Query gi|254780303|ref|YP_003064716.1| DNA protecting protein DprA [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 77
No_of_seqs 102 out of 154
Neff 3.5
Searched_HMMs 39220
Date Sun May 29 15:29:33 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780303.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0758 Smf Predicted Rossmann 98.2 3.2E-06 8.2E-11 56.6 5.8 63 13-75 1-66 (350)
2 pfam01367 5_3_exonuc 5'-3' exo 93.6 0.074 1.9E-06 31.9 3.2 32 27-58 23-54 (100)
3 cd00008 53EXOc 5'-3' exonuclea 93.4 0.091 2.3E-06 31.4 3.4 45 13-57 166-218 (240)
4 PRK09482 xni exonuclease IX; P 92.9 0.11 2.8E-06 30.9 3.2 32 27-58 187-218 (256)
5 smart00475 53EXOc 5'-3' exonuc 92.4 0.15 3.8E-06 30.2 3.4 46 13-58 169-222 (259)
6 cd00080 HhH2_motif Helix-hairp 91.6 0.29 7.4E-06 28.5 4.2 44 12-55 4-55 (75)
7 PRK08786 consensus 91.6 0.28 7.1E-06 28.6 4.1 45 13-57 166-218 (927)
8 PRK13766 Hef nuclease; Provisi 91.6 0.18 4.7E-06 29.7 3.1 30 26-55 710-739 (764)
9 PRK05929 consensus 91.3 0.24 6.1E-06 29.0 3.5 45 13-57 168-220 (870)
10 PRK08434 consensus 91.1 0.26 6.5E-06 28.8 3.5 44 13-56 167-218 (887)
11 PRK07300 consensus 91.0 0.28 7.1E-06 28.6 3.5 44 13-56 179-230 (880)
12 PRK08928 consensus 91.0 0.26 6.6E-06 28.8 3.4 43 14-56 170-220 (861)
13 PRK07898 consensus 90.9 0.3 7.7E-06 28.4 3.6 44 13-56 185-236 (902)
14 PRK05797 consensus 90.8 0.28 7.2E-06 28.6 3.5 44 13-56 171-222 (869)
15 PRK07625 consensus 90.8 0.29 7.5E-06 28.5 3.5 44 13-56 170-221 (922)
16 PRK07456 consensus 90.6 0.37 9.4E-06 27.9 3.9 46 13-58 188-241 (975)
17 PRK07556 consensus 90.5 0.33 8.4E-06 28.2 3.6 44 13-56 177-228 (977)
18 PRK07997 consensus 90.4 0.33 8.5E-06 28.2 3.5 45 13-57 171-223 (928)
19 PRK08835 consensus 90.3 0.32 8.2E-06 28.3 3.4 44 14-57 172-223 (931)
20 PRK08076 consensus 89.8 0.37 9.5E-06 27.9 3.3 44 13-56 171-222 (877)
21 PRK05755 DNA polymerase I; Pro 89.2 0.46 1.2E-05 27.4 3.5 44 13-56 169-220 (889)
22 PRK06887 consensus 89.0 0.47 1.2E-05 27.3 3.4 44 13-56 171-222 (954)
23 PRK00558 uvrC excinuclease ABC 88.5 0.53 1.3E-05 27.1 3.4 40 24-63 556-596 (609)
24 PTZ00217 flap endonuclease-1; 86.5 0.81 2.1E-05 26.0 3.4 44 9-52 216-265 (394)
25 cd00128 XPG Xeroderma pigmento 85.8 0.94 2.4E-05 25.6 3.4 45 8-52 203-253 (316)
26 PRK03980 flap endonuclease-1; 84.6 1.1 2.8E-05 25.3 3.3 43 10-52 171-219 (295)
27 TIGR03674 fen_arch flap struct 82.2 1.6 4.1E-05 24.3 3.3 43 10-52 218-266 (338)
28 COG0322 UvrC Nuclease subunit 81.4 1.7 4.3E-05 24.2 3.2 38 25-62 533-570 (581)
29 TIGR00593 pola DNA polymerase 76.6 2 5.2E-05 23.7 2.4 23 28-50 198-220 (1005)
30 COG0258 Exo 5'-3' exonuclease 74.6 3.7 9.5E-05 22.2 3.3 41 13-53 181-229 (310)
31 COG1948 MUS81 ERCC4-type nucle 73.3 7.5 0.00019 20.5 4.6 50 11-61 172-222 (254)
32 smart00279 HhH2 Helix-hairpin- 69.4 3.2 8.2E-05 22.6 2.0 16 27-42 21-36 (36)
33 COG3675 Predicted lipase [Lipi 66.3 1.8 4.6E-05 24.0 0.2 37 19-56 271-307 (332)
34 TIGR01091 upp uracil phosphori 61.1 6 0.00015 21.1 2.1 27 19-45 13-39 (213)
35 TIGR01371 met_syn_B12ind 5-met 53.5 6.9 0.00018 20.7 1.4 46 11-56 139-199 (778)
36 TIGR01313 therm_gnt_kin carboh 52.2 7.3 0.00019 20.6 1.3 19 8-26 47-65 (175)
37 cd03312 CIMS_N_terminal_like C 43.4 13 0.00032 19.2 1.4 45 11-55 129-180 (360)
38 pfam11662 DUF3263 Protein of u 43.1 25 0.00064 17.5 2.9 38 23-60 26-64 (77)
39 PRK11545 gntK gluconate kinase 42.8 21 0.00054 18.0 2.5 19 8-26 52-70 (177)
40 KOG1720 consensus 41.6 34 0.00087 16.8 3.6 32 11-42 173-205 (225)
41 TIGR02236 recomb_radA DNA repa 38.5 20 0.0005 18.2 1.8 35 27-61 5-41 (333)
42 PRK09825 idnK D-gluconate kina 37.4 28 0.00071 17.3 2.4 20 7-26 46-65 (176)
43 COG3265 GntK Gluconate kinase 37.2 19 0.0005 18.2 1.6 21 7-27 38-58 (161)
44 TIGR02169 SMC_prok_A chromosom 35.8 18 0.00046 18.3 1.2 28 11-38 581-608 (1202)
45 PRK00116 ruvA Holliday junctio 33.8 46 0.0012 16.1 3.6 34 12-45 63-96 (198)
46 TIGR00831 a_cpa1 Na+/H+ antipo 31.2 27 0.00068 17.4 1.5 28 34-61 426-453 (541)
47 COG1936 Predicted nucleotide k 30.9 37 0.00094 16.6 2.2 33 26-61 7-39 (180)
48 PRK09767 hypothetical protein; 27.4 21 0.00053 18.0 0.4 26 11-37 13-38 (116)
49 pfam07684 NODP NOTCH protein. 27.2 28 0.00072 17.3 1.0 33 40-72 22-54 (62)
50 pfam09012 FeoC FeoC like trans 26.7 49 0.0012 15.9 2.2 32 30-61 12-43 (68)
51 cd01079 NAD_bind_m-THF_DH NAD 24.7 52 0.0013 15.8 2.0 22 16-41 166-187 (197)
52 KOG3354 consensus 24.7 27 0.00068 17.4 0.5 18 8-25 56-73 (191)
53 COG0035 Upp Uracil phosphoribo 24.4 56 0.0014 15.6 2.1 39 14-52 8-48 (210)
54 KOG1223 consensus 23.2 6.5 0.00017 20.9 -2.8 58 9-73 259-316 (508)
55 TIGR01828 pyru_phos_dikin pyru 23.2 31 0.0008 17.0 0.7 24 11-45 126-149 (920)
56 COG0632 RuvA Holliday junction 23.1 72 0.0018 15.0 3.5 32 12-43 63-94 (201)
57 smart00278 HhH1 Helix-hairpin- 23.0 42 0.0011 16.3 1.3 21 23-43 2-22 (26)
58 pfam01474 DAHP_synth_2 Class-I 22.2 52 0.0013 15.7 1.6 49 7-59 285-334 (437)
59 PRK13901 ruvA Holliday junctio 22.1 75 0.0019 14.8 3.5 32 12-43 62-93 (196)
60 TIGR00575 dnlj DNA ligase, NAD 21.8 76 0.0019 14.8 2.4 28 27-54 526-553 (706)
No 1
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=98.20 E-value=3.2e-06 Score=56.60 Aligned_cols=63 Identities=21% Similarity=0.372 Sum_probs=52.2
Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHH-HHHHHHHHHHCCCCCCC--CCCHHHHHH
Q ss_conf 8999999999998658968999999999749999999-97099999614558876--789899754
Q gi|254780303|r 13 LTDDQKISWLRLIRSDNISPATCRDMINYFGSAEQAL-EMIPELAQRGAVYAGKR--AFVQKNQQK 75 (77)
Q Consensus 13 ls~~erlawLRL~Rt~~VGp~Tf~~Ll~~fGsA~aAL-~aLP~la~rgG~~~~~r--i~s~~~Ae~ 75 (77)
|++.|+++||||.+++++||.+|..++.+||+.+.++ ..++.+...|+..+.++ .+....++.
T Consensus 1 m~~~e~~~~l~L~~~~~l~~~~~~~ll~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~~~~~~ 66 (350)
T COG0758 1 MSDRERLAWLKLSSTNNLGPLNLLLLLKHFGNKESILKIPLPQLEIEGLSSRRLLAELARIELLEL 66 (350)
T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHHCCCHHHHHHHHCCHHHHHH
T ss_conf 963689999998617997769999999825877666333378999863554777754025778999
No 2
>pfam01367 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold.
Probab=93.57 E-value=0.074 Score=31.90 Aligned_cols=32 Identities=22% Similarity=0.366 Sum_probs=28.4
Q ss_pred CCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 58968999999999749999999970999996
Q gi|254780303|r 27 SDNISPATCRDMINYFGSAEQALEMIPELAQR 58 (77)
Q Consensus 27 t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~r 58 (77)
-++|||.|...||++|||-++.++.+.++..+
T Consensus 23 v~GiG~KtA~~Ll~~~gsle~i~~n~d~i~~k 54 (100)
T pfam01367 23 VPGIGEKTAAKLLKEYGSLENIYENLDKLKGK 54 (100)
T ss_pred CCCCCCHHHHHHHHHCCCHHHHHHHHHHCCHH
T ss_conf 99988168999999819899999819871799
No 3
>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=93.38 E-value=0.091 Score=31.39 Aligned_cols=45 Identities=27% Similarity=0.386 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHH--C------CCCCHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 89999999999986--5------896899999999974999999997099999
Q gi|254780303|r 13 LTDDQKISWLRLIR--S------DNISPATCRDMINYFGSAEQALEMIPELAQ 57 (77)
Q Consensus 13 ls~~erlawLRL~R--t------~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~ 57 (77)
++.++-.+++=|.= | ++|||.|...||+.|||-++.++++.++..
T Consensus 166 v~p~q~~d~~aL~GD~sDnIpGV~GiG~KtA~kLl~~~gsle~i~~~~~~~~~ 218 (240)
T cd00008 166 VTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKIKG 218 (240)
T ss_pred CCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHCCH
T ss_conf 89999987699728764688999985789999999980999999982985278
No 4
>PRK09482 xni exonuclease IX; Provisional
Probab=92.85 E-value=0.11 Score=30.94 Aligned_cols=32 Identities=25% Similarity=0.462 Sum_probs=28.0
Q ss_pred CCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 58968999999999749999999970999996
Q gi|254780303|r 27 SDNISPATCRDMINYFGSAEQALEMIPELAQR 58 (77)
Q Consensus 27 t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~r 58 (77)
-++|||.|...||++|||-++.++.+.++..+
T Consensus 187 V~GIG~KtA~~LL~~fgsle~i~~n~d~i~~k 218 (256)
T PRK09482 187 VAGIGPKSAAELLNQFRSLEGIYESLDALPEK 218 (256)
T ss_pred CCCCCHHHHHHHHHHHCCHHHHHHHHHHCCHH
T ss_conf 99858889999999855099999837755689
No 5
>smart00475 53EXOc 5'-3' exonuclease.
Probab=92.37 E-value=0.15 Score=30.18 Aligned_cols=46 Identities=30% Similarity=0.464 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 89999999999986--------58968999999999749999999970999996
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELAQR 58 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~r 58 (77)
++.++-.+++=|.= -++|||.|...||++|||-+..++++-++..+
T Consensus 169 v~P~q~~d~~aL~GD~sDnIpGV~GIG~KtA~kLL~~ygsle~i~~~~d~i~~k 222 (259)
T smart00475 169 LTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDKLKKK 222 (259)
T ss_pred CCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCHH
T ss_conf 998998637640464535899999847899999999839999999839854889
No 6
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=91.63 E-value=0.29 Score=28.54 Aligned_cols=44 Identities=30% Similarity=0.434 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 889999999999986--------58968999999999749999999970999
Q gi|254780303|r 12 SLTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPEL 55 (77)
Q Consensus 12 ~ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~l 55 (77)
.++.++-++..=|.= -++|||.|...||+.|||-+..++++...
T Consensus 4 g~~p~q~~d~~~L~GD~sDnipGV~GIG~ktA~~ll~~~~~l~~i~~~~~~~ 55 (75)
T cd00080 4 GLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDKI 55 (75)
T ss_pred CCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9799999999999196545887758637999999999909999999838777
No 7
>PRK08786 consensus
Probab=91.62 E-value=0.28 Score=28.63 Aligned_cols=45 Identities=16% Similarity=0.286 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 89999999999986--------5896899999999974999999997099999
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELAQ 57 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~ 57 (77)
.+.++-++.+=|.- -|+|||.|...||+.|||-+..++.+-++..
T Consensus 166 V~P~qviD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~I~~n~d~Ikg 218 (927)
T PRK08786 166 VRPDQIVDLLALMGDTVDNVPGVEKCGPKTAAKWLAEYDSLDGVIANADKIKG 218 (927)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 69899999999808764678999985689999999975769999999875546
No 8
>PRK13766 Hef nuclease; Provisional
Probab=91.60 E-value=0.18 Score=29.67 Aligned_cols=30 Identities=23% Similarity=0.478 Sum_probs=26.4
Q ss_pred HCCCCCHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 658968999999999749999999970999
Q gi|254780303|r 26 RSDNISPATCRDMINYFGSAEQALEMIPEL 55 (77)
Q Consensus 26 Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~l 55 (77)
--|+|||++.++||.+|||-++...|-.+=
T Consensus 710 ~~pgvg~~~a~~ll~~fgsi~~i~~a~~~e 739 (764)
T PRK13766 710 SLPDVGPVLARNLLDHFGSVENVMTASEEE 739 (764)
T ss_pred HCCCCCHHHHHHHHHHCCCHHHHHCCCHHH
T ss_conf 389999999999999719999996599999
No 9
>PRK05929 consensus
Probab=91.35 E-value=0.24 Score=29.00 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=36.6
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 89999999999986--------5896899999999974999999997099999
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELAQ 57 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~ 57 (77)
.+.++-++.+=|.- -|+|||.|...||+.|||-+..++.+-++..
T Consensus 168 v~P~qi~D~laL~GDsSDNIPGVpGIG~KTA~kLL~~ygsLE~Iy~n~d~ikg 220 (870)
T PRK05929 168 VPPGQIADYLALVGDSSDNIPGVSGCGPKKAAALLKEFQSVEGLLENLDRLSG 220 (870)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHCH
T ss_conf 69899999999728764689999976099999999867877799999986320
No 10
>PRK08434 consensus
Probab=91.11 E-value=0.26 Score=28.84 Aligned_cols=44 Identities=20% Similarity=0.302 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 89999999999986--------589689999999997499999999709999
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
.+.++-++.+=|.- -|+|||.|...||+.|||-+..++.+-++.
T Consensus 167 V~P~qv~D~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~I~~n~d~Ik 218 (887)
T PRK08434 167 VKPKQIRDFLALCGDSADNIPGVKGIGAKGAKKLLDEFGSLEGIYENLELVR 218 (887)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 6989999999981886457899998568999999998288899999887124
No 11
>PRK07300 consensus
Probab=90.96 E-value=0.28 Score=28.63 Aligned_cols=44 Identities=30% Similarity=0.326 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 89999999999986--------589689999999997499999999709999
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
.+.++-++.+=|.= -|+|||.|...||+.|||-+..++.+-++-
T Consensus 179 V~P~qiiD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~I~~n~d~Ik 230 (880)
T PRK07300 179 LTPNQFIDLKALMGDKSDNIPGVTKIGEKTGLKLLHEFGSLEGIYENIDGMK 230 (880)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf 8989999999980886246778898536999999997786999998575313
No 12
>PRK08928 consensus
Probab=90.95 E-value=0.26 Score=28.80 Aligned_cols=43 Identities=28% Similarity=0.474 Sum_probs=34.2
Q ss_pred CHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 9999999999986--------589689999999997499999999709999
Q gi|254780303|r 14 TDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 14 s~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
+.++-++.+=|.- -|+|||.|...||+.|||-+..++.+-++.
T Consensus 170 ~P~qiiD~laL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~Iy~n~d~Ik 220 (861)
T PRK08928 170 TSDKLLDVMALTGDRSDNIPGVPSIGPKTAAKLITQFGSLENILNSLDQIS 220 (861)
T ss_pred CHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 989999999980876468899988562899999996797999999886113
No 13
>PRK07898 consensus
Probab=90.86 E-value=0.3 Score=28.43 Aligned_cols=44 Identities=20% Similarity=0.242 Sum_probs=37.0
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 89999999999986--------589689999999997499999999709999
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
.+.++-++.+=|.- -|+|||.|...||+.|||-+..++.+-++.
T Consensus 185 V~P~qviD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~I~~n~d~Ik 236 (902)
T PRK07898 185 LTPAQYPDFAALRGDPSDNLPGIPGVGEKTAAKWIAQYGSLDGLVDHADEIK 236 (902)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 7989999999981886457999998447889999997677899999987521
No 14
>PRK05797 consensus
Probab=90.81 E-value=0.28 Score=28.59 Aligned_cols=44 Identities=30% Similarity=0.336 Sum_probs=36.0
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 89999999999986--------589689999999997499999999709999
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
.+.++-.+.+-|.- -|+|||.|...||+.|||-+..++.+-++.
T Consensus 171 v~P~q~~D~~aL~GD~sDNIPGVpGIG~KTA~kLL~eyGsLE~I~~n~deIk 222 (869)
T PRK05797 171 VTPTQFIDVKGLMGDKSDNIPGVPGIGEKTAFKLIKEYGSIENVLENIDNIK 222 (869)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 8999999999980886457899998781899999986787889998788505
No 15
>PRK07625 consensus
Probab=90.80 E-value=0.29 Score=28.49 Aligned_cols=44 Identities=20% Similarity=0.419 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 89999999999986--------589689999999997499999999709999
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
.+.++-++.+=|+= -|+|||.|...||+.|||-+..++.+-++.
T Consensus 170 V~P~qviD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~I~~n~d~Ik 221 (922)
T PRK07625 170 VPPERIVDYLSLIGDTVDNVPGVEKCGPKTAVKWLTQYGSLDGVVEHAGEIK 221 (922)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 7989999999971976357899998567989999997478999999887302
No 16
>PRK07456 consensus
Probab=90.56 E-value=0.37 Score=27.94 Aligned_cols=46 Identities=13% Similarity=0.271 Sum_probs=37.1
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 89999999999986--------58968999999999749999999970999996
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELAQR 58 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~r 58 (77)
.+.++-++.+=|+- -|+|||.|...||+.|||-+..++.+-++...
T Consensus 188 V~P~qiiD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~Iyen~d~i~~~ 241 (975)
T PRK07456 188 VAPEQVVDLKALTGDSSDNIPGVKGVGPKTAINLLKENGDLDGIYKALDEIEGE 241 (975)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHCCC
T ss_conf 598998999997288656889999855999999999849999999828762001
No 17
>PRK07556 consensus
Probab=90.53 E-value=0.33 Score=28.23 Aligned_cols=44 Identities=18% Similarity=0.256 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 89999999999986--------589689999999997499999999709999
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
.+.++-++.+=|.= -|+|||.|...||+.|||-+..++.+-++.
T Consensus 177 V~P~qv~D~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~Iy~n~deIk 228 (977)
T PRK07556 177 VPPEKVVDVQALAGDSVDNVPGIPGIGIKTAAQLINEYGDLDTLLARAGEIK 228 (977)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 6989999999971876467898998548999999997578999999886502
No 18
>PRK07997 consensus
Probab=90.38 E-value=0.33 Score=28.17 Aligned_cols=45 Identities=13% Similarity=0.258 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 89999999999986--------5896899999999974999999997099999
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELAQ 57 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~ 57 (77)
.+.++-++.+=|.- -|+|||.|...||+.|||-+..++.+-++..
T Consensus 171 V~P~qv~D~laL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~I~~n~d~i~g 223 (928)
T PRK07997 171 VPPELIIDFLALMGDSSDNIPGVPGVGEKTAQALLQGLGGLDTLYAEPEKIAG 223 (928)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHCC
T ss_conf 79898899999728865688999975489999999982779999980986045
No 19
>PRK08835 consensus
Probab=90.34 E-value=0.32 Score=28.29 Aligned_cols=44 Identities=14% Similarity=0.306 Sum_probs=35.5
Q ss_pred CHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 9999999999986--------5896899999999974999999997099999
Q gi|254780303|r 14 TDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELAQ 57 (77)
Q Consensus 14 s~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~ 57 (77)
+.++-++.+=|.- -|+|||.|...||+.|||-+..++.+-++..
T Consensus 172 ~P~qviD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLE~Iy~nld~Ik~ 223 (931)
T PRK08835 172 PPELIIDYLALMGDKVDNIPGVPGVGDKTATALLQGIGGLDALYDNLDDIAA 223 (931)
T ss_pred CHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHCCC
T ss_conf 9899899999718864688999974588899999984869999976986144
No 20
>PRK08076 consensus
Probab=89.77 E-value=0.37 Score=27.91 Aligned_cols=44 Identities=30% Similarity=0.429 Sum_probs=35.9
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 89999999999986--------589689999999997499999999709999
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
.+..+-++.+-|.= -|+|||.|...||+.|||-+..++.+-++.
T Consensus 171 v~P~q~~D~~aL~GDssDNIPGVpGiG~KtA~~ll~~~gsle~i~~~~~~ik 222 (877)
T PRK08076 171 LTPKQIIDMKGLMGDSSDNIPGVPGVGEKTAIKLLKQFGTVEEVLESIDEVS 222 (877)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 6989999999971876467999998637999999996686688998777326
No 21
>PRK05755 DNA polymerase I; Provisional
Probab=89.19 E-value=0.46 Score=27.38 Aligned_cols=44 Identities=27% Similarity=0.435 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 89999999999986--------589689999999997499999999709999
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
.+..+-++.+-|.- -|+|||.|...||+.|||-+..++.+-++.
T Consensus 169 v~P~q~~D~~aL~GD~sDNIPGVpGIG~KtA~kLl~~ygsle~i~~~~d~i~ 220 (889)
T PRK05755 169 VTPEQIIDFLALMGDSSDNIPGVPGVGEKTAAKLLKEFGSLEGLYENLDEIK 220 (889)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 6989999999980886457899886269999999986786899999898523
No 22
>PRK06887 consensus
Probab=88.99 E-value=0.47 Score=27.35 Aligned_cols=44 Identities=16% Similarity=0.296 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHH--------CCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 89999999999986--------589689999999997499999999709999
Q gi|254780303|r 13 LTDDQKISWLRLIR--------SDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 13 ls~~erlawLRL~R--------t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
.+.++-++.+=|.= -|+|||.|...||+.|||-+..++.+-++.
T Consensus 171 V~P~qiiD~lAL~GDsSDNIPGVpGIG~KTA~kLL~eyGsLe~Iy~nld~i~ 222 (954)
T PRK06887 171 IPPELIIDYLALMGDSSDNIPGVAGVGEKTALGLLQGIGSMAEIYANLDKVA 222 (954)
T ss_pred CCHHHHHHHHHHCCCCCCCCCCCCCEEHHHHHHHHHHHCCHHHHHHHHHHHC
T ss_conf 7989999999971885247788785416999999999577999998698732
No 23
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=88.51 E-value=0.53 Score=27.05 Aligned_cols=40 Identities=23% Similarity=0.235 Sum_probs=30.8
Q ss_pred HHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHH-HHHHCCCC
Q ss_conf 98658968999999999749999999970999-99614558
Q gi|254780303|r 24 LIRSDNISPATCRDMINYFGSAEQALEMIPEL-AQRGAVYA 63 (77)
Q Consensus 24 L~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~l-a~rgG~~~ 63 (77)
|---+||||.+-..||.+|||-+....|-.+= +.-.|..+
T Consensus 556 Ld~I~GIG~kr~~~Ll~~Fgs~~~i~~As~eeL~~v~Gi~~ 596 (609)
T PRK00558 556 LDDIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISK 596 (609)
T ss_pred CCCCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHCCCCCH
T ss_conf 64789979999999999707999997389999964899899
No 24
>PTZ00217 flap endonuclease-1; Provisional
Probab=86.48 E-value=0.81 Score=26.01 Aligned_cols=44 Identities=34% Similarity=0.508 Sum_probs=36.7
Q ss_pred CCCCCCHHHHHHHHHHHHC------CCCCHHHHHHHHHHCCCHHHHHHHH
Q ss_conf 4878899999999999865------8968999999999749999999970
Q gi|254780303|r 9 GGVSLTDDQKISWLRLIRS------DNISPATCRDMINYFGSAEQALEMI 52 (77)
Q Consensus 9 ~~~~ls~~erlawLRL~Rt------~~VGp~Tf~~Ll~~fGsA~aAL~aL 52 (77)
....||.++-++.==|.=| ++|||.|...||..|||-+..|+.+
T Consensus 216 ~~l~lt~eqfidlcIL~GcDY~~~I~GIGpk~A~klIk~~~sie~il~~~ 265 (394)
T PTZ00217 216 KGLGLSMDQFIDLCILCGCDYCDTIEGIGPKTAYELIKKYGSIEEILEHL 265 (394)
T ss_pred HHCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHH
T ss_conf 77499999999999981864468998748899999999959999999874
No 25
>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=85.82 E-value=0.94 Score=25.63 Aligned_cols=45 Identities=24% Similarity=0.408 Sum_probs=35.7
Q ss_pred CCCCCCCHHHHHHHHHHHHC------CCCCHHHHHHHHHHCCCHHHHHHHH
Q ss_conf 24878899999999999865------8968999999999749999999970
Q gi|254780303|r 8 KGGVSLTDDQKISWLRLIRS------DNISPATCRDMINYFGSAEQALEMI 52 (77)
Q Consensus 8 ~~~~~ls~~erlawLRL~Rt------~~VGp~Tf~~Ll~~fGsA~aAL~aL 52 (77)
.....||.++-++--=|.=| ++|||.|...||..|||-+..++.+
T Consensus 203 ~~~l~l~~~~~id~~iL~G~Dy~~gi~giG~k~A~kli~~~~~~e~~~~~l 253 (316)
T cd00128 203 LKELGLTREKLIDLAILLGCDYTEGIPGIGPVTALKLIKKYGDIEKDIERL 253 (316)
T ss_pred HHHCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHH
T ss_conf 877399999999999972988789999735999999999919999999999
No 26
>PRK03980 flap endonuclease-1; Provisional
Probab=84.56 E-value=1.1 Score=25.26 Aligned_cols=43 Identities=28% Similarity=0.441 Sum_probs=34.9
Q ss_pred CCCCCHHHHHHHHHHHHC------CCCCHHHHHHHHHHCCCHHHHHHHH
Q ss_conf 878899999999999865------8968999999999749999999970
Q gi|254780303|r 10 GVSLTDDQKISWLRLIRS------DNISPATCRDMINYFGSAEQALEMI 52 (77)
Q Consensus 10 ~~~ls~~erlawLRL~Rt------~~VGp~Tf~~Ll~~fGsA~aAL~aL 52 (77)
+..||.++-++--=|.=| ++|||.|...||..|||-+..|+.+
T Consensus 171 ~l~lt~eqfidlcIL~GcDY~~gI~gIGpk~Alklikk~~~ie~il~~~ 219 (295)
T PRK03980 171 ELGITREQLIDIAILVGTDYNPGVKGIGPKTALKLIKKHGDLEKVLEAV 219 (295)
T ss_pred HCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHC
T ss_conf 8399999999999845888999999842999999999969999999863
No 27
>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=82.19 E-value=1.6 Score=24.34 Aligned_cols=43 Identities=26% Similarity=0.375 Sum_probs=32.5
Q ss_pred CCCCCHHHHHHHHHHHHC------CCCCHHHHHHHHHHCCCHHHHHHHH
Q ss_conf 878899999999999865------8968999999999749999999970
Q gi|254780303|r 10 GVSLTDDQKISWLRLIRS------DNISPATCRDMINYFGSAEQALEMI 52 (77)
Q Consensus 10 ~~~ls~~erlawLRL~Rt------~~VGp~Tf~~Ll~~fGsA~aAL~aL 52 (77)
+..+|.++-++-==|.=| ++|||.|...||..|||-+..|+..
T Consensus 218 ~l~lt~eqfidlcIL~GcDY~~gI~GIG~k~A~klIkk~~~ie~i~~~~ 266 (338)
T TIGR03674 218 ELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVLKAR 266 (338)
T ss_pred HCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHC
T ss_conf 7389999999999970875678999856899999999859999999865
No 28
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=81.44 E-value=1.7 Score=24.21 Aligned_cols=38 Identities=16% Similarity=0.159 Sum_probs=29.7
Q ss_pred HHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 86589689999999997499999999709999961455
Q gi|254780303|r 25 IRSDNISPATCRDMINYFGSAEQALEMIPELAQRGAVY 62 (77)
Q Consensus 25 ~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~rgG~~ 62 (77)
---++|||.....||.+|||-...-+|..+=...-|..
T Consensus 533 d~I~GiG~~r~~~LL~~Fgs~~~i~~As~eel~~vgi~ 570 (581)
T COG0322 533 DDIPGIGPKRRKALLKHFGSLKGIKSASVEELAKVGIS 570 (581)
T ss_pred CCCCCCCHHHHHHHHHHHHCHHHHHHCCHHHHHHCCCC
T ss_conf 04888688999999998317888885599999874999
No 29
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries the biological information that instructs cells how to exist in an ordered fashion. Accurate replication is thus one of the most important events in the cell life cycle. This function is mediated by DNA-directed DNA polymerases, which add nucleotide triphosphate (dNTP) residues to the 5'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. DNA-dependent DNA polymerases have been grouped into families, denoted A, B and X, on the basis of sequence similarities , . Members of family A, which includes bacterial and bacteriophage polymerases, share significant similarity to Escherichia coli polymerase I; hence family A is also known as the pol I family. The bacterial polymerases also contain an exonuclease activity, which is coded for in the N-terminal portion. Three motifs, A, B and C , are seen to be conserved across all DNA polymerases, with motifs A and C also seen in RNA polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (E. coli) structure. Motif A contains a strictly-conserved aspartate at the junction of a beta-strand and an alpha-helix; motif B contains an alpha-helix with positive charges; and motif C has a doublet of negative charges, located in a beta-turn-beta secondary structure .; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication.
Probab=76.56 E-value=2 Score=23.73 Aligned_cols=23 Identities=30% Similarity=0.473 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHHHHCCCHHHHHH
Q ss_conf 89689999999997499999999
Q gi|254780303|r 28 DNISPATCRDMINYFGSAEQALE 50 (77)
Q Consensus 28 ~~VGp~Tf~~Ll~~fGsA~aAL~ 50 (77)
++|||.|-..||+.|||=+..++
T Consensus 198 ~GIGeKTA~kLL~~fgsLe~iy~ 220 (1005)
T TIGR00593 198 KGIGEKTAAKLLQEFGSLENIYE 220 (1005)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 97376568999987210899998
No 30
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=74.60 E-value=3.7 Score=22.23 Aligned_cols=41 Identities=32% Similarity=0.436 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHH--C------CCCCHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 89999999999986--5------89689999999997499999999709
Q gi|254780303|r 13 LTDDQKISWLRLIR--S------DNISPATCRDMINYFGSAEQALEMIP 53 (77)
Q Consensus 13 ls~~erlawLRL~R--t------~~VGp~Tf~~Ll~~fGsA~aAL~aLP 53 (77)
++..+-++..=|.= | ++|||.|...||++|||-+...+.+-
T Consensus 181 ~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~ 229 (310)
T COG0258 181 LTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLD 229 (310)
T ss_pred CCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHH
T ss_conf 9989988999982965357899998389999999998385999998775
No 31
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=73.33 E-value=7.5 Score=20.51 Aligned_cols=50 Identities=22% Similarity=0.238 Sum_probs=34.0
Q ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHH-HHHHHHCC
Q ss_conf 7889999999999986589689999999997499999999709-99996145
Q gi|254780303|r 11 VSLTDDQKISWLRLIRSDNISPATCRDMINYFGSAEQALEMIP-ELAQRGAV 61 (77)
Q Consensus 11 ~~ls~~erlawLRL~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP-~la~rgG~ 61 (77)
-..|..|.. ---|.--||||+...++|+.+|||-+..+.|-. +|..--|.
T Consensus 172 ~~~t~~e~q-~~il~s~pgig~~~a~~ll~~fgS~~~~~tas~~eL~~v~gi 222 (254)
T COG1948 172 KAKTLKELQ-LYILESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVKGI 222 (254)
T ss_pred CCCCHHHHH-HHHHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHHCCC
T ss_conf 224557899-999970899648999999998568887765599999774484
No 32
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=69.45 E-value=3.2 Score=22.61 Aligned_cols=16 Identities=25% Similarity=0.480 Sum_probs=14.3
Q ss_pred CCCCCHHHHHHHHHHC
Q ss_conf 5896899999999974
Q gi|254780303|r 27 SDNISPATCRDMINYF 42 (77)
Q Consensus 27 t~~VGp~Tf~~Ll~~f 42 (77)
-++|||.|+.+||++|
T Consensus 21 V~GIG~ktA~~ll~~~ 36 (36)
T smart00279 21 VKGIGPKTALKLLREF 36 (36)
T ss_pred CCCCCHHHHHHHHHHC
T ss_conf 9974789999999859
No 33
>COG3675 Predicted lipase [Lipid metabolism]
Probab=66.30 E-value=1.8 Score=24.00 Aligned_cols=37 Identities=22% Similarity=0.431 Sum_probs=26.4
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 99999986589689999999997499999999709999
Q gi|254780303|r 19 ISWLRLIRSDNISPATCRDMINYFGSAEQALEMIPELA 56 (77)
Q Consensus 19 lawLRL~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la 56 (77)
-+||||.+.|+||-++|..++..|.--.++ |-+|++.
T Consensus 271 p~~lrLy~yprVGl~~fae~il~YR~vNn~-d~~p~~p 307 (332)
T COG3675 271 PTWLRLYRYPRVGLIRFAEYILMYRYVNNK-DFFPERP 307 (332)
T ss_pred CHHHEEECCCCCCCCCHHHHHHHHHHCCHH-HHCCCCC
T ss_conf 536501115543564167777777610444-4135555
No 34
>TIGR01091 upp uracil phosphoribosyltransferase; InterPro: IPR005765 The enzyme uracil phosphoribosyltransferase (UPRT, 2.4.2.9 from EC) catalyzes conversion of uracil to uridine 5'-monophosphate utilizing 5'-phosphoribosyl--1-pyrophosphate (PRPP). UMP + diphosphate = uracil + 5-phospho-alpha-D-ribose 1-diphosphate ; GO: 0004845 uracil phosphoribosyltransferase activity, 0006223 uracil salvage.
Probab=61.11 E-value=6 Score=21.08 Aligned_cols=27 Identities=22% Similarity=0.382 Sum_probs=23.7
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHCCCH
Q ss_conf 999999865896899999999974999
Q gi|254780303|r 19 ISWLRLIRSDNISPATCRDMINYFGSA 45 (77)
Q Consensus 19 lawLRL~Rt~~VGp~Tf~~Ll~~fGsA 45 (77)
-.||-++|..|.++..||.++..-|+-
T Consensus 13 ~hkLt~lR~~~T~~~~FR~~l~elg~l 39 (213)
T TIGR01091 13 KHKLTLLRDKNTDTKEFRELLRELGRL 39 (213)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 998756532789818999899999889
No 35
>TIGR01371 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; InterPro: IPR006276 This group represents cobalamin-independent methionine synthase. A family of uncharacterised archaeal proteins having substantial homology to the C-terminal region of this family, are not included in this group, though they are contained in a larger family of vitamin-B12 independent methionine synthase.; GO: 0003871 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity, 0009086 methionine biosynthetic process.
Probab=53.55 E-value=6.9 Score=20.73 Aligned_cols=46 Identities=20% Similarity=0.231 Sum_probs=34.3
Q ss_pred CCCCHHHHHHHHHHHHCCC-C-------CHHHHHHHHHHC-C------CHHHHHHHHHHHH
Q ss_conf 7889999999999986589-6-------899999999974-9------9999999709999
Q gi|254780303|r 11 VSLTDDQKISWLRLIRSDN-I-------SPATCRDMINYF-G------SAEQALEMIPELA 56 (77)
Q Consensus 11 ~~ls~~erlawLRL~Rt~~-V-------Gp~Tf~~Ll~~f-G------sA~aAL~aLP~la 56 (77)
..|+...-|+-++=+...| | ||+||-.|-..+ | .....++.||.|.
T Consensus 139 F~L~~~k~l~e~~eAk~~GG~~~~PVl~GP~TfL~L~K~~~g~~eWir~~~~~~~~l~~Ll 199 (778)
T TIGR01371 139 FKLTSNKPLEEYLEAKELGGIETKPVLLGPITFLKLSKAKKGSDEWIREEFEPLELLEKLL 199 (778)
T ss_pred EEECCCHHHHHHHHHHHCCCCCEEEEEECCHHHHHHHCCCCCCHHHHCCCCHHHHHHHHHH
T ss_conf 4324000589999999708954233687302433331123553122237200799989999
No 36
>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family; InterPro: IPR006001 This family of proteins includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases (IPR000577 from INTERPRO).; GO: 0016301 kinase activity, 0005975 carbohydrate metabolic process.
Probab=52.18 E-value=7.3 Score=20.58 Aligned_cols=19 Identities=32% Similarity=0.796 Sum_probs=15.9
Q ss_pred CCCCCCCHHHHHHHHHHHH
Q ss_conf 2487889999999999986
Q gi|254780303|r 8 KGGVSLTDDQKISWLRLIR 26 (77)
Q Consensus 8 ~~~~~ls~~erlawLRL~R 26 (77)
..|.=|||++|..||....
T Consensus 47 s~GiPL~DdDR~pWL~~l~ 65 (175)
T TIGR01313 47 SRGIPLNDDDRWPWLKNLA 65 (175)
T ss_pred CCCCCCCCCCCHHHHHHHH
T ss_conf 1788887012043799999
No 37
>cd03312 CIMS_N_terminal_like CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers the N-terminal barrel, and a few single-barrel sequences most similar to the N-terminal barrel. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Side chains fro
Probab=43.38 E-value=13 Score=19.25 Aligned_cols=45 Identities=13% Similarity=0.192 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHHHHHHCCC-------CCHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 7889999999999986589-------68999999999749999999970999
Q gi|254780303|r 11 VSLTDDQKISWLRLIRSDN-------ISPATCRDMINYFGSAEQALEMIPEL 55 (77)
Q Consensus 11 ~~ls~~erlawLRL~Rt~~-------VGp~Tf~~Ll~~fGsA~aAL~aLP~l 55 (77)
..++...-++-.+-+..-+ |||+||-.|-...+.....++.|++|
T Consensus 129 f~l~~~~~l~e~~eAk~~g~~~kPvLvGPvTfL~LsK~~~~~~~~~~~l~~L 180 (360)
T cd03312 129 FKLASNKLLDEYLEAKALGINTKPVLLGPVTFLKLSKAKGGGFDRLSLLDKL 180 (360)
T ss_pred EECCCCHHHHHHHHHHHCCCCCCCEEECHHHHHHHHCCCCCCCCHHHHHHHH
T ss_conf 3035407899999999869988757974489988742247887989999999
No 38
>pfam11662 DUF3263 Protein of unknown function (DUF3263). This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=43.06 E-value=25 Score=17.54 Aligned_cols=38 Identities=24% Similarity=0.251 Sum_probs=32.2
Q ss_pred HHHHCC-CCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHC
Q ss_conf 998658-96899999999974999999997099999614
Q gi|254780303|r 23 RLIRSD-NISPATCRDMINYFGSAEQALEMIPELAQRGA 60 (77)
Q Consensus 23 RL~Rt~-~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~rgG 60 (77)
+-||.. ++.|+-|+++|+..=.-.+||++-|-+.+|--
T Consensus 26 ~AIRe~fglS~~rYYQ~LN~LiD~p~Ala~dP~lV~RLr 64 (77)
T pfam11662 26 QAIRELFGLSSTRYYQLLNALIDTPAALAYDPMLVKRLR 64 (77)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHCCHHHHHHCCHHHHHHH
T ss_conf 999999788889999999998688988886969999999
No 39
>PRK11545 gntK gluconate kinase 1; Provisional
Probab=42.85 E-value=21 Score=17.98 Aligned_cols=19 Identities=32% Similarity=0.746 Sum_probs=16.6
Q ss_pred CCCCCCCHHHHHHHHHHHH
Q ss_conf 2487889999999999986
Q gi|254780303|r 8 KGGVSLTDDQKISWLRLIR 26 (77)
Q Consensus 8 ~~~~~ls~~erlawLRL~R 26 (77)
.+|+-|+|++|..||.-++
T Consensus 52 ~~GiPLtD~DR~pWL~~l~ 70 (177)
T PRK11545 52 ASGEPLNDDDRKPWLQALN 70 (177)
T ss_pred HCCCCCCHHHHHHHHHHHH
T ss_conf 2899998688899999999
No 40
>KOG1720 consensus
Probab=41.56 E-value=34 Score=16.79 Aligned_cols=32 Identities=25% Similarity=0.480 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHHHHHHCCC-CCHHHHHHHHHHC
Q ss_conf 7889999999999986589-6899999999974
Q gi|254780303|r 11 VSLTDDQKISWLRLIRSDN-ISPATCRDMINYF 42 (77)
Q Consensus 11 ~~ls~~erlawLRL~Rt~~-VGp~Tf~~Ll~~f 42 (77)
-.||..|-++|||-.|.-- |||.-.+.+.+..
T Consensus 173 ~g~ta~eaI~~lR~~RpG~V~gpqQ~~l~~~q~ 205 (225)
T KOG1720 173 YGMTAGEAIAWLRICRPGAVIGPQQHKLLHKQR 205 (225)
T ss_pred HCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf 678999999999961886644778999999999
No 41
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=38.46 E-value=20 Score=18.16 Aligned_cols=35 Identities=20% Similarity=0.332 Sum_probs=22.3
Q ss_pred CCCCCHHHHHHHHHH-CCCHHH-HHHHHHHHHHHHCC
Q ss_conf 589689999999997-499999-99970999996145
Q gi|254780303|r 27 SDNISPATCRDMINY-FGSAEQ-ALEMIPELAQRGAV 61 (77)
Q Consensus 27 t~~VGp~Tf~~Ll~~-fGsA~a-AL~aLP~la~rgG~ 61 (77)
=|||||.|-.+|... |.+-++ |..-.-||+.-.|.
T Consensus 5 LPGVGp~TA~KL~EaGy~t~~~iA~A~~~EL~~~~gI 41 (333)
T TIGR02236 5 LPGVGPATAEKLREAGYDTLEAIAVASPKELSEIAGI 41 (333)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCC
T ss_conf 7897576889988610788999844585795320378
No 42
>PRK09825 idnK D-gluconate kinase; Provisional
Probab=37.41 E-value=28 Score=17.30 Aligned_cols=20 Identities=30% Similarity=0.870 Sum_probs=16.5
Q ss_pred CCCCCCCCHHHHHHHHHHHH
Q ss_conf 12487889999999999986
Q gi|254780303|r 7 LKGGVSLTDDQKISWLRLIR 26 (77)
Q Consensus 7 ~~~~~~ls~~erlawLRL~R 26 (77)
...|+-|+|++|..||.-++
T Consensus 46 M~~GiPL~D~DR~pWL~~l~ 65 (176)
T PRK09825 46 MSQGIPLTDEDRLPWLERLN 65 (176)
T ss_pred HHCCCCCCHHHHHHHHHHHH
T ss_conf 86899988667999999999
No 43
>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]
Probab=37.22 E-value=19 Score=18.18 Aligned_cols=21 Identities=29% Similarity=0.783 Sum_probs=17.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHC
Q ss_conf 124878899999999999865
Q gi|254780303|r 7 LKGGVSLTDDQKISWLRLIRS 27 (77)
Q Consensus 7 ~~~~~~ls~~erlawLRL~Rt 27 (77)
..+|+-|+|++|.-||..++.
T Consensus 38 M~~GiPL~DdDR~pWL~~l~~ 58 (161)
T COG3265 38 MSAGIPLNDDDRWPWLEALGD 58 (161)
T ss_pred HHCCCCCCCCHHHHHHHHHHH
T ss_conf 727998984112479999999
No 44
>TIGR02169 SMC_prok_A chromosome segregation protein SMC; InterPro: IPR011891 The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases . All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by IPR011890 from INTERPRO. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent ..
Probab=35.80 E-value=18 Score=18.35 Aligned_cols=28 Identities=18% Similarity=0.149 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf 7889999999999986589689999999
Q gi|254780303|r 11 VSLTDDQKISWLRLIRSDNISPATCRDM 38 (77)
Q Consensus 11 ~~ls~~erlawLRL~Rt~~VGp~Tf~~L 38 (77)
|-=+|..--.|+.+++..++||.||-=|
T Consensus 581 VV~dd~vA~~aI~~LK~~k~GRaTFLPL 608 (1202)
T TIGR02169 581 VVEDDAVAKEAIELLKRRKAGRATFLPL 608 (1202)
T ss_pred EECCHHHHHHHHHHHHHCCCCCCCCCCH
T ss_conf 4157589999999999707898765661
No 45
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=33.78 E-value=46 Score=16.07 Aligned_cols=34 Identities=15% Similarity=0.255 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCH
Q ss_conf 8899999999999865896899999999974999
Q gi|254780303|r 12 SLTDDQKISWLRLIRSDNISPATCRDMINYFGSA 45 (77)
Q Consensus 12 ~ls~~erlawLRL~Rt~~VGp~Tf~~Ll~~fGsA 45 (77)
.++.+||--...|+--.+|||.+.-.+|..++..
T Consensus 63 F~~~~Er~~F~~Li~V~GIGpK~AL~ILs~~~~~ 96 (198)
T PRK00116 63 FLTKEERELFRLLISVSGVGPKLALAILSGLSPE 96 (198)
T ss_pred ECCHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHH
T ss_conf 0888999999998566885789999887029999
No 46
>TIGR00831 a_cpa1 Na+/H+ antiporter; InterPro: IPR004705 Na^+/H^+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na^+/H^+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na^+ for H^+ in an electroneutral manner, and this activity is carried out by a family of Na^+/H^+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. In mammalian cells, Na^+/H^+ exchange activity is found in both the plasma membrane and inner mitochondrial membrane. To date, six mammalian isoforms have been identified (designated NHE1-NHE6) , . These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity with other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the region that is involved in the transport of sodium and hydrogen ions. The cytoplasmic region has little similarity throughout the family. There is some evidence that the exchangers may exist in the cell membrane as homodimers, but little is currently known about the mechanism of their antiport . This group is specific for the bacterial members of this family. .
Probab=31.22 E-value=27 Score=17.39 Aligned_cols=28 Identities=21% Similarity=0.137 Sum_probs=22.8
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 9999999749999999970999996145
Q gi|254780303|r 34 TCRDMINYFGSAEQALEMIPELAQRGAV 61 (77)
Q Consensus 34 Tf~~Ll~~fGsA~aAL~aLP~la~rgG~ 61 (77)
.-..-|+|+-||+.|+.+|+....+++.
T Consensus 426 ~~Ee~iAR~~~A~~A~~al~k~~e~l~a 453 (541)
T TIGR00831 426 EKEERIARAIAARAALVALQKVVERLAA 453 (541)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 9999999999999999998879973046
No 47
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=30.94 E-value=37 Score=16.60 Aligned_cols=33 Identities=18% Similarity=0.302 Sum_probs=23.6
Q ss_pred HCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 658968999999999749999999970999996145
Q gi|254780303|r 26 RSDNISPATCRDMINYFGSAEQALEMIPELAQRGAV 61 (77)
Q Consensus 26 Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~rgG~ 61 (77)
-||++|-.|+..+|+.+|---.-+- ++++.-|.
T Consensus 7 GTPGvGKTT~~~~L~~lg~~~i~l~---el~~e~~~ 39 (180)
T COG1936 7 GTPGVGKTTVCKLLRELGYKVIELN---ELAKENGL 39 (180)
T ss_pred CCCCCCHHHHHHHHHHHCCCEEEHH---HHHHHCCC
T ss_conf 7999866879999998298466199---99986697
No 48
>PRK09767 hypothetical protein; Provisional
Probab=27.45 E-value=21 Score=17.99 Aligned_cols=26 Identities=27% Similarity=0.427 Sum_probs=20.8
Q ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf 788999999999998658968999999
Q gi|254780303|r 11 VSLTDDQKISWLRLIRSDNISPATCRD 37 (77)
Q Consensus 11 ~~ls~~erlawLRL~Rt~~VGp~Tf~~ 37 (77)
-.||++|++=| ..+|...+|...|++
T Consensus 13 ~~~T~aE~~LW-~~LR~~~l~g~kFrR 38 (116)
T PRK09767 13 RNLTLQERKLW-RYLRSRRFGDFKFRR 38 (116)
T ss_pred CCCCHHHHHHH-HHHHHCCCCCCEEEE
T ss_conf 16999999999-999846768980573
No 49
>pfam07684 NODP NOTCH protein. NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. The role of the NOD and NODP domains remains to be elucidated.
Probab=27.24 E-value=28 Score=17.27 Aligned_cols=33 Identities=21% Similarity=0.247 Sum_probs=27.6
Q ss_pred HHCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHH
Q ss_conf 974999999997099999614558876789899
Q gi|254780303|r 40 NYFGSAEQALEMIPELAQRGAVYAGKRAFVQKN 72 (77)
Q Consensus 40 ~~fGsA~aAL~aLP~la~rgG~~~~~ri~s~~~ 72 (77)
+.|.+|..|.+-|-..+.+++...++-|.+...
T Consensus 22 ~CF~~a~~aA~fLaA~a~~~~L~~~~pI~~v~s 54 (62)
T pfam07684 22 ECFWSAQSAAAFLAALAAKGGLDTPYPISSVRS 54 (62)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEC
T ss_conf 556469999999999986456788862688525
No 50
>pfam09012 FeoC FeoC like transcriptional regulator. This family contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependant transcriptional repressor.
Probab=26.68 E-value=49 Score=15.91 Aligned_cols=32 Identities=19% Similarity=0.182 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf 68999999999749999999970999996145
Q gi|254780303|r 30 ISPATCRDMINYFGSAEQALEMIPELAQRGAV 61 (77)
Q Consensus 30 VGp~Tf~~Ll~~fGsA~aAL~aLP~la~rgG~ 61 (77)
=|.+++.+|-.+|+....++++.=+.-.+-|+
T Consensus 12 ~g~~s~~~Ls~~f~~~~~~v~~ML~~wi~kGk 43 (68)
T pfam09012 12 RGRASLAELARHFKMSPDAVEAMLEVWIRKGK 43 (68)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCC
T ss_conf 19847999998979399999999999998797
No 51
>cd01079 NAD_bind_m-THF_DH NAD binding domain of methylene-tetrahydrofolate dehydrogenase. The NAD-binding domain of methylene-tetrahydrofolate dehydrogenase (m-THF DH). M-THF is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. M-THF DH is a component of an unusual monofunctional enzyme; in eukaryotes, m-THF DH is typically found as part of a multifunctional protein. NADP-dependent m-THF DHs in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional DH/cyclodrolase form. In bacteria, monofunctional DH, as well as bifunctional DH/cyclodrolase are found. In addition, yeast (S. cerevisiae) also express an monofunctional DH. This family contains only the monofunctional
Probab=24.74 E-value=52 Score=15.77 Aligned_cols=22 Identities=18% Similarity=0.160 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 99999999986589689999999997
Q gi|254780303|r 16 DQKISWLRLIRSDNISPATCRDMINY 41 (77)
Q Consensus 16 ~erlawLRL~Rt~~VGp~Tf~~Ll~~ 41 (77)
.+.-.|+ ||.|||+|-.-||..
T Consensus 166 ~~~a~~i----tPvVGPmTvAmLl~N 187 (197)
T cd01079 166 KEKASIY----VPSIGKVTIAMLLRN 187 (197)
T ss_pred HHCCCEE----CCCCCHHHHHHHHHH
T ss_conf 3003133----898898999999999
No 52
>KOG3354 consensus
Probab=24.70 E-value=27 Score=17.41 Aligned_cols=18 Identities=39% Similarity=0.890 Sum_probs=15.0
Q ss_pred CCCCCCCHHHHHHHHHHH
Q ss_conf 248788999999999998
Q gi|254780303|r 8 KGGVSLTDDQKISWLRLI 25 (77)
Q Consensus 8 ~~~~~ls~~erlawLRL~ 25 (77)
.+|+-|+|++|..||.-+
T Consensus 56 ~~GipLnD~DR~pWL~~i 73 (191)
T KOG3354 56 TQGIPLNDDDRWPWLKKI 73 (191)
T ss_pred HCCCCCCCCCCCHHHHHH
T ss_conf 369988853211799999
No 53
>COG0035 Upp Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=24.41 E-value=56 Score=15.57 Aligned_cols=39 Identities=18% Similarity=0.264 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC--HHHHHHHH
Q ss_conf 9999999999986589689999999997499--99999970
Q gi|254780303|r 14 TDDQKISWLRLIRSDNISPATCRDMINYFGS--AEQALEMI 52 (77)
Q Consensus 14 s~~erlawLRL~Rt~~VGp~Tf~~Ll~~fGs--A~aAL~aL 52 (77)
+.-.-..+|-.+|..+.|+..|+.++.+-|+ +-+|.+.|
T Consensus 8 ~hpli~~~lt~lRdk~t~~~~Fr~~~~ei~~lL~yEa~~~l 48 (210)
T COG0035 8 DHPLVKHKLTILRDKNTGTKEFRELLDEIGRLLAYEATRDL 48 (210)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 72999989999981489918999999999999999985768
No 54
>KOG1223 consensus
Probab=23.21 E-value=6.5 Score=20.87 Aligned_cols=58 Identities=17% Similarity=0.092 Sum_probs=42.2
Q ss_pred CCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHH
Q ss_conf 48788999999999998658968999999999749999999970999996145588767898997
Q gi|254780303|r 9 GGVSLTDDQKISWLRLIRSDNISPATCRDMINYFGSAEQALEMIPELAQRGAVYAGKRAFVQKNQ 73 (77)
Q Consensus 9 ~~~~ls~~erlawLRL~Rt~~VGp~Tf~~Ll~~fGsA~aAL~aLP~la~rgG~~~~~ri~s~~~A 73 (77)
.-.++||...++|+|-+|+ |+|-+|.--|+.-| ..+..+-|++.-+.- ..|||+..-|
T Consensus 259 r~~r~td~~p~~~~~~lr~--vn~s~y~f~lq~~~--~i~ia~sPE~L~~~~---~~ri~~~~lA 316 (508)
T KOG1223 259 RIERLTDADPFNAYRALRI--VNPSPYMFYLQPRG--CIFIANSPERLCKSK---FGRILNRPLA 316 (508)
T ss_pred EEECCCCCCHHHHHHHHHH--CCCCCEEEEECCCC--CEEECCCHHHHHHHH---CCCEEEHHHH
T ss_conf 0200144352999999974--28995289982798--226628878999874---4764302120
No 55
>TIGR01828 pyru_phos_dikin pyruvate, phosphate dikinase; InterPro: IPR010121 Pyruvate phosphate dikinase (PPDK, or pyruvate orthophosphate dikinase) is found in plants, bacteria and archaea. The amino acid sequence identity between bacterial and plant enzymes is high, and they are similar in sequence to other PEP-utilizing enzymes. PPDK catalyses the reversible conversion of ATP and pyruvate to AMP and PEP (phosphoenolpyruvate). In bacteria such as Clostridium symbiosum, PPDK uses Mg2+ and NH4+ ions as cofactors . The enzyme has three domains: the N- and C-terminal domains each have an active site centre that catalyses a different step in the reaction, and the middle domain has a carrier histidine residue that moves between the two active centres. In plants, PPDK is localised predominantly in chloroplast stroma where it catalyses the rate-limiting step in the C4 photosynthetic pathway, namely the synthesis of PEP, which acts as the primary CO2 acceptor in C4 photosynthesis . PPDK activity in C4 plants is strictly regulated by light, its activity decreasing in darkness. This response is regulated by phosphorylation and dephosphorylation of the enzyme using ADP; such regulation is not seen in the bacterial form of the enzyme. PPDK is also found in C3 plants, but it is not known to have a photosynthetic role .; GO: 0050242 pyruvate phosphate dikinase activity.
Probab=23.17 E-value=31 Score=17.00 Aligned_cols=24 Identities=25% Similarity=0.599 Sum_probs=18.3
Q ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCH
Q ss_conf 78899999999999865896899999999974999
Q gi|254780303|r 11 VSLTDDQKISWLRLIRSDNISPATCRDMINYFGSA 45 (77)
Q Consensus 11 ~~ls~~erlawLRL~Rt~~VGp~Tf~~Ll~~fGsA 45 (77)
..+|.++|+|| -+|||+|+-||+-
T Consensus 126 A~~tgn~RFAy-----------DSYRRFiqMFG~v 149 (920)
T TIGR01828 126 AKLTGNARFAY-----------DSYRRFIQMFGDV 149 (920)
T ss_pred HHCCCCCCHHH-----------HHHHHHHHHHHHH
T ss_conf 61468842256-----------8778898842014
No 56
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=23.08 E-value=72 Score=14.96 Aligned_cols=32 Identities=19% Similarity=0.340 Sum_probs=23.7
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCC
Q ss_conf 88999999999998658968999999999749
Q gi|254780303|r 12 SLTDDQKISWLRLIRSDNISPATCRDMINYFG 43 (77)
Q Consensus 12 ~ls~~erlawLRL~Rt~~VGp~Tf~~Ll~~fG 43 (77)
..+.+||--+..|+...+|||.+--.+|+-+.
T Consensus 63 F~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~ 94 (201)
T COG0632 63 FLTEEERELFRLLISVNGIGPKLALAILSNLD 94 (201)
T ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHCCCC
T ss_conf 99889999999987118805899999984899
No 57
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=22.98 E-value=42 Score=16.30 Aligned_cols=21 Identities=19% Similarity=0.447 Sum_probs=17.5
Q ss_pred HHHHCCCCCHHHHHHHHHHCC
Q ss_conf 998658968999999999749
Q gi|254780303|r 23 RLIRSDNISPATCRDMINYFG 43 (77)
Q Consensus 23 RL~Rt~~VGp~Tf~~Ll~~fG 43 (77)
.|..-++||+.+..+++....
T Consensus 2 ~L~~v~GIG~k~A~~ll~~~~ 22 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAXX 22 (26)
T ss_pred CCCCCCCCCCHHHHHHHHHHH
T ss_conf 210179988115999999762
No 58
>pfam01474 DAHP_synth_2 Class-II DAHP synthetase family. Members of this family are aldolase enzymes that catalyse the first step of the shikimate pathway.
Probab=22.23 E-value=52 Score=15.75 Aligned_cols=49 Identities=27% Similarity=0.400 Sum_probs=35.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHCCCC-CHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 124878899999999999865896-89999999997499999999709999961
Q gi|254780303|r 7 LKGGVSLTDDQKISWLRLIRSDNI-SPATCRDMINYFGSAEQALEMIPELAQRG 59 (77)
Q Consensus 7 ~~~~~~ls~~erlawLRL~Rt~~V-Gp~Tf~~Ll~~fGsA~aAL~aLP~la~rg 59 (77)
+|.|++++.+|.+..++.+--.|. |-.| ||.|||. ..+-+.||.|.+.-
T Consensus 285 vKvGP~~~~~el~~l~~~LnP~~epGRlt---LI~RmGa-~~v~~~LP~li~aV 334 (437)
T pfam01474 285 VKVGPSTTPDELLRLIDRLNPDNEPGRLT---LITRMGA-DKVREVLPPLIRAV 334 (437)
T ss_pred EEECCCCCHHHHHHHHHHHCCCCCCCEEE---EEECCCH-HHHHHHHHHHHHHH
T ss_conf 66799999999999999739888997399---9852671-78987729999999
No 59
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional
Probab=22.08 E-value=75 Score=14.85 Aligned_cols=32 Identities=19% Similarity=0.282 Sum_probs=20.8
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHHHCC
Q ss_conf 88999999999998658968999999999749
Q gi|254780303|r 12 SLTDDQKISWLRLIRSDNISPATCRDMINYFG 43 (77)
Q Consensus 12 ~ls~~erlawLRL~Rt~~VGp~Tf~~Ll~~fG 43 (77)
..+.+||--+..|+--.+|||.+.-.+|..+.
T Consensus 62 F~~~~Er~~F~~LisVsGIGpk~Al~iLs~~~ 93 (196)
T PRK13901 62 FLNSSEREVFEELIGVDGIGPRAALRVLSGIK 93 (196)
T ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHCCCC
T ss_conf 59889999999987658826899999975799
No 60
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=21.76 E-value=76 Score=14.81 Aligned_cols=28 Identities=14% Similarity=0.217 Sum_probs=21.3
Q ss_pred CCCCCHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 5896899999999974999999997099
Q gi|254780303|r 27 SDNISPATCRDMINYFGSAEQALEMIPE 54 (77)
Q Consensus 27 t~~VGp~Tf~~Ll~~fGsA~aAL~aLP~ 54 (77)
-++||.+|-..|..+|+|=.+-.+|--|
T Consensus 526 Ir~VG~~~A~~La~~f~tl~~L~~A~~e 553 (706)
T TIGR00575 526 IRHVGEVTAKLLAKHFGTLDKLKAASLE 553 (706)
T ss_pred CHHHHHHHHHHHHHHCCCHHHHHHCCHH
T ss_conf 6035799999999855886899850821
Done!