Query 045823
Match_columns 233
No_of_seqs 113 out of 195
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 05:51:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045823.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045823hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2841 Structure-specific end 100.0 3E-52 6.5E-57 370.2 9.8 147 1-150 65-254 (254)
2 TIGR00597 rad10 DNA repair pro 100.0 4.8E-34 1E-38 229.4 4.6 75 1-78 10-112 (112)
3 COG5241 RAD10 Nucleotide excis 100.0 7.5E-32 1.6E-36 234.1 -0.3 142 1-148 43-224 (224)
4 PF03834 Rad10: Binding domain 99.9 1.4E-23 3E-28 156.5 2.4 41 1-41 10-51 (69)
5 PRK13766 Hef nuclease; Provisi 98.6 8.7E-08 1.9E-12 95.3 8.0 135 11-148 584-772 (773)
6 COG1948 MUS81 ERCC4-type nucle 97.1 0.0013 2.8E-08 60.1 6.8 140 11-151 49-242 (254)
7 TIGR00596 rad1 DNA repair prot 96.6 0.0054 1.2E-07 63.7 7.4 125 20-147 618-812 (814)
8 PF12826 HHH_2: Helix-hairpin- 96.6 0.00075 1.6E-08 48.8 0.8 31 109-139 7-47 (64)
9 PF14520 HHH_5: Helix-hairpin- 96.5 0.0027 5.9E-08 44.8 3.0 37 103-139 3-50 (60)
10 COG5241 RAD10 Nucleotide excis 95.8 0.0021 4.5E-08 57.2 -0.2 77 1-81 100-220 (224)
11 PRK13482 DNA integrity scannin 95.2 0.013 2.9E-07 55.8 2.8 45 95-139 277-331 (352)
12 KOG0442 Structure-specific end 87.7 1.4 3E-05 46.8 6.6 76 62-139 770-864 (892)
13 TIGR00575 dnlj DNA ligase, NAD 87.4 0.47 1E-05 48.3 3.0 47 100-147 494-554 (652)
14 TIGR00426 competence protein C 86.9 0.74 1.6E-05 33.1 3.1 35 105-139 16-59 (69)
15 PRK12766 50S ribosomal protein 86.9 0.56 1.2E-05 42.7 2.9 34 106-139 4-48 (232)
16 PRK00116 ruvA Holliday junctio 86.4 0.74 1.6E-05 39.8 3.3 37 103-139 71-120 (192)
17 COG1796 POL4 DNA polymerase IV 86.4 0.66 1.4E-05 44.1 3.3 70 69-139 11-105 (326)
18 PRK14605 ruvA Holliday junctio 85.8 0.77 1.7E-05 40.0 3.1 38 102-139 70-120 (194)
19 PRK07956 ligA NAD-dependent DN 85.2 1.9 4E-05 44.2 6.0 46 100-146 507-566 (665)
20 TIGR01259 comE comEA protein. 84.7 1.1 2.3E-05 36.3 3.3 36 104-139 67-110 (120)
21 PRK14666 uvrC excinuclease ABC 84.5 0.84 1.8E-05 47.3 3.2 37 103-139 635-681 (694)
22 PF00633 HHH: Helix-hairpin-he 83.2 0.44 9.5E-06 30.3 0.4 13 127-139 11-23 (30)
23 PRK00558 uvrC excinuclease ABC 83.2 0.94 2E-05 45.7 2.9 37 103-139 541-587 (598)
24 PRK02515 psbU photosystem II c 82.5 1.9 4.1E-05 36.4 4.0 39 104-142 60-102 (132)
25 PF12836 HHH_3: Helix-hairpin- 81.1 2.2 4.8E-05 30.6 3.5 36 104-139 13-56 (65)
26 PRK14601 ruvA Holliday junctio 78.4 1.9 4.1E-05 37.6 2.8 38 102-139 70-120 (183)
27 PRK13901 ruvA Holliday junctio 75.8 2.5 5.4E-05 37.4 2.8 38 102-139 69-119 (196)
28 PRK14602 ruvA Holliday junctio 75.3 3.1 6.6E-05 36.6 3.3 38 102-139 71-121 (203)
29 PRK14606 ruvA Holliday junctio 75.0 2.7 5.8E-05 36.7 2.8 38 102-139 70-120 (188)
30 PRK14603 ruvA Holliday junctio 74.5 2.8 6E-05 36.8 2.8 38 102-139 69-119 (197)
31 TIGR00084 ruvA Holliday juncti 71.9 3.9 8.5E-05 35.6 3.1 37 103-139 70-119 (191)
32 PRK14604 ruvA Holliday junctio 69.3 4.2 9.1E-05 35.6 2.7 38 102-139 70-120 (195)
33 PRK14600 ruvA Holliday junctio 67.3 5 0.00011 35.0 2.8 37 102-139 70-119 (186)
34 PRK14668 uvrC excinuclease ABC 67.0 4.7 0.0001 40.8 2.9 37 103-139 523-569 (577)
35 PRK02515 psbU photosystem II c 66.6 3.7 8.1E-05 34.6 1.8 21 127-147 61-83 (132)
36 TIGR01448 recD_rel helicase, p 65.3 6.7 0.00014 40.4 3.6 40 100-139 77-129 (720)
37 PRK14670 uvrC excinuclease ABC 65.1 4.6 9.9E-05 41.0 2.4 36 104-139 513-558 (574)
38 PRK14351 ligA NAD-dependent DN 62.3 6.9 0.00015 40.5 3.1 39 100-139 524-572 (689)
39 TIGR00608 radc DNA repair prot 57.7 5.9 0.00013 35.3 1.5 24 116-139 36-72 (218)
40 PRK00024 hypothetical protein; 57.4 5.9 0.00013 35.2 1.5 23 117-139 46-78 (224)
41 PRK14669 uvrC excinuclease ABC 56.8 10 0.00023 38.8 3.3 48 103-152 550-611 (624)
42 smart00278 HhH1 Helix-hairpin- 56.7 4.8 0.0001 24.2 0.5 18 127-144 1-19 (26)
43 PRK00254 ski2-like helicase; P 56.1 12 0.00025 38.2 3.5 33 107-139 647-690 (720)
44 PHA00439 exonuclease 55.3 9.1 0.0002 35.8 2.4 118 69-197 117-251 (286)
45 PRK14672 uvrC excinuclease ABC 55.1 13 0.00028 38.8 3.6 37 103-139 606-652 (691)
46 COG2003 RadC DNA repair protei 54.9 6.9 0.00015 35.6 1.5 32 108-139 36-78 (224)
47 COG0177 Nth Predicted EndoIII- 54.1 9.7 0.00021 34.2 2.3 31 119-149 94-136 (211)
48 COG0632 RuvA Holliday junction 54.0 37 0.0008 30.2 5.9 37 103-139 71-120 (201)
49 COG1623 Predicted nucleic-acid 53.4 8.9 0.00019 36.8 2.0 41 101-141 289-339 (349)
50 PRK10702 endonuclease III; Pro 48.5 11 0.00025 33.1 1.8 30 118-147 93-134 (211)
51 PRK14667 uvrC excinuclease ABC 41.4 29 0.00063 35.3 3.6 35 104-139 513-557 (567)
52 COG3727 Vsr DNA G:T-mismatch r 39.6 27 0.00058 30.1 2.6 16 19-34 48-63 (150)
53 KOG1921 Endonuclease III [Repl 38.6 22 0.00047 33.5 2.1 22 118-139 143-171 (286)
54 COG0272 Lig NAD-dependent DNA 37.1 27 0.00058 36.5 2.7 68 77-146 481-566 (667)
55 COG3526 Uncharacterized protei 35.4 23 0.00049 28.4 1.4 21 118-138 26-49 (99)
56 PRK08609 hypothetical protein; 34.9 25 0.00055 35.3 2.1 34 106-139 49-100 (570)
57 PRK00116 ruvA Holliday junctio 33.3 21 0.00045 30.9 1.0 13 127-139 73-85 (192)
58 PF02371 Transposase_20: Trans 31.8 40 0.00086 25.3 2.2 34 105-138 2-43 (87)
59 smart00279 HhH2 Helix-hairpin- 29.2 28 0.0006 22.8 0.9 19 121-139 10-28 (36)
60 PF03118 RNA_pol_A_CTD: Bacter 28.6 30 0.00064 25.3 1.0 38 99-139 19-56 (66)
61 smart00478 ENDO3c endonuclease 27.5 57 0.0012 26.0 2.6 23 127-149 72-99 (149)
62 PRK00199 ihfB integration host 26.9 79 0.0017 23.9 3.2 39 101-139 4-52 (94)
63 TIGR00987 himA integration hos 26.7 64 0.0014 24.6 2.6 39 101-139 5-52 (96)
64 PF00216 Bac_DNA_binding: Bact 26.5 50 0.0011 24.2 1.9 38 102-139 5-51 (90)
65 PRK14350 ligA NAD-dependent DN 26.3 56 0.0012 33.9 2.9 47 99-146 497-564 (669)
66 PRK00285 ihfA integration host 26.3 65 0.0014 24.6 2.6 39 101-139 6-53 (99)
67 TIGR01083 nth endonuclease III 26.3 49 0.0011 28.2 2.1 21 127-147 106-131 (191)
68 COG1555 ComEA DNA uptake prote 26.0 30 0.00066 29.1 0.8 13 127-139 97-109 (149)
69 PRK10664 transcriptional regul 25.0 70 0.0015 24.5 2.6 39 101-139 4-51 (90)
70 smart00411 BHL bacterial (prok 25.0 72 0.0016 23.4 2.6 39 101-139 4-51 (90)
71 PF00416 Ribosomal_S13: Riboso 24.7 82 0.0018 24.8 3.0 25 102-126 12-36 (107)
72 PRK09482 flap endonuclease-lik 24.4 41 0.00089 30.8 1.4 68 72-139 107-194 (256)
73 PRK10753 transcriptional regul 24.3 75 0.0016 24.2 2.6 39 101-139 4-51 (90)
74 PF12776 Myb_DNA-bind_3: Myb/S 24.1 1.8E+02 0.004 21.2 4.6 68 69-137 3-79 (96)
75 TIGR01084 mutY A/G-specific ad 23.0 48 0.001 30.5 1.5 21 127-147 105-130 (275)
76 PF14716 HHH_8: Helix-hairpin- 22.9 58 0.0013 23.4 1.7 11 128-138 48-58 (68)
77 PRK14363 Maf-like protein; Pro 22.4 33 0.00071 30.4 0.3 59 67-126 126-184 (204)
78 PF11798 IMS_HHH: IMS family H 21.3 70 0.0015 20.2 1.6 12 128-139 12-23 (32)
79 smart00027 EH Eps15 homology d 20.9 3.6E+02 0.0078 20.0 6.1 52 67-126 3-54 (96)
80 PF02764 Diphtheria_T: Diphthe 20.7 1.1E+02 0.0023 26.7 3.1 22 69-90 40-61 (180)
81 smart00483 POLXc DNA polymeras 20.3 39 0.00084 31.7 0.4 14 127-140 89-102 (334)
82 TIGR01201 HU_rel DNA-binding p 20.3 1.1E+02 0.0023 25.4 3.0 40 100-139 33-81 (145)
83 PF07279 DUF1442: Protein of u 20.2 67 0.0015 29.2 1.8 21 63-86 3-24 (218)
84 smart00475 53EXOc 5'-3' exonuc 20.1 1.2E+02 0.0025 27.7 3.4 13 127-139 186-198 (259)
No 1
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=100.00 E-value=3e-52 Score=370.22 Aligned_cols=147 Identities=44% Similarity=0.710 Sum_probs=140.6
Q ss_pred CCCccccccccCceeec-ccccceeecCceeEEEEeehhHHH---------hhhhHHH-----------------HHHHH
Q 045823 1 KGNPLLKHITYVRWAFA-DVVCDYLLGQNSCALYLRLCIYFL---------NLLFDNV-----------------LLWVF 53 (233)
Q Consensus 1 kGNPLLk~IrnVpwEy~-dIvpDYviG~t~cvLFLSLKYH~L---------q~L~k~y-----------------L~ELt 53 (233)
||||||+|||||+|+|+ ||+|||++|+++||||||||||.| +.|+++| |+||+
T Consensus 65 kGNplLk~vrnv~w~f~ddi~PDf~lg~~~cvLyLSl~yH~l~pdYi~~Ri~~l~k~yk~~VLl~~vd~~e~~~~l~el~ 144 (254)
T KOG2841|consen 65 KGNPLLKHVRNVKWEFGDDIIPDFVLGRGCCVLYLSLKYHKLHPDYIYRRIRKLGKNYKLRVLLVHVDMEEPYKPLLELT 144 (254)
T ss_pred ccChHHHHHhcCCeEecCCCCcceEecCceEEEEeehHhhhcCcHHHHHHHHHhcccccceEEEEEecCcchHHHHHHHH
Confidence 79999999999999998 899999999999999999999999 3455565 99999
Q ss_pred HHHhhccc--ccccCCCCHHHHHHHHHHHHhhcCCCcccccCCCCCchHHHHHHHhhcCCCccHhhHHHHHHhhh-----
Q 045823 54 STFGTSSC--LESWSNFSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG----- 126 (233)
Q Consensus 54 ~~c~~~~~--IlAW~~~S~EEAArYLEt~K~yEnk~~d~Ik~k~~~dy~s~v~~~LTsIrsVNKTDa~tLls~FG----- 126 (233)
++|++++| +||| |.||||+|||+||.||++|+|+|+++.+.||++++..+||+||+||||||.+||.+||
T Consensus 145 k~~~l~~~Tl~lA~---s~EeaaryIE~~k~~ek~p~dli~~~~~~d~ls~~~~~Lt~i~~VnKtda~~LL~~FgsLq~~ 221 (254)
T KOG2841|consen 145 KTCDLNDVTLVLAW---SMEEAARYIETYKEYEKKPIDLIMERKDRDLLSSLLGFLTTIPGVNKTDAQLLLQKFGSLQQI 221 (254)
T ss_pred HHHHhhceeeeeec---cHHHHHHHHHHHHHhhcCCchhhhhcccccHHHHHHHHHHhCCCCCcccHHHHHHhcccHHHH
Confidence 99999999 9999 9999999999999999999999999999999999999999999999999999999999
Q ss_pred -----hhccCCCCCcchh----hhhcCCCCCCC
Q 045823 127 -----EDLSHCPGIGERK----HVVSSHPPIPE 150 (233)
Q Consensus 127 -----EeLs~cPGiG~kK----~~v~~~PFi~~ 150 (233)
++|+.|||+||.| +.+|++||..+
T Consensus 222 ~~AS~~ele~~~G~G~~kak~l~~~l~~pf~~~ 254 (254)
T KOG2841|consen 222 SNASEGELEQCPGLGPAKAKRLHKFLHQPFLSN 254 (254)
T ss_pred HhcCHhHHHhCcCcCHHHHHHHHHHHhccccCC
Confidence 9999999999999 78999999753
No 2
>TIGR00597 rad10 DNA repair protein rad10. All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=4.8e-34 Score=229.44 Aligned_cols=75 Identities=47% Similarity=0.775 Sum_probs=71.1
Q ss_pred CCCccccccccCceeecccccceeecCceeEEEEeehhHHH---------hhhhHHH-----------------HHHHHH
Q 045823 1 KGNPLLKHITYVRWAFADVVCDYLLGQNSCALYLRLCIYFL---------NLLFDNV-----------------LLWVFS 54 (233)
Q Consensus 1 kGNPLLk~IrnVpwEy~dIvpDYviG~t~cvLFLSLKYH~L---------q~L~k~y-----------------L~ELt~ 54 (233)
||||||+|||||||||+||+|||++|+++||||||||||+| +.|+++| |+||++
T Consensus 10 kgNPlL~~i~nv~wey~di~~Dy~~g~~~~vLFLSLkYH~L~peYi~~Ri~~L~~~~~lrvLL~~VDv~~~~~~L~eL~k 89 (112)
T TIGR00597 10 KGNPLLKHVRNVPWEYGDVIPDYVLGQGTCALFLSLRYHNLHPDYIHRRLQSLGKNFNLRILLVQVDVKNPQQALKELAK 89 (112)
T ss_pred cCChHHHHHhcCCeEecCcCCCEEEcCccEEEEEEhhhhccCHHHHHHHHHHhccccceeEEEEEEeCCchHHHHHHHHH
Confidence 79999999999999999999999999999999999999999 4555666 999999
Q ss_pred HHhhccc--ccccCCCCHHHHHHHHH
Q 045823 55 TFGTSSC--LESWSNFSQEECGRYLE 78 (233)
Q Consensus 55 ~c~~~~~--IlAW~~~S~EEAArYLE 78 (233)
+|+.+|| |||| |+||||||||
T Consensus 90 ~~~~~~~TLilaw---s~eEaa~YlE 112 (112)
T TIGR00597 90 MCILNDCTLILAW---SFEEAARYLE 112 (112)
T ss_pred HHHHcCcEEEEEC---CHHHHHHhhC
Confidence 9999999 9999 9999999997
No 3
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=99.96 E-value=7.5e-32 Score=234.15 Aligned_cols=142 Identities=23% Similarity=0.243 Sum_probs=131.0
Q ss_pred CCCccccccccCceeecc-cccceeecCceeEEEEeehhHHH------hhhh--H--------------HH---HHHHHH
Q 045823 1 KGNPLLKHITYVRWAFAD-VVCDYLLGQNSCALYLRLCIYFL------NLLF--D--------------NV---LLWVFS 54 (233)
Q Consensus 1 kGNPLLk~IrnVpwEy~d-IvpDYviG~t~cvLFLSLKYH~L------q~L~--k--------------~y---L~ELt~ 54 (233)
+|||+|.|.+|++|+|++ |+|||++|+..|-||||||||.+ .++. | || |+||..
T Consensus 43 kgnp~l~~~~N~~w~y~~~i~Pd~~~~s~~~~lflslrfhs~~Peyi~~riSklKsYk~r~LL~hvd~~N~~asIqElv~ 122 (224)
T COG5241 43 KGNPQLSRRINSNWVYNAFIKPDEWTDSKATDLFLSLRFHSTRPEYIVLRISKLKSYKERPLLNHVDSTNWRASIQELVS 122 (224)
T ss_pred cCCCcccccccCcceeccccCcchhhcchHHHHHHHHhhhcCCCceEEEeeeccccccccceeeeeccccHHHHHHHHHH
Confidence 699999999999999998 99999999999999999999999 2222 2 23 899999
Q ss_pred HHhhcccccccCCCCHHHHHHHHHHHHhhcCCCcccccCCCCCchHHHHHHHhhcCCCccHhhHHHHHHhhh--------
Q 045823 55 TFGTSSCLESWSNFSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG-------- 126 (233)
Q Consensus 55 ~c~~~~~IlAW~~~S~EEAArYLEt~K~yEnk~~d~Ik~k~~~dy~s~v~~~LTsIrsVNKTDa~tLls~FG-------- 126 (233)
+..++.++++| |.|||+||+++|+.+++.++++|+++...|+ + .++|++|++|||+|+..+|..||
T Consensus 123 Tt~inti~l~~---svee~sry~~t~~~~~~~s~~iir~~~s~d~-s--~~fl~~i~~Vnksds~~~L~d~g~L~rf~ga 196 (224)
T COG5241 123 TTGINTIYLDY---SVEERSRYFLTLTYHKLYSDYIIRRMQSLDR-S--NEFLILIFIVNKSDSEDTLNDIGKLCRFNGA 196 (224)
T ss_pred hcccceeehhh---hhhHHHHHHHHhHHHhhcCHHHHHhcCCCcc-c--ccceEEEEeeccccHHHHHHHHHHHHHHhcc
Confidence 99988779999 9999999999999999999999999999987 3 89999999999999999999999
Q ss_pred --hhccCCCCCcchh----hhhcCCCCC
Q 045823 127 --EDLSHCPGIGERK----HVVSSHPPI 148 (233)
Q Consensus 127 --EeLs~cPGiG~kK----~~v~~~PFi 148 (233)
+++..+.|||+.| ..++++||+
T Consensus 197 SrdE~e~l~g~g~~ka~~~ieyln~pFm 224 (224)
T COG5241 197 SRDEFELLLGFGFEKAAKYIEYLNLPFM 224 (224)
T ss_pred chhHHHHHHccCHHHHHHHHHHhcccCC
Confidence 8899999999999 678999996
No 4
>PF03834 Rad10: Binding domain of DNA repair protein Ercc1 (rad10/Swi10); InterPro: IPR004579 All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. In yeast, Rad10 works as a heterodimer with Rad1, and is involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts or cross-linking agents. The complex forms an endonuclease which specifically degrades single-stranded DNA. Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA inter-strand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex [].; GO: 0003684 damaged DNA binding, 0004519 endonuclease activity, 0006281 DNA repair, 0005634 nucleus; PDB: 2JNW_A 2JPD_A 2A1I_A.
Probab=99.88 E-value=1.4e-23 Score=156.46 Aligned_cols=41 Identities=51% Similarity=0.977 Sum_probs=33.6
Q ss_pred CCCccccccccCceee-cccccceeecCceeEEEEeehhHHH
Q 045823 1 KGNPLLKHITYVRWAF-ADVVCDYLLGQNSCALYLRLCIYFL 41 (233)
Q Consensus 1 kGNPLLk~IrnVpwEy-~dIvpDYviG~t~cvLFLSLKYH~L 41 (233)
||||||++|||||||| +||+|||++|+++||||||||||+|
T Consensus 10 kGNplL~~i~nv~we~~~~i~~Dy~vg~~~~vLFLSLkYH~L 51 (69)
T PF03834_consen 10 KGNPLLKHIRNVPWEYDSDIVPDYVVGSTTCVLFLSLKYHRL 51 (69)
T ss_dssp TT-CHHHH--SS-EEE----SSSEEEETTEEEEEEEHHHHHH
T ss_pred cCChHHHHHhcCCeEecCCCCCCEEECCeEEEEEEeeeeecC
Confidence 7999999999999999 8999999999999999999999999
No 5
>PRK13766 Hef nuclease; Provisional
Probab=98.62 E-value=8.7e-08 Score=95.28 Aligned_cols=135 Identities=19% Similarity=0.115 Sum_probs=98.8
Q ss_pred cCceeecc-cccceeecCceeE-------EEEeehhHHH----hhhhHHH----------------------HHHHHHHH
Q 045823 11 YVRWAFAD-VVCDYLLGQNSCA-------LYLRLCIYFL----NLLFDNV----------------------LLWVFSTF 56 (233)
Q Consensus 11 nVpwEy~d-IvpDYviG~t~cv-------LFLSLKYH~L----q~L~k~y----------------------L~ELt~~c 56 (233)
.|+.+... -+-||+++..+|| |--||+=.+| .+|.+.| ...|..++
T Consensus 584 g~~~~~~~L~~gDy~~~~~~~vERK~~~Dl~~s~~~~r~~~q~~~l~~~~~~~~lliE~~~~~~~~~~~~~i~~~l~~l~ 663 (773)
T PRK13766 584 GAEVELKTLEVGDYVVSDRVAVERKTAEDFVDSIIDRRLFEQVKDLKRAYERPVLIIEGDLYTIRNIHPNAIRGALASIA 663 (773)
T ss_pred CCEEEEEecCCCCEEccCCeEEEeCcHHHHHHHhhcCcHHHHHHHHHhcCCCcEEEEEcCchhhcccCHHHHHHHHHHHH
Confidence 45555544 3579999988776 3334543444 4554433 46677888
Q ss_pred hhccc--ccccCCCCHHHHHHHHHHHHhhcCCC----cccccCCCCCchHHHHHHHhhcCCCccHhhHHHHHHhhh----
Q 045823 57 GTSSC--LESWSNFSQEECGRYLETIKVYENKP----ADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG---- 126 (233)
Q Consensus 57 ~~~~~--IlAW~~~S~EEAArYLEt~K~yEnk~----~d~Ik~k~~~dy~s~v~~~LTsIrsVNKTDa~tLls~FG---- 126 (233)
+..++ +.+| |++|+|+||+.++..+... .....++...+..++..-.|+.|+||+...+..|+..||
T Consensus 664 ~~~~~~ii~~~---~~~eta~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~ipgig~~~a~~Ll~~fgs~~~ 740 (773)
T PRK13766 664 VDFGIPILFTR---DEEETADLLKVIAKREQEEEKREVSVHGEKKAMTLKEQQEYIVESLPDVGPVLARNLLEHFGSVEA 740 (773)
T ss_pred HHcCceEEEeC---CHHHHHHHHHHHHhhccccCCCCcccccCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHcCCHHH
Confidence 87788 8888 9999999999999988622 234455555555444444799999999999999999999
Q ss_pred ------hhccCCCCCcchh----hhhcCCCCC
Q 045823 127 ------EDLSHCPGIGERK----HVVSSHPPI 148 (233)
Q Consensus 127 ------EeLs~cPGiG~kK----~~v~~~PFi 148 (233)
++|..+||+|+++ ..+++.||.
T Consensus 741 i~~as~~~L~~i~Gig~~~a~~i~~~~~~~~~ 772 (773)
T PRK13766 741 VMTASEEELMEVEGIGEKTAKRIREVVTSEYK 772 (773)
T ss_pred HHhCCHHHHHhCCCCCHHHHHHHHHHHhhhhc
Confidence 7899999999988 567777764
No 6
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=97.11 E-value=0.0013 Score=60.11 Aligned_cols=140 Identities=18% Similarity=0.087 Sum_probs=96.0
Q ss_pred cCceeecc-cccceeecCceeEE-------EEeehhHHH----hhhhHHH------------------------HHHHHH
Q 045823 11 YVRWAFAD-VVCDYLLGQNSCAL-------YLRLCIYFL----NLLFDNV------------------------LLWVFS 54 (233)
Q Consensus 11 nVpwEy~d-IvpDYviG~t~cvL-------FLSLKYH~L----q~L~k~y------------------------L~ELt~ 54 (233)
.|..+..- -+-||+++..+||= --||.=-+| ++|.+.| ..-|.-
T Consensus 49 gv~v~~~~LevGDYvvs~~v~VERKs~~Dfv~Si~dgRlfeQ~~rL~~~y~rpvliVegd~~~~~~~~i~~~av~~al~s 128 (254)
T COG1948 49 GVKVEVRTLEVGDYVVSDDVIVERKSISDFVSSIIDGRLFEQAKRLKKSYERPVLIVEGDDSFSRRPKIHPNAVRGALAS 128 (254)
T ss_pred CCeEEEEecccccEEeecCeeEEeccHHHHHHHHhcchHHHHHHHHHhcCCccEEEEEcccccccccccCHHHHHHHHHH
Confidence 34445544 46899999988873 224443344 4565544 111222
Q ss_pred HHhhcccccccCCCCHHHHHHHHHHHHhhcC---CCccccc-CCCCCchHHHHHHHhhcCCCccHhhHHHHHHhhh----
Q 045823 55 TFGTSSCLESWSNFSQEECGRYLETIKVYEN---KPADLTQ-GQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG---- 126 (233)
Q Consensus 55 ~c~~~~~IlAW~~~S~EEAArYLEt~K~yEn---k~~d~Ik-~k~~~dy~s~v~~~LTsIrsVNKTDa~tLls~FG---- 126 (233)
+.+-.++-+-||. |++|-+.+|..+..-++ +..=... .+...++.++-...|.+++||-...|..|+..||
T Consensus 129 ~~vdfg~~vi~t~-~~~~Ta~~i~~la~req~e~~r~v~~~~~~~~~t~~e~q~~il~s~pgig~~~a~~ll~~fgS~~~ 207 (254)
T COG1948 129 LAVDFGLPVIWTR-SPEETAELIHELARREQEERKRSVNPHGKKKAKTLKELQLYILESIPGIGPKLAERLLKKFGSVED 207 (254)
T ss_pred HHhhcCceEEEeC-CHHHHHHHHHHHHHHHHHhccccccccccccccchHHHHHHHHHcCCCccHHHHHHHHHHhcCHHH
Confidence 2222234445722 69999999999998666 4441112 2234578888999999999999999999999999
Q ss_pred ------hhccCCCCCcchh----hhhcCCCCCCCC
Q 045823 127 ------EDLSHCPGIGERK----HVVSSHPPIPET 151 (233)
Q Consensus 127 ------EeLs~cPGiG~kK----~~v~~~PFi~~~ 151 (233)
++|....|+|++| +++|-.|+.-.+
T Consensus 208 ~~tas~~eL~~v~gig~k~A~~I~~~~~t~~~~~~ 242 (254)
T COG1948 208 VLTASEEELMKVKGIGEKKAREIYRFLRTEYKLIE 242 (254)
T ss_pred HhhcCHHHHHHhcCccHHHHHHHHHHHhchhhhhc
Confidence 8899999999999 788888877433
No 7
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=96.61 E-value=0.0054 Score=63.69 Aligned_cols=125 Identities=18% Similarity=0.139 Sum_probs=84.8
Q ss_pred ccceeecCceeE-------EEEeehhHHH----hhhhHHH----------------H--------------H----HHHH
Q 045823 20 VCDYLLGQNSCA-------LYLRLCIYFL----NLLFDNV----------------L--------------L----WVFS 54 (233)
Q Consensus 20 vpDYviG~t~cv-------LFLSLKYH~L----q~L~k~y----------------L--------------~----ELt~ 54 (233)
+.||++++.+|| |.=||.=-+| ++|...| + + .|..
T Consensus 618 VGDYilS~~i~VERKSi~Dli~Sl~~gRL~~Q~~~m~~~Y~~PvLLIE~d~~~~f~l~~~~~~~~~~~~~~~~i~~~L~~ 697 (814)
T TIGR00596 618 VGDYILTPDICVERKSISDLIGSLNNGRLYNQCEKMLRYYAYPVLLIEFDQNKSFSLEPRNDLSQEISSVNNDIQQKLAL 697 (814)
T ss_pred cccEEecCCeEEEeCcHHHHHHHHhcchHHHHHHHHHHhcCCcEEEEEecCCcccccccccccccccCccHHHHHHHHHH
Confidence 569999999998 4445554455 4555444 1 1 2333
Q ss_pred HHhhc-ccccccCCCCHHHHHHHHHHHHhhcCCCcc----cccC-----CCCCchHHHHHHHhhcCCCccHhhHHHHHHh
Q 045823 55 TFGTS-SCLESWSNFSQEECGRYLETIKVYENKPAD----LTQG-----QMDTDYLSRLTHALTSVRSVNKTDVVNLGST 124 (233)
Q Consensus 55 ~c~~~-~~IlAW~~~S~EEAArYLEt~K~yEnk~~d----~Ik~-----k~~~dy~s~v~~~LTsIrsVNKTDa~tLls~ 124 (233)
+++.. ++=+-| .-|++|.|..|..+|.-+..|-. .|.. .....+.....++|.+++||+--.|..|+.+
T Consensus 698 L~l~fP~l~Iiw-S~s~~~TA~i~~~Lk~~e~epd~~~~v~i~~~~~~~~k~~~~~~~~q~~L~~lPgI~~~~a~~ll~~ 776 (814)
T TIGR00596 698 LTLHFPKLRIIW-SSSPYATAEIFEELKLGKEEPDPATAAALGSDENTTAEGLKFNDGPQDFLLKLPGVTKKNYRNLRKK 776 (814)
T ss_pred HHHhcCCceEEe-cCCHHHHHHHHHHHHhcCCCCCcccceecCcccccccccccccHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 44434 552236 35899999999999998875311 1220 1112356677889999999999999999999
Q ss_pred hh----------hhccCCCCCc-chh----hhhcCCCC
Q 045823 125 FG----------EDLSHCPGIG-ERK----HVVSSHPP 147 (233)
Q Consensus 125 FG----------EeLs~cPGiG-~kK----~~v~~~PF 147 (233)
|| ++|.. +|| +++ +++|+.++
T Consensus 777 f~si~~l~~as~eeL~~--~iG~~~~A~~i~~fl~~~~ 812 (814)
T TIGR00596 777 VKSIRELAKLSQNELNE--LIGDEEAAKRLYDFLRTEK 812 (814)
T ss_pred cCCHHHHHhCCHHHHHH--HhCCHHHHHHHHHHhcccc
Confidence 99 67766 599 555 67888774
No 8
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=96.60 E-value=0.00075 Score=48.81 Aligned_cols=31 Identities=35% Similarity=0.612 Sum_probs=26.2
Q ss_pred cCCCccHhhHHHHHHhhh----------hhccCCCCCcchh
Q 045823 109 SVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK 139 (233)
Q Consensus 109 sIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK 139 (233)
.|++|-.+.|..|+..|| |+|+.+||||++.
T Consensus 7 GI~~VG~~~ak~L~~~f~sl~~l~~a~~e~L~~i~gIG~~~ 47 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSLEALMNASVEELSAIPGIGPKI 47 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCHHHHCC--HHHHCTSTT--HHH
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHHcCHHHHhccCCcCHHH
Confidence 799999999999999999 9999999999998
No 9
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=96.48 E-value=0.0027 Score=44.84 Aligned_cols=37 Identities=27% Similarity=0.465 Sum_probs=34.2
Q ss_pred HHHHhhcCCCccHhhHHHHHHh-hh----------hhccCCCCCcchh
Q 045823 103 LTHALTSVRSVNKTDVVNLGST-FG----------EDLSHCPGIGERK 139 (233)
Q Consensus 103 v~~~LTsIrsVNKTDa~tLls~-FG----------EeLs~cPGiG~kK 139 (233)
+.+.|..|+||....+.+|... |+ ++|..+||||+++
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~ 50 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKT 50 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHH
T ss_pred HHHhhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHH
Confidence 5678999999999999999999 66 8999999999998
No 10
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=95.84 E-value=0.0021 Score=57.21 Aligned_cols=77 Identities=21% Similarity=0.362 Sum_probs=61.0
Q ss_pred CCCccccccccCcee-----ec------ccccceeecCceeEEEEeehhHHH------hhhh-----HHH----------
Q 045823 1 KGNPLLKHITYVRWA-----FA------DVVCDYLLGQNSCALYLRLCIYFL------NLLF-----DNV---------- 48 (233)
Q Consensus 1 kGNPLLk~IrnVpwE-----y~------dIvpDYviG~t~cvLFLSLKYH~L------q~L~-----k~y---------- 48 (233)
+-||||.|+.-..|. +- -|+-||.+-. ...+|+.++||.+ ++.+ +.|
T Consensus 100 k~r~LL~hvd~~N~~asIqElv~Tt~inti~l~~svee-~sry~~t~~~~~~~s~~iir~~~s~d~s~~fl~~i~~Vnks 178 (224)
T COG5241 100 KERPLLNHVDSTNWRASIQELVSTTGINTIYLDYSVEE-RSRYFLTLTYHKLYSDYIIRRMQSLDRSNEFLILIFIVNKS 178 (224)
T ss_pred cccceeeeeccccHHHHHHHHHHhcccceeehhhhhhH-HHHHHHHhHHHhhcCHHHHHhcCCCcccccceEEEEeeccc
Confidence 358999999888888 32 2678998865 6689999999999 2221 222
Q ss_pred -----HHHHHHHHhhcc-----c--ccccCCCCHHHHHHHHHHHH
Q 045823 49 -----LLWVFSTFGTSS-----C--LESWSNFSQEECGRYLETIK 81 (233)
Q Consensus 49 -----L~ELt~~c~~~~-----~--IlAW~~~S~EEAArYLEt~K 81 (233)
|.++.++|.++. + +++| .++.|++|||.+.
T Consensus 179 ds~~~L~d~g~L~rf~gaSrdE~e~l~g~---g~~ka~~~ieyln 220 (224)
T COG5241 179 DSEDTLNDIGKLCRFNGASRDEFELLLGF---GFEKAAKYIEYLN 220 (224)
T ss_pred cHHHHHHHHHHHHHHhccchhHHHHHHcc---CHHHHHHHHHHhc
Confidence 889999999887 5 9999 9999999999764
No 11
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=95.22 E-value=0.013 Score=55.75 Aligned_cols=45 Identities=33% Similarity=0.475 Sum_probs=40.0
Q ss_pred CCCchHHHHHHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchh
Q 045823 95 MDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK 139 (233)
Q Consensus 95 ~~~dy~s~v~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK 139 (233)
.|.....+-...|++|++|+|..|.+|+.+|| ++|..++|||+.+
T Consensus 277 ld~~v~prGyRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~r 331 (352)
T PRK13482 277 LDTPVSPRGYRLLSKIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVR 331 (352)
T ss_pred cccccCCcHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHH
Confidence 34445566778999999999999999999999 8999999999999
No 12
>KOG0442 consensus Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair]
Probab=87.74 E-value=1.4 Score=46.75 Aligned_cols=76 Identities=25% Similarity=0.312 Sum_probs=57.8
Q ss_pred ccccCCCCHHHHHHHHHHHHhhcCCCc-c-cc-cCC------CCCchHHHHHHHhhcCCCccHhhHHHHHHhhh------
Q 045823 62 LESWSNFSQEECGRYLETIKVYENKPA-D-LT-QGQ------MDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG------ 126 (233)
Q Consensus 62 IlAW~~~S~EEAArYLEt~K~yEnk~~-d-~I-k~k------~~~dy~s~v~~~LTsIrsVNKTDa~tLls~FG------ 126 (233)
-|-| .-|+.+-|..++.+|.-+..|- + .| -+. ....|.+...++|-+++||++.+..+|+..|+
T Consensus 770 RilW-S~Sp~~Ta~if~eLKl~~~epD~~~Ai~lg~~~~~~~~~~~~n~~~~~fll~lPgVs~~n~~~l~~k~ks~~~La 848 (892)
T KOG0442|consen 770 RILW-SSSPLATAEIFEELKLSEPEPDPARAISLGTDEEGNSESESYNSSALDFLLSLPGVSYINYRNLRHKFKSLKELA 848 (892)
T ss_pred EEEe-cCchhHHHHHHHHHhhcCCCCCcchheeecccccccccccccCchHHHHHhcCCCccHHHHHHHHHHhhHHHHHH
Confidence 3447 5589999999999999998872 1 22 122 23457888999999999999999999999999
Q ss_pred ----hhccCCCCCcchh
Q 045823 127 ----EDLSHCPGIGERK 139 (233)
Q Consensus 127 ----EeLs~cPGiG~kK 139 (233)
++|+.+=|. +.+
T Consensus 849 ~sS~~el~el~~~-~~~ 864 (892)
T KOG0442|consen 849 NSSQEELSELLGV-HEN 864 (892)
T ss_pred hCcHHHHHHHhcc-hHH
Confidence 666666554 444
No 13
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=87.40 E-value=0.47 Score=48.34 Aligned_cols=47 Identities=34% Similarity=0.541 Sum_probs=39.3
Q ss_pred HHHHHHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchh----hhhcCCCC
Q 045823 100 LSRLTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK----HVVSSHPP 147 (233)
Q Consensus 100 ~s~v~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK----~~v~~~PF 147 (233)
+.++..+| .|++|-...|..|+..|| ++|..+||||++. ...|+.|.
T Consensus 494 l~r~L~aL-gIpgVG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~~I~~ff~~~~ 554 (652)
T TIGR00575 494 LARLLFAL-GIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVGPKVAESIVNFFHDPN 554 (652)
T ss_pred HHHHHhhc-cCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHhhhh
Confidence 45666666 899999999999999999 7899999999999 45666654
No 14
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=86.92 E-value=0.74 Score=33.09 Aligned_cols=35 Identities=31% Similarity=0.527 Sum_probs=31.2
Q ss_pred HHhhc-CCCccHhhHHHHHHh---hh-----hhccCCCCCcchh
Q 045823 105 HALTS-VRSVNKTDVVNLGST---FG-----EDLSHCPGIGERK 139 (233)
Q Consensus 105 ~~LTs-IrsVNKTDa~tLls~---FG-----EeLs~cPGiG~kK 139 (233)
+.|.. +.+|...-|..|+.. || ++|..+||||+++
T Consensus 16 ~~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~v~gi~~~~ 59 (69)
T TIGR00426 16 EELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVPGIGNSL 59 (69)
T ss_pred HHHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHcCCCCCHHH
Confidence 45666 999999999999998 66 9999999999998
No 15
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=86.90 E-value=0.56 Score=42.72 Aligned_cols=34 Identities=24% Similarity=0.432 Sum_probs=32.3
Q ss_pred HhhcCCCccHhhHHHHHHh-hh----------hhccCCCCCcchh
Q 045823 106 ALTSVRSVNKTDVVNLGST-FG----------EDLSHCPGIGERK 139 (233)
Q Consensus 106 ~LTsIrsVNKTDa~tLls~-FG----------EeLs~cPGiG~kK 139 (233)
.|..|+||-+..+..|+.. || ++|..+||||+.+
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~ 48 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNAL 48 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHH
Confidence 4788999999999999999 99 8999999999999
No 16
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=86.43 E-value=0.74 Score=39.78 Aligned_cols=37 Identities=30% Similarity=0.442 Sum_probs=33.5
Q ss_pred HHHHhhcCCCccHhhHHHHHHhhh-------------hhccCCCCCcchh
Q 045823 103 LTHALTSVRSVNKTDVVNLGSTFG-------------EDLSHCPGIGERK 139 (233)
Q Consensus 103 v~~~LTsIrsVNKTDa~tLls~FG-------------EeLs~cPGiG~kK 139 (233)
+...|..|+||=.-=|..|++.|| ++|..+||||+++
T Consensus 71 ~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~ 120 (192)
T PRK00116 71 LFRLLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKT 120 (192)
T ss_pred HHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHH
Confidence 356788999999999999999999 5789999999999
No 17
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=86.42 E-value=0.66 Score=44.14 Aligned_cols=70 Identities=23% Similarity=0.300 Sum_probs=44.5
Q ss_pred CHHHHHHHHHHHHhhcCCCcccc-----cCCCCCchHHHHHHH--hhcCCCccHhhHHHHH--Hhhh-------------
Q 045823 69 SQEECGRYLETIKVYENKPADLT-----QGQMDTDYLSRLTHA--LTSVRSVNKTDVVNLG--STFG------------- 126 (233)
Q Consensus 69 S~EEAArYLEt~K~yEnk~~d~I-----k~k~~~dy~s~v~~~--LTsIrsVNKTDa~tLl--s~FG------------- 126 (233)
-++|-|.|+|.--.-.-|+.+.. .+..+.| ...+.+. +|.++||+|.=|.-|- -..|
T Consensus 11 ~le~iA~~me~~Gen~fk~~aYr~Aa~sle~~~e~-~~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~~le~lk~~~P 89 (326)
T COG1796 11 LLERIADYMELEGENPFKIRAYRKAAQSLENLTED-LEEIEERGRLTELPGIGKGIAEKISEYLDTGEVKKLEALKKEVP 89 (326)
T ss_pred HHHHHHHHHHhcCCCccchHHHHHHHHhhhhcccc-hHHHHhhcccCCCCCccHHHHHHHHHHHHcCccHHHHHHHHhCC
Confidence 45677777776322222332222 1222223 4557788 9999999998765543 3333
Q ss_pred ---hhccCCCCCcchh
Q 045823 127 ---EDLSHCPGIGERK 139 (233)
Q Consensus 127 ---EeLs~cPGiG~kK 139 (233)
++|..+||+||+|
T Consensus 90 ~gl~~Ll~v~GlGpkK 105 (326)
T COG1796 90 EGLEPLLKVPGLGPKK 105 (326)
T ss_pred cchHHHhhCCCCCcHH
Confidence 8999999999999
No 18
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.83 E-value=0.77 Score=40.04 Aligned_cols=38 Identities=29% Similarity=0.385 Sum_probs=34.7
Q ss_pred HHHHHhhcCCCccHhhHHHHHHhhh-------------hhccCCCCCcchh
Q 045823 102 RLTHALTSVRSVNKTDVVNLGSTFG-------------EDLSHCPGIGERK 139 (233)
Q Consensus 102 ~v~~~LTsIrsVNKTDa~tLls~FG-------------EeLs~cPGiG~kK 139 (233)
.+-..|.+|.||--.=|..+|++|+ ..|..+||||++.
T Consensus 70 ~lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKt 120 (194)
T PRK14605 70 SLFETLIDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKT 120 (194)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHH
Confidence 3667889999999999999999999 6789999999999
No 19
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=85.19 E-value=1.9 Score=44.24 Aligned_cols=46 Identities=30% Similarity=0.447 Sum_probs=38.5
Q ss_pred HHHHHHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchh----hhhcCCC
Q 045823 100 LSRLTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK----HVVSSHP 146 (233)
Q Consensus 100 ~s~v~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK----~~v~~~P 146 (233)
+.++.-+| .|++|-+..|..|+..|+ ++|..+||||++. ...|+.|
T Consensus 507 l~R~l~al-gi~~IG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~sI~~ff~~~ 566 (665)
T PRK07956 507 LARFLYAL-GIRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIVEFFAVE 566 (665)
T ss_pred HHHhhHhh-hccCcCHHHHHHHHHHcCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhh
Confidence 45667777 799999999999999999 8899999999999 4555554
No 20
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=84.73 E-value=1.1 Score=36.29 Aligned_cols=36 Identities=19% Similarity=0.350 Sum_probs=32.7
Q ss_pred HHHhhcCCCccHhhHHHHHHhhh--------hhccCCCCCcchh
Q 045823 104 THALTSVRSVNKTDVVNLGSTFG--------EDLSHCPGIGERK 139 (233)
Q Consensus 104 ~~~LTsIrsVNKTDa~tLls~FG--------EeLs~cPGiG~kK 139 (233)
.+-|.+++||...-|..|+..|. ++|..+||||+++
T Consensus 67 ~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~V~GIg~k~ 110 (120)
T TIGR01259 67 LEELQALPGIGPAKAKAIIEYREENGAFKSVDDLTKVSGIGEKS 110 (120)
T ss_pred HHHHhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHcCCCCCHHH
Confidence 56788999999999999999983 9999999999988
No 21
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=84.54 E-value=0.84 Score=47.25 Aligned_cols=37 Identities=35% Similarity=0.539 Sum_probs=34.9
Q ss_pred HHHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchh
Q 045823 103 LTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK 139 (233)
Q Consensus 103 v~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK 139 (233)
+...|..|+||-+..+..|+..|| ++|..+||||+++
T Consensus 635 ~~s~L~~IPGIGpkr~k~LL~~FGSle~I~~AS~eELa~V~Gig~k~ 681 (694)
T PRK14666 635 LTGELQRVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPAR 681 (694)
T ss_pred hHhHHhhCCCCCHHHHHHHHHHhCCHHHHHhcCHHHHHhcCCcCHHH
Confidence 567899999999999999999999 8899999999998
No 22
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=83.23 E-value=0.44 Score=30.29 Aligned_cols=13 Identities=46% Similarity=0.900 Sum_probs=11.4
Q ss_pred hhccCCCCCcchh
Q 045823 127 EDLSHCPGIGERK 139 (233)
Q Consensus 127 EeLs~cPGiG~kK 139 (233)
|+|..+||||++.
T Consensus 11 eeL~~lpGIG~~t 23 (30)
T PF00633_consen 11 EELMKLPGIGPKT 23 (30)
T ss_dssp HHHHTSTT-SHHH
T ss_pred HHHHhCCCcCHHH
Confidence 8999999999998
No 23
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=83.19 E-value=0.94 Score=45.71 Aligned_cols=37 Identities=32% Similarity=0.540 Sum_probs=34.8
Q ss_pred HHHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchh
Q 045823 103 LTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK 139 (233)
Q Consensus 103 v~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK 139 (233)
+...|+.|+||-..-+..|+..|| ++|..+||||++.
T Consensus 541 ~~s~L~~IpGIG~k~~k~Ll~~FgS~~~i~~As~eeL~~v~Gig~~~ 587 (598)
T PRK00558 541 LTSALDDIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKL 587 (598)
T ss_pred hhhhHhhCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCcCHHH
Confidence 567899999999999999999999 8999999999988
No 24
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=82.54 E-value=1.9 Score=36.37 Aligned_cols=39 Identities=21% Similarity=0.352 Sum_probs=29.6
Q ss_pred HHHhhcCCCccHhhHHHHHHh--hh--hhccCCCCCcchhhhh
Q 045823 104 THALTSVRSVNKTDVVNLGST--FG--EDLSHCPGIGERKHVV 142 (233)
Q Consensus 104 ~~~LTsIrsVNKTDa~tLls~--FG--EeLs~cPGiG~kK~~v 142 (233)
...|..++||=-+=|..++.+ |. |||..+||||+++.++
T Consensus 60 ~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V~GIgekqk~~ 102 (132)
T PRK02515 60 VRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNLPGLSERQKEL 102 (132)
T ss_pred HHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcCCCCCHHHHHH
Confidence 445777899999999998852 22 9999999999976333
No 25
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=81.14 E-value=2.2 Score=30.57 Aligned_cols=36 Identities=25% Similarity=0.469 Sum_probs=26.7
Q ss_pred HHHhhcCCCccHhhHHHHHHhh---h-----hhccCCCCCcchh
Q 045823 104 THALTSVRSVNKTDVVNLGSTF---G-----EDLSHCPGIGERK 139 (233)
Q Consensus 104 ~~~LTsIrsVNKTDa~tLls~F---G-----EeLs~cPGiG~kK 139 (233)
.+-|.++++|+...|..++.-- | ++|..+||||+.+
T Consensus 13 ~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~ 56 (65)
T PF12836_consen 13 AEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEVPGIGPKT 56 (65)
T ss_dssp HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGSTT--HHH
T ss_pred HHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHH
Confidence 4557889999999999999654 3 9999999999987
No 26
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.43 E-value=1.9 Score=37.60 Aligned_cols=38 Identities=21% Similarity=0.436 Sum_probs=34.1
Q ss_pred HHHHHhhcCCCccHhhHHHHHHhhh-------------hhccCCCCCcchh
Q 045823 102 RLTHALTSVRSVNKTDVVNLGSTFG-------------EDLSHCPGIGERK 139 (233)
Q Consensus 102 ~v~~~LTsIrsVNKTDa~tLls~FG-------------EeLs~cPGiG~kK 139 (233)
.+-..|.+|.||-=.=|..+|+++. ..|..+||||+|-
T Consensus 70 ~lF~~Li~VsGIGpK~Al~ILs~~~~~el~~aI~~~D~~~L~~vpGIGkKt 120 (183)
T PRK14601 70 KMFEMLLKVNGIGANTAMAVCSSLDVNSFYKALSLGDESVLKKVPGIGPKS 120 (183)
T ss_pred HHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHH
Confidence 3567789999999999999999998 6789999999988
No 27
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.77 E-value=2.5 Score=37.45 Aligned_cols=38 Identities=21% Similarity=0.306 Sum_probs=34.1
Q ss_pred HHHHHhhcCCCccHhhHHHHHHhhh-------------hhccCCCCCcchh
Q 045823 102 RLTHALTSVRSVNKTDVVNLGSTFG-------------EDLSHCPGIGERK 139 (233)
Q Consensus 102 ~v~~~LTsIrsVNKTDa~tLls~FG-------------EeLs~cPGiG~kK 139 (233)
.+-..|.+|.||-=.=|..+|+++. ..|..+||||++-
T Consensus 69 ~lF~~LisVsGIGPK~ALaILs~~~~~el~~aI~~~D~~~L~~vpGIGkKt 119 (196)
T PRK13901 69 EVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDREDIELISKVKGIGNKM 119 (196)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHH
Confidence 3667788999999999999999988 7799999999998
No 28
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.34 E-value=3.1 Score=36.62 Aligned_cols=38 Identities=24% Similarity=0.384 Sum_probs=34.3
Q ss_pred HHHHHhhcCCCccHhhHHHHHHhhh-------------hhccCCCCCcchh
Q 045823 102 RLTHALTSVRSVNKTDVVNLGSTFG-------------EDLSHCPGIGERK 139 (233)
Q Consensus 102 ~v~~~LTsIrsVNKTDa~tLls~FG-------------EeLs~cPGiG~kK 139 (233)
.+-..|.+|.||-=-=|..+|++++ ..|..+||||++.
T Consensus 71 ~lF~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~ipGIGkKt 121 (203)
T PRK14602 71 QTFIVLISISKVGAKTALAILSQFRPDDLRRLVAEEDVAALTRVSGIGKKT 121 (203)
T ss_pred HHHHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHhCCHHHHhcCCCcCHHH
Confidence 3567789999999999999999998 7799999999998
No 29
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.04 E-value=2.7 Score=36.69 Aligned_cols=38 Identities=29% Similarity=0.389 Sum_probs=34.1
Q ss_pred HHHHHhhcCCCccHhhHHHHHHhhh-------------hhccCCCCCcchh
Q 045823 102 RLTHALTSVRSVNKTDVVNLGSTFG-------------EDLSHCPGIGERK 139 (233)
Q Consensus 102 ~v~~~LTsIrsVNKTDa~tLls~FG-------------EeLs~cPGiG~kK 139 (233)
.+-..|.+|.||-=.=|..+|+++. ..|..+||||++-
T Consensus 70 ~lF~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~~D~~~L~~vpGIGkKt 120 (188)
T PRK14606 70 ELFLSLTKVSRLGPKTALKIISNEDAETLVTMIASQDVEGLSKLPGISKKT 120 (188)
T ss_pred HHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHH
Confidence 3667789999999999999999998 6799999999998
No 30
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=74.55 E-value=2.8 Score=36.79 Aligned_cols=38 Identities=24% Similarity=0.287 Sum_probs=34.2
Q ss_pred HHHHHhhcCCCccHhhHHHHHHhhh-------------hhccCCCCCcchh
Q 045823 102 RLTHALTSVRSVNKTDVVNLGSTFG-------------EDLSHCPGIGERK 139 (233)
Q Consensus 102 ~v~~~LTsIrsVNKTDa~tLls~FG-------------EeLs~cPGiG~kK 139 (233)
.+-..|.+|.||-=.=|..+|++++ ..|..+||+|++.
T Consensus 69 ~lF~~L~~V~GIGpK~AL~iLs~~~~~~l~~aI~~~D~~~L~kvpGIGkKt 119 (197)
T PRK14603 69 ELFELLLGVSGVGPKLALALLSALPPALLARALLEGDARLLTSASGVGKKL 119 (197)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHH
Confidence 3567788999999999999999988 6799999999998
No 31
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=71.89 E-value=3.9 Score=35.57 Aligned_cols=37 Identities=24% Similarity=0.409 Sum_probs=33.0
Q ss_pred HHHHhhcCCCccHhhHHHHHHhhh-------------hhccCCCCCcchh
Q 045823 103 LTHALTSVRSVNKTDVVNLGSTFG-------------EDLSHCPGIGERK 139 (233)
Q Consensus 103 v~~~LTsIrsVNKTDa~tLls~FG-------------EeLs~cPGiG~kK 139 (233)
+-..|.+|+||---=|..||+.|+ ..|..+||||++.
T Consensus 70 lF~~L~~V~GIGpK~Al~iL~~~~~~el~~aI~~~d~~~L~~ipGiGkKt 119 (191)
T TIGR00084 70 LFKELIKVNGVGPKLALAILSNMSPEEFVYAIETEEVKALVKIPGVGKKT 119 (191)
T ss_pred HHHHHhCCCCCCHHHHHHHHhcCCHHHHHHHHHhCCHHHHHhCCCCCHHH
Confidence 566788999999999999999998 5688999999999
No 32
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.33 E-value=4.2 Score=35.64 Aligned_cols=38 Identities=32% Similarity=0.438 Sum_probs=33.7
Q ss_pred HHHHHhhcCCCccHhhHHHHHHhhh-------------hhccCCCCCcchh
Q 045823 102 RLTHALTSVRSVNKTDVVNLGSTFG-------------EDLSHCPGIGERK 139 (233)
Q Consensus 102 ~v~~~LTsIrsVNKTDa~tLls~FG-------------EeLs~cPGiG~kK 139 (233)
.+-..|.+|.||-=.=|..+|+++. ..|..+||+|++-
T Consensus 70 ~lF~~Li~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~~~L~kvpGIGkKt 120 (195)
T PRK14604 70 QLFELLIGVSGVGPKAALNLLSSGTPDELQLAIAGGDVARLARVPGIGKKT 120 (195)
T ss_pred HHHHHHhCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHH
Confidence 3567788999999999999999987 7799999999998
No 33
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.26 E-value=5 Score=34.96 Aligned_cols=37 Identities=27% Similarity=0.350 Sum_probs=33.0
Q ss_pred HHHHHhhcCCCccHhhHHHHHHhhh-------------hhccCCCCCcchh
Q 045823 102 RLTHALTSVRSVNKTDVVNLGSTFG-------------EDLSHCPGIGERK 139 (233)
Q Consensus 102 ~v~~~LTsIrsVNKTDa~tLls~FG-------------EeLs~cPGiG~kK 139 (233)
.+-..|.+|.||-=-=|..+|++|+ ..| .+||+|++.
T Consensus 70 ~lF~~LisV~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L-~vpGIGkKt 119 (186)
T PRK14600 70 DCLRMLVKVSGVNYKTAMSILSKLTPEQLFSAIVNEDKAAL-KVNGIGEKL 119 (186)
T ss_pred HHHHHHhCcCCcCHHHHHHHHccCCHHHHHHHHHcCCHhhe-ECCCCcHHH
Confidence 3567788999999999999999998 668 999999998
No 34
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=67.05 E-value=4.7 Score=40.79 Aligned_cols=37 Identities=35% Similarity=0.593 Sum_probs=33.8
Q ss_pred HHHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchh
Q 045823 103 LTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK 139 (233)
Q Consensus 103 v~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK 139 (233)
+...|+.|+||-..-+..|+..|| ++|..+||+|++.
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~FGS~~~I~~As~eeL~~vpGi~~~~ 569 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRFGSVEGVREASVEDLRDVPGVGEKT 569 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHH
Confidence 457899999999999999999999 8999999999876
No 35
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=66.56 E-value=3.7 Score=34.64 Aligned_cols=21 Identities=19% Similarity=0.274 Sum_probs=15.1
Q ss_pred hhccCCCCCcchh-hh-hcCCCC
Q 045823 127 EDLSHCPGIGERK-HV-VSSHPP 147 (233)
Q Consensus 127 EeLs~cPGiG~kK-~~-v~~~PF 147 (233)
++|..+|||||+| .+ +-+-||
T Consensus 61 ~el~~lpGigP~~A~~IV~nGpf 83 (132)
T PRK02515 61 RAFRQFPGMYPTLAGKIVKNAPY 83 (132)
T ss_pred HHHHHCCCCCHHHHHHHHHCCCC
Confidence 6778899999999 33 334444
No 36
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=65.30 E-value=6.7 Score=40.39 Aligned_cols=40 Identities=30% Similarity=0.459 Sum_probs=35.9
Q ss_pred HHHHHHHhhc--CCCccHhhHHHHHHhhh-----------hhccCCCCCcchh
Q 045823 100 LSRLTHALTS--VRSVNKTDVVNLGSTFG-----------EDLSHCPGIGERK 139 (233)
Q Consensus 100 ~s~v~~~LTs--IrsVNKTDa~tLls~FG-----------EeLs~cPGiG~kK 139 (233)
.+.++.+|.+ |+||=+.-|..|...|| +.|..+||||++|
T Consensus 77 ~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~ 129 (720)
T TIGR01448 77 KEGIVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKAN 129 (720)
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHH
Confidence 3457889986 99999999999999999 6799999999999
No 37
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=65.09 E-value=4.6 Score=40.98 Aligned_cols=36 Identities=8% Similarity=0.244 Sum_probs=31.6
Q ss_pred HHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchh
Q 045823 104 THALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK 139 (233)
Q Consensus 104 ~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK 139 (233)
...|..|+||=+.=...||.+|| |+|+.+||||++.
T Consensus 513 ~s~L~~I~GiG~kr~~~LL~~Fgs~~~I~~As~eeL~~v~gi~~~~ 558 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKILKSLGTYKDILLLNEDEIAEKMKINIKM 558 (574)
T ss_pred ccccccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHhCCCCCHHH
Confidence 34677899999999999999999 9999999999776
No 38
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=62.25 E-value=6.9 Score=40.48 Aligned_cols=39 Identities=31% Similarity=0.438 Sum_probs=34.0
Q ss_pred HHHHHHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchh
Q 045823 100 LSRLTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK 139 (233)
Q Consensus 100 ~s~v~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK 139 (233)
+.+++-+| .|++|-+.-|..|+..|| ++|..++|||++.
T Consensus 524 l~r~l~AL-gIpgIG~~~ak~L~~~F~si~~L~~As~eeL~~i~GIG~k~ 572 (689)
T PRK14351 524 LADFLVAL-GIPEVGPTTARNLAREFGTFEAIMDADEEALRAVDDVGPTV 572 (689)
T ss_pred HHHHHHHc-CCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhccCCcCHHH
Confidence 45555555 589999999999999999 7899999999999
No 39
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=57.65 E-value=5.9 Score=35.30 Aligned_cols=24 Identities=46% Similarity=0.634 Sum_probs=20.3
Q ss_pred hhHHHHHHhh---h----------hhccCCCCCcchh
Q 045823 116 TDVVNLGSTF---G----------EDLSHCPGIGERK 139 (233)
Q Consensus 116 TDa~tLls~F---G----------EeLs~cPGiG~kK 139 (233)
.=|..|+..| | ++|..++|||+.|
T Consensus 36 ~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~ak 72 (218)
T TIGR00608 36 SLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAK 72 (218)
T ss_pred HHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHH
Confidence 3456677899 7 8999999999999
No 40
>PRK00024 hypothetical protein; Reviewed
Probab=57.40 E-value=5.9 Score=35.23 Aligned_cols=23 Identities=39% Similarity=0.524 Sum_probs=19.7
Q ss_pred hHHHHHHhhh----------hhccCCCCCcchh
Q 045823 117 DVVNLGSTFG----------EDLSHCPGIGERK 139 (233)
Q Consensus 117 Da~tLls~FG----------EeLs~cPGiG~kK 139 (233)
=|..|+..|| ++|..++|||+.|
T Consensus 46 LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~ak 78 (224)
T PRK00024 46 LARELLQRFGSLRGLLDASLEELQSIKGIGPAK 78 (224)
T ss_pred HHHHHHHHcCCHHHHHhCCHHHHhhccCccHHH
Confidence 3556668998 8999999999999
No 41
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=56.84 E-value=10 Score=38.82 Aligned_cols=48 Identities=21% Similarity=0.268 Sum_probs=37.0
Q ss_pred HHHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchh----hhhcCCCCCCCCC
Q 045823 103 LTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK----HVVSSHPPIPETP 152 (233)
Q Consensus 103 v~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK----~~v~~~PFi~~~~ 152 (233)
+...|..|+||-+.=+..||..|| ++|+.+ ||.++ ..+|+.+|-...|
T Consensus 550 ~~S~L~~IpGIG~kr~~~LL~~FgSi~~I~~As~eeL~~v--i~~k~A~~I~~~l~~~~~~~~~ 611 (624)
T PRK14669 550 RTSELLEIPGVGAKTVQRLLKHFGSLERVRAATETQLAAV--VGRAAAEAIIAHFTTEEAAPEP 611 (624)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHHH--hCHHHHHHHHHHhcCcCCCcch
Confidence 567788999999999999999999 788887 88777 5666655544333
No 42
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=56.67 E-value=4.8 Score=24.15 Aligned_cols=18 Identities=33% Similarity=0.663 Sum_probs=13.9
Q ss_pred hhccCCCCCcchh-hhhcC
Q 045823 127 EDLSHCPGIGERK-HVVSS 144 (233)
Q Consensus 127 EeLs~cPGiG~kK-~~v~~ 144 (233)
++|..+||||++. .++++
T Consensus 1 ~~L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 1 EELLKVPGIGPKTAEKILE 19 (26)
T ss_pred ChhhhCCCCCHHHHHHHHH
Confidence 4688999999998 45553
No 43
>PRK00254 ski2-like helicase; Provisional
Probab=56.07 E-value=12 Score=38.15 Aligned_cols=33 Identities=21% Similarity=0.372 Sum_probs=30.3
Q ss_pred hhcCCCccHhhHHHHHHh-hh----------hhccCCCCCcchh
Q 045823 107 LTSVRSVNKTDVVNLGST-FG----------EDLSHCPGIGERK 139 (233)
Q Consensus 107 LTsIrsVNKTDa~tLls~-FG----------EeLs~cPGiG~kK 139 (233)
|..|+||++.-+..|+.. |+ ++|..|||||++.
T Consensus 647 L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~ 690 (720)
T PRK00254 647 LMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKI 690 (720)
T ss_pred hhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHH
Confidence 557999999999999999 98 8899999999888
No 44
>PHA00439 exonuclease
Probab=55.30 E-value=9.1 Score=35.81 Aligned_cols=118 Identities=18% Similarity=0.155 Sum_probs=61.6
Q ss_pred CHHHHHHHHHHHHh-hcCCCc-ccccCCCCCchHHHHHHH--h-hcCCC---ccHhhHHHHH---Hhhh---hhccCCCC
Q 045823 69 SQEECGRYLETIKV-YENKPA-DLTQGQMDTDYLSRLTHA--L-TSVRS---VNKTDVVNLG---STFG---EDLSHCPG 134 (233)
Q Consensus 69 S~EEAArYLEt~K~-yEnk~~-d~Ik~k~~~dy~s~v~~~--L-TsIrs---VNKTDa~tLl---s~FG---EeLs~cPG 134 (233)
.--||=-.|-++-. .+.... +.+--..|.|+++ +.+. + ...+. ++..+...++ +--| +.+--|||
T Consensus 117 ~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~Q-Lv~~~~~~~~~~~~~~~~~~~p~~~~d~~AL~GDsSDNIPGVpG 195 (286)
T PHA00439 117 PGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKT-IPNCDFLWCTTGNILTQTPETADRWHLFQTIKGDSTDGYSGIPG 195 (286)
T ss_pred CCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhh-cCcceEEEccCCceEEcCcccHHHHHhhhhcccccccCCCCCCC
Confidence 44588888888754 333332 3333445566554 3221 1 01122 2222221111 1123 88999999
Q ss_pred Ccchh-hhhcCCCCCCCCCCCCCCCCCCCcchhhhhhchhHHHHhhhhhhhH--hHHHHHHHHHHH
Q 045823 135 IGERK-HVVSSHPPIPETPSQKDVEPSSVNEVTEVEKDAEDVNKRRKKELEL--TVKSALSAAFSK 197 (233)
Q Consensus 135 iG~kK-~~v~~~PFi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~ 197 (233)
|| +. .+++++||+-..-.. +=.|-. ...+...|++|+.|+. ++=-+.-++|+|
T Consensus 196 IG-KTA~kLL~~~~~~~~~~~--~~~sg~-------~~~~~~~~~~k~~~~~~~~~w~~~v~~~~k 251 (286)
T PHA00439 196 WG-DTAEAFLENPYIFEQVEK--VLKSGK-------RKGQTVTKWKKRAPEPEETLWDCIVTLGAK 251 (286)
T ss_pred cC-HHHHHHHhCccccchhhH--Hhhccc-------ccccchhhhhccCCCccccHHHHHHHHHHH
Confidence 99 55 889999988653211 100000 1234456777777664 666666666665
No 45
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=55.07 E-value=13 Score=38.84 Aligned_cols=37 Identities=22% Similarity=0.291 Sum_probs=33.8
Q ss_pred HHHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchh
Q 045823 103 LTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK 139 (233)
Q Consensus 103 v~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK 139 (233)
+...|..|+||=+.=...||..|| ++|+.+||||++.
T Consensus 606 ~~s~L~~IpGiG~kr~~~LL~~FgS~~~i~~As~eel~~v~gi~~~~ 652 (691)
T PRK14672 606 LVLSFERLPHVGKVRAHRLLAHFGSFRSLQSATPQDIATAIHIPLTQ 652 (691)
T ss_pred cccccccCCCCCHHHHHHHHHHhcCHHHHHhCCHHHHHhCCCCCHHH
Confidence 356688999999999999999999 9999999999988
No 46
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=54.95 E-value=6.9 Score=35.60 Aligned_cols=32 Identities=34% Similarity=0.420 Sum_probs=24.3
Q ss_pred hcCCCcc-HhhHHHHHHhhh----------hhccCCCCCcchh
Q 045823 108 TSVRSVN-KTDVVNLGSTFG----------EDLSHCPGIGERK 139 (233)
Q Consensus 108 TsIrsVN-KTDa~tLls~FG----------EeLs~cPGiG~kK 139 (233)
|.+++-+ ++=|..||.+|| ++|..+||+|+.|
T Consensus 36 tG~~~~~~~~la~~lL~~fg~L~~l~~a~~~el~~v~GiG~ak 78 (224)
T COG2003 36 TGTKGESVLDLAKELLQEFGSLAELLKASVEELSSVKGIGLAK 78 (224)
T ss_pred cCCCCCCHHHHHHHHHHHcccHHHHHhCCHHHHhhCCCccHHH
Confidence 3555443 333567889999 9999999999999
No 47
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=54.14 E-value=9.7 Score=34.17 Aligned_cols=31 Identities=32% Similarity=0.537 Sum_probs=22.5
Q ss_pred HHHHHhhh-------hhccCCCCCcchh-----hhhcCCCCCC
Q 045823 119 VNLGSTFG-------EDLSHCPGIGERK-----HVVSSHPPIP 149 (233)
Q Consensus 119 ~tLls~FG-------EeLs~cPGiG~kK-----~~v~~~PFi~ 149 (233)
..|+..|| ++|..+||+|++= ...|..|.|+
T Consensus 94 ~~l~e~~~g~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p~i~ 136 (211)
T COG0177 94 RILLEKFGGEVPDTREELLSLPGVGRKTANVVLSFAFGIPAIA 136 (211)
T ss_pred HHHHHHcCCCCCchHHHHHhCCCcchHHHHHHHHhhcCCCccc
Confidence 34567788 8999999999988 3345666554
No 48
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=54.00 E-value=37 Score=30.24 Aligned_cols=37 Identities=30% Similarity=0.452 Sum_probs=31.4
Q ss_pred HHHHhhcCCCccHhhHHHHHHhhh-------------hhccCCCCCcchh
Q 045823 103 LTHALTSVRSVNKTDVVNLGSTFG-------------EDLSHCPGIGERK 139 (233)
Q Consensus 103 v~~~LTsIrsVNKTDa~tLls~FG-------------EeLs~cPGiG~kK 139 (233)
+-.-|.+|.||=-.=|..+|+++. ..|..+||+|++-
T Consensus 71 lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKt 120 (201)
T COG0632 71 LFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKT 120 (201)
T ss_pred HHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCHHH
Confidence 455678899998888999998887 6799999999987
No 49
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=53.37 E-value=8.9 Score=36.76 Aligned_cols=41 Identities=34% Similarity=0.414 Sum_probs=36.3
Q ss_pred HHHHHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchhhh
Q 045823 101 SRLTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERKHV 141 (233)
Q Consensus 101 s~v~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK~~ 141 (233)
.+-...|..|+.+.+.++.+|...|| |+|..+.|||+.+.+
T Consensus 289 pRGYR~l~kIpRlp~~iv~nlV~~F~~l~~il~As~edL~~VeGIGe~rAr 339 (349)
T COG1623 289 PRGYRLLNKIPRLPFAIVENLVRAFGTLDGILEASAEDLDAVEGIGEARAR 339 (349)
T ss_pred chhhHHHhcCcCccHHHHHHHHHHHhhHHHHHHhcHhHHhhhcchhHHHHH
Confidence 34456788999999999999999999 999999999999844
No 50
>PRK10702 endonuclease III; Provisional
Probab=48.46 E-value=11 Score=33.15 Aligned_cols=30 Identities=20% Similarity=0.333 Sum_probs=21.5
Q ss_pred HHHHHHhhh-------hhccCCCCCcchh-----hhhcCCCC
Q 045823 118 VVNLGSTFG-------EDLSHCPGIGERK-----HVVSSHPP 147 (233)
Q Consensus 118 a~tLls~FG-------EeLs~cPGiG~kK-----~~v~~~PF 147 (233)
|..++..|| ++|..+||+|++= --.|++|-
T Consensus 93 a~~i~~~~~~~~p~~~~~Ll~lpGVG~ktA~~ill~a~~~~~ 134 (211)
T PRK10702 93 CRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGWPT 134 (211)
T ss_pred HHHHHHHcCCCCCchHHHHhcCCcccHHHHHHHHHHHcCCCc
Confidence 445566777 8999999999987 23455553
No 51
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=41.40 E-value=29 Score=35.28 Aligned_cols=35 Identities=17% Similarity=0.286 Sum_probs=29.7
Q ss_pred HHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchh
Q 045823 104 THALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK 139 (233)
Q Consensus 104 ~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK 139 (233)
...|..|+||=+.=...||..|| |+|+.+ |||++.
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~As~eeL~~v-gi~~~~ 557 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIYRNFKTLYDFLKADDEELKKL-GIPPSV 557 (567)
T ss_pred cCccccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHHc-CCCHHH
Confidence 45677889999999999999999 888888 888876
No 52
>COG3727 Vsr DNA G:T-mismatch repair endonuclease [DNA replication, recombination, and repair]
Probab=39.58 E-value=27 Score=30.12 Aligned_cols=16 Identities=19% Similarity=0.445 Sum_probs=14.8
Q ss_pred cccceeecCceeEEEE
Q 045823 19 VVCDYLLGQNSCALYL 34 (233)
Q Consensus 19 IvpDYviG~t~cvLFL 34 (233)
-.||+|+..+.||+|.
T Consensus 48 GkPDiVl~~y~~viFv 63 (150)
T COG3727 48 GKPDIVLPKYRCVIFV 63 (150)
T ss_pred CCCCEeecCceEEEEE
Confidence 3599999999999999
No 53
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=38.62 E-value=22 Score=33.46 Aligned_cols=22 Identities=36% Similarity=0.599 Sum_probs=18.6
Q ss_pred HHHHHHhhh-------hhccCCCCCcchh
Q 045823 118 VVNLGSTFG-------EDLSHCPGIGERK 139 (233)
Q Consensus 118 a~tLls~FG-------EeLs~cPGiG~kK 139 (233)
|.-|...|+ ++|..+||+||+=
T Consensus 143 a~IL~d~f~gDIP~~v~dLlsLPGVGPKM 171 (286)
T KOG1921|consen 143 AKILQDKFDGDIPDTVEDLLSLPGVGPKM 171 (286)
T ss_pred HHHHHHHhCCCCchhHHHHhcCCCCchHH
Confidence 555668888 9999999999986
No 54
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=37.11 E-value=27 Score=36.46 Aligned_cols=68 Identities=29% Similarity=0.450 Sum_probs=48.4
Q ss_pred HHHHHhhcCCCcc----cccCCCCCchHHHHHHHhhcCCCccHhhHHHHHHhhh----------hhccCCCCCcchh---
Q 045823 77 LETIKVYENKPAD----LTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG----------EDLSHCPGIGERK--- 139 (233)
Q Consensus 77 LEt~K~yEnk~~d----~Ik~k~~~dy~s~v~~~LTsIrsVNKTDa~tLls~FG----------EeLs~cPGiG~kK--- 139 (233)
|..++.+..+++. .|......+ +.+++-+| .||.|=.+-|..|...|| ++|..+||||++-
T Consensus 481 l~~l~~~~~ks~~nLl~aIe~sK~~~-l~r~l~aL-GIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l~~i~giG~~vA~s 558 (667)
T COG0272 481 LLSLEGFGEKSAENLLNAIEKSKKQP-LARFLYAL-GIRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEVVARS 558 (667)
T ss_pred HhhccchhhhHHHHHHHHHHHhccCC-HHHHHHHc-CCchhhHHHHHHHHHHhhhHHHHHhcCHHHHhhccchhHHHHHH
Confidence 3344444455544 345555544 56666555 699999999999999999 9999999999998
Q ss_pred -hhhcCCC
Q 045823 140 -HVVSSHP 146 (233)
Q Consensus 140 -~~v~~~P 146 (233)
...|+.|
T Consensus 559 i~~ff~~~ 566 (667)
T COG0272 559 IIEFFANE 566 (667)
T ss_pred HHHHHcCH
Confidence 4455554
No 55
>COG3526 Uncharacterized protein conserved in bacteria [Posttranslational modification, protein turnover, chaperones]
Probab=35.35 E-value=23 Score=28.44 Aligned_cols=21 Identities=33% Similarity=0.485 Sum_probs=17.4
Q ss_pred HHHHHHhhh---hhccCCCCCcch
Q 045823 118 VVNLGSTFG---EDLSHCPGIGER 138 (233)
Q Consensus 118 a~tLls~FG---EeLs~cPGiG~k 138 (233)
|+.||++|+ .+.+++||-|-.
T Consensus 26 aQElL~TF~~dlgeV~L~PgTGG~ 49 (99)
T COG3526 26 AQELLSTFADDLGEVALIPGTGGV 49 (99)
T ss_pred HHHHHHHHHhhhheEEEecCCCce
Confidence 688999999 667789998854
No 56
>PRK08609 hypothetical protein; Provisional
Probab=34.95 E-value=25 Score=35.29 Aligned_cols=34 Identities=24% Similarity=0.392 Sum_probs=23.3
Q ss_pred HhhcCCCccHhhHHHH--HHhhh----------------hhccCCCCCcchh
Q 045823 106 ALTSVRSVNKTDVVNL--GSTFG----------------EDLSHCPGIGERK 139 (233)
Q Consensus 106 ~LTsIrsVNKTDa~tL--ls~FG----------------EeLs~cPGiG~kK 139 (233)
-|+.|+||-+.=|..+ +-.-| .+|..|||+||++
T Consensus 49 ~l~~ipgIG~~ia~kI~Eil~tG~~~~le~l~~~~p~~~~~l~~i~GiGpk~ 100 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQEYRETGESSVLQELKKEVPEGLLPLLKLPGLGGKK 100 (570)
T ss_pred hhccCCCcCHHHHHHHHHHHHhCChHHHHHHHhhCcHHHHHHhcCCCCCHHH
Confidence 5778888888744322 12223 6688999999999
No 57
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=33.34 E-value=21 Score=30.88 Aligned_cols=13 Identities=23% Similarity=0.391 Sum_probs=11.8
Q ss_pred hhccCCCCCcchh
Q 045823 127 EDLSHCPGIGERK 139 (233)
Q Consensus 127 EeLs~cPGiG~kK 139 (233)
..|..+|||||+.
T Consensus 73 ~~L~~i~GIGpk~ 85 (192)
T PRK00116 73 RLLISVSGVGPKL 85 (192)
T ss_pred HHHhcCCCCCHHH
Confidence 5788999999999
No 58
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=31.83 E-value=40 Score=25.25 Aligned_cols=34 Identities=24% Similarity=0.419 Sum_probs=23.7
Q ss_pred HHhhcCCCccHhhHHHHHHhhh--------hhccCCCCCcch
Q 045823 105 HALTSVRSVNKTDVVNLGSTFG--------EDLSHCPGIGER 138 (233)
Q Consensus 105 ~~LTsIrsVNKTDa~tLls~FG--------EeLs~cPGiG~k 138 (233)
+.|++|+||-..=|.+|++.+| ..|...-|+-|.
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF~~~~~l~~~~Gl~P~ 43 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRFKSAKQLASYAGLAPR 43 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhcccchhhhhccccccc
Confidence 4578888888888888888776 455555555443
No 59
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=29.16 E-value=28 Score=22.82 Aligned_cols=19 Identities=21% Similarity=0.566 Sum_probs=13.2
Q ss_pred HHHhhhhhccCCCCCcchh
Q 045823 121 LGSTFGEDLSHCPGIGERK 139 (233)
Q Consensus 121 Lls~FGEeLs~cPGiG~kK 139 (233)
|+--+.+.+.-+||||+++
T Consensus 10 L~GD~~dni~Gv~giG~kt 28 (36)
T smart00279 10 LVGDYSDNIPGVKGIGPKT 28 (36)
T ss_pred HhCcCCCCCCCCCcccHHH
Confidence 3333446667899999988
No 60
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=28.65 E-value=30 Score=25.29 Aligned_cols=38 Identities=21% Similarity=0.185 Sum_probs=22.8
Q ss_pred hHHHHHHHhhcCCCccHhhHHHHHHhhhhhccCCCCCcchh
Q 045823 99 YLSRLTHALTSVRSVNKTDVVNLGSTFGEDLSHCPGIGERK 139 (233)
Q Consensus 99 y~s~v~~~LTsIrsVNKTDa~tLls~FGEeLs~cPGiG~kK 139 (233)
.-.|..+||... |-+-+..|+..=.++|..+||||++=
T Consensus 19 LS~Ra~n~L~~~---~I~tv~dL~~~s~~~L~~i~n~G~ks 56 (66)
T PF03118_consen 19 LSVRAYNCLKRA---GIHTVGDLVKYSEEDLLKIKNFGKKS 56 (66)
T ss_dssp SBHHHHHHHHCT---T--BHHHHHCS-HHHHHTSTTSHHHH
T ss_pred CCHHHHHHHHHh---CCcCHHHHHhCCHHHHHhCCCCCHhH
Confidence 345667777633 33334444444338999999999863
No 61
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=27.52 E-value=57 Score=26.05 Aligned_cols=23 Identities=35% Similarity=0.706 Sum_probs=16.8
Q ss_pred hhccCCCCCcchh-----hhhcCCCCCC
Q 045823 127 EDLSHCPGIGERK-----HVVSSHPPIP 149 (233)
Q Consensus 127 EeLs~cPGiG~kK-----~~v~~~PFi~ 149 (233)
+.|..+||||+.= ...+..|+.+
T Consensus 72 ~~L~~l~GIG~~tA~~~l~~~~~~~~~~ 99 (149)
T smart00478 72 EELLKLPGVGRKTANAVLSFALGKPFIP 99 (149)
T ss_pred HHHHcCCCCcHHHHHHHHHHHCCCCCCc
Confidence 6788999999988 4455655544
No 62
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=26.87 E-value=79 Score=23.89 Aligned_cols=39 Identities=23% Similarity=0.194 Sum_probs=29.6
Q ss_pred HHHHHHhhcC-CCccHhhHHHHHHhhh---------hhccCCCCCcchh
Q 045823 101 SRLTHALTSV-RSVNKTDVVNLGSTFG---------EDLSHCPGIGERK 139 (233)
Q Consensus 101 s~v~~~LTsI-rsVNKTDa~tLls~FG---------EeLs~cPGiG~kK 139 (233)
+.+++.+..- -++++.||..++..|- .+--.+||||-=.
T Consensus 4 ~eli~~ia~~~~~~s~~~~~~vv~~~~~~i~~~L~~g~~V~l~gfG~F~ 52 (94)
T PRK00199 4 SELIERLAARNPHLSAKDVENAVKEILEEMSDALARGDRIEIRGFGSFS 52 (94)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEcCCEEEE
Confidence 3466777653 4799999999999998 3345789999755
No 63
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=26.74 E-value=64 Score=24.62 Aligned_cols=39 Identities=18% Similarity=0.230 Sum_probs=29.9
Q ss_pred HHHHHHhhcCCCccHhhHHHHHHhhh----hhc-----cCCCCCcchh
Q 045823 101 SRLTHALTSVRSVNKTDVVNLGSTFG----EDL-----SHCPGIGERK 139 (233)
Q Consensus 101 s~v~~~LTsIrsVNKTDa~tLls~FG----EeL-----s~cPGiG~kK 139 (233)
+.+++.|....++++.||..++..|- +.| -.++|||-=+
T Consensus 5 ~eli~~ia~~~~~s~~~v~~vv~~~~~~i~~~L~~g~~V~l~gfG~F~ 52 (96)
T TIGR00987 5 AEMSEYLFDELGLSKREAKELVELFFEEIRRALENGEQVKLSGFGNFD 52 (96)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHcCCeEEecCCEEEE
Confidence 44667777777899999999999999 222 3578999765
No 64
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=26.46 E-value=50 Score=24.15 Aligned_cols=38 Identities=18% Similarity=0.261 Sum_probs=27.8
Q ss_pred HHHHHhhcCCCccHhhHHHHHHhhh---------hhccCCCCCcchh
Q 045823 102 RLTHALTSVRSVNKTDVVNLGSTFG---------EDLSHCPGIGERK 139 (233)
Q Consensus 102 ~v~~~LTsIrsVNKTDa~tLls~FG---------EeLs~cPGiG~kK 139 (233)
++++.+..--++++.|+..++..|- .+--.++|||-=.
T Consensus 5 eli~~ia~~~~~s~~~v~~vl~~~~~~i~~~L~~g~~V~l~g~G~F~ 51 (90)
T PF00216_consen 5 ELIKRIAEKTGLSKKDVEAVLDALFDVIKEALKEGESVKLPGFGTFS 51 (90)
T ss_dssp HHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHTT-EEEETTTEEEE
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHhcCCeEEeeceeEEE
Confidence 3455555445789999999999998 3334789999766
No 65
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=26.35 E-value=56 Score=33.93 Aligned_cols=47 Identities=17% Similarity=0.282 Sum_probs=37.2
Q ss_pred hHHHHHHHhhcCCCccHhhHHHHH-Hhhh----------------hhccCCCCCcchh----hhhcCCC
Q 045823 99 YLSRLTHALTSVRSVNKTDVVNLG-STFG----------------EDLSHCPGIGERK----HVVSSHP 146 (233)
Q Consensus 99 y~s~v~~~LTsIrsVNKTDa~tLl-s~FG----------------EeLs~cPGiG~kK----~~v~~~P 146 (233)
.+.+++-+|. |+.|=.+-|..|+ ..|+ ++|..++|||++- ...|+.|
T Consensus 497 ~l~r~l~ALG-I~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~e~l~~i~giG~~~a~si~~ff~~~ 564 (669)
T PRK14350 497 PFSKLLLSMG-IKDLGENTILLLINNNLNSFDKISTLCQDREFALSKLLKIKGIGEKIALNIIEAFNDK 564 (669)
T ss_pred CHHHHHHHcC-CCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCHHHHhhCCCccHHHHHHHHHHHcCH
Confidence 4678888887 9999999999999 6777 2578899999999 4455554
No 66
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=26.29 E-value=65 Score=24.59 Aligned_cols=39 Identities=23% Similarity=0.295 Sum_probs=30.3
Q ss_pred HHHHHHhhcCCCccHhhHHHHHHhhh----hhc-----cCCCCCcchh
Q 045823 101 SRLTHALTSVRSVNKTDVVNLGSTFG----EDL-----SHCPGIGERK 139 (233)
Q Consensus 101 s~v~~~LTsIrsVNKTDa~tLls~FG----EeL-----s~cPGiG~kK 139 (233)
+.+++.+..-.++++.||...+..|- +.| -.++|||-=+
T Consensus 6 ~el~~~ia~~~~~s~~~v~~vl~~~~~~i~~~L~~g~~V~l~gfG~F~ 53 (99)
T PRK00285 6 ADLAEALFEKVGLSKREAKELVELFFEEIRDALENGEQVKLSGFGNFQ 53 (99)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHcCCeEEEcCCEEEE
Confidence 44666777777899999999999998 333 4689999766
No 67
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=26.25 E-value=49 Score=28.21 Aligned_cols=21 Identities=33% Similarity=0.691 Sum_probs=16.0
Q ss_pred hhccCCCCCcchh-----hhhcCCCC
Q 045823 127 EDLSHCPGIGERK-----HVVSSHPP 147 (233)
Q Consensus 127 EeLs~cPGiG~kK-----~~v~~~PF 147 (233)
+.|..+||||++= ...|+.|.
T Consensus 106 ~~L~~l~GIG~ktA~~ill~~~~~~~ 131 (191)
T TIGR01083 106 EELVKLPGVGRKTANVVLNVAFGIPA 131 (191)
T ss_pred HHHHhCCCCcHHHHHHHHHHHcCCCc
Confidence 7899999999998 34455554
No 68
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=26.00 E-value=30 Score=29.08 Aligned_cols=13 Identities=54% Similarity=0.984 Sum_probs=11.1
Q ss_pred hhccCCCCCcchh
Q 045823 127 EDLSHCPGIGERK 139 (233)
Q Consensus 127 EeLs~cPGiG~kK 139 (233)
++|..+||||++|
T Consensus 97 eeL~~lpgIG~~k 109 (149)
T COG1555 97 EELQALPGIGPKK 109 (149)
T ss_pred HHHHHCCCCCHHH
Confidence 5667899999999
No 69
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=25.03 E-value=70 Score=24.48 Aligned_cols=39 Identities=15% Similarity=0.089 Sum_probs=30.4
Q ss_pred HHHHHHhhcCCCccHhhHHHHHHhhh---------hhccCCCCCcchh
Q 045823 101 SRLTHALTSVRSVNKTDVVNLGSTFG---------EDLSHCPGIGERK 139 (233)
Q Consensus 101 s~v~~~LTsIrsVNKTDa~tLls~FG---------EeLs~cPGiG~kK 139 (233)
+++++.|..--++++.||..++..|= .+=-.+||||-=+
T Consensus 4 ~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~~~~~v~l~gfG~F~ 51 (90)
T PRK10664 4 SQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFA 51 (90)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCCCEEEECCcEEEE
Confidence 34667777667999999999999998 2335789999766
No 70
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=25.01 E-value=72 Score=23.41 Aligned_cols=39 Identities=23% Similarity=0.273 Sum_probs=29.3
Q ss_pred HHHHHHhhcCCCccHhhHHHHHHhhh----h-----hccCCCCCcchh
Q 045823 101 SRLTHALTSVRSVNKTDVVNLGSTFG----E-----DLSHCPGIGERK 139 (233)
Q Consensus 101 s~v~~~LTsIrsVNKTDa~tLls~FG----E-----eLs~cPGiG~kK 139 (233)
+.+++.+..-.++++.||..++..|- + .--.++|||-=+
T Consensus 4 ~eli~~ia~~~~~~~~~v~~vl~~l~~~i~~~L~~g~~V~i~g~G~F~ 51 (90)
T smart00411 4 SELIDAIAEKAGLSKKDAKAAVDAFLEIITEALKKGEKVELRGFGTFE 51 (90)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCCCeEEEeCcEEEE
Confidence 34566666667899999999999998 2 234689999766
No 71
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=24.71 E-value=82 Score=24.81 Aligned_cols=25 Identities=16% Similarity=0.318 Sum_probs=22.9
Q ss_pred HHHHHhhcCCCccHhhHHHHHHhhh
Q 045823 102 RLTHALTSVRSVNKTDVVNLGSTFG 126 (233)
Q Consensus 102 ~v~~~LTsIrsVNKTDa~tLls~FG 126 (233)
.|.-+||.|.||++.=|..|+..+|
T Consensus 12 ~i~~aLt~IyGIG~~~A~~Ic~~lg 36 (107)
T PF00416_consen 12 PIYIALTKIYGIGRRKAKQICKKLG 36 (107)
T ss_dssp BHHHHHTTSTTBCHHHHHHHHHHTT
T ss_pred chHhHHhhhhccCHHHHHHHHHHcC
Confidence 4788999999999999999999998
No 72
>PRK09482 flap endonuclease-like protein; Provisional
Probab=24.39 E-value=41 Score=30.83 Aligned_cols=68 Identities=19% Similarity=0.248 Sum_probs=37.9
Q ss_pred HHHHHHHHHHh-hcCCCcccccCCCCCchHHHHHHHhhcC--CCccHhhHHHHHHhhh-----------------hhccC
Q 045823 72 ECGRYLETIKV-YENKPADLTQGQMDTDYLSRLTHALTSV--RSVNKTDVVNLGSTFG-----------------EDLSH 131 (233)
Q Consensus 72 EAArYLEt~K~-yEnk~~d~Ik~k~~~dy~s~v~~~LTsI--rsVNKTDa~tLls~FG-----------------EeLs~ 131 (233)
||=-.|-++-. +.....+.+--..|.|+++-+.+-.+-. ....--|...+...|| +.+--
T Consensus 107 EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~~v~~~~~~~~~~~~~~~v~~~~Gv~P~q~~D~~aL~GD~sDnIpG 186 (256)
T PRK09482 107 EADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRDYFQKRWLDAPFIEQEFGVEPQQLPDYWGLAGISSSKIPG 186 (256)
T ss_pred CHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCCCeEEEeccccccCCHHHHHHHhCCCHHHHHHHHHHhCCCccCCCC
Confidence 88888888754 3333333333344555543322211111 1111235666667788 67889
Q ss_pred CCCCcchh
Q 045823 132 CPGIGERK 139 (233)
Q Consensus 132 cPGiG~kK 139 (233)
||||||+.
T Consensus 187 VpGIG~Kt 194 (256)
T PRK09482 187 VAGIGPKS 194 (256)
T ss_pred CCCcChHH
Confidence 99999998
No 73
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=24.33 E-value=75 Score=24.23 Aligned_cols=39 Identities=18% Similarity=0.167 Sum_probs=29.6
Q ss_pred HHHHHHhhcCCCccHhhHHHHHHhhh---------hhccCCCCCcchh
Q 045823 101 SRLTHALTSVRSVNKTDVVNLGSTFG---------EDLSHCPGIGERK 139 (233)
Q Consensus 101 s~v~~~LTsIrsVNKTDa~tLls~FG---------EeLs~cPGiG~kK 139 (233)
+.+++.|..--++++.||...+..|- .+=-.++|||-=+
T Consensus 4 ~eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~~g~~V~i~gfG~F~ 51 (90)
T PRK10753 4 TQLIDVIADKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFK 51 (90)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHcCCeEEEcCCEEEE
Confidence 34566666666899999999999998 2234689999755
No 74
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=24.08 E-value=1.8e+02 Score=21.25 Aligned_cols=68 Identities=18% Similarity=0.214 Sum_probs=41.5
Q ss_pred CHHHHHHHHHHHHhhcCCCcccccCCCCCchHHHHHHHhhcCCCccHhhHHHHHHhhh---------hhccCCCCCcc
Q 045823 69 SQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG---------EDLSHCPGIGE 137 (233)
Q Consensus 69 S~EEAArYLEt~K~yEnk~~d~Ik~k~~~dy~s~v~~~LTsIrsVNKTDa~tLls~FG---------EeLs~cPGiG~ 137 (233)
++++-.-.|+.+...-++..-.=.+.........++..|-..-+.+.| ...|-++|+ ..|...+|+|=
T Consensus 3 t~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t-~~qlknk~~~lk~~y~~~~~l~~~sg~gw 79 (96)
T PF12776_consen 3 TPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYT-KKQLKNKWKTLKKDYRIWKELRNHSGFGW 79 (96)
T ss_pred ChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCccc-HHHHHHHHHHHHHHHHHHHHHHcCCCceE
Confidence 888888889888766444433101222223345566666655566554 344445554 88999999884
No 75
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=22.98 E-value=48 Score=30.52 Aligned_cols=21 Identities=33% Similarity=0.597 Sum_probs=15.8
Q ss_pred hhccCCCCCcchh-----hhhcCCCC
Q 045823 127 EDLSHCPGIGERK-----HVVSSHPP 147 (233)
Q Consensus 127 EeLs~cPGiG~kK-----~~v~~~PF 147 (233)
++|..+||||+.= .-.|+.|.
T Consensus 105 ~~L~~LpGIG~~TA~~Il~~a~~~~~ 130 (275)
T TIGR01084 105 EDLAALPGVGRYTAGAILSFALNKPY 130 (275)
T ss_pred HHHHhCCCCCHHHHHHHHHHHCCCCC
Confidence 8899999999977 23455553
No 76
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=22.85 E-value=58 Score=23.38 Aligned_cols=11 Identities=55% Similarity=1.020 Sum_probs=9.4
Q ss_pred hccCCCCCcch
Q 045823 128 DLSHCPGIGER 138 (233)
Q Consensus 128 eLs~cPGiG~k 138 (233)
++..+||||++
T Consensus 48 ~~~~l~gIG~~ 58 (68)
T PF14716_consen 48 DLKKLPGIGKS 58 (68)
T ss_dssp HHCTSTTTTHH
T ss_pred HHhhCCCCCHH
Confidence 48999999975
No 77
>PRK14363 Maf-like protein; Provisional
Probab=22.40 E-value=33 Score=30.41 Aligned_cols=59 Identities=12% Similarity=0.076 Sum_probs=49.9
Q ss_pred CCCHHHHHHHHHHHHhhcCCCcccccCCCCCchHHHHHHHhhcCCCccHhhHHHHHHhhh
Q 045823 67 NFSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG 126 (233)
Q Consensus 67 ~~S~EEAArYLEt~K~yEnk~~d~Ik~k~~~dy~s~v~~~LTsIrsVNKTDa~tLls~FG 126 (233)
.+|.+|-.+||++..-+....+-.|++. ...+..++....++|-|+.-.....+|..+|
T Consensus 126 ~ls~~~I~~Yv~~~ep~dkAG~y~Iqg~-g~~~i~~I~G~~~nV~GLPl~~l~~~L~~~g 184 (204)
T PRK14363 126 ELPESVIDYYVEKYRPLDKAGAYGIQDF-AAVFVEKIEGDFFTVVGFPLGMVWQYLYEKG 184 (204)
T ss_pred CCCHHHHHHHHhcCCChhhcceEEEccC-ccceEEeeECCCCceeCCCHHHHHHHHHHcC
Confidence 4499999999999888877777778884 4457788888889999999999999999987
No 78
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=21.34 E-value=70 Score=20.25 Aligned_cols=12 Identities=25% Similarity=0.498 Sum_probs=8.7
Q ss_pred hccCCCCCcchh
Q 045823 128 DLSHCPGIGERK 139 (233)
Q Consensus 128 eLs~cPGiG~kK 139 (233)
.+..++|||++=
T Consensus 12 pi~~~~GIG~kt 23 (32)
T PF11798_consen 12 PIRKFWGIGKKT 23 (32)
T ss_dssp BGGGSTTS-HHH
T ss_pred CHHhhCCccHHH
Confidence 678899999864
No 79
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=20.91 E-value=3.6e+02 Score=20.02 Aligned_cols=52 Identities=10% Similarity=0.118 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHHhhcCCCcccccCCCCCchHHHHHHHhhcCCCccHhhHHHHHHhhh
Q 045823 67 NFSQEECGRYLETIKVYENKPADLTQGQMDTDYLSRLTHALTSVRSVNKTDVVNLGSTFG 126 (233)
Q Consensus 67 ~~S~EEAArYLEt~K~yEnk~~d~Ik~k~~~dy~s~v~~~LTsIrsVNKTDa~tLls~FG 126 (233)
..|.+|-.+|-+.|+.+.....-.| + ...+..+|... +++..++..++..+.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~I------s-~~el~~~l~~~-~~~~~ev~~i~~~~d 54 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTV------T-GAQAKPILLKS-GLPQTLLAKIWNLAD 54 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeE------e-HHHHHHHHHHc-CCCHHHHHHHHHHhc
Confidence 4589999999999999985332222 2 34467777764 788999999998875
No 80
>PF02764 Diphtheria_T: Diphtheria toxin, T domain; InterPro: IPR022405 Diphtheria toxin (2.4.2.36 from EC) is a 58 kDa protein secreted by lysogenic strains of Corynebacterium diphtheriae. The toxin causes the disease diphtheria in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis []. The mechanism of inhibition involves transfer of the ADP-ribose group of NAD to elongation factor-2 (EF-2), rendering EF-2 inactive. The catalysed reaction is as follows: NAD+ + peptide diphthamide = nicotinamide + peptide N-(ADP-D-ribosyl)diphthamide The crystal structure of the diphtheria toxin homodimer has been determined to 2.5A resolution []. The structure reveals a Y-shaped molecule of 3 domains, a catalytic domain (fragment A), whose fold is of the alpha + beta type; a transmembrane (TM) domain, which consists of 9 alpha-helices, 2 pairs of which may participate in pH-triggered membrane insertion and translocation; and a receptor-binding domain, which forms a flattened beta-barrel with a jelly-roll-like topology []. The TM- and receptor binding-domains together constitute fragment B. This entry represents the translocation domain (also known as the T domain) found as the central domain in the Diphtheria toxin protein. The T domain has a multi-helical globin-like fold with two additional helices at N-termini, but which has no counterpart to the first globin helix. This domain is thought to unfold in the membrane []. pH-induced conformational change in the T domain triggers insertion into the endosomal membrane and facilitates the transfer of the catalytic domain into the cytoplasm [, ].; PDB: 1MDT_B 1SGK_A 1F0L_B 1DDT_A 1TOX_B 4AE0_A 1XDT_T 4AE1_A.
Probab=20.69 E-value=1.1e+02 Score=26.69 Aligned_cols=22 Identities=27% Similarity=0.413 Sum_probs=16.8
Q ss_pred CHHHHHHHHHHHHhhcCCCccc
Q 045823 69 SQEECGRYLETIKVYENKPADL 90 (233)
Q Consensus 69 S~EEAArYLEt~K~yEnk~~d~ 90 (233)
|.|.|..|||.|++..-.-|++
T Consensus 40 seekakqyleefhqtalehpel 61 (180)
T PF02764_consen 40 SEEKAKQYLEEFHQTALEHPEL 61 (180)
T ss_dssp -HHHHHHHHHHHHHHHTTSGGG
T ss_pred hHHHHHHHHHHHHHHHhcCchh
Confidence 8899999999999866555554
No 81
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=20.34 E-value=39 Score=31.68 Aligned_cols=14 Identities=14% Similarity=0.380 Sum_probs=12.6
Q ss_pred hhccCCCCCcchhh
Q 045823 127 EDLSHCPGIGERKH 140 (233)
Q Consensus 127 EeLs~cPGiG~kK~ 140 (233)
.+|..||||||+|.
T Consensus 89 ~~l~~i~GiGpk~a 102 (334)
T smart00483 89 KLFTNVFGVGPKTA 102 (334)
T ss_pred HHHHccCCcCHHHH
Confidence 78899999999993
No 82
>TIGR01201 HU_rel DNA-binding protein, histone-like, putative. This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe.
Probab=20.25 E-value=1.1e+02 Score=25.44 Aligned_cols=40 Identities=13% Similarity=0.213 Sum_probs=31.9
Q ss_pred HHHHHHHhhcCCCccHhhHHHHHHhhh----hh-----ccCCCCCcchh
Q 045823 100 LSRLTHALTSVRSVNKTDVVNLGSTFG----ED-----LSHCPGIGERK 139 (233)
Q Consensus 100 ~s~v~~~LTsIrsVNKTDa~tLls~FG----Ee-----Ls~cPGiG~kK 139 (233)
.+++++.+...-++++-||...+..+. +. --.++|||-=+
T Consensus 33 ~~el~~~Ia~~s~~s~~dv~~vl~~l~~~i~~~L~~G~~V~L~gfGtF~ 81 (145)
T TIGR01201 33 FEEIAELIAEESSLSPGDVKGIIDRLAYVLRRELANGKTVRLGEIGTFR 81 (145)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCCCeEEeCCCEEEE
Confidence 466788888778899999999999999 33 34689999655
No 83
>PF07279 DUF1442: Protein of unknown function (DUF1442); InterPro: IPR009902 This family consists of several hypothetical Arabidopsis thaliana proteins of around 225 residues in length. The function of this family is unknown.
Probab=20.17 E-value=67 Score=29.23 Aligned_cols=21 Identities=33% Similarity=0.616 Sum_probs=18.0
Q ss_pred cccCCCCHHHHH-HHHHHHHhhcCC
Q 045823 63 ESWSNFSQEECG-RYLETIKVYENK 86 (233)
Q Consensus 63 lAW~~~S~EEAA-rYLEt~K~yEnk 86 (233)
|+| |||-|- .||.|.|.+++.
T Consensus 3 l~W---Spe~AtkAYl~Tvk~c~~~ 24 (218)
T PF07279_consen 3 LVW---SPENATKAYLDTVKMCKKF 24 (218)
T ss_pred cee---ChhHHHHHHHHHHHHhhhc
Confidence 689 999986 599999998763
No 84
>smart00475 53EXOc 5'-3' exonuclease.
Probab=20.14 E-value=1.2e+02 Score=27.66 Aligned_cols=13 Identities=38% Similarity=0.971 Sum_probs=11.8
Q ss_pred hhccCCCCCcchh
Q 045823 127 EDLSHCPGIGERK 139 (233)
Q Consensus 127 EeLs~cPGiG~kK 139 (233)
+.+--+|||||++
T Consensus 186 DnipGV~GIG~Kt 198 (259)
T smart00475 186 DNIPGVPGIGEKT 198 (259)
T ss_pred cCCCCCCCCCHHH
Confidence 6788999999999
Done!