Query 029699
Match_columns 189
No_of_seqs 222 out of 1062
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 17:06:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029699.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029699hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13395 HNH_4: HNH endonuclea 99.2 2.6E-12 5.7E-17 87.5 1.7 36 74-109 18-53 (54)
2 PF01844 HNH: HNH endonuclease 99.1 1.6E-12 3.5E-17 84.0 -2.7 40 68-107 1-47 (47)
3 cd00085 HNHc HNH nucleases; HN 99.1 1.1E-10 2.3E-15 76.1 4.6 40 66-105 12-57 (57)
4 TIGR01865 cas_Csn1 CRISPR-asso 98.9 1.8E-09 3.9E-14 106.8 5.7 49 62-110 578-638 (805)
5 COG1403 McrA Restriction endon 98.9 1.7E-09 3.6E-14 82.2 4.1 51 60-110 64-118 (146)
6 smart00507 HNHc HNH nucleases. 98.8 6.2E-10 1.3E-14 71.2 -0.5 37 66-102 11-52 (52)
7 TIGR02646 conserved hypothetic 98.5 7.1E-08 1.5E-12 77.0 3.5 72 66-141 25-113 (144)
8 PRK11295 hypothetical protein; 98.5 3.3E-08 7.2E-13 77.5 0.9 47 63-109 22-77 (113)
9 PF14279 HNH_5: HNH endonuclea 96.7 0.00082 1.8E-08 48.6 1.5 39 68-109 1-45 (71)
10 PHA02565 49 recombination endo 91.8 0.11 2.3E-06 43.2 2.1 52 31-107 9-68 (157)
11 COG3513 Predicted CRISPR-assoc 90.1 0.083 1.8E-06 53.7 -0.2 49 62-110 568-628 (1088)
12 TIGR02986 restrict_Alw26I type 88.2 0.2 4.3E-06 47.1 0.9 82 19-109 205-291 (424)
13 PF13391 HNH_2: HNH endonuclea 86.8 0.12 2.6E-06 34.9 -1.1 31 73-103 14-57 (66)
14 TIGR03031 cas_csx12 CRISPR-ass 84.2 0.51 1.1E-05 46.8 1.4 25 63-87 758-787 (802)
15 PF05766 NinG: Bacteriophage L 83.6 0.84 1.8E-05 38.9 2.3 68 65-132 87-173 (189)
16 COG3183 Predicted restriction 83.5 0.77 1.7E-05 41.1 2.1 43 66-108 196-255 (272)
17 COG3440 Predicted restriction 74.8 1.5 3.2E-05 39.9 1.1 38 65-102 192-239 (301)
18 PF09665 RE_Alw26IDE: Type II 72.7 1.4 3E-05 42.5 0.5 36 73-109 256-291 (511)
19 PF06147 DUF968: Protein of un 65.3 4 8.7E-05 34.6 1.7 41 66-106 128-173 (200)
20 smart00782 PhnA_Zn_Ribbon PhnA 64.7 3.4 7.4E-05 27.7 1.0 38 63-103 5-45 (47)
21 PF07510 DUF1524: Protein of u 37.2 6.7 0.00014 29.5 -1.2 34 76-109 54-103 (142)
22 PF05315 ICEA: ICEA Protein; 28.7 99 0.0021 27.2 4.4 18 89-106 135-152 (230)
23 KOG3822 Succinyl-CoA:alpha-ket 25.0 45 0.00099 31.7 1.8 54 24-82 184-248 (516)
24 PF15446 zf-PHD-like: PHD/FYVE 23.0 1.8E+02 0.0038 24.8 4.8 48 30-84 92-144 (175)
No 1
>PF13395 HNH_4: HNH endonuclease
Probab=99.24 E-value=2.6e-12 Score=87.47 Aligned_cols=36 Identities=36% Similarity=0.557 Sum_probs=35.0
Q ss_pred CccceeEeccCCCCChHhHHHHHhHHHHhhccCCch
Q 029699 74 FEYDHIVPFSKGGESTADNCQILQTRVNRFKSDKEQ 109 (189)
Q Consensus 74 ~evDHIiP~S~GG~~~~~NLq~lC~~CN~~K~n~~~ 109 (189)
+++|||+|+|.+|.+++.||+++|..||+.|++++|
T Consensus 18 ~~iDHiiP~s~~~~~s~~Nlvl~~~~~N~~K~~k~P 53 (54)
T PF13395_consen 18 YEIDHIIPRSRGGDDSFWNLVLCCKECNRSKGNKTP 53 (54)
T ss_pred ceeEEEecccccCCCCcchhheECHHHhhcccccCC
Confidence 799999999999999999999999999999999987
No 2
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=99.14 E-value=1.6e-12 Score=84.03 Aligned_cols=40 Identities=38% Similarity=0.643 Sum_probs=30.2
Q ss_pred CCCC-------CCCccceeEeccCCCCChHhHHHHHhHHHHhhccCC
Q 029699 68 CHGC-------LCFEYDHIVPFSKGGESTADNCQILQTRVNRFKSDK 107 (189)
Q Consensus 68 C~~C-------~~~evDHIiP~S~GG~~~~~NLq~lC~~CN~~K~n~ 107 (189)
|++| ..+++|||+|++.||.++++||++||..||+.|+++
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~gg~~~~~Nl~~lC~~Ch~~k~~k 47 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSKGGKNDLENLILLCPSCHRKKHDK 47 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTTT---STTTEEEEEHHHHHHHH--
T ss_pred CCCCCCcCccCcceEeECcCchhcCCCCCHHHHHHHhHHHHHHhcCC
Confidence 6778 247999999999999999999999999999999864
No 3
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=99.11 E-value=1.1e-10 Score=76.12 Aligned_cols=40 Identities=38% Similarity=0.608 Sum_probs=36.4
Q ss_pred CCCCCCC------CCccceeEeccCCCCChHhHHHHHhHHHHhhcc
Q 029699 66 CNCHGCL------CFEYDHIVPFSKGGESTADNCQILQTRVNRFKS 105 (189)
Q Consensus 66 ~~C~~C~------~~evDHIiP~S~GG~~~~~NLq~lC~~CN~~K~ 105 (189)
+.|++|. .+++|||+|++.||.++++||+++|..||..|+
T Consensus 12 ~~C~~c~~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~~~c~~ch~~~~ 57 (57)
T cd00085 12 GLCPYCGKPGGTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKKH 57 (57)
T ss_pred CcCccCCCcCCCCCceEEeecchhhCCCCchHHhHHHHHHHhhccC
Confidence 4699993 579999999999999999999999999999874
No 4
>TIGR01865 cas_Csn1 CRISPR-associated protein, Csn1 family. CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only.
Probab=98.89 E-value=1.8e-09 Score=106.81 Aligned_cols=49 Identities=22% Similarity=0.299 Sum_probs=44.4
Q ss_pred eecCCCCCCCC------------CCccceeEeccCCCCChHhHHHHHhHHHHhhccCCchh
Q 029699 62 CKRFCNCHGCL------------CFEYDHIVPFSKGGESTADNCQILQTRVNRFKSDKEQV 110 (189)
Q Consensus 62 ~r~~~~C~~C~------------~~evDHIiP~S~GG~~~~~NLq~lC~~CN~~K~n~~~~ 110 (189)
.++++.|+||+ .+++|||+|+|+||.|+++|++++|..||+.|++++|.
T Consensus 578 ~~q~~~C~Y~g~~i~~~~l~~~~~~~iDHIiP~s~~~dds~~N~vl~~~~~N~~K~~~tp~ 638 (805)
T TIGR01865 578 YQQNGKCMYTGKEIDIDDLFDLSYYEIDHILPQSRSFDDSISNKVLVLASENQEKGDQTPY 638 (805)
T ss_pred HHcCCcCCCCCCcCccccccCCCCCceeeecccccCCCCcHHHHHHHhHHHHhhccCCCHH
Confidence 45677899992 26899999999999999999999999999999999995
No 5
>COG1403 McrA Restriction endonuclease [Defense mechanisms]
Probab=98.88 E-value=1.7e-09 Score=82.21 Aligned_cols=51 Identities=31% Similarity=0.504 Sum_probs=44.6
Q ss_pred eEeecCCCCCCC--C--CCccceeEeccCCCCChHhHHHHHhHHHHhhccCCchh
Q 029699 60 IVCKRFCNCHGC--L--CFEYDHIVPFSKGGESTADNCQILQTRVNRFKSDKEQV 110 (189)
Q Consensus 60 vv~r~~~~C~~C--~--~~evDHIiP~S~GG~~~~~NLq~lC~~CN~~K~n~~~~ 110 (189)
++.++.+.|.|| . ..++|||+|.+.||.+.++||++||..||..|++....
T Consensus 64 ~~~~d~~~c~~c~~~~~~~~~dHiip~~~g~~~~~~Nl~~lc~~c~~~k~~~~~~ 118 (146)
T COG1403 64 VLLRDNGLCQYCGSVGTDLEVDHIVPLSRGGASAWENLETLCERCHNKKGSRLPG 118 (146)
T ss_pred HHccccccccccCCcCCCCceeeEeecccCCcchHHHHHHHHHhhcccccccchh
Confidence 344455789999 3 58999999999999999999999999999999998874
No 6
>smart00507 HNHc HNH nucleases.
Probab=98.80 E-value=6.2e-10 Score=71.20 Aligned_cols=37 Identities=35% Similarity=0.605 Sum_probs=33.7
Q ss_pred CCCCCCC-----CCccceeEeccCCCCChHhHHHHHhHHHHh
Q 029699 66 CNCHGCL-----CFEYDHIVPFSKGGESTADNCQILQTRVNR 102 (189)
Q Consensus 66 ~~C~~C~-----~~evDHIiP~S~GG~~~~~NLq~lC~~CN~ 102 (189)
+.|++|. .+++|||+|++.||.++++||+++|..||.
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p~~~~~~~~~~Nl~~~c~~ch~ 52 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIPLSDGGNDDLDNLVLLCPKCHI 52 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCChhcCCCCChHhCeecChhhCc
Confidence 5799992 379999999999999999999999999984
No 7
>TIGR02646 conserved hypothetical protein TIGR02646. Members of this uncharacterized protein family are found exclusively in bacteria. Neighboring genes in various genomes are also uncharacterized or may annotated as similar to restriction system proteins.
Probab=98.52 E-value=7.1e-08 Score=77.03 Aligned_cols=72 Identities=14% Similarity=0.041 Sum_probs=52.9
Q ss_pred CCCCCCC------CCccceeEeccCCCCC--hHhHHHHHhHH---------HHhhccCCchhhhccccccCCCCCCChhh
Q 029699 66 CNCHGCL------CFEYDHIVPFSKGGES--TADNCQILQTR---------VNRFKSDKEQVDATKLKGFSCDVKFTDKE 128 (189)
Q Consensus 66 ~~C~~C~------~~evDHIiP~S~GG~~--~~~NLq~lC~~---------CN~~K~n~~~~~~~~~~~~s~~~~~t~~~ 128 (189)
+.|.||. .++||||+|.+..+.. +++||.++|.. ||..|++... ....-..++|..+.+.++
T Consensus 25 ~~C~YC~~~~~~~~~~ieH~~Pk~~~~~~~~~~~NL~~sC~~~n~~~~~~~Cn~~K~~~~~-~~~~~~~i~P~~~~~~~~ 103 (144)
T TIGR02646 25 GLCAYCEREIELLGSHIEHFRPKGAYPPLTLDWSNLFGSCHRESKQGNPLHCGRFKDNSCG-SNNFDELIDPLADDCEQL 103 (144)
T ss_pred CCcCccCCCcCCCCcceeeecccCCChhhhcChhhchhhccccCCCCCccccccccccccc-ccccccccCCCCCChHHh
Confidence 4699993 4899999999988885 56999999999 9999976544 222335677877766666
Q ss_pred hhhhheeeecccc
Q 029699 129 LDIIEMAVYGDVI 141 (189)
Q Consensus 129 ~~~ie~ai~g~v~ 141 (189)
|... ..|.|.
T Consensus 104 f~~~---~~G~i~ 113 (144)
T TIGR02646 104 FTYL---LTGKIE 113 (144)
T ss_pred eeec---CCCcEE
Confidence 6543 445554
No 8
>PRK11295 hypothetical protein; Provisional
Probab=98.49 E-value=3.3e-08 Score=77.46 Aligned_cols=47 Identities=15% Similarity=0.133 Sum_probs=39.2
Q ss_pred ecCCCCCCCCC---------CccceeEeccCCCCChHhHHHHHhHHHHhhccCCch
Q 029699 63 KRFCNCHGCLC---------FEYDHIVPFSKGGESTADNCQILQTRVNRFKSDKEQ 109 (189)
Q Consensus 63 r~~~~C~~C~~---------~evDHIiP~S~GG~~~~~NLq~lC~~CN~~K~n~~~ 109 (189)
++.+.|+.|.. .+||||+|...|+.++.+|||+||..||..|..+..
T Consensus 22 r~p~lC~~Cgr~~~~a~~~a~vVDHIip~~~gd~~D~sNLQ~LC~~CHn~kh~R~~ 77 (113)
T PRK11295 22 LYPWVCGRCSREFVYSNLRELTVHHIDHDHDNNPEDGSNWELLCLYCHDHEHSKYT 77 (113)
T ss_pred HCcchhhhhcChhccCCCCCceeeccCCCCCCCCCchhHHHHHhHHHHhHHHhhHH
Confidence 33457999933 499999999999999999999999999999875543
No 9
>PF14279 HNH_5: HNH endonuclease
Probab=96.69 E-value=0.00082 Score=48.56 Aligned_cols=39 Identities=31% Similarity=0.491 Sum_probs=31.7
Q ss_pred CCCC------CCCccceeEeccCCCCChHhHHHHHhHHHHhhccCCch
Q 029699 68 CHGC------LCFEYDHIVPFSKGGESTADNCQILQTRVNRFKSDKEQ 109 (189)
Q Consensus 68 C~~C------~~~evDHIiP~S~GG~~~~~NLq~lC~~CN~~K~n~~~ 109 (189)
|.|| ..+...||||-|-||.....| .|..||..=+....
T Consensus 1 Ci~C~~~~~~~~~s~EHIIP~sLGG~~~~~~---vC~~CN~~~g~~vD 45 (71)
T PF14279_consen 1 CIYCNKEKSESNFSEEHIIPESLGGKLKINN---VCDKCNNKFGSKVD 45 (71)
T ss_pred CccCCCCCCccCCCccccCchhcCCcccccc---hhHHHhHHHhHHHH
Confidence 7888 234589999999999888777 99999998876543
No 10
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=91.84 E-value=0.11 Score=43.17 Aligned_cols=52 Identities=15% Similarity=0.175 Sum_probs=36.5
Q ss_pred HHHHHHHHHHcCCCCCCCccchhccccCCeEeecCCCCCCCC--------CCccceeEeccCCCCChHhHHHHHhHHHHh
Q 029699 31 GKAKSMCWAKAETVPGRHPERWRKDAAGNIVCKRFCNCHGCL--------CFEYDHIVPFSKGGESTADNCQILQTRVNR 102 (189)
Q Consensus 31 ~~~R~~~w~ka~~v~Gr~p~r~R~da~gnvv~r~~~~C~~C~--------~~evDHIiP~S~GG~~~~~NLq~lC~~CN~ 102 (189)
++.++++++.++ | .|+.|. ..++||.-|.+.+.+ =.=-.+||..||.
T Consensus 9 ~~~k~~l~e~Q~---G--------------------~CaiC~~~l~~~~~~~~vDHDH~l~g~~T--G~VRGLLC~~CN~ 63 (157)
T PHA02565 9 KEEKQKLFEAQN---G--------------------ICPLCKRELDGDVSKNHLDHDHELNGPNA--GRVRGLLCNLCNA 63 (157)
T ss_pred HHHHHHHHHHhC---C--------------------cCCCCCCccCCCccccccCCCCCCCCccc--ccccccCchhhhh
Confidence 355667777777 4 599992 258999998873222 1125789999999
Q ss_pred hccCC
Q 029699 103 FKSDK 107 (189)
Q Consensus 103 ~K~n~ 107 (189)
..|.-
T Consensus 64 ~lG~~ 68 (157)
T PHA02565 64 LEGQM 68 (157)
T ss_pred hhhhh
Confidence 88764
No 11
>COG3513 Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]
Probab=90.12 E-value=0.083 Score=53.71 Aligned_cols=49 Identities=24% Similarity=0.306 Sum_probs=43.3
Q ss_pred eecCCCCCCC------------CCCccceeEeccCCCCChHhHHHHHhHHHHhhccCCchh
Q 029699 62 CKRFCNCHGC------------LCFEYDHIVPFSKGGESTADNCQILQTRVNRFKSDKEQV 110 (189)
Q Consensus 62 ~r~~~~C~~C------------~~~evDHIiP~S~GG~~~~~NLq~lC~~CN~~K~n~~~~ 110 (189)
.-+++.|.|- ...+||||+|.|+-=.|..+|.++.=..=|+.|+|.+|.
T Consensus 568 ~~Q~gkcmYsgqei~I~rL~dk~~~eIDHi~P~Sr~~DDS~~NkVLv~s~~Nq~KgnqtP~ 628 (1088)
T COG3513 568 YLQNGKCMYSGQEIDIHRLSDKGYYEIDHIVPQSRTWDDSIDNKVLVLSSENQEKGNQTPY 628 (1088)
T ss_pred HHhcCcccccCcccchhhcccccceeeceeccccccccccccceeEEeccccccccCCCCH
Confidence 3467789998 237999999999999999999999999999999999993
No 12
>TIGR02986 restrict_Alw26I type II restriction endonuclease, Alw26I/Eco31I/Esp3I family. Members of this family are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. Characterized specificities of three members are GGTCTC, CGTCTC, and the shared subsequence GTCTC.
Probab=88.21 E-value=0.2 Score=47.10 Aligned_cols=82 Identities=20% Similarity=0.246 Sum_probs=51.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHcCCCCCCCccchhc-cccCCeEeecCCCCCCC----CCCccceeEeccCCCCChHhHH
Q 029699 19 NNSNEERPRYFDGKAKSMCWAKAETVPGRHPERWRK-DAAGNIVCKRFCNCHGC----LCFEYDHIVPFSKGGESTADNC 93 (189)
Q Consensus 19 ~~~~~~~~R~F~~~~R~~~w~ka~~v~Gr~p~r~R~-da~gnvv~r~~~~C~~C----~~~evDHIiP~S~GG~~~~~NL 93 (189)
.|+-..+-+.++..-|..-|--++. |+. |+.=+......+.|+.| .....|||=|.|.|=.. .-+.
T Consensus 205 kGR~~eNlkSYt~DRRafEyWsDGn--------w~aAd~Lmg~~~~~~~~~~~~~~~p~~~saDHIGPISlGF~h-~P~F 275 (424)
T TIGR02986 205 PGRSDENLKSYTKDRRAFEYWSDGN--------WAAADQLMGKAGFNRCSIPECCKHPEKISADHIGPISLGFVH-DPRF 275 (424)
T ss_pred CCcchhhHhhhhhhHHHHHHHhcCc--------HHHHHHHhCcccCCcccCcccccCCCCCCccccCCccccccc-Cccc
Confidence 3444566667776666655554431 111 11111112233455666 35789999999997654 4456
Q ss_pred HHHhHHHHhhccCCch
Q 029699 94 QILQTRVNRFKSDKEQ 109 (189)
Q Consensus 94 q~lC~~CN~~K~n~~~ 109 (189)
|++|..||..|.++..
T Consensus 276 qplc~~cNSaKnnR~~ 291 (424)
T TIGR02986 276 QPLCSSCNSAKNDRLT 291 (424)
T ss_pred ccccccccccccccee
Confidence 9999999999999876
No 13
>PF13391 HNH_2: HNH endonuclease
Probab=86.79 E-value=0.12 Score=34.93 Aligned_cols=31 Identities=32% Similarity=0.533 Sum_probs=24.9
Q ss_pred CCccceeEeccCC--CCC-----------hHhHHHHHhHHHHhh
Q 029699 73 CFEYDHIVPFSKG--GES-----------TADNCQILQTRVNRF 103 (189)
Q Consensus 73 ~~evDHIiP~S~G--G~~-----------~~~NLq~lC~~CN~~ 103 (189)
.+|+=||+|++.+ +.. +.+|+.+||..+|..
T Consensus 14 ~~eaaHI~P~s~~~~~~~~~~~~~~~~~~~~~Ngl~L~~~lH~~ 57 (66)
T PF13391_consen 14 LLEAAHIVPFSLGSWWMNNWFGEYANDWISPSNGLLLRPDLHKL 57 (66)
T ss_pred cEEEEEcccCccCCCchhhhhhhhhccCCCccEEEEcCHhHHHH
Confidence 4678899999987 445 678999999988854
No 14
>TIGR03031 cas_csx12 CRISPR-associated protein, Csx12 family. Members of this family of CRISPR-associated (cas) protein are found, so far, in CRISPR/cas loci in Wolinella succinogenes DSM 1740, Legionella pneumophila str. Paris, and Francisella tularensis, where the last probably is an example of a degenerate CRISPR locus, having neither repeats nor a functional Cas1. The characteristic repeat length is 37 base pairs and period is about 72. One region of this large protein shows sequence similarity to PFAM model pfam01844, HNH endonuclease.
Probab=84.18 E-value=0.51 Score=46.81 Aligned_cols=25 Identities=28% Similarity=0.123 Sum_probs=20.1
Q ss_pred ecCCCCCCCC-----CCccceeEeccCCCC
Q 029699 63 KRFCNCHGCL-----CFEYDHIVPFSKGGE 87 (189)
Q Consensus 63 r~~~~C~~C~-----~~evDHIiP~S~GG~ 87 (189)
..-+.|+||+ .-|+|||+|+|+-|+
T Consensus 758 fs~gIcpY~Ga~iG~~gEiDHI~PRSht~k 787 (802)
T TIGR03031 758 FSMGICPYKGASIGGQGEIDHIYPRSHSKK 787 (802)
T ss_pred HhccCCCCCCCCCCCccccccccccccccc
Confidence 3456899993 469999999998765
No 15
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=83.61 E-value=0.84 Score=38.87 Aligned_cols=68 Identities=24% Similarity=0.165 Sum_probs=45.9
Q ss_pred CCCCCCC-----CCCccceeEeccCCCC--ChHhHHHHHhHHHHhhccCCchhhhccc------------cccCCCCCCC
Q 029699 65 FCNCHGC-----LCFEYDHIVPFSKGGE--STADNCQILQTRVNRFKSDKEQVDATKL------------KGFSCDVKFT 125 (189)
Q Consensus 65 ~~~C~~C-----~~~evDHIiP~S~GG~--~~~~NLq~lC~~CN~~K~n~~~~~~~~~------------~~~s~~~~~t 125 (189)
+..|.+| ..|+.-|...+..--. =+.+|+-..|..||+.++.....+...| ..-+...+|+
T Consensus 87 ~~~CiSCG~~~~~~~dagHy~s~g~~~~lRF~~~N~~~qC~~CN~~~sgn~~~Yr~~Li~kiG~~~ve~Le~~~~~~k~~ 166 (189)
T PF05766_consen 87 GKPCISCGRKHGGQWDAGHYRSRGAAPELRFNEDNIHAQCKHCNRHLSGNIVEYRIGLIEKIGQERVEWLEGPHEPRKWT 166 (189)
T ss_pred CCCcccCCCcCCCCcccccccccccCcccccChhhHhHcCCccccccccCHHHHHHHHHHHHhHHHHHHHhcCCCCCCCC
Confidence 4689999 3477778876532222 2788999999999999998766333322 2334556677
Q ss_pred hhhhhhh
Q 029699 126 DKELDII 132 (189)
Q Consensus 126 ~~~~~~i 132 (189)
.++++.|
T Consensus 167 ~~el~~i 173 (189)
T PF05766_consen 167 IEELKAI 173 (189)
T ss_pred HHHHHHH
Confidence 7776544
No 16
>COG3183 Predicted restriction endonuclease [Defense mechanisms]
Probab=83.45 E-value=0.77 Score=41.12 Aligned_cols=43 Identities=14% Similarity=0.271 Sum_probs=32.1
Q ss_pred CCCCCC-------------CCCccceeEeccCCC---C-ChHhHHHHHhHHHHhhccCCc
Q 029699 66 CNCHGC-------------LCFEYDHIVPFSKGG---E-STADNCQILQTRVNRFKSDKE 108 (189)
Q Consensus 66 ~~C~~C-------------~~~evDHIiP~S~GG---~-~~~~NLq~lC~~CN~~K~n~~ 108 (189)
..|..| ..-||+|++|.+.=+ . +...-|.++|.-||..-+.+.
T Consensus 196 ~vC~vC~fdF~k~YGe~gKgyIeVHH~~piae~e~~~~vnp~tDL~plCpNCH~mvHrr~ 255 (272)
T COG3183 196 TVCDVCEFDFQKKYGEIGKGYIEVHHKIPIAEFEGEYHVNPLTDLAPLCPNCHKMVHRRR 255 (272)
T ss_pred ceeeecCccHHHHhhhhccCeEEEeeccchhhhcCccccCchhhhhhcCccHHHHHhccC
Confidence 468999 124999999998322 2 678899999999997655433
No 17
>COG3440 Predicted restriction endonuclease [Defense mechanisms]
Probab=74.76 E-value=1.5 Score=39.93 Aligned_cols=38 Identities=21% Similarity=0.150 Sum_probs=31.9
Q ss_pred CCCCCCCC----------CCccceeEeccCCCCChHhHHHHHhHHHHh
Q 029699 65 FCNCHGCL----------CFEYDHIVPFSKGGESTADNCQILQTRVNR 102 (189)
Q Consensus 65 ~~~C~~C~----------~~evDHIiP~S~GG~~~~~NLq~lC~~CN~ 102 (189)
+++|+.|. ..+.-||.|.+++|.+.+.|..+||.-.|.
T Consensus 192 ~~RCalCG~e~~~~~~q~ii~~ahikp~~q~y~~~i~N~LaLC~nHh~ 239 (301)
T COG3440 192 DYRCALCGLEVLDFLEQNIIKAAHIKPFQQFYPDRIINGLALCKNHHW 239 (301)
T ss_pred cchhhhhcchhhhhhHHHHhhhhhcCcccccCcccccccchhchhhHH
Confidence 36899993 236779999999999999999999976664
No 18
>PF09665 RE_Alw26IDE: Type II restriction endonuclease (RE_Alw26IDE); InterPro: IPR014328 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
Probab=72.74 E-value=1.4 Score=42.49 Aligned_cols=36 Identities=31% Similarity=0.347 Sum_probs=30.3
Q ss_pred CCccceeEeccCCCCChHhHHHHHhHHHHhhccCCch
Q 029699 73 CFEYDHIVPFSKGGESTADNCQILQTRVNRFKSDKEQ 109 (189)
Q Consensus 73 ~~evDHIiP~S~GG~~~~~NLq~lC~~CN~~K~n~~~ 109 (189)
.+..|||=|.|.|=.. .-+.|++|..||..|.++..
T Consensus 256 ~~SaDHIGPISlGF~h-~P~Fqplc~~cNSaKnnR~~ 291 (511)
T PF09665_consen 256 CLSADHIGPISLGFVH-RPRFQPLCKSCNSAKNNRMY 291 (511)
T ss_pred ccCccccCCccccccc-Ccccccccccccccccccee
Confidence 4689999999997654 44569999999999999876
No 19
>PF06147 DUF968: Protein of unknown function (DUF968); InterPro: IPR010373 This is a family of uncharacterised prophage proteins that are also found in bacteria and humans.
Probab=65.26 E-value=4 Score=34.62 Aligned_cols=41 Identities=17% Similarity=0.105 Sum_probs=32.0
Q ss_pred CCCCCCC--CCccceeEeccCCCC---ChHhHHHHHhHHHHhhccC
Q 029699 66 CNCHGCL--CFEYDHIVPFSKGGE---STADNCQILQTRVNRFKSD 106 (189)
Q Consensus 66 ~~C~~C~--~~evDHIiP~S~GG~---~~~~NLq~lC~~CN~~K~n 106 (189)
-.|..|+ .-+++||+..-.||. ..-..+.+||+.||....+
T Consensus 128 ~~C~iCGk~~~d~hH~iG~g~~~~~~~~~d~~~ipLCr~hH~e~H~ 173 (200)
T PF06147_consen 128 RPCVICGKPPADIHHIIGMGRGRMGIKHHDLFVIPLCREHHRELHR 173 (200)
T ss_pred CccccCCCCccccceeeccccCccccccCCCeehhccHHHHHHHhC
Confidence 4788995 579999987665554 3445899999999998887
No 20
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=64.70 E-value=3.4 Score=27.72 Aligned_cols=38 Identities=24% Similarity=0.279 Sum_probs=24.7
Q ss_pred ecCCCCCCCC---CCccceeEeccCCCCChHhHHHHHhHHHHhh
Q 029699 63 KRFCNCHGCL---CFEYDHIVPFSKGGESTADNCQILQTRVNRF 103 (189)
Q Consensus 63 r~~~~C~~C~---~~evDHIiP~S~GG~~~~~NLq~lC~~CN~~ 103 (189)
|.+..|+.|. .+.+-+|-| +. ....+|.+++|..|...
T Consensus 5 Rs~~kCELC~a~~~L~vy~Vpp-~~--~~~~d~~iliC~tC~~Q 45 (47)
T smart00782 5 RCESKCELCGSDSPLVVYAVPP-SS--DVTADNSVMLCDTCHSQ 45 (47)
T ss_pred HcCCcccCcCCCCCceEEecCC-CC--CCCccceeeechHHHHh
Confidence 4456799994 344544434 22 25567889999999853
No 21
>PF07510 DUF1524: Protein of unknown function (DUF1524); InterPro: IPR011089 The family contains RloF from Campylobacter jejuni, its function and those of the other members are unknown.
Probab=37.20 E-value=6.7 Score=29.54 Aligned_cols=34 Identities=26% Similarity=0.342 Sum_probs=27.3
Q ss_pred cceeEeccCCCC----------------ChHhHHHHHhHHHHhhccCCch
Q 029699 76 YDHIVPFSKGGE----------------STADNCQILQTRVNRFKSDKEQ 109 (189)
Q Consensus 76 vDHIiP~S~GG~----------------~~~~NLq~lC~~CN~~K~n~~~ 109 (189)
+|||+|.+.... +.+.||++|=..=|..+++...
T Consensus 54 iEHI~Pq~~~~~~~~~~~~~~~~~~~~~~~igNL~LL~~~~N~~~~n~~f 103 (142)
T PF07510_consen 54 IEHIFPQNPKKESKSEKDWDEEEREIYLNSIGNLTLLSKSLNSSISNKPF 103 (142)
T ss_pred eEeeccCCCCcccccccccCHHHHHHHhcccccEEEeccchhhccchhhh
Confidence 999999885553 4667999999888988887665
No 22
>PF05315 ICEA: ICEA Protein; InterPro: IPR007979 This family consists of several ICEA proteins from Helicobacter pylori, infection of which causes gastritis and peptic ulcer disease, and the bacteria is classified as a definite carcinogen of gastric cancer. ICEA1 is speculated to be associated with peptic ulcer disease and may have endonuclease activity [].
Probab=28.71 E-value=99 Score=27.21 Aligned_cols=18 Identities=33% Similarity=0.230 Sum_probs=14.9
Q ss_pred hHhHHHHHhHHHHhhccC
Q 029699 89 TADNCQILQTRVNRFKSD 106 (189)
Q Consensus 89 ~~~NLq~lC~~CN~~K~n 106 (189)
+++-.|+||..||..|.-
T Consensus 135 ~~~dFQ~Lck~~N~~KRq 152 (230)
T PF05315_consen 135 TFDDFQPLCKACNDQKRQ 152 (230)
T ss_pred hHHHHHHHHHHHhHHHHH
Confidence 557789999999999853
No 23
>KOG3822 consensus Succinyl-CoA:alpha-ketoacid-CoA transferase [Energy production and conversion]
Probab=24.97 E-value=45 Score=31.70 Aligned_cols=54 Identities=30% Similarity=0.485 Sum_probs=37.9
Q ss_pred CCCCCCCHH---HHHHHHHHcCCCCCCCccchhccccCCeEeec---CCCCCCCC-----CCccceeEec
Q 029699 24 ERPRYFDGK---AKSMCWAKAETVPGRHPERWRKDAAGNIVCKR---FCNCHGCL-----CFEYDHIVPF 82 (189)
Q Consensus 24 ~~~R~F~~~---~R~~~w~ka~~v~Gr~p~r~R~da~gnvv~r~---~~~C~~C~-----~~evDHIiP~ 82 (189)
...|.|+.. +-+++|.....++ .|+-|..||++||. +++=+.|. .-|++.|++.
T Consensus 184 revreFNG~~~v~EeaI~~DFAlvK-----awkAD~~GNvvFr~sArNFN~PMCkAak~TvvEVEEIV~i 248 (516)
T KOG3822|consen 184 REVREFNGDHFVLEEAIRADFALVK-----AWKADRAGNVVFRKSARNFNVPMCKAAKVTVVEVEEIVEI 248 (516)
T ss_pred chhhhcCCceeeehhhhhhhhhhhh-----hhhcCcccceeeehhhccCCcccchhccceEEEEeeeecc
Confidence 445556543 3456776666555 59999999999984 66778883 3578888875
No 24
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=23.02 E-value=1.8e+02 Score=24.79 Aligned_cols=48 Identities=19% Similarity=0.419 Sum_probs=28.1
Q ss_pred CHHHHHHHHHHcCCCCCCCc----cchhccccCCeEeecCCCCCCC-CCCccceeEeccC
Q 029699 30 DGKAKSMCWAKAETVPGRHP----ERWRKDAAGNIVCKRFCNCHGC-LCFEYDHIVPFSK 84 (189)
Q Consensus 30 ~~~~R~~~w~ka~~v~Gr~p----~r~R~da~gnvv~r~~~~C~~C-~~~evDHIiP~S~ 84 (189)
+.++-+++.+..+ |.+| +--......|||| +|..| ..|+++|.-|.+.
T Consensus 92 T~kQEe~~ReeNg---G~DPit~Vd~~lvnN~~nVLF----RC~~C~RawH~~HLP~~~~ 144 (175)
T PF15446_consen 92 TPKQEEKLREENG---GVDPITPVDPELVNNPDNVLF----RCTSCHRAWHFEHLPPPSG 144 (175)
T ss_pred CcHHHHHHHHHcC---CCCCCccCCHHHccChhheEE----ecCCccceeehhhCCCCcC
Confidence 3344445555444 3333 2233444456665 58899 6899999988653
Done!