Query psy9493
Match_columns 175
No_of_seqs 87 out of 104
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 20:47:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9493.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9493hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3956|consensus 100.0 1.1E-44 2.4E-49 315.3 12.2 162 4-175 15-181 (359)
2 PF06400 Alpha-2-MRAP_N: Alpha 100.0 1.2E-41 2.6E-46 263.6 8.8 110 3-120 3-113 (120)
3 PF06401 Alpha-2-MRAP_C: Alpha 99.9 6.3E-26 1.4E-30 191.1 7.8 116 46-175 1-138 (214)
4 KOG3956|consensus 99.8 1E-19 2.2E-24 159.4 11.0 116 45-175 149-285 (359)
5 PF06401 Alpha-2-MRAP_C: Alpha 97.3 0.00046 9.9E-09 59.0 5.1 44 45-88 106-150 (214)
6 PF06400 Alpha-2-MRAP_N: Alpha 91.8 0.14 3E-06 40.5 2.6 34 142-175 36-69 (120)
7 TIGR03798 ocin_TIGR03798 bacte 71.1 6.4 0.00014 26.9 3.4 25 151-175 27-53 (64)
8 PF07862 Nif11: Nitrogen fixat 59.3 8.8 0.00019 24.7 2.2 19 151-169 29-49 (49)
9 PRK02539 hypothetical protein; 39.2 31 0.00068 25.8 2.6 22 49-70 5-27 (85)
10 PF05979 DUF896: Bacterial pro 36.9 38 0.00083 24.0 2.7 21 50-70 4-25 (65)
11 PRK01631 hypothetical protein; 34.5 41 0.00089 24.7 2.6 21 50-70 5-26 (76)
12 PRK01546 hypothetical protein; 34.2 41 0.0009 24.8 2.6 22 49-70 6-28 (79)
13 cd08325 CARD_CASP1-like Caspas 31.6 66 0.0014 23.1 3.3 25 150-174 17-42 (83)
14 PF09968 DUF2202: Uncharacteri 31.1 66 0.0014 26.6 3.6 42 107-165 44-86 (162)
15 PF05979 DUF896: Bacterial pro 30.6 54 0.0012 23.3 2.6 21 149-169 5-25 (65)
16 PF02787 CPSase_L_D3: Carbamoy 28.8 68 0.0015 24.9 3.1 20 153-172 63-82 (123)
17 cd07313 terB_like_2 tellurium 26.5 90 0.0019 22.2 3.3 24 150-173 75-99 (104)
18 PF06569 DUF1128: Protein of u 24.8 87 0.0019 22.7 2.9 26 150-175 40-66 (71)
19 cd07316 terB_like_DjlA N-termi 24.7 1.1E+02 0.0023 21.7 3.4 24 150-173 76-100 (106)
20 PF14771 DUF4476: Domain of un 24.1 86 0.0019 22.5 2.8 31 142-172 18-49 (95)
21 PF01476 LysM: LysM domain; I 23.6 99 0.0021 18.5 2.6 20 153-172 8-27 (44)
22 PF04032 Rpr2: RNAse P Rpr2/Rp 23.5 1.3E+02 0.0027 20.8 3.5 26 51-76 1-28 (85)
23 cd08804 Death_ank2 Death domai 23.0 92 0.002 22.5 2.7 20 155-174 18-38 (84)
24 PF08671 SinI: Anti-repressor 22.6 1.5E+02 0.0033 17.9 3.2 23 149-171 3-25 (30)
25 COG5018 KapD Inhibitor of the 22.5 42 0.00091 28.7 1.0 24 144-167 139-164 (210)
26 PRK01631 hypothetical protein; 22.1 84 0.0018 23.1 2.4 21 149-169 6-26 (76)
27 PRK02539 hypothetical protein; 22.1 85 0.0018 23.5 2.4 21 149-169 7-27 (85)
28 cd08318 Death_NMPP84 Death dom 21.7 96 0.0021 22.3 2.6 21 154-174 20-41 (86)
29 PRK01546 hypothetical protein; 21.6 86 0.0019 23.1 2.3 21 149-169 8-28 (79)
30 PF04679 DNA_ligase_A_C: ATP d 20.9 49 0.0011 23.8 1.0 15 161-175 28-42 (97)
31 PF14440 XOO_2897-deam: Xantho 20.5 1.1E+02 0.0023 24.0 2.8 32 47-78 43-75 (118)
No 1
>KOG3956|consensus
Probab=100.00 E-value=1.1e-44 Score=315.31 Aligned_cols=162 Identities=30% Similarity=0.501 Sum_probs=141.1
Q ss_pred hhhhhhhhcccCCCCCcchhhhcccccccCCCCCcccccCCCCccchhhhHHHHHHHHccCCHH-HHHHHHHHhhhhHHH
Q psy9493 4 LCVFALLYTVAVSSENIYSRESNVRFKSQLDVEPNIQLRHLDNPFRMGKLNLLWKKAQVRLSEP-KLKSIYNELKIHDKE 82 (175)
Q Consensus 4 ~~~~~~~~~~~~~~~~kys~e~n~~~~~~~~~~~~~~~~~~~~~FR~~KLN~LWeKAq~~fs~~-eL~~L~~ELk~qeK~ 82 (175)
|.+.++|+|+++.+++|||+|+|.| +| .|.+.++. ||||+|||+||+|||+++|++ .|++|+.||++||++
T Consensus 15 llll~~G~~~~kkqskKySkEaNdP-ky------dPdfkSiq-pFRmeklN~iweKAq~~~t~p~~La~L~~eLki~d~~ 86 (359)
T KOG3956|consen 15 LLLLVIGSAHNKKQSKKYSKEANDP-KY------DPDFKSIQ-PFRMEKLNFIWEKAQQHVTDPQNLARLEKELKIYDAI 86 (359)
T ss_pred HHHHHhCcccchhhccccchhccCC-CC------Cccccccc-hhHHHHHHHHHHHHHHhcCCHhHHHHHHHHhhhhhHH
Confidence 3445578999999999999999999 63 67777777 999999999999999977775 599999999999999
Q ss_pred HHHHHhhhhcCCCCCchhHHHHHHHHHHHHHhhccccccchhhccccccccCCC---C-CCCCCCCCCCChhHHHHHHHH
Q psy9493 83 EILFKKVKADGLDPDGQREGILRKRLVGIMSTYGLLEHFEDIQGEKIKLDTDDN---A-PVHKPRAVFKDKKLNKLWEKA 158 (175)
Q Consensus 83 e~~~k~LK~eg~D~dG~kEa~Lr~kl~~Il~kYgL~~~~~~~~~~~~~~h~~l~---d-~~~~~~~~F~DpKl~kLW~kA 158 (175)
+++||.|+..+.|.+|+++++|+|+|++||++|||.+++++++++ ..|+.+. | ....+++.|.||+|++||++|
T Consensus 87 elAwK~lns~~~d~dg~k~d~l~rkL~~Il~kYgL~~~~da~q~t--~k~k~l~~~~d~~e~~~~~~f~D~~L~kLW~kA 164 (359)
T KOG3956|consen 87 ELAWKSLNSRQGDQDGKKIDKLDRKLGKILEKYGLEKAVDAFQET--YKHKNLFQQTDDNEPLPSGKFTDQNLQKLWSKA 164 (359)
T ss_pred HHHHHHhhhcccCcchHHHHHHHHHHHHHHHHcchhhhhHHHHHH--HhccchhhcccccccCcccccCchhHHHHHHHH
Confidence 999999999999999999999999999999999999998877641 1222222 2 336678899999999999999
Q ss_pred HhCCCCHHHHHHHhhhC
Q psy9493 159 EHSGFTCKNVKFNNQEL 175 (175)
Q Consensus 159 ~~sgFS~eEL~sLk~EL 175 (175)
++||||.+||.+||.|+
T Consensus 165 ~~sgFs~eEL~~L~~Ef 181 (359)
T KOG3956|consen 165 QNSGFSQEELNALHGEF 181 (359)
T ss_pred hccCCCHHHHHHHHHHH
Confidence 99999999999999985
No 2
>PF06400 Alpha-2-MRAP_N: Alpha-2-macroglobulin RAP, N-terminal domain; InterPro: IPR009066 The alpha-2-macroglobulin receptor-associated protein (RAP) is a glycoprotein that binds to the alpha-2-macroglobulin receptor, as well as to other members of the low density lipoprotein receptor family (IPR002172 from INTERPRO). RAP acts to inhibit the binding of all know ligands for these receptors, and may prevent receptor aggregation and degradation in the endoplasmic reticulum, thereby acting as a molecular chaperone []. RAP may be under the regulatory control of calmodulin, since it is able to bind calmodulin and be phosphorylated by calmodulin-dependent kinase II (IPR002048 from INTERPRO). RAP is comprised of three domains. Both domains 1 and 3 are involved in binding to the alpha-2-macroglobulin receptor, while domain 1 is also involved in inhibiting the binding of activated alpha-2-macroglobulin (IPR001599 from INTERPRO). Structural studies have revealed the RAP domain 1 to be comprised of a partly opened bundle of three helices, the first one being shorter than the other two.; PDB: 1NRE_A 2P03_A 1OV2_A 1LRE_A 2FYL_A 1OP1_A 2P01_A.
Probab=100.00 E-value=1.2e-41 Score=263.58 Aligned_cols=110 Identities=55% Similarity=0.811 Sum_probs=70.6
Q ss_pred hhhhhhhhhcccCCCCCcchhhhcccccccCCCCCcccccCCCCccchhhhHHHHHHHHc-cCCHHHHHHHHHHhhhhHH
Q psy9493 3 ILCVFALLYTVAVSSENIYSRESNVRFKSQLDVEPNIQLRHLDNPFRMGKLNLLWKKAQV-RLSEPKLKSIYNELKIHDK 81 (175)
Q Consensus 3 ~~~~~~~~~~~~~~~~~kys~e~n~~~~~~~~~~~~~~~~~~~~~FR~~KLN~LWeKAq~-~fs~~eL~~L~~ELk~qeK 81 (175)
++|+++++++.++.+++|||||+|++ . +|++|.++.||||+||||||+||++ +||+++|++||+||++|||
T Consensus 3 ~~~~ll~~~~~~~~~~~KYSre~Ne~-~-------~~~~~~~~~~FRm~KLN~lW~KA~r~~Ls~~kLk~L~~dLKi~dk 74 (120)
T PF06400_consen 3 LLLLLLLFPIAAVKAAGKYSREANEP-K-------PPSFRELDRPFRMAKLNQLWEKAQRLRLSEVKLKSLYSDLKIHDK 74 (120)
T ss_dssp ----------------------------------------S---SSSSHHHHHHHHHHHHHT--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhHHHHhccccCHhhCCC-C-------CCccccccccHHHHHHHHHHHHHHHccCChHHHHHHHHHHHHhHH
Confidence 45666777777788899999999987 3 6789999999999999999999997 9999999999999999999
Q ss_pred HHHHHHhhhhcCCCCCchhHHHHHHHHHHHHHhhccccc
Q psy9493 82 EEILFKKVKADGLDPDGQREGILRKRLVGIMSTYGLLEH 120 (175)
Q Consensus 82 ~e~~~k~LK~eg~D~dG~kEa~Lr~kl~~Il~kYgL~~~ 120 (175)
+|++||+||++|.|++|++||+||++|++||++|||.++
T Consensus 75 eEl~wKklk~~g~D~dG~kEa~Lrrkl~~Im~kYgL~g~ 113 (120)
T PF06400_consen 75 EELAWKKLKAEGKDKDGEKEAELRRKLNVIMSKYGLDGK 113 (120)
T ss_dssp HHHHHHHHHHHTS-SSSHHHHHHHHHHHHHHHHHTSSSS
T ss_pred HHHHHHHHhhhCCCccccHHHHHHHHHHHHHHHhCCCCC
Confidence 999999999999999999999999999999999999864
No 3
>PF06401 Alpha-2-MRAP_C: Alpha-2-macroglobulin RAP, C-terminal domain ; InterPro: IPR010483 The alpha-2-macroglobulin receptor-associated protein (RAP) is a intracellular glycoprotein that binds to the 2-macroglobulin receptor and other members of the low density lipoprotein receptor family. The protein inhibits binding of all currently known ligands of these receptors []. Two different studies have provided conflicting domain boundaries.; GO: 0008201 heparin binding, 0050750 low-density lipoprotein particle receptor binding, 0005783 endoplasmic reticulum; PDB: 2FCW_A 2P03_A 2FTU_A 2P01_A.
Probab=99.93 E-value=6.3e-26 Score=191.05 Aligned_cols=116 Identities=21% Similarity=0.336 Sum_probs=87.6
Q ss_pred CccchhhhHHHHHHHHc-c-CCHHHHHHHHHHhhh-hHHHHHHHHhhhhcCC------------C-CC------chhHHH
Q psy9493 46 NPFRMGKLNLLWKKAQV-R-LSEPKLKSIYNELKI-HDKEEILFKKVKADGL------------D-PD------GQREGI 103 (175)
Q Consensus 46 ~~FR~~KLN~LWeKAq~-~-fs~~eL~~L~~ELk~-qeK~e~~~k~LK~eg~------------D-~d------G~kEa~ 103 (175)
+.|.|+|||+||.||++ + ||+++|.+|+.||+| |+|+..|+..|...+. + .. ..+.+.
T Consensus 1 ~~F~D~kL~KLW~kA~~sGkFt~eEL~~Lk~Ef~hHqeKi~eY~~LL~~~~~~~~~~~N~i~~~~~~~~k~~~~~~k~~~ 80 (214)
T PF06401_consen 1 DLFKDKKLNKLWHKAETSGKFTDEELDKLKEEFQHHQEKIDEYNSLLETLSRTEEIHENSISPNEMNPEKEEQLHEKHNE 80 (214)
T ss_dssp -SS-SHHHHHHHHHHHHHS---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTTSS---S-TTTT-SSSSCHHHHHH
T ss_pred CCCCChHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccccCCccccchhHHHHHHHHHHH
Confidence 47999999999999999 7 999999999999999 7788888887755221 1 01 236789
Q ss_pred HHHHHHHHHHhhccccccchhhccccccccCCCCCCCCCCCCCCChhHHHHHHHHHhCCCCHHHHHHHhhhC
Q psy9493 104 LRKRLVGIMSTYGLLEHFEDIQGEKIKLDTDDNAPVHKPRAVFKDKKLNKLWEKAEHSGFTCKNVKFNNQEL 175 (175)
Q Consensus 104 Lr~kl~~Il~kYgL~~~~~~~~~~~~~~h~~l~d~~~~~~~~F~DpKl~kLW~kA~~sgFS~eEL~sLk~EL 175 (175)
||.+.+.|.+.|+-+.. ..+. ++.+..+|++|||++||..|++++||++||+||++||
T Consensus 81 Lk~k~r~i~~~~drL~r---------~~~~-----g~~~~~eF~epkV~~LW~~A~~~nFT~~ELeSlkeEL 138 (214)
T PF06401_consen 81 LKEKHREINDGYDRLRR---------VSHQ-----GPNSDKEFIEPKVQGLWKLAQNANFTEDELESLKEEL 138 (214)
T ss_dssp HHHHHHHHHHHHHHHHH---------HHHT-----SSSSS-SSSSTTHHHHHHHHCTTT--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH---------HHhc-----CCCcccccccHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 99999999999977731 1122 2223378999999999999999999999999999997
No 4
>KOG3956|consensus
Probab=99.81 E-value=1e-19 Score=159.42 Aligned_cols=116 Identities=19% Similarity=0.281 Sum_probs=88.0
Q ss_pred CCccchhhhHHHHHHHHc-cCCHHHHHHHHHHhhh-hHHHHHHHHhhhhcCCCCC-------------------chhHHH
Q psy9493 45 DNPFRMGKLNLLWKKAQV-RLSEPKLKSIYNELKI-HDKEEILFKKVKADGLDPD-------------------GQREGI 103 (175)
Q Consensus 45 ~~~FR~~KLN~LWeKAq~-~fs~~eL~~L~~ELk~-qeK~e~~~k~LK~eg~D~d-------------------G~kEa~ 103 (175)
.+.|.|.+||+||+||++ +||.++|.+|+.||+| ++|...|+..|..-..+++ +.+.-+
T Consensus 149 ~~~f~D~~L~kLW~kA~~sgFs~eEL~~L~~Ef~hh~~Kv~vY~~lLe~~tv~~~~HEN~I~~~dlsDvneik~h~~~~k 228 (359)
T KOG3956|consen 149 SGKFTDQNLQKLWSKAQNSGFSQEELNALHGEFKHHEQKVRVYEDLLEDFTVKKVPHENSIQHDDLSDVNEIKIHDKTKK 228 (359)
T ss_pred ccccCchhHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccCCchhhhhhhhccccchHHH
Confidence 468999999999999999 9999999999999999 5677777777755311211 123344
Q ss_pred HHHHHHHHHHhhccccccchhhccccccccCCCCCCCCCCCCCCChhHHHHHHHHHhCCCCHHHHHHHhhhC
Q psy9493 104 LRKRLVGIMSTYGLLEHFEDIQGEKIKLDTDDNAPVHKPRAVFKDKKLNKLWEKAEHSGFTCKNVKFNNQEL 175 (175)
Q Consensus 104 Lr~kl~~Il~kYgL~~~~~~~~~~~~~~h~~l~d~~~~~~~~F~DpKl~kLW~kA~~sgFS~eEL~sLk~EL 175 (175)
|..+...|.+.|+-+.. .. .+++..++|.+|||++||..||.++||+.||++|++||
T Consensus 229 lke~~r~~n~glDrl~R-------------~v--~sg~h~~~F~EPrV~~LW~lAQ~~nlT~kELe~~k~EL 285 (359)
T KOG3956|consen 229 LKEANRELNDGLDRLHR-------------KV--TSGEHFSPFNEPRVKRLWKLAQENNLTPKELEVLKDEL 285 (359)
T ss_pred HHHHHHHHHhhHHHHHH-------------Hh--ccCCcccccccHHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence 55555555554433311 00 24567899999999999999999999999999999997
No 5
>PF06401 Alpha-2-MRAP_C: Alpha-2-macroglobulin RAP, C-terminal domain ; InterPro: IPR010483 The alpha-2-macroglobulin receptor-associated protein (RAP) is a intracellular glycoprotein that binds to the 2-macroglobulin receptor and other members of the low density lipoprotein receptor family. The protein inhibits binding of all currently known ligands of these receptors []. Two different studies have provided conflicting domain boundaries.; GO: 0008201 heparin binding, 0050750 low-density lipoprotein particle receptor binding, 0005783 endoplasmic reticulum; PDB: 2FCW_A 2P03_A 2FTU_A 2P01_A.
Probab=97.26 E-value=0.00046 Score=58.95 Aligned_cols=44 Identities=34% Similarity=0.431 Sum_probs=35.7
Q ss_pred CCccchhhhHHHHHHHHc-cCCHHHHHHHHHHhhhhHHHHHHHHh
Q psy9493 45 DNPFRMGKLNLLWKKAQV-RLSEPKLKSIYNELKIHDKEEILFKK 88 (175)
Q Consensus 45 ~~~FR~~KLN~LWeKAq~-~fs~~eL~~L~~ELk~qeK~e~~~k~ 88 (175)
+.+|..+|+..||.-|+. .||+.+|.+|+.||.|.|..-.....
T Consensus 106 ~~eF~epkV~~LW~~A~~~nFT~~ELeSlkeEL~HfE~rl~K~~H 150 (214)
T PF06401_consen 106 DKEFIEPKVQGLWKLAQNANFTEDELESLKEELKHFEKRLEKHRH 150 (214)
T ss_dssp S-SSSSTTHHHHHHHHCTTT--HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccccHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999 99999999999999998876443333
No 6
>PF06400 Alpha-2-MRAP_N: Alpha-2-macroglobulin RAP, N-terminal domain; InterPro: IPR009066 The alpha-2-macroglobulin receptor-associated protein (RAP) is a glycoprotein that binds to the alpha-2-macroglobulin receptor, as well as to other members of the low density lipoprotein receptor family (IPR002172 from INTERPRO). RAP acts to inhibit the binding of all know ligands for these receptors, and may prevent receptor aggregation and degradation in the endoplasmic reticulum, thereby acting as a molecular chaperone []. RAP may be under the regulatory control of calmodulin, since it is able to bind calmodulin and be phosphorylated by calmodulin-dependent kinase II (IPR002048 from INTERPRO). RAP is comprised of three domains. Both domains 1 and 3 are involved in binding to the alpha-2-macroglobulin receptor, while domain 1 is also involved in inhibiting the binding of activated alpha-2-macroglobulin (IPR001599 from INTERPRO). Structural studies have revealed the RAP domain 1 to be comprised of a partly opened bundle of three helices, the first one being shorter than the other two.; PDB: 1NRE_A 2P03_A 1OV2_A 1LRE_A 2FYL_A 1OP1_A 2P01_A.
Probab=91.83 E-value=0.14 Score=40.46 Aligned_cols=34 Identities=32% Similarity=0.439 Sum_probs=27.3
Q ss_pred CCCCCCChhHHHHHHHHHhCCCCHHHHHHHhhhC
Q psy9493 142 PRAVFKDKKLNKLWEKAEHSGFTCKNVKFNNQEL 175 (175)
Q Consensus 142 ~~~~F~DpKl~kLW~kA~~sgFS~eEL~sLk~EL 175 (175)
...+|.=-|||.||.+|+...+|+--|.+|..||
T Consensus 36 ~~~~FRm~KLN~lW~KA~r~~Ls~~kLk~L~~dL 69 (120)
T PF06400_consen 36 LDRPFRMAKLNQLWEKAQRLRLSEVKLKSLYSDL 69 (120)
T ss_dssp ---SSSSHHHHHHHHHHHHHT--HHHHHHHHHHH
T ss_pred ccccHHHHHHHHHHHHHHHccCChHHHHHHHHHH
Confidence 4568999999999999999999999999998875
No 7
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=71.11 E-value=6.4 Score=26.91 Aligned_cols=25 Identities=28% Similarity=0.339 Sum_probs=20.3
Q ss_pred HHHHHHHHHhCC--CCHHHHHHHhhhC
Q psy9493 151 LNKLWEKAEHSG--FTCKNVKFNNQEL 175 (175)
Q Consensus 151 l~kLW~kA~~sg--FS~eEL~sLk~EL 175 (175)
.+.++..|+..| ||.+||.+...||
T Consensus 27 ~e~~~~lA~~~Gf~ft~~el~~~~~el 53 (64)
T TIGR03798 27 PEDRVAIAKEAGFEFTGEDLKEAGEEL 53 (64)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHhhC
Confidence 567899999999 9999998765554
No 8
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=59.27 E-value=8.8 Score=24.70 Aligned_cols=19 Identities=21% Similarity=0.342 Sum_probs=16.1
Q ss_pred HHHHHHHHHhCC--CCHHHHH
Q psy9493 151 LNKLWEKAEHSG--FTCKNVK 169 (175)
Q Consensus 151 l~kLW~kA~~sg--FS~eEL~ 169 (175)
...++..|+..| ||.+||.
T Consensus 29 ~~e~~~lA~~~Gy~ft~~el~ 49 (49)
T PF07862_consen 29 PEEVVALAREAGYDFTEEELE 49 (49)
T ss_pred HHHHHHHHHHcCCCCCHHHhC
Confidence 467899999999 9999873
No 9
>PRK02539 hypothetical protein; Provisional
Probab=39.22 E-value=31 Score=25.81 Aligned_cols=22 Identities=23% Similarity=0.315 Sum_probs=18.6
Q ss_pred chhhhHHHHHHHHc-cCCHHHHH
Q psy9493 49 RMGKLNLLWKKAQV-RLSEPKLK 70 (175)
Q Consensus 49 R~~KLN~LWeKAq~-~fs~~eL~ 70 (175)
.+.|+|-|-.|++. +||++|.+
T Consensus 5 ~I~RINeLakK~K~~gLT~eEk~ 27 (85)
T PRK02539 5 KIARINELAKKKKTEGLTGEEKV 27 (85)
T ss_pred HHHHHHHHHHHhcccCCCHHHHH
Confidence 36899999999999 99996554
No 10
>PF05979 DUF896: Bacterial protein of unknown function (DUF896); InterPro: IPR009242 This family consists of several short, hypothetical bacterial proteins of unknown function. They may be involved in the bacterial SOS response [].; PDB: 2HEP_A 3BHP_C 2JVD_A.
Probab=36.95 E-value=38 Score=24.04 Aligned_cols=21 Identities=29% Similarity=0.365 Sum_probs=14.6
Q ss_pred hhhhHHHHHHHHc-cCCHHHHH
Q psy9493 50 MGKLNLLWKKAQV-RLSEPKLK 70 (175)
Q Consensus 50 ~~KLN~LWeKAq~-~fs~~eL~ 70 (175)
+.|+|-|-.|++. +||++|..
T Consensus 4 i~RINeLa~K~K~~gLT~eE~~ 25 (65)
T PF05979_consen 4 IDRINELAKKSKEEGLTEEEKA 25 (65)
T ss_dssp HHHHHHHHHHHHTT---HHHHH
T ss_pred HHHHHHHHHHhccCCCCHHHHH
Confidence 5789999999998 99986654
No 11
>PRK01631 hypothetical protein; Provisional
Probab=34.53 E-value=41 Score=24.68 Aligned_cols=21 Identities=24% Similarity=0.244 Sum_probs=17.7
Q ss_pred hhhhHHHHHHHHc-cCCHHHHH
Q psy9493 50 MGKLNLLWKKAQV-RLSEPKLK 70 (175)
Q Consensus 50 ~~KLN~LWeKAq~-~fs~~eL~ 70 (175)
+.|+|-|-.|++. +||++|.+
T Consensus 5 i~RINeLakK~K~~gLT~eE~~ 26 (76)
T PRK01631 5 LFRINELSKKEKATGLTVDEKQ 26 (76)
T ss_pred HHHHHHHHHHhcccCCCHHHHH
Confidence 5789999999999 99986654
No 12
>PRK01546 hypothetical protein; Provisional
Probab=34.20 E-value=41 Score=24.81 Aligned_cols=22 Identities=32% Similarity=0.465 Sum_probs=18.4
Q ss_pred chhhhHHHHHHHHc-cCCHHHHH
Q psy9493 49 RMGKLNLLWKKAQV-RLSEPKLK 70 (175)
Q Consensus 49 R~~KLN~LWeKAq~-~fs~~eL~ 70 (175)
.+.|+|-|-.|++. +||++|.+
T Consensus 6 ~i~RINeLakK~K~~gLT~eEk~ 28 (79)
T PRK01546 6 LVERINFLAKKAKAEGLTEEEQR 28 (79)
T ss_pred HHHHHHHHHHhhcccCCCHHHHH
Confidence 36899999999999 99986554
No 13
>cd08325 CARD_CASP1-like Caspase activation and recruitment domain found in Caspase-1 and related proteins. Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) and CASP4 (TX, ICH-2). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. CASP1 plays a central role in the cellular response to a wide variety of microbial and non-microbial stimuli, being activated by the inflammasome or the pyroptosome. CARD8 binds itself and the initiator caspase-9, interfering with the binding of APAF-1 and suppressing caspase-9 activation. CARD12 is a Nod-like receptor (NLR) that plays an important role in the innate immune response to Gram-negative bacteria. Caspase-4 (CASP4), -5 (CASP5),
Probab=31.61 E-value=66 Score=23.14 Aligned_cols=25 Identities=12% Similarity=0.157 Sum_probs=21.8
Q ss_pred hHHHHHHHHHhCC-CCHHHHHHHhhh
Q psy9493 150 KLNKLWEKAEHSG-FTCKNVKFNNQE 174 (175)
Q Consensus 150 Kl~kLW~kA~~sg-FS~eEL~sLk~E 174 (175)
=+++||+-=...+ ||.+|.++++.|
T Consensus 17 ~i~~llD~Ll~~~Vl~~~E~e~i~~~ 42 (83)
T cd08325 17 VINGLLDDLLEKNVLNEEEMEKIKEE 42 (83)
T ss_pred hHHHHHHHHHHcCCCCHHHHHHHHhc
Confidence 4678998889999 999999999875
No 14
>PF09968 DUF2202: Uncharacterized protein domain (DUF2202); InterPro: IPR019243 This domain, found in various hypothetical archaeal proteins, has no known function.; PDB: 3Q4O_A 3Q4Q_A 3Q4R_A 3Q4N_A.
Probab=31.13 E-value=66 Score=26.56 Aligned_cols=42 Identities=21% Similarity=0.430 Sum_probs=25.9
Q ss_pred HHHHHHHhhccccccchhhccccccccCCCCCCCCCCCCCCChhHHHHHHHHHhCC-CCH
Q psy9493 107 RLVGIMSTYGLLEHFEDIQGEKIKLDTDDNAPVHKPRAVFKDKKLNKLWEKAEHSG-FTC 165 (175)
Q Consensus 107 kl~~Il~kYgL~~~~~~~~~~~~~~h~~l~d~~~~~~~~F~DpKl~kLW~kA~~sg-FS~ 165 (175)
.+..+|++||+..- . .+.....|.+|.||.|...-...| .|.
T Consensus 44 av~~Ll~kY~l~dP-------------~----~~~~~G~f~~~~lq~LY~~Lv~~G~~S~ 86 (162)
T PF09968_consen 44 AVKALLEKYGLEDP-------------V----EGDPVGVFTNPELQELYNQLVEQGSKSL 86 (162)
T ss_dssp HHHHHHHHTT---S------------------SS-STT--SSHHHHHHHHHHHHHHTS-H
T ss_pred HHHHHHHHhCCCCC-------------C----ccCCCCCcCcHHHHHHHHHHHHHhhhcH
Confidence 67788999998621 1 112346799999999999888777 553
No 15
>PF05979 DUF896: Bacterial protein of unknown function (DUF896); InterPro: IPR009242 This family consists of several short, hypothetical bacterial proteins of unknown function. They may be involved in the bacterial SOS response [].; PDB: 2HEP_A 3BHP_C 2JVD_A.
Probab=30.57 E-value=54 Score=23.27 Aligned_cols=21 Identities=24% Similarity=0.427 Sum_probs=15.7
Q ss_pred hhHHHHHHHHHhCCCCHHHHH
Q psy9493 149 KKLNKLWEKAEHSGFTCKNVK 169 (175)
Q Consensus 149 pKl~kLW~kA~~sgFS~eEL~ 169 (175)
.|.|.|=+++++.|+|++|..
T Consensus 5 ~RINeLa~K~K~~gLT~eE~~ 25 (65)
T PF05979_consen 5 DRINELAKKSKEEGLTEEEKA 25 (65)
T ss_dssp HHHHHHHHHHHTT---HHHHH
T ss_pred HHHHHHHHHhccCCCCHHHHH
Confidence 478999999999999999875
No 16
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=28.85 E-value=68 Score=24.87 Aligned_cols=20 Identities=25% Similarity=0.308 Sum_probs=12.2
Q ss_pred HHHHHHHhCCCCHHHHHHHh
Q psy9493 153 KLWEKAEHSGFTCKNVKFNN 172 (175)
Q Consensus 153 kLW~kA~~sgFS~eEL~sLk 172 (175)
.+...|+.-|||+..+..|+
T Consensus 63 ~~L~~aK~~GFsD~~IA~l~ 82 (123)
T PF02787_consen 63 ELLRKAKRLGFSDRQIARLW 82 (123)
T ss_dssp HHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHhcc
Confidence 36677777777777776664
No 17
>cd07313 terB_like_2 tellurium resistance terB-like protein, subgroup 2. This family includes several uncharacterized bacterial proteins. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
Probab=26.54 E-value=90 Score=22.23 Aligned_cols=24 Identities=21% Similarity=0.332 Sum_probs=20.7
Q ss_pred hHHHHHHHHHhCC-CCHHHHHHHhh
Q psy9493 150 KLNKLWEKAEHSG-FTCKNVKFNNQ 173 (175)
Q Consensus 150 Kl~kLW~kA~~sg-FS~eEL~sLk~ 173 (175)
-|.-||..|..-| +++.|.+-|++
T Consensus 75 ~l~~L~~vA~ADG~~~~~E~~~l~~ 99 (104)
T cd07313 75 LVEALWEVAYADGELDEYEEHLIRR 99 (104)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHH
Confidence 4667999999999 99999988764
No 18
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=24.81 E-value=87 Score=22.68 Aligned_cols=26 Identities=19% Similarity=0.340 Sum_probs=22.1
Q ss_pred hHHHHHHHHHhCC-CCHHHHHHHhhhC
Q psy9493 150 KLNKLWEKAEHSG-FTCKNVKFNNQEL 175 (175)
Q Consensus 150 Kl~kLW~kA~~sg-FS~eEL~sLk~EL 175 (175)
-|..||....+-+ ||..|...|=+||
T Consensus 40 dl~diy~~V~~K~~fS~sEm~aI~~EL 66 (71)
T PF06569_consen 40 DLKDIYEMVMSKDSFSPSEMQAIAEEL 66 (71)
T ss_pred HHHHHHHHHHhccCCCHHHHHHHHHHH
Confidence 3667898888877 9999999998886
No 19
>cd07316 terB_like_DjlA N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins. Tellurium resistance terB-like domain of the DnaJ-like DjlA proteins. This family represents the terB-like domain of DjlA-like proteins, a subgroup of heat shock DnaJ-like proteins. Escherichia coli DjlA is a type III membrane protein with a small N-terminal transmembrane region and DnaJ-like domain on the extreme C-terminus. Overproduction has been shown to activate the RcsC pathway, which regulates the production of the capsular exopolysaccharide colanic acid. The specific function of this domain is unknown.
Probab=24.66 E-value=1.1e+02 Score=21.74 Aligned_cols=24 Identities=17% Similarity=0.192 Sum_probs=20.8
Q ss_pred hHHHHHHHHHhCC-CCHHHHHHHhh
Q psy9493 150 KLNKLWEKAEHSG-FTCKNVKFNNQ 173 (175)
Q Consensus 150 Kl~kLW~kA~~sg-FS~eEL~sLk~ 173 (175)
-|.-||..|..=| +++.|-+-|++
T Consensus 76 ~l~~l~~vA~ADG~~~~~E~~~l~~ 100 (106)
T cd07316 76 LLEFLFQIAYADGELSEAERELLRR 100 (106)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 4677999999999 99999988764
No 20
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=24.11 E-value=86 Score=22.52 Aligned_cols=31 Identities=32% Similarity=0.424 Sum_probs=26.7
Q ss_pred CCCCCCChhHHHHHHHHHhCC-CCHHHHHHHh
Q psy9493 142 PRAVFKDKKLNKLWEKAEHSG-FTCKNVKFNN 172 (175)
Q Consensus 142 ~~~~F~DpKl~kLW~kA~~sg-FS~eEL~sLk 172 (175)
....|.+.|+.-|...+.+.+ ||..+...|=
T Consensus 18 k~~~fd~dkl~~l~~~~~~~~~~T~~Qv~~il 49 (95)
T PF14771_consen 18 KKESFDSDKLKVLEAAAKTNNCFTCAQVKQIL 49 (95)
T ss_pred HcCCCcHHHHHHHHHHHhcCCceeHHHHHHHH
Confidence 345799999999999999999 9999987764
No 21
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=23.65 E-value=99 Score=18.48 Aligned_cols=20 Identities=25% Similarity=0.443 Sum_probs=16.2
Q ss_pred HHHHHHHhCCCCHHHHHHHh
Q psy9493 153 KLWEKAEHSGFTCKNVKFNN 172 (175)
Q Consensus 153 kLW~kA~~sgFS~eEL~sLk 172 (175)
-||..|+.-|.|.++|.++-
T Consensus 8 tl~~IA~~~~~~~~~l~~~N 27 (44)
T PF01476_consen 8 TLWSIAKRYGISVDELMELN 27 (44)
T ss_dssp -HHHHHHHTTS-HHHHHHHC
T ss_pred cHHHHHhhhhhhHhHHHHhc
Confidence 58999999999999998764
No 22
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=23.52 E-value=1.3e+02 Score=20.84 Aligned_cols=26 Identities=27% Similarity=0.528 Sum_probs=19.7
Q ss_pred hhhHHHHHHHH-c-cCCHHHHHHHHHHh
Q psy9493 51 GKLNLLWKKAQ-V-RLSEPKLKSIYNEL 76 (175)
Q Consensus 51 ~KLN~LWeKAq-~-~fs~~eL~~L~~EL 76 (175)
.++|.||.-|. . ..+.+.|.+.+...
T Consensus 1 ~Ri~~L~~~a~~~~~~~~~~lsr~y~~~ 28 (85)
T PF04032_consen 1 QRINFLYQAAHLLLADGSPSLSRHYMKL 28 (85)
T ss_dssp HHHHHHHHHHH-HHCCC-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence 47999999999 5 77778888776543
No 23
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=23.02 E-value=92 Score=22.46 Aligned_cols=20 Identities=30% Similarity=0.428 Sum_probs=17.3
Q ss_pred H-HHHHhCCCCHHHHHHHhhh
Q psy9493 155 W-EKAEHSGFTCKNVKFNNQE 174 (175)
Q Consensus 155 W-~kA~~sgFS~eEL~sLk~E 174 (175)
| ..|...|||+.+++.++.+
T Consensus 18 Wk~LAr~Lg~se~dI~~i~~~ 38 (84)
T cd08804 18 WTELARELDFTEEQIHQIRIE 38 (84)
T ss_pred HHHHHHHcCCCHHHHHHHHHH
Confidence 6 5799999999999998765
No 24
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=22.57 E-value=1.5e+02 Score=17.95 Aligned_cols=23 Identities=17% Similarity=0.287 Sum_probs=15.7
Q ss_pred hhHHHHHHHHHhCCCCHHHHHHH
Q psy9493 149 KKLNKLWEKAEHSGFTCKNVKFN 171 (175)
Q Consensus 149 pKl~kLW~kA~~sgFS~eEL~sL 171 (175)
+-=..|=..|+.+|+|.+|...+
T Consensus 3 ~EW~~Li~eA~~~Gls~eeir~F 25 (30)
T PF08671_consen 3 EEWVELIKEAKESGLSKEEIREF 25 (30)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHH
Confidence 33445667899999999998764
No 25
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=22.47 E-value=42 Score=28.70 Aligned_cols=24 Identities=38% Similarity=0.511 Sum_probs=20.3
Q ss_pred CCCCChhHHHHHHHHHhCC--CCHHH
Q psy9493 144 AVFKDKKLNKLWEKAEHSG--FTCKN 167 (175)
Q Consensus 144 ~~F~DpKl~kLW~kA~~sg--FS~eE 167 (175)
..|.+||+-+||..++..| |+-.+
T Consensus 139 ~v~~~pr~tgln~ale~~G~sf~G~~ 164 (210)
T COG5018 139 NVFGDPRLTGLNKALEEYGDSFTGTH 164 (210)
T ss_pred HHhcCCccccHHHHHHHhccccCCch
Confidence 4589999999999999999 66444
No 26
>PRK01631 hypothetical protein; Provisional
Probab=22.13 E-value=84 Score=23.06 Aligned_cols=21 Identities=24% Similarity=0.422 Sum_probs=18.6
Q ss_pred hhHHHHHHHHHhCCCCHHHHH
Q psy9493 149 KKLNKLWEKAEHSGFTCKNVK 169 (175)
Q Consensus 149 pKl~kLW~kA~~sgFS~eEL~ 169 (175)
.|.|-|=+++++.|+|.+|..
T Consensus 6 ~RINeLakK~K~~gLT~eE~~ 26 (76)
T PRK01631 6 FRINELSKKEKATGLTVDEKQ 26 (76)
T ss_pred HHHHHHHHHhcccCCCHHHHH
Confidence 478999999999999999875
No 27
>PRK02539 hypothetical protein; Provisional
Probab=22.12 E-value=85 Score=23.51 Aligned_cols=21 Identities=24% Similarity=0.373 Sum_probs=18.5
Q ss_pred hhHHHHHHHHHhCCCCHHHHH
Q psy9493 149 KKLNKLWEKAEHSGFTCKNVK 169 (175)
Q Consensus 149 pKl~kLW~kA~~sgFS~eEL~ 169 (175)
.|.|-|-+++++.|+|++|..
T Consensus 7 ~RINeLakK~K~~gLT~eEk~ 27 (85)
T PRK02539 7 ARINELAKKKKTEGLTGEEKV 27 (85)
T ss_pred HHHHHHHHHhcccCCCHHHHH
Confidence 378899999999999999875
No 28
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=21.66 E-value=96 Score=22.30 Aligned_cols=21 Identities=19% Similarity=0.321 Sum_probs=17.7
Q ss_pred HH-HHHHhCCCCHHHHHHHhhh
Q psy9493 154 LW-EKAEHSGFTCKNVKFNNQE 174 (175)
Q Consensus 154 LW-~kA~~sgFS~eEL~sLk~E 174 (175)
=| ..|..-|||+.+++.++.+
T Consensus 20 ~Wk~Lar~LGls~~dI~~i~~~ 41 (86)
T cd08318 20 DWKTLAPHLEMKDKEIRAIESD 41 (86)
T ss_pred hHHHHHHHcCCCHHHHHHHHhc
Confidence 37 6799999999999998753
No 29
>PRK01546 hypothetical protein; Provisional
Probab=21.57 E-value=86 Score=23.14 Aligned_cols=21 Identities=29% Similarity=0.420 Sum_probs=18.6
Q ss_pred hhHHHHHHHHHhCCCCHHHHH
Q psy9493 149 KKLNKLWEKAEHSGFTCKNVK 169 (175)
Q Consensus 149 pKl~kLW~kA~~sgFS~eEL~ 169 (175)
.|.|-|=+++++.|+|.+|..
T Consensus 8 ~RINeLakK~K~~gLT~eEk~ 28 (79)
T PRK01546 8 ERINFLAKKAKAEGLTEEEQR 28 (79)
T ss_pred HHHHHHHHhhcccCCCHHHHH
Confidence 378999999999999999865
No 30
>PF04679 DNA_ligase_A_C: ATP dependent DNA ligase C terminal region ; InterPro: IPR012309 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase []. ; GO: 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 2CFM_A 1X9N_A 1VS0_B 3GDE_A 2HIX_A 2HIV_A 3L2P_A 4EQ5_A.
Probab=20.91 E-value=49 Score=23.84 Aligned_cols=15 Identities=20% Similarity=0.434 Sum_probs=10.1
Q ss_pred CCCCHHHHHHHhhhC
Q psy9493 161 SGFTCKNVKFNNQEL 175 (175)
Q Consensus 161 sgFS~eEL~sLk~EL 175 (175)
+|||++++..|.+.|
T Consensus 28 tG~~~~~~~~l~~~l 42 (97)
T PF04679_consen 28 TGFSDEELRELRERL 42 (97)
T ss_dssp SS--HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHh
Confidence 579999998887653
No 31
>PF14440 XOO_2897-deam: Xanthomonas XOO_2897-like deaminase
Probab=20.46 E-value=1.1e+02 Score=24.02 Aligned_cols=32 Identities=9% Similarity=0.160 Sum_probs=25.4
Q ss_pred ccchhhhHHHHHHHHc-cCCHHHHHHHHHHhhh
Q psy9493 47 PFRMGKLNLLWKKAQV-RLSEPKLKSIYNELKI 78 (175)
Q Consensus 47 ~FR~~KLN~LWeKAq~-~fs~~eL~~L~~ELk~ 78 (175)
+.++.==-.||..++. .++++++.+||+||.-
T Consensus 43 ~~~~H~E~~il~~l~~~~v~p~~I~elYtEl~P 75 (118)
T PF14440_consen 43 GGKPHSERAILHQLRAHGVPPEQITELYTELEP 75 (118)
T ss_pred CCCCChHHHHHHHHHHcCCcHHHHHHHHHhccc
Confidence 3444444678888886 9999999999999976
Done!