASIKAMSIKVIE---------------- 42 (72)
Q Consensus 2 t~R~~~~p~YKanR~~~Pe~L-----------------------~~Ql~~i~~~l~~lgi~~~~---------------- 42 (72)
++|++.++.||++|+++|+++ ..|++.++++|+.||||++.
T Consensus 93 ~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~EAdaq~A~L~~~g 172 (393)
T PTZ00217 93 ELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKG 172 (393)
T ss_pred hhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCcCHHHHHHHHHHCC
Confidence 578999999999999999998 78899999999999999999
Q ss_pred --EEEecCCCCc-cccCCCEEEEEe
Q 035140 43 --IQVVSPNKDS-QILSHSLCLLRI 64 (72)
Q Consensus 43 --v~IvS~DKD~-QLv~~~v~v~~~ 64 (72)
..|+|.|+|+ |+.++. .+++.
T Consensus 173 ~v~~ViS~D~D~l~fg~~~-vi~~l 196 (393)
T PTZ00217 173 KVYAVATEDMDALTFGTPV-LLRNL 196 (393)
T ss_pred CeEEEeCCCcCeeecCCcE-EEEcc
Confidence 5589999999 998774 34433
>TIGR03674 fen_arch flap structure-specific endonuclease
Back Show alignment and domain information
Probab=98.57 E-value=2.4e-08 Score=73.53 Aligned_cols=62 Identities=15% Similarity=0.158 Sum_probs=51.8
Q ss_pred CcccccCccccCCCCCCchhHHH-----------------------hHHHHHHHHHHcCCccEE----------------
Q 035140 2 NFRHTLYPSYKNNRPPTPDTMVQ-----------------------GLQYLKASIKAMSIKVIE---------------- 42 (72)
Q Consensus 2 t~R~~~~p~YKanR~~~Pe~L~~-----------------------Ql~~i~~~l~~lgi~~~~---------------- 42 (72)
+||++.++.||+.|+++++++.. |++.++++|++||||++.
T Consensus 85 ~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~EAeaq~a~L~~~g 164 (338)
T TIGR03674 85 ELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKG 164 (338)
T ss_pred hhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCccHHHHHHHHHHCC
Confidence 57788888888888887777654 489999999999999999
Q ss_pred -E-EEecCCCCc-cccCCCEEEEEe
Q 035140 43 -I-QVVSPNKDS-QILSHSLCLLRI 64 (72)
Q Consensus 43 -v-~IvS~DKD~-QLv~~~v~v~~~ 64 (72)
| .|+|+|+|+ |+.+++| +.+.
T Consensus 165 ~vd~v~S~D~D~l~fg~~~v-i~~~ 188 (338)
T TIGR03674 165 DVDYVGSQDYDSLLFGAPRL-VRNL 188 (338)
T ss_pred CeeEEecCCcCeeeecCCEE-EEec
Confidence 4 889999999 9999987 4443
Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases
Back Show alignment and domain information
Probab=98.27 E-value=1.8e-07 Score=67.44 Aligned_cols=57 Identities=12% Similarity=0.102 Sum_probs=49.9
Q ss_pred ccccCccccCCCCCCch----------------hHHHhHHHHHHHHHHcCCccEE------------------EEEecCC
Q 035140 4 RHTLYPSYKNNRPPTPD----------------TMVQGLQYLKASIKAMSIKVIE------------------IQVVSPN 49 (72)
Q Consensus 4 R~~~~p~YKanR~~~Pe----------------~L~~Ql~~i~~~l~~lgi~~~~------------------v~IvS~D 49 (72)
|++..++||++|.++|+ ....|++.++++|++||++++. ..|+|.|
T Consensus 92 R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap~EAdaq~a~l~~~g~v~~i~S~D 171 (316)
T cd00128 92 RRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAPYEAEAQCAYLAKKGLVDAIITED 171 (316)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECCcCHHHHHHHHHhCCCeeEEEecC
Confidence 88999999999998887 2478899999999999999998 5799999
Q ss_pred CCc-cccCCCEE
Q 035140 50 KDS-QILSHSLC 60 (72)
Q Consensus 50 KD~-QLv~~~v~ 60 (72)
+|+ |+-.++|.
T Consensus 172 sD~l~fg~~~vi 183 (316)
T cd00128 172 SDLLLFGAPRVY 183 (316)
T ss_pred CCeeeecCceEE
Confidence 999 98776554
XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
>TIGR00288 conserved hypothetical protein TIGR00288
Back Show alignment and domain information
Probab=87.58 E-value=0.57 Score=31.84 Aligned_cols=28 Identities=14% Similarity=0.290 Sum_probs=21.9
Q ss_pred HHHHHHHcCCccEE------------------------EEEecCCCCc-cccC
Q 035140 29 LKASIKAMSIKVIE------------------------IQVVSPNKDS-QILS 56 (72)
Q Consensus 29 i~~~l~~lgi~~~~------------------------v~IvS~DKD~-QLv~ 56 (72)
+.+.+..+|+..+. ++|+|||.|| -|+.
T Consensus 71 l~~~l~~~Gf~pv~~kG~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv~ 123 (160)
T TIGR00288 71 LIEAVVNQGFEPIIVAGDVDVRMAVEAMELIYNPNIDAVALVTRDADFLPVIN 123 (160)
T ss_pred HHHHHHHCCceEEEecCcccHHHHHHHHHHhccCCCCEEEEEeccHhHHHHHH
Confidence 35677778876543 8999999999 9983
This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
>TIGR00264 alpha-NAC-related protein
Back Show alignment and domain information
Probab=84.69 E-value=2.6 Score=27.44 Aligned_cols=42 Identities=12% Similarity=0.236 Sum_probs=34.8
Q ss_pred HhHHHHHHHHHHcCCccEE-----EEEecCCCCccccCCCEEEEEec
Q 035140 24 QGLQYLKASIKAMSIKVIE-----IQVVSPNKDSQILSHSLCLLRIA 65 (72)
Q Consensus 24 ~Ql~~i~~~l~~lgi~~~~-----v~IvS~DKD~QLv~~~v~v~~~~ 65 (72)
.|+..+++.+..||+..-+ |+|-+.|+++=+-+++|.+++..
T Consensus 9 r~~~~mkkmMk~MGi~~~eidV~~ViIk~~~k~ivf~~p~V~~m~~~ 55 (116)
T TIGR00264 9 KMLKQMQKMMKQMGMEMEDLDVEEVIIVFDDEEWIFENPKVQVMDIL 55 (116)
T ss_pred ccHHHHHHHHHHcCCCccccccEEEEEEeCCceEEEecCeeEEEecC
Confidence 4567789999999987764 99999999997778899998754
This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function
Back Show alignment and domain information
Probab=82.36 E-value=0.51 Score=29.27 Aligned_cols=14 Identities=29% Similarity=0.399 Sum_probs=9.8
Q ss_pred EEEecCCCCc-cccC
Q 035140 43 IQVVSPNKDS-QILS 56 (72)
Q Consensus 43 v~IvS~DKD~-QLv~ 56 (72)
++|+|||.|| .++.
T Consensus 99 ivLvSgD~Df~~~v~ 113 (146)
T PF01936_consen 99 IVLVSGDSDFAPLVR 113 (146)
T ss_dssp EEEE---GGGHHHHH
T ss_pred EEEEECcHHHHHHHH
Confidence 8999999999 8874
However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
>PLN02320 seryl-tRNA synthetase
Back Show alignment and domain information
Probab=81.87 E-value=4.5 Score=31.97 Aligned_cols=50 Identities=2% Similarity=0.007 Sum_probs=42.2
Q ss_pred hhHHHhHHHHHHHHHHcCCccEEEEEecCCCCc-cccCCCEEEEEecCCce
Q 035140 20 DTMVQGLQYLKASIKAMSIKVIEIQVVSPNKDS-QILSHSLCLLRIAPRGF 69 (72)
Q Consensus 20 e~L~~Ql~~i~~~l~~lgi~~~~v~IvS~DKD~-QLv~~~v~v~~~~k~~~ 69 (72)
+++..-+..+.+++..||+|.-.+.+.|+|=.+ .-..=.+.+|-|..+.+
T Consensus 359 ~e~e~ll~~~e~i~~~LgLpyrvv~l~tgDLg~~a~kkyDiEvW~P~~~~y 409 (502)
T PLN02320 359 SFHEELIQIEEDLFTSLGLHFKTLDMATADLGAPAYRKFDIEAWMPGLGRY 409 (502)
T ss_pred HHHHHHHHHHHHHHHHcCCCeEEEEecCCccchhhhheEEEEEEecCCCcE
Confidence 345666788899999999999999999999988 77777899999986654
Homologous Structure Domains
