Query gi|254780469|ref|YP_003064882.1| zinc-binding protein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 63 No_of_seqs 121 out of 410 Neff 4.0 Searched_HMMs 39220 Date Sun May 29 17:33:56 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780469.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK00418 zinc-binding protein; 99.9 6.6E-23 1.7E-27 151.7 3.7 54 7-60 3-60 (62) 2 pfam03884 DUF329 Domain of unk 99.9 2E-22 5.2E-27 149.0 3.7 49 9-57 1-53 (57) 3 PRK01343 zinc-binding protein; 99.8 1E-21 2.7E-26 144.9 3.7 50 8-57 7-56 (56) 4 COG3024 Uncharacterized protei 99.8 1.4E-21 3.5E-26 144.2 3.3 49 7-55 4-56 (65) 5 pfam09889 DUF2116 Uncharacteri 91.1 0.12 3.1E-06 31.3 1.8 24 11-35 4-27 (59) 6 COG4068 Uncharacterized protei 90.7 0.13 3.3E-06 31.2 1.7 24 11-35 9-32 (64) 7 pfam10013 DUF2256 Uncharacteri 88.3 0.29 7.5E-06 29.2 2.0 24 11-34 9-40 (42) 8 COG4338 Uncharacterized protei 80.4 0.33 8.5E-06 28.8 -0.7 29 11-39 13-49 (54) 9 pfam04640 PLATZ PLATZ transcri 69.2 1.8 4.7E-05 24.6 0.7 30 4-34 43-72 (72) 10 pfam10071 DUF2310 Zn-ribbon-co 67.7 1.6 4.1E-05 25.0 0.2 35 6-40 217-256 (259) 11 LOAD_FCS consensus 64.2 2.8 7E-05 23.6 0.8 28 7-34 3-38 (40) 12 pfam11023 DUF2614 Protein of u 62.2 3.4 8.7E-05 23.1 1.0 17 5-21 64-80 (114) 13 pfam04945 YHS YHS domain. This 61.2 2.9 7.4E-05 23.5 0.5 22 14-35 1-32 (44) 14 PRK02935 hypothetical protein; 61.1 3.7 9.4E-05 22.9 1.0 17 5-21 64-80 (117) 15 TIGR00354 polC DNA polymerase 58.0 2.7 6.8E-05 23.7 -0.1 29 10-38 679-707 (1173) 16 PRK05776 DNA topoisomerase III 57.1 6.5 0.00017 21.5 1.7 28 10-39 602-629 (675) 17 TIGR01405 polC_Gram_pos DNA po 55.7 6.2 0.00016 21.7 1.4 39 6-46 738-786 (1264) 18 COG2260 Predicted Zn-ribbon RN 52.6 7.8 0.0002 21.1 1.5 17 8-24 15-31 (59) 19 pfam04135 Nop10p Nucleolar RNA 51.6 7.3 0.00019 21.3 1.3 18 7-24 14-31 (53) 20 KOG0978 consensus 50.7 5.8 0.00015 21.8 0.6 21 6-26 674-695 (698) 21 PRK05638 threonine synthase; V 50.5 7.5 0.00019 21.2 1.2 24 9-34 1-24 (443) 22 PRK13130 H/ACA RNA-protein com 50.4 8.7 0.00022 20.8 1.5 17 8-24 15-31 (54) 23 KOG2879 consensus 47.5 9.8 0.00025 20.5 1.4 22 3-24 232-253 (298) 24 pfam06467 zf-FCS MYM-type Zinc 41.0 9.9 0.00025 20.5 0.6 28 7-34 3-39 (41) 25 PRK00415 rps27e 30S ribosomal 40.6 15 0.00038 19.5 1.4 19 2-20 3-21 (59) 26 PTZ00083 40S ribosomal protein 38.2 16 0.00041 19.3 1.3 20 1-20 26-45 (85) 27 CHL00174 accD acetyl-CoA carbo 36.4 14 0.00037 19.6 0.8 15 6-20 44-58 (305) 28 COG2176 PolC DNA polymerase II 35.6 18 0.00047 19.0 1.3 41 4-46 933-981 (1444) 29 pfam12156 ATPase-cat_bd Putati 35.2 28 0.00071 18.0 2.1 26 11-36 1-36 (88) 30 smart00746 TRASH metallochaper 34.3 17 0.00043 19.2 0.9 22 13-34 1-33 (39) 31 pfam04159 NB NB glycoprotein. 33.0 14 0.00036 19.6 0.3 15 10-32 59-73 (100) 32 pfam04423 Rad50_zn_hook Rad50 32.4 13 0.00033 19.9 0.0 14 11-24 21-34 (54) 33 COG3350 Uncharacterized conser 32.3 21 0.00054 18.7 1.1 27 9-35 1-38 (53) 34 cd01057 AAMH_A Aromatic and Al 30.8 28 0.00071 18.0 1.5 38 7-46 377-430 (465) 35 pfam10122 Mu-like_Com Mu-like 30.7 22 0.00055 18.6 1.0 16 4-19 18-33 (51) 36 pfam05573 NosL NosL. NosL is o 29.7 29 0.00074 17.9 1.5 27 11-37 17-57 (140) 37 PHA00732 hypothetical protein 29.4 7.6 0.00019 21.2 -1.6 38 10-49 27-66 (79) 38 TIGR00538 hemN oxygen-independ 28.7 16 0.0004 19.4 -0.1 11 22-32 55-65 (462) 39 pfam04570 DUF581 Protein of un 28.3 29 0.00075 17.8 1.3 27 9-35 16-50 (59) 40 pfam09986 DUF2225 Uncharacteri 27.9 24 0.0006 18.4 0.8 10 10-19 48-57 (214) 41 pfam02891 zf-MIZ MIZ/SP-RING z 27.2 25 0.00065 18.2 0.8 12 11-22 3-14 (50) 42 PRK08173 DNA topoisomerase III 26.5 18 0.00047 19.0 -0.0 27 5-32 619-646 (857) 43 TIGR02300 FYDLN_acid conserved 25.9 26 0.00066 18.1 0.7 45 1-46 1-47 (157) 44 KOG3362 consensus 25.8 34 0.00086 17.5 1.2 33 3-35 111-147 (156) 45 KOG4317 consensus 25.0 27 0.00069 18.0 0.6 24 9-32 6-34 (383) 46 PRK05978 hypothetical protein; 24.2 26 0.00065 18.2 0.4 14 7-20 31-44 (149) 47 pfam10571 UPF0547 Uncharacteri 24.1 38 0.00097 17.2 1.2 19 11-29 1-21 (26) 48 PRK07379 coproporphyrinogen II 23.9 19 0.00049 18.9 -0.3 17 23-39 15-31 (399) 49 PRK08446 coproporphyrinogen II 23.6 21 0.00053 18.7 -0.2 15 24-38 6-20 (351) 50 PRK05799 coproporphyrinogen II 23.4 19 0.00049 18.9 -0.4 17 24-40 9-25 (374) 51 pfam01667 Ribosomal_S27e Ribos 23.4 36 0.00093 17.3 1.0 16 5-20 2-17 (55) 52 smart00734 ZnF_Rad18 Rad18-lik 23.0 19 0.00048 18.9 -0.5 11 10-20 1-11 (26) 53 cd00729 rubredoxin_SM Rubredox 22.5 35 0.00089 17.4 0.8 10 11-20 19-28 (34) 54 PRK05628 coproporphyrinogen II 22.3 23 0.00058 18.5 -0.2 17 24-40 8-24 (376) 55 PRK06294 coproporphyrinogen II 21.9 22 0.00057 18.5 -0.3 17 23-39 11-27 (374) 56 PRK08208 coproporphyrinogen II 21.5 23 0.00057 18.5 -0.3 16 24-39 51-66 (436) 57 pfam12230 PRP21_like_P Pre-mRN 21.3 48 0.0012 16.6 1.3 13 8-20 160-172 (223) 58 cd00350 rubredoxin_like Rubred 20.9 39 0.001 17.1 0.8 10 11-20 18-27 (33) 59 KOG0801 consensus 20.9 36 0.00092 17.3 0.6 10 11-20 139-148 (205) 60 PRK09057 coproporphyrinogen II 20.7 24 0.00062 18.3 -0.3 16 24-39 10-25 (381) 61 PRK06582 coproporphyrinogen II 20.7 25 0.00063 18.3 -0.3 17 23-39 16-32 (390) 62 PRK13347 coproporphyrinogen II 20.5 27 0.00068 18.1 -0.2 20 23-42 55-74 (453) 63 pfam06827 zf-FPG_IleRS Zinc fi 20.0 40 0.001 17.1 0.7 25 11-35 2-30 (30) No 1 >PRK00418 zinc-binding protein; Reviewed Probab=99.87 E-value=6.6e-23 Score=151.73 Aligned_cols=54 Identities=31% Similarity=0.681 Sum_probs=48.1 Q ss_pred CCEECCCCCCCCCC----CCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHH Q ss_conf 63044568887877----7886876107774433565308983035788886687143 Q gi|254780469|r 7 RSLKSICPECRKGS----MVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEEEVK 60 (63) Q Consensus 7 k~~k~~CP~C~k~~----~~~~rPFCS~RC~~iDLg~W~~e~Y~Ip~~~~~~~~~e~~ 60 (63) +.++++||+|++++ +|+||||||+|||+||||+||+|+|+||++..++++++.. T Consensus 3 ~~~~V~CP~C~~~v~w~~~n~~RPFCS~RCkliDLG~Wa~E~y~Ip~~~~~~~~dd~~ 60 (62) T PRK00418 3 EPITVNCPTCGKPVEWGEISPFRPFCSKRCQLIDLGEWAAEEKRIPSSGDLSESDDWS 60 (62) T ss_pred CCCEEECCCCCCCCCCCCCCCCCCCHHHHHHCCHHHHHHCCCCCCCCCCCCCCCCCCC T ss_conf 9727479899895445778886873457760340777755574477989888642322 No 2 >pfam03884 DUF329 Domain of unknown function (DUF329). The function of this short domain is unknown it contains four conserved cysteines and may therefore be involved in zinc binding. Probab=99.85 E-value=2e-22 Score=148.96 Aligned_cols=49 Identities=41% Similarity=0.849 Sum_probs=42.7 Q ss_pred EECCCCCCCCCC----CCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC Q ss_conf 044568887877----7886876107774433565308983035788886687 Q gi|254780469|r 9 LKSICPECRKGS----MVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEE 57 (63) Q Consensus 9 ~k~~CP~C~k~~----~~~~rPFCS~RC~~iDLg~W~~e~Y~Ip~~~~~~~~~ 57 (63) |+++||+|+|++ +++||||||+||++||||+||+|+|+||+++.+++.+ T Consensus 1 m~v~CP~C~k~~~~~~~~~~rPFCS~RC~~iDLg~W~~e~y~Ip~~~~~~~~~ 53 (57) T pfam03884 1 MTVKCPTCGKPVVWSEENPFRPFCSERCKLIDLGAWASEEYRIPGEPDDEDEE 53 (57) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCC T ss_conf 94268699897555766886884037775310889866783367989887433 No 3 >PRK01343 zinc-binding protein; Provisional Probab=99.84 E-value=1e-21 Score=144.94 Aligned_cols=50 Identities=52% Similarity=1.058 Sum_probs=45.4 Q ss_pred CEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC Q ss_conf 30445688878777886876107774433565308983035788886687 Q gi|254780469|r 8 SLKSICPECRKGSMVEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKSEE 57 (63) Q Consensus 8 ~~k~~CP~C~k~~~~~~rPFCS~RC~~iDLg~W~~e~Y~Ip~~~~~~~~~ 57 (63) ..+..||+|+|++++.||||||+||++||||+||+|+|+||+.+.+++++ T Consensus 7 ~~~~~CPiC~k~~~~~~rPFCS~RC~~iDLgrWl~g~Y~IP~~~~~~ddE 56 (56) T PRK01343 7 RPTRPCPECGKPSTREAYPFCSERCRDVDLNRWLSGSYVIPGAPDEEDDE 56 (56) T ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC T ss_conf 89998988899774444773436672635889865861357988676677 No 4 >COG3024 Uncharacterized protein conserved in bacteria [Function unknown] Probab=99.83 E-value=1.4e-21 Score=144.24 Aligned_cols=49 Identities=35% Similarity=0.807 Sum_probs=42.5 Q ss_pred CCEECCCCCCCCCCC----CCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCC Q ss_conf 630445688878777----8868761077744335653089830357888866 Q gi|254780469|r 7 RSLKSICPECRKGSM----VEFYPFCSTQCRSIDLSRWLHGEYVIAAVEDEKS 55 (63) Q Consensus 7 k~~k~~CP~C~k~~~----~~~rPFCS~RC~~iDLg~W~~e~Y~Ip~~~~~~~ 55 (63) ..++++||+|||+++ ++||||||+|||+||||+||+|+|+||+++...+ T Consensus 4 ~~~~v~CP~Cgkpv~w~~~s~frPFCSkRCklIDLg~Wa~eey~Ip~~~e~~~ 56 (65) T COG3024 4 LRITVPCPTCGKPVVWGEESPFRPFCSKRCKLIDLGEWAAEEYAIPDETEDSD 56 (65) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCHHHHHCCCCCCCCCCCCCC T ss_conf 66215388778833346667767633676621215365436702578755676 No 5 >pfam09889 DUF2116 Uncharacterized protein containing a Zn-ribbon (DUF2116). This domain, found in various hypothetical archaeal proteins, has no known function. Probab=91.09 E-value=0.12 Score=31.34 Aligned_cols=24 Identities=25% Similarity=0.498 Sum_probs=18.5 Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHH Q ss_conf 4568887877788687610777443 Q gi|254780469|r 11 SICPECRKGSMVEFYPFCSTQCRSI 35 (63) Q Consensus 11 ~~CP~C~k~~~~~~rPFCS~RC~~i 35 (63) .-|++||++... -.-|||++|+.+ T Consensus 4 kHC~vCG~~Ipp-~e~fCS~kC~~~ 27 (59) T pfam09889 4 KHCIVCGTAIPP-DESFCSEKCQEE 27 (59) T ss_pred CCCCCCCCCCCC-CCCCCCHHHHHH T ss_conf 535657997894-322314889999 No 6 >COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown] Probab=90.72 E-value=0.13 Score=31.16 Aligned_cols=24 Identities=29% Similarity=0.605 Sum_probs=18.4 Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHH Q ss_conf 4568887877788687610777443 Q gi|254780469|r 11 SICPECRKGSMVEFYPFCSTQCRSI 35 (63) Q Consensus 11 ~~CP~C~k~~~~~~rPFCS~RC~~i 35 (63) .-||+||++.... .-|||++|+-| T Consensus 9 ~HC~VCg~aIp~d-e~~CSe~C~ei 32 (64) T COG4068 9 RHCVVCGKAIPPD-EQVCSEECGEI 32 (64) T ss_pred CCCCCCCCCCCCC-CCHHHHHHHHH T ss_conf 6566058868974-03688999999 No 7 >pfam10013 DUF2256 Uncharacterized protein conserved in bacteria (DUF2256). Members of this family of hypothetical bacterial proteins have no known function. Probab=88.32 E-value=0.29 Score=29.17 Aligned_cols=24 Identities=33% Similarity=0.836 Sum_probs=18.8 Q ss_pred CCCCCCCCCCC--------CCCCCCHHHHHHH Q ss_conf 45688878777--------8868761077744 Q gi|254780469|r 11 SICPECRKGSM--------VEFYPFCSTQCRS 34 (63) Q Consensus 11 ~~CP~C~k~~~--------~~~rPFCS~RC~~ 34 (63) ..|++||.|.. ..---|||+||+- T Consensus 9 K~C~~C~rpf~WRKKW~r~Wd~VkyCS~rCrr 40 (42) T pfam10013 9 KICPVCGRPFTWRKKWARNWDEVKYCSERCRR 40 (42) T ss_pred CCCCCCCCCCHHHHHHHHHCCHHCCHHHHHCC T ss_conf 64654699528999998717023008888732 No 8 >COG4338 Uncharacterized protein conserved in bacteria [Function unknown] Probab=80.38 E-value=0.33 Score=28.84 Aligned_cols=29 Identities=31% Similarity=0.775 Sum_probs=20.6 Q ss_pred CCCCCCCCCCCC--------CCCCCHHHHHHHHHHHH Q ss_conf 456888787778--------86876107774433565 Q gi|254780469|r 11 SICPECRKGSMV--------EFYPFCSTQCRSIDLSR 39 (63) Q Consensus 11 ~~CP~C~k~~~~--------~~rPFCS~RC~~iDLg~ 39 (63) ..||.|+.|... .---+||+||+-.--|+ T Consensus 13 KICpvCqRPFsWRkKW~~cWDeVKyCSeRCrr~Rs~~ 49 (54) T COG4338 13 KICPVCQRPFSWRKKWARCWDEVKYCSERCRRLRSGR 49 (54) T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 4515426961899999999999889999999986225 No 9 >pfam04640 PLATZ PLATZ transcription factor. Plant AT-rich sequence and zinc-binding proteins (PLATZ) are zinc dependant DNA binding proteins. They bind to AT rich sequences and functions in transcriptional repression. Probab=69.20 E-value=1.8 Score=24.65 Aligned_cols=30 Identities=27% Similarity=0.603 Sum_probs=22.3 Q ss_pred CCCCCEECCCCCCCCCCCCCCCCCHHHHHHH Q ss_conf 7766304456888787778868761077744 Q gi|254780469|r 4 SDFRSLKSICPECRKGSMVEFYPFCSTQCRS 34 (63) Q Consensus 4 ~~~k~~k~~CP~C~k~~~~~~rPFCS~RC~~ 34 (63) ..++.....|-+|+.....+|+ |||-.||. T Consensus 43 r~~~~~~~~C~~C~R~L~d~~~-fCSl~CKv 72 (72) T pfam04640 43 RPGKGSGNICETCDRSLQDPFR-FCSLGCKV 72 (72) T ss_pred CCCCCCCCCCCCCCCCCCCCCC-EEEEEEEC T ss_conf 8889999811626563788775-74535559 No 10 >pfam10071 DUF2310 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310). Members of this family of proteobacterial zinc ribbon proteins are thought to bind to nucleic acids, however their exact function has not as yet been defined. Probab=67.74 E-value=1.6 Score=24.97 Aligned_cols=35 Identities=20% Similarity=0.541 Sum_probs=25.0 Q ss_pred CCCEECCCCCCCCCC--C---CCCCCCHHHHHHHHHHHHH Q ss_conf 663044568887877--7---8868761077744335653 Q gi|254780469|r 6 FRSLKSICPECRKGS--M---VEFYPFCSTQCRSIDLSRW 40 (63) Q Consensus 6 ~k~~k~~CP~C~k~~--~---~~~rPFCS~RC~~iDLg~W 40 (63) -+...++||.||+.- . ...+.|+.+.|++|-=-.| T Consensus 217 ~~e~~r~CP~Cg~dW~L~~plh~iF~FKCd~CRLVSnlSw 256 (259) T pfam10071 217 ASEQARKCPSCGGDWRLAEPLHDIFDFKCDKCRLVSNLSW 256 (259) T ss_pred HHHHCCCCCCCCCCCCCCCCHHHHCCCCCCCCCEECCCCC T ss_conf 6673299989997516698557501203775301103565 No 11 >LOAD_FCS consensus Probab=64.20 E-value=2.8 Score=23.64 Aligned_cols=28 Identities=32% Similarity=0.495 Sum_probs=22.0 Q ss_pred CCEECCCCCCCCCCCC--------CCCCCHHHHHHH Q ss_conf 6304456888787778--------868761077744 Q gi|254780469|r 7 RSLKSICPECRKGSMV--------EFYPFCSTQCRS 34 (63) Q Consensus 7 k~~k~~CP~C~k~~~~--------~~rPFCS~RC~~ 34 (63) .....+|..|++.... ..+.|||+-|.. T Consensus 3 ~~~~~~C~~C~~~~~~~~~~~~~g~~~~FCS~~C~~ 38 (40) T LOAD_FCS 3 GSKLRKCAFCGKEIQPKEEVYFVGKVKRFCSESCLS 38 (40) T ss_pred CCHHHHHHCCCCCCCCCCEEEEEHHHHHHHHHHHHH T ss_conf 640023111265468540477642677773587774 No 12 >pfam11023 DUF2614 Protein of unknown function (DUF2614). This is a family of proteins conserved in the Bacillaceae family. Some members are annotated as being protein YgzB. The function is not known. Probab=62.19 E-value=3.4 Score=23.11 Aligned_cols=17 Identities=24% Similarity=0.778 Sum_probs=14.2 Q ss_pred CCCCEECCCCCCCCCCC Q ss_conf 76630445688878777 Q gi|254780469|r 5 DFRSLKSICPECRKGSM 21 (63) Q Consensus 5 ~~k~~k~~CP~C~k~~~ 21 (63) ..|+.++.||.|+|++. T Consensus 64 STkAvqV~CP~C~K~TK 80 (114) T pfam11023 64 STKAVQVVCPNCGKPTK 80 (114) T ss_pred CCCEEEEECCCCCCCHH T ss_conf 04405778989997113 No 13 >pfam04945 YHS YHS domain. This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterized membrane proteins. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases. Probab=61.19 E-value=2.9 Score=23.53 Aligned_cols=22 Identities=32% Similarity=0.624 Sum_probs=15.9 Q ss_pred CCCCCCCC----------CCCCCCHHHHHHHH Q ss_conf 88878777----------88687610777443 Q gi|254780469|r 14 PECRKGSM----------VEFYPFCSTQCRSI 35 (63) Q Consensus 14 P~C~k~~~----------~~~rPFCS~RC~~i 35 (63) |+||-.+. .+.+=|||+.|+.. T Consensus 1 PVCGM~V~~~~~~~~~y~G~~Y~FCS~~C~~k 32 (44) T pfam04945 1 PVCGMYVKPRAAYKLEYEGRRYHFCSEGCKDK 32 (44) T ss_pred CCCCCEECCCCCCCEEECCEEEEEECHHHHHH T ss_conf 98887868888871689994899858888699 No 14 >PRK02935 hypothetical protein; Provisional Probab=61.12 E-value=3.7 Score=22.94 Aligned_cols=17 Identities=29% Similarity=0.796 Sum_probs=14.2 Q ss_pred CCCCEECCCCCCCCCCC Q ss_conf 76630445688878777 Q gi|254780469|r 5 DFRSLKSICPECRKGSM 21 (63) Q Consensus 5 ~~k~~k~~CP~C~k~~~ 21 (63) ..|+.++.||.|+|++. T Consensus 64 STkAvqV~CP~C~K~TK 80 (117) T PRK02935 64 STKAVQVICPSCDKPTK 80 (117) T ss_pred CCCEEEEECCCCCCCHH T ss_conf 04405778989997113 No 15 >TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, of a two subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process. Probab=58.00 E-value=2.7 Score=23.72 Aligned_cols=29 Identities=24% Similarity=0.588 Sum_probs=19.2 Q ss_pred ECCCCCCCCCCCCCCCCCHHHHHHHHHHH Q ss_conf 44568887877788687610777443356 Q gi|254780469|r 10 KSICPECRKGSMVEFYPFCSTQCRSIDLS 38 (63) Q Consensus 10 k~~CP~C~k~~~~~~rPFCS~RC~~iDLg 38 (63) ..+||.||+.+-..-=|||-.|--+...| T Consensus 679 ~~~CP~Cgk~s~~~~Cp~CG~~te~~~~g 707 (1173) T TIGR00354 679 IAKCPSCGKESLYRVCPVCGEKTELDEYG 707 (1173) T ss_pred CCCCCCCCCCCEEEECCCCCCEEEECCCC T ss_conf 12188766400001457788545445778 No 16 >PRK05776 DNA topoisomerase III; Provisional Probab=57.06 E-value=6.5 Score=21.53 Aligned_cols=28 Identities=21% Similarity=0.465 Sum_probs=20.9 Q ss_pred ECCCCCCCCCCCCCCCCCHHHHHHHHHHHH Q ss_conf 445688878777886876107774433565 Q gi|254780469|r 10 KSICPECRKGSMVEFYPFCSTQCRSIDLSR 39 (63) Q Consensus 10 k~~CP~C~k~~~~~~rPFCS~RC~~iDLg~ 39 (63) .++||.||+.+... +-||-.|..++.-+ T Consensus 602 ~g~Cp~Cg~~~~~~--~~c~~~~~~~~~~~ 629 (675) T PRK05776 602 PRKCKLCGREAEKD--GLCKYHYNAIDRLR 629 (675) T ss_pred CCCCCCCCCHHHCC--CCHHHHHHHHHHHH T ss_conf 78898766023118--71187899999998 No 17 >TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308 These are the polypeptide chains of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm. Probab=55.66 E-value=6.2 Score=21.66 Aligned_cols=39 Identities=31% Similarity=0.560 Sum_probs=29.8 Q ss_pred CCCEECCCCCCC--CCCC--------CCCCCCHHHHHHHHHHHHHCCCCCC Q ss_conf 663044568887--8777--------8868761077744335653089830 Q gi|254780469|r 6 FRSLKSICPECR--KGSM--------VEFYPFCSTQCRSIDLSRWLHGEYV 46 (63) Q Consensus 6 ~k~~k~~CP~C~--k~~~--------~~~rPFCS~RC~~iDLg~W~~e~Y~ 46 (63) |=-.-..||.|| .+-. ..|-=|=...-=+|||+ +||+|. T Consensus 738 fDLp~K~CP~Cgak~pl~kDG~~IPFETFLGF~GDKVPDIDLN--FSGEYQ 786 (1264) T TIGR01405 738 FDLPDKDCPKCGAKAPLKKDGQDIPFETFLGFKGDKVPDIDLN--FSGEYQ 786 (1264) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCHHHH T ss_conf 7685788888887776345736998500167788846864467--872247 No 18 >COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis] Probab=52.56 E-value=7.8 Score=21.09 Aligned_cols=17 Identities=35% Similarity=0.714 Sum_probs=12.3 Q ss_pred CEECCCCCCCCCCCCCC Q ss_conf 30445688878777886 Q gi|254780469|r 8 SLKSICPECRKGSMVEF 24 (63) Q Consensus 8 ~~k~~CP~C~k~~~~~~ 24 (63) +++-+||.||..+..++ T Consensus 15 TLke~Cp~CG~~t~~~~ 31 (59) T COG2260 15 TLKEKCPVCGGDTKVPH 31 (59) T ss_pred EECCCCCCCCCCCCCCC T ss_conf 61133778887454678 No 19 >pfam04135 Nop10p Nucleolar RNA-binding protein, Nop10p family. Nop10p is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10p is probably necessary for the stability of these RNPs. Probab=51.63 E-value=7.3 Score=21.26 Aligned_cols=18 Identities=33% Similarity=0.645 Sum_probs=13.2 Q ss_pred CCEECCCCCCCCCCCCCC Q ss_conf 630445688878777886 Q gi|254780469|r 7 RSLKSICPECRKGSMVEF 24 (63) Q Consensus 7 k~~k~~CP~C~k~~~~~~ 24 (63) =+++.+||.||.++.+.+ T Consensus 14 YTLk~~cp~cG~~t~~ah 31 (53) T pfam04135 14 YTLKDKCPECGGPTKSAH 31 (53) T ss_pred EECCCCCCCCCCCCCCCC T ss_conf 767784688988467678 No 20 >KOG0978 consensus Probab=50.66 E-value=5.8 Score=21.80 Aligned_cols=21 Identities=14% Similarity=0.480 Sum_probs=11.7 Q ss_pred CCCEECCCCCCCCCC-CCCCCC Q ss_conf 663044568887877-788687 Q gi|254780469|r 6 FRSLKSICPECRKGS-MVEFYP 26 (63) Q Consensus 6 ~k~~k~~CP~C~k~~-~~~~rP 26 (63) +.++.++||+|+.+. .|.++| T Consensus 674 ~etRqRKCP~Cn~aFganDv~~ 695 (698) T KOG0978 674 YETRQRKCPKCNAAFGANDVHR 695 (698) T ss_pred HHHHCCCCCCCCCCCCCCCCCC T ss_conf 9885487999888878531100 No 21 >PRK05638 threonine synthase; Validated Probab=50.46 E-value=7.5 Score=21.19 Aligned_cols=24 Identities=33% Similarity=0.827 Sum_probs=18.4 Q ss_pred EECCCCCCCCCCCCCCCCCHHHHHHH Q ss_conf 04456888787778868761077744 Q gi|254780469|r 9 LKSICPECRKGSMVEFYPFCSTQCRS 34 (63) Q Consensus 9 ~k~~CP~C~k~~~~~~rPFCS~RC~~ 34 (63) ++.+|+.||+..++...++| +|-. T Consensus 1 ~~LkC~~CG~~y~~~~~~~C--~CG~ 24 (443) T PRK05638 1 VKVKCPKCGREYNSYIPPFC--ICGE 24 (443) T ss_pred CCCCCCCCCCCCCCCCCCCC--CCCC T ss_conf 96888764775688899447--9998 No 22 >PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed Probab=50.37 E-value=8.7 Score=20.82 Aligned_cols=17 Identities=35% Similarity=0.718 Sum_probs=11.9 Q ss_pred CEECCCCCCCCCCCCCC Q ss_conf 30445688878777886 Q gi|254780469|r 8 SLKSICPECRKGSMVEF 24 (63) Q Consensus 8 ~~k~~CP~C~k~~~~~~ 24 (63) +++..||.||..+.+.+ T Consensus 15 TL~~~CP~CG~~t~~~~ 31 (54) T PRK13130 15 TLKETCPECGGKTKNPH 31 (54) T ss_pred ECCCCCCCCCCCCCCCC T ss_conf 03252866887267679 No 23 >KOG2879 consensus Probab=47.47 E-value=9.8 Score=20.53 Aligned_cols=22 Identities=18% Similarity=0.445 Sum_probs=16.3 Q ss_pred CCCCCCEECCCCCCCCCCCCCC Q ss_conf 7776630445688878777886 Q gi|254780469|r 3 TSDFRSLKSICPECRKGSMVEF 24 (63) Q Consensus 3 ~~~~k~~k~~CP~C~k~~~~~~ 24 (63) ++...+.++.||+||++.+.+| T Consensus 232 sss~~t~~~~C~~Cg~~PtiP~ 253 (298) T KOG2879 232 SSSTGTSDTECPVCGEPPTIPH 253 (298) T ss_pred CCCCCCCCCEEECCCCCCCCCE T ss_conf 6665647755006699999873 No 24 >pfam06467 zf-FCS MYM-type Zinc finger with FCS sequence motif. MYM-type zinc fingers were identified in MYM family proteins. Human zinc finger protein 261 is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1. Human zinc finger protein 198 is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1; in atypical myeloproliferative disorders it is rearranged. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons. Probab=41.01 E-value=9.9 Score=20.52 Aligned_cols=28 Identities=32% Similarity=0.558 Sum_probs=20.9 Q ss_pred CCEECCCCCCCCCC---------CCCCCCCHHHHHHH Q ss_conf 63044568887877---------78868761077744 Q gi|254780469|r 7 RSLKSICPECRKGS---------MVEFYPFCSTQCRS 34 (63) Q Consensus 7 k~~k~~CP~C~k~~---------~~~~rPFCS~RC~~ 34 (63) ...+..|-.|++.. ......|||+-|.. T Consensus 3 ~~~~~~C~~C~~~~~~~~~~~~~~g~~~~FCS~~C~~ 39 (41) T pfam06467 3 NLVKARCTYCKKYLPSKPTALQWDGSVKQFCSTTCLD 39 (41) T ss_pred CEEEEECCCCCCCCCCCCHHHHCCCCHHHEEECCCCC T ss_conf 5012210004763466844542077532023031015 No 25 >PRK00415 rps27e 30S ribosomal protein S27e; Reviewed Probab=40.57 E-value=15 Score=19.52 Aligned_cols=19 Identities=32% Similarity=0.625 Sum_probs=15.0 Q ss_pred CCCCCCCEECCCCCCCCCC Q ss_conf 8777663044568887877 Q gi|254780469|r 2 QTSDFRSLKSICPECRKGS 20 (63) Q Consensus 2 ~~~~~k~~k~~CP~C~k~~ 20 (63) +.++-+-++++||-|+... T Consensus 3 ~~p~S~FlkVkC~~C~neq 21 (59) T PRK00415 3 PQPRSRFLKVKCPDCGNEQ 21 (59) T ss_pred CCCCCCEEEEECCCCCCEE T ss_conf 7898728987999999867 No 26 >PTZ00083 40S ribosomal protein S27; Provisional Probab=38.24 E-value=16 Score=19.34 Aligned_cols=20 Identities=20% Similarity=0.389 Sum_probs=16.1 Q ss_pred CCCCCCCCEECCCCCCCCCC Q ss_conf 98777663044568887877 Q gi|254780469|r 1 MQTSDFRSLKSICPECRKGS 20 (63) Q Consensus 1 m~~~~~k~~k~~CP~C~k~~ 20 (63) ++.+|-.-|.++||.|++.. T Consensus 26 Vq~PnS~FmdVkCpgC~~it 45 (85) T PTZ00083 26 VQGPNSYFMDVKCPGCLTIT 45 (85) T ss_pred ECCCCCEEEEEECCCCCCEE T ss_conf 03998307986899999703 No 27 >CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed Probab=36.35 E-value=14 Score=19.58 Aligned_cols=15 Identities=27% Similarity=0.539 Sum_probs=13.2 Q ss_pred CCCEECCCCCCCCCC Q ss_conf 663044568887877 Q gi|254780469|r 6 FRSLKSICPECRKGS 20 (63) Q Consensus 6 ~k~~k~~CP~C~k~~ 20 (63) ++++++|||.|++.. T Consensus 44 ~~nLW~KCp~C~~~i 58 (305) T CHL00174 44 YRHLWVQCENCYGLN 58 (305) T ss_pred CCCCCCCCCCCCCHH T ss_conf 177465498766224 No 28 >COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair] Probab=35.61 E-value=18 Score=18.97 Aligned_cols=41 Identities=32% Similarity=0.555 Sum_probs=29.7 Q ss_pred CCCCCEECCCCCCCCCCC--------CCCCCCHHHHHHHHHHHHHCCCCCC Q ss_conf 776630445688878777--------8868761077744335653089830 Q gi|254780469|r 4 SDFRSLKSICPECRKGSM--------VEFYPFCSTQCRSIDLSRWLHGEYV 46 (63) Q Consensus 4 ~~~k~~k~~CP~C~k~~~--------~~~rPFCS~RC~~iDLg~W~~e~Y~ 46 (63) +-|--.-..||.||.+-. ..|.-|=...--+|||+ ++|+|. T Consensus 933 sGfDLpdK~CPkCg~pl~kDG~dIPFETFlGF~GDKVPDIDLN--FSGeYQ 981 (1444) T COG2176 933 SGFDLPDKDCPKCGTPLKKDGHDIPFETFLGFKGDKVPDIDLN--FSGEYQ 981 (1444) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCC--CCCCCC T ss_conf 7888899989867994356898787255327788878876676--786441 No 29 >pfam12156 ATPase-cat_bd Putative metal-binding domain of cation transport ATPase. This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with pfam00403, pfam00122, pfam00702. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases. Probab=35.17 E-value=28 Score=17.96 Aligned_cols=26 Identities=19% Similarity=0.482 Sum_probs=19.9 Q ss_pred CCCCCCCCCCC----------CCCCCCHHHHHHHHH Q ss_conf 45688878777----------886876107774433 Q gi|254780469|r 11 SICPECRKGSM----------VEFYPFCSTQCRSID 36 (63) Q Consensus 11 ~~CP~C~k~~~----------~~~rPFCS~RC~~iD 36 (63) .+|=.||.+.. ..-|+||..-|+.|= T Consensus 1 ~~C~HCg~~~p~~~~~~~~i~g~~~~fCC~GC~~V~ 36 (88) T pfam12156 1 TKCFHCGLPVPEGEPFTAEIDGQERDFCCPGCQAVA 36 (88) T ss_pred CCCCCCCCCCCCCCCEEEEECCCCCCCCCHHHHHHH T ss_conf 967678997899885567778973441477899999 No 30 >smart00746 TRASH metallochaperone-like domain. Probab=34.35 E-value=17 Score=19.22 Aligned_cols=22 Identities=36% Similarity=0.833 Sum_probs=15.7 Q ss_pred CCCCCCCCC-----------CCCCCCHHHHHHH Q ss_conf 688878777-----------8868761077744 Q gi|254780469|r 13 CPECRKGSM-----------VEFYPFCSTQCRS 34 (63) Q Consensus 13 CP~C~k~~~-----------~~~rPFCS~RC~~ 34 (63) |+.|++... ..-+-|||+.|.. T Consensus 1 C~~Cg~~i~~~~~~~~~~~~g~~~~FCs~~C~~ 33 (39) T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVFYFCSSKCLS 33 (39) T ss_pred CCCCCCCCCCCCCEEEEECCCCEEEEECHHHHH T ss_conf 935578632799508998289689982777876 No 31 >pfam04159 NB NB glycoprotein. The NB glycoprotein is found in Influenza type B virus. Its function is unknown. Probab=32.99 E-value=14 Score=19.65 Aligned_cols=15 Identities=33% Similarity=1.048 Sum_probs=10.7 Q ss_pred ECCCCCCCCCCCCCCCCCHHHHH Q ss_conf 44568887877788687610777 Q gi|254780469|r 10 KSICPECRKGSMVEFYPFCSTQC 32 (63) Q Consensus 10 k~~CP~C~k~~~~~~rPFCS~RC 32 (63) ..||+-|. |||.+|= T Consensus 59 rikcs~ce--------pfcnkr~ 73 (100) T pfam04159 59 RIKCSGCE--------PFCNKRD 73 (100) T ss_pred CCCCCCCC--------CHHCCCC T ss_conf 03368872--------1002667 No 32 >pfam04423 Rad50_zn_hook Rad50 zinc hook motif. The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side. Probab=32.36 E-value=13 Score=19.87 Aligned_cols=14 Identities=29% Similarity=0.586 Sum_probs=10.5 Q ss_pred CCCCCCCCCCCCCC Q ss_conf 45688878777886 Q gi|254780469|r 11 SICPECRKGSMVEF 24 (63) Q Consensus 11 ~~CP~C~k~~~~~~ 24 (63) ..||+||.+.+... T Consensus 21 ~~CPvC~r~l~~e~ 34 (54) T pfam04423 21 GCCPVCGRPLDEEH 34 (54) T ss_pred CCCCCCCCCCCHHH T ss_conf 87776699766788 No 33 >COG3350 Uncharacterized conserved protein [Function unknown] Probab=32.31 E-value=21 Score=18.66 Aligned_cols=27 Identities=30% Similarity=0.604 Sum_probs=19.1 Q ss_pred EECCCCCCCCCCCC-----------CCCCCHHHHHHHH Q ss_conf 04456888787778-----------8687610777443 Q gi|254780469|r 9 LKSICPECRKGSMV-----------EFYPFCSTQCRSI 35 (63) Q Consensus 9 ~k~~CP~C~k~~~~-----------~~rPFCS~RC~~i 35 (63) +.+.=|+||..+++ +.+=|||+.|+.- T Consensus 1 ~~~iDPVcgm~v~~~~a~~k~~Y~GktYYFcse~~~~~ 38 (53) T COG3350 1 IDVIDPVCGMKVDNENAEYKSSYGGKTYYFCSEECKEK 38 (53) T ss_pred CCCCCCCCCCCCCCCCCCEEEEECCEEEEEECHHHHHH T ss_conf 96536776765266555105875887899708999999 No 34 >cd01057 AAMH_A Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain. Aromatic and Alkene Monooxygenase Hydroxylases, subunit A (AAMH_A). Subunit A of the soluble hydroxylase of multicomponent, aromatic and alkene monooxygenases are members of a superfamily of ferritin-like iron-storage proteins. AAMH exists as a hexamer (an alpha2-beta2-gamma2 homodimer) with each alpha-subunit housing one nonheme diiron center embedded in a four-helix bundle. The N-terminal domain of the alpha- and noncatalytic beta-subunits possess nearly identical folds, however, the beta-subunit lacks critical diiron ligands and a C-terminal domain found in the alpha-subunit. Methane monooxygenase is a multicomponent enzyme found in methanotrophic bacteria that catalyzes the hydroxylation of methane and higher alkenes (as large as octane). Phenol monooxygenase, found in a diverse group of bacteria, catalyses the hydroxylation of phenol, chloro- and methyl-phenol and naphtho Probab=30.77 E-value=28 Score=17.97 Aligned_cols=38 Identities=26% Similarity=0.508 Sum_probs=26.1 Q ss_pred CCEECCCCCCCCCCC----------------CCCCCCHHHHHHHHHHHHHCCCCCC Q ss_conf 630445688878777----------------8868761077744335653089830 Q gi|254780469|r 7 RSLKSICPECRKGSM----------------VEFYPFCSTQCRSIDLSRWLHGEYV 46 (63) Q Consensus 7 k~~k~~CP~C~k~~~----------------~~~rPFCS~RC~~iDLg~W~~e~Y~ 46 (63) .++-..|=+|+-|.. .+-+.|||+-|+-|... --|.|+ T Consensus 377 ~tlP~lC~~Cq~P~~~~~~~~~~~~r~~ey~G~~y~fcSe~c~wiF~~--ePerY~ 430 (465) T cd01057 377 ETLPPLCNVCQVPCVFTEDLTAEAPRVLEYNGRKYHFCSEGCEWIFEQ--EPERYA 430 (465) T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCEEECCCCHHHHHHHHH--CHHHHC T ss_conf 989871236678606177777665136778887650268066767775--968653 No 35 >pfam10122 Mu-like_Com Mu-like prophage protein Com. Members of this family of proteins comprise the translational regulator of mom. Probab=30.68 E-value=22 Score=18.59 Aligned_cols=16 Identities=31% Similarity=0.717 Sum_probs=12.6 Q ss_pred CCCCCEECCCCCCCCC Q ss_conf 7766304456888787 Q gi|254780469|r 4 SDFRSLKSICPECRKG 19 (63) Q Consensus 4 ~~~k~~k~~CP~C~k~ 19 (63) -.|-.+.+|||.||.- T Consensus 18 g~~~elqIKCpRCgtl 33 (51) T pfam10122 18 GAFSELQIKCPRCGTL 33 (51) T ss_pred CCCEEEEEECCCCCCC T ss_conf 6750588856866751 No 36 >pfam05573 NosL NosL. NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallo-centre assembly. Probab=29.71 E-value=29 Score=17.86 Aligned_cols=27 Identities=30% Similarity=0.261 Sum_probs=17.3 Q ss_pred CCCCCCCCCC------------C-C-CCCCCHHHHHHHHHH Q ss_conf 4568887877------------7-8-868761077744335 Q gi|254780469|r 11 SICPECRKGS------------M-V-EFYPFCSTQCRSIDL 37 (63) Q Consensus 11 ~~CP~C~k~~------------~-~-~~rPFCS~RC~~iDL 37 (63) .+||+||=.+ . . +.+=|||-+|-..-| T Consensus 17 ~~C~vCgM~i~~~Pg~~aqi~~~~g~~~~~Fds~~~m~~~~ 57 (140) T pfam05573 17 ARCHLCGMNITEYPGPKGQIHLKGGPEPLFFCSTRDMFAFL 57 (140) T ss_pred CCCCCCCCCHHHCCCCCEEEEECCCCCCEEECCHHHHHHHH T ss_conf 70188996963589820899978998411178999999998 No 37 >PHA00732 hypothetical protein Probab=29.37 E-value=7.6 Score=21.17 Aligned_cols=38 Identities=21% Similarity=0.379 Sum_probs=18.9 Q ss_pred ECCCCCCCCCCCCCCCCCHHHHHHHHH--HHHHCCCCCCCCC Q ss_conf 445688878777886876107774433--5653089830357 Q gi|254780469|r 10 KSICPECRKGSMVEFYPFCSTQCRSID--LSRWLHGEYVIAA 49 (63) Q Consensus 10 k~~CP~C~k~~~~~~rPFCS~RC~~iD--Lg~W~~e~Y~Ip~ 49 (63) -.+||+||+.--+-..-|-|+ .+|| +--||=+.|.+|- T Consensus 27 l~kCPVC~~~y~~l~QHfy~~--~D~~HL~~cyLfstyklP~ 66 (79) T PHA00732 27 LTKCPVCNNSYRRLNQHFYSQ--YDIEHLIYCYLFSTYKLPK 66 (79) T ss_pred CCCCCCCCHHHHHHHHHHHHH--CCCHHHHHHEEEECCCCCH T ss_conf 522775047899999877643--4205620111111576758 No 38 >TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase; InterPro: IPR004558 This family represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. HemN catalyses the anaerobic transformation of coproporhyrinogen-III into protoporphyrinogen-IX during porphyrin biosynthesis. Several species, including Escherichia coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity, IPR004559 from INTERPRO. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterised protein.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin biosynthetic process, 0005737 cytoplasm. Probab=28.73 E-value=16 Score=19.39 Aligned_cols=11 Identities=36% Similarity=1.026 Sum_probs=8.8 Q ss_pred CCCCCCHHHHH Q ss_conf 88687610777 Q gi|254780469|r 22 VEFYPFCSTQC 32 (63) Q Consensus 22 ~~~rPFCS~RC 32 (63) --|-|||.++| T Consensus 55 Y~HiPFC~~~C 65 (462) T TIGR00538 55 YVHIPFCEKAC 65 (462) T ss_pred CCCCHHHHCCC T ss_conf 24552341213 No 39 >pfam04570 DUF581 Protein of unknown function (DUF581). Family of uncharacterized proteins. Probab=28.35 E-value=29 Score=17.84 Aligned_cols=27 Identities=33% Similarity=0.541 Sum_probs=19.0 Q ss_pred EECCCCCCCCCCCC--------CCCCCHHHHHHHH Q ss_conf 04456888787778--------8687610777443 Q gi|254780469|r 9 LKSICPECRKGSMV--------EFYPFCSTQCRSI 35 (63) Q Consensus 9 ~k~~CP~C~k~~~~--------~~rPFCS~RC~~i 35 (63) .-..|-.|+|.... --++|||.-|+.- T Consensus 16 FL~~C~~Ckk~L~~~~DIymYrG~~aFCS~eCR~~ 50 (59) T pfam04570 16 FLSSCFLCKKKLGPGKDIYMYRGDKAFCSEECRQQ 50 (59) T ss_pred HHHHHHHCCCCCCCCCCEEEECCCCCCCCHHHHHH T ss_conf 99987621872789985577789953128899899 No 40 >pfam09986 DUF2225 Uncharacterized protein conserved in bacteria (DUF2225). This domain, found in various hypothetical bacterial proteins, has no known function. Probab=27.95 E-value=24 Score=18.36 Aligned_cols=10 Identities=30% Similarity=0.883 Sum_probs=4.7 Q ss_pred ECCCCCCCCC Q ss_conf 4456888787 Q gi|254780469|r 10 KSICPECRKG 19 (63) Q Consensus 10 k~~CP~C~k~ 19 (63) ...||.||=. T Consensus 48 v~vCp~CgyA 57 (214) T pfam09986 48 VWVCPHCGYA 57 (214) T ss_pred EEECCCCCCC T ss_conf 1699999854 No 41 >pfam02891 zf-MIZ MIZ/SP-RING zinc finger. This domain has SUMO (small ubiquitin-like modifier) ligase activity and is involved in DNA repair and chromosome organisation. Probab=27.20 E-value=25 Score=18.19 Aligned_cols=12 Identities=17% Similarity=0.205 Sum_probs=4.9 Q ss_pred CCCCCCCCCCCC Q ss_conf 456888787778 Q gi|254780469|r 11 SICPECRKGSMV 22 (63) Q Consensus 11 ~~CP~C~k~~~~ 22 (63) .+||+....... T Consensus 3 L~CPis~~~i~~ 14 (50) T pfam02891 3 LKCPISYLRISI 14 (50) T ss_pred EECCCCCCEEEC T ss_conf 368888888743 No 42 >PRK08173 DNA topoisomerase III; Validated Probab=26.54 E-value=18 Score=18.98 Aligned_cols=27 Identities=30% Similarity=0.903 Sum_probs=16.2 Q ss_pred CCCCEECCCCCCCCCCCCCCCCC-HHHHH Q ss_conf 76630445688878777886876-10777 Q gi|254780469|r 5 DFRSLKSICPECRKGSMVEFYPF-CSTQC 32 (63) Q Consensus 5 ~~k~~k~~CP~C~k~~~~~~rPF-CS~RC 32 (63) ++.++...||.||..+...++=| || -| T Consensus 619 ~~~~~~~~CP~Cg~~i~~~~k~y~C~-~C 646 (857) T PRK08173 619 DYATLQTPCPNCGGVVKENYRRFACT-KC 646 (857) T ss_pred CCCCCCCCCCCCCCEEEECCCEEECC-CC T ss_conf 22333578888895167556189779-99 No 43 >TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300; InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.. Probab=25.87 E-value=26 Score=18.12 Aligned_cols=45 Identities=29% Similarity=0.356 Sum_probs=23.9 Q ss_pred CCCCCCCCEECCCCCCCCCC-CCCCCCCHHHHH-HHHHHHHHCCCCCC Q ss_conf 98777663044568887877-788687610777-44335653089830 Q gi|254780469|r 1 MQTSDFRSLKSICPECRKGS-MVEFYPFCSTQC-RSIDLSRWLHGEYV 46 (63) Q Consensus 1 m~~~~~k~~k~~CP~C~k~~-~~~~rPFCS~RC-~~iDLg~W~~e~Y~ 46 (63) |..++.= .|..||.||+-. +=.-+|--|-.| +..+|..-+.-+.+ T Consensus 1 mAkpdLG-tKrIcP~tg~KFYDLNr~P~vsPytGe~~p~~~~~~~r~~ 47 (157) T TIGR02300 1 MAKPDLG-TKRICPETGKKFYDLNRDPVVSPYTGEQFPLEEVLKSRRV 47 (157) T ss_pred CCCCCCC-CCCCCCCCCCCCCCCCCCCEECCCCCCCCCHHHHHCCCEE T ss_conf 9887678-6220687777220007895341778870475430045402 No 44 >KOG3362 consensus Probab=25.84 E-value=34 Score=17.50 Aligned_cols=33 Identities=24% Similarity=0.549 Sum_probs=22.9 Q ss_pred CCCCCCEECCCCCCCCCCC----CCCCCCHHHHHHHH Q ss_conf 7776630445688878777----88687610777443 Q gi|254780469|r 3 TSDFRSLKSICPECRKGSM----VEFYPFCSTQCRSI 35 (63) Q Consensus 3 ~~~~k~~k~~CP~C~k~~~----~~~rPFCS~RC~~i 35 (63) ...+|.....|-+||-.+. +=---+||.||..+ T Consensus 111 ~p~~KP~r~fCaVCG~~S~ysC~~CG~kyCsv~C~~~ 147 (156) T KOG3362 111 KPSFKPLRKFCAVCGYDSKYSCVNCGTKYCSVRCLKT 147 (156) T ss_pred CCCCCCCCHHHHHCCCCCHHHHHHCCCCEEECHHHHH T ss_conf 8877874103242489860277754874250225432 No 45 >KOG4317 consensus Probab=24.99 E-value=27 Score=18.03 Aligned_cols=24 Identities=21% Similarity=0.353 Sum_probs=14.3 Q ss_pred EECCCCCCCCCCCC-----CCCCCHHHHH Q ss_conf 04456888787778-----8687610777 Q gi|254780469|r 9 LKSICPECRKGSMV-----EFYPFCSTQC 32 (63) Q Consensus 9 ~k~~CP~C~k~~~~-----~~rPFCS~RC 32 (63) -...||+|++.... =..|+||-|| T Consensus 6 ~~~~C~ic~vq~~~YtCPRCn~~YCsl~C 34 (383) T KOG4317 6 SFLACGICGVQKREYTCPRCNLLYCSLKC 34 (383) T ss_pred CEEECCCCCCCCCCCCCCCCCCCCEEEEE T ss_conf 50342345544200558777764200343 No 46 >PRK05978 hypothetical protein; Provisional Probab=24.18 E-value=26 Score=18.16 Aligned_cols=14 Identities=36% Similarity=1.087 Sum_probs=11.1 Q ss_pred CCEECCCCCCCCCC Q ss_conf 63044568887877 Q gi|254780469|r 7 RSLKSICPECRKGS 20 (63) Q Consensus 7 k~~k~~CP~C~k~~ 20 (63) |.++.+||.||+.. T Consensus 31 RGlr~rCP~CG~G~ 44 (149) T PRK05978 31 RGFRGRCPHCGEGK 44 (149) T ss_pred HHHCCCCCCCCCCH T ss_conf 88737598999941 No 47 >pfam10571 UPF0547 Uncharacterized protein family UPF0547. This domain contains a zinc-ribbon motif. Probab=24.06 E-value=38 Score=17.19 Aligned_cols=19 Identities=32% Similarity=0.894 Sum_probs=12.2 Q ss_pred CCCCCCCCCC--CCCCCCCHH Q ss_conf 4568887877--788687610 Q gi|254780469|r 11 SICPECRKGS--MVEFYPFCS 29 (63) Q Consensus 11 ~~CP~C~k~~--~~~~rPFCS 29 (63) ..||.|++.+ ....=|+|- T Consensus 1 K~CP~C~~~vp~~~~~Cp~CG 21 (26) T pfam10571 1 KTCPECGAEVPLAAKICPHCG 21 (26) T ss_pred CCCCCCCCCCCHHCCCCCCCC T ss_conf 968755483640034477888 No 48 >PRK07379 coproporphyrinogen III oxidase; Provisional Probab=23.93 E-value=19 Score=18.90 Aligned_cols=17 Identities=29% Similarity=0.659 Sum_probs=12.6 Q ss_pred CCCCCHHHHHHHHHHHH Q ss_conf 86876107774433565 Q gi|254780469|r 23 EFYPFCSTQCRSIDLSR 39 (63) Q Consensus 23 ~~rPFCS~RC~~iDLg~ 39 (63) -|-|||..||.-=|+.. T Consensus 15 iHIPFC~~~C~YCdF~~ 31 (399) T PRK07379 15 LHIPFCRRRCFYCDFPI 31 (399) T ss_pred EECCCCCCCCCCCCCCC T ss_conf 86500669288999975 No 49 >PRK08446 coproporphyrinogen III oxidase; Provisional Probab=23.58 E-value=21 Score=18.71 Aligned_cols=15 Identities=27% Similarity=0.857 Sum_probs=9.6 Q ss_pred CCCCHHHHHHHHHHH Q ss_conf 687610777443356 Q gi|254780469|r 24 FYPFCSTQCRSIDLS 38 (63) Q Consensus 24 ~rPFCS~RC~~iDLg 38 (63) |-|||..+|.-=|+. T Consensus 6 HiPFC~~~C~YCdF~ 20 (351) T PRK08446 6 HIPFCESKCGYCAFN 20 (351) T ss_pred ECCCCCCCCCCCCCC T ss_conf 817838808999792 No 50 >PRK05799 coproporphyrinogen III oxidase; Provisional Probab=23.41 E-value=19 Score=18.88 Aligned_cols=17 Identities=29% Similarity=0.866 Sum_probs=12.6 Q ss_pred CCCCHHHHHHHHHHHHH Q ss_conf 68761077744335653 Q gi|254780469|r 24 FYPFCSTQCRSIDLSRW 40 (63) Q Consensus 24 ~rPFCS~RC~~iDLg~W 40 (63) |-|||.+||.-=|+... T Consensus 9 HiPFC~~~C~yC~f~~~ 25 (374) T PRK05799 9 HIPFCKQKCLYCDFPSY 25 (374) T ss_pred EECCCCCCCCCCCCCCC T ss_conf 94899985899979474 No 51 >pfam01667 Ribosomal_S27e Ribosomal protein S27. Probab=23.35 E-value=36 Score=17.31 Aligned_cols=16 Identities=25% Similarity=0.476 Sum_probs=11.9 Q ss_pred CCCCEECCCCCCCCCC Q ss_conf 7663044568887877 Q gi|254780469|r 5 DFRSLKSICPECRKGS 20 (63) Q Consensus 5 ~~k~~k~~CP~C~k~~ 20 (63) |-+=|+++||-|++.. T Consensus 2 nS~F~~VkCp~C~n~~ 17 (55) T pfam01667 2 NSYFLDVKCPGCGNIT 17 (55) T ss_pred CCEEEEEECCCCCCEE T ss_conf 8615884999999756 No 52 >smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids. Probab=23.00 E-value=19 Score=18.94 Aligned_cols=11 Identities=27% Similarity=0.649 Sum_probs=8.4 Q ss_pred ECCCCCCCCCC Q ss_conf 44568887877 Q gi|254780469|r 10 KSICPECRKGS 20 (63) Q Consensus 10 k~~CP~C~k~~ 20 (63) .+.||+|++.. T Consensus 1 ~v~CPVC~~~v 11 (26) T smart00734 1 LVQCPVCFREV 11 (26) T ss_pred CCCCCHHHHHC T ss_conf 97576259883 No 53 >cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity. Probab=22.48 E-value=35 Score=17.40 Aligned_cols=10 Identities=30% Similarity=0.770 Sum_probs=6.4 Q ss_pred CCCCCCCCCC Q ss_conf 4568887877 Q gi|254780469|r 11 SICPECRKGS 20 (63) Q Consensus 11 ~~CP~C~k~~ 20 (63) .+||+|+.+. T Consensus 19 ~~CPvC~~~~ 28 (34) T cd00729 19 EKCPICGAPK 28 (34) T ss_pred CCCCCCCCCH T ss_conf 7586999967 No 54 >PRK05628 coproporphyrinogen III oxidase; Validated Probab=22.33 E-value=23 Score=18.47 Aligned_cols=17 Identities=35% Similarity=0.960 Sum_probs=12.5 Q ss_pred CCCCHHHHHHHHHHHHH Q ss_conf 68761077744335653 Q gi|254780469|r 24 FYPFCSTQCRSIDLSRW 40 (63) Q Consensus 24 ~rPFCS~RC~~iDLg~W 40 (63) |-|||..+|.-=|+... T Consensus 8 HiPFC~~~C~yC~f~~~ 24 (376) T PRK05628 8 HVPFCATRCGYCDFNTY 24 (376) T ss_pred ECCCCCCCCCCCCCCCC T ss_conf 70576460899979573 No 55 >PRK06294 coproporphyrinogen III oxidase; Provisional Probab=21.88 E-value=22 Score=18.49 Aligned_cols=17 Identities=29% Similarity=0.704 Sum_probs=12.3 Q ss_pred CCCCCHHHHHHHHHHHH Q ss_conf 86876107774433565 Q gi|254780469|r 23 EFYPFCSTQCRSIDLSR 39 (63) Q Consensus 23 ~~rPFCS~RC~~iDLg~ 39 (63) -|-|||..||.-=|+.. T Consensus 11 iHIPFC~~~C~yC~f~~ 27 (374) T PRK06294 11 IHIPFCSKKCHYCSFYT 27 (374) T ss_pred EECCCCCCCCCCCCCEE T ss_conf 86278998799998810 No 56 >PRK08208 coproporphyrinogen III oxidase; Validated Probab=21.54 E-value=23 Score=18.49 Aligned_cols=16 Identities=31% Similarity=0.798 Sum_probs=11.1 Q ss_pred CCCCHHHHHHHHHHHH Q ss_conf 6876107774433565 Q gi|254780469|r 24 FYPFCSTQCRSIDLSR 39 (63) Q Consensus 24 ~rPFCS~RC~~iDLg~ 39 (63) |-|||.+||.-=|+.. T Consensus 51 HiPFC~~~C~YC~f~~ 66 (436) T PRK08208 51 HIPFCESRCGFCNLFT 66 (436) T ss_pred ECCCCCCCCCCCCCCC T ss_conf 7044079588999837 No 57 >pfam12230 PRP21_like_P Pre-mRNA splicing factor PRP21 like protein. This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with pfam01805. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. Probab=21.28 E-value=48 Score=16.61 Aligned_cols=13 Identities=15% Similarity=0.094 Sum_probs=9.7 Q ss_pred CEECCCCCCCCCC Q ss_conf 3044568887877 Q gi|254780469|r 8 SLKSICPECRKGS 20 (63) Q Consensus 8 ~~k~~CP~C~k~~ 20 (63) +...+||+||+.+ T Consensus 160 ~~~~~cPitGq~I 172 (223) T pfam12230 160 AKMIKCPITGELI 172 (223) T ss_pred CCEEECCCCCCCC T ss_conf 8865778777817 No 58 >cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity. Probab=20.86 E-value=39 Score=17.12 Aligned_cols=10 Identities=30% Similarity=0.853 Sum_probs=5.8 Q ss_pred CCCCCCCCCC Q ss_conf 4568887877 Q gi|254780469|r 11 SICPECRKGS 20 (63) Q Consensus 11 ~~CP~C~k~~ 20 (63) -+||+||.+. T Consensus 18 ~~CP~Cg~~k 27 (33) T cd00350 18 WVCPVCGAPK 27 (33) T ss_pred CCCCCCCCCH T ss_conf 7287889978 No 59 >KOG0801 consensus Probab=20.85 E-value=36 Score=17.33 Aligned_cols=10 Identities=40% Similarity=0.823 Sum_probs=8.5 Q ss_pred CCCCCCCCCC Q ss_conf 4568887877 Q gi|254780469|r 11 SICPECRKGS 20 (63) Q Consensus 11 ~~CP~C~k~~ 20 (63) .|||+|.|.+ T Consensus 139 ~KCPvC~K~V 148 (205) T KOG0801 139 MKCPVCHKVV 148 (205) T ss_pred CCCCCCCCCC T ss_conf 5477434402 No 60 >PRK09057 coproporphyrinogen III oxidase; Provisional Probab=20.74 E-value=24 Score=18.29 Aligned_cols=16 Identities=31% Similarity=0.939 Sum_probs=11.3 Q ss_pred CCCCHHHHHHHHHHHH Q ss_conf 6876107774433565 Q gi|254780469|r 24 FYPFCSTQCRSIDLSR 39 (63) Q Consensus 24 ~rPFCS~RC~~iDLg~ 39 (63) |-|||..+|.-=|+.. T Consensus 10 HIPFC~~~C~YCdf~~ 25 (381) T PRK09057 10 HWPFCLAKCPYCDFNS 25 (381) T ss_pred EECCCCCCCCCCCCCC T ss_conf 8178888289994987 No 61 >PRK06582 coproporphyrinogen III oxidase; Provisional Probab=20.69 E-value=25 Score=18.25 Aligned_cols=17 Identities=29% Similarity=0.848 Sum_probs=12.7 Q ss_pred CCCCCHHHHHHHHHHHH Q ss_conf 86876107774433565 Q gi|254780469|r 23 EFYPFCSTQCRSIDLSR 39 (63) Q Consensus 23 ~~rPFCS~RC~~iDLg~ 39 (63) -|-|||..+|.-=|+.. T Consensus 16 iHIPFC~~~C~yC~f~~ 32 (390) T PRK06582 16 IHWPFCLSKCPYCDFNS 32 (390) T ss_pred EEECCCCCCCCCCCCCC T ss_conf 98389988089993907 No 62 >PRK13347 coproporphyrinogen III oxidase; Provisional Probab=20.49 E-value=27 Score=18.08 Aligned_cols=20 Identities=20% Similarity=0.464 Sum_probs=14.5 Q ss_pred CCCCCHHHHHHHHHHHHHCC Q ss_conf 86876107774433565308 Q gi|254780469|r 23 EFYPFCSTQCRSIDLSRWLH 42 (63) Q Consensus 23 ~~rPFCS~RC~~iDLg~W~~ 42 (63) -|-|||..+|--=|+..-.. T Consensus 55 iHIPFC~~~C~YC~f~~~~~ 74 (453) T PRK13347 55 LHVPFCRSLCWFCGCNTIIT 74 (453) T ss_pred EECCCCCCCCCCCCCCCCCC T ss_conf 85277168089998973377 No 63 >pfam06827 zf-FPG_IleRS Zinc finger found in FPG and IleRS. This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23. Probab=20.05 E-value=40 Score=17.07 Aligned_cols=25 Identities=20% Similarity=0.456 Sum_probs=16.6 Q ss_pred CCCCCCCCCCC----CCCCCCHHHHHHHH Q ss_conf 45688878777----88687610777443 Q gi|254780469|r 11 SICPECRKGSM----VEFYPFCSTQCRSI 35 (63) Q Consensus 11 ~~CP~C~k~~~----~~~rPFCS~RC~~i 35 (63) .+||.|+.... +...+|-..||+.+ T Consensus 2 ~kC~RCw~~~~~~~~~~r~~~~C~rCq~~ 30 (30) T pfam06827 2 EKCPRCWTYIEKVGQGGRSTFLCPRCQKV 30 (30) T ss_pred CCCCCCCCEEEEEEECCCCCCCCCCCCCC T ss_conf 82774799715768558888118053249 Done!