Query 042232
Match_columns 144
No_of_seqs 11 out of 13
Neff 1.9
Searched_HMMs 46136
Date Fri Mar 29 04:11:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042232.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042232hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00008 53EXOc 5'-3' exonuclea 97.5 9.5E-05 2.1E-09 58.7 3.7 51 88-144 2-54 (240)
2 PRK14976 5'-3' exonuclease; Pr 97.5 0.0001 2.2E-09 60.5 3.8 56 87-144 3-59 (281)
3 smart00475 53EXOc 5'-3' exonuc 97.4 0.00017 3.7E-09 58.6 4.3 51 88-144 2-53 (259)
4 PRK09482 flap endonuclease-lik 97.3 0.00029 6.4E-09 58.1 4.3 47 88-144 4-51 (256)
5 PF02739 5_3_exonuc_N: 5'-3' e 97.2 0.00014 3.1E-09 55.5 1.3 52 88-143 2-54 (169)
6 PRK05755 DNA polymerase I; Pro 97.1 0.00069 1.5E-08 62.5 4.7 53 87-144 2-55 (880)
7 PHA00439 exonuclease 96.9 0.0013 2.7E-08 55.8 4.6 59 85-144 4-68 (286)
8 TIGR00593 pola DNA polymerase 96.5 0.003 6.5E-08 59.6 4.0 52 89-144 1-53 (887)
9 COG0258 Exo 5'-3' exonuclease 95.6 0.026 5.7E-07 46.0 5.2 54 85-143 9-63 (310)
10 PHA02567 rnh RnaseH; Provision 92.7 0.058 1.3E-06 46.4 1.4 52 86-143 13-66 (304)
11 PTZ00217 flap endonuclease-1; 90.3 0.46 9.9E-06 41.3 4.5 54 85-140 26-83 (393)
12 TIGR03674 fen_arch flap struct 88.1 0.65 1.4E-05 39.1 3.8 50 86-138 20-71 (338)
13 cd00128 XPG Xeroderma pigmento 81.7 3.2 6.8E-05 33.8 4.9 21 86-106 23-43 (316)
14 PF09228 Prok-TraM: Prokaryoti 52.1 8.7 0.00019 29.0 1.4 32 96-141 69-101 (102)
15 PF00752 XPG_N: XPG N-terminal 52.0 19 0.00041 24.4 2.9 48 83-133 22-69 (101)
16 cd06409 PB1_MUG70 The MUG70 pr 39.0 13 0.00027 26.9 0.5 13 111-123 45-57 (86)
17 PF10707 YrbL-PhoP_reg: PhoP r 37.0 33 0.00071 27.1 2.6 38 69-106 141-182 (199)
18 PF13591 MerR_2: MerR HTH fami 25.0 1.6E+02 0.0035 20.1 4.1 25 100-124 14-38 (84)
19 PRK10265 chaperone-modulator p 24.8 1.5E+02 0.0033 21.0 4.1 25 101-125 22-47 (101)
20 PF14427 Pput2613-deam: Pput_2 24.0 47 0.001 26.1 1.4 9 87-95 66-74 (118)
21 smart00485 XPGN Xeroderma pigm 22.7 1.3E+02 0.0028 20.3 3.3 43 87-133 24-67 (99)
22 PRK10345 hypothetical protein; 21.8 73 0.0016 24.9 2.1 24 71-94 130-153 (210)
No 1
>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. 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.
Probab=97.51 E-value=9.5e-05 Score=58.67 Aligned_cols=51 Identities=27% Similarity=0.593 Sum_probs=40.8
Q ss_pred eEEEEeCchHHHHHHHHHHHhcCCccCCCC-CCCeehhHHHHHHHHHHHhhcc-CCCCC
Q 042232 88 RVMLIDGTSIIYRAYYKILLHHGHLSHADG-NGDWVLTIFSALSLIIDVLEFI-PSHVV 144 (144)
Q Consensus 88 rimLiDGtsiiyRaYyKlllhhg~l~hadg-n~DWVLTiF~Als~iid~L~~~-PSH~~ 144 (144)
++|||||++++||+||-.. ...+. +|.++-.++..+..++.+++-. |+|++
T Consensus 2 ~~llIDg~~l~yr~~~a~~------~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~ 54 (240)
T cd00008 2 RLLLIDGSSLAYRAYFALP------PLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVA 54 (240)
T ss_pred cEEEEEChHHHHHHHHCCC------CcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeEE
Confidence 6999999999999999752 11222 7888889999999999999754 98864
No 2
>PRK14976 5'-3' exonuclease; Provisional
Probab=97.49 E-value=0.0001 Score=60.48 Aligned_cols=56 Identities=32% Similarity=0.601 Sum_probs=38.8
Q ss_pred CeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh-ccCCCCC
Q 042232 87 GRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVV 144 (144)
Q Consensus 87 grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~-~~PSH~~ 144 (144)
.+++||||++++|||||..+-+-..+...+|+-.. .++.-+..++.+++ +.|+|++
T Consensus 3 ~~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~--a~~gf~~~l~~ll~~~~p~~~~ 59 (281)
T PRK14976 3 KKALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTN--AIHTFLTMIFKILKKLNPSYIL 59 (281)
T ss_pred CcEEEEeCcHHHHHHHHccCccCCCccCCCCCCch--HHHHHHHHHHHHHHhcCCCEEE
Confidence 47999999999999999975111224444555444 45666777888885 5798864
No 3
>smart00475 53EXOc 5'-3' exonuclease.
Probab=97.43 E-value=0.00017 Score=58.59 Aligned_cols=51 Identities=24% Similarity=0.611 Sum_probs=37.5
Q ss_pred eEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh-ccCCCCC
Q 042232 88 RVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVV 144 (144)
Q Consensus 88 rimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~-~~PSH~~ 144 (144)
+++||||++++|||||-.- .+...+ |..+=.++.-+..++.+++ +.|+|++
T Consensus 2 ~lllIDg~~~i~R~~~a~~----~l~~~~--G~~t~a~~g~~~~l~~l~~~~~p~~~~ 53 (259)
T smart00475 2 KLLLVDGSSLAFRAYFALP----PLKNSK--GEPTNAVYGFLRMLLKLIKEEKPTYVA 53 (259)
T ss_pred cEEEEeCcHHHHHHHHCCC----cccCCC--CCcccHHHHHHHHHHHHHHHcCCCeEE
Confidence 5899999999999999751 244344 4455566777778888886 5699874
No 4
>PRK09482 flap endonuclease-like protein; Provisional
Probab=97.31 E-value=0.00029 Score=58.07 Aligned_cols=47 Identities=15% Similarity=0.217 Sum_probs=35.2
Q ss_pred eEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHh-hccCCCCC
Q 042232 88 RVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVL-EFIPSHVV 144 (144)
Q Consensus 88 rimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L-~~~PSH~~ 144 (144)
+++||||++++||+||-. +..+|. +=.|+.-+..++.++ ++.|+|++
T Consensus 4 ~llLiDg~~l~~R~~~a~-------~~~~g~---t~av~gf~~~l~~ll~~~~p~~i~ 51 (256)
T PRK09482 4 HLLIIDALNLIRRIHAVQ-------PSPNDI---NACVETCQHALDKLIRHSQPTHAV 51 (256)
T ss_pred eEEEEeCcHHHHHHHhCC-------CCCCCc---chHHHHHHHHHHHHHHHcCCCEEE
Confidence 599999999999999862 223343 555777778888888 56699974
No 5
>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. 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 ....
Probab=97.20 E-value=0.00014 Score=55.54 Aligned_cols=52 Identities=31% Similarity=0.683 Sum_probs=36.5
Q ss_pred eEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh-ccCCCC
Q 042232 88 RVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHV 143 (144)
Q Consensus 88 rimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~-~~PSH~ 143 (144)
+++||||++++|||||-.-. . .-...+|.++=.|+..+..+..+++ +.|+|+
T Consensus 2 ~llLIDg~~l~~Ra~~a~~~--~--~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~ 54 (169)
T PF02739_consen 2 KLLLIDGNSLLFRAYYALPK--D--PLRNSDGEPTNAIYGFLRMLLKLLKDFKPDYV 54 (169)
T ss_dssp EEEEEEHHHHHHHCCCCCTT--S--T-BETTSEB-HHHHHHHHHHHHHHHHTTEEEE
T ss_pred eEEEEechHHHHHHHHhhcc--C--CCcCCCCCChHHHHHHHHHHHHHHHHcCCceE
Confidence 79999999999999974321 1 3345567787788887777777665 446775
No 6
>PRK05755 DNA polymerase I; Provisional
Probab=97.08 E-value=0.00069 Score=62.47 Aligned_cols=53 Identities=30% Similarity=0.624 Sum_probs=38.5
Q ss_pred CeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHh-hccCCCCC
Q 042232 87 GRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVL-EFIPSHVV 144 (144)
Q Consensus 87 grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L-~~~PSH~~ 144 (144)
.++|||||++++|||||-. . -.+.. .+|..+=.|+..+..++.++ ++.|+|++
T Consensus 2 ~~~~liDg~~~~~r~~~a~--~-~~~~~--~~g~~~~a~~g~~~~l~~~~~~~~p~~~~ 55 (880)
T PRK05755 2 KTLLLIDGSSLLFRAFYAL--L-PTLRN--SDGLPTGAVYGFLNMLLKLLKEEKPTHVA 55 (880)
T ss_pred CeEEEEeCcHHHHHHHHCC--C-CcccC--CCCCcccHHHHHHHHHHHHHHhcCCCEEE
Confidence 3699999999999999975 1 12233 34555666777778888888 46699964
No 7
>PHA00439 exonuclease
Probab=96.92 E-value=0.0013 Score=55.76 Aligned_cols=59 Identities=15% Similarity=0.125 Sum_probs=44.0
Q ss_pred CCCeEEEEeCchHHHHHHHHHH--HhcCCccCCCCCCCeehhHHHHHHHHHHHhh----ccCCCCC
Q 042232 85 SNGRVMLIDGTSIIYRAYYKIL--LHHGHLSHADGNGDWVLTIFSALSLIIDVLE----FIPSHVV 144 (144)
Q Consensus 85 s~grimLiDGtsiiyRaYyKll--lhhg~l~hadgn~DWVLTiF~Als~iid~L~----~~PSH~~ 144 (144)
++-.++||||.+++|||||-+- ..-+. .-...+|+.+=.++.-+..++.+++ +.|+|++
T Consensus 4 ~~~~llLIDG~~l~fRA~~A~~~~~~~~~-~l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~ 68 (286)
T PHA00439 4 SDKGVLVMDGDYLVFQAMAAAEVETDWGE-DIWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIV 68 (286)
T ss_pred CCCcEEEEeCcHHHHHHHHccCcccccCC-CCCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEE
Confidence 3678999999999999999863 11111 1125788888888888888888885 4899874
No 8
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.45 E-value=0.003 Score=59.62 Aligned_cols=52 Identities=25% Similarity=0.578 Sum_probs=39.7
Q ss_pred EEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhh-ccCCCCC
Q 042232 89 VMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVV 144 (144)
Q Consensus 89 imLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~-~~PSH~~ 144 (144)
++||||++++|||||-+- .. .+. .++|..+=.|+.-+..++.+++ +.|+|++
T Consensus 1 l~lIDg~~l~~Ra~~a~~-~~-~l~--~~~G~~t~av~Gf~~~l~~ll~~~~p~~i~ 53 (887)
T TIGR00593 1 LLLIDGHSLAFRAYFALK-NK-PLT--NSKGEPTNAVYGFTKMLLKLLKEEKPTYVA 53 (887)
T ss_pred CEEEeCcHHHHHHHHCCC-cc-cCc--CCCCCEecHHHHHHHHHHHHHHhcCCCEEE
Confidence 589999999999999751 00 132 4567778888888999999995 6799964
No 9
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=95.57 E-value=0.026 Score=45.98 Aligned_cols=54 Identities=24% Similarity=0.505 Sum_probs=36.6
Q ss_pred CCCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHHHHhhccC-CCC
Q 042232 85 SNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIP-SHV 143 (144)
Q Consensus 85 s~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~iid~L~~~P-SH~ 143 (144)
..|++++|||.+.+||+||-+-.. +..-+|.-.| +++.-...+..++...+ .|.
T Consensus 9 ~~~~l~~IDg~~~lyr~~~a~~~~---~~~~~g~~~~--~~~~~~~~l~~~~~~~~~~~~ 63 (310)
T COG0258 9 KSGKLLLIDGSSLLYRALHALPQP---LGNPLGDPTG--AVSGFLGMLYRLIRLLEPTHP 63 (310)
T ss_pred ccCcEEEEechHHHHHHHHhcchh---cCCCCCCCcc--HHHHHHHHHHHHHHhcCCCcE
Confidence 457999999999999999988644 4445555555 55555555555554433 554
No 10
>PHA02567 rnh RnaseH; Provisional
Probab=92.65 E-value=0.058 Score=46.40 Aligned_cols=52 Identities=17% Similarity=0.160 Sum_probs=30.8
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcCCccCCCC-CCCeeh-hHHHHHHHHHHHhhccCCCC
Q 042232 86 NGRVMLIDGTSIIYRAYYKILLHHGHLSHADG-NGDWVL-TIFSALSLIIDVLEFIPSHV 143 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKlllhhg~l~hadg-n~DWVL-TiF~Als~iid~L~~~PSH~ 143 (144)
+--++||||++++|||||.- ++..+| +..=+. .|+..|--+++...-.|.|+
T Consensus 13 ~~~~~LiDgs~i~~~~~~a~------l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i 66 (304)
T PHA02567 13 KEGVNLIDFSQIIIATIMAN------FKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEI 66 (304)
T ss_pred CCCEEEEehHHHHHHHHHhh------CCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeE
Confidence 56799999999999999984 333332 222221 25555555555433345554
No 11
>PTZ00217 flap endonuclease-1; Provisional
Probab=90.29 E-value=0.46 Score=41.25 Aligned_cols=54 Identities=28% Similarity=0.363 Sum_probs=37.3
Q ss_pred CCCeEEEEeCchHHHHHHHHHHH--hcCCccCCCCCCCeehhHHHHHHHHHHHhhc--cC
Q 042232 85 SNGRVMLIDGTSIIYRAYYKILL--HHGHLSHADGNGDWVLTIFSALSLIIDVLEF--IP 140 (144)
Q Consensus 85 s~grimLiDGtsiiyRaYyKlll--hhg~l~hadgn~DWVLTiF~Als~iid~L~~--~P 140 (144)
-.|+.++|||.+.|||+||.+-. +++.|...+|+- .-.++..+..++.+|+. .|
T Consensus 26 l~gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~--t~~l~g~~~r~~~Ll~~gikP 83 (393)
T PTZ00217 26 YFGRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEV--TSHISGLFNRTIRLLEAGIKP 83 (393)
T ss_pred hCCcEEEEeHHHHHHHHHHHcccccccccchhccCCc--cHHHHHHHHHHHHHHHCCCCE
Confidence 35899999999999999998642 334455444443 34566667777777763 55
No 12
>TIGR03674 fen_arch flap structure-specific endonuclease. 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
Probab=88.09 E-value=0.65 Score=39.13 Aligned_cols=50 Identities=24% Similarity=0.350 Sum_probs=32.9
Q ss_pred CCeEEEEeCchHHHHHHHHHHHhcC-CccCCCCCCCe-ehhHHHHHHHHHHHhhc
Q 042232 86 NGRVMLIDGTSIIYRAYYKILLHHG-HLSHADGNGDW-VLTIFSALSLIIDVLEF 138 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKlllhhg-~l~hadgn~DW-VLTiF~Als~iid~L~~ 138 (144)
.|++++|||.+.+||+||.+-..+| .+..++|+-.. +..+| .-++.+++.
T Consensus 20 ~gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~---~~~~~ll~~ 71 (338)
T TIGR03674 20 SGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLF---YRTINLLEN 71 (338)
T ss_pred CCCEEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHH---HHHHHHHHC
Confidence 5889999999999999998643333 55556666543 33333 455555554
No 13
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. 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.
Probab=81.74 E-value=3.2 Score=33.81 Aligned_cols=21 Identities=19% Similarity=0.309 Sum_probs=18.8
Q ss_pred CCeEEEEeCchHHHHHHHHHH
Q 042232 86 NGRVMLIDGTSIIYRAYYKIL 106 (144)
Q Consensus 86 ~grimLiDGtsiiyRaYyKll 106 (144)
+|+.++|||.+.+||+||..-
T Consensus 23 ~gk~laID~~~~l~r~~~a~~ 43 (316)
T cd00128 23 RGKKVAIDASIWLYQFLKACR 43 (316)
T ss_pred CCcEEEecHHHHHHHHHHHhh
Confidence 688999999999999999863
No 14
>PF09228 Prok-TraM: Prokaryotic Transcriptional repressor TraM; InterPro: IPR015309 Members of this family of transcriptional repressors adopt a T-shaped structure, with a core composed of two antiparallel alpha-helices. These proteins can be divided into two parts, a globular head and an elongated tail, and they negatively regulate conjugation and the expression of tra genes by antagonising traR/AAI-dependent activation []. ; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 2Q0O_D 2HJD_D 1UPG_A 1US6_B 1RFY_B.
Probab=52.09 E-value=8.7 Score=28.97 Aligned_cols=32 Identities=31% Similarity=0.471 Sum_probs=24.9
Q ss_pred hHHHHHHHHHH-HhcCCccCCCCCCCeehhHHHHHHHHHHHhhccCC
Q 042232 96 SIIYRAYYKIL-LHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPS 141 (144)
Q Consensus 96 siiyRaYyKll-lhhg~l~hadgn~DWVLTiF~Als~iid~L~~~PS 141 (144)
....++|..-+ -+|-+ -.+|++|||.|.|+|-
T Consensus 69 ~~~~~eY~~~~~e~hAQ--------------~~~lstli~~LGyvPk 101 (102)
T PF09228_consen 69 GELQLEYIERQIEMHAQ--------------QSALSTLIDILGYVPK 101 (102)
T ss_dssp SHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHTSEE-
T ss_pred hHHHHHHHHHHHHhHHH--------------HHHHHHHHHHhCCCCC
Confidence 45788898888 55543 4799999999999994
No 15
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=52.03 E-value=19 Score=24.38 Aligned_cols=48 Identities=17% Similarity=0.328 Sum_probs=28.6
Q ss_pred CCCCCeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCCeehhHHHHHHHHH
Q 042232 83 APSNGRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGDWVLTIFSALSLII 133 (144)
Q Consensus 83 ~~s~grimLiDGtsiiyRaYyKlllhhg~l~hadgn~DWVLTiF~Als~ii 133 (144)
..-+|..+-|||+..+||.++.. +.......++..++-++|.-+..++
T Consensus 22 ~~l~g~~vaID~s~wl~~~~~~~---~~~~~~~~~~~~~~~~~~~r~~~L~ 69 (101)
T PF00752_consen 22 SELRGKRVAIDASCWLHQFLFSC---REELGQGVGTDSHLRGLFSRLCRLL 69 (101)
T ss_dssp GGGTTCEEEEEHHHHHHHHHHHS---BCTTSCB-BS-HHHHHHHHHHHHHH
T ss_pred HHhCCCEEEEEcHHHHHHHHHHh---HHHhccccchHHHHHHHHHHHHHHH
Confidence 33456789999999999998764 2222222222356666666655443
No 16
>cd06409 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is
Probab=38.95 E-value=13 Score=26.92 Aligned_cols=13 Identities=54% Similarity=0.664 Sum_probs=11.0
Q ss_pred CccCCCCCCCeeh
Q 042232 111 HLSHADGNGDWVL 123 (144)
Q Consensus 111 ~l~hadgn~DWVL 123 (144)
.|+-.|.+||||+
T Consensus 45 ~L~YlDDEgD~Vl 57 (86)
T cd06409 45 ALSYVDDEGDIVL 57 (86)
T ss_pred cEEEEcCCCCEEE
Confidence 4677899999997
No 17
>PF10707 YrbL-PhoP_reg: PhoP regulatory network protein YrbL; InterPro: IPR019647 This entry represents proteins that are activated by the protein PhoP. PhoP controls the expression of a large number of genes that mediate adaptation to low Mg2+ environments and/or virulence in several bacterial species. YbrL is proposed to be acting in a loop activity with PhoP and PrmA analogous to the multi-component loop in Salmonella sp., where the PhoP-dependent PmrD protein activates the regulatory protein PmrA, and the activated PmrA then represses transcription from the PmrD promoter which harbours binding sites for both the PhoP and PmrA proteins. Expression of YrbL is induced in low Mg2+ in a PhoP-dependent fashion and repressed by Fe3+ in a PmrA-dependent manner [].
Probab=37.03 E-value=33 Score=27.11 Aligned_cols=38 Identities=32% Similarity=0.460 Sum_probs=26.2
Q ss_pred cccccccceeecccCCCCCeEEEEeC----chHHHHHHHHHH
Q 042232 69 VGHANFHSIVTCKKAPSNGRVMLIDG----TSIIYRAYYKIL 106 (144)
Q Consensus 69 ~~~a~p~si~~~~~~~s~grimLiDG----tsiiyRaYyKll 106 (144)
..+.+|+.|.+-..+....+++|||| +-|=.++|.+.+
T Consensus 141 ~~dl~~~NIv~~~~~~~~~~lvlIDG~G~~~~ipl~~~~~~~ 182 (199)
T PF10707_consen 141 IRDLNPHNIVVQRRDSGEFRLVLIDGLGEKELIPLASWSKFL 182 (199)
T ss_pred ecCCCcccEEEEecCCCceEEEEEeCCCCcccccHHHHhHHH
Confidence 35678888887776666679999999 233345565555
No 18
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=25.00 E-value=1.6e+02 Score=20.10 Aligned_cols=25 Identities=12% Similarity=0.482 Sum_probs=19.5
Q ss_pred HHHHHHHHhcCCccCCCCCCCeehh
Q 042232 100 RAYYKILLHHGHLSHADGNGDWVLT 124 (144)
Q Consensus 100 RaYyKlllhhg~l~hadgn~DWVLT 124 (144)
+++..-|+.+|.++-...++.|.+.
T Consensus 14 ~~~l~~lve~Gli~p~~~~~~~~f~ 38 (84)
T PF13591_consen 14 PEFLRELVEEGLIEPEGEEEEWYFS 38 (84)
T ss_pred HHHHHHHHHCCCeeecCCCCeeeEC
Confidence 4556667889999988888899854
No 19
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=24.76 E-value=1.5e+02 Score=21.01 Aligned_cols=25 Identities=12% Similarity=0.218 Sum_probs=16.5
Q ss_pred HHHHHHHhcCCccCCCCC-CCeehhH
Q 042232 101 AYYKILLHHGHLSHADGN-GDWVLTI 125 (144)
Q Consensus 101 aYyKlllhhg~l~hadgn-~DWVLTi 125 (144)
++-.-|+.+|.++...++ +.|+.+-
T Consensus 22 ~~l~eLve~GlIep~~~~~~~~~F~~ 47 (101)
T PRK10265 22 EELNEIVGLGVIEPREIQETTWVFDD 47 (101)
T ss_pred HHHHHHHHCCCeecCCCCcccceECH
Confidence 344456888888765554 8887654
No 20
>PF14427 Pput2613-deam: Pput_2613-like deaminase
Probab=23.98 E-value=47 Score=26.05 Aligned_cols=9 Identities=67% Similarity=1.032 Sum_probs=8.6
Q ss_pred CeEEEEeCc
Q 042232 87 GRVMLIDGT 95 (144)
Q Consensus 87 grimLiDGt 95 (144)
|+.|+|||+
T Consensus 66 Gd~m~I~G~ 74 (118)
T PF14427_consen 66 GDRMLIDGQ 74 (118)
T ss_pred CceEEEeee
Confidence 999999996
No 21
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=22.65 E-value=1.3e+02 Score=20.34 Aligned_cols=43 Identities=14% Similarity=0.246 Sum_probs=27.5
Q ss_pred CeEEEEeCchHHHHHHHHHHHhcCCccCCCCCCC-eehhHHHHHHHHH
Q 042232 87 GRVMLIDGTSIIYRAYYKILLHHGHLSHADGNGD-WVLTIFSALSLII 133 (144)
Q Consensus 87 grimLiDGtsiiyRaYyKlllhhg~l~hadgn~D-WVLTiF~Als~ii 133 (144)
|..+-||++..+||+++..=..++. +-+++ ++-.+|.=+..++
T Consensus 24 g~~vaIDa~~wl~~~~~~~~~~~~~----~~~~~~~l~~~~~rl~~L~ 67 (99)
T smart00485 24 GKTLAIDASIWLYQFLTACREKLGT----PLPNSKHLMGLFYRTCRLL 67 (99)
T ss_pred CceEeccHHHHHHHHHHHHhhhhcC----CCCchHHHHHHHHHHHHHH
Confidence 6778999999999999975222111 11223 7777776655544
No 22
>PRK10345 hypothetical protein; Provisional
Probab=21.78 E-value=73 Score=24.94 Aligned_cols=24 Identities=13% Similarity=0.077 Sum_probs=18.6
Q ss_pred cccccceeecccCCCCCeEEEEeC
Q 042232 71 HANFHSIVTCKKAPSNGRVMLIDG 94 (144)
Q Consensus 71 ~a~p~si~~~~~~~s~grimLiDG 94 (144)
+..|..|-+...+.+++++.||||
T Consensus 130 DlKp~NILl~~~~~~~~~~~LiDg 153 (210)
T PRK10345 130 ELKPQNILCQRISESEVIPVVCDN 153 (210)
T ss_pred CCCHHHEEEeccCCCCCcEEEEEC
Confidence 367777777666677889999994
Done!