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 95
cd09859 174
cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuc
2e-31 smart00475 259
smart00475, 53EXOc, 5'-3' exonuclease
5e-31 PRK05755 880
PRK05755, PRK05755, DNA polymerase I; Provisional
1e-26 pfam02739 169
pfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-term
9e-25 TIGR00593 887
TIGR00593, pola, DNA polymerase I
2e-20 PRK14976 281
PRK14976, PRK14976, 5'-3' exonuclease; Provisional
7e-18 COG0258 310
COG0258, Exo, 5'-3' exonuclease (including N-termi
5e-16 PRK09482 256
PRK09482, PRK09482, flap endonuclease-like protein
2e-15 cd00008 160
cd00008, PIN_53EXO-like, PIN domains of the 5'-3'
3e-10 cd09860 170
cd09860, PIN_T4-like, PIN domain of bacteriophage
5e-09 PHA00439 286
PHA00439, PHA00439, exonuclease
2e-08 PHA02567 304
PHA02567, rnh, RnaseH; Provisional
2e-04
>gnl|CDD|189029 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs
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Score = 107 bits (271), Expect = 2e-31
Identities = 38/91 (41%), Positives = 59/91 (64%), Gaps = 1/91 (1%)
Query: 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVD 61
FRH LYP YK NRPP P+ + L +K ++A+ I V+EV G EADDVIG LA ++ +
Sbjct: 61 TFRHELYPEYKANRPPMPEELRPQLPLIKELLEALGIPVLEVEGYEADDVIGTLAKKAEE 120
Query: 62 DGFKIQVVSPNKDS-QILSHSLCLLRIAPRG 91
+G+++ +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|214682 smart00475, 53EXOc, 5'-3' exonuclease
Back Show alignment and domain information
Score = 109 bits (274), Expect = 5e-31
Identities = 38/95 (40%), Positives = 59/95 (62%), Gaps = 1/95 (1%)
Query: 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSV 60
FRH LYP YK NRP TPD +++ + +K + A+ I V+EV G EADDVI LA ++
Sbjct: 61 KTFRHELYPEYKANRPKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAE 120
Query: 61 DDGFKIQVVSPNKDS-QILSHSLCLLRIAPRGFEL 94
+G+++++VS +KD Q++S + +L E
Sbjct: 121 AEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEF 155
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional
Back Show alignment and domain information
Score = 101 bits (254), Expect = 1e-26
Identities = 30/73 (41%), Positives = 50/73 (68%)
Query: 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVD 61
FRH LYP YK NRPP P+ + + + ++ ++A+ I ++E+ G EADDVIG LA ++
Sbjct: 64 TFRHELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEA 123
Query: 62 DGFKIQVVSPNKD 74
G+++ +V+ +KD
Sbjct: 124 AGYEVLIVTGDKD 136
>gnl|CDD|145734 pfam02739, 5_3_exonuc_N, 5'-3' exonuclease, N-terminal resolvase-like domain
Back Show alignment and domain information
Score = 90.7 bits (226), Expect = 9e-25
Identities = 34/73 (46%), Positives = 48/73 (65%)
Query: 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVD 61
FRH LY YK NR TPD + + +K + A+ I V+EVPG EADDVIG LA ++
Sbjct: 64 TFRHELYEEYKANRAKTPDELPPQIPLIKELLDALGIPVLEVPGYEADDVIGTLAKKAEK 123
Query: 62 DGFKIQVVSPNKD 74
+G+ +++VS +KD
Sbjct: 124 EGYDVRIVSGDKD 136
>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I
Back Show alignment and domain information
Score = 83.5 bits (207), Expect = 2e-20
Identities = 31/79 (39%), Positives = 53/79 (67%), Gaps = 1/79 (1%)
Query: 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVD 61
FRH Y YK NR PTP+ +++ + +K + A+ I ++EV G EADDVI LA ++
Sbjct: 62 TFRHEAYAEYKANRAPTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEK 121
Query: 62 DGFKIQVVSPNKDS-QILS 79
+G++++++S +KD Q++S
Sbjct: 122 EGYEVRIISGDKDLLQLVS 140
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|237877 PRK14976, PRK14976, 5'-3' exonuclease; Provisional
Back Show alignment and domain information
Score = 75.0 bits (185), Expect = 7e-18
Identities = 29/73 (39%), Positives = 40/73 (54%)
Query: 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVD 61
FRH LY YK R TP++++ + LK +K IK E PG EADD+IG LA +
Sbjct: 68 TFRHQLYDEYKQGRKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSK 127
Query: 62 DGFKIQVVSPNKD 74
+ + S +KD
Sbjct: 128 QNITVLIYSSDKD 140
>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 = 70.4 bits (173), Expect = 5e-16
Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 2 NFRHTLYPSYKNNRPP-TPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSV 60
FRH L YK NR PD + + L + A+ I ++E+ G+EADD I LA ++
Sbjct: 73 TFRHELLEEYKANREKEMPDELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAY 132
Query: 61 DDGFKIQVVSPNKDSQIL 78
G + ++S +KD L
Sbjct: 133 KKGDVVLIISGDKDLLQL 150
>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional
Back Show alignment and domain information
Score = 68.4 bits (168), Expect = 2e-15
Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 4 RHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDG 63
RH L P YK R P P+ + QGL ++A+ + + I G EADD+I LAV+ G
Sbjct: 64 RHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAG 123
Query: 64 FKIQVVSPNKD-SQILSHSLCL 84
+ +VS +K Q+LS ++ +
Sbjct: 124 HQATIVSTDKGYCQLLSPTIQI 145
>gnl|CDD|189019 cd00008, PIN_53EXO-like, PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H and T5-5' nucleases, and homologs
Back Show alignment and domain information
Score = 53.0 bits (127), Expect = 3e-10
Identities = 21/85 (24%), Positives = 35/85 (41%), Gaps = 8/85 (9%)
Query: 3 FRHTLYPSYKNNRPP-------TPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKL 55
FR P YK NR + + L+ KA + + G EADD+ L
Sbjct: 60 FRLEHLPEYKGNRDEKYAEEKALDEQFFEYLKDAFELCKATTFPTFTIRGYEADDMAAYL 119
Query: 56 AVRSVDDGFKIQVVSPNKD-SQILS 79
+ +G + ++S + D Q+L+
Sbjct: 120 VKKIGHEGDHVWIISTDGDWDQLLT 144
PIN (PilT N terminus) domains of the 5'-3' exonucleases (53EXO) of mutli-domain DNA polymerase I and single domain protein homologs, as well as, the PIN domains of bacteriophage T5-5'nuclease (T5FEN or 5'-3'exonuclease), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar nucleases are included in this family. The 53EXO of DNA polymerase I 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 T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. These nucleases 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. They contain a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 16 to 30 residues in 53EXO-like 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 binding. The active site of the 53EXO of Taq DNA polymerase I includes a set of conserved acidic residues that are essential for binding three divalent metal ions (two Mn2+ ions and one Zn2+ ion) required for nuclease activity. T5-5'nuclease requires at least two bound divalent metal ions for nuclease activity and is reported to be able to use Mg2+, Mn2+ or Co2+ as co-factors. Length = 160
>gnl|CDD|189030 cd09860, PIN_T4-like, PIN domain of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs
Back Show alignment and domain information
Score = 50.1 bits (120), Expect = 5e-09
Identities = 26/78 (33%), Positives = 36/78 (46%), Gaps = 6/78 (7%)
Query: 3 FRHTLYPSYKNNRPPTPDT--MVQGLQYLKASI----KAMSIKVIEVPGVEADDVIGKLA 56
+R L P YK NR TPD + K I + M + I +PG EADDV L
Sbjct: 60 WRRDLLPYYKANRDKTPDKRAWEGYFEAQKPYIEEMKENMPVIQIRIPGAEADDVAAVLV 119
Query: 57 VRSVDDGFKIQVVSPNKD 74
+ G K+ ++S + D
Sbjct: 120 KKLSAFGHKVLLISSDGD 137
PIN (PilT N terminus) domain of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases 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. They have a PIN domain with a helical arch/clamp region (I domain) of variable length (approximately 20 to 30 residues in PIN T5-like 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. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, metal binding site 1, whereas exonuclease activity requires both, the high-affinity, metal binding site 1 and the low-affinity, metal binding site 2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors. Length = 170
>gnl|CDD|222794 PHA00439, PHA00439, exonuclease
Back Show alignment and domain information
Score = 49.4 bits (118), Expect = 2e-08
Identities = 28/76 (36%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 2 NFRHTLYPSYKNNRPPT--PDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRS 59
N+R + P+YK NR P + L+ L A + SI PG+E DDV+G +
Sbjct: 76 NWRKEVVPTYKANRKAKRKPVGYRKFLEELMAREEWKSILE---PGLEGDDVMGIIGTNP 132
Query: 60 VDDGFKIQV-VSPNKD 74
GFK V VS +KD
Sbjct: 133 SLFGFKKAVLVSCDKD 148
>gnl|CDD|222882 PHA02567, rnh, RnaseH; Provisional
Back Show alignment and domain information
Score = 38.1 bits (89), Expect = 2e-04
Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 4 RHTLYPSYKNNR-------PPTPDTMVQGLQYLKASIKA-MSIKVIEVPGVEADDVIGKL 55
R + YK NR P + + + + + IK M KV+++ EADD+I L
Sbjct: 79 RRDIAWYYKKNRKKDREESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVL 138
Query: 56 AVRSVDDGFKIQVVSPNKD 74
+ +G + +VS + D
Sbjct: 139 TKKFSAEGRPVLIVSSDGD 157
Conserved Domains Detected by HHsearch
Original result of HHsearch against CDD database
ID Alignment Graph Length
Definition
Probability Query
95
PF02739 169
5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolv
100.0 PRK09482 256
flap endonuclease-like protein; Provisional
100.0 smart00475 259
53EXOc 5'-3' exonuclease.
99.97 PRK14976 281
5'-3' exonuclease; Provisional
99.97 PHA02567 304
rnh RnaseH; Provisional
99.97 cd00008 240
53EXOc 5'-3' exonuclease; T5 type 5'-3' exonucleas
99.97 PHA00439 286
exonuclease
99.96 TIGR00593 887
pola DNA polymerase I. This family is based on the
99.96 PRK05755 880
DNA polymerase I; Provisional
99.95 COG0258 310
Exo 5'-3' exonuclease (including N-terminal domain
99.91 PTZ00217 393
flap endonuclease-1; Provisional
99.32 PRK03980 292
flap endonuclease-1; Provisional
99.22 TIGR03674 338
fen_arch flap structure-specific endonuclease. End
99.19 cd00128 316
XPG Xeroderma pigmentosum G N- and I-regions (XPGN
99.12 PF12813 246
XPG_I_2: XPG domain containing
97.36 TIGR00600 1034
rad2 DNA excision repair protein (rad2). All prote
95.94 PF05991 166
NYN_YacP: YacP-like NYN domain; InterPro: IPR01029
95.78 cd06167 149
LabA_like LabA_like proteins. A well conserved gro
95.12 PF01936 146
NYN: NYN domain; InterPro: IPR021139 This highly c
94.79 TIGR00288 160
conserved hypothetical protein TIGR00288. This fam
93.29 cd00431 161
cysteine_hydrolases Cysteine hydrolases; This fami
91.5 PF00867 94
XPG_I: XPG I-region; InterPro: IPR006086 This entr
91.41 cd01015 179
CSHase N-carbamoylsarcosine amidohydrolase (CSHase
91.34 COG1412 136
Uncharacterized proteins of PilT N-term./Vapc supe
91.16 cd01012 157
YcaC_related YcaC related amidohydrolases; E.coli
90.78 PRK11440 188
putative hydrolase; Provisional
90.37 TIGR00028 142
Mtu_PIN_fam Mycobacterium tuberculosis PIN domain
90.14 cd01013 203
isochorismatase Isochorismatase, also known as 2,3
89.85 TIGR03614 226
RutB pyrimidine utilization protein B. RL Proc Nat
89.65 cd01014 155
nicotinamidase_related Nicotinamidase_ related ami
89.03 smart00484 73
XPGI Xeroderma pigmentosum G I-region. domain in n
88.51 PLN02621 197
nicotinamidase
88.36 PF00857 174
Isochorismatase: Isochorismatase family; InterPro:
87.84 COG1335 205
PncA Amidases related to nicotinamidase [Secondary
87.09 PF04900 101
Fcf1: Fcf1; InterPro: IPR006984 This family is com
86.89 cd01011 196
nicotinamidase Nicotinamidase/pyrazinamidase (PZas
85.48 PRK11609 212
nicotinamidase/pyrazinamidase; Provisional
85.23 PTZ00331 212
alpha/beta hydrolase; Provisional
83.9
>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
Back Hide alignment and domain information
Probab=100.00 E-value=2e-36 Score=215.08 Aligned_cols=86 Identities=44% Similarity=0.816 Sum_probs=80.1
Q ss_pred ccccccChhhhcCCCCCChhhHHhHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-ccccC
Q 034414 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILSH 80 (95)
Q Consensus 2 ~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~~ 80 (95)
|||+++||+||+||+++|++|..|++.++++++.+|+++++.+|+||||+|||+|+++...|.+|+|+|+|||| ||+++
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 79999999999999999999999999999999999999999999999999999999999999999999999999 99999
Q ss_pred --CeEEEEe
Q 034414 81 --SLCLLRI 87 (95)
Q Consensus 81 --~v~v~~~ 87 (95)
+|.++++
T Consensus 144 ~~~V~~~~~ 152 (169)
T PF02739_consen 144 NVNVYLLDP 152 (169)
T ss_dssp -TSEEEEET
T ss_pred CceEEEeec
Confidence 5666655
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=100.00 E-value=5.9e-34 Score=214.26 Aligned_cols=87 Identities=34% Similarity=0.597 Sum_probs=84.4
Q ss_pred ccccccChhhhcCCCCCChhhHHhHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-ccccC
Q 034414 2 NFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILSH 80 (95)
Q Consensus 2 ~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~~ 80 (95)
+|||++||+||+||+++|++|..|++.++++++++|++++..||+||||+|||+|+++.+.|.+|+|+|+|||| ||+++
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 39999999999999999999999999999999999999999999999999999999999889999999999999 99999
Q ss_pred CeEEEEec
Q 034414 81 SLCLLRIA 88 (95)
Q Consensus 81 ~v~v~~~~ 88 (95)
+|++|.+.
T Consensus 142 ~v~~~~~~ 149 (256)
T PRK09482 142 TIQIRDYF 149 (256)
T ss_pred CeEEEecc
Confidence 99999864
>smart00475 53EXOc 5'-3' exonuclease
Back Show alignment and domain information
Probab=99.97 E-value=3.1e-32 Score=204.66 Aligned_cols=89 Identities=42% Similarity=0.746 Sum_probs=85.8
Q ss_pred CccccccChhhhcCCCCCChhhHHhHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-cccc
Q 034414 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILS 79 (95)
Q Consensus 1 ~~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~ 79 (95)
.+||+++||+||+||+++|++|..|++.++++++.+|++++..+|+||||+|||+|+++...|..++|+|+|||| ||++
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 489999999999999999999999999999999999999999999999999999999988889999999999999 9999
Q ss_pred CCeEEEEecc
Q 034414 80 HSLCLLRIAP 89 (95)
Q Consensus 80 ~~v~v~~~~k 89 (95)
++|++|.+.+
T Consensus 141 ~~v~~~~~~~ 150 (259)
T smart00475 141 DKVSVLDPTK 150 (259)
T ss_pred CCEEEEeccC
Confidence 9999998765
>PRK14976 5'-3' exonuclease; Provisional
Back Show alignment and domain information
Probab=99.97 E-value=4.6e-32 Score=205.66 Aligned_cols=90 Identities=34% Similarity=0.541 Sum_probs=86.2
Q ss_pred CccccccChhhhcCCCCCChhhHHhHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-cccc
Q 034414 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILS 79 (95)
Q Consensus 1 ~~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~ 79 (95)
.+||+++||+||+||+++|++|..|++.++++++.+||+++..||+||||+|||+|+++...|..|+|+|+|||| ||++
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 489999999999999999999999999999999999999999999999999999999999889999999999999 9999
Q ss_pred CCeEEEEeccC
Q 034414 80 HSLCLLRIAPR 90 (95)
Q Consensus 80 ~~v~v~~~~k~ 90 (95)
++|+++.+.++
T Consensus 147 ~~v~~~~~~~~ 157 (281)
T PRK14976 147 ENTDVLLKKKG 157 (281)
T ss_pred CCeEEEEecCC
Confidence 99999987543
>PHA02567 rnh RnaseH; Provisional
Back Show alignment and domain information
Probab=99.97 E-value=1.1e-31 Score=205.92 Aligned_cols=89 Identities=21% Similarity=0.248 Sum_probs=82.5
Q ss_pred CccccccChhhhcCCCCCChhhHHhH--------HHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCC
Q 034414 1 MNFRHTLYPSYKNNRPPTPDTMVQGL--------QYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPN 72 (95)
Q Consensus 1 ~~~R~~l~p~YKanR~~~p~~l~~q~--------~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~D 72 (95)
++|||++||+||+||+++|++|..|+ +.+++++..||++++..+|+||||+|||+|+++...|.+|+|+|+|
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 37999999999999999999987776 6788889999999999999999999999999999889999999999
Q ss_pred CCc-cccc-CCeEEEEecc
Q 034414 73 KDS-QILS-HSLCLLRIAP 89 (95)
Q Consensus 73 kDl-QLv~-~~v~v~~~~k 89 (95)
||| ||++ ++|++|.+.+
T Consensus 156 KDl~QLv~~~~v~~~~~~~ 174 (304)
T PHA02567 156 GDFTQLHKYPGVKQWSPMQ 174 (304)
T ss_pred CChhhccCCCCeEEeecCC
Confidence 999 9995 8999998753
>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=99.97 E-value=5.4e-31 Score=195.33 Aligned_cols=88 Identities=39% Similarity=0.693 Sum_probs=85.0
Q ss_pred CccccccChhhhcCCCCCChhhHHhHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-cccc
Q 034414 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILS 79 (95)
Q Consensus 1 ~~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~ 79 (95)
.+||+++||+||+||+++|++|..|++.++++++.+|++++..+|+||||+|||+|+++...|.+++|+|+|||| ||++
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 489999999999999999999999999999999999999999999999999999999998889999999999999 9999
Q ss_pred CCeEEEEec
Q 034414 80 HSLCLLRIA 88 (95)
Q Consensus 80 ~~v~v~~~~ 88 (95)
++|+++++.
T Consensus 142 ~~v~~~~~~ 150 (240)
T cd00008 142 DNVKVVSPM 150 (240)
T ss_pred CCEEEEeCC
Confidence 999999864
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.
>PHA00439 exonuclease
Back Show alignment and domain information
Probab=99.96 E-value=8.7e-30 Score=194.21 Aligned_cols=83 Identities=33% Similarity=0.436 Sum_probs=77.2
Q ss_pred CccccccChhhhcCCCCCChhhHHhHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCC-cEEEEcCCCCc-ccc
Q 034414 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGF-KIQVVSPNKDS-QIL 78 (95)
Q Consensus 1 ~~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~-~v~IvS~DkDl-QLv 78 (95)
+||||++||+||+||+++|++ ..|++.++++++.+|++++..+|+||||+|||+|+++...|+ +|+|+|+|||| ||+
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 589999999999999999999 789999999999999999999999999999999999988888 99999999999 999
Q ss_pred cCCeEEE
Q 034414 79 SHSLCLL 85 (95)
Q Consensus 79 ~~~v~v~ 85 (95)
+. +.++
T Consensus 154 ~~-~~~~ 159 (286)
T PHA00439 154 NC-DFLW 159 (286)
T ss_pred cc-eEEE
Confidence 76 3344
>TIGR00593 pola DNA polymerase I
Back Show alignment and domain information
Probab=99.96 E-value=2.3e-29 Score=213.63 Aligned_cols=89 Identities=36% Similarity=0.670 Sum_probs=85.9
Q ss_pred CccccccChhhhcCCCCCChhhHHhHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-cccc
Q 034414 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILS 79 (95)
Q Consensus 1 ~~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~ 79 (95)
+|||+++||+||+||+++|++|..|++.++++++.+||++++.+||||||+|||+|+++...|++|+|+|+|||+ ||++
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 489999999999999999999999999999999999999999999999999999999999899999999999999 9999
Q ss_pred CCeEEEEecc
Q 034414 80 HSLCLLRIAP 89 (95)
Q Consensus 80 ~~v~v~~~~k 89 (95)
++|+++++.+
T Consensus 141 ~~v~~~~~~~ 150 (887)
T TIGR00593 141 DNVKVLIPKG 150 (887)
T ss_pred CCEEEEeccC
Confidence 9999998753
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=99.95 E-value=4.3e-28 Score=205.01 Aligned_cols=88 Identities=38% Similarity=0.747 Sum_probs=85.1
Q ss_pred CccccccChhhhcCCCCCChhhHHhHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-cccc
Q 034414 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILS 79 (95)
Q Consensus 1 ~~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~ 79 (95)
+|||+++||+||+||+++|++|..|++.++++|+.+|++++..||+||||+|||+|+++...|..|+|+|+|||| ||++
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 489999999999999999999999999999999999999999999999999999999988889999999999999 9999
Q ss_pred CCeEEEEec
Q 034414 80 HSLCLLRIA 88 (95)
Q Consensus 80 ~~v~v~~~~ 88 (95)
++|+++.+.
T Consensus 143 ~~v~~~~~~ 151 (880)
T PRK05755 143 DNVTLLDTM 151 (880)
T ss_pred CCEEEeecc
Confidence 999999874
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Back Show alignment and domain information
Probab=99.91 E-value=8.7e-25 Score=166.60 Aligned_cols=91 Identities=31% Similarity=0.483 Sum_probs=87.3
Q ss_pred CccccccChhhhcCCCC-CChhhHHhHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-ccc
Q 034414 1 MNFRHTLYPSYKNNRPP-TPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QIL 78 (95)
Q Consensus 1 ~~~R~~l~p~YKanR~~-~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv 78 (95)
++||+++|++||++|++ +|++|..|++.+.+++.++|+++++.+|+||||+|||+|+++.+.|+.+.|+|+|||+ ||+
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 58999999999999999 9999999999999999999999999999999999999999999889999999999999 999
Q ss_pred cCCeEEEEeccCC
Q 034414 79 SHSLCLLRIAPRG 91 (95)
Q Consensus 79 ~~~v~v~~~~k~~ 91 (95)
+++|+++++.++.
T Consensus 152 ~~~~~~~~~~~~~ 164 (310)
T COG0258 152 SPNVLVINGKKGE 164 (310)
T ss_pred CCCcEEEeccCCC
Confidence 9999999876654
>PTZ00217 flap endonuclease-1; Provisional
Back Show alignment and domain information
Probab=99.32 E-value=1.5e-12 Score=103.03 Aligned_cols=80 Identities=20% Similarity=0.264 Sum_probs=69.4
Q ss_pred ccccccChhhhcCCCCCChhh-----------------------HHhHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHH
Q 034414 2 NFRHTLYPSYKNNRPPTPDTM-----------------------VQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVR 58 (95)
Q Consensus 2 ~~R~~l~p~YKanR~~~p~~l-----------------------~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~ 58 (95)
++|++.++.||++|.+.++++ ..|++.++++|+.|||+++..|+ ||||.+|+|++
T Consensus 93 ~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~-EAdaq~A~L~~- 170 (393)
T PTZ00217 93 ELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPC-EAEAQCAELVK- 170 (393)
T ss_pred hhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCc-CHHHHHHHHHH-
Confidence 578999999999999998887 67889999999999999999998 99999999874
Q ss_pred hhhCCCcEEEEcCCCCc-ccccCCeEEEEe
Q 034414 59 SVDDGFKIQVVSPNKDS-QILSHSLCLLRI 87 (95)
Q Consensus 59 ~~~~~~~v~IvS~DkDl-QLv~~~v~v~~~ 87 (95)
.|.-..|+|.|+|+ |+..+.| ++++
T Consensus 171 ---~g~v~~ViS~D~D~l~fg~~~v-i~~l 196 (393)
T PTZ00217 171 ---KGKVYAVATEDMDALTFGTPVL-LRNL 196 (393)
T ss_pred ---CCCeEEEeCCCcCeeecCCcEE-EEcc
Confidence 46667799999999 9988743 4444
>PRK03980 flap endonuclease-1; Provisional
Back Show alignment and domain information
Probab=99.22 E-value=7.9e-12 Score=95.68 Aligned_cols=75 Identities=19% Similarity=0.170 Sum_probs=65.8
Q ss_pred ccccccChhhhcCCCCCChhhHH-----------------------hHHHHHHHHHHCCCcEEecCCc-chhHHHHHHHH
Q 034414 2 NFRHTLYPSYKNNRPPTPDTMVQ-----------------------GLQYLKASIKAMSIKVIEVPGV-EADDVIGKLAV 57 (95)
Q Consensus 2 ~~R~~l~p~YKanR~~~p~~l~~-----------------------q~~~i~~~l~~~gi~~~~~~g~-EADDvIatla~ 57 (95)
++|++.++.||++|.+.++.+.. |++.++++|..|||+++..|+. ||+ +|+|++
T Consensus 38 ~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~vt~~~~~~~k~lL~~~GIp~i~AP~EAEAq--~A~L~~ 115 (292)
T PRK03980 38 ELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQ--AAYMAK 115 (292)
T ss_pred hHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccCCHHHHHHHHHHHHHCCCCEEecCchHHHH--HHHHHH
Confidence 57899999999999999988766 8999999999999999999996 666 887773
Q ss_pred HhhhCCCcEEEEcCCCCc-ccccCCe
Q 034414 58 RSVDDGFKIQVVSPNKDS-QILSHSL 82 (95)
Q Consensus 58 ~~~~~~~~v~IvS~DkDl-QLv~~~v 82 (95)
.|.-..|+|+|+|+ |+.+++|
T Consensus 116 ----~g~vd~V~S~D~D~l~fg~~~v 137 (292)
T PRK03980 116 ----KGDAWAVGSQDYDSLLFGAPRL 137 (292)
T ss_pred ----CCCeEEEecCCcCeeeecCCEE
Confidence 46667899999999 9999876
>TIGR03674 fen_arch flap structure-specific endonuclease
Back Show alignment and domain information
Probab=99.19 E-value=1.9e-11 Score=94.93 Aligned_cols=81 Identities=16% Similarity=0.158 Sum_probs=64.3
Q ss_pred ccccccChhhhcCCCCCChhhHH-----------------------hHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHH
Q 034414 2 NFRHTLYPSYKNNRPPTPDTMVQ-----------------------GLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVR 58 (95)
Q Consensus 2 ~~R~~l~p~YKanR~~~p~~l~~-----------------------q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~ 58 (95)
+||++.++.||+.|.+.++.+.. |++.++++|+.+||+++..|| |||+.+|.|++
T Consensus 85 ~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~-EAeaq~a~L~~- 162 (338)
T TIGR03674 85 ELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPS-EGEAQAAYMAK- 162 (338)
T ss_pred hhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCc-cHHHHHHHHHH-
Confidence 46777777787777665555432 488899999999999999999 99999888774
Q ss_pred hhhCCCcEEEEcCCCCc-ccccCCeEEEEec
Q 034414 59 SVDDGFKIQVVSPNKDS-QILSHSLCLLRIA 88 (95)
Q Consensus 59 ~~~~~~~v~IvS~DkDl-QLv~~~v~v~~~~ 88 (95)
.|.-..|+|+|+|+ |+.+++| +.++.
T Consensus 163 ---~g~vd~v~S~D~D~l~fg~~~v-i~~~~ 189 (338)
T TIGR03674 163 ---KGDVDYVGSQDYDSLLFGAPRL-VRNLT 189 (338)
T ss_pred ---CCCeeEEecCCcCeeeecCCEE-EEecc
Confidence 35444889999999 9999987 55543
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=99.12 E-value=3.4e-11 Score=91.86 Aligned_cols=76 Identities=17% Similarity=0.177 Sum_probs=63.8
Q ss_pred ccccChhhhcCCCCCCh----------------hhHHhHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEE
Q 034414 4 RHTLYPSYKNNRPPTPD----------------TMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQ 67 (95)
Q Consensus 4 R~~l~p~YKanR~~~p~----------------~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~ 67 (95)
|++..++||++|..+++ ....|++.++++|+.+|++++..| +||||.+|+|++. |.-..
T Consensus 92 R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap-~EAdaq~a~l~~~----g~v~~ 166 (316)
T cd00128 92 RRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAP-YEAEAQCAYLAKK----GLVDA 166 (316)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECC-cCHHHHHHHHHhC----CCeeE
Confidence 88889999999987776 236778999999999999999988 6999999998763 44557
Q ss_pred EEcCCCCc-ccccCCeEE
Q 034414 68 VVSPNKDS-QILSHSLCL 84 (95)
Q Consensus 68 IvS~DkDl-QLv~~~v~v 84 (95)
|+|+|+|+ |+..++|..
T Consensus 167 i~S~DsD~l~fg~~~vi~ 184 (316)
T cd00128 167 IITEDSDLLLFGAPRVYR 184 (316)
T ss_pred EEecCCCeeeecCceEEE
Confidence 99999999 988776543
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.
>PF12813 XPG_I_2: XPG domain containing
Back Show alignment and domain information
Probab=97.36 E-value=0.00031 Score=52.73 Aligned_cols=43 Identities=23% Similarity=0.365 Sum_probs=36.3
Q ss_pred HHHHHHHHHC---CCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc
Q 034414 27 QYLKASIKAM---SIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS 75 (95)
Q Consensus 27 ~~i~~~l~~~---gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl 75 (95)
+.+.+.|..+ |..++..+| |||.-+|++|++. .+.|+|+|.||
T Consensus 7 ~~~~e~L~~~~~~~~~~~~~~~-EAD~~~A~~A~~~-----~~~VLt~DSDf 52 (246)
T PF12813_consen 7 PAFIEALRESWRYGVPVVQCPG-EADRECAALARKW-----GCPVLTNDSDF 52 (246)
T ss_pred HHHHHHHHHHhhcCCcEEEcCc-cchHHHHHHHHHc-----CCeEEccCCCE
Confidence 4566777777 999999988 9999999999655 34899999998
>TIGR00600 rad2 DNA excision repair protein (rad2)
Back Show alignment and domain information
Probab=95.94 E-value=0.018 Score=51.16 Aligned_cols=46 Identities=15% Similarity=0.161 Sum_probs=40.3
Q ss_pred hHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc
Q 034414 25 GLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS 75 (95)
Q Consensus 25 q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl 75 (95)
.+..++++|..|||+++..| +||+..+|.|++ .|.-..|+|.|.|.
T Consensus 773 m~~~~~~LL~~~GIP~i~AP-~EAEAqcA~L~~----~G~vd~V~TeDsD~ 818 (1034)
T TIGR00600 773 MILESQELLRLFGIPYIVAP-MEAEAQCAILDL----LDQTSGTITDDSDI 818 (1034)
T ss_pred HHHHHHHHHHHCCCCeeeCC-ccHHHHHHHHHh----CCCeEEEEccccce
Confidence 36779999999999999999 999999998854 56677899999998
All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana
Back Show alignment and domain information
Probab=95.78 E-value=0.0088 Score=42.31 Aligned_cols=50 Identities=20% Similarity=0.272 Sum_probs=39.0
Q ss_pred CCcEEec-CCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-cccc-CCeEEEE
Q 034414 37 SIKVIEV-PGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILS-HSLCLLR 86 (95)
Q Consensus 37 gi~~~~~-~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~-~~v~v~~ 86 (95)
|+.++-. +|-.||++|--++......+.+|+|||+|+.. +.+. -+..++.
T Consensus 67 gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~~GA~~is 119 (166)
T PF05991_consen 67 GIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREIQRAARGRGAKRIS 119 (166)
T ss_pred ceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhhCCCEEEc
Confidence 6665544 47999999999999888767899999999999 6654 4555543
The function of this family is unknown.
>cd06167 LabA_like LabA_like proteins
Back Show alignment and domain information
Probab=95.12 E-value=0.055 Score=36.29 Aligned_cols=54 Identities=15% Similarity=0.103 Sum_probs=37.9
Q ss_pred HHHHHHHHHHCCCcEEecCCc-------chhHHHHHHHHHhhh-C-CCcEEEEcCCCCc-cccc
Q 034414 26 LQYLKASIKAMSIKVIEVPGV-------EADDVIGKLAVRSVD-D-GFKIQVVSPNKDS-QILS 79 (95)
Q Consensus 26 ~~~i~~~l~~~gi~~~~~~g~-------EADDvIatla~~~~~-~-~~~v~IvS~DkDl-QLv~ 79 (95)
.....+.|...|+.++..+.. .+|=-|++-+..... . -..++|+|+|+|| .++.
T Consensus 54 ~~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i~ 117 (149)
T cd06167 54 QRGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLVE 117 (149)
T ss_pred HHHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHHH
Confidence 344556688899999988854 377667655543322 2 3578999999999 8875
A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function
Back Show alignment and domain information
Probab=94.79 E-value=0.055 Score=35.73 Aligned_cols=54 Identities=17% Similarity=0.166 Sum_probs=29.5
Q ss_pred HHHHHHHHHHCCCcEEecCC--------cchhHHHHHHHHHhh--hCCCcEEEEcCCCCc-cccc
Q 034414 26 LQYLKASIKAMSIKVIEVPG--------VEADDVIGKLAVRSV--DDGFKIQVVSPNKDS-QILS 79 (95)
Q Consensus 26 ~~~i~~~l~~~gi~~~~~~g--------~EADDvIatla~~~~--~~~~~v~IvS~DkDl-QLv~ 79 (95)
...+.+.|...|+.+...+. -.+|=-|++-+.... ..-..++|+|+|+|| .+++
T Consensus 49 ~~~~~~~L~~~g~~v~~~~~~~~~~~~k~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~v~ 113 (146)
T PF01936_consen 49 QKSFQEALQRAGIKVRHFPLRKRGGGGKKGVDVALAVDILELAYENPPDTIVLVSGDSDFAPLVR 113 (146)
T ss_dssp HHHHHHHHHHHT-EEEE------S---S---HHHHHHHHHHHG--GG-SEEEEE---GGGHHHHH
T ss_pred hhhHHHHHHhCeeeEEeeecccccccccCCcHHHHHHHHHHHhhccCCCEEEEEECcHHHHHHHH
Confidence 34455677888997766544 236666665554433 223789999999999 8886
However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
>TIGR00288 conserved hypothetical protein TIGR00288
Back Show alignment and domain information
Probab=93.29 E-value=0.26 Score=35.20 Aligned_cols=57 Identities=14% Similarity=0.172 Sum_probs=36.5
Q ss_pred HHHHHHHCCCcEEecCCcchhHHHHHHHHHhh--hCCCcEEEEcCCCCc-cccc----CCeEEEE
Q 034414 29 LKASIKAMSIKVIEVPGVEADDVIGKLAVRSV--DDGFKIQVVSPNKDS-QILS----HSLCLLR 86 (95)
Q Consensus 29 i~~~l~~~gi~~~~~~g~EADDvIatla~~~~--~~~~~v~IvS~DkDl-QLv~----~~v~v~~ 86 (95)
+.+.+...|+..+...| -.|=-|+.=|-... .+=..++|+|+|.|| .|+. .+.+|.-
T Consensus 71 l~~~l~~~Gf~pv~~kG-~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv~~lre~G~~V~v 134 (160)
T TIGR00288 71 LIEAVVNQGFEPIIVAG-DVDVRMAVEAMELIYNPNIDAVALVTRDADFLPVINKAKENGKETIV 134 (160)
T ss_pred HHHHHHHCCceEEEecC-cccHHHHHHHHHHhccCCCCEEEEEeccHhHHHHHHHHHHCCCEEEE
Confidence 46678889999887777 34433333332222 233578899999999 9984 4555543
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.
>cd00431 cysteine_hydrolases Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle
Back Show alignment and domain information
Probab=91.50 E-value=0.47 Score=31.97 Aligned_cols=43 Identities=23% Similarity=0.342 Sum_probs=39.4
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+.++|...|+..+..-|.++|=++.+-+..+.+.|++|+|++
T Consensus 100 ~l~~~L~~~~i~~vil~G~~t~~CV~~T~~~a~~~G~~v~vi~ 142 (161)
T cd00431 100 DLDELLRERGIDTLVVCGIATDICVLATARDALDLGYRVIVVE 142 (161)
T ss_pred CHHHHHHHCCCCEEEEEecCcChhHHHHHHHHHHCCCEEEEeh
Confidence 4677888999999999999999999999999999999999976
It also contains isochorismatase, an enzyme that catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of the vinyl ether bond, and other related enzymes with unknown function.
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment
Back Show alignment and domain information
Probab=91.41 E-value=0.2 Score=32.01 Aligned_cols=36 Identities=25% Similarity=0.347 Sum_probs=25.0
Q ss_pred HCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc
Q 034414 35 AMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS 75 (95)
Q Consensus 35 ~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl 75 (95)
.+|++++..| +|||=.+|.|.+ .|.==.|+|.|.|+
T Consensus 2 ~~gv~~i~AP-~EAeAq~A~L~~----~g~vd~V~t~DsD~ 37 (94)
T PF00867_consen 2 LMGVPYIVAP-YEAEAQCAYLER----NGLVDAVITEDSDL 37 (94)
T ss_dssp HHT-EEEE-S-S-HHHHHHHHHH----TTSSSEEE-SSSHH
T ss_pred CCCCeEEEcC-chHHHHHHHHHH----hcceeEEEecCCCE
Confidence 5799999999 999999998774 33333578999998
Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
>cd01015 CSHase N-carbamoylsarcosine amidohydrolase (CSHase) hydrolyzes N-carbamoylsarcosine to sarcosine, carbon dioxide and ammonia
Back Show alignment and domain information
Probab=91.34 E-value=0.53 Score=32.86 Aligned_cols=43 Identities=28% Similarity=0.421 Sum_probs=39.7
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+.++|...|+..+..-|.++|=++-+-+..+...|++|++++
T Consensus 104 ~L~~~L~~~gi~~vvi~G~~t~~CV~~Ta~~A~~~Gy~v~vv~ 146 (179)
T cd01015 104 SLAATLTARGVDTLIVAGCSTSGCIRATAVDAMQHGFRPIVVR 146 (179)
T ss_pred cHHHHHHHcCCCEEEEeeecccHhHHHHHHHHHHCCCeEEEee
Confidence 4777889999999999999999999999999999999999976
CSHase is involved in one of the two alternative pathways for creatinine degradation to glycine in microorganisms.This CSHase-containing pathway degrades creatinine via N-methylhydantoin N-carbamoylsarcosine and sarcosine to glycine. Enzymes of this pathway are used in the diagnosis for renal disfunction, for determining creatinine levels in urine and serum.
>COG1412 Uncharacterized proteins of PilT N-term
Back Show alignment and domain information
Probab=91.16 E-value=0.6 Score=32.54 Aligned_cols=49 Identities=18% Similarity=0.283 Sum_probs=38.1
Q ss_pred HCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-cccc-CCeEEEEec
Q 034414 35 AMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILS-HSLCLLRIA 88 (95)
Q Consensus 35 ~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~-~~v~v~~~~ 88 (95)
..+++++.. +-.|||.|-.+|.+.. .++|+|+|+.| |-+. .+|-+....
T Consensus 74 ~er~~~~~~-~~~aDe~i~~~a~~~~----~~iVaTnD~eLk~rlr~~GIPvi~lr 124 (136)
T COG1412 74 AERLECIHK-GRYADECLLEAALKHG----RYIVATNDKELKRRLRENGIPVITLR 124 (136)
T ss_pred hhccCcccc-CCChHHHHHHHHHHcC----CEEEEeCCHHHHHHHHHcCCCEEEEe
Confidence 457778887 8888999998876553 79999999999 8765 477666553
/Vapc superfamily [General function prediction only]
>cd01012 YcaC_related YcaC related amidohydrolases; E
Back Show alignment and domain information
Probab=90.78 E-value=0.62 Score=31.89 Aligned_cols=43 Identities=21% Similarity=0.414 Sum_probs=39.2
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+.+.|+..|+..+..-|..+|=++.+-+..+...|++|++++
T Consensus 78 ~L~~~L~~~gi~~lii~G~~T~~CV~~Ta~~a~~~g~~v~v~~ 120 (157)
T cd01012 78 AFRKALKATGRKQVVLAGLETHVCVLQTALDLLEEGYEVFVVA 120 (157)
T ss_pred HHHHHHHhcCCCEEEEEEeeccHHHHHHHHHHHHCCCEEEEEe
Confidence 4677888999999999999999999999999999999999975
coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them. Multimerisation interface seems not to be conserved in all members.
>PRK11440 putative hydrolase; Provisional
Back Show alignment and domain information
Probab=90.37 E-value=0.75 Score=32.34 Aligned_cols=43 Identities=16% Similarity=0.265 Sum_probs=39.0
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+..+|...|+..+..-|.+++=++.+-+..+...|++|++++
T Consensus 111 ~L~~~L~~~gi~~lii~Gv~T~~CV~~Ta~~A~~~gy~v~vv~ 153 (188)
T PRK11440 111 DLELQLRRRGIDTIVLCGISTNIGVESTARNAWELGFNLVIAE 153 (188)
T ss_pred CHHHHHHHCCCCEEEEeeechhHHHHHHHHHHHHCCCEEEEec
Confidence 3666788999999999999999999999999999999999975
>TIGR00028 Mtu_PIN_fam Mycobacterium tuberculosis PIN domain family
Back Show alignment and domain information
Probab=90.14 E-value=0.39 Score=31.33 Aligned_cols=36 Identities=14% Similarity=0.159 Sum_probs=24.7
Q ss_pred chhHHHHHHHHHhhhCCCcEEEEcCCCCc-ccccCCeEEEEecc
Q 034414 47 EADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILSHSLCLLRIAP 89 (95)
Q Consensus 47 EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~~~v~v~~~~k 89 (95)
-+|-+|+..|... | ..++|.|+|| +. +++++++|.-
T Consensus 105 ~~D~~i~a~A~~~---~--~~lvT~D~~f~~~--~~~~i~~P~~ 141 (142)
T TIGR00028 105 VTDAHLAALAREH---G--AELVTFDRGFARF--AGIRWRDPLT 141 (142)
T ss_pred chHHHHHHHHHHc---C--CEEEecCCCcccc--CCCeeeCCCC
Confidence 4677777655433 3 4677999999 64 5788888753
Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see Pfam pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis. Two more are now found in Synechococcus sp. WH8102. The specific function is unknown but may be in signal transduction.
>cd01013 isochorismatase Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in biological systems
Back Show alignment and domain information
Probab=89.85 E-value=0.66 Score=33.27 Aligned_cols=43 Identities=21% Similarity=0.068 Sum_probs=39.5
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+.++|...|+..+.+-|.++|=++-+-|..+...|++|+|++
T Consensus 132 ~L~~~Lr~~gi~~lii~Gv~T~~CV~~Ta~~A~~~Gy~v~vv~ 174 (203)
T cd01013 132 PLLERLKESGRDQLIITGVYAHIGCLSTAVDAFMRDIQPFVVA 174 (203)
T ss_pred CHHHHHHHcCCCEEEEEEeccChhHHHHHHHHHHCCCeEEEec
Confidence 4677889999999999999999999999999999999999976
Isochorismatase is part of the phenazine biosynthesis pathway. Phenazines are antimicrobial compounds that provide the competitive advantage for certain bacteria.
>TIGR03614 RutB pyrimidine utilization protein B
Back Show alignment and domain information
Probab=89.65 E-value=0.85 Score=33.23 Aligned_cols=43 Identities=12% Similarity=0.140 Sum_probs=39.9
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+..+|...|+..+..-|...|=++.+-+..+...|++|+|++
T Consensus 141 ~L~~~Lr~~gI~~lvi~Gv~T~~CV~sTar~A~~~Gy~v~vv~ 183 (226)
T TIGR03614 141 PLDSMLRARGIRNLVFTGIATNVCVESTLRDGFHLEYFGVVLE 183 (226)
T ss_pred CHHHHHHHCCCCEEEEeccCccHhHHHHHHHHHHCCCEEEEec
Confidence 3778889999999999999999999999999999999999976
RL Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5114-9. Epub 2006 Mar 15.
>cd01014 nicotinamidase_related Nicotinamidase_ related amidohydrolases
Back Show alignment and domain information
Probab=89.03 E-value=1 Score=30.70 Aligned_cols=44 Identities=16% Similarity=0.287 Sum_probs=39.3
Q ss_pred HHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 27 QYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 27 ~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
+.+.+.|...|+..+..-|..+|=++.+-|..+.+.|++|+|++
T Consensus 88 t~l~~~L~~~gi~~viv~G~~td~CV~~Ta~~a~~~g~~v~vi~ 131 (155)
T cd01014 88 TDLEEWLREAGIDHLVICGAMTEMCVDTTVRSAFDLGYDVTVVA 131 (155)
T ss_pred CCHHHHHHHCCCCEEEEEeeccchhHHHHHHHHHHCCCcEEEec
Confidence 34677889999999999999999999998988999999999975
Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia.
>smart00484 XPGI Xeroderma pigmentosum G I-region
Back Show alignment and domain information
Probab=88.51 E-value=2.7 Score=26.05 Aligned_cols=42 Identities=24% Similarity=0.246 Sum_probs=31.4
Q ss_pred HCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-ccccCC
Q 034414 35 AMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILSHS 81 (95)
Q Consensus 35 ~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~~~ 81 (95)
.+|++++..|+ ||+--.|.|.+ .|.==.|+|.|.|+ -.-.+.
T Consensus 2 ~~gi~~i~AP~-eAeAq~A~L~~----~g~vdav~s~D~D~llfG~~~ 44 (73)
T smart00484 2 LMGIPYIVAPY-EAEAQCAYLAK----SGLVDAIITEDSDLLLFGAPR 44 (73)
T ss_pred cCCCeEEEcCC-cHHHHHHHHHh----CCCeeEEEcCccceEecCCcE
Confidence 47999999998 99988887775 34333699999999 443343
>PLN02621 nicotinamidase
Back Show alignment and domain information
Probab=88.36 E-value=1.1 Score=31.86 Aligned_cols=43 Identities=19% Similarity=0.307 Sum_probs=38.9
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+.++|...|+..+.+-|.++|=++-+-+..+.+.|++|++++
T Consensus 117 ~L~~~L~~~gi~~lvi~Gv~T~~CV~~Ta~~a~~~gy~v~v~~ 159 (197)
T PLN02621 117 RLEERLRKIGVKEVIVTGVMTNLCCETTAREAFVRGFRVFFST 159 (197)
T ss_pred cHHHHHHHCCCCEEEEEecccchhHHHHHHHHHHCCCEEEEec
Confidence 4677788999999999999999999999998999999999974
>PF00857 Isochorismatase: Isochorismatase family; InterPro: IPR000868 This is a family of hydrolase enzymes
Back Show alignment and domain information
Probab=87.84 E-value=0.94 Score=30.81 Aligned_cols=43 Identities=23% Similarity=0.350 Sum_probs=37.9
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+.++|...|+..+.+-|+.+|=+|-+-+..+.+.|++|+|++
T Consensus 102 ~L~~~L~~~gi~~vil~G~~t~~CV~~Ta~~a~~~g~~v~v~~ 144 (174)
T PF00857_consen 102 DLDEILRKRGIDTVILCGVATDVCVLATARDAFDRGYRVIVVE 144 (174)
T ss_dssp SHHHHHHHTTESEEEEEEESTTTHHHHHHHHHHHTT-EEEEEE
T ss_pred cccccccccccceEEEcccccCcEEehhHHHHHHCCCEEEEEC
Confidence 3667788899999999999999999999999999999999976
Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate (3.3.2.1 from EC).; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1XN4_A 3KL2_F 1YZV_A 3IRV_A 1IM5_A 1ILW_A 3PL1_A 1NF9_A 1NF8_A 1X9G_A ....
>COG1335 PncA Amidases related to nicotinamidase [Secondary metabolites biosynthesis, transport, and catabolism]
Back Show alignment and domain information
Probab=87.09 E-value=1.7 Score=30.52 Aligned_cols=43 Identities=21% Similarity=0.357 Sum_probs=39.1
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+..+|+..|+..+..-|..+|=++-+-+..+...|++|++++
T Consensus 123 ~L~~~Lr~~~i~~l~v~G~~td~CV~~T~~~A~~~gy~v~v~~ 165 (205)
T COG1335 123 DLDDILRNLGIDTVVVCGIATDICVLATARDAFDLGYQVTLVE 165 (205)
T ss_pred CHHHHHHHCCCCEEEEeeeehhHHHHHHHHHHHHCCCeEEEeh
Confidence 4777888899999999999999999999999999999998865
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins
Back Show alignment and domain information
Probab=86.89 E-value=0.42 Score=30.77 Aligned_cols=42 Identities=19% Similarity=0.169 Sum_probs=31.3
Q ss_pred CcchhHHHHHHHHHhhhCCCcEEEEcCCCCc--ccc-cCCeEEEEeccC
Q 034414 45 GVEADDVIGKLAVRSVDDGFKIQVVSPNKDS--QIL-SHSLCLLRIAPR 90 (95)
Q Consensus 45 g~EADDvIatla~~~~~~~~~v~IvS~DkDl--QLv-~~~v~v~~~~k~ 90 (95)
+.-|||.|-.++. +.+. .+|+|.|++| +|- .++|-++.+.+.
T Consensus 50 ~~~addci~~~~~---~~~~-~~VaT~D~~Lr~~lr~~~GvPvi~l~~~ 94 (101)
T PF04900_consen 50 PGSADDCILDLAG---KNNK-YIVATQDKELRRRLRKIPGVPVIYLRRN 94 (101)
T ss_pred CcCHHHHHHHHhc---cCCe-EEEEecCHHHHHHHhcCCCCCEEEEECC
Confidence 3568999988885 2222 8999999999 566 578888877543
>cd01011 nicotinamidase Nicotinamidase/pyrazinamidase (PZase)
Back Show alignment and domain information
Probab=85.48 E-value=1.9 Score=30.67 Aligned_cols=44 Identities=20% Similarity=0.416 Sum_probs=40.3
Q ss_pred HHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 27 QYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 27 ~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
..+.++|...|+..+.+-|...|=++.+-+..+...|++|+|++
T Consensus 127 t~L~~~L~~~~i~~lii~G~~t~~CV~~T~~~a~~~g~~v~v~~ 170 (196)
T cd01011 127 TGLAEYLRERGIDRVDVVGLATDYCVKATALDALKAGFEVRVLE 170 (196)
T ss_pred hhHHHHHHHCCCCEEEEEEecccHHHHHHHHHHHHCCCEEEEec
Confidence 45788899999999999999999999999999999999999976
Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is also called pyrazinamidase, because in converts the tuberculosis drug pyrazinamide (PZA) into its active form pyrazinoic acid (POA).
>PRK11609 nicotinamidase/pyrazinamidase; Provisional
Back Show alignment and domain information
Probab=85.23 E-value=1.9 Score=30.80 Aligned_cols=43 Identities=16% Similarity=0.312 Sum_probs=39.3
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+..+|...|+..+..-|...|=++-+-+..+...|++|+|++
T Consensus 132 ~L~~~L~~~gi~~lii~G~~T~~CV~~Ta~dA~~~gy~v~v~~ 174 (212)
T PRK11609 132 ALDDWLREHGITELIVMGLATDYCVKFTVLDALALGYQVNVIT 174 (212)
T ss_pred cHHHHHHHcCCCEEEEEEeccCHHHHHHHHHHHHCCCEEEEEe
Confidence 4677889999999999999999999999999999999999975
>PTZ00331 alpha/beta hydrolase; Provisional
Back Show alignment and domain information
Probab=83.90 E-value=2.4 Score=30.74 Aligned_cols=44 Identities=25% Similarity=0.283 Sum_probs=39.5
Q ss_pred HHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 27 QYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 27 ~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
..+.++|+..|+..+..-|.+.|=++.+-+..+...|++|+|++
T Consensus 135 t~L~~~L~~~gi~~lvi~G~~t~~CV~~Ta~~a~~~g~~v~vv~ 178 (212)
T PTZ00331 135 TGLAQILKAHGVRRVFICGLAFDFCVLFTALDAVKLGFKVVVLE 178 (212)
T ss_pred chHHHHHHHCCCCEEEEEEeccCHHHHHHHHHHHHCCCEEEEeC
Confidence 34667888999999999999999999999998999999999976
Homologous Structure Domains
Homologous Domains Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
ID Alignment Graph Length
Definition
Probability Query 95
d1cmwa2 164
5' to 3' exonuclease domain of DNA polymerase Taq
100.0 d1tfra2 169
T4 RNase H {Bacteriophage T4 [TaxId: 10665]}
99.97 d1xo1a2 167
T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]
99.97 d1b43a2 219
Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyr
96.59 d1a77a2 207
Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Met
96.27 d1ul1x2 216
Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo
96.16 d1rxwa2 217
Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Arc
95.61 d1j2ra_ 188
Hypothetical protein YecD {Escherichia coli [TaxId
91.66 d1im5a_ 179
Pyrazinamidase/nicotinamidase {Archaeon Pyrococcus
91.48 d1nf9a_ 207
Phenazine biosynthesis protein PhzD {Pseudomonas a
89.39 d1yaca_ 204
YcaC {Escherichia coli [TaxId: 562]}
88.73 d1o4wa_ 125
Hypothetical protein AF0591 {Archaeon Archaeoglobu
86.22 d1nbaa_ 253
N-carbamoylsarcosine amidohydrolase {Arthrobacter
82.38
>d1cmwa2 c.120.1.2 (A:10-173) 5' to 3' exonuclease domain of DNA polymerase Taq {Thermus aquaticus [TaxId: 271]}
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class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: 5' to 3' exonuclease domain of DNA polymerase Taq
species: Thermus aquaticus [TaxId: 271]
Probab=100.00 E-value=5.2e-35 Score=202.77 Aligned_cols=89 Identities=34% Similarity=0.655 Sum_probs=85.8
Q ss_pred CccccccChhhhcCCCCCChhhHHhHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-cccc
Q 034414 1 MNFRHTLYPSYKNNRPPTPDTMVQGLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILS 79 (95)
Q Consensus 1 ~~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~ 79 (95)
++||+++||+||+||.++|+++..|++.+++++..+|++++..+|+||||+|||+|+++...+.+|+|+|+|||| |||+
T Consensus 62 ~~~R~~l~p~YK~~R~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~EADDvIa~la~~~~~~~~~v~IvS~DkD~~QLv~ 141 (164)
T d1cmwa2 62 PSFRHEAYGGYKAGRAPTPEDFPRQLALIKELVDLLGLARLEVPGYEADDVLASLAKKAEKEGYEVRILTADKDLYQLLS 141 (164)
T ss_dssp SCTTGGGGSTTTSCCCCCCSSHHHHHHHHHHHHHHTTCEEECCTTSCHHHHHHHHHHHHHHTTEEEEEECSSGGGGGSCC
T ss_pred ccchhhhhhhhhhccccCchhHHHHHHHHHHHHhhcCceEEEecCcchHHHHHHHHHHhccccceEEEecCCCChHHhee
Confidence 489999999999999999999999999999999999999999999999999999999999888999999999999 9999
Q ss_pred CCeEEEEecc
Q 034414 80 HSLCLLRIAP 89 (95)
Q Consensus 80 ~~v~v~~~~k 89 (95)
++|+||+|.+
T Consensus 142 ~~v~i~~~~~ 151 (164)
T d1cmwa2 142 DRIHVLHPEG 151 (164)
T ss_dssp SSCEEECSSS
T ss_pred CCEEEEeCCC
Confidence 9999999854
>d1tfra2 c.120.1.2 (A:12-180) T4 RNase H {Bacteriophage T4 [TaxId: 10665]}
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class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: T4 RNase H
species: Bacteriophage T4 [TaxId: 10665]
Probab=99.97 E-value=2.6e-32 Score=191.32 Aligned_cols=90 Identities=21% Similarity=0.235 Sum_probs=72.6
Q ss_pred ccccccChhhhcCCCCCChhhHHhH--------HHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCC
Q 034414 2 NFRHTLYPSYKNNRPPTPDTMVQGL--------QYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNK 73 (95)
Q Consensus 2 ~~R~~l~p~YKanR~~~p~~l~~q~--------~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~Dk 73 (95)
.||+++||+||+||+++|+++..|+ +.+.++++.+|++++..+|+||||+||++|+++...|.+|+|+|+||
T Consensus 66 ~~R~~l~p~YKanR~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~EADDvIa~la~~~~~~~~~vvIvS~Dk 145 (169)
T d1tfra2 66 YWRRDFAYYYKKNRGKAREESTWDWEGYFESSHKVIDELKAYMPYIVMDIDKYEADDHIAVLVKKFSLEGHKILIISSDG 145 (169)
T ss_dssp CGGGGTCTTTTC---------CCCHHHHHHHHHHHHHHHHHHSSSEEECCTTCCHHHHHHHHHHHHHHTTCCEEEECCCG
T ss_pred chhhhhHHHHhhCCCCCcccchhhhhHHHHHHHHHHHHHHHHhhhhccccCCcccccHHHHHHHHHHHCCCcEEEEeCCC
Confidence 5899999999999999998866554 44566777899999999999999999999999988899999999999
Q ss_pred Cc-cccc-CCeEEEEeccCC
Q 034414 74 DS-QILS-HSLCLLRIAPRG 91 (95)
Q Consensus 74 Dl-QLv~-~~v~v~~~~k~~ 91 (95)
|| ||++ ++|++|+|.+|.
T Consensus 146 D~~QLv~~~~V~~~~p~~Kk 165 (169)
T d1tfra2 146 DFTQLHKYPNVKQWSPMHKK 165 (169)
T ss_dssp GGGGGTTSTTEEEEETTTTE
T ss_pred CHHHhCcCCCeEEeeCCCce
Confidence 99 9998 899999997664
>d1xo1a2 c.120.1.2 (A:19-185) T5 5'-exonuclease {Bacteriophage T5 [TaxId: 10726]}
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class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: T5 5'-exonuclease
species: Bacteriophage T5 [TaxId: 10726]
Probab=99.97 E-value=2.1e-31 Score=185.45 Aligned_cols=90 Identities=21% Similarity=0.276 Sum_probs=67.7
Q ss_pred CccccccChhhhcCCCCCChhhHH--------hHHHHHHHH--HHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 1 MNFRHTLYPSYKNNRPPTPDTMVQ--------GLQYLKASI--KAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 1 ~~~R~~l~p~YKanR~~~p~~l~~--------q~~~i~~~l--~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+||+++||+||+||++.|+++.. ++..+.+++ ..+|++++..+|+||||+||++++++...+.+|+|+|
T Consensus 54 ~~~R~~l~p~YKanR~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~EADDiIa~l~~~~~~~~~~v~IvS 133 (167)
T d1xo1a2 54 SVFRLEHLPEYAGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLIS 133 (167)
T ss_dssp CHHHHTTCTTCC--------------------CHHHHHHHHHHHHTTSCEECCTTBCHHHHHHHHHHHHGGGSSCEEEEC
T ss_pred CCcccccchhhhhcCCCCchhcccchhHHHHHHHHHHHHHHHHhhccccEEEeccccchhHHHHHHHHhhcCCCEEEEEe
Confidence 379999999999999887765432 233344333 3479999999999999999999999988899999999
Q ss_pred CCCCc-ccccCCeEEEEeccC
Q 034414 71 PNKDS-QILSHSLCLLRIAPR 90 (95)
Q Consensus 71 ~DkDl-QLv~~~v~v~~~~k~ 90 (95)
+|||| |||+++|++|+|.++
T Consensus 134 ~DkD~~QLv~~~v~~~~~~~k 154 (167)
T d1xo1a2 134 TDGDWDTLLTDKVSRFSFTTR 154 (167)
T ss_dssp SCGGGGGGCBTTEEEECTTTC
T ss_pred CCccHHHheeCCEEEEeCCCC
Confidence 99999 999999999998765
>d1b43a2 c.120.1.2 (A:1-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Pyrococcus furiosus [TaxId: 2261]}
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class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Pyrococcus furiosus [TaxId: 2261]
Probab=96.59 E-value=0.001 Score=45.74 Aligned_cols=46 Identities=20% Similarity=0.276 Sum_probs=37.3
Q ss_pred hHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc
Q 034414 25 GLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS 75 (95)
Q Consensus 25 q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl 75 (95)
.+..++++|+.+|++++..| +|||-.+|.|++.-. ==.|+|.|.|+
T Consensus 130 ~~~~~~~lL~~~gv~~i~Ap-~EAdaqcA~L~~~g~----vd~v~SeDsD~ 175 (219)
T d1b43a2 130 LIEDAKKLLELMGIPIVQAP-SEGEAQAAYMAAKGS----VYASASQDYDS 175 (219)
T ss_dssp HHHHHHHHHHHHTCCEEECS-SCHHHHHHHHHHHTS----SSEEECSSSHH
T ss_pred HHHHHHHHHHHcCCceeeCc-hHHHHHHHHHHhcCC----eEEEEecccce
Confidence 36678999999999999998 599999998876422 22578999998
>d1a77a2 c.120.1.2 (A:2-208) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Methanococcus jannaschii [TaxId: 2190]}
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class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Methanococcus jannaschii [TaxId: 2190]
Probab=96.27 E-value=0.0024 Score=43.47 Aligned_cols=51 Identities=22% Similarity=0.190 Sum_probs=39.4
Q ss_pred hHHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-ccccC
Q 034414 25 GLQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILSH 80 (95)
Q Consensus 25 q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~~ 80 (95)
.+..++++|..+|++++..| +|||=.+|.|++.-. .. .|+|.|.|+ -.-.+
T Consensus 130 ~~~~~~~ll~~~gi~yi~Ap-~EAeaqcA~L~~~g~---vd-~v~seDsD~l~yG~~ 181 (207)
T d1a77a2 130 MVENCKYLLSLMGIPYVEAP-SEGEAQASYMAKKGD---VW-AVVSQDYDALLYGAP 181 (207)
T ss_dssp HHHHHHHHHHHHTCCEEECS-SCHHHHHHHHHHHTS---SS-EEECSSSGGGGGTCS
T ss_pred HHHHHHHHHHHcCCceEecC-ccHHHHHHHHHHcCC---eE-EEEecccceeccCCC
Confidence 46778999999999999998 899999998876322 13 367999998 54333
>d1ul1x2 c.120.1.2 (X:2-217) Flap endonuclease-1 (Fen-1 nuclease) {Human (Homo sapiens) [TaxId: 9606]}
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class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Human (Homo sapiens) [TaxId: 9606]
Probab=96.16 E-value=0.0033 Score=42.50 Aligned_cols=52 Identities=21% Similarity=0.211 Sum_probs=38.2
Q ss_pred HHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-ccccCCe
Q 034414 26 LQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILSHSL 82 (95)
Q Consensus 26 ~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~~~v 82 (95)
+..++++|+.+|++++..|+ |||=.+|.|++. |.==.|+|.|.|+ -.-.+.|
T Consensus 137 ~~~~~~ll~~~gv~~i~Ap~-EAdaq~A~L~~~----g~vd~v~S~DsD~l~fG~~~v 189 (216)
T d1ul1x2 137 NDECKHLLSLMGIPYLDAPS-EAEASCAALVKA----GKVYAAATEDMDCLTFGSPVL 189 (216)
T ss_dssp HHHHHHHHHHHTCCEEECSS-CHHHHHHHHHHH----TSSSEEECSCTHHHHTTCSEE
T ss_pred HHHHHHHHHhcCeeeEeccc-hHHHHHHHHHhc----CceEEEEccccceeccCCcEE
Confidence 45688999999999999876 999888777652 2211578999999 5433433
>d1rxwa2 c.120.1.2 (A:3-219) Flap endonuclease-1 (Fen-1 nuclease) {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}
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class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: 5' to 3' exonuclease catalytic domain
domain: Flap endonuclease-1 (Fen-1 nuclease)
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]
Probab=95.61 E-value=0.0096 Score=40.52 Aligned_cols=50 Identities=22% Similarity=0.209 Sum_probs=38.8
Q ss_pred HHHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc-ccccC
Q 034414 26 LQYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS-QILSH 80 (95)
Q Consensus 26 ~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl-QLv~~ 80 (95)
+..++++|+.+|++++..| +|||-..|.|++. |.==.|+|.|.|+ -.-.+
T Consensus 129 ~~~~~~lL~~~gi~~i~Ap-~EAeaqcA~L~~~----g~vd~v~seDsD~l~fG~~ 179 (217)
T d1rxwa2 129 VDSAKTLLSYMGIPFVDAP-SEGEAQAAYMAAK----GDVEYTGSQDYDSLLFGSP 179 (217)
T ss_dssp HHHHHHHHHHTTCCEEECS-SCHHHHHHHHHHT----TSSSEEECSSSHHHHTTCS
T ss_pred HHHHHHHHHHcCceEEecC-chHHHHHHHHHhC----CCeEEEEecccceeeeCCC
Confidence 5678899999999999986 6999999988762 3322478999998 55333
>d1j2ra_ c.33.1.3 (A:) Hypothetical protein YecD {Escherichia coli [TaxId: 562]}
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class: Alpha and beta proteins (a/b)
fold: Isochorismatase-like hydrolases
superfamily: Isochorismatase-like hydrolases
family: Isochorismatase-like hydrolases
domain: Hypothetical protein YecD
species: Escherichia coli [TaxId: 562]
Probab=91.66 E-value=0.11 Score=33.63 Aligned_cols=43 Identities=16% Similarity=0.265 Sum_probs=39.6
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+.++|...|+..+.+-|.++|=++-+-+..+.+.|++|++++
T Consensus 111 ~L~~~L~~~gi~~liv~Gv~t~~CV~~Ta~~A~~~G~~v~vv~ 153 (188)
T d1j2ra_ 111 DLELQLRRRGIDTIVLCGISTNIGVESTARNAWELGFNLVIAE 153 (188)
T ss_dssp SHHHHHHHTTCCEEEEEEECTTTHHHHHHHHHHHTTCEEEEEE
T ss_pred cHHHHHHhcCCceEEEEEeccCchHHHHHHHHHHCCCeEEEeC
Confidence 4778889999999999999999999999999999999999975
>d1im5a_ c.33.1.3 (A:) Pyrazinamidase/nicotinamidase {Archaeon Pyrococcus horikoshii [TaxId: 53953]}
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class: Alpha and beta proteins (a/b)
fold: Isochorismatase-like hydrolases
superfamily: Isochorismatase-like hydrolases
family: Isochorismatase-like hydrolases
domain: Pyrazinamidase/nicotinamidase
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]
Probab=91.48 E-value=0.12 Score=32.98 Aligned_cols=43 Identities=16% Similarity=0.356 Sum_probs=39.1
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+..+|...|+..+.+-|.++|=++-+-+..+...|++|+|++
T Consensus 109 ~L~~~Lr~~gi~~liv~G~~t~~CV~~T~~~a~~~g~~V~vv~ 151 (179)
T d1im5a_ 109 DLAKILRGNGVKRVYICGVATEYCVRATALDALKHGFEVYLLR 151 (179)
T ss_dssp SHHHHHHHTTCCEEEEEEECTTTHHHHHHHHHHHTTCEEEEEE
T ss_pred HHHHHHHHCCCCEEEEEEeccchhHHHHHHHHHHcCCEEEEec
Confidence 4667788999999999999999999999999999999999976
>d1nf9a_ c.33.1.3 (A:) Phenazine biosynthesis protein PhzD {Pseudomonas aeruginosa [TaxId: 287]}
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class: Alpha and beta proteins (a/b)
fold: Isochorismatase-like hydrolases
superfamily: Isochorismatase-like hydrolases
family: Isochorismatase-like hydrolases
domain: Phenazine biosynthesis protein PhzD
species: Pseudomonas aeruginosa [TaxId: 287]
Probab=89.39 E-value=0.22 Score=32.99 Aligned_cols=42 Identities=17% Similarity=0.109 Sum_probs=38.7
Q ss_pred HHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 29 LKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 29 i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
+.++|+..|+..+.+-|...|=++.+-+..+...|++|+|++
T Consensus 133 L~~~L~~~gi~~lvv~Gv~T~~CV~~Ta~~A~~~gy~v~Vv~ 174 (207)
T d1nf9a_ 133 LLQRMRAAGRDQLVLCGVYAHVGVLISTVDAYSNDIQPFLVA 174 (207)
T ss_dssp HHHHHHHTTCCEEEEEEECTTTHHHHHHHHHHHTTCEEEEEE
T ss_pred HHHHHHHcCCceeEEecccccccHHHHHHHHHHCCCEEEEEc
Confidence 777888999999999999999999988988999999999976
>d1yaca_ c.33.1.3 (A:) YcaC {Escherichia coli [TaxId: 562]}
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class: Alpha and beta proteins (a/b)
fold: Isochorismatase-like hydrolases
superfamily: Isochorismatase-like hydrolases
family: Isochorismatase-like hydrolases
domain: YcaC
species: Escherichia coli [TaxId: 562]
Probab=88.73 E-value=0.14 Score=34.08 Aligned_cols=44 Identities=23% Similarity=0.414 Sum_probs=40.4
Q ss_pred HHHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 27 QYLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 27 ~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
..+.++|+..|+..+..-|.+.|=++.+-|..+.+.|++|+|++
T Consensus 93 t~L~~~L~~~gi~~lil~G~~T~~CV~~Ta~dA~~~Gy~V~vv~ 136 (204)
T d1yaca_ 93 EDFVKAVKATGKKQLIIAGVVTEVCVAFPALSAIEEGFDVFVVT 136 (204)
T ss_dssp HHHHHHHHHTTCSEEEEEEBSCCCCCHHHHHHHHHTTCEEEEET
T ss_pred hhHHHHHHhcCCCEEEEEEeecccHHHHHHHHHHHcCCEEEEeC
Confidence 34778899999999999999999999999999999999999986
>d1o4wa_ c.120.1.1 (A:) Hypothetical protein AF0591 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}
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class: Alpha and beta proteins (a/b)
fold: PIN domain-like
superfamily: PIN domain-like
family: PIN domain
domain: Hypothetical protein AF0591
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]
Probab=86.22 E-value=0.13 Score=31.84 Aligned_cols=47 Identities=13% Similarity=0.156 Sum_probs=34.7
Q ss_pred CCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEcCCCCc--ccccCCeEEEEecc
Q 034414 37 SIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVSPNKDS--QILSHSLCLLRIAP 89 (95)
Q Consensus 37 gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkDl--QLv~~~v~v~~~~k 89 (95)
.++.+..+ -.|||.|=.+|... +++++|.|+.| ++..++|.|+.+..
T Consensus 68 ~~~~~~~~-~~~Dd~il~~a~~~-----~~iv~T~D~~Lr~~~~~~GVpvi~l~~ 116 (125)
T d1o4wa_ 68 HFEVVETE-SEGDPSLIEAAEKY-----GCILITNDKELKRKAKQRGIPVGYLKE 116 (125)
T ss_dssp TSEEECCS-SCSHHHHHHHHHHH-----TCEEECCCHHHHHHHHHTTCCEECCCC
T ss_pred hCCCCCCC-CcHHHHHHHHHhhC-----CeEEEecCHHHHHHHHHcCCcEEEEeC
Confidence 45555544 46999887776543 57899999999 67779999988754
>d1nbaa_ c.33.1.3 (A:) N-carbamoylsarcosine amidohydrolase {Arthrobacter sp. [TaxId: 1667]}
Back Show information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Isochorismatase-like hydrolases
superfamily: Isochorismatase-like hydrolases
family: Isochorismatase-like hydrolases
domain: N-carbamoylsarcosine amidohydrolase
species: Arthrobacter sp. [TaxId: 1667]
Probab=82.38 E-value=0.59 Score=32.10 Aligned_cols=43 Identities=16% Similarity=0.272 Sum_probs=39.1
Q ss_pred HHHHHHHHCCCcEEecCCcchhHHHHHHHHHhhhCCCcEEEEc
Q 034414 28 YLKASIKAMSIKVIEVPGVEADDVIGKLAVRSVDDGFKIQVVS 70 (95)
Q Consensus 28 ~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS 70 (95)
.+..+|...|+..+.+-|...|=++-+-+..+...|++|+|++
T Consensus 148 ~L~~~Lr~~gI~~liv~Gv~Td~CV~~Ta~dA~~~Gy~V~Vv~ 190 (253)
T d1nbaa_ 148 NLELFLTSNRIDTLIVTGATAAGCVRHTVEDAIAKGFRPIIPR 190 (253)
T ss_dssp SHHHHHHHTTCCEEEEEEECTTTHHHHHHHHHHHHTCEEEEEG
T ss_pred cHHHHHhhhccceEEEEeecccchHHHHHHHHHHCCCEEEEec
Confidence 3677899999999999999999999999988888999999976
