Query         gi|254781076|ref|YP_003065489.1| ribonuclease HII [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 209
No_of_seqs    132 out of 2742
Neff          6.2 
Searched_HMMs 39220
Date          Mon May 30 04:13:51 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781076.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK13926 junction RNase; Provi 100.0       0       0  493.0  17.8  200    7-208     5-205 (212)
  2 PRK00015 rnhB ribonuclease HII 100.0       0       0  468.1  16.1  195    8-204     2-197 (197)
  3 PRK13925 rnhB ribonuclease HII 100.0       0       0  460.0  15.5  184   23-206     7-195 (200)
  4 cd07182 RNaseH_typeII_bacteria 100.0       0       0  445.8  12.9  178   27-205     1-179 (179)
  5 COG0164 RnhB Ribonuclease HII  100.0       0       0  430.8  14.8  184   25-208     1-188 (199)
  6 cd06266 RNaseH_typeII Ribonucl 100.0       0       0  389.5  13.1  179   27-205     1-193 (193)
  7 pfam01351 RNase_HII Ribonuclea 100.0       0       0  385.6  11.0  177   27-204     1-197 (197)
  8 cd07180 RNaseH_typeII_Archaea_ 100.0       0       0  376.7  14.1  177   27-207     1-203 (204)
  9 cd07181 RNaseH_typeII_eukaryot 100.0       0       0  362.6  12.8  181   27-207     1-215 (216)
 10 cd06590 RNaseH_typeII_bacteria 100.0       0       0  338.8  11.5  178   27-207     1-207 (208)
 11 TIGR00729 TIGR00729 ribonuclea 100.0       0       0  329.2  10.4  179   26-208     1-234 (235)
 12 KOG2299 consensus              100.0 2.2E-36 5.7E-41  247.8   9.8  182   21-207    25-248 (301)
 13 PRK00996 ribonuclease HIII; Pr 100.0 3.2E-35 8.1E-40  240.6  12.1  182   22-206    86-299 (303)
 14 COG1039 RnhC Ribonuclease HIII 100.0 1.3E-29 3.2E-34  205.7   9.7  180   23-205    82-294 (297)
 15 TIGR00716 rnhC ribonuclease HI  99.9 5.7E-26 1.5E-30  182.9   9.5  170   25-197    92-289 (298)
 16 cd06559 Endonuclease_V Endonuc  64.9       3 7.6E-05   22.4   1.1   26  102-127    81-106 (208)
 17 pfam04493 Endonuclease_5 Endon  62.8     3.5 8.9E-05   22.0   1.1   80   23-127    21-101 (205)
 18 PRK11617 endonuclease V; Provi  62.5     3.3 8.3E-05   22.2   1.0   25  103-127    85-109 (223)
 19 TIGR00538 hemN oxygen-independ  55.2      15 0.00038   18.1   3.3   31   63-93    118-154 (462)
 20 cd01674 Homoaconitase_Swivel H  52.2      15 0.00039   18.0   3.0   30  175-204    53-84  (129)
 21 pfam06135 DUF965 Bacterial pro  48.7      16  0.0004   17.9   2.6   32  137-168    44-77  (79)
 22 PRK05473 hypothetical protein;  46.4      17 0.00043   17.7   2.5   31  138-168    48-80  (86)
 23 COG1515 Nfi Deoxyinosine 3'end  42.2      11 0.00027   19.0   0.9   26  101-126    82-107 (212)
 24 pfam01314 AFOR_C Aldehyde ferr  40.9      20 0.00052   17.3   2.2   32  155-187   348-379 (382)
 25 pfam08893 DUF1839 Domain of un  40.1      20 0.00051   17.3   2.0   27  182-208   219-245 (320)
 26 PRK01641 leuD isopropylmalate   39.2      32 0.00082   16.0   3.0   12  155-166   164-175 (201)
 27 KOG3407 consensus               38.1      16 0.00042   17.8   1.3   17  114-130    53-69  (151)
 28 PRK09849 putative oxidoreducta  37.3      24 0.00062   16.8   2.1   32  154-185   651-682 (702)
 29 cd01218 PH_phafin2 Phafin2  Pl  34.9      28  0.0007   16.4   2.1   31  134-167    67-97  (104)
 30 COG0066 LeuD 3-isopropylmalate  34.4      39 0.00099   15.5   2.8   11   68-78     78-88  (191)
 31 pfam07286 DUF1445 Protein of u  34.1      28 0.00073   16.3   2.0   44   11-54      8-63  (143)
 32 pfam04084 ORC2 Origin recognit  34.0      20 0.00052   17.3   1.3   13   66-78    118-130 (316)
 33 cd01577 IPMI_Swivel Aconatase-  31.2      44  0.0011   15.2   2.8   30  175-204    25-56  (91)
 34 TIGR01070 mutS1 DNA mismatch r  30.5      15 0.00037   18.1   0.1   15  116-130   410-424 (863)
 35 KOG2745 consensus               29.4      47  0.0012   15.0   2.6   27  146-172    93-119 (321)
 36 pfam11641 Antigen_Bd37 Glycosy  29.4      47  0.0012   15.0   2.9   34  154-187   138-179 (224)
 37 cd01220 PH_CDEP Chondrocyte-de  29.1      39   0.001   15.5   2.1   34  131-167    63-96  (99)
 38 KOG3495 consensus               28.7      48  0.0012   14.9   2.7   21  146-166    12-32  (50)
 39 pfam04870 DUF644 Protein of un  27.4      51  0.0013   14.8   2.7   31  178-208   286-316 (323)
 40 COG2238 RPS19A Ribosomal prote  26.1      54  0.0014   14.6   2.6   55  140-194    47-111 (147)
 41 PRK00439 leuD 3-isopropylmalat  24.7      57  0.0015   14.5   2.9   12   68-79     64-75  (163)
 42 cd01219 PH_FGD FGD (faciogenit  23.3      59  0.0015   14.4   2.1   36  129-167    63-98  (101)
 43 TIGR02177 PorB_KorB 2-oxoacid:  23.3      61  0.0015   14.3   3.0   39  137-175    77-115 (302)
 44 pfam08589 DUF1770 Fungal prote  23.2      50  0.0013   14.8   1.7   15    6-20     67-81  (96)
 45 COG2247 LytB Putative cell wal  22.9      62  0.0016   14.2   3.0   13  183-196   146-158 (337)
 46 pfam12149 HSV_VP16_C Herpes si  22.8      38 0.00096   15.6   1.0   21    8-33      9-29  (30)
 47 pfam09974 DUF2209 Uncharacteri  22.8      62  0.0016   14.2   5.6  116   27-166     1-127 (128)
 48 PRK11181 23S rRNA (guanosine-2  22.4      63  0.0016   14.2   3.4   15  115-129    95-109 (244)
 49 pfam08459 UvrC_HhH_N UvrC Heli  22.1      64  0.0016   14.1   2.9   37  106-142    70-116 (154)
 50 KOG3668 consensus               21.4      55  0.0014   14.5   1.6   15  152-167   212-226 (269)
 51 COG3081 Nucleoid-associated pr  21.4      66  0.0017   14.1   3.4   22  161-182   242-269 (335)
 52 pfam09288 UBA_3 Fungal ubiquit  21.0      68  0.0017   14.0   2.5   25  177-206    19-43  (55)
 53 pfam09010 AsiA Anti-Sigma Fact  20.7      68  0.0017   14.0   2.2   23  144-166    10-32  (91)
 54 pfam08714 Fae Formaldehyde-act  20.6      62  0.0016   14.2   1.7   34   80-114   106-144 (160)
 55 KOG3062 consensus               20.6      69  0.0018   13.9   2.6   34  113-146    72-105 (281)
 56 pfam02334 RTP Replication term  20.3      51  0.0013   14.8   1.3   13  154-166   104-116 (122)
 57 COG3596 Predicted GTPase [Gene  20.2      59  0.0015   14.4   1.6   23  144-166   221-243 (296)

No 1  
>PRK13926 junction RNase; Provisional
Probab=100.00  E-value=0  Score=492.97  Aligned_cols=200  Identities=36%  Similarity=0.527  Sum_probs=190.7

Q ss_pred             CCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEEC
Q ss_conf             7886888999999779948999842787775222559999987010823311520289999987552110123-078851
Q gi|254781076|r    7 PERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSA-IISISS   85 (209)
Q Consensus         7 ~~~p~~~~E~~l~~~~~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~   85 (209)
                      +..|||++|++|++.|+.+|||||||||||||||||+|||+++......+++|||+||+++|++||+.|++++ .|++++
T Consensus         5 ~~~p~~~~E~~l~~~G~~~I~GVDEaGRG~laGPvvvaaVil~~~~~~~~~~DSKkLs~kkRe~l~~~I~~~~~~~~i~~   84 (212)
T PRK13926          5 STMPDWALEREHWRRGLFRVAGVDEAGRGAWAGPITVAAVILPGTPGEYPFRDSKQLSPAARERLAAKVREVAVAWAVEH   84 (212)
T ss_pred             CCCCCHHHHHHHHHCCCCEEEEECCCCCCCCHHHHEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHEEEE
T ss_conf             89969799999998799719866576866553433479999788666357870353999999999999986412331366


Q ss_pred             CCHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             56799852047999886543210025753211012653224662122687114786520023666654775899999998
Q gi|254781076|r   86 ASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAH  165 (209)
Q Consensus        86 ~~~~eID~~ni~~A~~~a~~~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~  165 (209)
                      ++++|||++||++||.+||++|+.+|...++.+++|+...+.  +.++.+++|||+++++||||||||||+||++|.+|+
T Consensus        85 ~s~~eID~~nI~~At~~am~rai~~l~~~~~~v~~D~~~~~~--~~~~~~~~KGD~~~~~IAAASIiAKV~RD~~M~~l~  162 (212)
T PRK13926         85 AWPEEIDRLNVLGATHAAAERALARLPPPPQALVTDYLRLRT--PLPLLAPPKADALSYSVAAASLLAKTERDRLMAELD  162 (212)
T ss_pred             ECHHHHHHHCHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCC--CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             589998750709999999999998658887679856874799--988050278634433127889999999899999999


Q ss_pred             HHCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHC
Q ss_conf             8777988102899999899999998285830107848886403
Q gi|254781076|r  166 KKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLTFRPLRNLS  208 (209)
Q Consensus       166 ~~~p~Ygf~~nkGYgT~~H~~ai~~~G~~~~HR~Sf~~vk~l~  208 (209)
                      ++||+|||++||||||++|+++|++||+|++||+||+||+++-
T Consensus       163 ~~yP~Ygf~~nkGYgTk~H~~ai~~~G~~~~HR~Sf~Pi~~~~  205 (212)
T PRK13926        163 ALYPGYGFAAHKGYGAPAHRAALLALGVSEVHRRRYAPIAQLL  205 (212)
T ss_pred             HHCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHCCCCHHHHHHH
T ss_conf             8787998200579782999999998495976768868799999


No 2  
>PRK00015 rnhB ribonuclease HII; Validated
Probab=100.00  E-value=0  Score=468.07  Aligned_cols=195  Identities=51%  Similarity=0.766  Sum_probs=187.3

Q ss_pred             CCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECC
Q ss_conf             886888999999779948999842787775222559999987010823311520289999987552110123-0788515
Q gi|254781076|r    8 ERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSA-IISISSA   86 (209)
Q Consensus         8 ~~p~~~~E~~l~~~~~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~   86 (209)
                      .+|++++|+.|+..|+.+|+|||||||||++||||+|||+++++..+.||+|||+||+++|++||+.|++++ .|+++++
T Consensus         2 ~~p~~~~e~~l~~~g~~~ViGiDEaGRG~~~GP~vvaav~~~~~~~~~gv~DSK~Ls~~kR~~l~~~I~~~~~~~~i~~~   81 (197)
T PRK00015          2 LVPMLSFEKALLKQGLGLIAGVDEAGRGPLAGPVVAAAVILDPNRIILGLNDSKKLSEKKREALYEEIKEKALAWSVGIA   81 (197)
T ss_pred             CCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHEEEC
T ss_conf             98727999999987990799863688787600016899998875676777310109999999999999998877631315


Q ss_pred             CHHHHHHHCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             67998520479998865432100257532110126532246621226871147865200236666547758999999988
Q gi|254781076|r   87 SHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHK  166 (209)
Q Consensus        87 ~~~eID~~ni~~A~~~a~~~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~  166 (209)
                      +|+|||++||++|+.++|++++.+|..+|+.++|||+..+.  +.++.+++|||++|++||||||||||+||++|.+|++
T Consensus        82 ~~~eID~~ni~~a~~~a~~~al~~l~~~~~~i~vDg~~~~~--~~~~~~~~KaD~~~~~VaAASIvAKv~RD~~m~~l~~  159 (197)
T PRK00015         82 SPEEIDELNILEATMLAMRRAVAGLSVKPDYVLIDGNPVPV--PIPQEAIVKGDAKSPSIAAASILAKVTRDRLMEELDK  159 (197)
T ss_pred             CHHHHHHHCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCC--CCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             79997400709999999999999649999999985999999--9974888525210035778899999899999999998


Q ss_pred             HCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHH
Q ss_conf             77798810289999989999999828583010784888
Q gi|254781076|r  167 KYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLTFRPL  204 (209)
Q Consensus       167 ~~p~Ygf~~nkGYgT~~H~~ai~~~G~~~~HR~Sf~~v  204 (209)
                      +||+|||++||||||++|+++|+++|+|++||+||+||
T Consensus       160 ~yp~Yg~~~nkGY~T~~H~~ai~~~G~~~~HR~S~~pi  197 (197)
T PRK00015        160 EYPGYGFAKHKGYGTKAHLEALKKHGPTPIHRRSFAPV  197 (197)
T ss_pred             HCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHCCCCCCC
T ss_conf             78898986587869799999999849698873998899


No 3  
>PRK13925 rnhB ribonuclease HII; Provisional
Probab=100.00  E-value=0  Score=459.96  Aligned_cols=184  Identities=43%  Similarity=0.618  Sum_probs=174.7

Q ss_pred             CCEEEEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECCCHHHHHHHCHH
Q ss_conf             9489998427877752225599999870108----23311520289999987552110123-078851567998520479
Q gi|254781076|r   23 MWPVAGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSA-IISISSASHQYIDKHNIH   97 (209)
Q Consensus        23 ~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~~~~eID~~ni~   97 (209)
                      -.+|||||||||||||||||+|||+++++..    ..||+|||+||+++|++||+.|++++ .|+++.++++|||++||+
T Consensus         7 ~g~IiGvDEaGRG~laGPvvvaav~~~~~~~~~l~~~gv~DSKkLs~kkR~~l~~~I~~~~~~~~i~~~s~~eID~~nI~   86 (200)
T PRK13925          7 SGLIAGVDEVGRGCLFGPVVAAAVILPESAAEELLAAGLTDSKKLSQRRRAQLVPLIETVAIAWGIGQASAREIDRLNIL   86 (200)
T ss_pred             CCCEEEECCCCCCCCHHCEEEEEEEEECCCCHHHHHCCCHHHHHCCHHHHHHHHHHHHHHHHEEEEEEECHHHHHHHCHH
T ss_conf             99899872888666410017999998065542230123404551578889999887875211028999089999875849


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             99886543210025753211012653224662122687114786520023666654775899999998877798810289
Q gi|254781076|r   98 KATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHV  177 (209)
Q Consensus        98 ~A~~~a~~~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~Ygf~~nk  177 (209)
                      +||.+||++|+.+|..+|+.++|||+...+.++.++.+++|||+++++||||||||||+||++|.+|+++||+|||++||
T Consensus        87 ~At~~am~~ai~~l~~~~~~vlvDG~~~~~~~~~~~~~ivKgD~~~~~IaAASIIAKV~RD~~M~~l~~~yP~Y~f~~nk  166 (200)
T PRK13925         87 QATELAMLRALQKLPSPPDLCLVDGNQPIRLLPGPQRTVVKGDSRSAAIAAASILAKVWRDALIKRLARRYPGYGLERNK  166 (200)
T ss_pred             HHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCEEEECCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             99999999999863899778997368556778867477528971111005888999999999999999878699841265


Q ss_pred             CCCCHHHHHHHHHCCCCCCCCCCHHHHHH
Q ss_conf             99998999999982858301078488864
Q gi|254781076|r  178 GYPTAKHQQVIKEKGPSCIHRLTFRPLRN  206 (209)
Q Consensus       178 GYgT~~H~~ai~~~G~~~~HR~Sf~~vk~  206 (209)
                      ||||++|+++|++||+|++||+||+||..
T Consensus       167 GYgTk~H~~ai~~~G~s~~HRkSf~P~~~  195 (200)
T PRK13925        167 GYGTAKHRQALLQLGPTPLHRQSFLPCLI  195 (200)
T ss_pred             CCCCHHHHHHHHHHCCCHHHCCCCHHHHH
T ss_conf             87819999999983949778698687999


No 4  
>cd07182 RNaseH_typeII_bacteria_HII_like bacterial Ribonuclease HII-like. Bacterial ribonuclease (RNase) HII has a role in primer removal based on its involvement in ribonucleotide-specific catalytic activity in the presence of RNA/DNA hybrid substrates. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII- double deletion of these leads to cellular lethality. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli.
Probab=100.00  E-value=0  Score=445.76  Aligned_cols=178  Identities=56%  Similarity=0.803  Sum_probs=171.6

Q ss_pred             EEEECCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECCCHHHHHHHCHHHHHHHHHH
Q ss_conf             99842787775222559999987010823311520289999987552110123-07885156799852047999886543
Q gi|254781076|r   27 AGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSA-IISISSASHQYIDKHNIHKATLDAIY  105 (209)
Q Consensus        27 iGvDEaGRG~~~GPlvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~~~~eID~~ni~~A~~~a~~  105 (209)
                      +|||||||||++||||+|+|+++.+..+.||+|||+||+++|++||+.|++++ .|++++++|+|||++||++|+.+||+
T Consensus         1 aGiDEaGRG~~~GP~vvaav~~~~~~~~~gv~DSK~Lt~k~R~~l~~~I~~~~~~~~v~~~s~~eID~~ni~~A~~~a~~   80 (179)
T cd07182           1 AGVDEAGRGPLAGPVVAAAVILPPDFEIEGLNDSKKLSEKKREELYEEIKEKALAWGIGIASPEEIDRINILQATLLAMR   80 (179)
T ss_pred             CCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCHHHHCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHCCHHHHHHHHHH
T ss_conf             99876686662100158999988867866542665389999999999986211306778669999986399999999999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHH
Q ss_conf             21002575321101265322466212268711478652002366665477589999999887779881028999998999
Q gi|254781076|r  106 HAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQ  185 (209)
Q Consensus       106 ~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~Ygf~~nkGYgT~~H~  185 (209)
                      +++++|...++.++|||+.++ .+++++.+++|||++|++||||||||||+||++|.+|+++||+|||++||||||++|+
T Consensus        81 ~ai~~l~~~~~~i~vDg~~~~-~~~~~~~~i~kaD~~~~~VaaASIiAKv~RD~~m~~l~~~yP~Yg~~~nkGYgT~~H~  159 (179)
T cd07182          81 RAVEGLPVKPDYVLVDGNRLP-PLPIPQEAIVKGDAKSASIAAASILAKVTRDRLMIELDKKYPGYGFAKHKGYGTKEHL  159 (179)
T ss_pred             HHHHHCCCCCCEEEEECCCCC-CCCCCEEEEECCCCEEEEEEHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHH
T ss_conf             999866899868997466388-9998869995487356565277889898899999999987879884127688809999


Q ss_pred             HHHHHCCCCCCCCCCHHHHH
Q ss_conf             99998285830107848886
Q gi|254781076|r  186 QVIKEKGPSCIHRLTFRPLR  205 (209)
Q Consensus       186 ~ai~~~G~~~~HR~Sf~~vk  205 (209)
                      ++|++||+|++||+||+|++
T Consensus       160 ~aI~~~G~~~~HR~Sf~~~~  179 (179)
T cd07182         160 EALKKYGPTPIHRRSFAPVK  179 (179)
T ss_pred             HHHHHHCCCHHHCCCCCCCC
T ss_conf             99998494977757986869


No 5  
>COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair]
Probab=100.00  E-value=0  Score=430.82  Aligned_cols=184  Identities=52%  Similarity=0.788  Sum_probs=174.6

Q ss_pred             EEEEEECCCCCCCCCCEEEEEEEECCCCCC--CCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECCCHHHHHHHCHHHHHH
Q ss_conf             899984278777522255999998701082--3311520289999987552110123-0788515679985204799988
Q gi|254781076|r   25 PVAGIDEVGRGALAGPVVVAAIILDPNNIP--FGINDSKKISHKKREELYEKITSSA-IISISSASHQYIDKHNIHKATL  101 (209)
Q Consensus        25 ~IiGvDEaGRG~~~GPlvvaav~~~~~~~~--~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~~~~eID~~ni~~A~~  101 (209)
                      +|+|||||||||++||||+|||+++++..+  .|++||||||+++|++||+.|++.+ .|+++++++++||++||++|++
T Consensus         1 ~vaGIDEAGRGpl~GPvV~Aavil~~~~~~~~~Gl~DSKkLs~~kRe~L~~~I~~~a~~~~v~~~~~~~Id~~ni~~a~~   80 (199)
T COG0164           1 LVAGVDEAGRGPLAGPVVAAAVILPPDRLPKKLGLKDSKKLSPKKREELFEEIKEKALAWGVGIIPAEEIDELNILEATK   80 (199)
T ss_pred             CCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEECCHHHHHHHHHHHHHH
T ss_conf             92760577867752622589999773223334586652307999999999999865227999972789886742999999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             65432100257532110126532246621226871147865200236666547758999999988777988102899999
Q gi|254781076|r  102 DAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPT  181 (209)
Q Consensus       102 ~a~~~ai~~l~~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~Ygf~~nkGYgT  181 (209)
                      +||++|+.+|..+++.++|||+.++..++.+..+++|||++|++||||||||||+||++|.+|++.||+|||+.||||||
T Consensus        81 ~am~~av~~l~~~~~~vlvD~~~~~~~l~~~~~a~~KgDa~~~~IaAASIvAKV~RDr~m~~l~~~yp~Y~~~~~~GY~T  160 (199)
T COG0164          81 LAMRRAVAGLSSQPDLVLVDGNDLPLGLPQPAVAIIKGDAKSPSIAAASILAKVTRDRLMEELAKEYPEYGFDKGSGYPT  160 (199)
T ss_pred             HHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             99999998266668889981788642378776034535311378999999999999999999986586767625787798


Q ss_pred             HHHHHHHHHCCCCC-CCCCCHHHHHHHC
Q ss_conf             89999999828583-0107848886403
Q gi|254781076|r  182 AKHQQVIKEKGPSC-IHRLTFRPLRNLS  208 (209)
Q Consensus       182 ~~H~~ai~~~G~~~-~HR~Sf~~vk~l~  208 (209)
                      +.|.+++.++|+++ +||+||+|++++.
T Consensus       161 ~~h~~a~~~~~~~~~~hR~Sf~~vk~~~  188 (199)
T COG0164         161 DPHTEALLKKGGTPGIHRRSFAPVRRLL  188 (199)
T ss_pred             HHHHHHHHHHCCCCCEEECCCHHHHHHH
T ss_conf             3999999985699862222428899874


No 6  
>cd06266 RNaseH_typeII Ribonuclease H type II. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, however, no prokaryotic genome contained the combination of only RNase HI and HIII. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escheri
Probab=100.00  E-value=0  Score=389.53  Aligned_cols=179  Identities=53%  Similarity=0.779  Sum_probs=167.3

Q ss_pred             EEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECCCHHHHHHHCHHHHHH
Q ss_conf             998427877752225599999870108----23311520289999987552110123-0788515679985204799988
Q gi|254781076|r   27 AGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSA-IISISSASHQYIDKHNIHKATL  101 (209)
Q Consensus        27 iGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~~~~eID~~ni~~A~~  101 (209)
                      +|||||||||+|||||+|||+++.+..    ..||+|||+||+++|++||+.|++.+ .|++++++|+|||++||++++.
T Consensus         1 ~GiDEaGRG~~~GP~vvaav~~~~~~~~~l~~~gv~DSK~Ls~~kR~~l~~~I~~~~~~~~v~~~s~~~Id~~ni~~~~~   80 (193)
T cd06266           1 AGIDEAGRGPLAGPVVAAAVILPKENIEILKILGVKDSKKLSEKKREELFEEIKEEALAYAIGIISPEEIDELNILQATA   80 (193)
T ss_pred             CCCCCCCCCCCCCCEEEEEEEECHHHHHHHHHCCCCCHHHCCHHHHHHHHHHHCCCCEEEEEEECCHHHHHHCCHHHHHH
T ss_conf             99857786772044068999981354003432577511018999999998752356448999967899997557899999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCC--------CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             65432100257532110126532246--------6212268711478652002366665477589999999887779881
Q gi|254781076|r  102 DAIYHAVENLQVIPRSALIDGRSIPE--------DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGF  173 (209)
Q Consensus       102 ~a~~~ai~~l~~~~~~ilIDg~~~~~--------~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~Ygf  173 (209)
                      ++|.+++.++..+++.++|||+..++        ..+.++.+++|||++|++||||||+|||+||++|.+|+++||+|+|
T Consensus        81 ~~~~~ai~~l~~~~~~v~vD~~~~~~~~~~~~~~~~~~~~~~~~kaD~~~~~VaAASIiAKv~RD~~m~~l~~~~p~y~~  160 (193)
T cd06266          81 LAMARAILNLGVKPDEVLVDGNGVPEKYFALEKKFLPIPVTAIVKGDSKSPSVAAASILAKVTRDRLMEELDEEYPGYGF  160 (193)
T ss_pred             HHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHCCCCCCCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             99999999648999999989999827776542026898717886155421788899999999999999999987879998


Q ss_pred             CCCCCCCCHHHHHHHHHCCCC-CCCCCCHHHHH
Q ss_conf             028999998999999982858-30107848886
Q gi|254781076|r  174 DSHVGYPTAKHQQVIKEKGPS-CIHRLTFRPLR  205 (209)
Q Consensus       174 ~~nkGYgT~~H~~ai~~~G~~-~~HR~Sf~~vk  205 (209)
                      +.|+||||+.|.+++.++|++ ++||+||+|++
T Consensus       161 ~~g~GY~t~~h~~~~~~~g~~~~~hR~sf~~~~  193 (193)
T cd06266         161 AKGKGYPTDPHTEAILKYGPTEPIHRRSFKTVK  193 (193)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCCHHHCCCCCCCC
T ss_conf             577583999999999986859566566876869


No 7  
>pfam01351 RNase_HII Ribonuclease HII.
Probab=100.00  E-value=0  Score=385.57  Aligned_cols=177  Identities=46%  Similarity=0.674  Sum_probs=159.5

Q ss_pred             EEEECCCCCCCCCCEEEEEEEECCCCCC----CCCCCCCCCCHHHHHHHHHHHCCCC------EEEEECCCHHHHHHHCH
Q ss_conf             9984278777522255999998701082----3311520289999987552110123------07885156799852047
Q gi|254781076|r   27 AGIDEVGRGALAGPVVVAAIILDPNNIP----FGINDSKKISHKKREELYEKITSSA------IISISSASHQYIDKHNI   96 (209)
Q Consensus        27 iGvDEaGRG~~~GPlvvaav~~~~~~~~----~~i~DSK~Ls~~~R~~l~~~i~~~~------~~~i~~~~~~eID~~ni   96 (209)
                      +|||||||||+|||||+|||+++++...    .||+|||+||+++|+++++.|++.+      .|.+...++++||+.||
T Consensus         1 aGiDEaGRG~~~GPlvvaav~l~~~~~~~l~~~gv~DSK~Ls~kkR~~l~~~I~~~~~~~~~~~~~i~~~~~~~id~~~i   80 (197)
T pfam01351         1 AGIDEVGRGPLAGPLVVAAVYLPPERLIELRKLGVKDSKKLSDKKREELAELIKKRIETRKLVAGNIKYAEANEINLNNI   80 (197)
T ss_pred             CCCCCCCCCCCCCCEEEEEEEEECCCCHHHHHCCCHHHHHCCHHHHHHHHHHHHHHHHHHHCEEEEEEEECHHHHCHHHH
T ss_conf             99877587676022068999980221556664332022017999999999999974101110244556603756269999


Q ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC------EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             9998865432100257532110126532246621------2268711478652002366665477589999999887779
Q gi|254781076|r   97 HKATLDAIYHAVENLQVIPRSALIDGRSIPEDLP------CQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPD  170 (209)
Q Consensus        97 ~~A~~~a~~~ai~~l~~~~~~ilIDg~~~~~~~~------~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~  170 (209)
                      .+++..+|.+++..+...++.++|||+..+..+.      .++.+++|||++|++||||||||||+||+.|+ +..+||+
T Consensus        81 ~~a~~~~~~~~l~~~~~~~~~i~vD~~~~~~~~~~~~~~~~~~~~~~KaD~~~~~VAAASIlAKv~RD~~i~-~~~~~p~  159 (197)
T pfam01351        81 LHALHLAMIRAVQKLGVKPDEILVDGFTPPKSLPMKQEAIFKVTAEHKADSKYLSVAAASIIAKVTRDEMLE-LLKRFPG  159 (197)
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-HHHHCCC
T ss_conf             999999999999845999998998898894201222430257623232012203431437899999999999-9866879


Q ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCC----CCCCCHHHH
Q ss_conf             8810289999989999999828583----010784888
Q gi|254781076|r  171 YGFDSHVGYPTAKHQQVIKEKGPSC----IHRLTFRPL  204 (209)
Q Consensus       171 Ygf~~nkGYgT~~H~~ai~~~G~~~----~HR~Sf~~v  204 (209)
                      |+|++||||||++|+++|.++|++|    +||+||+||
T Consensus       160 y~f~~~~GY~t~~h~~~i~~~g~~~~~~~~hR~Sf~~v  197 (197)
T pfam01351       160 YGLDKGSGYPSDPHTEALLKLGATPWLPDFHRRSFATV  197 (197)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf             99624868498999999999682999884126888897


No 8  
>cd07180 RNaseH_typeII_Archaea_like Archaeal ribonuclease  HII. Ribonuclease (RNase) H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair. Some archaeal RNase HII show broad divalent cation specificity. It is proposed that three of the four acidic residues at the active site are involved in metal binding and the fourth one involved in the catalytic process in archaea. Most archaeal genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears tha
Probab=100.00  E-value=0  Score=376.72  Aligned_cols=177  Identities=36%  Similarity=0.585  Sum_probs=154.4

Q ss_pred             EEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCC-EEEEECCCHHHHHH----HCHH
Q ss_conf             998427877752225599999870108----23311520289999987552110123-07885156799852----0479
Q gi|254781076|r   27 AGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSA-IISISSASHQYIDK----HNIH   97 (209)
Q Consensus        27 iGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~-~~~i~~~~~~eID~----~ni~   97 (209)
                      ||||||||||||||||+|||+++++..    ..||+|||+||+++|++|++.|++++ .|++++++++|||+    .||+
T Consensus         1 ~GvDEaGRG~laGPvvvaav~~~~~~~~~l~~~gv~DSKkLs~kkR~~l~~~I~~~~~~~~i~~~s~~eID~~~~~~nln   80 (204)
T cd07180           1 CGIDEAGRGPVIGPMVVAGVAIDEESLKKLKSLGVKDSKKLTPKKREELYNEILKVADDVVIVIVSPEEIDERREAHNLN   80 (204)
T ss_pred             CCCCCCCCCCCCCCCEEEEEEECHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEEECHHHHHHHHHHHHHH
T ss_conf             99987787662101168999984553335553677535008899999999999973537899997799997885899999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCCC---------C--CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99886543210025753211012653224---------6--621226871147865200236666547758999999988
Q gi|254781076|r   98 KATLDAIYHAVENLQVIPRSALIDGRSIP---------E--DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHK  166 (209)
Q Consensus        98 ~A~~~a~~~ai~~l~~~~~~ilIDg~~~~---------~--~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~  166 (209)
                      .++..+|.++++++..+++.+++|+....         .  ..+..+.+++|||+++++||||||||||+||++|.+|++
T Consensus        81 ~~~~~a~~~~i~~l~~~~~~i~iD~~~~~~~~~~~~~~~~~~~~~~v~~~~KgD~k~~~IAAASIiAKv~RD~~M~~l~~  160 (204)
T cd07180          81 ELEAEAFAELINRLSDKPDIVYVDACDVNEERFAEELRERLNSGVEVIAEHKADAKYPVVSAASIIAKVERDREIEELKE  160 (204)
T ss_pred             HHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHCCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999955778999998167876134433033235888726873375222177899999999999999999998


Q ss_pred             HCCCCCCCCCCCCCC-HHHHHH----HHHCC-CCCCCCCCHHHHHHH
Q ss_conf             777988102899999-899999----99828-583010784888640
Q gi|254781076|r  167 KYPDYGFDSHVGYPT-AKHQQV----IKEKG-PSCIHRLTFRPLRNL  207 (209)
Q Consensus       167 ~~p~Ygf~~nkGYgT-~~H~~a----i~~~G-~~~~HR~Sf~~vk~l  207 (209)
                      +||+||    +|||| |.|+++    |+++| ++++||+||+|||+|
T Consensus       161 ~yp~yG----~GYpsd~~t~~~l~~~i~~~g~~~~~hR~S~~~vk~~  203 (204)
T cd07180         161 EYGDFG----SGYPSDPRTIKFLRNYYREHGELPPIVRKSWKTVKRL  203 (204)
T ss_pred             HCCCCC----CCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHH
T ss_conf             769989----8799977899999999873289996631881758975


No 9  
>cd07181 RNaseH_typeII_eukaryota_like Eukaryotic Ribonuclease HII; putative role in Okazaki fragment removal during replication. Ribonuclease (RNase) HII endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is a type II RNase H that is active during replication and is believed to play a role in removal
Probab=100.00  E-value=0  Score=362.64  Aligned_cols=181  Identities=31%  Similarity=0.390  Sum_probs=146.0

Q ss_pred             EEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCC---EEEEECCCHHHHHHH-----
Q ss_conf             998427877752225599999870108----23311520289999987552110123---078851567998520-----
Q gi|254781076|r   27 AGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSA---IISISSASHQYIDKH-----   94 (209)
Q Consensus        27 iGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~---~~~i~~~~~~eID~~-----   94 (209)
                      ||||||||||||||||+|||+++.+..    ..||+|||+||+++|++||+.|++.+   .|+++.++++|||+.     
T Consensus         1 IGvDEaGRGplaGPvV~aav~~~~~~~~~l~~~gv~DSKkLs~kkRe~l~~~I~~~~~~~~~~i~~~~~~eId~~~l~~~   80 (216)
T cd07181           1 LGIDEAGRGPVLGPMVYGIAYCPISYEEDLKKLGFADSKTLTEEKREELFKKIKEKSEALGWATRILSPQYISAKMLART   80 (216)
T ss_pred             CCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHCCCCHHCCCCHHHHHHHHHHHHHHCCCEEEEEEEECHHHHHHHHHHHH
T ss_conf             99778786662164057999970222303431487120119999999999999852735078999946999889898864


Q ss_pred             --CHHHHHHHHHHH---HCCCCCCCCCCCCCCCCCCCC---------CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             --479998865432---100257532110126532246---------621226871147865200236666547758999
Q gi|254781076|r   95 --NIHKATLDAIYH---AVENLQVIPRSALIDGRSIPE---------DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRL  160 (209)
Q Consensus        95 --ni~~A~~~a~~~---ai~~l~~~~~~ilIDg~~~~~---------~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~  160 (209)
                        |++.....++.+   .+.....+++.++||+...+.         ..+.+..+++|||++|++||||||||||+||++
T Consensus        81 ~~~ln~l~~~~~~~~i~~~~~~~~~~~~i~iD~~g~~~~~~~~l~~~~~~~~~~~~~KgD~~~~~IaAASIlAKV~RD~~  160 (216)
T cd07181          81 KYNLNEISHDAAIGLIKSVLDKGVNVTEVYVDTVGPPEKYQAKLKKLFPGIKFTVEKKADSLYPIVSAASIVAKVTRDRA  160 (216)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCHH
T ss_conf             75599999999999999999659998779981899867887653103899654772126545520237888999974599


Q ss_pred             HHHHHHHCCCCCCCCC--CCCCC-HHHHHHHHH-----CCCCCCCCCCHHHHHHH
Q ss_conf             9999887779881028--99999-899999998-----28583010784888640
Q gi|254781076|r  161 MRIAHKKYPDYGFDSH--VGYPT-AKHQQVIKE-----KGPSCIHRLTFRPLRNL  207 (209)
Q Consensus       161 m~~l~~~~p~Ygf~~n--kGYgT-~~H~~ai~~-----~G~~~~HR~Sf~~vk~l  207 (209)
                      |.+|+..||.|+|..|  +|||| +.|+++|++     +|+|++||+||+||++|
T Consensus       161 m~~l~~~~~~~~~~~~~GsGYPsdp~t~~~L~~~~~~~~g~~~~hR~Sw~~v~~l  215 (216)
T cd07181         161 LKNWQFDEYLIDPDGDFGSGYPSDPKTKKWLKKNVDPVFGFPSLVRFSWSTAKKL  215 (216)
T ss_pred             HHHHHHHCCCCCCCCCCCEECCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHH
T ss_conf             9987645645544688785789838899999955556689996640782999985


No 10 
>cd06590 RNaseH_typeII_bacteria_HIII_like bacterial Ribonuclease HIII-like. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII. RNases HIII are distinguished by having a large (70-90 residues) N-terminal extension of unknown function. In addition, the active site of RNase HIII differs from that of other RNases H; replacing the fourth residue (aspartate) of the acidic "DEDD" motif with a glutamate. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, however, no prokaryotic genomes contain the combination of both RNase HI and HIII. This mutual exclusive gen
Probab=100.00  E-value=0  Score=338.80  Aligned_cols=178  Identities=30%  Similarity=0.358  Sum_probs=147.5

Q ss_pred             EEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCHHHH---
Q ss_conf             998427877752225599999870108----2331152028999998755211012307885156799852047999---
Q gi|254781076|r   27 AGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKA---   99 (209)
Q Consensus        27 iGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~ni~~A---   99 (209)
                      ||+|||||||||||||+|||+++++..    ..||+|||+||+++|++||+.|++.+.|++..+++++||.+.....   
T Consensus         1 IGiDEaGRG~l~GPvv~aav~~~~~~~~~l~~lgv~DSKkLs~kkR~~l~~~I~~~~~~~~~~~~~~~~n~~~~~~~n~n   80 (208)
T cd06590           1 IGSDEVGKGDYFGPLVVAAVYVDKENISKLKKLGVKDSKKLTDKKIIRLAPKIKKKIPYSVLSLGPEKYNELYKKGKNLN   80 (208)
T ss_pred             CCCCCCCCCCCHHCCEEEEEEECHHHHHHHHHCCCCCHHHCCHHHHHHHHHHHHHHCCEEEEEECHHHHHHHHHHHHHHH
T ss_conf             98767787765102078999986575477876598532125899999999999984866899987899999998798899


Q ss_pred             --HHHHHHHHCCCCC---CCCCCCCCCCCCCC-----------CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             --8865432100257---53211012653224-----------6621226871147865200236666547758999999
Q gi|254781076|r  100 --TLDAIYHAVENLQ---VIPRSALIDGRSIP-----------EDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRI  163 (209)
Q Consensus       100 --~~~a~~~ai~~l~---~~~~~ilIDg~~~~-----------~~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~  163 (209)
                        ...++.++++++.   ..++.++||++..+           ...+.++.+++|||++|++||||||||||+||+.|.+
T Consensus        81 ~~~~~~~~~ai~~~~~~~~~~~~v~iD~~~~~~~~~~~l~~~~~~~~~~~~~~~KgD~k~~~VaAASIiAKv~rd~~m~~  160 (208)
T cd06590          81 KLKALLHNKAINNLLEKPKKPVAILIDQFASEKVYKRYLKKEKKIVKEPLIFRTKAESKHLAVAAASILARYAFLEKMEK  160 (208)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHCCCCCCCCCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999836899998998898870478898731367889876998223332278899999999999999999


Q ss_pred             HHHHCCCCCCCCCCCCCCHHHHHH---HHHCCCCCCCCC---CHHHHHHH
Q ss_conf             988777988102899999899999---998285830107---84888640
Q gi|254781076|r  164 AHKKYPDYGFDSHVGYPTAKHQQV---IKEKGPSCIHRL---TFRPLRNL  207 (209)
Q Consensus       164 l~~~~p~Ygf~~nkGYgT~~H~~a---i~~~G~~~~HR~---Sf~~vk~l  207 (209)
                      |+++   |||..||||||+.|+++   |++||++++||.   +|+|+++.
T Consensus       161 l~~~---Yg~~~~kGyGt~~~~~a~~~i~~yG~~~lhr~~k~~f~~~k~~  207 (208)
T cd06590         161 LSKQ---YGMKLPKGASSKVDEQAAEIIKKYGLEELKKVAKLHFKNTKKA  207 (208)
T ss_pred             HHHH---CCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHCHHHHHH
T ss_conf             8786---4987688998288999999999849618788998702158750


No 11 
>TIGR00729 TIGR00729 ribonuclease HII; InterPro: IPR004649   Ribonuclease HII 3.1.26.4 from EC cleaves RNA from DNA-RNA hybrids. Archaeal members of this subfamily of RNase H are designated RNase HII and one has been shown to be active as a monomer. A member from Homo sapiens was characterised as RNase HI, large subunit.; GO: 0004523 ribonuclease H activity, 0016070 RNA metabolic process.
Probab=100.00  E-value=0  Score=329.17  Aligned_cols=179  Identities=34%  Similarity=0.521  Sum_probs=149.6

Q ss_pred             EEEEECCCCCCCCCCEEEE-EEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCC------CCEEEEECCCHHHHHH-
Q ss_conf             9998427877752225599-999870108----233115202899999875521101------2307885156799852-
Q gi|254781076|r   26 VAGIDEVGRGALAGPVVVA-AIILDPNNI----PFGINDSKKISHKKREELYEKITS------SAIISISSASHQYIDK-   93 (209)
Q Consensus        26 IiGvDEaGRG~~~GPlvva-av~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~------~~~~~i~~~~~~eID~-   93 (209)
                      |+|||||||||+.|||||| +.+.++..+    ..||+|||+||+.+|+.||..|.+      .+.|.+..++|+|||+ 
T Consensus         1 v~GiDEAGRGpV~GPlVvag~~~~e~~~~~~L~~lGVkDSK~Lt~~~R~~L~~~i~~DneeL~~~~~~~~~i~p~eId~G   80 (235)
T TIGR00729         1 VAGIDEAGRGPVIGPLVVAGVFAIEEKREEELRKLGVKDSKKLTPGRRRELFRKIRQDNEELKLGRVEVLKITPEEIDRG   80 (235)
T ss_pred             CCEEECCCCCCCCCCCEEEEEEEECHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEEEEEECCCCCCC
T ss_conf             91110058887206523687765313566454406844630169668999999860886527886689998630014662


Q ss_pred             ----HC-HH----HHHHHHHHHHCCCCCCCC------CCCCCCCCCCCC------------------CCCEEEEEECCCC
Q ss_conf             ----04-79----998865432100257532------110126532246------------------6212268711478
Q gi|254781076|r   94 ----HN-IH----KATLDAIYHAVENLQVIP------RSALIDGRSIPE------------------DLPCQAFAVIKGD  140 (209)
Q Consensus        94 ----~n-i~----~A~~~a~~~ai~~l~~~~------~~ilIDg~~~~~------------------~~~~~~~~i~KgD  140 (209)
                          .+ ++    .+..+....++..|..+|      +.++||.....+                  ..+.++...||||
T Consensus        81 mskf~~~~~~~~n~~e~~~~~~~~~~l~~kpnir~~~~~vyvD~~~~~~~rfedsfk~~~~~~~~~~~~~~~v~aEhKAD  160 (235)
T TIGR00729        81 MSKFERTRNINLNENEIEKFSAAVIILIVKPNIRVKLSEVYVDSVDVKPKRFEDSFKLKREIKLKERGEEIKVIAEHKAD  160 (235)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCC
T ss_conf             12014227662058899999999864420466321412788833888840112457679999987517981899974778


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHH---CCCCCCCCCCCCCC-HHHHHHHHH----C-C-CCCCCCCCHHHHHHHC
Q ss_conf             652002366665477589999999887---77988102899999-899999998----2-8-5830107848886403
Q gi|254781076|r  141 SISLSIAAASIIAKVTRDRLMRIAHKK---YPDYGFDSHVGYPT-AKHQQVIKE----K-G-PSCIHRLTFRPLRNLS  208 (209)
Q Consensus       141 ~~~~~VaaASIiAKv~RD~~m~~l~~~---~p~Ygf~~nkGYgT-~~H~~ai~~----~-G-~~~~HR~Sf~~vk~l~  208 (209)
                      ++|+.||||||||||+||+.++.|.++   |+..|    +|||| |.|++||++    | | ++++.|.||+||++|.
T Consensus       161 ~kY~~VSAASIiAKV~RD~~ie~lk~~~rkyG~~G----SGYPSDP~T~ewL~~~~~~~mG~~P~~vR~~W~Tv~~l~  234 (235)
T TIGR00729       161 SKYPVVSAASIIAKVERDREIESLKRKPRKYGDIG----SGYPSDPRTREWLEEYFKSLMGELPDIVRRSWKTVRKLL  234 (235)
T ss_pred             CCCCCEEEEEEEEHHHHHHHHHHHHHCCCCCCCCC----CCCCCCHHHHHHHHHHHHHHCCCCCCCEECCCHHHHHCC
T ss_conf             88862232334202245688998720232146557----878976356899999999862765300006506755115


No 12 
>KOG2299 consensus
Probab=100.00  E-value=2.2e-36  Score=247.81  Aligned_cols=182  Identities=32%  Similarity=0.448  Sum_probs=140.1

Q ss_pred             CCCCEEEEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCC------CEEEEECCCHHH
Q ss_conf             799489998427877752225599999870108----2331152028999998755211012------307885156799
Q gi|254781076|r   21 KNMWPVAGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSS------AIISISSASHQY   90 (209)
Q Consensus        21 ~~~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~------~~~~i~~~~~~e   90 (209)
                      +....+.|||||||||+.||||.|+++.|.+..    ..|+.|||+|++.+|++||+.|++.      .-|++..++|.+
T Consensus        25 ~~~PcvlGIDEAGRGPVLGPMVYa~~ycP~~~~~~l~~lgfaDSK~L~e~kRe~lf~~i~~d~~~~~~vgwA~~~isP~~  104 (301)
T KOG2299          25 KSEPCVLGIDEAGRGPVLGPMVYAAAYCPLDYLEDLENLGFADSKTLTEAKREELFNKIKEDEELTSNVGWATDCISPRE  104 (301)
T ss_pred             CCCCEEEECCCCCCCCCCCCEEEEEEECCCHHHHHHHHCCCCCHHHCCHHHHHHHHHHHHHHHHHHHCEEEEEEECCHHH
T ss_conf             48864864343577875442045788435045435654586631110678999999998630133210035765268899


Q ss_pred             HH-------HHCHHHHHHHHH----HHHCCCCCCCCCCCCCCCCCCCC--------CCC-EEEEEECCCCCCCHHHHHHH
Q ss_conf             85-------204799988654----32100257532110126532246--------621-22687114786520023666
Q gi|254781076|r   91 ID-------KHNIHKATLDAI----YHAVENLQVIPRSALIDGRSIPE--------DLP-CQAFAVIKGDSISLSIAAAS  150 (209)
Q Consensus        91 ID-------~~ni~~A~~~a~----~~ai~~l~~~~~~ilIDg~~~~~--------~~~-~~~~~i~KgD~~~~~VaaAS  150 (209)
                      |-       ++|+++....+.    +++++. ......++||....+.        .+| +++..-.|||+.|+.|+|||
T Consensus       105 IS~~Ml~r~kynLNevshdsam~LI~~v~~~-gvnvteiyVDTVGpp~~Yq~kLek~FP~~k~tV~kKADSlfpiVS~AS  183 (301)
T KOG2299         105 ISASMLRRNKYNLNEVSHDSAMGLIDEVLDQ-GVNVTEIYVDTVGPPAKYQEKLEKRFPGIKFTVTKKADSLFPIVSAAS  183 (301)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH-CCCEEEEEEECCCCHHHHHHHHHHHCCCEEEEEEECCCCCCCCHHHHH
T ss_conf             8899888714780134358899999999984-875279997057985999999996589708998503665243201545


Q ss_pred             HHHHHHHHHHHHHHHH------HCCCCCCCCCCCCCC-HHHHHHHHH-----CCCCCCCCCCHHHHHHH
Q ss_conf             6547758999999988------777988102899999-899999998-----28583010784888640
Q gi|254781076|r  151 IIAKVTRDRLMRIAHK------KYPDYGFDSHVGYPT-AKHQQVIKE-----KGPSCIHRLTFRPLRNL  207 (209)
Q Consensus       151 IiAKv~RD~~m~~l~~------~~p~Ygf~~nkGYgT-~~H~~ai~~-----~G~~~~HR~Sf~~vk~l  207 (209)
                      |+|||+||+.+++..-      .-..||    +|||+ |++++||++     ||.+.+.|.||+|+++|
T Consensus       184 I~AKVtRD~alk~w~~~E~~~~~d~~~G----SGYP~DP~T~~wLk~~v~~VFGfp~lVRfSW~Ta~t~  248 (301)
T KOG2299         184 IVAKVTRDRALKEWQFEEKLSDPDEDLG----SGYPSDPETKAWLKENVDSVFGFPSLVRFSWKTAKTL  248 (301)
T ss_pred             HHHHHHHCCCCCEEEEEEECCCCCCCCC----CCCCCCHHHHHHHHHCCCCCCCCCCCEEEEHHHHHHH
T ss_conf             6665530110100454440346775556----8899980678999964640026850206438889998


No 13 
>PRK00996 ribonuclease HIII; Provisional
Probab=100.00  E-value=3.2e-35  Score=240.62  Aligned_cols=182  Identities=28%  Similarity=0.382  Sum_probs=142.0

Q ss_pred             CCCEEEEEECCCCCCCCCCEEEEEEEECCCCC----CCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHH---
Q ss_conf             99489998427877752225599999870108----23311520289999987552110123078851567998520---
Q gi|254781076|r   22 NMWPVAGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKH---   94 (209)
Q Consensus        22 ~~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~----~~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~---   94 (209)
                      ..+++||+||||+||+|||||||||+++++.+    ..||+|||+||+++|.+|++.|++.+.|++..++|+++|++   
T Consensus        86 ~~~~~iGsDE~G~Gd~FGPlvVaav~v~~~~~~~L~~lGVkDSK~Lsd~kI~~la~~I~~~~~~~~~~l~p~kYNel~~k  165 (303)
T PRK00996         86 DLRPHIGSDEVGKGDYFGPLTVAAVYVDKEQIPFLKKLGVDDSKKLTDTKIRQIAPQLREKIPHSVLLLSPEKYNELQAK  165 (303)
T ss_pred             CCCCCEEECCCCCCCCCCCCEEEEEEECHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCEEEEEECHHHHHHHHHH
T ss_conf             56762003587788876771899999779999999975996601189999999999999748779999886878999984


Q ss_pred             CHHHHHHHHHH--HHCCCC---CCCCCCCCCCCCCCCC-----------CCCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             47999886543--210025---7532110126532246-----------6212268711478652002366665477589
Q gi|254781076|r   95 NIHKATLDAIY--HAVENL---QVIPRSALIDGRSIPE-----------DLPCQAFAVIKGDSISLSIAAASIIAKVTRD  158 (209)
Q Consensus        95 ni~~A~~~a~~--~ai~~l---~~~~~~ilIDg~~~~~-----------~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD  158 (209)
                      +++...++||.  +||.+|   ...|+.++||++..+.           ....+....+|||+++++||||||||   |+
T Consensus       166 ~~Nln~ika~lH~~aI~~ll~k~~~~~~ilIDqF~~~~~~~~yl~~~~~~~~~~i~~~~Kae~~~~aVAAASIiA---R~  242 (303)
T PRK00996        166 GYNQNKLKAWLHNQAIDNLLQKPSQPEAIVIDQFASPEVYLKYLAKEKNKFRDPVTFETKAESKHLAVAAASIIA---RY  242 (303)
T ss_pred             HCCHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHH---HH
T ss_conf             348999999999999999983578998799716888078999987540478764488731554007899999999---99


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCHHH---HHHHHHCC------CCCCCCCCHHHHHH
Q ss_conf             99999988777988102899999899---99999828------58301078488864
Q gi|254781076|r  159 RLMRIAHKKYPDYGFDSHVGYPTAKH---QQVIKEKG------PSCIHRLTFRPLRN  206 (209)
Q Consensus       159 ~~m~~l~~~~p~Ygf~~nkGYgT~~H---~~ai~~~G------~~~~HR~Sf~~vk~  206 (209)
                      .++..++++-.+||+.--+|-|++.-   .+.++++|      ++..|=++.+-++.
T Consensus       243 ~Fl~~m~~ls~~~g~~lPkGAg~~v~~~a~~i~~~~G~~~L~~~aKlHFknt~ka~~  299 (303)
T PRK00996        243 AFLENMDKLSKEAGMTLPKGAGAKVDKVAAQIIKKYGKEALEKIAKLHFANTEKAQK  299 (303)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999998199787888788999999999985999999999886113999999


No 14 
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=99.96  E-value=1.3e-29  Score=205.70  Aligned_cols=180  Identities=27%  Similarity=0.382  Sum_probs=138.7

Q ss_pred             CCEEEEEECCCCCCCCCCEEEEEEEECCCCCC----CCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHH---C
Q ss_conf             94899984278777522255999998701082----3311520289999987552110123078851567998520---4
Q gi|254781076|r   23 MWPVAGIDEVGRGALAGPVVVAAIILDPNNIP----FGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKH---N   95 (209)
Q Consensus        23 ~~~IiGvDEaGRG~~~GPlvvaav~~~~~~~~----~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~---n   95 (209)
                      ..+++|+||+|.|++||||+||||+++++.++    .||+|||+|++.++.+|++.|++.+.+.+..++|++.+++   +
T Consensus        82 ~~~~IGsDEvG~GDyFGpl~v~av~v~~e~~~~L~~lgV~DSKkL~D~kI~~la~~ik~~i~~~~l~l~p~kYNel~~k~  161 (297)
T COG1039          82 AKNLIGSDEVGKGDYFGPLVVCAVYVSKENLPKLKELGVKDSKKLSDKKIQQLAPIIKPLIPHSVLTLDPKKYNELYKKF  161 (297)
T ss_pred             CCCCCCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEECHHHHHHHHHHH
T ss_conf             46314777878887557716899973899979998639853032887889999999997568249997868889999854


Q ss_pred             HHHHHHHHHH--HHCC----CCCCCCCCCCCCCCCCCC-----------CCCEEEEEECCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             7999886543--2100----257532110126532246-----------6212268711478652002366665477589
Q gi|254781076|r   96 IHKATLDAIY--HAVE----NLQVIPRSALIDGRSIPE-----------DLPCQAFAVIKGDSISLSIAAASIIAKVTRD  158 (209)
Q Consensus        96 i~~A~~~a~~--~ai~----~l~~~~~~ilIDg~~~~~-----------~~~~~~~~i~KgD~~~~~VaaASIiAKv~RD  158 (209)
                      .+...++++.  +|+.    .....++.++||.+...+           ...-+.....||++++.+||+|||+|   ||
T Consensus       162 ~N~n~mkt~lH~~ai~~ll~~~~~~~~~ivIDqFa~~~~~~~yl~k~~~~~~~p~~f~~kaEs~~laVAvASIiA---R~  238 (297)
T COG1039         162 NNANSMKTFLHNQAIQNLLPQKGAQPEFIVIDQFASSENYKNYLQKETNKFSEPVLFLTKAESKSLAVAVASIIA---RY  238 (297)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHH---HH
T ss_conf             239999999999999999875368973887320136568999988602578996024423354102688899999---99


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCH---HHHHHHHHCC------CCCCCCCCHHHHH
Q ss_conf             999999887779881028999998---9999999828------5830107848886
Q gi|254781076|r  159 RLMRIAHKKYPDYGFDSHVGYPTA---KHQQVIKEKG------PSCIHRLTFRPLR  205 (209)
Q Consensus       159 ~~m~~l~~~~p~Ygf~~nkGYgT~---~H~~ai~~~G------~~~~HR~Sf~~vk  205 (209)
                      .++..+++...+||..--||-|..   .-.+-++++|      .+..|-++|.-+.
T Consensus       239 ~Fl~~~~~l~~~~gv~LPkGAg~~V~~~a~~i~~k~g~~~L~~~~k~hf~n~~k~~  294 (297)
T COG1039         239 AFLQSLKQLSRQYGVQLPKGAGPAVDQAAAEIIQKRGFSKLEQVAKLHFKNFQKAL  294 (297)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999959737788746489999999987427999999999998799887


No 15 
>TIGR00716 rnhC ribonuclease HIII; InterPro: IPR004641   Ribonuclease HIII 3.1.26 from EC cleaves RNA from DNA-RNA hybrids. It catalyses endonucleolytic cleavage to 5'-phospho-monoesters. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homologue in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This family describes bacterial RNase HIII .; GO: 0004523 ribonuclease H activity, 0016070 RNA metabolic process, 0005737 cytoplasm.
Probab=99.93  E-value=5.7e-26  Score=182.89  Aligned_cols=170  Identities=24%  Similarity=0.352  Sum_probs=133.2

Q ss_pred             EEEEEECCCCCCCCCCEEEEEEEECC-CCCC----CCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHH---CH
Q ss_conf             89998427877752225599999870-1082----3311520289999987552110123078851567998520---47
Q gi|254781076|r   25 PVAGIDEVGRGALAGPVVVAAIILDP-NNIP----FGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKH---NI   96 (209)
Q Consensus        25 ~IiGvDEaGRG~~~GPlvvaav~~~~-~~~~----~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~---ni   96 (209)
                      .+||+||+|+|++||||++|||+++. ..++    .+++|||.|+++|+++|+..|+..+.+.+..+-||+.+.+   +.
T Consensus        92 S~IG~DEsGkGD~FGpl~~~cvy~~~P~~~~~~~~l~~~DsK~l~D~~i~~la~nl~~l~~~~~~~lkpEkYN~ly~kf~  171 (298)
T TIGR00716        92 SVIGVDESGKGDYFGPLVVVCVYVDEPEALEKLKELSVKDSKRLKDKKILELARNLKKLVKAKVLVLKPEKYNKLYEKFR  171 (298)
T ss_pred             CEEECCCCCCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCEEEEEECCCCHHHHHHHCC
T ss_conf             23302456887634141688775187568899884688655558867899999987764122455753740378886002


Q ss_pred             HHHHHHHHH--HHCCCC-----CCCCCCCCCCCCCCCCCC----------CEEEEEECCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             999886543--210025-----753211012653224662----------122687114786520023666654775899
Q gi|254781076|r   97 HKATLDAIY--HAVENL-----QVIPRSALIDGRSIPEDL----------PCQAFAVIKGDSISLSIAAASIIAKVTRDR  159 (209)
Q Consensus        97 ~~A~~~a~~--~ai~~l-----~~~~~~ilIDg~~~~~~~----------~~~~~~i~KgD~~~~~VaaASIiAKv~RD~  159 (209)
                      +...++|+.  .+|++|     +..|+.+++|.+..+..+          +......++|+...++||||||+|   |..
T Consensus       172 nlnkm~a~~h~~~I~~l~~~~~Gv~Pe~~~~Dqfa~s~~~l~~~~~~~~~~~~~if~t~AE~i~laVAaASI~A---Ry~  248 (298)
T TIGR00716       172 NLNKMLALLHKLLIERLLKKEAGVKPEAVVVDQFAESERYLLQLKRKDIVDEEVIFETKAERIDLAVAAASILA---RYK  248 (298)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHCCCCCCEEEEEECCCCCCCHHHHHHHHHH---HHH
T ss_conf             65579999999999975111048985547872004733788864214200000022101253305777888999---999


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCHHHHHH---HHHCCCCCCC
Q ss_conf             9999988777988102899999899999---9982858301
Q gi|254781076|r  160 LMRIAHKKYPDYGFDSHVGYPTAKHQQV---IKEKGPSCIH  197 (209)
Q Consensus       160 ~m~~l~~~~p~Ygf~~nkGYgT~~H~~a---i~~~G~~~~H  197 (209)
                      |+..+++..-+||..--||-+.+.-..|   |.+-|.+.+-
T Consensus       249 FL~s~~~ler~~gi~lpKGas~~Vke~Ak~l~~~Kg~~~Le  289 (298)
T TIGR00716       249 FLSSLKKLERELGIKLPKGASKKVKELAKELLLKKGAVVLE  289 (298)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCHHHHH
T ss_conf             99899998898486714899854899999997605844545


No 16 
>cd06559 Endonuclease_V Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases. Endonuclease_V (EndoV) is an enzyme that can initiate repair of all possible deaminated DNA bases.  EndoV cleaves the DNA strand containing lesions at the second phosphodiester bond 3' to the lesion using Mg2+ as a cofactor.  EndoV homologs are conserved throughout all domains of life from bacteria to humans. EndoV is encoded by the nfi gene and nfi null mutant mice have a phenotype prone to cancer. The ability of endonuclease V to recognize mismatches and abnormal replicative DNA structures suggests that the enzyme plays an important role in DNA metabolism. The details of downstream processing for the EndoV pathway remain unknown.
Probab=64.94  E-value=3  Score=22.44  Aligned_cols=26  Identities=31%  Similarity=0.551  Sum_probs=20.1

Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             65432100257532110126532246
Q gi|254781076|r  102 DAIYHAVENLQVIPRSALIDGRSIPE  127 (209)
Q Consensus       102 ~a~~~ai~~l~~~~~~ilIDg~~~~~  127 (209)
                      -.|..|+++|...||.++|||+....
T Consensus        81 p~~l~a~~~l~~~PdlllvDG~Gi~H  106 (208)
T cd06559          81 PPLLEALEKLKTKPDLLLVDGHGIAH  106 (208)
T ss_pred             HHHHHHHHHCCCCCCEEEECCCCCCC
T ss_conf             89999998557799999986887526


No 17 
>pfam04493 Endonuclease_5 Endonuclease V. Endonuclease V is specific for single-stranded DNA or for duplex DNA that contains uracil or that is damaged by a variety of agents.
Probab=62.77  E-value=3.5  Score=22.04  Aligned_cols=80  Identities=21%  Similarity=0.194  Sum_probs=41.2

Q ss_pred             CCEEEEEECCC-CCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCHHHHHH
Q ss_conf             94899984278-77752225599999870108233115202899999875521101230788515679985204799988
Q gi|254781076|r   23 MWPVAGIDEVG-RGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATL  101 (209)
Q Consensus        23 ~~~IiGvDEaG-RG~~~GPlvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~ni~~A~~  101 (209)
                      .+.|+|+|=+= +|..   .++|+|+++..++..  -+.          .+....-...|-=|..+=.|          .
T Consensus        21 l~~VaGvDvSf~~~~~---~~aa~Vvl~~p~l~~--v~~----------~~~~~~~~fPYIPG~LaFRE----------~   75 (205)
T pfam04493        21 LRYVAGVDVSYDKETR---AVAALVVLDFPSLEV--IEK----------KVIRGEISFPYIPGFLAFRE----------L   75 (205)
T ss_pred             EEEEEEEEEEEECCCE---EEEEEEEEECCCCCE--EEE----------EEEEEEECCCCCCCHHHHHH----------H
T ss_conf             5699999973757984---999999998899839--999----------99997623665540343310----------1


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             65432100257532110126532246
Q gi|254781076|r  102 DAIYHAVENLQVIPRSALIDGRSIPE  127 (209)
Q Consensus       102 ~a~~~ai~~l~~~~~~ilIDg~~~~~  127 (209)
                      -+|.+++++|...||.++|||+.+..
T Consensus        76 p~~l~a~~~L~~~PDvllvDG~Gi~H  101 (205)
T pfam04493        76 PLLLKALKKLYDEPDVLLVDGNGIAH  101 (205)
T ss_pred             HHHHHHHHHCCCCCCEEEECCCCCCC
T ss_conf             89999999657799999987876437


No 18 
>PRK11617 endonuclease V; Provisional
Probab=62.49  E-value=3.3  Score=22.20  Aligned_cols=25  Identities=32%  Similarity=0.489  Sum_probs=19.6

Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             5432100257532110126532246
Q gi|254781076|r  103 AIYHAVENLQVIPRSALIDGRSIPE  127 (209)
Q Consensus       103 a~~~ai~~l~~~~~~ilIDg~~~~~  127 (209)
                      ++..++++|+..||.++|||+.+..
T Consensus        85 ~ll~a~~~L~~~PDvllvDG~Gi~H  109 (223)
T PRK11617         85 ALLAAWEQLSQKPDLVFVDGHGISH  109 (223)
T ss_pred             HHHHHHHHCCCCCCEEEECCCCCCC
T ss_conf             9999999627799999987975437


No 19 
>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=55.23  E-value=15  Score=18.12  Aligned_cols=31  Identities=26%  Similarity=0.340  Sum_probs=21.6

Q ss_pred             CCHHHHHHHHHHHCCCCE-EE-----EECCCHHHHHH
Q ss_conf             899999875521101230-78-----85156799852
Q gi|254781076|r   63 ISHKKREELYEKITSSAI-IS-----ISSASHQYIDK   93 (209)
Q Consensus        63 Ls~~~R~~l~~~i~~~~~-~~-----i~~~~~~eID~   93 (209)
                      ||+.|.+.|.+.|++... ++     -..++|.++|+
T Consensus       118 L~~~Q~~~l~~~i~~~F~nf~~daEiSiEidPR~~~~  154 (462)
T TIGR00538       118 LSPEQIEELMKEIREAFPNFSEDAEISIEIDPRYLTK  154 (462)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCH
T ss_conf             7889999999999987320115844776523741378


No 20 
>cd01674 Homoaconitase_Swivel Homoaconitase swivel domain. This family includes homoaconitase and other uncharacterized proteins of the Aconitase family. Homoaconitase is part of an unusual lysine biosynthesis pathway found only in filamentous fungi, in which lysine is synthesized via the alpha-aminoadipate pathway. In this pathway, homoaconitase catalyzes the conversion of cis-homoaconitic acid into homoisocitric acid. The reaction mechanism is believed to be similar to that of other aconitases. This is the swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism.
Probab=52.21  E-value=15  Score=18.01  Aligned_cols=30  Identities=13%  Similarity=0.196  Sum_probs=23.2

Q ss_pred             CCCCCCC-HHH-HHHHHHCCCCCCCCCCHHHH
Q ss_conf             2899999-899-99999828583010784888
Q gi|254781076|r  175 SHVGYPT-AKH-QQVIKEKGPSCIHRLTFRPL  204 (209)
Q Consensus       175 ~nkGYgT-~~H-~~ai~~~G~~~~HR~Sf~~v  204 (209)
                      .|.|-|| .+| ..+|+.+|+..+.-+||.-|
T Consensus        53 ~NFGcGSSREhA~~aL~~~Gi~aVIA~SFa~I   84 (129)
T cd01674          53 FNFGTGSSREQAATALLAKGIPLVVSGSFGNI   84 (129)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCCEEEECHHHHH
T ss_conf             86576734889999999849979998529999


No 21 
>pfam06135 DUF965 Bacterial protein of unknown function (DUF965). This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=48.74  E-value=16  Score=17.93  Aligned_cols=32  Identities=28%  Similarity=0.513  Sum_probs=22.7

Q ss_pred             CCCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             147865200--23666654775899999998877
Q gi|254781076|r  137 IKGDSISLS--IAAASIIAKVTRDRLMRIAHKKY  168 (209)
Q Consensus       137 ~KgD~~~~~--VaaASIiAKv~RD~~m~~l~~~~  168 (209)
                      .-||-.|.+  --|-|++-|+.||.++++|=+.|
T Consensus        44 lSgDPtYItsh~nAR~lIrkiERDEilEelv~~Y   77 (79)
T pfam06135        44 LSGDPAYITRHNDARNLIRKIERDEILEELVKSY   77 (79)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             2489775277525999999985889999999997


No 22 
>PRK05473 hypothetical protein; Provisional
Probab=46.42  E-value=17  Score=17.75  Aligned_cols=31  Identities=29%  Similarity=0.474  Sum_probs=22.4

Q ss_pred             CCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             47865200--23666654775899999998877
Q gi|254781076|r  138 KGDSISLS--IAAASIIAKVTRDRLMRIAHKKY  168 (209)
Q Consensus       138 KgD~~~~~--VaaASIiAKv~RD~~m~~l~~~~  168 (209)
                      -||-.|.+  --|-|++-|+.||.++++|=+.|
T Consensus        48 SGDPaYItsh~~AR~lIrk~eRDEilEELv~~Y   80 (86)
T PRK05473         48 SGDPAYIPRHNDARNLIRKLERDEILEELVKSY   80 (86)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             489763167402999999986889999999999


No 23 
>COG1515 Nfi Deoxyinosine 3'endonuclease (endonuclease V) [DNA replication, recombination, and repair]
Probab=42.16  E-value=11  Score=19.02  Aligned_cols=26  Identities=38%  Similarity=0.607  Sum_probs=21.2

Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             86543210025753211012653224
Q gi|254781076|r  101 LDAIYHAVENLQVIPRSALIDGRSIP  126 (209)
Q Consensus       101 ~~a~~~ai~~l~~~~~~ilIDg~~~~  126 (209)
                      .-+|.++++.|..+++.++|||+.+.
T Consensus        82 ~p~~l~a~~~l~~~~d~ilVDG~Gia  107 (212)
T COG1515          82 LPLLLKALEKLSVKPDLLLVDGHGIA  107 (212)
T ss_pred             HHHHHHHHHHCCCCCCEEEECCCCEE
T ss_conf             28899999864888889998686514


No 24 
>pfam01314 AFOR_C Aldehyde ferredoxin oxidoreductase, domains 2 & 3. Aldehyde ferredoxin oxidoreductase (AOR) catalyses the reversible oxidation of aldehydes to their corresponding carboxylic acids with their accompanying reduction of the redox protein ferredoxin. This family is composed of two structural domains that bind the tungsten cofactor via DXXGL(C/D) motifs. In addition to maintaining specific binding interactions with the cofactor, another role for domains 2 and 3 may be to regulate substrate access to AOR.
Probab=40.91  E-value=20  Score=17.25  Aligned_cols=32  Identities=25%  Similarity=0.430  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHH
Q ss_conf             758999999988777988102899999899999
Q gi|254781076|r  155 VTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQV  187 (209)
Q Consensus       155 v~RD~~m~~l~~~~p~Ygf~~nkGYgT~~H~~a  187 (209)
                      +.|+.+-+.+...|...||+. .|-||+++.+-
T Consensus       348 ~~~e~~~~~l~~YY~~rGWd~-~G~Pt~e~L~~  379 (382)
T pfam01314       348 LDREDLEEMLDEYYRLRGWDE-EGVPTPETLKE  379 (382)
T ss_pred             CCHHHHHHHHHHHHHHCCCCC-CCCCCHHHHHH
T ss_conf             699999999999999829898-99889899987


No 25 
>pfam08893 DUF1839 Domain of unknown function (DUF1839). This family of proteins are functionally uncharacterized.
Probab=40.05  E-value=20  Score=17.28  Aligned_cols=27  Identities=26%  Similarity=0.492  Sum_probs=24.4

Q ss_pred             HHHHHHHHHCCCCCCCCCCHHHHHHHC
Q ss_conf             899999998285830107848886403
Q gi|254781076|r  182 AKHQQVIKEKGPSCIHRLTFRPLRNLS  208 (209)
Q Consensus       182 ~~H~~ai~~~G~~~~HR~Sf~~vk~l~  208 (209)
                      +.|.++|...|..-+|-+||.+.++|+
T Consensus       219 ~~~l~~l~~r~~~~FH~YsFn~lRQlG  245 (320)
T pfam08893       219 PAHLETLLARGEPFFHLYAFNVLRQLG  245 (320)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHCC
T ss_conf             999999985895400076540387633


No 26 
>PRK01641 leuD isopropylmalate isomerase small subunit; Provisional
Probab=39.21  E-value=32  Score=16.02  Aligned_cols=12  Identities=17%  Similarity=0.144  Sum_probs=5.8

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             758999999988
Q gi|254781076|r  155 VTRDRLMRIAHK  166 (209)
Q Consensus       155 v~RD~~m~~l~~  166 (209)
                      ..|.++|.-++.
T Consensus       164 ~~k~~LL~GlD~  175 (201)
T PRK01641        164 FRRHCLLNGLDD  175 (201)
T ss_pred             HHHHHHHHCCCH
T ss_conf             999999919688


No 27 
>KOG3407 consensus
Probab=38.10  E-value=16  Score=17.82  Aligned_cols=17  Identities=35%  Similarity=0.630  Sum_probs=6.7

Q ss_pred             CCCCCCCCCCCCCCCCC
Q ss_conf             32110126532246621
Q gi|254781076|r  114 IPRSALIDGRSIPEDLP  130 (209)
Q Consensus       114 ~~~~ilIDg~~~~~~~~  130 (209)
                      .|+.-..||+..++.++
T Consensus        53 ~Pe~e~~~g~~~p~~~~   69 (151)
T KOG3407          53 KPEVEPKDGFVVPPELP   69 (151)
T ss_pred             CCCCCCCCCCCCCCCCC
T ss_conf             97533334734797643


No 28 
>PRK09849 putative oxidoreductase; Provisional
Probab=37.35  E-value=24  Score=16.78  Aligned_cols=32  Identities=28%  Similarity=0.486  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHH
Q ss_conf             77589999999887779881028999998999
Q gi|254781076|r  154 KVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQ  185 (209)
Q Consensus       154 Kv~RD~~m~~l~~~~p~Ygf~~nkGYgT~~H~  185 (209)
                      |..|+.+-+.|.+.|..-||+...|-||+++.
T Consensus       651 ~~d~e~~e~ml~~YY~~rGWD~e~G~Pt~etL  682 (702)
T PRK09849        651 KMDRDDMQASLTMFYKEMGWDPQTGCPTRATL  682 (702)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHH
T ss_conf             68999999999999997099855884289999


No 29 
>cd01218 PH_phafin2 Phafin2  Pleckstrin Homology (PH) domain. Phafin contains a PH domain and a FYVE domain.  PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding.  Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=34.94  E-value=28  Score=16.43  Aligned_cols=31  Identities=23%  Similarity=0.121  Sum_probs=24.7

Q ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8711478652002366665477589999999887
Q gi|254781076|r  134 FAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKK  167 (209)
Q Consensus       134 ~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~  167 (209)
                      ...+.+-.++.+|+|+|--.   ++.||..|.+-
T Consensus        67 ~f~I~s~~KSF~v~A~s~~E---k~~Wm~~i~~a   97 (104)
T cd01218          67 GWIIKTPTKSFAVYAATETE---KREWMLHINKC   97 (104)
T ss_pred             EEEEECCCCEEEEEECCHHH---HHHHHHHHHHH
T ss_conf             69997388189999699999---99999999999


No 30 
>COG0066 LeuD 3-isopropylmalate dehydratase small subunit [Amino acid transport and metabolism]
Probab=34.42  E-value=39  Score=15.51  Aligned_cols=11  Identities=18%  Similarity=0.039  Sum_probs=3.6

Q ss_pred             HHHHHHHHCCC
Q ss_conf             98755211012
Q gi|254781076|r   68 REELYEKITSS   78 (209)
Q Consensus        68 R~~l~~~i~~~   78 (209)
                      ||...-.|+..
T Consensus        78 REHApwALk~~   88 (191)
T COG0066          78 REHAPWALKDY   88 (191)
T ss_pred             HHHHHHHHHHC
T ss_conf             77899999975


No 31 
>pfam07286 DUF1445 Protein of unknown function (DUF1445). This family represents a conserved region approximately 150 residues long within a number of hypothetical bacterial and eukaryotic proteins of unknown function.
Probab=34.13  E-value=28  Score=16.34  Aligned_cols=44  Identities=18%  Similarity=0.286  Sum_probs=30.9

Q ss_pred             CHHHHHHHHHCCCCE------------EEEEECCCCCCCCCCEEEEEEEECCCCCC
Q ss_conf             888999999779948------------99984278777522255999998701082
Q gi|254781076|r   11 HFELEAMVREKNMWP------------VAGIDEVGRGALAGPVVVAAIILDPNNIP   54 (209)
Q Consensus        11 ~~~~E~~l~~~~~~~------------IiGvDEaGRG~~~GPlvvaav~~~~~~~~   54 (209)
                      +|++|..|.+.|..+            .--++=.--|++.|||||.---++++.+.
T Consensus         8 SFSFE~aL~~aGip~rhi~~~~nV~MY~Tni~~~~aG~F~g~mVVSMRp~~~~~~~   63 (143)
T pfam07286         8 SFSFEEALLAAGIPVRHIEEGRNVPMYRTNIPCRPAGPFSGPMVVSMRPIPADDVI   63 (143)
T ss_pred             CCCHHHHHHHCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCEEEEEECCCHHHHH
T ss_conf             30589999987998533235866683865865535677567547874038989988


No 32 
>pfam04084 ORC2 Origin recognition complex subunit 2. All DNA replication initiation is driven by a single conserved eukaryotic initiator complex termed he origin recognition complex (ORC). The ORC is a six protein complex. The function of ORC is reviewed in.
Probab=33.98  E-value=20  Score=17.25  Aligned_cols=13  Identities=8%  Similarity=0.115  Sum_probs=6.4

Q ss_pred             HHHHHHHHHHCCC
Q ss_conf             9998755211012
Q gi|254781076|r   66 KKREELYEKITSS   78 (209)
Q Consensus        66 ~~R~~l~~~i~~~   78 (209)
                      .+-..+.+.+.+.
T Consensus       118 ~~~~~i~~~~~~~  130 (316)
T pfam04084       118 EQLDFIVSYLNSR  130 (316)
T ss_pred             HHHHHHHHHHHCC
T ss_conf             9999999998368


No 33 
>cd01577 IPMI_Swivel Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-isopropylmalate. IPMI is involved in fungal and bacterial leucine biosynthesis and is also found in eukaryotes. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism.
Probab=31.19  E-value=44  Score=15.18  Aligned_cols=30  Identities=17%  Similarity=0.347  Sum_probs=19.6

Q ss_pred             CCCCCCC-HHHH-HHHHHCCCCCCCCCCHHHH
Q ss_conf             2899999-8999-9999828583010784888
Q gi|254781076|r  175 SHVGYPT-AKHQ-QVIKEKGPSCIHRLTFRPL  204 (209)
Q Consensus       175 ~nkGYgT-~~H~-~ai~~~G~~~~HR~Sf~~v  204 (209)
                      .|.|-|| .+|- .+++.+|+..+.-+||.-+
T Consensus        25 ~NFG~GSSREhA~~al~~~Gi~~VIa~SFa~I   56 (91)
T cd01577          25 KNFGCGSSREHAPWALKDAGIRAVIAESFARI   56 (91)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCEEEEEHHHHHH
T ss_conf             86577852899999999849549997239999


No 34 
>TIGR01070 mutS1 DNA mismatch repair protein MutS; InterPro: IPR005748   Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication . MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base . MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch . MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level . Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA.    MutS is a modular protein with a complex structure , and is composed of:    N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts.    Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions . Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts .    This entry represents a family of MutS proteins.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair.
Probab=30.54  E-value=15  Score=18.14  Aligned_cols=15  Identities=27%  Similarity=0.266  Sum_probs=6.3

Q ss_pred             CCCCCCCCCCCCCCC
Q ss_conf             110126532246621
Q gi|254781076|r  116 RSALIDGRSIPEDLP  130 (209)
Q Consensus       116 ~~ilIDg~~~~~~~~  130 (209)
                      ..++=||.-+..+++
T Consensus       410 P~~v~dGG~I~~GYd  424 (863)
T TIGR01070       410 PLVVRDGGVIREGYD  424 (863)
T ss_pred             CCEEECCCEECCCCC
T ss_conf             926504861235788


No 35 
>KOG2745 consensus
Probab=29.38  E-value=47  Score=14.99  Aligned_cols=27  Identities=33%  Similarity=0.536  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             236666547758999999988777988
Q gi|254781076|r  146 IAAASIIAKVTRDRLMRIAHKKYPDYG  172 (209)
Q Consensus       146 VaaASIiAKv~RD~~m~~l~~~~p~Yg  172 (209)
                      -=|||+++-|.+|+..+.+++.||+-|
T Consensus        93 rL~a~~v~~v~~~rv~q~l~~~~p~~~  119 (321)
T KOG2745          93 RLAASAVQTVVSDRVLQYLDEYYPNEG  119 (321)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999999999971179987521086768


No 36 
>pfam11641 Antigen_Bd37 Glycosylphosphatidylinositol-anchored merozoite surface protein. This family of proteins represents the core region of Bd37, a surface antigen of B.divergens which is GPI-anchored at the surface of the merozoite. The structure of the protein consists of mainly alpha folds and has three sub domains.
Probab=29.36  E-value=47  Score=14.98  Aligned_cols=34  Identities=24%  Similarity=0.369  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHHHHCCC-------CCCCCCCCCCCH-HHHHH
Q ss_conf             77589999999887779-------881028999998-99999
Q gi|254781076|r  154 KVTRDRLMRIAHKKYPD-------YGFDSHVGYPTA-KHQQV  187 (209)
Q Consensus       154 Kv~RD~~m~~l~~~~p~-------Ygf~~nkGYgT~-~H~~a  187 (209)
                      ++.||.+|+++....|.       |||-.---||.| .|-.|
T Consensus       138 ~~~~del~kKf~a~~psflt~eDIs~fLTVPeYG~p~na~kw  179 (224)
T pfam11641       138 RVQRDELVKKFTARAPSFLTSEDISGFLTVPEYGVPMNAAKW  179 (224)
T ss_pred             HHHHHHHHHHHHHCCCCCCCHHHHHHHEECCCCCCCCCHHHH
T ss_conf             553999999888508976648766222106656897638899


No 37 
>cd01220 PH_CDEP Chondrocyte-derived ezrin-like domain containing protein (CDEP) Pleckstrin homology (PH) domain. CDEP consists of a Ferm domain, a rhoGEF (DH) domain followed by two PH domains.  PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding.  Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=29.14  E-value=39  Score=15.45  Aligned_cols=34  Identities=15%  Similarity=0.220  Sum_probs=26.0

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             2268711478652002366665477589999999887
Q gi|254781076|r  131 CQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKK  167 (209)
Q Consensus       131 ~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~  167 (209)
                      .+....+.+-+++..|+|+|---   ||.||..+.+.
T Consensus        63 ~~n~f~I~~~~ks~~v~A~s~~E---k~~W~~~i~~a   96 (99)
T cd01220          63 VPHCFTIFGGQCAITVAASTRAE---KEKWLADLSKA   96 (99)
T ss_pred             CCCEEEEECCCEEEEEEECCHHH---HHHHHHHHHHH
T ss_conf             87379996588799999599999---99999999998


No 38 
>KOG3495 consensus
Probab=28.69  E-value=48  Score=14.91  Aligned_cols=21  Identities=29%  Similarity=0.267  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             236666547758999999988
Q gi|254781076|r  146 IAAASIIAKVTRDRLMRIAHK  166 (209)
Q Consensus       146 VaaASIiAKv~RD~~m~~l~~  166 (209)
                      |.=++|.|++.|+.++.++..
T Consensus        12 i~Ys~I~A~vvR~~LK~e~ka   32 (50)
T KOG3495          12 IRYSQIAAQVVRQALKTELKA   32 (50)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999998577777


No 39 
>pfam04870 DUF644 Protein of unknown function (DUF644). This family of proteins with unknown function are from C.elegans. The GO annotation for this protein indicates that this protein is involved in nematode larval development and is a positive regulator of growth rate. This protein is possibly an integral membrane protein.
Probab=27.37  E-value=51  Score=14.76  Aligned_cols=31  Identities=13%  Similarity=0.215  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHHHCCCCCCCCCCHHHHHHHC
Q ss_conf             9999899999998285830107848886403
Q gi|254781076|r  178 GYPTAKHQQVIKEKGPSCIHRLTFRPLRNLS  208 (209)
Q Consensus       178 GYgT~~H~~ai~~~G~~~~HR~Sf~~vk~l~  208 (209)
                      -|.+++-.+..+.+-...+||.=|++|+.|+
T Consensus       286 p~~ns~~L~~~k~lt~~~~~~sI~~tIr~lA  316 (323)
T pfam04870       286 PFNNSKALKEYRNLTRAEIPRSIHSTIRDIA  316 (323)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             8888899999874587679999999999999


No 40 
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=26.11  E-value=54  Score=14.62  Aligned_cols=55  Identities=20%  Similarity=0.115  Sum_probs=37.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHH--HHHHHHHCCCC------CCCCCCCCCC--HHHHHHHHHCCCC
Q ss_conf             865200236666547758999--99998877798------8102899999--8999999982858
Q gi|254781076|r  140 DSISLSIAAASIIAKVTRDRL--MRIAHKKYPDY------GFDSHVGYPT--AKHQQVIKEKGPS  194 (209)
Q Consensus       140 D~~~~~VaaASIiAKv~RD~~--m~~l~~~~p~Y------gf~~nkGYgT--~~H~~ai~~~G~~  194 (209)
                      +....-+-||||+-|+.=|-.  +..|...|++-      -...-+|+|+  ..-.+.|++.|.-
T Consensus        47 ~~DWwY~RaASilRkiyi~gpvGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V  111 (147)
T COG2238          47 QEDWWYVRAASILRKIYIDGPVGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLV  111 (147)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHCCCE
T ss_conf             87549999999999998537601999999878666688894344237736999999999977856


No 41 
>PRK00439 leuD 3-isopropylmalate dehydratase small subunit; Reviewed
Probab=24.73  E-value=57  Score=14.46  Aligned_cols=12  Identities=17%  Similarity=0.191  Sum_probs=4.8

Q ss_pred             HHHHHHHHCCCC
Q ss_conf             987552110123
Q gi|254781076|r   68 REELYEKITSSA   79 (209)
Q Consensus        68 R~~l~~~i~~~~   79 (209)
                      ||.....++...
T Consensus        64 RE~A~~al~~~G   75 (163)
T PRK00439         64 REHAPLALKAAG   75 (163)
T ss_pred             HHHHHHHHHHCC
T ss_conf             799999999859


No 42 
>cd01219 PH_FGD FGD (faciogenital dysplasia protein) pleckstrin homology (PH) domain. FGD has a RhoGEF (DH) domain, followed by a PH domain, a FYVE domain and a C-terminal PH domain. FGD is a guanine nucleotide exchange factor that activates the Rho GTPase Cdc42. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding.  Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=23.33  E-value=59  Score=14.35  Aligned_cols=36  Identities=11%  Similarity=0.137  Sum_probs=28.3

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             212268711478652002366665477589999999887
Q gi|254781076|r  129 LPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKK  167 (209)
Q Consensus       129 ~~~~~~~i~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~  167 (209)
                      ...++...+.|.+++..++|.|---   ||.||+.+...
T Consensus        63 ~~~~~~F~I~~~~rsl~l~A~s~eE---k~~W~~~i~~a   98 (101)
T cd01219          63 LERPHSFLVSGKQRCLELQARTQKE---KNDWVQAIFSI   98 (101)
T ss_pred             CCCCEEEEEEECCEEEEEECCCHHH---HHHHHHHHHHH
T ss_conf             7877079998465699998799899---99999999987


No 43 
>TIGR02177 PorB_KorB 2-oxoacid:acceptor oxidoreductase, beta subunit, pyruvate/2-ketoisovalerate family; InterPro: IPR011896    A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This entry describes the beta subunits, representing mostly pyruvate and 2-ketoisovalerate specific enzymes..
Probab=23.25  E-value=61  Score=14.29  Aligned_cols=39  Identities=18%  Similarity=0.271  Sum_probs=22.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             147865200236666547758999999988777988102
Q gi|254781076|r  137 IKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDS  175 (209)
Q Consensus       137 ~KgD~~~~~VaaASIiAKv~RD~~m~~l~~~~p~Ygf~~  175 (209)
                      ..||-.-..++++=.||---|--=|..|=-...-||.-+
T Consensus        77 ~GGDGD~~GIG~~Hfva~gRRN~dIt~l~~DN~VYGLTK  115 (302)
T TIGR02177        77 VGGDGDLYGIGGNHFVAAGRRNVDITVLVHDNQVYGLTK  115 (302)
T ss_pred             EECCCCCHHHHHHHHHHHHCCCCCCEEEEECCEECCCCC
T ss_conf             606864101105778754114788248842470546665


No 44 
>pfam08589 DUF1770 Fungal protein of unknown function (DUF1770). The function of this family is unknown. These proteins are rather dissimilar except for a single strongly conserved motif (PDLRFEQ).
Probab=23.24  E-value=50  Score=14.82  Aligned_cols=15  Identities=20%  Similarity=0.419  Sum_probs=5.8

Q ss_pred             CCCCCCHHHHHHHHH
Q ss_conf             878868889999997
Q gi|254781076|r    6 IPERPHFELEAMVRE   20 (209)
Q Consensus         6 ~~~~p~~~~E~~l~~   20 (209)
                      +|-.|||++|+.+++
T Consensus        67 lPPlPDLRFEQSYL~   81 (96)
T pfam08589        67 LPPLPDLRFEQSYLA   81 (96)
T ss_pred             CCCCCCHHHHHHHHH
T ss_conf             988965137899999


No 45 
>COG2247 LytB Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]
Probab=22.86  E-value=62  Score=14.24  Aligned_cols=13  Identities=23%  Similarity=0.322  Sum_probs=8.2

Q ss_pred             HHHHHHHHCCCCCC
Q ss_conf             99999998285830
Q gi|254781076|r  183 KHQQVIKEKGPSCI  196 (209)
Q Consensus       183 ~H~~ai~~~G~~~~  196 (209)
                      +.++++++ |++|.
T Consensus       146 ~~~e~~k~-~~~p~  158 (337)
T COG2247         146 ALMELMKE-GIVPV  158 (337)
T ss_pred             HHHHHHHC-CCCEE
T ss_conf             78888753-75326


No 46 
>pfam12149 HSV_VP16_C Herpes simplex virus virion protein 16 C terminal. This domain is found in viruses, and is about 30 amino acids in length. It is found in association with pfam02232. This domain is the C terminal of the HSV virion protein 16. This protein is a transcription promoter. The C terminal domain is the carboxyl subdomain of the acidic transcriptional activation domain. The protein binds to DNA binding proteins to carry out its function. Such proteins include TATA binding protein, CBP, TBP-binding protein, etc.
Probab=22.85  E-value=38  Score=15.58  Aligned_cols=21  Identities=38%  Similarity=0.757  Sum_probs=15.5

Q ss_pred             CCCCHHHHHHHHHCCCCEEEEEECCC
Q ss_conf             88688899999977994899984278
Q gi|254781076|r    8 ERPHFELEAMVREKNMWPVAGIDEVG   33 (209)
Q Consensus         8 ~~p~~~~E~~l~~~~~~~IiGvDEaG   33 (209)
                      +..+|++|+++-..     .|+||-|
T Consensus         9 dmadfefeqmftda-----lgidd~g   29 (30)
T pfam12149         9 DMADFEFEQMFTDA-----LGIDDFG   29 (30)
T ss_pred             HHHHHHHHHHHHHH-----HCCCCCC
T ss_conf             05567899998664-----0764558


No 47 
>pfam09974 DUF2209 Uncharacterized protein conserved in archaea (DUF2209). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=22.82  E-value=62  Score=14.23  Aligned_cols=116  Identities=15%  Similarity=0.182  Sum_probs=60.2

Q ss_pred             EEEECCCCCCCCCC--EEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCHHHHHHHHH
Q ss_conf             99842787775222--5599999870108233115202899999875521101230788515679985204799988654
Q gi|254781076|r   27 AGIDEVGRGALAGP--VVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLDAI  104 (209)
Q Consensus        27 iGvDEaGRG~~~GP--lvvaav~~~~~~~~~~i~DSK~Ls~~~R~~l~~~i~~~~~~~i~~~~~~eID~~ni~~A~~~a~  104 (209)
                      +|||=.||--..|-  +|.|||.+.-+....             +    .+.+...+.+-.-.+     -|+ .....-.
T Consensus         1 vaVDISGRH~e~dgy~~V~AaV~~ev~a~~I-------------~----~Ve~v~v~~v~~~~~-----~~L-~diV~~v   57 (128)
T pfam09974         1 IAVDISGRHAEKDGYYRVCAAVALEVSADHI-------------E----TVRQVNVFPVCTREP-----PNL-RDIVEEV   57 (128)
T ss_pred             CEEECCCCCCCCCCEEEEEEEEEEEECHHHE-------------E----EEECCEEEEEECCCC-----CCH-HHHHHHH
T ss_conf             9140456431168479999889899724465-------------7----653132799864788-----518-9999999


Q ss_pred             HHHCCCCCCCCCC-CCCC-CCCCCCCCCEEEEEECCCCCCCH-------HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3210025753211-0126-53224662122687114786520-------0236666547758999999988
Q gi|254781076|r  105 YHAVENLQVIPRS-ALID-GRSIPEDLPCQAFAVIKGDSISL-------SIAAASIIAKVTRDRLMRIAHK  166 (209)
Q Consensus       105 ~~ai~~l~~~~~~-ilID-g~~~~~~~~~~~~~i~KgD~~~~-------~VaaASIiAKv~RD~~m~~l~~  166 (209)
                      .++++++...++. ++.. |.++ ....+.+.++-+++=+|+       +|-.|-=++-..|+-+|.+|..
T Consensus        58 ~~~v~~l~~~f~g~Iv~E~Gefy-n~P~w~v~a~l~~~fky~es~gEreaIe~AHhvSysvrklL~~el~i  127 (128)
T pfam09974        58 ERTLDGLDKDFEYTIVAEKGEFF-NQPEWRVSAMLSAPFKYQETVAEREAIEMAHHVSYSVRKLLIKELKI  127 (128)
T ss_pred             HHHHHHCCCCCCCCEEECCCCCC-CCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99997267688852895173201-48166888772566204154888999999999999999999886057


No 48 
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=22.43  E-value=63  Score=14.19  Aligned_cols=15  Identities=33%  Similarity=0.620  Sum_probs=8.1

Q ss_pred             CCCCCCCCCCCCCCC
Q ss_conf             211012653224662
Q gi|254781076|r  115 PRSALIDGRSIPEDL  129 (209)
Q Consensus       115 ~~~ilIDg~~~~~~~  129 (209)
                      |-.+++|+-.-|.++
T Consensus        95 ~lil~LD~I~DP~Nl  109 (244)
T PRK11181         95 PFLLILDGVTDPHNL  109 (244)
T ss_pred             CEEEEECCCCCCCHH
T ss_conf             879998188787389


No 49 
>pfam08459 UvrC_HhH_N UvrC Helix-hairpin-helix N-terminal. This domain is found in the C subunits of the bacterial and archaeal UvrABC system which catalyses nucleotide excision repair in a multi-step process. UvrC catalyses the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised. The domain described here is found to the N-terminus of a helix hairpin helix (pfam00633) motif and also co-occurs with the pfam01541 catalytic domain which is found at the N-terminus of the same proteins.
Probab=22.07  E-value=64  Score=14.14  Aligned_cols=37  Identities=22%  Similarity=0.345  Sum_probs=23.2

Q ss_pred             HHCCCCCCCCCCCCCCCCC---------C-CCCCCEEEEEECCCCCC
Q ss_conf             2100257532110126532---------2-46621226871147865
Q gi|254781076|r  106 HAVENLQVIPRSALIDGRS---------I-PEDLPCQAFAVIKGDSI  142 (209)
Q Consensus       106 ~ai~~l~~~~~~ilIDg~~---------~-~~~~~~~~~~i~KgD~~  142 (209)
                      +..+.-..-|+.++|||-.         + ..+++.++.++.|++..
T Consensus        70 ~~~~~~~~~PDLilIDGGkgQl~~a~~~l~~~~~~i~vi~iaK~~~~  116 (154)
T pfam08459        70 RLLKEKLPLPDLILIDGGKGQLNAAKEVLEELGLDIPVIGLAKGEEH  116 (154)
T ss_pred             HHHHCCCCCCCEEEECCCHHHHHHHHHHHHHCCCCCEEEEEEECCCC
T ss_conf             65411689998899759989999999999985999529999735655


No 50 
>KOG3668 consensus
Probab=21.44  E-value=55  Score=14.55  Aligned_cols=15  Identities=47%  Similarity=0.722  Sum_probs=7.7

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             5477589999999887
Q gi|254781076|r  152 IAKVTRDRLMRIAHKK  167 (209)
Q Consensus       152 iAKv~RD~~m~~l~~~  167 (209)
                      +-||.| ++|...+.+
T Consensus       212 Ihk~~~-rv~~~~HRq  226 (269)
T KOG3668         212 IHKVER-RVFTRAHRQ  226 (269)
T ss_pred             HHHHHH-HHHHHHHHH
T ss_conf             999999-999998878


No 51 
>COG3081 Nucleoid-associated protein [General function prediction only]
Probab=21.36  E-value=66  Score=14.05  Aligned_cols=22  Identities=27%  Similarity=0.584  Sum_probs=16.1

Q ss_pred             HHHHHHHCCC------CCCCCCCCCCCH
Q ss_conf             9999887779------881028999998
Q gi|254781076|r  161 MRIAHKKYPD------YGFDSHVGYPTA  182 (209)
Q Consensus       161 m~~l~~~~p~------Ygf~~nkGYgT~  182 (209)
                      +.+|++.-|.      |.|..++|||-.
T Consensus       242 l~~LS~~lp~~~e~~F~~f~~eq~YgLe  269 (335)
T COG3081         242 LQELSKELPGLNEVAFYDFTAEKGYGLE  269 (335)
T ss_pred             HHHHHHHCCCCCCCHHHHHHHHCCCCCC
T ss_conf             9998734788674129998886056777


No 52 
>pfam09288 UBA_3 Fungal ubiquitin-associated domain. Members of this family of ubiquitin binding domains adopt a structure consisting of a three alpha-helix bundle. They are predominantly found in fungal ubiquitin-protein ligases.
Probab=20.96  E-value=68  Score=14.00  Aligned_cols=25  Identities=28%  Similarity=0.444  Sum_probs=17.4

Q ss_pred             CCCCCHHHHHHHHHCCCCCCCCCCHHHHHH
Q ss_conf             999998999999982858301078488864
Q gi|254781076|r  177 VGYPTAKHQQVIKEKGPSCIHRLTFRPLRN  206 (209)
Q Consensus       177 kGYgT~~H~~ai~~~G~~~~HR~Sf~~vk~  206 (209)
                      -|++..+.++.+|+.|+-     |+.|+.|
T Consensus        19 ~GF~r~KvIevLrRlgiK-----s~~~~~n   43 (55)
T pfam09288        19 QGFEKDKVIEVLKRLGIK-----SMDPNDN   43 (55)
T ss_pred             CCCCHHHHHHHHHHHCCC-----CCCCCCH
T ss_conf             488623399999995856-----5797552


No 53 
>pfam09010 AsiA Anti-Sigma Factor A. Anti-sigma factor A is a transcriptional inhibitor that inhibits sigma 70-directed transcription by weakening its interaction with the core of the host's RNA polymerase. It is an all-helical protein, composed of six helical segments and intervening loops and turns, as well as a helix-turn-helix DNA binding motif, although neither free anti-sigma factor nor anti-sigma factor bound to sigma-70 has been shown to interact directly with DNA. In solution, the protein forms a symmetric dimer of small (10.59 kDa) protomers, which are composed of helix and coil regions and are devoid of beta-strand/sheet secondary structural elements.
Probab=20.73  E-value=68  Score=13.97  Aligned_cols=23  Identities=26%  Similarity=0.316  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00236666547758999999988
Q gi|254781076|r  144 LSIAAASIIAKVTRDRLMRIAHK  166 (209)
Q Consensus       144 ~~VaaASIiAKv~RD~~m~~l~~  166 (209)
                      -.||-|||+-|..||.++..-+.
T Consensus        10 eIia~aSlLIK~~~edI~~~q~~   32 (91)
T pfam09010        10 DIIATASLLIKFGREDIVENQAN   32 (91)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHH
T ss_conf             99999999998269999871999


No 54 
>pfam08714 Fae Formaldehyde-activating enzyme (Fae). Formaldehyde-activating enzyme is an enzyme required for energy metabolism and formaldehyde detoxification. It catalyses the condensation of formaldehyde and tetrahydromethanopterin to methylene tetrahydromethanopterin.
Probab=20.58  E-value=62  Score=14.24  Aligned_cols=34  Identities=29%  Similarity=0.187  Sum_probs=20.3

Q ss_pred             EEEEECCCHHHHH-----HHCHHHHHHHHHHHHCCCCCCC
Q ss_conf             0788515679985-----2047999886543210025753
Q gi|254781076|r   80 IISISSASHQYID-----KHNIHKATLDAIYHAVENLQVI  114 (209)
Q Consensus        80 ~~~i~~~~~~eID-----~~ni~~A~~~a~~~ai~~l~~~  114 (209)
                      +..-.+++|+-.|     ++| .+||.+|++||++..+..
T Consensus       106 iiv~V~i~p~a~D~~kiy~~N-y~ATk~AI~rAm~~~Ps~  144 (160)
T pfam08714       106 IIVSVFIHPEALDDKKIYRYN-YEATKLAIKRAMKGEPSI  144 (160)
T ss_pred             EEEEEECCCCCCCHHHHHHHH-HHHHHHHHHHHHCCCCCH
T ss_conf             999997183303689999999-999999999998089998


No 55 
>KOG3062 consensus
Probab=20.56  E-value=69  Score=13.95  Aligned_cols=34  Identities=6%  Similarity=0.123  Sum_probs=24.2

Q ss_pred             CCCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHH
Q ss_conf             5321101265322466212268711478652002
Q gi|254781076|r  113 VIPRSALIDGRSIPEDLPCQAFAVIKGDSISLSI  146 (209)
Q Consensus       113 ~~~~~ilIDg~~~~~~~~~~~~~i~KgD~~~~~V  146 (209)
                      .+.+.|++|.-...+++.+...|+.|+-..-.+|
T Consensus        72 sk~~iVI~DslNyIKGfRYeLyC~ak~~~tt~Cv  105 (281)
T KOG3062          72 SKGDIVIVDSLNYIKGFRYELYCEAKAARTTYCV  105 (281)
T ss_pred             CCCCEEEEECCCCCCCCEEEEEEEHHCCCEEEEE
T ss_conf             5686899814441122020365510105446899


No 56 
>pfam02334 RTP Replication terminator protein. The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.
Probab=20.29  E-value=51  Score=14.75  Aligned_cols=13  Identities=38%  Similarity=0.491  Sum_probs=6.5

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             7758999999988
Q gi|254781076|r  154 KVTRDRLMRIAHK  166 (209)
Q Consensus       154 Kv~RD~~m~~l~~  166 (209)
                      |+.=||....+++
T Consensus       104 K~eLdRc~~ll~K  116 (122)
T pfam02334       104 KVELDRCKKLIEK  116 (122)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9889999999999


No 57 
>COG3596 Predicted GTPase [General function prediction only]
Probab=20.16  E-value=59  Score=14.36  Aligned_cols=23  Identities=26%  Similarity=0.294  Sum_probs=13.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00236666547758999999988
Q gi|254781076|r  144 LSIAAASIIAKVTRDRLMRIAHK  166 (209)
Q Consensus       144 ~~VaaASIiAKv~RD~~m~~l~~  166 (209)
                      .++.++|++|+..-|.+=.....
T Consensus       221 lp~e~rs~~a~~~~d~~~~~~~~  243 (296)
T COG3596         221 LPVEARSPLAARLQDELRTQSAR  243 (296)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             73100240243301687777788


Done!