Query 040614
Match_columns 475
No_of_seqs 58 out of 60
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 10:04:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040614.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040614hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00465 GIYc GIY-YIG type n 97.5 0.00021 4.5E-09 55.7 5.7 82 62-154 2-83 (84)
2 PHA02598 denA endonuclease II; 96.3 0.0058 1.3E-07 56.4 4.8 82 61-151 33-132 (138)
3 PRK10545 nucleotide excision r 95.9 0.0092 2E-07 60.4 4.7 81 53-151 28-108 (286)
4 TIGR00194 uvrC excinuclease AB 95.0 0.034 7.4E-07 61.0 5.5 83 52-150 4-86 (574)
5 PRK14668 uvrC excinuclease ABC 95.0 0.034 7.3E-07 61.0 5.4 80 52-149 9-88 (577)
6 PRK07883 hypothetical protein; 94.8 0.038 8.2E-07 60.1 5.2 82 50-146 208-289 (557)
7 PRK14669 uvrC excinuclease ABC 94.8 0.04 8.7E-07 61.0 5.5 81 52-146 6-86 (624)
8 PRK00558 uvrC excinuclease ABC 94.2 0.058 1.3E-06 59.3 4.9 81 52-147 7-87 (598)
9 PRK12306 uvrC excinuclease ABC 94.0 0.083 1.8E-06 57.5 5.5 80 53-147 4-83 (519)
10 PRK14667 uvrC excinuclease ABC 93.8 0.087 1.9E-06 57.9 5.4 79 52-146 9-87 (567)
11 PRK14671 uvrC excinuclease ABC 93.7 0.096 2.1E-06 58.0 5.4 83 50-146 13-95 (621)
12 COG0322 UvrC Nuclease subunit 93.6 0.068 1.5E-06 58.9 4.1 82 53-150 9-90 (581)
13 PRK14666 uvrC excinuclease ABC 93.4 0.11 2.3E-06 58.5 5.3 81 52-146 5-85 (694)
14 PF01541 GIY-YIG: GIY-YIG cata 91.5 0.24 5.3E-06 38.5 3.6 62 78-147 14-76 (80)
15 PRK14672 uvrC excinuclease ABC 91.2 0.31 6.7E-06 55.0 5.4 84 50-149 12-95 (691)
16 PRK14670 uvrC excinuclease ABC 84.4 1.1 2.4E-05 49.6 4.3 59 78-146 8-66 (574)
17 PF09740 DUF2043: Uncharacteri 72.6 2 4.4E-05 38.7 1.5 24 450-475 70-93 (110)
18 PF11722 zf-TRM13_CCCH: CCCH z 53.1 6.9 0.00015 28.0 0.9 26 353-378 4-30 (31)
19 TIGR01453 grpIintron_endo grou 52.4 47 0.001 32.1 6.8 81 78-168 14-109 (214)
20 PF08313 SCA7: SCA7, zinc-bind 46.4 9.5 0.00021 32.3 0.9 26 228-258 19-44 (73)
21 PF08313 SCA7: SCA7, zinc-bind 40.4 11 0.00024 31.9 0.5 26 347-377 18-43 (73)
22 PF09740 DUF2043: Uncharacteri 38.7 17 0.00036 33.0 1.3 24 232-258 71-94 (110)
23 PRK00329 GIY-YIG nuclease supe 36.1 90 0.0019 26.6 5.2 52 78-141 18-70 (86)
24 PF14852 Fis1_TPR_N: Fis1 N-te 32.4 14 0.00031 26.9 -0.1 6 144-149 4-9 (35)
25 PF09329 zf-primase: Primase z 25.3 30 0.00065 26.5 0.6 32 406-437 7-40 (46)
26 PF13072 DUF3936: Protein of u 23.5 56 0.0012 24.9 1.7 20 79-98 11-30 (38)
27 PF10544 T5orf172: T5orf172 do 21.5 1E+02 0.0022 24.9 3.1 19 79-97 17-35 (100)
28 PF11767 SET_assoc: Histone ly 21.3 1E+02 0.0022 25.5 2.9 27 84-123 14-40 (66)
No 1
>smart00465 GIYc GIY-YIG type nucleases (URI domain).
Probab=97.52 E-value=0.00021 Score=55.68 Aligned_cols=82 Identities=17% Similarity=0.256 Sum_probs=57.2
Q ss_pred CceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCCchHHHHHHHHHH
Q 040614 62 PGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNKEDAEKTERKI 141 (475)
Q Consensus 62 pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K~~Ae~tE~~l 141 (475)
||+|-+=- . .-.++|+|+|.|+++|+.+|-.... ....+...+...|..+.+.+...... .|...|..|
T Consensus 2 ~gvY~i~~--~--~~~~~YVG~t~nl~~R~~~h~~~~~------~~~~~~~~~~~~~~~f~~~~~~~~~~-~~~~~E~~~ 70 (84)
T smart00465 2 PGVYYITN--K--KNGKLYVGKAKNLRNRLKRHFSGSR------KGRLLIDALLKYGGNFEFIILESFDE-SALELEKYL 70 (84)
T ss_pred CEEEEEEE--C--CCCEEEEEEccCHHHHHHHHHhCCC------CChHHHHHHHHhcCCeEEEEeecChH-hHHHHHHHH
Confidence 56665532 1 2347899999999999999875544 22355566667776555555544433 299999999
Q ss_pred hhcchhhhccCCC
Q 040614 142 LDKFDYAWNKGNN 154 (475)
Q Consensus 142 L~~fdYAWN~~~N 154 (475)
+..|+..||..-+
T Consensus 71 i~~~~~~~N~~~~ 83 (84)
T smart00465 71 IKEYKPKYNLLLK 83 (84)
T ss_pred HHhcCCCcceeeC
Confidence 9999999997544
No 2
>PHA02598 denA endonuclease II; Provisional
Probab=96.28 E-value=0.0058 Score=56.42 Aligned_cols=82 Identities=22% Similarity=0.454 Sum_probs=56.5
Q ss_pred CCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCC-------CCccCCCCCChhHHHHHhcceee---------EEe
Q 040614 61 GPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTG-------AHLNSGCDSGRYFEDIFRRGYSI---------VYR 124 (475)
Q Consensus 61 ~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~G-------aHL~~~~~~~~Lf~eif~~g~sI---------~~R 124 (475)
--|||-+- ..| .++|+|+|.|+|.|+.+|=+++ +|+. .+..|.+.|.. |-.+ +|-
T Consensus 33 ~n~VY~~~----~~~-~viYVGKAknLkkRv~sYf~~~~~r~~~~sn~~---Kt~~L~~~I~~-g~~ve~~~~~cf~~~I 103 (138)
T PHA02598 33 KNVIYAIA----VDD-ELVYIGKTKNLRKRIDYYRNSKNWRNTNTSDIT---KSALLEEALKK-GKKVEFYARQCFNLSI 103 (138)
T ss_pred ceEEEEEE----eCC-eEEEEeehhhHHHHHHHHhCccccccccccccH---HHHHHHHHHhc-CCceEEEeeccceeEE
Confidence 46888874 223 6899999999999999995554 4653 23466666655 2222 223
Q ss_pred ecCCCc--hHHHHHHHHHHhhcchhhhcc
Q 040614 125 SAPMKN--KEDAEKTERKILDKFDYAWNK 151 (475)
Q Consensus 125 ~a~t~~--K~~Ae~tE~~lL~~fdYAWN~ 151 (475)
..++.. ..+|+-.|.+|+..|+=.||.
T Consensus 104 ~t~~~~~~~~~a~llE~~lIk~~~P~~N~ 132 (138)
T PHA02598 104 TNPLGSMTIATMDLEEPKFIKKFNPEWNK 132 (138)
T ss_pred ecCCCcchhhhHHhhHHHHHHHhCChHHH
Confidence 344433 337888999999999999985
No 3
>PRK10545 nucleotide excision repair endonuclease; Provisional
Probab=95.93 E-value=0.0092 Score=60.38 Aligned_cols=81 Identities=22% Similarity=0.368 Sum_probs=58.8
Q ss_pred eecCCCCCCCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCCchH
Q 040614 53 VHNLPNDTGPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNKE 132 (475)
Q Consensus 53 v~nLp~~~~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K~ 132 (475)
+.+|| +-||||=+= ...|-+++|+|.|.|||+|+.+|=++. .... +..+...|- |-.|.+--
T Consensus 28 l~~LP--~~PGVYlf~---d~~g~~~LYVGKAknLR~RV~syF~~~-------k~~~----m~~~i~~Ie--~i~T~sEl 89 (286)
T PRK10545 28 LEDLP--KLPGVYLFH---GESDTMPLYIGKSVNIRSRVLSHLRTP-------DEAA----MLRQSRRIS--WICTAGEI 89 (286)
T ss_pred HHhCC--CCCeEEEEE---cCCCCEEEEEechHhHHHHHHHHcCcH-------HHHH----HHHhcceEE--EEEeCCHH
Confidence 67888 899999772 235667899999999999999998641 1123 444444444 45677777
Q ss_pred HHHHHHHHHhhcchhhhcc
Q 040614 133 DAEKTERKILDKFDYAWNK 151 (475)
Q Consensus 133 ~Ae~tE~~lL~~fdYAWN~ 151 (475)
+|.-.|.+|+..+---.|+
T Consensus 90 eALLLE~~LIK~~~P~yN~ 108 (286)
T PRK10545 90 GALLLEARLIKEQQPLFNK 108 (286)
T ss_pred HHHHHHHHHHHHhCCcchh
Confidence 9999999998877655543
No 4
>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=95.02 E-value=0.034 Score=60.98 Aligned_cols=83 Identities=27% Similarity=0.486 Sum_probs=59.5
Q ss_pred eeecCCCCCCCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCCch
Q 040614 52 KVHNLPNDTGPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNK 131 (475)
Q Consensus 52 Rv~nLp~~~~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K 131 (475)
.+.+|| .-||||=+= ...|- ++|+|.|.|+|+|+.+|=... | ...+..|.++|.. +.|-.|.|.
T Consensus 4 kl~~lP--~~PGVYl~~---d~~g~-viYVGKAknLr~Rv~sYF~~~-~---~~K~~~mv~~i~~------ie~ivt~sE 67 (574)
T TIGR00194 4 KLKNLP--DKPGCYLMK---DRNGQ-VLYVGKAKNLKKRVSSYFREN-N---SAKTQALVKQIAD------IEYILTKNE 67 (574)
T ss_pred hHhhCC--CCCeEEEEE---CCCCC-EEEEecHHHHHHHHHHhcCCC-C---CchHHHHHHhcCe------EEEEEeCCH
Confidence 467888 899999762 23343 399999999999999998853 4 1233456666644 345568888
Q ss_pred HHHHHHHHHHhhcchhhhc
Q 040614 132 EDAEKTERKILDKFDYAWN 150 (475)
Q Consensus 132 ~~Ae~tE~~lL~~fdYAWN 150 (475)
-+|.-.|.+|+..|.=-+|
T Consensus 68 ~eALlLE~~lIK~~~P~YN 86 (574)
T TIGR00194 68 NEALILEANLIKQYQPRYN 86 (574)
T ss_pred HHHHHHHHHHHHHhCCCcc
Confidence 8999999999886654443
No 5
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=94.98 E-value=0.034 Score=61.03 Aligned_cols=80 Identities=25% Similarity=0.439 Sum_probs=57.2
Q ss_pred eeecCCCCCCCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCCch
Q 040614 52 KVHNLPNDTGPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNK 131 (475)
Q Consensus 52 Rv~nLp~~~~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K 131 (475)
.+.+|| .-||||=+- . .| -++|+|.|.|+|+|+.+|=+. | . ..+..|.++|.. | -|-.|.|.
T Consensus 9 k~~~LP--~~PGVYl~~---d-~g-~viYVGKAknLr~RV~sYF~~--~-~--~k~~~lv~~i~~----i--e~i~t~sE 70 (577)
T PRK14668 9 RAAELP--REPGVYQFV---A-GG-TVLYVGKAVDLRDRVRSYADP--R-S--ERIRRMVERADD----I--DFAVTDTE 70 (577)
T ss_pred HHHhCC--CCCEEEEEc---C-CC-eEEEeeCcHhHHHHHHHHcCC--C-C--hHHHHHHHhhCe----E--EEEEeCCH
Confidence 578899 899999974 2 45 569999999999999999642 2 1 122345555533 3 34457788
Q ss_pred HHHHHHHHHHhhcchhhh
Q 040614 132 EDAEKTERKILDKFDYAW 149 (475)
Q Consensus 132 ~~Ae~tE~~lL~~fdYAW 149 (475)
-+|.-.|..|+..|.=-+
T Consensus 71 ~eALlLE~~LIK~~~P~Y 88 (577)
T PRK14668 71 TQALLLEANLIKRHQPRY 88 (577)
T ss_pred HHHHHHHHHHHHHhCCcc
Confidence 899999999988654444
No 6
>PRK07883 hypothetical protein; Validated
Probab=94.83 E-value=0.038 Score=60.11 Aligned_cols=82 Identities=23% Similarity=0.339 Sum_probs=59.3
Q ss_pred ceeeecCCCCCCCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCC
Q 040614 50 RYKVHNLPNDTGPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMK 129 (475)
Q Consensus 50 RyRv~nLp~~~~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~ 129 (475)
|-.+.+|| .-||||=+= ...|- ++|+|.|.|+|+|+.+|=+...|-. .+..|.++|-. +.|-.|.
T Consensus 208 ~~~~~~lP--~~PGVY~~~---d~~g~-viYVGKAknLr~Rv~sYF~~~~~~~---k~~~lv~~i~~------ie~i~t~ 272 (557)
T PRK07883 208 RHLADGLP--HAPGVYLFR---GPSGE-VLYVGTAVNLRRRVRSYFTAAETRG---RMREMVALAER------VDHVECA 272 (557)
T ss_pred hHHHhhCC--CCceEEEEE---CCCCc-EEEeehhhhHHHHHHHHcCCCCCCc---hHHHHHhhhce------EEEEEeC
Confidence 34678888 899999773 23343 8999999999999999987543211 23456666633 3455688
Q ss_pred chHHHHHHHHHHhhcch
Q 040614 130 NKEDAEKTERKILDKFD 146 (475)
Q Consensus 130 ~K~~Ae~tE~~lL~~fd 146 (475)
+.-+|.-.|..|+..+.
T Consensus 273 sE~eAllLE~~lIk~~~ 289 (557)
T PRK07883 273 HALEAEVRELRLIAAHK 289 (557)
T ss_pred CHHHHHHHHHHHHHHhC
Confidence 88899999999988553
No 7
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=94.83 E-value=0.04 Score=61.05 Aligned_cols=81 Identities=26% Similarity=0.509 Sum_probs=58.6
Q ss_pred eeecCCCCCCCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCCch
Q 040614 52 KVHNLPNDTGPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNK 131 (475)
Q Consensus 52 Rv~nLp~~~~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K 131 (475)
.+.+|| .-||||=+= ...| -++|+|.|.|+|+|+.+|=+...+.. ..+..|.++|.. +.|-.|.|.
T Consensus 6 kl~~lP--~~PGVYl~~---d~~g-~viYVGKAknLr~RV~sYF~~~~~~~--~K~~~lv~~i~~------ie~i~t~sE 71 (624)
T PRK14669 6 KIRTLP--TSPGVYLYK---NAGG-EVIYVGKAKNLRSRVRSYFSEDKLGN--IKTGSLIREAVD------IDYILVDNE 71 (624)
T ss_pred HHHhCC--CCCeEEEEE---CCCC-CEEEeeCchhHHHHHHHHhccCccCC--hHHHHHHHhhce------EEEEEeCCH
Confidence 467888 899999872 2333 37899999999999999988653222 123456666644 445567888
Q ss_pred HHHHHHHHHHhhcch
Q 040614 132 EDAEKTERKILDKFD 146 (475)
Q Consensus 132 ~~Ae~tE~~lL~~fd 146 (475)
-+|.-.|..|+..|.
T Consensus 72 ~EALlLE~~LIk~~~ 86 (624)
T PRK14669 72 KEALALENNLIKQYK 86 (624)
T ss_pred HHHHHHHHHHHhhhC
Confidence 899999999988654
No 8
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=94.18 E-value=0.058 Score=59.33 Aligned_cols=81 Identities=23% Similarity=0.484 Sum_probs=57.0
Q ss_pred eeecCCCCCCCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCCch
Q 040614 52 KVHNLPNDTGPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNK 131 (475)
Q Consensus 52 Rv~nLp~~~~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K 131 (475)
.+.+|| .-||||=+= ...|. ++|+|.|.|+|+|+.+|=+...|.. .+..|.++|.. +-|-.|.|-
T Consensus 7 ~l~~lP--~~PGVY~~~---d~~g~-viYVGKAknLr~Rv~sYF~~~~~~~---k~~~lv~~i~~------ie~i~t~sE 71 (598)
T PRK00558 7 KLKTLP--DSPGVYRMK---DANGT-VIYVGKAKNLKNRVRSYFRKSHDSP---KTRAMVSEIAD------IEYIVTRSE 71 (598)
T ss_pred HHhhCC--CCCeEEEEE---CCCCC-EEEecCchhHHHHHHhhCCCCCcCh---HHHHHHHhcCe------EEEEEeCCH
Confidence 467888 799999772 23343 4999999999999999987543322 22345555533 334567788
Q ss_pred HHHHHHHHHHhhcchh
Q 040614 132 EDAEKTERKILDKFDY 147 (475)
Q Consensus 132 ~~Ae~tE~~lL~~fdY 147 (475)
-+|.-.|..|+..+-=
T Consensus 72 ~eALlLE~~LIK~~~P 87 (598)
T PRK00558 72 TEALLLENNLIKKYKP 87 (598)
T ss_pred HHHHHHHHHHHHHhCC
Confidence 8999999999885543
No 9
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed
Probab=93.96 E-value=0.083 Score=57.47 Aligned_cols=80 Identities=23% Similarity=0.375 Sum_probs=56.3
Q ss_pred eecCCCCCCCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCCchH
Q 040614 53 VHNLPNDTGPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNKE 132 (475)
Q Consensus 53 v~nLp~~~~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K~ 132 (475)
+.+|| .-||||-+= ...| -++|+|.|.|+|+|+.+|=+...| . ..+..|.++|.. +-|-.|.+.-
T Consensus 4 l~~lP--~~PGVYl~~---d~~g-~vIYVGKAknLr~RV~sYF~~~~~-~--~K~~~lv~~i~~------ie~ivt~sE~ 68 (519)
T PRK12306 4 LSTIP--TNPGCYLYK---DEEG-TIIYVGKAKNLKKRVSSYFQKKDH-D--PKTQSLVKAIRD------IEFIVTDNEV 68 (519)
T ss_pred hhHCC--CCCeEEEEE---CCCC-CEEEeccchhHHHHHHHhCCCCCC-C--hHHHHHHHHhcE------EEEEEeCCHH
Confidence 56788 789999873 2334 349999999999999999875222 2 122346666644 3344577888
Q ss_pred HHHHHHHHHhhcchh
Q 040614 133 DAEKTERKILDKFDY 147 (475)
Q Consensus 133 ~Ae~tE~~lL~~fdY 147 (475)
+|.-.|..|+..+.=
T Consensus 69 eALlLE~~LIK~~~P 83 (519)
T PRK12306 69 EALLLENTLIKKHWP 83 (519)
T ss_pred HHHHHHHHHHHHhCc
Confidence 999999999885543
No 10
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=93.85 E-value=0.087 Score=57.86 Aligned_cols=79 Identities=16% Similarity=0.316 Sum_probs=57.1
Q ss_pred eeecCCCCCCCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCCch
Q 040614 52 KVHNLPNDTGPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNK 131 (475)
Q Consensus 52 Rv~nLp~~~~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K 131 (475)
.+.+|| .-||||=+= ..| -++|+|.|.|+|+|+.+|=+. ++.. ..+..|.++|.. +-|-.|.|.
T Consensus 9 ~l~~lP--~~PGVYl~~----~~g-~viYVGKAknLr~RV~sYF~~-~~~~--~K~~~lv~~i~~------ie~i~t~sE 72 (567)
T PRK14667 9 LIEKAP--EEPGVYLFK----KKK-RYIYIGKAKNIKNRLLQHYKQ-SETD--PKERAIFSESSS------LEWIITRNE 72 (567)
T ss_pred HHHhCC--CCCeEEEEe----cCC-eEEEeeCcHhHHHHHHHHcCC-CCCC--hHHHHHHHhhCe------EEEEEeCCH
Confidence 477899 899999774 222 478999999999999999874 3222 123456666644 334567888
Q ss_pred HHHHHHHHHHhhcch
Q 040614 132 EDAEKTERKILDKFD 146 (475)
Q Consensus 132 ~~Ae~tE~~lL~~fd 146 (475)
-+|.-.|.+|+..+.
T Consensus 73 ~EALlLE~~LIK~~~ 87 (567)
T PRK14667 73 YEALVLEIDLIQQYK 87 (567)
T ss_pred HHHHHHHHHHHHHhC
Confidence 899999999988554
No 11
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=93.68 E-value=0.096 Score=58.01 Aligned_cols=83 Identities=27% Similarity=0.447 Sum_probs=59.0
Q ss_pred ceeeecCCCCCCCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCC
Q 040614 50 RYKVHNLPNDTGPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMK 129 (475)
Q Consensus 50 RyRv~nLp~~~~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~ 129 (475)
+..+.+|| .-||||=+= ...|- ++|+|.|.|+|+|+.+|=+...+.. ..+..|.++|.. +.|-.|.
T Consensus 13 ~~~l~~lP--~~PGVYl~~---d~~g~-viYVGKAknLr~RV~sYF~~~~~~~--~K~~~lv~~i~~------ie~i~t~ 78 (621)
T PRK14671 13 VEKLASLP--TSPGVYQFK---NAAGR-VIYVGKAKNLRNRVRSYFRNSRQLS--GKTLVLVGHIAD------LEVIITS 78 (621)
T ss_pred HHHHHhCC--CCCeEEEEE---CCCCC-EEEeecchhHHHHHHHHcCCCCCCC--hHHHHHHHhhce------EEEEEeC
Confidence 34678899 899999773 23342 4999999999999999987544322 122345666644 3455678
Q ss_pred chHHHHHHHHHHhhcch
Q 040614 130 NKEDAEKTERKILDKFD 146 (475)
Q Consensus 130 ~K~~Ae~tE~~lL~~fd 146 (475)
+.-+|.-.|.+|+..|-
T Consensus 79 sE~EALlLE~~LIk~~~ 95 (621)
T PRK14671 79 SEVEALILENNLIKELK 95 (621)
T ss_pred CHHHHHHHHHHHHHHhC
Confidence 88899999999988553
No 12
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=93.62 E-value=0.068 Score=58.93 Aligned_cols=82 Identities=26% Similarity=0.405 Sum_probs=60.3
Q ss_pred eecCCCCCCCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCCchH
Q 040614 53 VHNLPNDTGPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNKE 132 (475)
Q Consensus 53 v~nLp~~~~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K~ 132 (475)
+.+|| +-||||-+-= .. =.|.|+|.|.|+|.|+++|-+...| ..+..|..+|.. +.|-.|++-.
T Consensus 9 l~~lP--~~PGvY~~~d---~~-g~VlYVGKAknLr~Rv~sYF~~~~~----~kt~~lv~~i~~------iE~ivt~~E~ 72 (581)
T COG0322 9 LKNLP--HSPGVYLMKD---EN-GTVLYVGKAKNLRKRVSSYFRGRLD----PKTAALVENIAD------IEYIVTDTET 72 (581)
T ss_pred HHhCC--CCCeeEEEEC---CC-CCEEEEeehhhHHHHHHHhhcCCCc----HHHHHHHHhhcc------eeEEEeCCHH
Confidence 77888 8999997631 11 3579999999999999999987777 223456666644 2334577788
Q ss_pred HHHHHHHHHhhcchhhhc
Q 040614 133 DAEKTERKILDKFDYAWN 150 (475)
Q Consensus 133 ~Ae~tE~~lL~~fdYAWN 150 (475)
+|.-.|..|+.+|.=-.|
T Consensus 73 EALlLE~nLIK~~~PrYN 90 (581)
T COG0322 73 EALLLENNLIKKHKPRYN 90 (581)
T ss_pred HHHHHHHhHHHhhCCcee
Confidence 999999999987764443
No 13
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=93.41 E-value=0.11 Score=58.52 Aligned_cols=81 Identities=22% Similarity=0.394 Sum_probs=57.2
Q ss_pred eeecCCCCCCCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCCch
Q 040614 52 KVHNLPNDTGPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNK 131 (475)
Q Consensus 52 Rv~nLp~~~~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K 131 (475)
.+.+|| .-||||=+= ...| -++|+|.|.|+|+|+.+|=+...+.. ..+..|.++|.. +.|-.|.+.
T Consensus 5 ~l~~LP--~~PGVYlfk---D~~G-~VIYVGKAKNLR~RV~SYF~~~~~~~--~K~~~Lv~~i~~------Ie~ivT~sE 70 (694)
T PRK14666 5 DLSTIP--LTPGVYLYK---DEAG-RIIYVGKARHLRRRVASYFRDVSALT--PKTVAMLRHAVT------IDTLSTTTE 70 (694)
T ss_pred hHhhCC--CCCeEEEEE---CCCC-CEEEeeCcHhHHHHHHHHcCCCCCCC--hHHHHHHHhcCe------eEEEEeCCH
Confidence 467888 899999873 2334 34999999999999999986433222 122355655544 344567888
Q ss_pred HHHHHHHHHHhhcch
Q 040614 132 EDAEKTERKILDKFD 146 (475)
Q Consensus 132 ~~Ae~tE~~lL~~fd 146 (475)
-+|.-.|..|+..|.
T Consensus 71 ~EALLLE~~LIK~~k 85 (694)
T PRK14666 71 KEALLLEASLIKKHR 85 (694)
T ss_pred HHHHHHHHHHHHHhC
Confidence 899999999988653
No 14
>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=91.52 E-value=0.24 Score=38.46 Aligned_cols=62 Identities=15% Similarity=0.234 Sum_probs=37.3
Q ss_pred EEeecchhhHHHHHHhccC-CCCCccCCCCCChhHHHHHhcceeeEEeecCCCchHHHHHHHHHHhhcchh
Q 040614 78 VVYVGQAESVRARLQAYGR-TGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNKEDAEKTERKILDKFDY 147 (475)
Q Consensus 78 vvYlGqa~nvR~RLq~Ygr-~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K~~Ae~tE~~lL~~fdY 147 (475)
.+|+|+|.|++.||.+|-. .+.+-.. .+. --...+.+. =+....+..++...|..++..|+-
T Consensus 14 ~~YIG~t~nl~~R~~~H~~~~~~~~~~-----~~~--~~~~~~~~~-~~~~~~~~~~~~~~E~~~i~~~~~ 76 (80)
T PF01541_consen 14 KIYIGSTKNLKKRLNEHFSGNKSKKKK-----QKK--YGWDNFEFI-IIEEFNTKSEALKLEQYLIKKLKP 76 (80)
T ss_dssp EEEEEEESSHHHHHHHHHHHCTHCSHC-----HHH--HHSSCEEEE-EEEEESSHHHHHHHHHHHHHHHHH
T ss_pred EEEEEEECCHHHHHHHHhcCCCCCcch-----hhh--cccccEEEE-eeEEeCCHHHHHHHHHHHHHHHcC
Confidence 4699999999999998722 2222110 111 112223332 133455666779999999998876
No 15
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=91.19 E-value=0.31 Score=54.99 Aligned_cols=84 Identities=24% Similarity=0.363 Sum_probs=58.7
Q ss_pred ceeeecCCCCCCCceeeeeeecCCCcEEEEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCC
Q 040614 50 RYKVHNLPNDTGPGLYELGIAVPGAGVIVVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMK 129 (475)
Q Consensus 50 RyRv~nLp~~~~pGlYELGVa~~~~~vvvvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~ 129 (475)
+-.+.+|| .-||||=+= ...| -++|+|.|.|+|+|+.+|=+. +|=. .+..|.++|.. +-|-.|.
T Consensus 12 ~~~~~~LP--~~PGVYlfk---d~~G-~VLYVGKAKNLR~RV~SYF~~-~~~~---K~~~Lv~~i~~------Ie~ivT~ 75 (691)
T PRK14672 12 RIQALSAP--STSGVYLWK---DVHG-VVIYVGKAKSLRTRLTSYFRC-RHDP---KTRVLMSRAAA------LEYLQTQ 75 (691)
T ss_pred HHHHHhCC--CCCeEEEEE---CCCC-CEEEeeCcHHHHHHHHHHcCC-CCCc---hHHHHHHhhCc------EEEEEeC
Confidence 44678899 899999873 1222 468999999999999999875 3311 11235555543 3344678
Q ss_pred chHHHHHHHHHHhhcchhhh
Q 040614 130 NKEDAEKTERKILDKFDYAW 149 (475)
Q Consensus 130 ~K~~Ae~tE~~lL~~fdYAW 149 (475)
+.-+|.-.|.+|+..|-=..
T Consensus 76 sE~EALLLE~~LIK~~kP~Y 95 (691)
T PRK14672 76 HEYEALLLENTLIKKHTPRY 95 (691)
T ss_pred CHHHHHHHHHHHHHHhCchh
Confidence 88899999999988664444
No 16
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=84.44 E-value=1.1 Score=49.57 Aligned_cols=59 Identities=14% Similarity=0.283 Sum_probs=43.9
Q ss_pred EEeecchhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEEeecCCCchHHHHHHHHHHhhcch
Q 040614 78 VVYVGQAESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNKEDAEKTERKILDKFD 146 (475)
Q Consensus 78 vvYlGqa~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K~~Ae~tE~~lL~~fd 146 (475)
++|+|.|.|+|+|+.+|=+. +| . ..+..|.++|.. +-|-.|.|.-+|.-.|..|+..|.
T Consensus 8 vIYVGKAknLr~RV~sYF~~-~~-~--~K~~~lv~~i~~------ie~ivt~sE~EALlLE~~LIK~~~ 66 (574)
T PRK14670 8 ILYIGKAKNLRSRVKNYFLE-KI-S--HKTKILMKNVKN------IEVITTNSEYEALLLECNLIKTHK 66 (574)
T ss_pred EEEeeCcHhHHHHHHHHcCC-CC-C--chHHHHHHhcCe------EEEEEeCCHHHHHHHHHHHHHHhC
Confidence 68999999999999999875 23 1 233456666644 344567888899999999988553
No 17
>PF09740 DUF2043: Uncharacterized conserved protein (DUF2043); InterPro: IPR018610 This entry consists of uncharacterised proteins of unknown function. They contain three conserved cysteines and a {CP}{y/l}{HG} motif.
Probab=72.60 E-value=2 Score=38.68 Aligned_cols=24 Identities=38% Similarity=0.713 Sum_probs=20.1
Q ss_pred cccccccCCCCcccccccCcCcccCC
Q 040614 450 SLCGAPTRNGSSCRRSVKGGGRCWQH 475 (475)
Q Consensus 450 ~~CG~~~~~Gs~C~~~v~GrkRC~~H 475 (475)
-.|.|+|.||+-|.|+ -+++|+.|
T Consensus 70 ~~CrAPL~~G~LC~Rr--D~~kCPfH 93 (110)
T PF09740_consen 70 HACRAPLPNGGLCPRR--DRKKCPFH 93 (110)
T ss_pred hhhcCCCCCCCcCCcc--CcccCCCC
Confidence 4499999999999998 23479988
No 18
>PF11722 zf-TRM13_CCCH: CCCH zinc finger in TRM13 protein; InterPro: IPR021721 This domain is found at the N terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain. ; GO: 0008168 methyltransferase activity
Probab=53.05 E-value=6.9 Score=28.00 Aligned_cols=26 Identities=27% Similarity=0.498 Sum_probs=21.0
Q ss_pred eeEEec-CCceeeeeccCCcccccccc
Q 040614 353 CGVELG-GGTFCTRQPVKGRVRCEQHK 378 (475)
Q Consensus 353 CGv~L~-dg~~C~r~PV~GRkRCeeHK 378 (475)
|...|. -+++|++++.+|.+.|-||.
T Consensus 4 C~f~l~~K~R~C~m~~~~g~~fC~~H~ 30 (31)
T PF11722_consen 4 CEFFLPRKKRFCKMTRKPGSRFCGEHM 30 (31)
T ss_pred ceEECCccccccCCeecCcCCccccCC
Confidence 554444 36899999999999999994
No 19
>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=52.42 E-value=47 Score=32.12 Aligned_cols=81 Identities=19% Similarity=0.333 Sum_probs=49.4
Q ss_pred EEeecchhhHHHHHHhccC---CCCCccCCCCCChhHHHHHhcce-----eeEEeecCCCchHHHHHHHHHHhhcchh--
Q 040614 78 VVYVGQAESVRARLQAYGR---TGAHLNSGCDSGRYFEDIFRRGY-----SIVYRSAPMKNKEDAEKTERKILDKFDY-- 147 (475)
Q Consensus 78 vvYlGqa~nvR~RLq~Ygr---~GaHL~~~~~~~~Lf~eif~~g~-----sI~~R~a~t~~K~~Ae~tE~~lL~~fdY-- 147 (475)
.+|+|++.|+..|+.+|=. .|.|- -|...|-.-|. .|+--. -++++....|..+++.|+=
T Consensus 14 k~YIGss~nl~~R~~~h~~~~~~~~~~-------~l~~ai~kyG~~nF~~~ile~~---~~~~~l~~lE~~~I~~l~~~~ 83 (214)
T TIGR01453 14 KIYVGSSVNLEKRLKEHLKLLKKGNRI-------KLQKALNKYGWSNFSFEILEYY---CNKDDLIERETYYIKLLNPDA 83 (214)
T ss_pred cEEEEeccCHHHHHHHHHHHHhcCChH-------HHHHHHHHhChHheEEEEEEEe---CCHHHHHHHHHHHHHHcCCcC
Confidence 5799999999999998854 33331 23333333332 222211 3566777889999988876
Q ss_pred hhccCC-----CCcccchHHHHHhhh
Q 040614 148 AWNKGN-----NGKRRHADVRRKLDE 168 (475)
Q Consensus 148 AWN~~~-----Ng~rR~~DIl~kl~~ 168 (475)
-.|-.. .|-..++|..+|+.+
T Consensus 84 ~YNi~~~~~s~~G~khs~etk~k~s~ 109 (214)
T TIGR01453 84 GYNILKIAGSSLGYKHSEETKAKMSK 109 (214)
T ss_pred ccccccccccccccccCHHHHHhhhH
Confidence 666322 345556666555554
No 20
>PF08313 SCA7: SCA7, zinc-binding domain; InterPro: IPR013243 SAGA (Spt-Ada-Gcn5 acetyltransferase), a coactivator complex involved in chromatin remodelling, harbours both histone acetylation and deubiquitination activities. SAGA-associated factor 73 (Sgf734/ATXN7) and Ataxin-7-like protein 3 (ATXN7L3), two subunits of the SAGA deubiquitination module, contain an ~50-residue SCA7 domain characterised by an atypical zinc- finger (Znf) with a Cys-X(9,10)-Cys-X(5)-Cys-X(2)-His motif and a long sequence insertion between the first two zinc coordinating residues. The SCA7 domain is found exclusively in members of the ATXN7 gene family, which includes two distinct subunits of SAGA complexes: ATXN7 and ATXN7L3 orthologues. The analysis of multiple alignments highlights the consensus signature for the SCA7 domain, encompassing the putative zinc- coordinating residues, but also reveals the distinct features of the two proteins. Marked differences are found mostly in the carboxy-terminal of the domain, suggesting that divergent evolution of the SCA7 Znf domain occurred in order to achieve specific functions in the SAGA complex. Both SCA7 domains contain disordered regions, albeit not in the same region. Whereas the first and last 10 residues of ATXN7-SCA7 are not folded, the N- terminal region of ATXN7L3-SCA7 is well structured and the last 30 residues of this domain are not folded. In both ATXN7-SCA7 and ATXN7L3-SCA7, the large sequence insertion between the first and second zinc- coordinating cysteines corresponds to a protruding extended hairpin structure. The core of the zinc-binding sites shows a conserved structure formed by two short adjacent loops located at the bottom of the hairpin. Although the SCA7 domains of both ATXN7 and ATXN7L3 contain two alpha-helices, these are not located at similar positions in the sequences. In ATXN7-SCA7, the two alpha- helices are located downstream from the zinc-binding site and are separated by a loop containing a large number of positively charged residues. In ATXN7L3- SCA7, the two helices lie to either side of the zinc-binding site, leading to a different packing of the two helices. In ATXN7-SCA7, the two helices have an almost perpendicular orientation, the alpha2 helix being anchored to the zinc- binding site. In ATXN7L3-SCA7, the helices alpha1 and alpha2 adopt an anti- parallel orientation defined by hydrophobic interactions. The ATXN7-SCA7 domain binds to the core or the C-terminal ends of the histone H2A and H2B dimer, a region located on the lateral face of the nucleosome that contains the ubiquitinated Lys 120 of H2B. This property is lost in the ATXN7-SCA7 domain [, ]. This entry represents the SCA7 domain.; PDB: 2KKR_A 2KKT_A.
Probab=46.36 E-value=9.5 Score=32.31 Aligned_cols=26 Identities=27% Similarity=0.526 Sum_probs=15.4
Q ss_pred CCcccceeecCCCCccCCCCCCCCccccccc
Q 040614 228 GHTGICGVSLGDGSVCQMPPVEQRKRCIEHR 258 (475)
Q Consensus 228 ~~~~~CGv~l~dG~~C~~~Pv~grKRC~~HK 258 (475)
+.+..|||++++|.+|.+. -.|..|.
T Consensus 19 D~d~~CGV~~~~~~~CtRS-----LtCk~Hs 44 (73)
T PF08313_consen 19 DPDKQCGVIDPEGKPCTRS-----LTCKSHS 44 (73)
T ss_dssp -TTTC--S-BTTTTS--SB-----TTSTTS-
T ss_pred CCCccCCeECCCCCCCCCc-----cccCCCC
Confidence 5567899999999999875 4688883
No 21
>PF08313 SCA7: SCA7, zinc-binding domain; InterPro: IPR013243 SAGA (Spt-Ada-Gcn5 acetyltransferase), a coactivator complex involved in chromatin remodelling, harbours both histone acetylation and deubiquitination activities. SAGA-associated factor 73 (Sgf734/ATXN7) and Ataxin-7-like protein 3 (ATXN7L3), two subunits of the SAGA deubiquitination module, contain an ~50-residue SCA7 domain characterised by an atypical zinc- finger (Znf) with a Cys-X(9,10)-Cys-X(5)-Cys-X(2)-His motif and a long sequence insertion between the first two zinc coordinating residues. The SCA7 domain is found exclusively in members of the ATXN7 gene family, which includes two distinct subunits of SAGA complexes: ATXN7 and ATXN7L3 orthologues. The analysis of multiple alignments highlights the consensus signature for the SCA7 domain, encompassing the putative zinc- coordinating residues, but also reveals the distinct features of the two proteins. Marked differences are found mostly in the carboxy-terminal of the domain, suggesting that divergent evolution of the SCA7 Znf domain occurred in order to achieve specific functions in the SAGA complex. Both SCA7 domains contain disordered regions, albeit not in the same region. Whereas the first and last 10 residues of ATXN7-SCA7 are not folded, the N- terminal region of ATXN7L3-SCA7 is well structured and the last 30 residues of this domain are not folded. In both ATXN7-SCA7 and ATXN7L3-SCA7, the large sequence insertion between the first and second zinc- coordinating cysteines corresponds to a protruding extended hairpin structure. The core of the zinc-binding sites shows a conserved structure formed by two short adjacent loops located at the bottom of the hairpin. Although the SCA7 domains of both ATXN7 and ATXN7L3 contain two alpha-helices, these are not located at similar positions in the sequences. In ATXN7-SCA7, the two alpha- helices are located downstream from the zinc-binding site and are separated by a loop containing a large number of positively charged residues. In ATXN7L3- SCA7, the two helices lie to either side of the zinc-binding site, leading to a different packing of the two helices. In ATXN7-SCA7, the two helices have an almost perpendicular orientation, the alpha2 helix being anchored to the zinc- binding site. In ATXN7L3-SCA7, the helices alpha1 and alpha2 adopt an anti- parallel orientation defined by hydrophobic interactions. The ATXN7-SCA7 domain binds to the core or the C-terminal ends of the histone H2A and H2B dimer, a region located on the lateral face of the nucleosome that contains the ubiquitinated Lys 120 of H2B. This property is lost in the ATXN7-SCA7 domain [, ]. This entry represents the SCA7 domain.; PDB: 2KKR_A 2KKT_A.
Probab=40.38 E-value=11 Score=31.88 Aligned_cols=26 Identities=38% Similarity=0.733 Sum_probs=14.7
Q ss_pred ccccceeeEEecCCceeeeeccCCccccccc
Q 040614 347 LQYDTICGVELGGGTFCTRQPVKGRVRCEQH 377 (475)
Q Consensus 347 ~~~~~iCGv~L~dg~~C~r~PV~GRkRCeeH 377 (475)
.+.+..|||++.++..|.+. =.|..|
T Consensus 18 ~D~d~~CGV~~~~~~~CtRS-----LtCk~H 43 (73)
T PF08313_consen 18 VDPDKQCGVIDPEGKPCTRS-----LTCKSH 43 (73)
T ss_dssp --TTTC--S-BTTTTS--SB-----TTSTTS
T ss_pred cCCCccCCeECCCCCCCCCc-----cccCCC
Confidence 46789999999999999875 345555
No 22
>PF09740 DUF2043: Uncharacterized conserved protein (DUF2043); InterPro: IPR018610 This entry consists of uncharacterised proteins of unknown function. They contain three conserved cysteines and a {CP}{y/l}{HG} motif.
Probab=38.74 E-value=17 Score=33.01 Aligned_cols=24 Identities=33% Similarity=0.761 Sum_probs=20.9
Q ss_pred cceeecCCCCccCCCCCCCCccccccc
Q 040614 232 ICGVSLGDGSVCQMPPVEQRKRCIEHR 258 (475)
Q Consensus 232 ~CGv~l~dG~~C~~~Pv~grKRC~~HK 258 (475)
.|..-|.+|.-|. ...+++||.|-
T Consensus 71 ~CrAPL~~G~LC~---RrD~~kCPfHG 94 (110)
T PF09740_consen 71 ACRAPLPNGGLCP---RRDRKKCPFHG 94 (110)
T ss_pred hhcCCCCCCCcCC---ccCcccCCCCC
Confidence 5999999999995 56788999994
No 23
>PRK00329 GIY-YIG nuclease superfamily protein; Validated
Probab=36.06 E-value=90 Score=26.58 Aligned_cols=52 Identities=21% Similarity=0.394 Sum_probs=32.9
Q ss_pred EEeecchhhHHHHHHhccCC-CCCccCCCCCChhHHHHHhcceeeEEeecCCCchHHHHHHHHHH
Q 040614 78 VVYVGQAESVRARLQAYGRT-GAHLNSGCDSGRYFEDIFRRGYSIVYRSAPMKNKEDAEKTERKI 141 (475)
Q Consensus 78 vvYlGqa~nvR~RLq~Ygr~-GaHL~~~~~~~~Lf~eif~~g~sI~~R~a~t~~K~~Ae~tE~~l 141 (475)
..|+|.|.|+-.||.+.-.. |+ ..+.. .+-.-++|= ..-.|+.+|.+.|.+|
T Consensus 18 ~~Y~G~T~dl~~Rl~qH~~g~ga--~~tr~---------~~p~~Lv~~-e~~~~~~~A~~~E~~l 70 (86)
T PRK00329 18 SLYTGITTDVERRFAQHQSGKGA--KYTRG---------RPPLTLVFV-EPVGDRSEALRAEYRF 70 (86)
T ss_pred CEEEEEcCCHHHHHHHHHcCCCC--CCccC---------CCceEEEEE-EECCCHHHHHHHHHHH
Confidence 69999999999999976321 22 11111 001123332 2455999999999997
No 24
>PF14852 Fis1_TPR_N: Fis1 N-terminal tetratricopeptide repeat; PDB: 1IYG_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A 1PC2_A 1NZN_A.
Probab=32.45 E-value=14 Score=26.88 Aligned_cols=6 Identities=67% Similarity=1.946 Sum_probs=5.6
Q ss_pred cchhhh
Q 040614 144 KFDYAW 149 (475)
Q Consensus 144 ~fdYAW 149 (475)
.|+|||
T Consensus 4 ~FnyAw 9 (35)
T PF14852_consen 4 QFNYAW 9 (35)
T ss_dssp HHHHHH
T ss_pred hhHHHH
Confidence 699999
No 25
>PF09329 zf-primase: Primase zinc finger; InterPro: IPR015408 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger domain is found in Mcm10 proteins and DnaG-type primases []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0006260 DNA replication, 0005634 nucleus; PDB: 3H15_A 3EBE_C.
Probab=25.31 E-value=30 Score=26.49 Aligned_cols=32 Identities=22% Similarity=0.337 Sum_probs=19.5
Q ss_pred eeeeEEeCCCcceecc--ccccccccccCCceee
Q 040614 406 FVCGAQTLDGSYCRRQ--VKANTKCWQHSDKSLT 437 (475)
Q Consensus 406 ~~Cga~t~nGS~C~~~--v~G~kRC~~Hkg~~v~ 437 (475)
-+|.++..||.+|.+. ..-.+.|.-|-.+.+.
T Consensus 7 G~Ck~~kkdG~~C~~~Vn~~~~~~C~yH~~~~~~ 40 (46)
T PF09329_consen 7 GYCKAVKKDGKPCTNPVNKSKGEYCDYHVESAYR 40 (46)
T ss_dssp EE-SSB-TTSSB---EEETTT-SS-TTTHHHHHC
T ss_pred ccccCCCCCCCcccCceeCCCCcccHHHHHHHHH
Confidence 4799999999999999 6677889888655443
No 26
>PF13072 DUF3936: Protein of unknown function (DUF3936)
Probab=23.46 E-value=56 Score=24.85 Aligned_cols=20 Identities=40% Similarity=0.720 Sum_probs=17.2
Q ss_pred EeecchhhHHHHHHhccCCC
Q 040614 79 VYVGQAESVRARLQAYGRTG 98 (475)
Q Consensus 79 vYlGqa~nvR~RLq~Ygr~G 98 (475)
+-+|.|=.||+.|++|++..
T Consensus 11 ~lvGKAWeIr~~Lkey~k~~ 30 (38)
T PF13072_consen 11 ILVGKAWEIRAKLKEYGKQF 30 (38)
T ss_pred EEEehHHHHHHHHHHHHHhh
Confidence 44699999999999999864
No 27
>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=21.53 E-value=1e+02 Score=24.91 Aligned_cols=19 Identities=21% Similarity=0.352 Sum_probs=17.0
Q ss_pred EeecchhhHHHHHHhccCC
Q 040614 79 VYVGQAESVRARLQAYGRT 97 (475)
Q Consensus 79 vYlGqa~nvR~RLq~Ygr~ 97 (475)
+=+|.|.++.+||++|.++
T Consensus 17 ~KIG~T~~~~~Rl~~~~~~ 35 (100)
T PF10544_consen 17 YKIGYTTNPERRLRELNRN 35 (100)
T ss_pred EEEeeECCHHHHHHHhhcc
Confidence 6789999999999999863
No 28
>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes. This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].
Probab=21.29 E-value=1e+02 Score=25.46 Aligned_cols=27 Identities=30% Similarity=0.479 Sum_probs=20.3
Q ss_pred hhhHHHHHHhccCCCCCccCCCCCChhHHHHHhcceeeEE
Q 040614 84 AESVRARLQAYGRTGAHLNSGCDSGRYFEDIFRRGYSIVY 123 (475)
Q Consensus 84 a~nvR~RLq~Ygr~GaHL~~~~~~~~Lf~eif~~g~sI~~ 123 (475)
.+++|.||..|+-.=--. -.-||+|+|
T Consensus 14 v~d~K~~Lr~y~~~~I~~-------------d~tGfYIvF 40 (66)
T PF11767_consen 14 VEDFKKRLRKYRWDRIRD-------------DRTGFYIVF 40 (66)
T ss_pred HHHHHHHHhcCCcceEEe-------------cCCEEEEEE
Confidence 579999999997543322 356999999
Done!