Query 047362
Match_columns 109
No_of_seqs 120 out of 1010
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 10:22:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047362.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047362hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00329 GIY-YIG nuclease supe 99.9 9.6E-24 2.1E-28 143.5 7.2 61 44-109 2-62 (86)
2 COG2827 Predicted endonuclease 99.9 2.1E-22 4.5E-27 140.3 6.4 58 47-109 3-60 (95)
3 KOG3005 GIY-YIG type nuclease 99.3 3.5E-12 7.5E-17 102.7 6.7 65 43-107 3-69 (276)
4 PF01541 GIY-YIG: GIY-YIG cata 99.1 7.5E-11 1.6E-15 74.8 4.2 57 48-108 1-61 (80)
5 smart00465 GIYc GIY-YIG type n 98.3 9.5E-07 2.1E-11 55.8 4.7 32 49-81 2-33 (84)
6 TIGR01453 grpIintron_endo grou 97.2 0.00057 1.2E-08 52.6 4.8 31 50-81 3-33 (214)
7 PF10544 T5orf172: T5orf172 do 97.1 0.0035 7.5E-08 41.1 7.0 43 50-98 2-46 (100)
8 PHA02598 denA endonuclease II; 94.5 0.054 1.2E-06 40.3 3.8 33 46-80 31-63 (138)
9 PRK10545 nucleotide excision r 94.0 0.056 1.2E-06 44.0 3.3 32 48-80 34-66 (286)
10 PRK14671 uvrC excinuclease ABC 90.3 0.3 6.5E-06 43.5 3.5 33 47-80 21-53 (621)
11 PRK12306 uvrC excinuclease ABC 90.3 0.29 6.2E-06 42.8 3.3 31 49-80 11-41 (519)
12 PRK07883 hypothetical protein; 90.0 0.31 6.8E-06 42.6 3.3 34 46-80 215-248 (557)
13 PRK00558 uvrC excinuclease ABC 89.9 0.29 6.4E-06 43.2 3.0 34 46-80 12-45 (598)
14 TIGR00194 uvrC excinuclease AB 89.2 0.37 8E-06 42.6 3.2 32 48-80 11-42 (574)
15 PRK14666 uvrC excinuclease ABC 89.0 0.4 8.7E-06 43.5 3.3 32 48-80 12-43 (694)
16 PRK14669 uvrC excinuclease ABC 88.5 0.47 1E-05 42.4 3.4 33 47-80 12-44 (624)
17 PRK14672 uvrC excinuclease ABC 88.0 0.47 1E-05 43.1 3.1 32 48-80 21-52 (691)
18 PRK14667 uvrC excinuclease ABC 87.6 0.51 1.1E-05 41.7 3.0 29 50-80 18-46 (567)
19 PRK14668 uvrC excinuclease ABC 85.5 0.73 1.6E-05 40.8 2.9 31 48-80 16-46 (577)
20 PF13455 MUG113: Meiotically u 79.9 1.2 2.7E-05 29.9 1.7 16 65-80 3-18 (83)
21 COG0322 UvrC Nuclease subunit 78.1 2.5 5.4E-05 37.7 3.5 32 48-80 15-46 (581)
22 KOG3005 GIY-YIG type nuclease 60.7 5.1 0.00011 33.0 1.5 83 5-87 28-120 (276)
23 COG3680 Uncharacterized protei 57.8 9.8 0.00021 30.9 2.6 30 48-79 15-44 (259)
24 PRK14670 uvrC excinuclease ABC 51.9 10 0.00022 33.8 1.9 24 56-80 3-26 (574)
25 PRK11901 hypothetical protein; 49.3 21 0.00045 30.1 3.3 56 44-109 241-296 (327)
26 smart00800 uDENN Domain always 36.9 63 0.0014 21.1 3.6 23 44-68 63-85 (89)
27 PF01986 DUF123: Domain of unk 35.8 35 0.00076 23.8 2.3 20 62-81 9-31 (99)
28 COG3266 DamX Uncharacterized p 31.3 68 0.0015 26.7 3.6 53 43-108 206-261 (292)
29 PF07935 SSV1_ORF_D-335: ORF D 30.9 34 0.00074 23.0 1.5 32 47-78 15-48 (72)
30 PRK10905 cell division protein 29.5 58 0.0013 27.5 3.0 37 70-109 260-298 (328)
31 PF05036 SPOR: Sporulation rel 26.6 39 0.00085 20.2 1.2 38 70-109 17-56 (76)
32 PF03456 uDENN: uDENN domain; 21.6 1E+02 0.0023 18.7 2.5 23 44-68 39-61 (65)
No 1
>PRK00329 GIY-YIG nuclease superfamily protein; Validated
Probab=99.90 E-value=9.6e-24 Score=143.49 Aligned_cols=61 Identities=28% Similarity=0.540 Sum_probs=55.7
Q ss_pred CCCCccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhcCCCCCccccCCCCCcEEEEEEeeeCCCCC
Q 047362 44 SNSRSWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNGELRGGAKASQAGRPWISACIIQGFHDQSD 109 (109)
Q Consensus 44 ~~~~~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~~~~~gak~Tr~~~Pw~LV~~~E~f~~kse 109 (109)
+..++||||||+|.++. +|||+|+||.+||+|||. +.|++||++++||+|| |+|.|++++|
T Consensus 2 ~~~~~~~vYil~~~~~~--~Y~G~T~dl~~Rl~qH~~--g~ga~~tr~~~p~~Lv-~~e~~~~~~~ 62 (86)
T PRK00329 2 AEMKPWFLYLLRCADGS--LYTGITTDVERRFAQHQS--GKGAKYTRGRPPLTLV-FVEPVGDRSE 62 (86)
T ss_pred CCCCceEEEEEEcCCCC--EEEEEcCCHHHHHHHHHc--CCCCCCccCCCceEEE-EEEECCCHHH
Confidence 45788999999998876 999999999999999998 4689999999999999 8999999764
No 2
>COG2827 Predicted endonuclease containing a URI domain [DNA replication, recombination, and repair]
Probab=99.87 E-value=2.1e-22 Score=140.30 Aligned_cols=58 Identities=33% Similarity=0.568 Sum_probs=54.6
Q ss_pred CccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhcCCCCCccccCCCCCcEEEEEEeeeCCCCC
Q 047362 47 RSWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNGELRGGAKASQAGRPWISACIIQGFHDQSD 109 (109)
Q Consensus 47 ~~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~~~~~gak~Tr~~~Pw~LV~~~E~f~~kse 109 (109)
+.||||||.|.||. ||||+|+||.+|+.|||+ ++|++||+.++|.+|| |+|.|+++++
T Consensus 3 ~~~~vYil~c~dgt--lY~GvT~D~~rR~~~H~~--GkgakyT~~~~~~~Lv-~~e~~~~~~~ 60 (95)
T COG2827 3 NNWYVYILRCADGT--LYTGVTTDLERRLAEHNS--GKGAKYTRRYGPVRLV-WYEEFDDKSE 60 (95)
T ss_pred cceEEEEEEeCCCC--EEEEecCCHHHHHHHHhc--ccccchhccCCceEEE-EEeecCCHHH
Confidence 47999999999888 999999999999999998 5799999999999999 9999999864
No 3
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=99.32 E-value=3.5e-12 Score=102.69 Aligned_cols=65 Identities=38% Similarity=0.721 Sum_probs=57.0
Q ss_pred CCCCCccEEEEeEeCC--CCCceEEEEeCCHHHHHHHHhcCCCCCccccCCCCCcEEEEEEeeeCCC
Q 047362 43 NSNSRSWSVYLIISTN--PPIKTYVGTTTNFPRRLKQHNGELRGGAKASQAGRPWISACIIQGFHDQ 107 (109)
Q Consensus 43 ~~~~~~yyVYIL~s~~--~~~~lYiG~T~DL~rRl~qHn~~~~~gak~Tr~~~Pw~LV~~~E~f~~k 107 (109)
.+....|++|+|.|.+ ..++.|||+|.|+.+||+|||+...+||.-|++++||+||+.+..|+++
T Consensus 3 ~~~~~Fy~cYlL~s~sp~~r~~~yigst~nP~rRlRqhNg~~~gga~kt~~~~PWeMv~iV~GFPn~ 69 (276)
T KOG3005|consen 3 KDGKGFYCCYLLTSLSPRYKGRTYIGSTVNPSRRLRQHNGEIKGGAWKTKKRRPWEMVMIVHGFPNK 69 (276)
T ss_pred cccCceEEEEEEeecCcCcCCceEEeeeCCCchhHHhhCCcccCcccccCCCCCceEEEEeccCCcc
Confidence 3456789999999977 2247999999999999999998667889999999999999999999985
No 4
>PF01541 GIY-YIG: GIY-YIG catalytic domain; InterPro: IPR000305 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. It is found in the amino terminal region of excinuclease abc subunit c (uvrC), Bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage.; GO: 0004518 nuclease activity, 0006281 DNA repair, 0005622 intracellular; PDB: 1YWL_A 1YD6_D 1YD5_A 1YD1_A 1YCZ_A 1YD0_A 1YD3_A 1YD4_A 1YD2_A 1LN0_A ....
Probab=99.12 E-value=7.5e-11 Score=74.84 Aligned_cols=57 Identities=26% Similarity=0.511 Sum_probs=45.3
Q ss_pred ccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhcCCCCCccccC----CCCCcEEEEEEeeeCCCC
Q 047362 48 SWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNGELRGGAKASQ----AGRPWISACIIQGFHDQS 108 (109)
Q Consensus 48 ~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~~~~~gak~Tr----~~~Pw~LV~~~E~f~~ks 108 (109)
+++||+|.|.++. .+|||.|.||.+||.+|..+ .+...+. ....+.++ +++.+.+..
T Consensus 1 k~gIY~i~~~~~~-~~YIG~t~nl~~R~~~H~~~--~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 61 (80)
T PF01541_consen 1 KYGIYIIYNKDNK-KIYIGSTKNLKKRLNEHFSG--NKSKKKKQKKYGWDNFEFI-IIEEFNTKS 61 (80)
T ss_dssp -EEEEEEEETTTE-EEEEEEESSHHHHHHHHHHH--CTHCSHCHHHHHSSCEEEE-EEEEESSHH
T ss_pred CcEEEEEEECCCC-EEEEEEECCHHHHHHHHhcC--CCCCcchhhhcccccEEEE-eeEEeCCHH
Confidence 4789999999998 89999999999999999874 2333333 26889998 788887653
No 5
>smart00465 GIYc GIY-YIG type nucleases (URI domain).
Probab=98.34 E-value=9.5e-07 Score=55.84 Aligned_cols=32 Identities=38% Similarity=0.531 Sum_probs=28.6
Q ss_pred cEEEEeEeCCCCCceEEEEeCCHHHHHHHHhcC
Q 047362 49 WSVYLIISTNPPIKTYVGTTTNFPRRLKQHNGE 81 (109)
Q Consensus 49 yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~~ 81 (109)
..||++.+.++. ++|||.|.||.+|+.+|...
T Consensus 2 ~gvY~i~~~~~~-~~YVG~t~nl~~R~~~h~~~ 33 (84)
T smart00465 2 PGVYYITNKKNG-KLYVGKAKNLRNRLKRHFSG 33 (84)
T ss_pred CEEEEEEECCCC-EEEEEEccCHHHHHHHHHhC
Confidence 369999997777 89999999999999999964
No 6
>TIGR01453 grpIintron_endo group I intron endonuclease. This model represents one subfamily of endonucleases containing the endo/excinuclease amino terminal domain, Pfam:PF01541 at its amino end. A distinct subfamily includes excinuclease abc subunit c (uvrC). Members of pfam01541 are often termed GIY-YIG endonucleases after conserved motifs near the amino end. This subfamily in this model is found in open reading frames of group I introns in both phage and mitochondria. The closely related endonucleases of phage T4: segA, segB, segC, segD and segE, score below the trusted cutoff for the family.
Probab=97.22 E-value=0.00057 Score=52.61 Aligned_cols=31 Identities=35% Similarity=0.568 Sum_probs=27.8
Q ss_pred EEEEeEeCCCCCceEEEEeCCHHHHHHHHhcC
Q 047362 50 SVYLIISTNPPIKTYVGTTTNFPRRLKQHNGE 81 (109)
Q Consensus 50 yVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~~ 81 (109)
.||+|.|...+ ++|||.|.||.+||.+|...
T Consensus 3 GIY~i~n~~ng-k~YIGss~nl~~R~~~h~~~ 33 (214)
T TIGR01453 3 GIYKITNNING-KIYVGSSVNLEKRLKEHLKL 33 (214)
T ss_pred EEEEEEECCCC-cEEEEeccCHHHHHHHHHHH
Confidence 59999997766 79999999999999999864
No 7
>PF10544 T5orf172: T5orf172 domain; InterPro: IPR018306 This entry represents a DNA-binding domain found in bacteriophage T5, ORF172 []. The domain is related to the Bro-N and KilA-N domains that are widespread in large-DNA viruses infecting bacteria and eukaryotes [].
Probab=97.10 E-value=0.0035 Score=41.09 Aligned_cols=43 Identities=26% Similarity=0.322 Sum_probs=32.5
Q ss_pred EEEEeEeCCCCCc--eEEEEeCCHHHHHHHHhcCCCCCccccCCCCCcEEE
Q 047362 50 SVYLIISTNPPIK--TYVGTTTNFPRRLKQHNGELRGGAKASQAGRPWISA 98 (109)
Q Consensus 50 yVYIL~s~~~~~~--lYiG~T~DL~rRl~qHn~~~~~gak~Tr~~~Pw~LV 98 (109)
||||+.+...... +=||.|+|+.+|+.|++. ..+....+|.++
T Consensus 2 yiYi~~~~~~~~~~~~KIG~T~~~~~Rl~~~~~------~~~~~~~~~~~~ 46 (100)
T PF10544_consen 2 YIYILTSPSNPGYNIYKIGYTTNPERRLRELNR------NSTGSPFDFEVI 46 (100)
T ss_pred EEEEEEecCCCCceeEEEeeECCHHHHHHHhhc------cccCCCCceeEE
Confidence 8999977665434 779999999999999993 133446677776
No 8
>PHA02598 denA endonuclease II; Provisional
Probab=94.51 E-value=0.054 Score=40.34 Aligned_cols=33 Identities=21% Similarity=0.440 Sum_probs=28.9
Q ss_pred CCccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 46 SRSWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 46 ~~~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
.+...||++. .++. .+|||-+.||.+|+.++..
T Consensus 31 ~~~n~VY~~~-~~~~-viYVGKAknLkkRv~sYf~ 63 (138)
T PHA02598 31 NKKNVIYAIA-VDDE-LVYIGKTKNLRKRIDYYRN 63 (138)
T ss_pred ccceEEEEEE-eCCe-EEEEeehhhHHHHHHHHhC
Confidence 4666899999 6667 8999999999999999975
No 9
>PRK10545 nucleotide excision repair endonuclease; Provisional
Probab=94.01 E-value=0.056 Score=43.98 Aligned_cols=32 Identities=25% Similarity=0.362 Sum_probs=27.8
Q ss_pred ccEEEEeEeCCCCCc-eEEEEeCCHHHHHHHHhc
Q 047362 48 SWSVYLIISTNPPIK-TYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 48 ~yyVYIL~s~~~~~~-lYiG~T~DL~rRl~qHn~ 80 (109)
.-=||+....++. . +|||=+.||.+|+.+|=.
T Consensus 34 ~PGVYlf~d~~g~-~~LYVGKAknLR~RV~syF~ 66 (286)
T PRK10545 34 LPGVYLFHGESDT-MPLYIGKSVNIRSRVLSHLR 66 (286)
T ss_pred CCeEEEEEcCCCC-EEEEEechHhHHHHHHHHcC
Confidence 3459999998886 5 899999999999999964
No 10
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=90.32 E-value=0.3 Score=43.50 Aligned_cols=33 Identities=24% Similarity=0.296 Sum_probs=29.4
Q ss_pred CccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 47 RSWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 47 ~~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
..-=||++...++. .+|||=+.||.+|+.+|=.
T Consensus 21 ~~PGVYl~~d~~g~-viYVGKAknLr~RV~sYF~ 53 (621)
T PRK14671 21 TSPGVYQFKNAAGR-VIYVGKAKNLRNRVRSYFR 53 (621)
T ss_pred CCCeEEEEECCCCC-EEEeecchhHHHHHHHHcC
Confidence 33459999999999 9999999999999999964
No 11
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed
Probab=90.28 E-value=0.29 Score=42.84 Aligned_cols=31 Identities=23% Similarity=0.308 Sum_probs=28.6
Q ss_pred cEEEEeEeCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 49 WSVYLIISTNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 49 yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
-=||++...++. .+|||=+.||.+|+.+|=.
T Consensus 11 PGVYl~~d~~g~-vIYVGKAknLr~RV~sYF~ 41 (519)
T PRK12306 11 PGCYLYKDEEGT-IIYVGKAKNLKKRVSSYFQ 41 (519)
T ss_pred CeEEEEECCCCC-EEEeccchhHHHHHHHhCC
Confidence 359999999999 9999999999999999974
No 12
>PRK07883 hypothetical protein; Validated
Probab=90.00 E-value=0.31 Score=42.58 Aligned_cols=34 Identities=29% Similarity=0.404 Sum_probs=30.4
Q ss_pred CCccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 46 SRSWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 46 ~~~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
+..-=||+....++. .+|||=+.||.+|+.+|=.
T Consensus 215 P~~PGVY~~~d~~g~-viYVGKAknLr~Rv~sYF~ 248 (557)
T PRK07883 215 PHAPGVYLFRGPSGE-VLYVGTAVNLRRRVRSYFT 248 (557)
T ss_pred CCCceEEEEECCCCc-EEEeehhhhHHHHHHHHcC
Confidence 455569999999999 9999999999999999964
No 13
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=89.86 E-value=0.29 Score=43.23 Aligned_cols=34 Identities=26% Similarity=0.348 Sum_probs=30.0
Q ss_pred CCccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 46 SRSWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 46 ~~~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
+...=||++...++. .+|||=+.||.+|+.+|=.
T Consensus 12 P~~PGVY~~~d~~g~-viYVGKAknLr~Rv~sYF~ 45 (598)
T PRK00558 12 PDSPGVYRMKDANGT-VIYVGKAKNLKNRVRSYFR 45 (598)
T ss_pred CCCCeEEEEECCCCC-EEEecCchhHHHHHHhhCC
Confidence 344569999999999 9999999999999999964
No 14
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=89.24 E-value=0.37 Score=42.58 Aligned_cols=32 Identities=25% Similarity=0.355 Sum_probs=29.0
Q ss_pred ccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 48 SWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 48 ~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
.-=||++...++. .+|||=+.||.+|+.+|=.
T Consensus 11 ~PGVYl~~d~~g~-viYVGKAknLr~Rv~sYF~ 42 (574)
T TIGR00194 11 KPGCYLMKDRNGQ-VLYVGKAKNLKKRVSSYFR 42 (574)
T ss_pred CCeEEEEECCCCC-EEEEecHHHHHHHHHHhcC
Confidence 3359999999999 9999999999999999974
No 15
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=88.98 E-value=0.4 Score=43.54 Aligned_cols=32 Identities=25% Similarity=0.309 Sum_probs=28.9
Q ss_pred ccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 48 SWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 48 ~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
.-=||++...++. .+|||=+.||.+|+.+|=.
T Consensus 12 ~PGVYlfkD~~G~-VIYVGKAKNLR~RV~SYF~ 43 (694)
T PRK14666 12 TPGVYLYKDEAGR-IIYVGKARHLRRRVASYFR 43 (694)
T ss_pred CCeEEEEECCCCC-EEEeeCcHhHHHHHHHHcC
Confidence 3359999999999 9999999999999999964
No 16
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=88.52 E-value=0.47 Score=42.41 Aligned_cols=33 Identities=27% Similarity=0.356 Sum_probs=29.3
Q ss_pred CccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 47 RSWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 47 ~~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
..-=||+....++. .+|||=+.||.+|+.+|=.
T Consensus 12 ~~PGVYl~~d~~g~-viYVGKAknLr~RV~sYF~ 44 (624)
T PRK14669 12 TSPGVYLYKNAGGE-VIYVGKAKNLRSRVRSYFS 44 (624)
T ss_pred CCCeEEEEECCCCC-EEEeeCchhHHHHHHHHhc
Confidence 33459999999999 9999999999999999964
No 17
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=88.03 E-value=0.47 Score=43.09 Aligned_cols=32 Identities=25% Similarity=0.303 Sum_probs=28.9
Q ss_pred ccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 48 SWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 48 ~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
.-=||++...++. .+|||=+.||.+|+.+|=.
T Consensus 21 ~PGVYlfkd~~G~-VLYVGKAKNLR~RV~SYF~ 52 (691)
T PRK14672 21 TSGVYLWKDVHGV-VIYVGKAKSLRTRLTSYFR 52 (691)
T ss_pred CCeEEEEECCCCC-EEEeeCcHHHHHHHHHHcC
Confidence 3459999999998 9999999999999999974
No 18
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=87.64 E-value=0.51 Score=41.71 Aligned_cols=29 Identities=34% Similarity=0.539 Sum_probs=26.5
Q ss_pred EEEEeEeCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 50 SVYLIISTNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 50 yVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
=||+.. .++. .+|||=+.||.+|+.+|=.
T Consensus 18 GVYl~~-~~g~-viYVGKAknLr~RV~sYF~ 46 (567)
T PRK14667 18 GVYLFK-KKKR-YIYIGKAKNIKNRLLQHYK 46 (567)
T ss_pred eEEEEe-cCCe-EEEeeCcHhHHHHHHHHcC
Confidence 499999 8888 9999999999999999964
No 19
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=85.49 E-value=0.73 Score=40.77 Aligned_cols=31 Identities=19% Similarity=0.375 Sum_probs=26.3
Q ss_pred ccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 48 SWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 48 ~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
.-=||+... ++. .+|||=+.||.+|+.+|-.
T Consensus 16 ~PGVYl~~d-~g~-viYVGKAknLr~RV~sYF~ 46 (577)
T PRK14668 16 EPGVYQFVA-GGT-VLYVGKAVDLRDRVRSYAD 46 (577)
T ss_pred CCEEEEEcC-CCe-EEEeeCcHhHHHHHHHHcC
Confidence 335898886 677 8999999999999999964
No 20
>PF13455 MUG113: Meiotically up-regulated gene 113
Probab=79.93 E-value=1.2 Score=29.87 Aligned_cols=16 Identities=50% Similarity=0.707 Sum_probs=14.9
Q ss_pred EEEeCCHHHHHHHHhc
Q 047362 65 VGTTTNFPRRLKQHNG 80 (109)
Q Consensus 65 iG~T~DL~rRl~qHn~ 80 (109)
||.|.|+.+||.|.+.
T Consensus 3 IGrt~nv~rRl~qW~~ 18 (83)
T PF13455_consen 3 IGRTTNVERRLNQWSR 18 (83)
T ss_pred ccccCCHHHHHHHHHH
Confidence 7999999999999984
No 21
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=78.06 E-value=2.5 Score=37.69 Aligned_cols=32 Identities=31% Similarity=0.414 Sum_probs=28.8
Q ss_pred ccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 48 SWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 48 ~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
.-=||+....++. .+|||=..||.+|+.++=.
T Consensus 15 ~PGvY~~~d~~g~-VlYVGKAknLr~Rv~sYF~ 46 (581)
T COG0322 15 SPGVYLMKDENGT-VLYVGKAKNLRKRVSSYFR 46 (581)
T ss_pred CCeeEEEECCCCC-EEEEeehhhHHHHHHHhhc
Confidence 3359999999999 9999999999999999864
No 22
>KOG3005 consensus GIY-YIG type nuclease [General function prediction only]
Probab=60.69 E-value=5.1 Score=32.97 Aligned_cols=83 Identities=23% Similarity=0.167 Sum_probs=60.9
Q ss_pred cccccccccc--cCC--CCCCCCCCCCCC---CCCCCCCCCCCCCCCCCCccEEEEeEeCCCCCceEEE---EeCCHHHH
Q 047362 5 LSRKFPAVKN--RNP--NPSKLSSSSSSP---TPIRSQSQSKRTPNSNSRSWSVYLIISTNPPIKTYVG---TTTNFPRR 74 (109)
Q Consensus 5 ~~~~~~~~~~--~~~--~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~yyVYIL~s~~~~~~lYiG---~T~DL~rR 74 (109)
.+..+|+.|+ .|+ +.|+-..+...| ...--+.++....+.+...|-+|.+...-.....|.+ ++.+...|
T Consensus 28 gst~nP~rRlRqhNg~~~gga~kt~~~~PWeMv~iV~GFPn~vsALqFEwAWQ~p~~S~~~k~~~~~~k~~~~et~F~~~ 107 (276)
T KOG3005|consen 28 GSTVNPSRRLRQHNGEIKGGAWKTKKRRPWEMVMIVHGFPNKVSALQFEWAWQHPLISRYLKEKDTRLKSKSIETDFMYR 107 (276)
T ss_pred eeeCCCchhHHhhCCcccCcccccCCCCCceEEEEeccCCccchhcchhhhccCcchhhhhhhhhhhhhhhhhhhHHHHH
Confidence 4567888888 455 444444444444 4556678888899999999999988776555346999 99999999
Q ss_pred HHHHhcCCCCCcc
Q 047362 75 LKQHNGELRGGAK 87 (109)
Q Consensus 75 l~qHn~~~~~gak 87 (109)
|++|+.....|+.
T Consensus 108 Lr~l~~~~~~~aw 120 (276)
T KOG3005|consen 108 LRILNHVLRSGAW 120 (276)
T ss_pred HHHHHhhhcCCch
Confidence 9999987655543
No 23
>COG3680 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.84 E-value=9.8 Score=30.85 Aligned_cols=30 Identities=23% Similarity=0.401 Sum_probs=23.5
Q ss_pred ccEEEEeEeCCCCCceEEEEeCCHHHHHHHHh
Q 047362 48 SWSVYLIISTNPPIKTYVGTTTNFPRRLKQHN 79 (109)
Q Consensus 48 ~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn 79 (109)
.||||+|.....+-.||+|--.- +|+-+|.
T Consensus 15 G~YVY~l~Dpr~~~ifYVGKG~G--nRVf~H~ 44 (259)
T COG3680 15 GFYVYCLTDPRKDKIFYVGKGCG--NRVFEHE 44 (259)
T ss_pred eeEEEEEecCCCCcEEEEecCCc--cchHHhh
Confidence 59999998876554899997642 4888887
No 24
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=51.87 E-value=10 Score=33.84 Aligned_cols=24 Identities=29% Similarity=0.344 Sum_probs=21.0
Q ss_pred eCCCCCceEEEEeCCHHHHHHHHhc
Q 047362 56 STNPPIKTYVGTTTNFPRRLKQHNG 80 (109)
Q Consensus 56 s~~~~~~lYiG~T~DL~rRl~qHn~ 80 (109)
..+|. .+|||=+.||.+|+.+|=.
T Consensus 3 d~~g~-vIYVGKAknLr~RV~sYF~ 26 (574)
T PRK14670 3 SENNK-ILYIGKAKNLRSRVKNYFL 26 (574)
T ss_pred CCCCC-EEEeeCcHhHHHHHHHHcC
Confidence 45667 8999999999999999974
No 25
>PRK11901 hypothetical protein; Reviewed
Probab=49.34 E-value=21 Score=30.09 Aligned_cols=56 Identities=11% Similarity=0.259 Sum_probs=34.6
Q ss_pred CCCCccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhcCCCCCccccCCCCCcEEEEEEeeeCCCCC
Q 047362 44 SNSRSWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNGELRGGAKASQAGRPWISACIIQGFHDQSD 109 (109)
Q Consensus 44 ~~~~~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~~~~~gak~Tr~~~Pw~LV~~~E~f~~kse 109 (109)
-....|.+=|+-..+.. +|..=+++|+...-.--+.++.++||-+| .+=.|.++.+
T Consensus 241 ~p~~~YTLQL~Aas~~~---------~L~~f~~~~~L~~~~VYqT~RnGkpWYVV-vyG~Y~Sr~e 296 (327)
T PRK11901 241 APASHYTLQLSSASRSD---------TLNAYAKKQNLSHYHVYETKRDGKPWYVL-VSGNYASSAE 296 (327)
T ss_pred CCCCCeEEEeecCCCHH---------HHHHHHHHcCcCceEEEEEEECCceEEEE-EecCcCCHHH
Confidence 33456666666665555 67777777763110011235678999999 6778888753
No 26
>smart00800 uDENN Domain always found upstream of DENN domain, found in a variety of signalling proteins. The uDENN domain is part of the tripartite DENN domain. It is always found upstream of the DENN domain itself, which is found in a variety of signalling proteins involved in Rab-mediated processes or regulation of MAPKs signalling pathways. The DENN domain is always encircled on both sides by more divergent domains, called uDENN (for upstream DENN) and dDENN (for downstream DENN). The function of the DENN domain remains to date unclear, although it appears to represent a good candidate for a GTP/GDP exchange activity.
Probab=36.87 E-value=63 Score=21.09 Aligned_cols=23 Identities=13% Similarity=0.390 Sum_probs=18.5
Q ss_pred CCCCccEEEEeEeCCCCCceEEEEe
Q 047362 44 SNSRSWSVYLIISTNPPIKTYVGTT 68 (109)
Q Consensus 44 ~~~~~yyVYIL~s~~~~~~lYiG~T 68 (109)
.....+++++|...+|. +.| |++
T Consensus 63 ~~~~~~f~FvLT~~dG~-r~y-G~C 85 (89)
T smart00800 63 SKDPQFFSFVLTDIDGS-RRY-GFC 85 (89)
T ss_pred CCCCcEEEEEEECCCCC-EEE-EEE
Confidence 44568899999999999 888 654
No 27
>PF01986 DUF123: Domain of unknown function DUF123; InterPro: IPR002837 This archaebacterial domain has no known function. In Methanocaldococcus jannaschii (Methanococcus jannaschii) it occurs with an endonuclease domain IPR003265 from INTERPRO.
Probab=35.84 E-value=35 Score=23.83 Aligned_cols=20 Identities=25% Similarity=0.501 Sum_probs=14.0
Q ss_pred ceEEEEeC---CHHHHHHHHhcC
Q 047362 62 KTYVGTTT---NFPRRLKQHNGE 81 (109)
Q Consensus 62 ~lYiG~T~---DL~rRl~qHn~~ 81 (109)
.+|||..- +|..|+..|-..
T Consensus 9 Y~YvGSA~G~~gL~~Ri~RHl~~ 31 (99)
T PF01986_consen 9 YVYVGSAMGPGGLRSRISRHLRR 31 (99)
T ss_pred EEEEecCCCCCCChHHHHHHhhh
Confidence 34455443 799999999863
No 28
>COG3266 DamX Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.25 E-value=68 Score=26.71 Aligned_cols=53 Identities=19% Similarity=0.355 Sum_probs=36.6
Q ss_pred CCCCCccEEEEeEeCCCCCceEEEEeCCHHHHHHHHhcCCCCCc---cccCCCCCcEEEEEEeeeCCCC
Q 047362 43 NSNSRSWSVYLIISTNPPIKTYVGTTTNFPRRLKQHNGELRGGA---KASQAGRPWISACIIQGFHDQS 108 (109)
Q Consensus 43 ~~~~~~yyVYIL~s~~~~~~lYiG~T~DL~rRl~qHn~~~~~ga---k~Tr~~~Pw~LV~~~E~f~~ks 108 (109)
......|.+=|+.+..-+ |+..=..||+. +|- .-|+...||-+| .+=.|.+|.
T Consensus 206 ~~p~~~yTLQl~a~~s~~---------nv~~fa~k~~l---~~~~vy~t~rnG~pWYvv-~~G~Yatrq 261 (292)
T COG3266 206 SAPSSHYTLQLSASGSYD---------NVNGFAKKQNL---KGYVVYETTRNGKPWYVV-VYGNYATRQ 261 (292)
T ss_pred hCCCCceEEEEecccchH---------HHHHHHHhcCC---CceEEeEeecCCceeEEE-EecCcccHH
Confidence 333455556666555555 89999999985 332 237889999999 578887764
No 29
>PF07935 SSV1_ORF_D-335: ORF D-335-like protein; InterPro: IPR012922 The sequences featured in this family are similar to a probable integrase (P20214 from SWISSPROT) expressed by the SSV1 virus of the archaeon Sulfolobus shibatae. This protein may be necessary for the integration of the virus into the host genome by a process of site-specific recombination [].
Probab=30.87 E-value=34 Score=22.98 Aligned_cols=32 Identities=25% Similarity=0.304 Sum_probs=22.1
Q ss_pred CccEEEEeEe-CCCC-CceEEEEeCCHHHHHHHH
Q 047362 47 RSWSVYLIIS-TNPP-IKTYVGTTTNFPRRLKQH 78 (109)
Q Consensus 47 ~~yyVYIL~s-~~~~-~~lYiG~T~DL~rRl~qH 78 (109)
..||||.|+. .++. -..|+|-=.|+..-.-.-
T Consensus 15 GkYYVY~iE~~~~G~~re~YVGpL~~VVe~Yik~ 48 (72)
T PF07935_consen 15 GKYYVYKIEKDINGERRETYVGPLDDVVETYIKL 48 (72)
T ss_pred CeEEEEEEEeccCCceeeeeeccHHHHHHHHHhc
Confidence 4799999999 4443 268999877766544443
No 30
>PRK10905 cell division protein DamX; Validated
Probab=29.50 E-value=58 Score=27.50 Aligned_cols=37 Identities=16% Similarity=0.384 Sum_probs=23.2
Q ss_pred CHHHHHHHHhcCCCCCc--cccCCCCCcEEEEEEeeeCCCCC
Q 047362 70 NFPRRLKQHNGELRGGA--KASQAGRPWISACIIQGFHDQSD 109 (109)
Q Consensus 70 DL~rRl~qHn~~~~~ga--k~Tr~~~Pw~LV~~~E~f~~kse 109 (109)
++..-+++|.. .... .-++.+.||-+| .+=.|.+|.|
T Consensus 260 ~l~~fakKlgL--~~y~vy~TtRnGkpWYVV-~yG~YaSrae 298 (328)
T PRK10905 260 NLNGWAKKENL--KNYVVYETTRNGQPWYVL-VSGVYASKEE 298 (328)
T ss_pred HHHHHHHHcCC--CceEEEEeccCCceEEEE-EecCCCCHHH
Confidence 55556666642 2111 134677899999 6888888753
No 31
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=26.56 E-value=39 Score=20.22 Aligned_cols=38 Identities=21% Similarity=0.359 Sum_probs=23.1
Q ss_pred CHHHHHHHHhcCCCCCc--cccCCCCCcEEEEEEeeeCCCCC
Q 047362 70 NFPRRLKQHNGELRGGA--KASQAGRPWISACIIQGFHDQSD 109 (109)
Q Consensus 70 DL~rRl~qHn~~~~~ga--k~Tr~~~Pw~LV~~~E~f~~kse 109 (109)
+..+.+.+.... +.-+ ..+....+|-.| ++-.|.++.|
T Consensus 17 ~A~~~~~~l~~~-g~~~~~~~~~~~~~~yrV-~~G~f~~~~~ 56 (76)
T PF05036_consen 17 NAERLLAKLKKK-GPDAYVVQVSKGGPWYRV-RVGPFSSREE 56 (76)
T ss_dssp HHHHHHHHHHHH-T-----EEEEEETTCEEE-EECCECTCCH
T ss_pred HHHHHHHHHHhc-CCCcceEEEecCCceEEE-EECCCCCHHH
Confidence 455555555531 1111 566778889888 6888888753
No 32
>PF03456 uDENN: uDENN domain; InterPro: IPR005113 This region is always found associated with IPR001194 from INTERPRO. It is predicted to form an all beta domain [].; PDB: 3TW8_A.
Probab=21.57 E-value=1e+02 Score=18.74 Aligned_cols=23 Identities=9% Similarity=0.325 Sum_probs=16.0
Q ss_pred CCCCccEEEEeEeCCCCCceEEEEe
Q 047362 44 SNSRSWSVYLIISTNPPIKTYVGTT 68 (109)
Q Consensus 44 ~~~~~yyVYIL~s~~~~~~lYiG~T 68 (109)
...-.+++.+|...+|. ++| |++
T Consensus 39 ~~~~~~f~FvLT~~~G~-r~Y-g~C 61 (65)
T PF03456_consen 39 RPPPQFFSFVLTDEDGS-RLY-GYC 61 (65)
T ss_dssp -GSSCEEEEEEE-TTS--EEE-EEE
T ss_pred cCCCeEEEEEEECCCCC-EEE-EEE
Confidence 34567899999999999 898 543
Done!