Query 021549
Match_columns 311
No_of_seqs 197 out of 795
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 03:52:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021549.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021549hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR03033 phage_rel_nuc putati 100.0 2.4E-40 5.3E-45 283.7 13.4 151 66-226 1-153 (153)
2 PF09588 YqaJ: YqaJ-like viral 100.0 1.5E-35 3.3E-40 252.1 4.2 142 73-216 1-152 (152)
3 COG5377 Phage-related protein, 100.0 4.7E-34 1E-38 256.5 8.0 196 63-268 2-206 (319)
4 PF01771 Herpes_alk_exo: Herpe 99.4 2.5E-13 5.5E-18 135.0 6.5 114 65-187 102-231 (465)
5 PHA03293 deoxyribonuclease; Pr 98.8 1E-08 2.2E-13 102.5 6.4 110 67-186 133-282 (523)
6 TIGR00372 cas4 CRISPR-associat 97.0 0.022 4.7E-07 49.2 13.5 154 82-261 1-158 (178)
7 PF01930 Cas_Cas4: Domain of u 96.8 0.025 5.3E-07 48.4 12.0 143 83-264 1-146 (162)
8 PHA00619 CRISPR-associated Cas 93.6 1.5 3.2E-05 39.3 12.1 158 78-261 19-178 (201)
9 COG1468 CRISPR-associated prot 85.3 24 0.00052 31.4 12.5 151 78-263 12-171 (190)
10 PF13366 PDDEXK_3: PD-(D/E)XK 79.5 2.5 5.3E-05 34.9 3.6 47 164-225 62-108 (118)
11 PHA01622 CRISPR-associated Cas 71.6 76 0.0016 28.5 11.8 114 120-248 46-164 (204)
12 PF15649 Tox-REase-7: Restrict 42.7 53 0.0011 25.6 4.5 69 126-217 2-73 (87)
13 PF12705 PDDEXK_1: PD-(D/E)XK 35.1 34 0.00074 29.6 2.8 84 160-251 130-224 (257)
14 TIGR01896 cas_AF1879 CRISPR-as 33.1 4.2E+02 0.0091 25.0 9.7 83 165-263 165-256 (271)
15 PF08774 VRR_NUC: VRR-NUC doma 31.9 83 0.0018 24.3 4.2 50 160-223 44-97 (100)
16 PHA02943 hypothetical protein; 31.0 2E+02 0.0042 25.1 6.5 51 205-258 40-90 (165)
17 PF03749 SfsA: Sugar fermentat 29.7 2.8E+02 0.0062 25.1 7.8 90 158-248 99-192 (215)
18 KOG4309 Transcription mediator 29.5 84 0.0018 27.8 4.1 61 216-278 120-192 (217)
19 PRK14676 hypothetical protein; 28.8 1E+02 0.0022 25.2 4.4 56 119-183 3-58 (117)
20 PF13588 HSDR_N_2: Type I rest 28.2 52 0.0011 25.9 2.5 61 164-238 38-103 (112)
21 PRK12497 hypothetical protein; 27.7 74 0.0016 25.9 3.4 52 124-184 7-58 (119)
22 PF10122 Mu-like_Com: Mu-like 26.7 35 0.00076 24.0 1.1 11 176-186 21-31 (51)
23 PHA01753 Holliday junction res 25.8 1.3E+02 0.0029 24.9 4.5 98 126-238 7-108 (121)
24 PRK14683 hypothetical protein; 25.6 96 0.0021 25.6 3.7 54 121-183 11-64 (122)
25 PRK14673 hypothetical protein; 24.9 1.3E+02 0.0029 25.4 4.5 53 123-184 26-79 (137)
26 PRK14684 hypothetical protein; 23.9 95 0.0021 25.5 3.4 52 124-184 7-58 (120)
27 PRK14689 hypothetical protein; 22.9 1.3E+02 0.0028 25.0 3.9 53 123-184 8-60 (124)
28 PRK14681 hypothetical protein; 22.6 1.8E+02 0.0039 25.2 4.9 53 123-184 43-96 (158)
29 PRK14679 hypothetical protein; 22.6 1E+02 0.0022 25.7 3.2 57 121-186 13-69 (128)
30 cd00523 archeal_HJR Holliday j 22.4 1.2E+02 0.0027 25.0 3.7 50 124-184 3-56 (123)
31 PRK14677 hypothetical protein; 21.8 95 0.0021 25.0 2.9 49 126-183 3-51 (107)
32 PRK14675 hypothetical protein; 21.7 84 0.0018 26.0 2.6 54 122-184 7-60 (125)
33 TIGR00252 conserved hypothetic 21.3 1.2E+02 0.0025 24.9 3.4 52 124-184 7-58 (119)
34 PRK14685 hypothetical protein; 20.2 1.2E+02 0.0025 26.9 3.3 56 120-184 39-94 (177)
35 PRK14686 hypothetical protein; 20.0 1.3E+02 0.0028 24.6 3.4 52 124-184 6-57 (119)
No 1
>TIGR03033 phage_rel_nuc putative phage-type endonuclease. Members of this protein family are found often in phage genomes and in prokaryotic genomes in uncharacterized regions that resemble integrated prophage regions.
Probab=100.00 E-value=2.4e-40 Score=283.69 Aligned_cols=151 Identities=30% Similarity=0.424 Sum_probs=126.6
Q ss_pred cCCCCCHHHHHHhhCCCccchHHHhhCCCCCCChHHHHHHHHcCccccccccchhHHHHHHHHhHHHHHHHHHhHhCCee
Q 021549 66 DMLQRSDEWFALRRDKLTTSTFSTALGFWKGKRRSELWHEKVFSLETQVIENSKRCAMEWGVLNEAAAIDRYKSITGHDV 145 (311)
Q Consensus 66 ~~~q~s~eW~~~R~~rITAS~~a~ilg~~~~~s~~~L~~eK~~g~~~~~~~~~~n~am~~G~~~E~~a~~~ye~~~g~~V 145 (311)
+++|+|++|+++|+++||||++++++|.++|+|+++||++|+|...+ . ..|++|+||+.+||.|++.|+..++. +
T Consensus 1 ~~~Q~s~eWl~~R~~~ItaS~~~~i~g~s~~~t~~~L~~ek~g~~~~-~---~~~~~~~~G~~~Ep~a~~~~~~~~~~-~ 75 (153)
T TIGR03033 1 DLVQRTEEWHAWRKGGITASDIAAIMGLNPYKTPEELWKEKTGFVEP-E---DMNEAMYHGVKLEPEAREAFRDKYGI-M 75 (153)
T ss_pred CcccCHHHHHHHHhcCCCHhHHHHHHCCCccCCHHHHHHHHhCCCCC-c---cccHHHHHhHhhhHHHHHHHHhcCCe-E
Confidence 47999999999999999999999999999999999999999854332 2 25899999999999999987776654 3
Q ss_pred eeccceeeccccccccccCCCcccccCCCCcEEEEecCCCCC--CCcccCCCCCCCcccHHHHHHHhHhhcCCcEEEEEE
Q 021549 146 SSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCPYNKG--KPEIALPWSTVPFYYMPQVQGQMEILDREWVDLYCW 223 (311)
Q Consensus 146 ~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP~~~~--~~~~~~~~~~iP~~Y~~QVQ~qM~Vtg~~~~~fvv~ 223 (311)
..++++.++ ++||++|||||++.+ +.++||||||+... .|.... .+.+|.+|++|||+||+|+|+++|||++|
T Consensus 76 ~~~~~~~~~--~~~~~~aSpDg~~~~--~~~ilEiK~~~~~~~~~w~~~~-~~~iP~~Y~~QvQ~ql~vtg~~~~~f~~~ 150 (153)
T TIGR03033 76 AEPFCLEHD--EYPWMAASLDGLVAD--DKQILEIKCPSERVSKLWVSEL-SGEVPAYYQAQVQWQLYVSGSQAAYFAVY 150 (153)
T ss_pred EeCcEEecC--CCCeEEECCceeecC--CCceEEEecCCcccchhhhhhc-cCCCcHHHHHHHHHHHhccCCCeEEEEEE
Confidence 456666665 589999999999853 25999999998653 443221 36899999999999999999999999999
Q ss_pred cCC
Q 021549 224 TPN 226 (311)
Q Consensus 224 ~~~ 226 (311)
+++
T Consensus 151 ~~~ 153 (153)
T TIGR03033 151 IGG 153 (153)
T ss_pred eCc
Confidence 874
No 2
>PF09588 YqaJ: YqaJ-like viral recombinase domain; InterPro: IPR019080 This protein is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit []. ; PDB: 3SZ5_A 3SZ4_A 3SYY_A 3K93_A 1AVQ_A 3SM4_C 3SLP_A.
Probab=100.00 E-value=1.5e-35 Score=252.14 Aligned_cols=142 Identities=39% Similarity=0.587 Sum_probs=103.4
Q ss_pred HHHHHhhCCCccchHHHhhCCCCCCChHHHHHHHHcCccccc--cccchhHHHHHHHHhHHHHHHHHHhHhCCeeee-cc
Q 021549 73 EWFALRRDKLTTSTFSTALGFWKGKRRSELWHEKVFSLETQV--IENSKRCAMEWGVLNEAAAIDRYKSITGHDVSS-LG 149 (311)
Q Consensus 73 eW~~~R~~rITAS~~a~ilg~~~~~s~~~L~~eK~~g~~~~~--~~~~~n~am~~G~~~E~~a~~~ye~~~g~~V~~-~G 149 (311)
||+++|+++||||++++|+|.++++++.+||.+|++....+. .++.+|.+|+||+.+|+.|++.|++.+|..|.+ .|
T Consensus 1 eW~~~R~~~ItaS~~~~i~g~~~~~~~~~l~~~k~~~~~~~~~~~~~~~~~~~~~G~~~E~~a~~~~~~~~~~~v~~~~~ 80 (152)
T PF09588_consen 1 EWLELRRGGITASEAAAILGISPYKTPFSLWREKLGERITEDLESPFSGNKAMQWGHELEPLARQFYEEKTGLEVKEPNG 80 (152)
T ss_dssp HHHHHCTT-EEGGGHHHHH---SS-HHHHHHHHHHHHHHHSCH--S--SHHHHHHHHHHHHHHHHHHHHHHT--EE---S
T ss_pred ChhHHHCCCcCHhHHHHHHCCCCCCCHHHHHHHHhCccccCCcCCcchhHHHHHHHHHhhHHHHHHHHHHhccceEecce
Confidence 799999999999999999999999999999999998743221 134579999999999999999999999999998 58
Q ss_pred ceeeccccccccccCCCcccccCC-C--CcEEEEecCCCCCC----CcccCCCCCCCcccHHHHHHHhHhhcCC
Q 021549 150 FAVHAEEQLDWLGASPDGLLGCFP-G--GGILEVKCPYNKGK----PEIALPWSTVPFYYMPQVQGQMEILDRE 216 (311)
Q Consensus 150 l~i~~~~~~p~lgASPDGli~~~~-~--~~iLEIKcP~~~~~----~~~~~~~~~iP~~Y~~QVQ~qM~Vtg~~ 216 (311)
+++++ ++|||+|||||++.+++ + .++||||||+.... |......+++|++|++|||+||+|+|++
T Consensus 81 ~~~~~--~~~~l~aSpDg~~~~~~~~~~~~~lEiK~~~~~~~~~~~~~~~~~~~~ip~~Y~~QvQ~qm~vtg~e 152 (152)
T PF09588_consen 81 LFIHP--DHPWLGASPDGLVVCPSGGEERGLLEIKCPYSPKFISYKWGEAGESDKIPHYYYAQVQHQMAVTGAE 152 (152)
T ss_dssp -EESS--CTTSEEE--SEEE--GCTT-CTEEEEEEE-SHHHHHHHHHHCGG-HHCCHHHHHHHHHHHHHHHT-S
T ss_pred eEEcC--ccceeeecCCEEEeeccCCCccceEEEecCCchhhhhhhhcccccccCCCHHHHHHHHHHHHHHCcC
Confidence 88875 58999999999997753 3 79999999986221 2211112478999999999999999975
No 3
>COG5377 Phage-related protein, predicted endonuclease [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.7e-34 Score=256.53 Aligned_cols=196 Identities=22% Similarity=0.264 Sum_probs=173.0
Q ss_pred ccccCCCCCH-----HHHHHhhCCCccchHHHhhCCCCCCChHHHHHHHHcCccccccccchhHHHHHHHHhHHHHHHHH
Q 021549 63 TQNDMLQRSD-----EWFALRRDKLTTSTFSTALGFWKGKRRSELWHEKVFSLETQVIENSKRCAMEWGVLNEAAAIDRY 137 (311)
Q Consensus 63 ~~~~~~q~s~-----eW~~~R~~rITAS~~a~ilg~~~~~s~~~L~~eK~~g~~~~~~~~~~n~am~~G~~~E~~a~~~y 137 (311)
++.++.|+++ +|+..|+.+|+||+++.+||+|+|+|+++||++|+++.++. ....++-.||..+|++++..|
T Consensus 2 k~~ev~~~t~dm~~~qWl~~R~~glggSDA~~imGln~ykt~fELwlekt~qv~p~---~~qseaayfg~~~Eevva~ef 78 (319)
T COG5377 2 KIIEVLAKTPDMSRTQWLTHRRQGLGGSDAPIIMGLNKYKTPFELWLEKTGQVTPD---ESQSEAAYFGELLEEVVAKEF 78 (319)
T ss_pred chhhhhhcCCcccHHHHHHHHHhcCCCcchhhhhcCCccCCHHHHHHHhcCCCCCC---cchHHHHHHHHHHHHHHHHHH
Confidence 3455667777 99999999999999999999999999999999999988653 247789999999999999999
Q ss_pred HhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEec--CCCCCCCcccCCCCCCCcccHHHHHHHhHhhc-
Q 021549 138 KSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKC--PYNKGKPEIALPWSTVPFYYMPQVQGQMEILD- 214 (311)
Q Consensus 138 e~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKc--P~~~~~~~~~~~~~~iP~~Y~~QVQ~qM~Vtg- 214 (311)
++++|.+|..|..+..+ +.+.|++|+.|..+... ..+||||| .|..+.|+. +++|..|..|||||+.|+|
T Consensus 79 errtGkkvrr~~~i~~h-p~~~F~~anvdr~vVgE--~aiLeckT~sA~m~~ew~~----~eiP~~Y~vQmqHyl~V~Ge 151 (319)
T COG5377 79 ERRTGKKVRRCNAILRH-PEYDFILANVDRDVVGE--KAILECKTTSAYMAKEWED----DEIPFHYIVQMQHYLGVLGE 151 (319)
T ss_pred HHHhccchhhhhhhhcC-ccchhhhhhhHHHhhhh--hhhhccchHHHHHhccccc----ccCcHHHHHHHHHHHhhhhh
Confidence 99999999998876654 57999999999987542 58999999 466677774 7899999999999999999
Q ss_pred CCcEEEEEEcCC-CeEEEEEECCHHHHHHHHHHHHHHHHHhcCCCCCCCCCCchh
Q 021549 215 REWVDLYCWTPN-GSTIFRVIRRRDYWELIHGILQEFWWENVVPAKEALSMGREE 268 (311)
Q Consensus 215 ~~~~~fvv~~~~-~~~v~rV~RD~~~~~~i~~~~~~Fw~~~V~p~~~p~~~~~~~ 268 (311)
.+.++|+|++++ .+...+|+||++.++.|+..+.+||+++|+-..||+++|+.+
T Consensus 152 ~rk~y~AvligG~kfiwkeierddeLin~Ii~~e~~fw~d~v~~~~pPaldgssa 206 (319)
T COG5377 152 YRKAYFAVLIGGNKFIWKEIERDDELINMIINAEIDFWNDIVLGPVPPALDGSSA 206 (319)
T ss_pred hhhhhheeeeccchhHHHHhhhhHHHHHHHHHHHHHHHhhccccCCCCCcccccc
Confidence 788899888865 678889999999999999999999999999999999998853
No 4
>PF01771 Herpes_alk_exo: Herpesvirus alkaline exonuclease; InterPro: IPR001616 Equid herpesvirus 1 (Equine herpesvirus 1) is a respiratory virus capable of causing abortion and neurological disease. Its complete DNA sequence has been determined [] and the constituent genes found to be arranged co-linearly with those in the genomes of other alphaherpesviruses, namely Human herpesvirus 3 (HHV-3) and Human herpesvirus 1 (HHV-1) []. Comparisons of the predicted amino acid sequences have allowed functions of many EHV-1 proteins to be inferred. For example, detailed analysis of HHV-1 and Human herpesvirus 2 (HHV-2) DNA has revealed an open reading frame sufficient to encode 626 amino acids for the HHV-1 alkaline exonuclease (620 amino acids for HHV-2) []. Comparison of the predicted amino acid sequences of the viral enzymes has revealed significant differences in the N-terminal portions of the proteins; nevertheless, their three-dimensional structures are believed to be similar.; GO: 0003677 DNA binding, 0004527 exonuclease activity; PDB: 3FHD_A 3POV_A 2W45_B 2W4B_B.
Probab=99.41 E-value=2.5e-13 Score=134.96 Aligned_cols=114 Identities=20% Similarity=0.288 Sum_probs=73.3
Q ss_pred ccCCCCCHHHHHHhhCCCccchHHHhhCCCCCCChHHHHHHHHcCccccccccchhHHHHHHHHhHHHHHHHHHhHhC--
Q 021549 65 NDMLQRSDEWFALRRDKLTTSTFSTALGFWKGKRRSELWHEKVFSLETQVIENSKRCAMEWGVLNEAAAIDRYKSITG-- 142 (311)
Q Consensus 65 ~~~~q~s~eW~~~R~~rITAS~~a~ilg~~~~~s~~~L~~eK~~g~~~~~~~~~~n~am~~G~~~E~~a~~~ye~~~g-- 142 (311)
+.-|++++.|+.+|.+++|||.+...+....... .+..... ... ....+++|.+|..+|+.|+..+++..-
T Consensus 102 TRGQS~N~LW~lLR~~riTAS~~~~~~~~~~~~~--~l~~~~~--~~~---~~~~~~av~fG~~~E~~vk~li~~~v~~~ 174 (465)
T PF01771_consen 102 TRGQSENPLWHLLRLGRITASKFYWVCKGPNSSP--ALFKGNP--IQN---NHYQSEAVAFGLRNEPVVKKLIEELVVKT 174 (465)
T ss_dssp TTTGCCSCCHHHHCTTSEECCCHHHHHCT-CTTT--GCCS------------SS--SHHHHHHHHHHHHHHHHHHCTSS-
T ss_pred hhcCccchhHHHHHCCceeeccceeeccCCcCcH--HHhcccc--ccc---cccCcHHHHhchhhHHHHHHHHHHhhccc
Confidence 3356689999999999999999999886322111 0000000 000 113678999999999999999988763
Q ss_pred ---CeeeeccceeeccccccccccCCCcccc-cC----------CCCcEEEEecCCCCC
Q 021549 143 ---HDVSSLGFAVHAEEQLDWLGASPDGLLG-CF----------PGGGILEVKCPYNKG 187 (311)
Q Consensus 143 ---~~V~~~Gl~i~~~~~~p~lgASPDGli~-~~----------~~~~iLEIKcP~~~~ 187 (311)
..|.+|||++++ ..+.+|||||.++. .. ....++||||+|++.
T Consensus 175 ~~~~~v~~CGLfisp--~~Gl~gASpD~~f~r~~~g~~~~~~~~~~~~vyEIKCr~KY~ 231 (465)
T PF01771_consen 175 RDSEEVLDCGLFISP--RTGLFGASPDAYFCRDETGELGPLEFEPDIVVYEIKCRYKYL 231 (465)
T ss_dssp TTSTCE-----EE-T--TTSSEEE--SEEEC-EEEECTTEEEEECCCEEEEEEEEGCC-
T ss_pred cCCCcccceeeeecC--CCCccccchhheeeeccCCCCCccccCCceEEEEEecccccc
Confidence 578999999986 47999999999987 21 136789999998864
No 5
>PHA03293 deoxyribonuclease; Provisional
Probab=98.77 E-value=1e-08 Score=102.52 Aligned_cols=110 Identities=24% Similarity=0.254 Sum_probs=73.5
Q ss_pred CCCCCHHHHHHhhCCCccchHHHhhCCCCCCCh-HHHHHHHHcCccccccccchhHHHHHHHHhHHHHHHHHHhHhC---
Q 021549 67 MLQRSDEWFALRRDKLTTSTFSTALGFWKGKRR-SELWHEKVFSLETQVIENSKRCAMEWGVLNEAAAIDRYKSITG--- 142 (311)
Q Consensus 67 ~~q~s~eW~~~R~~rITAS~~a~ilg~~~~~s~-~~L~~eK~~g~~~~~~~~~~n~am~~G~~~E~~a~~~ye~~~g--- 142 (311)
-|+.++.|+.+|.+++|||.+.- | +.+.. .--|.+.-.... ....+.+|.+|+.+|+.|+...+...-
T Consensus 133 GQS~N~LW~lLR~~~iTAS~~~w--~--~~g~~~~p~~~~~~~~~~----~~~~s~Av~FG~~nE~~vK~Ll~~~~~~~~ 204 (523)
T PHA03293 133 NQAECDLWALLRRGLLTASTLKW--G--ANGPCFPPQWCKVNTGAR----GIPQSAAVAFGRTNEPLARALIEAYCVGPS 204 (523)
T ss_pred cCccCHHHHHHHcCCceecceec--c--CCCCccCccccccccccc----ccccchHhhhchhhhHHHHHHHHHHccCCc
Confidence 46689999999999999998763 1 11110 001221110000 012468999999999999998887431
Q ss_pred ------------------------CeeeeccceeeccccccccccCCCccccc-C--C---------CCcEEEEecCCCC
Q 021549 143 ------------------------HDVSSLGFAVHAEEQLDWLGASPDGLLGC-F--P---------GGGILEVKCPYNK 186 (311)
Q Consensus 143 ------------------------~~V~~~Gl~i~~~~~~p~lgASPDGli~~-~--~---------~~~iLEIKcP~~~ 186 (311)
.....|||++++ .-+.+|||+|-++.. + + ...+.||||-+.+
T Consensus 205 ~~~~~~~~~~~~~f~f~~~~~~~~~~~~~cGlLiDp--~tG~~GASLDm~v~~rd~~G~L~~~~~~~~~~iyEIKCRaKY 282 (523)
T PHA03293 205 TDDGGTDPDDGEFFVFDEPVGSPPEEAYACGLLIDA--RTGMVGASLDMLVCDRDPHGVLAPHPTQTTLEFFEIKCRAKY 282 (523)
T ss_pred ccccccccccccceecccccCCCCCcceeeeeEecC--CCCcccccCceEecccCCCCcccccCCCCceeEEEEeccccc
Confidence 124469999986 479999999998733 1 1 2579999997654
No 6
>TIGR00372 cas4 CRISPR-associated protein Cas4. This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p.
Probab=97.02 E-value=0.022 Score=49.25 Aligned_cols=154 Identities=18% Similarity=0.078 Sum_probs=93.6
Q ss_pred CccchHHHhhCCCCCCChHHHHHHHHcCccccccccchhHHHHHHHHhHHHHHHHHHhHhCCeeeeccceeecccccccc
Q 021549 82 LTTSTFSTALGFWKGKRRSELWHEKVFSLETQVIENSKRCAMEWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWL 161 (311)
Q Consensus 82 ITAS~~a~ilg~~~~~s~~~L~~eK~~g~~~~~~~~~~n~am~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~l 161 (311)
|+.|.+...+=+ |...|.+...+... .++..|.-|......+.+......+.. .+....+..+ .+ -+
T Consensus 1 i~~s~i~~~~~C-----pR~~~~~~~~~~~~-----~~~~~~~~G~~~h~~~~~~~~~~~~~~-~~~~v~l~~~-~~-~l 67 (178)
T TIGR00372 1 ITVSDVLEYLYC-----PRKLWYMKKGGSER-----FSEVRMILGRLIHERAESFLKSLGGVR-EEKEVPLKSK-KL-GL 67 (178)
T ss_pred CChHHhHHHHhC-----hHHHHHHHhhcccc-----cchhHHHHHHHHHHHhhhhhhccCCEE-EEEeeEeEcc-cC-Cc
Confidence 345555544433 56788888766543 234569999987666653332222222 2334445442 23 47
Q ss_pred ccCCCcccccCCCCcEEEEecCCCCCCCcccCCCCCCCcccHHHHHHHhHhhcCCcE----EEEEEcCCCeEEEEEECCH
Q 021549 162 GASPDGLLGCFPGGGILEVKCPYNKGKPEIALPWSTVPFYYMPQVQGQMEILDREWV----DLYCWTPNGSTIFRVIRRR 237 (311)
Q Consensus 162 gASPDGli~~~~~~~iLEIKcP~~~~~~~~~~~~~~iP~~Y~~QVQ~qM~Vtg~~~~----~fvv~~~~~~~v~rV~RD~ 237 (311)
.+.+|.+...+++..++|+|+..... ...|..|++.|.+++..... -+++|...+. ...|+.|+
T Consensus 68 ~G~iD~i~~~~~~~~ive~Ktg~~~~-----------~~~~~~Ql~~Ya~~l~~~~~~v~~g~l~y~~~~~-~~~v~~~~ 135 (178)
T TIGR00372 68 KGVIDVVLEADGELVPVEVKSGKPKL-----------REAHKYQLLAYAYLLEEMYGEIVRGYILYIEAGK-KLEVEISE 135 (178)
T ss_pred EEEEEEEEEECCeEEEEEEecCCCCC-----------ChhHHHHHHHHHHHHHHhhCCCCcEEEEEEeCCc-EEEecCCH
Confidence 88899888766456799999953211 14477899999888775542 2333444433 34888999
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCC
Q 021549 238 DYWELIHGILQEFWWENVVPAKEA 261 (311)
Q Consensus 238 ~~~~~i~~~~~~Fw~~~V~p~~~p 261 (311)
+..+.+.+.+.+.- +.+..+.+|
T Consensus 136 ~~~~~~~~~~~~i~-~~~~~~~~P 158 (178)
T TIGR00372 136 ELRKKAEKLIEKIR-ELLEGGKPP 158 (178)
T ss_pred HHHHHHHHHHHHHH-HHHhCCCCC
Confidence 88888887777764 455555555
No 7
>PF01930 Cas_Cas4: Domain of unknown function DUF83; InterPro: IPR022765 This entry represents an uncharacterised domain found in several proteins, including DNA replication helicase Dna2, clustered regularly interspaced short palindromic repeats (CRISPR)-associated exonuclease Cas4 and putative RecB family exonuclease proteins.
Probab=96.82 E-value=0.025 Score=48.42 Aligned_cols=143 Identities=14% Similarity=0.006 Sum_probs=88.7
Q ss_pred ccchHHHhhCCCCCCChHHHHHHHHcCccccccccchhHHHHHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccc
Q 021549 83 TTSTFSTALGFWKGKRRSELWHEKVFSLETQVIENSKRCAMEWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLG 162 (311)
Q Consensus 83 TAS~~a~ilg~~~~~s~~~L~~eK~~g~~~~~~~~~~n~am~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lg 162 (311)
|+|++-..+=+ |..+|....+.... ..+..|..|+.... ..|.+.. .++.+ ++ .
T Consensus 1 t~s~v~~y~~C-----pR~~~l~~~~~~~~-----~~~~~~~~G~~~h~---~~~~~~~------~~v~v-s~------~ 54 (162)
T PF01930_consen 1 TGSMVNEYVYC-----PRRAYLERVGIEPE-----EPTESMELGRELHE---ERYEREK------REVPV-SE------S 54 (162)
T ss_pred CHHHhhHHHHc-----cHHHHHHHcCCccc-----CCHhHHHhhHHhhh---hhhhhcc------eeecc-CC------c
Confidence 45555544432 56788888732221 24568888988766 2222211 12222 21 7
Q ss_pred cCCCcccccCCCCcEEEEecCCCCCCCcccCCCCCCCcccHHHHHHHhHhhc---CCcEEEEEEcCCCeEEEEEECCHHH
Q 021549 163 ASPDGLLGCFPGGGILEVKCPYNKGKPEIALPWSTVPFYYMPQVQGQMEILD---REWVDLYCWTPNGSTIFRVIRRRDY 239 (311)
Q Consensus 163 ASPDGli~~~~~~~iLEIKcP~~~~~~~~~~~~~~iP~~Y~~QVQ~qM~Vtg---~~~~~fvv~~~~~~~v~rV~RD~~~ 239 (311)
+-+|.+...++...++|+|..... ...+..|+..|+++.. .+.-.-+++..++-...+|+-|++.
T Consensus 55 G~iD~v~~~~~~~~~~E~K~~~~~------------~~~~~~Ql~~Y~~lL~~~g~~v~~G~i~y~~~~~~~~v~~~~~~ 122 (162)
T PF01930_consen 55 GKIDIVEKGGGEIIPVEIKSGRKP------------REEHRMQLAAYALLLEEFGIPVKRGYIYYIEDRKRVRVEITEEL 122 (162)
T ss_pred EEEEEEEEeCCEEEEEEEecCCCC------------cchhHHHHHHHHHHHHhcCccceeEEEEEecCCeEEEEeCCHHH
Confidence 888988855556789999985322 1123679999988877 2222123344455556669999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCCCC
Q 021549 240 WELIHGILQEFWWENVVPAKEALSM 264 (311)
Q Consensus 240 ~~~i~~~~~~Fw~~~V~p~~~p~~~ 264 (311)
.+.+.+.+.++- +.+..+.+|++.
T Consensus 123 ~~~v~~~i~~i~-~~~~~~~~P~~~ 146 (162)
T PF01930_consen 123 RRKVEKLIEEIR-KILEGESPPPPE 146 (162)
T ss_pred HHHHHHHHHHHH-HHHhCCCcCCCC
Confidence 999999999886 566666666654
No 8
>PHA00619 CRISPR-associated Cas4-like protein
Probab=93.58 E-value=1.5 Score=39.29 Aligned_cols=158 Identities=12% Similarity=-0.026 Sum_probs=87.7
Q ss_pred hhCCCccchHHHhhCCCCCCChHHHHHHHHcCccccccccchhHHHHHHHHhHHHHHHHHHhHhCCeeeecc-ceeeccc
Q 021549 78 RRDKLTTSTFSTALGFWKGKRRSELWHEKVFSLETQVIENSKRCAMEWGVLNEAAAIDRYKSITGHDVSSLG-FAVHAEE 156 (311)
Q Consensus 78 R~~rITAS~~a~ilg~~~~~s~~~L~~eK~~g~~~~~~~~~~n~am~~G~~~E~~a~~~ye~~~g~~V~~~G-l~i~~~~ 156 (311)
|.+.|..|+++. -+..+|.......... +......|.-|+..-....+...+ .+....... ..+.
T Consensus 19 ~~~~i~~sd~~~--------CpRk~w~~~~~~~~~~--~~~~~~~~~~G~~iHe~~~~~~~~-~sy~~e~~ve~~i~--- 84 (201)
T PHA00619 19 DLQTIWVTELSR--------CLRRSWLMRKNGGVKL--ALEEAMKMHIGSGLHMRLQRILKK-HGFETECRVERKTA--- 84 (201)
T ss_pred CCCeEEeeehhc--------CccHHHHHHhcccccc--ccccchHHHhhHHHHHHHHHHHhh-cCceeEEEEEEecc---
Confidence 446677777652 2356788876543221 122456778998886555555543 222222100 0111
Q ss_pred cccc-cccCCCcccccCCCCcEEEEecCCCCCCCcccCCCCCCCcccHHHHHHHhHhhcCCcEEEEEEcCCCeEEEEEEC
Q 021549 157 QLDW-LGASPDGLLGCFPGGGILEVKCPYNKGKPEIALPWSTVPFYYMPQVQGQMEILDREWVDLYCWTPNGSTIFRVIR 235 (311)
Q Consensus 157 ~~p~-lgASPDGli~~~~~~~iLEIKcP~~~~~~~~~~~~~~iP~~Y~~QVQ~qM~Vtg~~~~~fvv~~~~~~~v~rV~R 235 (311)
..+ +.+..|.+. +++..|+|+|+.-....+ ...-..+..|++.||+..+...+.++.+..+. ....|+-
T Consensus 85 -~~~~i~G~ID~i~--~~~~~vvEiK~s~~~~~~------~~~~~~~~~QL~~Yl~lL~~~~G~l~~~~~~r-k~~eV~~ 154 (201)
T PHA00619 85 -LGFEIVGKIDVYD--KEENTIYELKYTHMDDLD------KGRLNNYLRQLNYYIEMANAMAGYLIIVHADG-RVEEIKR 154 (201)
T ss_pred -cceEEEEEEEEEe--CCCcEEEEEEccCCCccc------ccchHHHHHHHHHHHHHHHhcCcEEEEEcCCC-ceEEeec
Confidence 123 667888883 234589999995322111 11234577899999999987666665444443 2334443
Q ss_pred CHHHHHHHHHHHHHHHHHhcCCCCCC
Q 021549 236 RRDYWELIHGILQEFWWENVVPAKEA 261 (311)
Q Consensus 236 D~~~~~~i~~~~~~Fw~~~V~p~~~p 261 (311)
| .-.+++.+.+.+.. +.|..+.+|
T Consensus 155 ~-~~~~~l~~~i~~I~-~ii~~~~~P 178 (201)
T PHA00619 155 D-WSETDLENRANAFG-ISVEENILP 178 (201)
T ss_pred c-ccHHHHHHHHHHHH-HHHhcCcCC
Confidence 3 44466666666665 556555555
No 9
>COG1468 CRISPR-associated protein Cas4 (RecB family exonuclease) [Defense mechanisms]
Probab=85.27 E-value=24 Score=31.41 Aligned_cols=151 Identities=17% Similarity=0.140 Sum_probs=82.2
Q ss_pred hhCCCccchHHHhhCCCCCCChHHHHHHHHcCccccccccchhHHHHHHHHhHHHHHHHHHhHh--CCeeeeccceeecc
Q 021549 78 RRDKLTTSTFSTALGFWKGKRRSELWHEKVFSLETQVIENSKRCAMEWGVLNEAAAIDRYKSIT--GHDVSSLGFAVHAE 155 (311)
Q Consensus 78 R~~rITAS~~a~ilg~~~~~s~~~L~~eK~~g~~~~~~~~~~n~am~~G~~~E~~a~~~ye~~~--g~~V~~~Gl~i~~~ 155 (311)
+...+++|++...+-+ +..+|....++... .++++.-|......+....+... ...|.-.|..+
T Consensus 12 ~~~~i~~~~v~~y~~C-----prk~w~~~~~~~~~------~~~~~~~~~~l~~~i~~~~~~~~~~~~~v~l~~~~i--- 77 (190)
T COG1468 12 NSMRITGSDVNEYLYC-----PRKLWLFSRGGPEE------SPEVYSEGVELGKLIHEKLEKFLRDEKEVELEGEWI--- 77 (190)
T ss_pred cceeecHHHHHHHHhc-----CHHHHHHHhcCccc------cchhcchhhhhhHHHHHHHHHHhcccccceecceee---
Confidence 3456888888887766 36799988876543 22333344444333333332211 11121112111
Q ss_pred ccccccccCCCcccccCC---CCcEEEEecCCCCCCCcccCCCCCCCcccHHHHHHHhHhhcCCcEEE---EEEcCCCeE
Q 021549 156 EQLDWLGASPDGLLGCFP---GGGILEVKCPYNKGKPEIALPWSTVPFYYMPQVQGQMEILDREWVDL---YCWTPNGST 229 (311)
Q Consensus 156 ~~~p~lgASPDGli~~~~---~~~iLEIKcP~~~~~~~~~~~~~~iP~~Y~~QVQ~qM~Vtg~~~~~f---vv~~~~~~~ 229 (311)
..|++.+... ...++|||...... ..| ...|++.+|++.....+.. +.+-+..-.
T Consensus 78 --------~~d~lk~~~~~~~~~~~vEiK~~~~~~---------~~~--~~~Ql~~ylyl~e~~g~~v~~g~i~Y~~~~k 138 (190)
T COG1468 78 --------KIDFLKGRMDLEVKDVVVEIKKSKKME---------KAP--HKLQLAYYLYLEEKLGIAVAKGYIYYPKLKK 138 (190)
T ss_pred --------eeeeecccceeeccceeEEEecCcCcc---------cch--HHHHHHHHHHHHHhhCceeeeEEEEecccCc
Confidence 3333332210 12689999854332 223 4579999999988333331 223333347
Q ss_pred EEEEECCHHHHHHHHHHHHHHHHHhcCCC-CCCCC
Q 021549 230 IFRVIRRRDYWELIHGILQEFWWENVVPA-KEALS 263 (311)
Q Consensus 230 v~rV~RD~~~~~~i~~~~~~Fw~~~V~p~-~~p~~ 263 (311)
.+.|+-|++..+.+.+.+.+- +.++.+ .||++
T Consensus 139 ~~~Vei~~~~~e~v~~~~~ei--~~ile~~~~p~~ 171 (190)
T COG1468 139 RVEVELTEELREEVERVLKEI--EEILEGGKPPPP 171 (190)
T ss_pred EEEEEeCHHHHHHHHHHHHHH--HHHHhCCCCCCC
Confidence 888999999888888888776 344444 44433
No 10
>PF13366 PDDEXK_3: PD-(D/E)XK nuclease superfamily
Probab=79.46 E-value=2.5 Score=34.92 Aligned_cols=47 Identities=15% Similarity=-0.036 Sum_probs=37.3
Q ss_pred CCCcccccCCCCcEEEEecCCCCCCCcccCCCCCCCcccHHHHHHHhHhhcCCcEEEEEEcC
Q 021549 164 SPDGLLGCFPGGGILEVKCPYNKGKPEIALPWSTVPFYYMPQVQGQMEILDREWVDLYCWTP 225 (311)
Q Consensus 164 SPDGli~~~~~~~iLEIKcP~~~~~~~~~~~~~~iP~~Y~~QVQ~qM~Vtg~~~~~fvv~~~ 225 (311)
-+|-++.+. .|+|+|+-- .+...+.+|+..||-.+|.+.+.++-+..
T Consensus 62 r~DllV~~~---vIvElKav~------------~l~~~h~aQll~YLk~~~~~lGlLiNF~~ 108 (118)
T PF13366_consen 62 RADLLVENK---VIVELKAVE------------ELNPVHEAQLLNYLKATGLPLGLLINFGV 108 (118)
T ss_pred EeeEEEcCe---EEEEEeeHh------------hcCHHHHHHHHHHHHHhCCCEEEEEecCC
Confidence 678777664 899999942 23344779999999999999999987765
No 11
>PHA01622 CRISPR-associated Cas4-like protein
Probab=71.61 E-value=76 Score=28.45 Aligned_cols=114 Identities=12% Similarity=0.020 Sum_probs=59.3
Q ss_pred hHHHHHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecCCCCCCCcccCCCCCCC
Q 021549 120 RCAMEWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCPYNKGKPEIALPWSTVP 199 (311)
Q Consensus 120 n~am~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP~~~~~~~~~~~~~~iP 199 (311)
++.+.-|...-...-+.+.+..+.+. +..+.+..+ . -.+.+..|.+... .++|+|+.-.. . ...-
T Consensus 46 ~~~~~~G~~ihe~~~~~~~~~~~~e~-Ekei~~~i~-~-i~i~GkID~l~~~----~iiEvKsS~k~-~-------~~~~ 110 (204)
T PHA01622 46 EIYLDLGEQYHERIEQYFKEKLNCQT-EVEIKDEIE-G-IKISGRIDIVCNN----DLLEIKTISYN-Y-------FQVK 110 (204)
T ss_pred chHHHHHHHHHHHHHHHHHHHhCcee-EEEEEEEEC-C-EEEEEEEEEEeCC----ceEEEEecCCC-C-------Cccc
Confidence 78899999875555444444322211 111111111 1 1245577777633 48999996421 0 1223
Q ss_pred cccHHHHHHHhHhhcC---C-cEEEEEEcCCC-eEEEEEECCHHHHHHHHHHHH
Q 021549 200 FYYMPQVQGQMEILDR---E-WVDLYCWTPNG-STIFRVIRRRDYWELIHGILQ 248 (311)
Q Consensus 200 ~~Y~~QVQ~qM~Vtg~---~-~~~fvv~~~~~-~~v~rV~RD~~~~~~i~~~~~ 248 (311)
..|..|++.|+++... + ..-+.++..+. ..+..+.-|++..+.++..+.
T Consensus 111 ~~~~~Qla~Yl~~Lk~~Gi~v~g~~l~~i~~k~~~v~~~~~~e~~le~~i~~I~ 164 (204)
T PHA01622 111 EYHLYQVALYYHILKKQNYQINNVYIVYLNRNTREVKQFKIDEKVLETYYQKVI 164 (204)
T ss_pred HhHHHHHHHHHHHHHHcCCCCCceEEEEecCCCCceeEEEcChHHHHHHHHHHH
Confidence 4578899999988763 1 12233333332 245556666555554444443
No 12
>PF15649 Tox-REase-7: Restriction endonuclease fold toxin 7
Probab=42.70 E-value=53 Score=25.61 Aligned_cols=69 Identities=19% Similarity=0.144 Sum_probs=40.3
Q ss_pred HHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecCCCCCCCcccCCCCCCCcccHHH
Q 021549 126 GVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCPYNKGKPEIALPWSTVPFYYMPQ 205 (311)
Q Consensus 126 G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP~~~~~~~~~~~~~~iP~~Y~~Q 205 (311)
|...|..|...+... ...+. +.. +....-.-=||++... .+.++|||..-.. .|=.|
T Consensus 2 G~~~E~~a~~~~~~~-~~~i~-----~~~-~~~~~~~rIPD~~~~~--~~~l~EVKNV~~~--------------s~t~Q 58 (87)
T PF15649_consen 2 GREGERRAGIDLNKN-KKNIT-----VNN-GNGGQGNRIPDGLDKN--NGQLVEVKNVKYQ--------------SLTKQ 58 (87)
T ss_pred hhhHHHHHhhhhcCC-ceEEE-----ecc-CcccCCcCCCcccccC--CCcEEEEechhhc--------------cchHH
Confidence 677888888777511 11111 100 0111223458888753 3589999986321 24579
Q ss_pred HHHHhHhh---cCCc
Q 021549 206 VQGQMEIL---DREW 217 (311)
Q Consensus 206 VQ~qM~Vt---g~~~ 217 (311)
+..|+..+ |.+.
T Consensus 59 lr~~~~~A~~~G~~~ 73 (87)
T PF15649_consen 59 LRDYVKYAKENGYRF 73 (87)
T ss_pred HHHHHHHHHHcCCcE
Confidence 99999997 6653
No 13
>PF12705 PDDEXK_1: PD-(D/E)XK nuclease superfamily; PDB: 1W36_B 3K70_B 3U4Q_A 3U44_A.
Probab=35.05 E-value=34 Score=29.63 Aligned_cols=84 Identities=13% Similarity=0.020 Sum_probs=49.6
Q ss_pred ccccCCCccccc-CCCCcEEEEecCCCCCCCcccCCCCCCCcccHHHHHHHhHhhcCCc-------EEEEEEcCCCe-EE
Q 021549 160 WLGASPDGLLGC-FPGGGILEVKCPYNKGKPEIALPWSTVPFYYMPQVQGQMEILDREW-------VDLYCWTPNGS-TI 230 (311)
Q Consensus 160 ~lgASPDGli~~-~~~~~iLEIKcP~~~~~~~~~~~~~~iP~~Y~~QVQ~qM~Vtg~~~-------~~fvv~~~~~~-~v 230 (311)
.+.+-+|.+... ++...|++.||.-...... ...|..|+-.|+.+..... +.++.+...+. ..
T Consensus 130 ~l~G~iD~i~~~~~g~~~IvDyKt~~~~~~~~--------~~~~~~Ql~~Y~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 201 (257)
T PF12705_consen 130 RLRGRIDRIDRDKDGRVRIVDYKTGSSPDDKS--------DLKYDLQLALYALALEQQFPGKPPDKIGLVYLFLRQPKSP 201 (257)
T ss_dssp EEEEEEEEEEECESSTEEEEEEESSS-SSSHH--------HHHCHHHHHHHHHHHHHHHHTSHEEEEEEEEEESSS--CC
T ss_pred EEEEEEeEEEEeCCCcEEEEEEcCCCCCCccc--------hhhhHHHHHHHHHHHHhccccCCceeEEEEEEEecCCCcc
Confidence 578999999888 6677899999964322110 1127789999988765444 44454554322 22
Q ss_pred --EEEECCHHHHHHHHHHHHHHH
Q 021549 231 --FRVIRRRDYWELIHGILQEFW 251 (311)
Q Consensus 231 --~rV~RD~~~~~~i~~~~~~Fw 251 (311)
..+..+++.++...+.+.+.+
T Consensus 202 ~~~~~~~~~~~~~~~~~~~~~~~ 224 (257)
T PF12705_consen 202 RRRKVDFSDEELEEFRERIRELL 224 (257)
T ss_dssp -TT--EE-HHHHHHHHHHHHHHH
T ss_pred ccccccCcHHHHHHHHHHHHHHH
Confidence 355556666665555555555
No 14
>TIGR01896 cas_AF1879 CRISPR-associated protein, Csa1 family. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model describes a particularly strongly conserved family found so only in the APERN subtype of CRISPR/Cas loci and represented by AF1879 from Archaeoglobus fulgidus. This family has four perfectly preserved Cys residues. This subfamily is found in a CRISPR/Cas locus we designate APERN, so the family is designated Csa1, for CRISPR/Cas Subtype Protein 1.
Probab=33.07 E-value=4.2e+02 Score=25.01 Aligned_cols=83 Identities=13% Similarity=-0.035 Sum_probs=52.4
Q ss_pred CCcccccCCCCcEEEEecCCCCCCCcccCCCCCCCcccHHHHHHHhHhhc------CCcEEEEEEcCC---CeEEEEEEC
Q 021549 165 PDGLLGCFPGGGILEVKCPYNKGKPEIALPWSTVPFYYMPQVQGQMEILD------REWVDLYCWTPN---GSTIFRVIR 235 (311)
Q Consensus 165 PDGli~~~~~~~iLEIKcP~~~~~~~~~~~~~~iP~~Y~~QVQ~qM~Vtg------~~~~~fvv~~~~---~~~v~rV~R 235 (311)
+|+++.. ...++|+|.-. . + .++. .|+-+|-.+.. ++.+.++-...+ ...+..|.-
T Consensus 165 ~Da~~~~--~~~pVEyK~G~-~--~--------~~hk--lQLaaYALllEe~yg~pVd~G~I~y~~~~~r~~~~~~~V~I 229 (271)
T TIGR01896 165 VDALVGI--LPVVVEMKVGS-Y--Q--------ERHE--LALAGYALAIEADLEVPVDYGLLVYVNVNDGVEIKARLVYI 229 (271)
T ss_pred cchhhcc--cceeEEEecCC-C--C--------chhH--HHHHHHHHHHHHHHCCCCcceeEEEEeeccccccceEEEEC
Confidence 6774333 23689999831 0 0 1233 48877755544 344444433322 345778999
Q ss_pred CHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 021549 236 RRDYWELIHGILQEFWWENVVPAKEALS 263 (311)
Q Consensus 236 D~~~~~~i~~~~~~Fw~~~V~p~~~p~~ 263 (311)
|++..++.++...+-- +.|..+..|++
T Consensus 230 ~d~LR~~v~e~~dei~-~iI~~g~~P~p 256 (271)
T TIGR01896 230 SDDLRTEFLERRDEAI-RIIEYGSDPGL 256 (271)
T ss_pred CHHHHHHHHHHHHHHH-HHHhCCCCCCC
Confidence 9999999999888876 66777776666
No 15
>PF08774 VRR_NUC: VRR-NUC domain; InterPro: IPR014883 This entry contains proteins with the VRR-NUC domain. It is associated with members of the PD-(D/E)XK nuclease superfamily, which include the type III restriction modification enzymes, for example StyLTI: (P40815 from SWISSPROT).; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=31.86 E-value=83 Score=24.30 Aligned_cols=50 Identities=20% Similarity=0.077 Sum_probs=32.5
Q ss_pred ccccCCCcccccCCC----CcEEEEecCCCCCCCcccCCCCCCCcccHHHHHHHhHhhcCCcEEEEEE
Q 021549 160 WLGASPDGLLGCFPG----GGILEVKCPYNKGKPEIALPWSTVPFYYMPQVQGQMEILDREWVDLYCW 223 (311)
Q Consensus 160 ~lgASPDGli~~~~~----~~iLEIKcP~~~~~~~~~~~~~~iP~~Y~~QVQ~qM~Vtg~~~~~fvv~ 223 (311)
.-.+-||-++..+.+ ...+|+|.|... . -. .|..+.-.+.+.-....||+
T Consensus 44 ~~~G~PDl~~~~~~~~~~~~~~iEvK~p~~~--l---------s~---~Q~~~~~~l~~~G~~v~V~~ 97 (100)
T PF08774_consen 44 VRSGFPDLILWRPRGKRDIFLFIEVKGPGDR--L---------SP---NQKEWIDKLREAGFRVAVCR 97 (100)
T ss_pred CCCCCCcEEEEecCCCccEEEEEEEcCCCCC--c---------CH---HHHHHHHHHHHCCCEEEEEE
Confidence 447788888876543 578999999522 1 11 37777777776655555554
No 16
>PHA02943 hypothetical protein; Provisional
Probab=30.96 E-value=2e+02 Score=25.06 Aligned_cols=51 Identities=20% Similarity=0.276 Sum_probs=39.1
Q ss_pred HHHHHhHhhcCCcEEEEEEcCCCeEEEEEECCHHHHHHHHHHHHHHHHHhcCCC
Q 021549 205 QVQGQMEILDREWVDLYCWTPNGSTIFRVIRRRDYWELIHGILQEFWWENVVPA 258 (311)
Q Consensus 205 QVQ~qM~Vtg~~~~~fvv~~~~~~~v~rV~RD~~~~~~i~~~~~~Fw~~~V~p~ 258 (311)
|+|+.+++...+....=|- .|..-++.-.|+++...+.+..+++| ..|-..
T Consensus 40 qa~~~LyvLErEG~VkrV~--~G~~tyw~l~~day~~~v~~~~Relw-rlv~s~ 90 (165)
T PHA02943 40 MARNALYQLAKEGMVLKVE--IGRAAIWCLDEDAYTNLVFEIKRELW-RLVCNS 90 (165)
T ss_pred HHHHHHHHHHHcCceEEEe--ecceEEEEEChHHHHHHHHHHHHHHH-HHHHhc
Confidence 9999999999998776643 45555666667888888999999999 455433
No 17
>PF03749 SfsA: Sugar fermentation stimulation protein; InterPro: IPR005224 The sugar fermentation stimulation protein is a probable regulatory factor involved in maltose metabolism. It contains a putative DNA-binding domain, and was isolated as a gene which enabled Escherichia coli W3110 (strain MK2001) to use maltose [].
Probab=29.73 E-value=2.8e+02 Score=25.09 Aligned_cols=90 Identities=14% Similarity=0.041 Sum_probs=49.0
Q ss_pred ccccccCCCcccccCCCCcEEEEecCCCCCCCcccCCCCCCCcccHHHHHHHhHhh--cCCcEEEEEEcCCCeEEEEE--
Q 021549 158 LDWLGASPDGLLGCFPGGGILEVKCPYNKGKPEIALPWSTVPFYYMPQVQGQMEIL--DREWVDLYCWTPNGSTIFRV-- 233 (311)
Q Consensus 158 ~p~lgASPDGli~~~~~~~iLEIKcP~~~~~~~~~~~~~~iP~~Y~~QVQ~qM~Vt--g~~~~~fvv~~~~~~~v~rV-- 233 (311)
..+-....|-++.++++...+|+|+-.-..+-...+| +.+..-=..+++--+.+. |.+.+.+++..-.+...+..
T Consensus 99 v~~g~sR~Dfll~~~~~~~~vEVKsvtL~~~~~a~FP-DApT~RG~kHL~eL~~l~~~G~ra~vlFvvqr~d~~~f~p~~ 177 (215)
T PF03749_consen 99 VKYGNSRFDFLLEDNGGKCYVEVKSVTLVEDGIAMFP-DAPTERGRKHLRELAELAEEGYRAAVLFVVQRPDAERFRPNR 177 (215)
T ss_pred eeeCCccEEEEEEcCCCCEEEEEeeeEeccCCcccCC-CccchHHHHHHHHHHHHHhccCcEEEEEEEECCCCCEEeECh
Confidence 4566777888888766678999997422222111111 222222223555544443 44544444433334444443
Q ss_pred ECCHHHHHHHHHHHH
Q 021549 234 IRRRDYWELIHGILQ 248 (311)
Q Consensus 234 ~RD~~~~~~i~~~~~ 248 (311)
+-|++|.+.+.++..
T Consensus 178 ~~Dp~fa~~l~~A~~ 192 (215)
T PF03749_consen 178 EIDPEFAEALREAAE 192 (215)
T ss_pred hcCHHHHHHHHHHHH
Confidence 568899888877654
No 18
>KOG4309 consensus Transcription mediator-related factor [Transcription]
Probab=29.49 E-value=84 Score=27.83 Aligned_cols=61 Identities=18% Similarity=0.359 Sum_probs=42.5
Q ss_pred CcEEEEEEcCC-------CeEEEEEECCH-----HHHHHHHHHHHHHHHHhcCCCCCCCCCCchhhhhccCCCCC
Q 021549 216 EWVDLYCWTPN-------GSTIFRVIRRR-----DYWELIHGILQEFWWENVVPAKEALSMGREELATSYDPTST 278 (311)
Q Consensus 216 ~~~~fvv~~~~-------~~~v~rV~RD~-----~~~~~i~~~~~~Fw~~~V~p~~~p~~~~~~~e~~~~~p~~~ 278 (311)
.+|||++..+. .-.++.|+.|+ .-|+.|++-++.|+..++ |. .|...|....-+.|.|..|
T Consensus 120 ~Y~Df~IkvGtvTmg~tvKGi~vEIEY~pcvI~~~Cw~M~~Eflqsflg~~~-p~-aP~~fg~t~h~~~y~p~DT 192 (217)
T KOG4309|consen 120 QYCDFLIKVGTVTMGPTVKGISVEIEYGPCVIASDCWSMLLEFLQSFLGSHT-PG-APAVFGNTRHDAVYGPADT 192 (217)
T ss_pred eecceEEEEcceEeccccceEEEEEeeCCEEEhHHHHHHHHHHHHHHhcccC-CC-chHhhcCccCccccCcHHH
Confidence 46899987763 22578899998 357778889999997666 44 5566666555667777543
No 19
>PRK14676 hypothetical protein; Provisional
Probab=28.76 E-value=1e+02 Score=25.20 Aligned_cols=56 Identities=18% Similarity=0.066 Sum_probs=36.6
Q ss_pred hhHHHHHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecC
Q 021549 119 KRCAMEWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCP 183 (311)
Q Consensus 119 ~n~am~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP 183 (311)
+..+...|..-|..|.+.++. .|..|...++-.. .+-.|-+..+++....+|+|+.
T Consensus 3 ~~~~~~~G~~gE~~A~~~L~~-~Gy~Il~rN~r~~--------~GEIDiIa~~~~~lVFVEVKt~ 58 (117)
T PRK14676 3 GEVSYYAGQTAEEAVARIYDR-SGRPVAARRWRGV--------SGEIDLIAREGAEVIFIEVKKS 58 (117)
T ss_pred chHHHHHHHHHHHHHHHHHHH-CCCEEeeeecCCC--------CCeEEEEEeeCCEEEEEEEeeC
Confidence 345667899999999887765 5777766554322 3455555544334567999983
No 20
>PF13588 HSDR_N_2: Type I restriction enzyme R protein N terminus (HSDR_N); PDB: 3H1T_A.
Probab=28.24 E-value=52 Score=25.91 Aligned_cols=61 Identities=15% Similarity=-0.028 Sum_probs=34.1
Q ss_pred CCCcccccCC----CCcEEEEecCCCCCCCcccCCCCCCCcccHHHHHHHhHhhcCCcEEEEEEcCC-CeEEEEEECCHH
Q 021549 164 SPDGLLGCFP----GGGILEVKCPYNKGKPEIALPWSTVPFYYMPQVQGQMEILDREWVDLYCWTPN-GSTIFRVIRRRD 238 (311)
Q Consensus 164 SPDGli~~~~----~~~iLEIKcP~~~~~~~~~~~~~~iP~~Y~~QVQ~qM~Vtg~~~~~fvv~~~~-~~~v~rV~RD~~ 238 (311)
-+|-++..+. ...++|+|.+...- -.....|+-.+|..++++ |++++.+ +..++.+..++.
T Consensus 38 r~Divv~~~~~~~~p~~iIE~K~~~~~~-----------~~~~~~Q~~~Y~~~~~~~---~~i~tNG~~~~~~~~~~~~~ 103 (112)
T PF13588_consen 38 RADIVVFRDDKDNKPLIIIECKAPSVSL-----------SEKAVEQLKSYARALGAP---YGILTNGKEFRFYDVDEGKK 103 (112)
T ss_dssp EEEEEEEEET--TEEEEEEEE--TTS-G-----------GG-SHHHHHHHHHHHT-S---EEEEE-SS-EEEEETTT--E
T ss_pred eeEEEEEeCCCCCCeEEEEEECCCCCCc-----------cHHHHHHHHHHHHhCCCC---EEEEECCCeEEEEEEeCCCc
Confidence 3565554332 35689999985321 113568999999998655 6666654 677777766654
No 21
>PRK12497 hypothetical protein; Reviewed
Probab=27.73 E-value=74 Score=25.95 Aligned_cols=52 Identities=17% Similarity=0.019 Sum_probs=35.5
Q ss_pred HHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecCC
Q 021549 124 EWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCPY 184 (311)
Q Consensus 124 ~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP~ 184 (311)
.-|..-|..|...++ ..|..|...++-. =.+..|-+..+++....+|+|+-.
T Consensus 7 ~~G~~gE~~A~~~L~-~~Gy~Il~rN~r~--------~~GEIDiIa~~~~~lvFVEVK~R~ 58 (119)
T PRK12497 7 QLGAAGEDLAARYLE-SKGLRILARNFRC--------RFGEIDLIARDGDTLVFVEVKTRR 58 (119)
T ss_pred HHHHHHHHHHHHHHH-HCCCEEEcceecC--------CCCcEeeeEEeCCEEEEEEEEecc
Confidence 469999999988876 4677766655422 245667666554445689999953
No 22
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=26.67 E-value=35 Score=23.97 Aligned_cols=11 Identities=55% Similarity=0.769 Sum_probs=8.4
Q ss_pred cEEEEecCCCC
Q 021549 176 GILEVKCPYNK 186 (311)
Q Consensus 176 ~iLEIKcP~~~ 186 (311)
.-||||||--.
T Consensus 21 ~~leIKCpRC~ 31 (51)
T PF10122_consen 21 IELEIKCPRCK 31 (51)
T ss_pred cEEEEECCCCC
Confidence 45899999654
No 23
>PHA01753 Holliday junction resolvase
Probab=25.77 E-value=1.3e+02 Score=24.91 Aligned_cols=98 Identities=14% Similarity=0.051 Sum_probs=54.0
Q ss_pred HHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecCCCCCCCcccCCCCCCCcccHHH
Q 021549 126 GVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCPYNKGKPEIALPWSTVPFYYMPQ 205 (311)
Q Consensus 126 G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP~~~~~~~~~~~~~~iP~~Y~~Q 205 (311)
|...|..|.+.+++ .|..|....+-... =.+-||-+..+++....+|+|+..+. .. .+...=..+
T Consensus 7 G~~~E~~a~~~L~~-~G~~il~rn~~~~~------~~GEiDIIA~~~~~lvfVEVKtR~~~-~~-------~V~~~Ki~k 71 (121)
T PHA01753 7 GKYYEYKTLEILES-NGFKALRIPVSGTG------KQALPDIIATKNNTIYPIEVKSTSKD-VV-------TVDKFQIEK 71 (121)
T ss_pred hHHHHHHHHHHHHH-CCCEEEEeccccCC------CCCCccEEEeeCCEEEEEEEEeCCCC-cE-------ecCHHHHHH
Confidence 99999999888876 56665544322100 13567877766555678999997431 11 222221223
Q ss_pred HHHHhHhhcC--CcEEEEEEcC--CCeEEEEEECCHH
Q 021549 206 VQGQMEILDR--EWVDLYCWTP--NGSTIFRVIRRRD 238 (311)
Q Consensus 206 VQ~qM~Vtg~--~~~~fvv~~~--~~~~v~rV~RD~~ 238 (311)
+..-....|. -...+.|-.. .+-.++.|.+|..
T Consensus 72 Li~fa~~fg~~~~~p~i~vkf~~~~~w~~~~~~~~~~ 108 (121)
T PHA01753 72 LFRFCEIFSFCECKPLVMVRYKKYKQVIVYELTQDVR 108 (121)
T ss_pred HHHHHHHhCccCCeEEEEEEecCccceEEEEeeccCC
Confidence 3322333331 3345555544 3667777776654
No 24
>PRK14683 hypothetical protein; Provisional
Probab=25.61 E-value=96 Score=25.65 Aligned_cols=54 Identities=17% Similarity=-0.032 Sum_probs=36.5
Q ss_pred HHHHHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecC
Q 021549 121 CAMEWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCP 183 (311)
Q Consensus 121 ~am~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP 183 (311)
.+-.-|..-|..|.+.++. .|..|.+.++-. =.+..|-+..+++....+|+|+-
T Consensus 11 ~~~~lG~~gE~~A~~~L~~-~Gy~Il~rN~r~--------~~GEIDIIa~~~~~lVFVEVKtR 64 (122)
T PRK14683 11 AYNTLGYLGEVLIILFLKC-KLYHIIKHRYRC--------PLGEIDIIAHKNKQLVFIEVKTS 64 (122)
T ss_pred HHHHHHHHHHHHHHHHHHH-CCCEEEeeecCC--------CCCcEEEEEEeCCEEEEEEEeec
Confidence 4667899999999777765 566666554432 24566666655444578999995
No 25
>PRK14673 hypothetical protein; Provisional
Probab=24.94 E-value=1.3e+02 Score=25.35 Aligned_cols=53 Identities=15% Similarity=0.108 Sum_probs=34.4
Q ss_pred HHHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCC-CCcEEEEecCC
Q 021549 123 MEWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFP-GGGILEVKCPY 184 (311)
Q Consensus 123 m~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~-~~~iLEIKcP~ 184 (311)
...|..-|..|...++. .|..|.+.++-.. .+..|-+..++. ....+|||+-.
T Consensus 26 ~~~G~~gE~~A~~~L~~-~Gy~IL~rN~r~~--------~GEIDLIa~~~~~~lVFVEVKtR~ 79 (137)
T PRK14673 26 RAVGAAFEDRALAFLQR-AGLALVARNYRCR--------GGEIDLVMRERDGTLVFVEVRARA 79 (137)
T ss_pred HHHHHHHHHHHHHHHHH-CCCEEeEeEecCC--------CCccCHHHccCCcEEEEEEEEeCC
Confidence 34699999999777754 5777766554332 445565554432 34679999953
No 26
>PRK14684 hypothetical protein; Provisional
Probab=23.93 E-value=95 Score=25.52 Aligned_cols=52 Identities=15% Similarity=0.073 Sum_probs=34.2
Q ss_pred HHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecCC
Q 021549 124 EWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCPY 184 (311)
Q Consensus 124 ~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP~ 184 (311)
.-|..-|..|...++. .|..|...++-. -.+-.|-+..++.....+|||+-.
T Consensus 7 ~~G~~gE~~A~~~L~~-~Gy~Il~rN~r~--------~~GEIDiIa~~~~~lvFVEVK~R~ 58 (120)
T PRK14684 7 KIGFNAEKTACRYLQK-QGLSFITKNFRY--------KQGEIDLIMSDQSMLVFIEVRYRR 58 (120)
T ss_pred HHhHHHHHHHHHHHHH-CCCEEEEEEecC--------CCCeEEEEEEeCCEEEEEEEeEcC
Confidence 5799999999777655 566666555432 245566555554345689999953
No 27
>PRK14689 hypothetical protein; Provisional
Probab=22.95 E-value=1.3e+02 Score=25.01 Aligned_cols=53 Identities=15% Similarity=0.080 Sum_probs=34.6
Q ss_pred HHHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecCC
Q 021549 123 MEWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCPY 184 (311)
Q Consensus 123 m~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP~ 184 (311)
.+-|..-|..|.+.+++ .|..|...++-.. .+-.|-+...++....+|+|+-.
T Consensus 8 ~~~G~~gE~~Aa~~L~~-~Gy~Il~rN~r~~--------~GEIDIIa~~~~~lVFVEVKtR~ 60 (124)
T PRK14689 8 QALGAWAEERVLRLLQR-RGWRLLDRNWSCR--------WGELDLVLEKQQRLLVVEVKGRR 60 (124)
T ss_pred HHHHHHHHHHHHHHHHH-CCCEEEEEecCCC--------CCcccEEeeeCCEEEEEEEEECC
Confidence 35799999999777765 5677666554322 34556555444345679999953
No 28
>PRK14681 hypothetical protein; Provisional
Probab=22.59 E-value=1.8e+02 Score=25.22 Aligned_cols=53 Identities=19% Similarity=-0.009 Sum_probs=34.1
Q ss_pred HHHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccC-CCCcEEEEecCC
Q 021549 123 MEWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCF-PGGGILEVKCPY 184 (311)
Q Consensus 123 m~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~-~~~~iLEIKcP~ 184 (311)
-..|..-|..|.+.+ +..|..|...++-.. .+-.|-+..++ +....+|||+-.
T Consensus 43 ~~~G~~gE~~Aa~~L-~~~Gy~IL~rN~R~~--------~GEIDIIa~d~~~~LVFVEVKtR~ 96 (158)
T PRK14681 43 KQIGALGEQYAAAWL-EEHGWTTLSRNWHCR--------YGELDIVALNPEYTIVFVEVKTRR 96 (158)
T ss_pred HHHHHHHHHHHHHHH-HHCCCEEEEEEEeCC--------CCcEEEEEEcCCceEEEEEEEecc
Confidence 346999999998866 446777766554332 34555555442 245789999953
No 29
>PRK14679 hypothetical protein; Provisional
Probab=22.56 E-value=1e+02 Score=25.74 Aligned_cols=57 Identities=19% Similarity=0.086 Sum_probs=38.2
Q ss_pred HHHHHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecCCCC
Q 021549 121 CAMEWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCPYNK 186 (311)
Q Consensus 121 ~am~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP~~~ 186 (311)
.+-..|..-|..|.+.++. .|.+|...++-.. .+..|-+..+++....+|||+-.+.
T Consensus 13 ~~~~~G~~gE~~A~~~L~~-~Gy~Il~rN~r~~--------~GEIDiIa~~~~~lVFVEVKtR~~~ 69 (128)
T PRK14679 13 ATHGRGLSAEGLALLALML-KGYRPLARRFAAA--------GGEIDLIVRRGRTIAFVEVKARATL 69 (128)
T ss_pred HHHHHHHHHHHHHHHHHHH-CCCEEEeeeccCC--------CCeEEEEEEeCCEEEEEEEEecCCC
Confidence 4557999999999887764 6777766554322 3456666555444567999996443
No 30
>cd00523 archeal_HJR Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain eukaryotes, however this CD includes only the archeal HJR's. The bacterial and archeal HJRs perform a similar function but differ in both sequence and structure. Structural similarity does however, exist between the archeal HJRs and type II restriction endonucleases, such as EcoRV, BglII, and Fok, and this similarity includes their active site configurations.
Probab=22.41 E-value=1.2e+02 Score=25.01 Aligned_cols=50 Identities=22% Similarity=0.115 Sum_probs=34.4
Q ss_pred HHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccc----cCCCcccccCCCCcEEEEecCC
Q 021549 124 EWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLG----ASPDGLLGCFPGGGILEVKCPY 184 (311)
Q Consensus 124 ~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lg----ASPDGli~~~~~~~iLEIKcP~ 184 (311)
+.|..-|..|.+.+.+ .|..|..+ +--| +.||-+...++....+|||+..
T Consensus 3 ~~G~~~E~~a~~~L~~-~G~~vlR~----------~~sG~~~~~eiDIIA~~~~~lvfVEVK~r~ 56 (123)
T cd00523 3 RKGSRAERELVKILEE-KGFAVVRA----------PGSGGGPRPLPDIVAGNGGTYLAIEVKSTK 56 (123)
T ss_pred chHHHHHHHHHHHHHh-CCCEEEEE----------cCCCCCCCCceeEEEecCCEEEEEEEEecC
Confidence 4688999999888877 66666532 1112 2677777665556789999974
No 31
>PRK14677 hypothetical protein; Provisional
Probab=21.78 E-value=95 Score=24.99 Aligned_cols=49 Identities=16% Similarity=-0.067 Sum_probs=31.4
Q ss_pred HHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecC
Q 021549 126 GVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCP 183 (311)
Q Consensus 126 G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP 183 (311)
|..-|..|...++. .|..|...++-. =.+..|-+..+++....+|+|+.
T Consensus 3 G~~~E~~A~~~L~~-~Gy~Il~rN~r~--------~~GEIDlIa~~~~~lvFVEVK~~ 51 (107)
T PRK14677 3 WKEAEELACKFLKK-KGYKILERNYRT--------KYGEIDIVARDGREIVFVEVKSG 51 (107)
T ss_pred hHHHHHHHHHHHHH-CCCEEEEEEecC--------CCceeeEEEEECCEEEEEEEecC
Confidence 67788888776644 577766555432 23566666655444578999983
No 32
>PRK14675 hypothetical protein; Provisional
Probab=21.67 E-value=84 Score=26.00 Aligned_cols=54 Identities=17% Similarity=0.058 Sum_probs=35.2
Q ss_pred HHHHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecCC
Q 021549 122 AMEWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCPY 184 (311)
Q Consensus 122 am~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP~ 184 (311)
.-.-|..-|..|...+++ .|..|...++-.. .+..|-+..++....++|||+-.
T Consensus 7 ~~~~G~~gE~~A~~~L~~-~G~~il~rn~r~~--------~GEIDlIa~d~~~lvFVEVK~R~ 60 (125)
T PRK14675 7 NKSLGEIGESIAVTYLKG-LRYKIVERNFRCR--------CGEIDIIARDGKTLVFVEVKTRK 60 (125)
T ss_pred HHHHhHHHHHHHHHHHHH-CCCEEEEEEEeCC--------CCeEEEEEEeCCEEEEEEEEecc
Confidence 334799999999777765 5777666554322 44555555544345789999953
No 33
>TIGR00252 conserved hypothetical protein TIGR00252. the scores for Mycobacterium tuberculosis and Treponema pallidum are low considering the alignment
Probab=21.35 E-value=1.2e+02 Score=24.94 Aligned_cols=52 Identities=13% Similarity=0.074 Sum_probs=34.0
Q ss_pred HHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecCC
Q 021549 124 EWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCPY 184 (311)
Q Consensus 124 ~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP~ 184 (311)
.-|..-|..|.+.++. .|..|...++-.. .+-.|-+..+++....+|||+-.
T Consensus 7 ~~G~~gE~~A~~~L~~-~Gy~Il~rN~r~~--------~GEIDiIa~~~~~lvFVEVK~R~ 58 (119)
T TIGR00252 7 QLGQAGESQARAWLEQ-KGLKFIAANWNSP--------WGEIDLIMHDTKTIAFVEVRTRS 58 (119)
T ss_pred HHhHHHHHHHHHHHHH-CCCEEeEEEecCC--------CCcEEEEEeeCCEEEEEEEEecC
Confidence 3699999999777655 5677666554322 35566555544345779999953
No 34
>PRK14685 hypothetical protein; Provisional
Probab=20.18 E-value=1.2e+02 Score=26.92 Aligned_cols=56 Identities=14% Similarity=-0.014 Sum_probs=36.9
Q ss_pred hHHHHHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecCC
Q 021549 120 RCAMEWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCPY 184 (311)
Q Consensus 120 n~am~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP~ 184 (311)
...-..|..-|..|.+.++. .|..|....+- .-.+-.|-+..+++....+|||+-.
T Consensus 39 ~~~~~~G~~gE~~Aa~yL~~-~Gy~IL~RN~R--------~~~GEIDIIA~dg~~LVFVEVKtR~ 94 (177)
T PRK14685 39 SPTQRCGQAYESAALRWLAR-QGLRPLARNLR--------CRAGEIDLAMRDGEVLVLVEVRARA 94 (177)
T ss_pred chHHHHhHHHHHHHHHHHHH-CCCEEeEeeec--------CCCCcEEEEEecCCEEEEEEEeECC
Confidence 34567899999999877765 56666554432 2245666665554345679999953
No 35
>PRK14686 hypothetical protein; Provisional
Probab=20.04 E-value=1.3e+02 Score=24.57 Aligned_cols=52 Identities=21% Similarity=0.076 Sum_probs=34.6
Q ss_pred HHHHHhHHHHHHHHHhHhCCeeeeccceeeccccccccccCCCcccccCCCCcEEEEecCC
Q 021549 124 EWGVLNEAAAIDRYKSITGHDVSSLGFAVHAEEQLDWLGASPDGLLGCFPGGGILEVKCPY 184 (311)
Q Consensus 124 ~~G~~~E~~a~~~ye~~~g~~V~~~Gl~i~~~~~~p~lgASPDGli~~~~~~~iLEIKcP~ 184 (311)
..|..-|..|...++. .|..|.+.++-.. .+..|-+..+++....+|||+-.
T Consensus 6 ~~G~~gE~~A~~~L~~-~Gy~il~rN~r~~--------~GEIDlIa~~~~~lvFVEVKtR~ 57 (119)
T PRK14686 6 ELGKEGEDLAVEFLIK-KGYTILERNYRFQ--------KAEIDIIAQKGNILVIVEVKTRS 57 (119)
T ss_pred HHHHHHHHHHHHHHHH-CCCEEEEEEecCC--------CCcEEEEECcCCEEEEEEEEecC
Confidence 3699999999777655 5777766654332 34555555554445679999954
Done!