Query 019701
Match_columns 337
No_of_seqs 121 out of 143
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 03:51:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019701.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019701hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00767 DCD DCD is a plant 100.0 4.1E-60 8.8E-65 405.6 11.9 130 202-334 1-132 (132)
2 PF10539 Dev_Cell_Death: Devel 100.0 5.6E-60 1.2E-64 403.8 12.2 128 204-332 1-130 (130)
3 PRK00809 hypothetical protein; 98.5 4.3E-07 9.3E-12 79.0 8.0 97 208-308 5-109 (144)
4 COG1673 Uncharacterized protei 97.5 0.00013 2.8E-09 65.1 5.4 85 221-308 23-114 (151)
5 PF01878 EVE: EVE domain; Int 97.1 0.00094 2E-08 56.2 5.0 97 234-331 36-143 (143)
6 PRK02268 hypothetical protein; 96.9 0.0019 4.1E-08 57.0 5.9 97 221-330 19-134 (141)
7 COG2947 Uncharacterized conser 58.6 10 0.00022 34.7 3.1 98 232-331 36-149 (156)
8 KOG1901 Uncharacterized high-g 58.3 24 0.00052 37.2 6.2 123 206-335 299-439 (487)
9 PF08442 ATP-grasp_2: ATP-gras 53.3 3.2 6.9E-05 38.2 -0.9 130 197-336 49-191 (202)
10 PLN00124 succinyl-CoA ligase [ 40.5 35 0.00077 34.9 4.1 121 204-335 93-226 (422)
11 PF04146 YTH: YT521-B-like dom 36.7 60 0.0013 28.1 4.4 120 212-335 11-140 (140)
12 PF14875 PIP49_N: N-term cyste 32.0 14 0.00029 33.4 -0.3 32 300-331 127-158 (158)
13 PF12419 DUF3670: SNF2 Helicas 29.4 57 0.0012 28.2 3.1 47 289-335 74-124 (141)
14 KOG1447 GTP-specific succinyl- 26.0 30 0.00065 35.0 0.9 75 249-334 139-216 (412)
15 PHA02902 putative IMV membrane 23.3 93 0.002 25.3 3.0 21 314-334 48-68 (70)
16 PF08321 PPP5: PPP5 TPR repeat 20.1 83 0.0018 26.1 2.2 26 310-335 41-67 (95)
No 1
>smart00767 DCD DCD is a plant specific domain in proteins involved in development and programmed cell death. The domain is shared by several proteins in the Arabidopsis and the rice genomes, which otherwise show a different protein architecture. Biological studies indicate a role of these proteins in phytohormone response, embryo development and programmed cell death by pathogens or ozone.
Probab=100.00 E-value=4.1e-60 Score=405.57 Aligned_cols=130 Identities=66% Similarity=1.159 Sum_probs=124.5
Q ss_pred CCcceEEEeecCcChHHhhhhhhccCCccchhhhhccCCCCcEEEEeccCceEeeeeeeccCCCCccCCcCccCCCCCCC
Q 019701 202 ETIGGYIFVCNNDTMAENLKRQLFGLPPRYRDSVRAITPGLPLFLYNYSTHQLHGIFEAASFGGTNIDPTAWEDKKCPGE 281 (337)
Q Consensus 202 ~~lgG~IFmCN~~T~~ECf~r~LFGLP~~h~d~VrkIKPGmpLFLYnys~RkLhGIFEAaS~Gg~NIdP~AF~s~~~~g~ 281 (337)
+++||+|||||++|++|||+++|||||+.++++|++|||||+||||||++|+|||||||+|+|+|||+|.||.+++ +
T Consensus 1 ~~lgG~IF~Cn~~T~~Ecf~~~lFGLP~~~~~~V~~IkpG~~LFLfn~~~r~L~GifeA~S~G~~ni~p~Af~~~~---~ 77 (132)
T smart00767 1 ETLGGYIFMCNNDTKEECFRRQLFGLPRGYRDFVRNIKPGLPLFLYNYDTRKLHGIFEATSFGGLNIDPNAFEGKK---E 77 (132)
T ss_pred CCcceEEEEeCCCCHHHHHhcccccCChhhhhhhheeCCCCEEEEEecCCceeeeEEEeccCCcCCcChhHhcCCC---C
Confidence 4699999999999999999999999999999999999999999999999999999999999999999999999875 5
Q ss_pred CcCCceEEEEEeeeccCCCcccchhhh-hccCCC-CccccCCHHHHHHHHHhhhh
Q 019701 282 SRFPAQVRVVTRKICEPLEEDSFRPIL-HHYDGP-KFRLELNVPEAISLLDIFEE 334 (337)
Q Consensus 282 s~FPAQVRf~i~k~C~PL~EseFKpiI-~~Y~~~-KF~fELs~~QV~~Ll~LF~~ 334 (337)
++|||||||+|+|+|+||+|++||++| +||.++ ||++|||++||++|++||++
T Consensus 78 s~fPaQVrf~i~~~C~PL~E~~f~~aI~~nY~~~~kF~~eLs~~Qv~~L~~LF~~ 132 (132)
T smart00767 78 SRFPAQVRFRIRKDCKPLPESEFRSAILENYDGPSKFRFELSHAQVLRLLDLFAP 132 (132)
T ss_pred CccCcEEEEEEeeeecCCCHHHHHHHHHHhCcCCccccccCCHHHHHHHHHHhcC
Confidence 899999999999999999999999977 678775 99999999999999999975
No 2
>PF10539 Dev_Cell_Death: Development and cell death domain; InterPro: IPR013989 The DCD (Development and Cell Death) domain is found in plant proteins involved in development and cell death. The DCD domain is an ~130 amino acid long stretch that contains several mostly invariable motifs. These include a FGLP and a LFL motif at the N terminus and a PAQV and a PLxE motif towards the C terminus of the domain. The DCD domain is present in proteins with different architectures. Some of these proteins contain additional recognizable motifs, like the KELCH repeats or the ParB domain []. Biological studies indicate a role of these proteins in phytohormone response, embryo development and programmed cell death by pathogens or ozone. The predicted secondary structure of the DCD domain is mostly composed of beta strands and confined by an alpha-helix at the N- and at the C terminus []. Proteins known to contain a DCD domain are listed below: Carrot B2 protein. Pea Gda-1 protein. Soybean N-rich protein (NRP).
Probab=100.00 E-value=5.6e-60 Score=403.79 Aligned_cols=128 Identities=52% Similarity=0.931 Sum_probs=123.1
Q ss_pred cceEEEeecCcChHHhhhhhhccCCccchhhhhccCCCCcEEEEeccCceEeeeeeeccCCCCccCCcCccCCCCCCCCc
Q 019701 204 IGGYIFVCNNDTMAENLKRQLFGLPPRYRDSVRAITPGLPLFLYNYSTHQLHGIFEAASFGGTNIDPTAWEDKKCPGESR 283 (337)
Q Consensus 204 lgG~IFmCN~~T~~ECf~r~LFGLP~~h~d~VrkIKPGmpLFLYnys~RkLhGIFEAaS~Gg~NIdP~AF~s~~~~g~s~ 283 (337)
|||||||||++|++|||+++|||||++|+++|++||||||||||||++|+|||||||+|+|+|||+|.||.+++ .++++
T Consensus 1 lgG~IF~Cn~~T~~ECf~~~lFGLP~~~~~~V~~I~pG~~LFLfn~~~r~L~GifeA~S~G~~ni~p~Af~~~~-~~~~~ 79 (130)
T PF10539_consen 1 LGGFIFMCNNKTKPECFRRQLFGLPAGHKDFVKKIKPGMPLFLFNYSDRKLYGIFEATSDGGMNIEPYAFSGSG-SGESP 79 (130)
T ss_pred CceEEEEECCCCHHHHHhcccccCChhhhhHHheeCCCCEEEEEEcCCCEEEEEEEecCCCccCcChhhhCCCC-CCCcc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999987 46799
Q ss_pred CCceEEEEEeeeccCCCcccchhhh-h-ccCCCCccccCCHHHHHHHHHhh
Q 019701 284 FPAQVRVVTRKICEPLEEDSFRPIL-H-HYDGPKFRLELNVPEAISLLDIF 332 (337)
Q Consensus 284 FPAQVRf~i~k~C~PL~EseFKpiI-~-~Y~~~KF~fELs~~QV~~Ll~LF 332 (337)
|||||||+|+++|+||+|++||++| + ||.++||+||||++||++|++||
T Consensus 80 fPAQVrf~i~~~C~PL~E~~fk~aI~~Ny~~~~kF~~eLs~~Qv~~L~~LF 130 (130)
T PF10539_consen 80 FPAQVRFRIRWDCPPLPESQFKPAIKDNYYDKNKFRFELSHQQVRKLLSLF 130 (130)
T ss_pred cceEEEEEEeeeeecCCHHHHHHHHHHhCCCCCcccCcCCHHHHHHHHHhC
Confidence 9999999999999999999999999 4 55668999999999999999998
No 3
>PRK00809 hypothetical protein; Provisional
Probab=98.50 E-value=4.3e-07 Score=78.98 Aligned_cols=97 Identities=25% Similarity=0.473 Sum_probs=76.9
Q ss_pred EEeecCcChHHhhhhhhccCCccchhhhhccCCCCcEEEEecc-------CceEeeeeeeccCCCCccCCcCc-cCCCCC
Q 019701 208 IFVCNNDTMAENLKRQLFGLPPRYRDSVRAITPGLPLFLYNYS-------THQLHGIFEAASFGGTNIDPTAW-EDKKCP 279 (337)
Q Consensus 208 IFmCN~~T~~ECf~r~LFGLP~~h~d~VrkIKPGmpLFLYnys-------~RkLhGIFEAaS~Gg~NIdP~AF-~s~~~~ 279 (337)
|++-+.+....|.++.+||+|.+++.++++++|||.||.|.-. ...+.||.|.+++.. .||.+| .+.+.+
T Consensus 5 i~~~~~~~~~~~~~~gv~g~~~~~rn~lr~Mk~GD~v~fYhs~~~~~~~~~~~ivgi~eV~~~~y--~D~t~~~p~~~~~ 82 (144)
T PRK00809 5 LCITNEDNWEVIKDKNVWGVPERYKNTIEKVKPGDKLIIYVSQEYGAERLPGKIVGIYEVVSEWY--EDSTPIFPAEPVR 82 (144)
T ss_pred EEecCHHHHHHHHhCCEeecchhhhhHHhhCCCCCEEEEEECCccCCCCCCceEEEEEEEecCcc--cCCccCCCccccC
Confidence 5566778889999999999999999999999999999999998 578999999999875 455544 333334
Q ss_pred CCCcCCceEEEEEeeeccCCCcccchhhh
Q 019701 280 GESRFPAQVRVVTRKICEPLEEDSFRPIL 308 (337)
Q Consensus 280 g~s~FPAQVRf~i~k~C~PL~EseFKpiI 308 (337)
.+.+||.+|+++....++ .+..++++|
T Consensus 83 ~~~~~p~rvdV~~~~~~~--~~v~l~~L~ 109 (144)
T PRK00809 83 PKEIYPYRVKLKPVKIFE--EPIDFKPLI 109 (144)
T ss_pred CCCCceEEEEEEEeeecC--CcccHHHHH
Confidence 678999999999885544 224455553
No 4
>COG1673 Uncharacterized protein conserved in archaea [Function unknown]
Probab=97.55 E-value=0.00013 Score=65.14 Aligned_cols=85 Identities=20% Similarity=0.389 Sum_probs=71.5
Q ss_pred hhhhccCCccchhhhhccCCCCcEEEEeccCc-------eEeeeeeeccCCCCccCCcCccCCCCCCCCcCCceEEEEEe
Q 019701 221 KRQLFGLPPRYRDSVRAITPGLPLFLYNYSTH-------QLHGIFEAASFGGTNIDPTAWEDKKCPGESRFPAQVRVVTR 293 (337)
Q Consensus 221 ~r~LFGLP~~h~d~VrkIKPGmpLFLYnys~R-------kLhGIFEAaS~Gg~NIdP~AF~s~~~~g~s~FPAQVRf~i~ 293 (337)
.+.++|.|..+..+...|++|+.|..|..... ++.|||||+|... -.+...|...+.++...||-+|+++++
T Consensus 23 ~k~i~g~~~k~~~v~~~ik~g~~~v~y~~~~~~~~~~~~~iv~v~ev~se~y-~ds~r~f~~~~~~~~~~~~~r~k~~p~ 101 (151)
T COG1673 23 EKGIYGVREKHENVEEKIKEGDRLVIYVRQRGEKERHEPKIVGVFEVGSEPY-SDSSRIFKIDPFRGDETFPYRVKIRPV 101 (151)
T ss_pred ccceeecCCCCccHHHhhCccceeEEEeeecchhhccCccEEEEEEeecccc-ccccccccCCCCCCccccccccCcceE
Confidence 45789999999999999999999999986654 8999999999988 455556887776667899999999999
Q ss_pred eeccCCCcccchhhh
Q 019701 294 KICEPLEEDSFRPIL 308 (337)
Q Consensus 294 k~C~PL~EseFKpiI 308 (337)
+..+ ....|++.|
T Consensus 102 ~i~e--~~i~~k~~~ 114 (151)
T COG1673 102 KVGE--VHIKFKPLI 114 (151)
T ss_pred EEEe--cccCcchhh
Confidence 9866 347788765
No 5
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=97.06 E-value=0.00094 Score=56.17 Aligned_cols=97 Identities=15% Similarity=0.218 Sum_probs=60.0
Q ss_pred hhhccCCCCcEEEEecc--CceEeeeeeeccCCCCccCCcCccCCCCCCC--CcCCceEEEEEeeecc-CCCcccchh--
Q 019701 234 SVRAITPGLPLFLYNYS--THQLHGIFEAASFGGTNIDPTAWEDKKCPGE--SRFPAQVRVVTRKICE-PLEEDSFRP-- 306 (337)
Q Consensus 234 ~VrkIKPGmpLFLYnys--~RkLhGIFEAaS~Gg~NIdP~AF~s~~~~g~--s~FPAQVRf~i~k~C~-PL~EseFKp-- 306 (337)
.+++||||+.+|+|.-. .+.++||.|++++...+-.+. +...+.... .++|..|+++...... ||+-.+.|.
T Consensus 36 ~l~~mk~GD~vifY~s~~~~~~ivai~~V~~~~~~d~~~~-~~~~~~~~~~~~~~~~~v~v~~~~~~~~pi~l~~Lk~~~ 114 (143)
T PF01878_consen 36 NLKRMKPGDKVIFYHSGCKERGIVAIGEVVSEPYPDPTAF-DPDSPYYDPKSNPKPYRVDVEYVKIFEKPIPLKELKAEP 114 (143)
T ss_dssp HHHC--TT-EEEEEETSSSS-EEEEEEEEEEEEEE-GGGT-STTSTTBTTTSCSSSEEEEEEEEEEEEEEEEHHHHHC-G
T ss_pred hhhcCCCCCEEEEEEcCCCCCEEEEEEEEeccccCCCccc-cccccCcCCccCCCeeEEEEEEEEecCCCcCHHHHhcCC
Confidence 78899999999999998 689999999999866443332 111111111 3588888888876555 665444443
Q ss_pred hhhc---cCCCCcc-ccCCHHHHHHHHHh
Q 019701 307 ILHH---YDGPKFR-LELNVPEAISLLDI 331 (337)
Q Consensus 307 iI~~---Y~~~KF~-fELs~~QV~~Ll~L 331 (337)
.++. ...+.+. ++||.+|...|++|
T Consensus 115 ~l~~l~~i~~~r~s~~~it~~~~~~I~~~ 143 (143)
T PF01878_consen 115 ELENLSFIRNKRLSVFPITEEDFEAIMEM 143 (143)
T ss_dssp GGTTSHHHHTTT-SEEEE-HHHHHHHHHH
T ss_pred ccccChhhhcCCcCeEEECHHHHHHHHhC
Confidence 2432 2233454 59999999999886
No 6
>PRK02268 hypothetical protein; Provisional
Probab=96.93 E-value=0.0019 Score=56.98 Aligned_cols=97 Identities=18% Similarity=0.233 Sum_probs=69.9
Q ss_pred hhhhccCCccchhhhhccCCCCcEEEEeccC--------ceEeeeeeeccCCCCccCCcCccCCCCCCCCcCCceEEEEE
Q 019701 221 KRQLFGLPPRYRDSVRAITPGLPLFLYNYST--------HQLHGIFEAASFGGTNIDPTAWEDKKCPGESRFPAQVRVVT 292 (337)
Q Consensus 221 ~r~LFGLP~~h~d~VrkIKPGmpLFLYnys~--------RkLhGIFEAaS~Gg~NIdP~AF~s~~~~g~s~FPAQVRf~i 292 (337)
+..+++++.+++..+++|||||.|..|--.+ ..+.||++.+++-... . .++.+-||.+++++.
T Consensus 19 ~~gf~qv~hgK~apl~RmkpGD~ivyYsp~~~~~~~~~~qaftAig~V~~~~~Yq-------~--~m~~~f~P~Rr~v~~ 89 (141)
T PRK02268 19 EGGFMQVCHGKAAPLRRMKPGDWIIYYSPKTTFGGKDKLQAFTAIGKVKDDEPYQ-------V--EMAPGFIPWRRDVDY 89 (141)
T ss_pred hCCEEEeCCCccchhhcCCCCCEEEEEeceEecCCCcccceEEEEEEEcCCceEe-------c--ccCCCceeEEEEeeE
Confidence 3467899999999999999999999998433 3788899988763322 1 134567999999988
Q ss_pred eeeccCCCcccchhhhh--ccC------CCCcc---ccCCHHHHHHHHH
Q 019701 293 RKICEPLEEDSFRPILH--HYD------GPKFR---LELNVPEAISLLD 330 (337)
Q Consensus 293 ~k~C~PL~EseFKpiI~--~Y~------~~KF~---fELs~~QV~~Ll~ 330 (337)
. |..|..++|+|. .+. +.+|+ +|++.+..+-+.+
T Consensus 90 ~----~~~e~pi~pLi~~L~Fi~~k~~Wg~~fr~g~~eI~e~Df~~I~~ 134 (141)
T PRK02268 90 Y----PCAETPIRPLLDHLDFTEDRKNWGYQFRFGHFEISKHDFETIAS 134 (141)
T ss_pred e----ecCccchHHhhcccceeeCcchhhHhhcCCcEecCHHHHHHHHH
Confidence 7 347788999885 232 23666 4777776654444
No 7
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=58.61 E-value=10 Score=34.69 Aligned_cols=98 Identities=17% Similarity=0.228 Sum_probs=59.2
Q ss_pred hhhhhccCCCCcEEEEeccCc--eEeeeeeeccCCCCccCCcCccCCC-----CCCCCcCCce-EEEEEeeecc-CCCcc
Q 019701 232 RDSVRAITPGLPLFLYNYSTH--QLHGIFEAASFGGTNIDPTAWEDKK-----CPGESRFPAQ-VRVVTRKICE-PLEED 302 (337)
Q Consensus 232 ~d~VrkIKPGmpLFLYnys~R--kLhGIFEAaS~Gg~NIdP~AF~s~~-----~~g~s~FPAQ-VRf~i~k~C~-PL~Es 302 (337)
+.+++.+++|+..|+|.-..+ -+.||-|.++... .||.+|.... +...+.=+++ |.|+.+..|. |++-.
T Consensus 36 RNfmR~M~iGD~~fFYHSNc~~pgIvGl~~V~~~a~--pD~tq~d~~spYyDPka~~e~pRW~~Vdv~~v~~~~~~vtL~ 113 (156)
T COG2947 36 RNFMRDMKIGDLGFFYHSNCKPPGIVGLAEVCALAH--PDPTQFDPASPYYDPKATPEDPRWYCVDVRFVRKLPRPVTLK 113 (156)
T ss_pred HHHHHhcccCceEEEEecCCCCCCceehhhhhhccC--CCccccCCCCcccCcccccCCCCeeEEeeHHHhhcCCCccHH
Confidence 678999999999999998866 7889999888544 6888886431 1111122232 4444444444 55444
Q ss_pred cchh--hhhc----cCCCCcc-ccCCHHHHHHHHHh
Q 019701 303 SFRP--ILHH----YDGPKFR-LELNVPEAISLLDI 331 (337)
Q Consensus 303 eFKp--iI~~----Y~~~KF~-fELs~~QV~~Ll~L 331 (337)
+.|. -++. -.+..-. +..|.+|-+.+++|
T Consensus 114 ~lK~~~~~~~~~~l~~g~RLSV~PVt~~ew~~i~~l 149 (156)
T COG2947 114 ELKANPELAEMSLLVKGNRLSVQPVTPEEWKEILRL 149 (156)
T ss_pred HHhcCcchhhhhhhhccCeeeeeeCCHHHHHHHHHh
Confidence 4332 1111 1123332 37788888877776
No 8
>KOG1901 consensus Uncharacterized high-glucose-regulated protein [General function prediction only]
Probab=58.27 E-value=24 Score=37.23 Aligned_cols=123 Identities=20% Similarity=0.316 Sum_probs=88.2
Q ss_pred eEEEeecCcCh---HHhhhhhhccCCc-cc--h-hhhhccC---CCCcEEEE--eccCceEeeeeeeccCCCCccCCcCc
Q 019701 206 GYIFVCNNDTM---AENLKRQLFGLPP-RY--R-DSVRAIT---PGLPLFLY--NYSTHQLHGIFEAASFGGTNIDPTAW 273 (337)
Q Consensus 206 G~IFmCN~~T~---~ECf~r~LFGLP~-~h--~-d~VrkIK---PGmpLFLY--nys~RkLhGIFEAaS~Gg~NIdP~AF 273 (337)
+-.|...+-.. --|.++.||.=.. +. . +.-+.-+ -+-||||| .=..++..||-|-++.-.++-+-..|
T Consensus 299 AkfFVIKSySEDdVHkSIKY~vWsST~~GNKkLdaAYreak~~~~~cPvfLfFSVNaSGqFCGvAEMvgPVdfn~~~~~W 378 (487)
T KOG1901|consen 299 AKFFVIKSYSEDDVHKSIKYNVWSSTLNGNKKLDAAYREAKKKSGKCPVFLFFSVNASGQFCGVAEMVGPVDFNKDMEYW 378 (487)
T ss_pred ceEEEEeccChhhhhhhcccceeecccCCchhhHHHHHHhhhccCCCCceEEEEEcCCccccceeeeccceecccccchh
Confidence 45566666444 4477788885321 11 1 2344444 78899888 34567999999999999999999999
Q ss_pred cCCCCCCCCcCCceEEEEEeeeccCCCcccchhhh-hccCCC-----CccccCCHHHHHHHHHhhhhc
Q 019701 274 EDKKCPGESRFPAQVRVVTRKICEPLEEDSFRPIL-HHYDGP-----KFRLELNVPEAISLLDIFEEQ 335 (337)
Q Consensus 274 ~s~~~~g~s~FPAQVRf~i~k~C~PL~EseFKpiI-~~Y~~~-----KF~fELs~~QV~~Ll~LF~~~ 335 (337)
..+++. ..|| ||..|+++ ++-..||+|| ++=..+ .=..|.-..|+.+.|.+|.+-
T Consensus 379 qQDKW~--G~Fp--VKWhiVKD---VPNs~lrHI~LeNNeNKPVTnSRDTQEV~leqGievlkIfk~y 439 (487)
T KOG1901|consen 379 QQDKWS--GSFP--VKWHIVKD---VPNSQLRHIILENNENKPVTNSRDTQEVPLEQGIEVLKIFKSY 439 (487)
T ss_pred hhcccc--eecc--eeeEEEee---CCccceeEEEeecCCCCCcccccccceecHHHHHHHHHHHHhh
Confidence 998874 6788 67888888 5789999976 543321 224688889999999999763
No 9
>PF08442 ATP-grasp_2: ATP-grasp domain; InterPro: IPR013650 The ATP-grasp superfamily currently includes 17 groups of enzymes, catalyzing ATP-dependent ligation of a carboxylate containing molecule to an amino or thiol group-containing molecule []. They contribute predominantly to macromolecular synthesis. ATP-hydrolysis is used to activate a substrate. For example, DD-ligase transfers phosphate from ATP to D-alanine on the first step of catalysis. On the second step the resulting acylphosphate is attacked by a second D-alanine to produce a DD dipeptide following phosphate elimination []. The ATP-grasp domain contains three conserved motifs, corresponding to the phosphate binding loop and the Mg(2+) binding site []. The fold is characterised by two alpha-beta subdomains that grasp the ATP molecule between them. Each subdomain provides a variable loop that forms a part of the active site, completed by region of other domains not conserved between the various ATP-grasp enzymes []. The ATP-grasp domain represented by this entry is found primarily in succinyl-CoA synthetases (6.2.1.5 from EC).; PDB: 3PFF_A 3MWD_A 3MWE_A 1CQI_E 1SCU_B 2NU9_G 2NU6_E 1CQJ_E 2NU7_B 1JLL_E ....
Probab=53.30 E-value=3.2 Score=38.20 Aligned_cols=130 Identities=18% Similarity=0.144 Sum_probs=65.6
Q ss_pred CCCCCCCcceEEEeecCcChHHhhhhhhccCCcc------------chhhhhccCCCCcEEEEeccCceEee-eeeeccC
Q 019701 197 ALPRNETIGGYIFVCNNDTMAENLKRQLFGLPPR------------YRDSVRAITPGLPLFLYNYSTHQLHG-IFEAASF 263 (337)
Q Consensus 197 ~~~r~~~lgG~IFmCN~~T~~ECf~r~LFGLP~~------------h~d~VrkIKPGmpLFLYnys~RkLhG-IFEAaS~ 263 (337)
-....++.||+-| |.+.-.-+.+.+.++|..-. +.-+-..|..--=++|=-.-+|.-.+ +.-|...
T Consensus 49 l~GgRGK~GgVk~-~~s~~ea~~~a~~mlg~~l~T~Qtg~~G~~v~~vlvee~v~~~~E~Ylsi~~DR~~~~p~ii~S~~ 127 (202)
T PF08442_consen 49 LAGGRGKAGGVKI-AKSPEEAKEAAKEMLGKTLKTKQTGPKGEKVNKVLVEEFVDIKREYYLSITLDRESRGPVIIASKE 127 (202)
T ss_dssp SSSTTTTTTCEEE-ESSHHHHHHHHHTTTTSEEE-TTSTTTEEEE--EEEEE---CCEEEEEEEEEETTTTEEEEEEESS
T ss_pred eecCcccCCceee-cCCHHHHHHHHHHHhCCceEeeecCCCCCEeeEEEEEecCccCceEEEEEEeccCCCceEEEEecc
Confidence 3445567788888 55444445556667776422 11112222222233333333344444 3556779
Q ss_pred CCCccCCcCccCCCCCCCCcCCceEEEEEeeeccCCCcccchhhhhccCCCCccccCCHHHHHHHHHhhhhcC
Q 019701 264 GGTNIDPTAWEDKKCPGESRFPAQVRVVTRKICEPLEEDSFRPILHHYDGPKFRLELNVPEAISLLDIFEEQD 336 (337)
Q Consensus 264 Gg~NIdP~AF~s~~~~g~s~FPAQVRf~i~k~C~PL~EseFKpiI~~Y~~~KF~fELs~~QV~~Ll~LF~~~~ 336 (337)
|||+|+--|-+ .|..|.-..+-.-..|.+.+.+.++....-+.=..+-=.+.+.+|.++|.+.+
T Consensus 128 GGvdIEeva~~---------~P~~i~~~~id~~~g~~~~~~~~i~~~lg~~~~~~~~~~~~l~~Ly~~F~~~D 191 (202)
T PF08442_consen 128 GGVDIEEVAAE---------NPEKIIKFPIDPTEGLTPYQAREIAKKLGLPGKLAEQLADILKKLYRLFREYD 191 (202)
T ss_dssp TSSTHHHHHHH---------SGGGEEEEEEBTTTB--HHHHHHHHHHTTS-CHHHHHHHHHHHHHHHHHHHTT
T ss_pred CCccHHHHhhh---------ChhhEEEEecCCCCCCCHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHcC
Confidence 99999988765 45555433332333445555555554332111011222456789999998764
No 10
>PLN00124 succinyl-CoA ligase [GDP-forming] subunit beta; Provisional
Probab=40.49 E-value=35 Score=34.93 Aligned_cols=121 Identities=17% Similarity=0.208 Sum_probs=74.0
Q ss_pred cceEEEeecCcChHHhhhhhhccC--------Cccc----hhhhhccCCCCcEEEEeccCceEeeeee-eccCCCCccCC
Q 019701 204 IGGYIFVCNNDTMAENLKRQLFGL--------PPRY----RDSVRAITPGLPLFLYNYSTHQLHGIFE-AASFGGTNIDP 270 (337)
Q Consensus 204 lgG~IFmCN~~T~~ECf~r~LFGL--------P~~h----~d~VrkIKPGmpLFLYnys~RkLhGIFE-AaS~Gg~NIdP 270 (337)
.||+.+. +++-..+.+ .+++|. |... .-+++.+.++.=++|=-.-+|...|+.- +...||++||-
T Consensus 93 ~GGV~l~-~~eea~~aa-~~il~~~lvt~qtg~~G~~v~~vlv~e~~~~~~E~ylgi~~Dr~~~gpvil~s~~GGv~IEe 170 (422)
T PLN00124 93 KGGVHIV-KKDKAEELA-GKMLGQILVTKQTGPAGKPVNKVYLCEKMSLVNEMYFAILLDRASAGPLIIACSKGGTSIED 170 (422)
T ss_pred CCeEEEC-CHHHHHHHH-HHHhccchhhcccCCCCceeceEEEEEeecCCceEEEEEEeccccCCcEEEEECCCCccHHH
Confidence 5777665 433333333 356675 2221 2236666677777777777777788887 78899999986
Q ss_pred cCccCCCCCCCCcCCceEEEEEeeeccCCCcccchhhhhccCCCCccccCCHHHHHHHHHhhhhc
Q 019701 271 TAWEDKKCPGESRFPAQVRVVTRKICEPLEEDSFRPILHHYDGPKFRLELNVPEAISLLDIFEEQ 335 (337)
Q Consensus 271 ~AF~s~~~~g~s~FPAQVRf~i~k~C~PL~EseFKpiI~~Y~~~KF~fELs~~QV~~Ll~LF~~~ 335 (337)
-|=. +|-.+.-...-...||.+.+-+.++..+..+.-..+==.+.+.+|.++|.+.
T Consensus 171 va~~---------~pd~i~~~~id~~~~l~~~~a~~~~~~L~~~~~~~~~l~~ii~~L~~lf~~~ 226 (422)
T PLN00124 171 LAEK---------FPEKIIKVPIDIFKGITDEDAAKVVDGLAPKVADRNDAIEQVKKLYKLFCKC 226 (422)
T ss_pred hhhh---------CchheeEEecCcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 5332 4555555555567788888888888765443222222234567888888764
No 11
>PF04146 YTH: YT521-B-like domain; InterPro: IPR007275 A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells []. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanaisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B, Q9QY02 from SWISSPROT, is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner []. The domain is predicted to have four alpha helices and six beta strands []. In plant cells environmental stimuli, which light, pathogens, hormones, and abiotic stresses, elicit changes in the cytosolic Ca levels but little is known of the cytosolic-nuclear Ca-signaling pathway; where gene regulation occurs to respond appropriately to the stress. It has been demonstrated that two novel Arabidopsis thaliana (Mouse-ear cress) proteins, (ECT1 and ECT2), specifically associated with Calcineurin B-Like-Interacting Protein Kinase1 (CIPK1), a member of Ser/Thr protein kinases that interact with the calcineurin B-like Ca-binding proteins. These two proteins contain a very similar C-terminal region (180 amino acids in length, 81% similarity), which is required and sufficient for both interaction with CIPK1 and translocation to the nucleus. This domain, the YTH-domain, is conserved across all eukaryotes and suggests that the conserved C-terminal region plays a critical role in relaying the cytosolic Ca-signals to the nucleus, thereby regulating gene expression [].; PDB: 2YUD_A 2YU6_A.
Probab=36.71 E-value=60 Score=28.09 Aligned_cols=120 Identities=14% Similarity=0.229 Sum_probs=66.6
Q ss_pred cCcChHHhhhhhhccCCccchh-hhhccCCCCcEEEE--eccCceEeeeeeeccCCCCccCCcCccCCCCCCCCcCCceE
Q 019701 212 NNDTMAENLKRQLFGLPPRYRD-SVRAITPGLPLFLY--NYSTHQLHGIFEAASFGGTNIDPTAWEDKKCPGESRFPAQV 288 (337)
Q Consensus 212 N~~T~~ECf~r~LFGLP~~h~d-~VrkIKPGmpLFLY--nys~RkLhGIFEAaS~Gg~NIdP~AF~s~~~~g~s~FPAQV 288 (337)
+..-...++++.+|.+++.... .-++-+-+.+++|+ .-..++..|+=+-+|..........|.... ...++.-.
T Consensus 11 ~~~ni~~s~~~gvW~t~~~~~~~L~~Af~~~~~V~L~FSvn~S~~F~G~A~M~s~~~~~~~~~~w~~~~--~~~~~~g~- 87 (140)
T PF04146_consen 11 NEENIHLSIKYGVWATQPKNEKKLNEAFKESRNVYLFFSVNGSGHFQGYARMTSPIDPDSPKPFWQQDS--SSSKWGGP- 87 (140)
T ss_dssp SCHHHHHHHHCTEEE--CCCHHHHHHHHHHSS-EEEEEEETTTSEEEEEEEEECECCSSS------SS---SGCGG-SE-
T ss_pred CHHHHHHHHhCCEEcccccchHHHHHHHHhCCCEEEEEeecCcceEEEEEEEccCCCCcccCccccccc--cccccCCc-
Confidence 3466788999999999988755 34455555566655 347789999999999877676666773210 11233333
Q ss_pred EEEEeeecc-CCCcccchhhhhccCC------CCccccCCHHHHHHHHHhhhhc
Q 019701 289 RVVTRKICE-PLEEDSFRPILHHYDG------PKFRLELNVPEAISLLDIFEEQ 335 (337)
Q Consensus 289 Rf~i~k~C~-PL~EseFKpiI~~Y~~------~KF~fELs~~QV~~Ll~LF~~~ 335 (337)
|+|.|.+. +||=..++++...+.. .+=-.||+...-++|+.||.++
T Consensus 88 -F~v~Wl~~~~lpf~~~~hl~n~~n~~~pV~~~rDgqEi~~~~G~~l~~~f~~~ 140 (140)
T PF04146_consen 88 -FRVEWLRVKDLPFSKLRHLRNPLNENKPVKISRDGQEIEPEIGEQLLKIFDNQ 140 (140)
T ss_dssp -EEEEEEE-S-EEHHHHTT-EETTTTTEETTS--TTEEE-CCHHHHHHHHCGT-
T ss_pred -eEEEEEECCcCChHHhcccccccCCCcEEEECCCCEEeCHHHHHHHHHHHhhC
Confidence 44544443 2444445555433322 1224689988999999999763
No 12
>PF14875 PIP49_N: N-term cysteine-rich ER, FAM69
Probab=31.98 E-value=14 Score=33.39 Aligned_cols=32 Identities=19% Similarity=0.267 Sum_probs=29.7
Q ss_pred CcccchhhhhccCCCCccccCCHHHHHHHHHh
Q 019701 300 EEDSFRPILHHYDGPKFRLELNVPEAISLLDI 331 (337)
Q Consensus 300 ~EseFKpiI~~Y~~~KF~fELs~~QV~~Ll~L 331 (337)
++++|+.++..+...++-.+|+..+|..|+.|
T Consensus 127 s~~ef~eMV~~~lk~~lG~~~~~~lv~~ll~l 158 (158)
T PF14875_consen 127 SMEEFREMVKSFLKNKLGDQLSNNLVERLLSL 158 (158)
T ss_pred CHHHHHHHHHHHHHHHhCCCCCHHHHHHHhcC
Confidence 88999999999999999999999999999875
No 13
>PF12419 DUF3670: SNF2 Helicase protein ; InterPro: IPR022138 This domain family is found in bacteria, archaea and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF00271 from PFAM, PF00176 from PFAM. Most of the proteins in this family are annotated as SNF2 helicases but there is little accompanying literature to confirm this.
Probab=29.44 E-value=57 Score=28.15 Aligned_cols=47 Identities=19% Similarity=0.138 Sum_probs=35.7
Q ss_pred EEEEeeeccCCCcccchhhhhccCC----CCccccCCHHHHHHHHHhhhhc
Q 019701 289 RVVTRKICEPLEEDSFRPILHHYDG----PKFRLELNVPEAISLLDIFEEQ 335 (337)
Q Consensus 289 Rf~i~k~C~PL~EseFKpiI~~Y~~----~KF~fELs~~QV~~Ll~LF~~~ 335 (337)
+.++..-=.+|+++||+.+++.-.+ +.=|++|++++++++++.+...
T Consensus 74 ~W~lalGd~~Ls~eEf~~L~~~~~~LV~~rg~WV~ld~~~l~~~~~~~~~~ 124 (141)
T PF12419_consen 74 DWELALGDEELSEEEFEQLVEQKRPLVRFRGRWVELDPEELRRALAFLEKA 124 (141)
T ss_pred eEEEEECCEECCHHHHHHHHHcCCCeEEECCEEEEECHHHHHHHHHHHHhc
Confidence 3444445578999999999875443 3447899999999999998774
No 14
>KOG1447 consensus GTP-specific succinyl-CoA synthetase, beta subunit [Energy production and conversion]
Probab=26.01 E-value=30 Score=35.03 Aligned_cols=75 Identities=21% Similarity=0.268 Sum_probs=49.9
Q ss_pred ccCceEeeeeeecc-CCCCccCCcCccCCCCCCCCcCCceEEEEEeeeccCCCcccchhhhhc--cCCCCccccCCHHHH
Q 019701 249 YSTHQLHGIFEAAS-FGGTNIDPTAWEDKKCPGESRFPAQVRVVTRKICEPLEEDSFRPILHH--YDGPKFRLELNVPEA 325 (337)
Q Consensus 249 ys~RkLhGIFEAaS-~Gg~NIdP~AF~s~~~~g~s~FPAQVRf~i~k~C~PL~EseFKpiI~~--Y~~~KF~fELs~~QV 325 (337)
+-+|.--|+--.+| .|+|+|+.-|=+. |..+.-.++-+++|++|++--.+-++ |.++-- .--.+|.
T Consensus 139 LmDRe~NGPVlvaSP~GGmDIEaVAe~t---------PE~Ifk~piDI~~gi~esq~l~~Ak~L~F~G~l~--~~aA~eI 207 (412)
T KOG1447|consen 139 LMDRECNGPVLVASPQGGMDIEAVAEST---------PELIFKEPIDIFEGIKESQALRMAKNLGFVGPLK--SQAADEI 207 (412)
T ss_pred eeccccCCCEEEecCCCCccHHHHhhhC---------hHhhccccchhccCCchHHHHHHHHhccccCcHH--HHHHHHH
Confidence 34566677766666 8999999887654 44444455667899999876655443 444311 2236789
Q ss_pred HHHHHhhhh
Q 019701 326 ISLLDIFEE 334 (337)
Q Consensus 326 ~~Ll~LF~~ 334 (337)
.+|+.||-.
T Consensus 208 ~kLY~LF~a 216 (412)
T KOG1447|consen 208 TKLYNLFLA 216 (412)
T ss_pred HHHHHHHhh
Confidence 999999964
No 15
>PHA02902 putative IMV membrane protein; Provisional
Probab=23.32 E-value=93 Score=25.26 Aligned_cols=21 Identities=19% Similarity=0.246 Sum_probs=18.8
Q ss_pred CCccccCCHHHHHHHHHhhhh
Q 019701 314 PKFRLELNVPEAISLLDIFEE 334 (337)
Q Consensus 314 ~KF~fELs~~QV~~Ll~LF~~ 334 (337)
+-|+-+||.+||++|-.|+.+
T Consensus 48 ~~F~D~lTpDQirAlHrlvT~ 68 (70)
T PHA02902 48 PLFKDSLTPDQIKALHRLVSL 68 (70)
T ss_pred chhhccCCHHHHHHHHHHHhc
Confidence 588999999999999999875
No 16
>PF08321 PPP5: PPP5 TPR repeat region; InterPro: IPR013235 This domain is specific to the PPP5 subfamily of serine/threonine phosphatases.; GO: 0004722 protein serine/threonine phosphatase activity, 0046872 metal ion binding; PDB: 3ICF_B 3H60_B 3H63_A 3H66_A 3H62_B 1A17_A 1S95_B 3H69_A 3H68_D 3H64_D ....
Probab=20.08 E-value=83 Score=26.11 Aligned_cols=26 Identities=23% Similarity=0.595 Sum_probs=17.9
Q ss_pred ccCCCCcc-ccCCHHHHHHHHHhhhhc
Q 019701 310 HYDGPKFR-LELNVPEAISLLDIFEEQ 335 (337)
Q Consensus 310 ~Y~~~KF~-fELs~~QV~~Ll~LF~~~ 335 (337)
-|+||+.. ..||.+.|..|++.|...
T Consensus 41 sY~GP~l~~~~it~efv~~mie~FK~~ 67 (95)
T PF08321_consen 41 SYDGPRLEDEPITLEFVKAMIEWFKNQ 67 (95)
T ss_dssp S--SS--BTTB--HHHHHHHHHHHHCT
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhC
Confidence 69999998 899999999999999864
Done!