Query psy7641
Match_columns 85
No_of_seqs 131 out of 692
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 23:38:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7641.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7641hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13529 malate dehydrogenase; 99.9 1.3E-23 2.8E-28 169.8 6.9 76 10-85 3-81 (563)
2 PTZ00317 NADP-dependent malic 99.9 3.2E-23 7E-28 167.5 6.4 72 14-85 9-83 (559)
3 PLN03129 NADP-dependent malic 99.9 1.2E-22 2.5E-27 164.8 5.9 65 21-85 39-106 (581)
4 KOG1257|consensus 99.9 4.9E-22 1.1E-26 159.9 6.0 68 18-85 25-95 (582)
5 COG0281 SfcA Malic enzyme [Ene 71.8 2.4 5.1E-05 34.5 1.5 27 54-81 1-28 (432)
6 PF09036 Bcr-Abl_Oligo: Bcr-Ab 65.4 3.4 7.4E-05 26.2 1.0 32 53-84 27-62 (79)
7 PF13877 RPAP3_C: Potential Mo 53.4 18 0.0004 22.3 2.9 31 51-84 1-31 (94)
8 PF04697 Pinin_SDK_N: pinin/SD 49.6 9.7 0.00021 26.5 1.2 27 52-78 3-29 (134)
9 PF14743 DNA_ligase_OB_2: DNA 47.2 8.8 0.00019 23.1 0.6 17 32-48 25-41 (66)
10 PF10410 DnaB_bind: DnaB-helic 44.7 28 0.00061 19.3 2.5 23 62-84 26-48 (59)
11 COG4235 Cytochrome c biogenesi 38.6 45 0.00098 25.7 3.5 33 50-82 131-163 (287)
12 PF09006 Surfac_D-trimer: Lung 38.4 15 0.00033 21.2 0.7 25 55-79 2-26 (46)
13 cd06150 YjgF_YER057c_UK114_lik 36.6 40 0.00087 21.1 2.5 25 46-70 15-40 (105)
14 COG0669 CoaD Phosphopantethein 36.2 19 0.00042 25.6 1.1 19 26-44 35-54 (159)
15 PF06737 Transglycosylas: Tran 34.9 72 0.0016 20.1 3.4 39 32-70 29-68 (77)
16 TIGR00004 endoribonuclease L-P 34.5 45 0.00099 21.4 2.6 16 55-70 44-59 (124)
17 TIGR03391 FeS_syn_CsdE cystein 33.8 63 0.0014 22.1 3.3 27 58-84 9-35 (138)
18 PF00373 FERM_M: FERM central 33.8 43 0.00092 20.8 2.3 33 52-84 83-115 (126)
19 PF02731 SKIP_SNW: SKIP/SNW do 33.6 30 0.00064 24.6 1.7 42 25-80 50-92 (158)
20 cd08041 OBF_kDNA_ligase_like T 32.4 29 0.00062 20.9 1.3 14 32-45 36-49 (77)
21 cd06156 eu_AANH_C_2 A group of 30.0 65 0.0014 20.9 2.8 16 55-70 29-44 (118)
22 cd07971 OBF_DNA_ligase_LigD Th 30.0 31 0.00068 22.1 1.2 13 32-44 39-51 (115)
23 PF15225 IL32: Interleukin 32 29.3 50 0.0011 21.8 2.1 37 35-71 4-50 (104)
24 cd08040 OBF_DNA_ligase_family 28.9 34 0.00074 21.7 1.3 13 32-44 40-52 (108)
25 cd06155 eu_AANH_C_1 A group of 27.6 81 0.0018 19.6 2.8 17 54-70 21-37 (101)
26 cd00448 YjgF_YER057c_UK114_fam 27.2 86 0.0019 18.8 2.9 17 54-70 27-43 (107)
27 KOG4117|consensus 26.8 44 0.00096 20.8 1.4 28 52-79 30-57 (73)
28 cd06154 YjgF_YER057c_UK114_lik 24.7 78 0.0017 20.3 2.4 16 55-70 40-55 (119)
29 PF09776 Mitoc_L55: Mitochondr 23.6 90 0.0019 21.1 2.6 47 5-52 45-92 (116)
30 PF04679 DNA_ligase_A_C: ATP d 23.0 44 0.00095 20.7 0.9 13 32-44 26-38 (97)
31 cd06152 YjgF_YER057c_UK114_lik 22.0 1.1E+02 0.0025 19.7 2.8 16 55-70 30-45 (114)
32 KOG0969|consensus 21.5 55 0.0012 29.3 1.5 48 28-79 602-649 (1066)
33 cd06151 YjgF_YER057c_UK114_lik 20.4 87 0.0019 20.3 2.0 16 55-70 37-52 (126)
No 1
>PRK13529 malate dehydrogenase; Provisional
Probab=99.89 E-value=1.3e-23 Score=169.84 Aligned_cols=76 Identities=32% Similarity=0.512 Sum_probs=72.1
Q ss_pred cCCCCCcceecccchhhhhhCC---CCCCCCHHHHhhcccCCCCCCcccCHHHHHHHHHHHhhccCChhhHHHHHHhcC
Q psy7641 10 EDEQGFPSSQVNLRLHSILRQS---MGLAFSLRERQQLGIHGLMPPTIKNQDQQIEVCRESVRRFQEDLNKFTYLSELQ 85 (85)
Q Consensus 10 ~~~~~~~~~~~~~~g~~~l~~p---KGtaFt~eER~~lgl~GLLPp~v~tle~Q~~R~~~~l~~~~t~L~Ky~yL~~L~ 85 (85)
.+..+.....+..+|.++|+|| ||||||.+||++|||+|||||+|+|+|+|++||+.||+++++||+||+||++||
T Consensus 3 ~~~~~~~~~~~~~~G~~lL~~p~~NKgtaFt~~ER~~lgl~GLLPp~v~t~e~Q~~R~~~~~~~~~~~l~ky~~L~~L~ 81 (563)
T PRK13529 3 RDEKKKRPLYTPLRGPALLNNPLLNKGTAFTEEEREEFGLEGLLPPAVETLEEQAERAYRQYQSKPTDLEKHIYLRNLQ 81 (563)
T ss_pred cccCCCcceeecccchhhhcCcccccccCCCHHHHHhcCCCCCCCCCccCHHHHHHHHHHHHhcCCChHHHHHHHHHHH
Confidence 4566777888899999999999 999999999999999999999999999999999999999999999999999986
No 2
>PTZ00317 NADP-dependent malic enzyme; Provisional
Probab=99.88 E-value=3.2e-23 Score=167.47 Aligned_cols=72 Identities=33% Similarity=0.594 Sum_probs=68.4
Q ss_pred CCcceecccchhhhhhCC---CCCCCCHHHHhhcccCCCCCCcccCHHHHHHHHHHHhhccCChhhHHHHHHhcC
Q psy7641 14 GFPSSQVNLRLHSILRQS---MGLAFSLRERQQLGIHGLMPPTIKNQDQQIEVCRESVRRFQEDLNKFTYLSELQ 85 (85)
Q Consensus 14 ~~~~~~~~~~g~~~l~~p---KGtaFt~eER~~lgl~GLLPp~v~tle~Q~~R~~~~l~~~~t~L~Ky~yL~~L~ 85 (85)
+.+...+..+|.++|+|| ||||||.+||++|||+|||||+|+|+|+|++||+.+++++++||+||+||++||
T Consensus 9 ~~~~~~~~~~G~~lL~~p~~NKgtAFt~~ER~~l~l~GLlPp~v~t~e~Q~~R~~~~~~~~~~~l~Ky~~L~~L~ 83 (559)
T PTZ00317 9 SKEKVPSNARGVDVLRNRFLNKGTAFTAEEREHLGIEGLLPPTVETLEQQVERLWTQFNRIETPINKYQFLRNIH 83 (559)
T ss_pred cccccccCCcchhhhcCcccccccCCCHHHHHhcCCCCCCCCCccCHHHHHHHHHHHHhhCCChHHHHHHHHHHh
Confidence 455667888999999999 999999999999999999999999999999999999999999999999999986
No 3
>PLN03129 NADP-dependent malic enzyme; Provisional
Probab=99.87 E-value=1.2e-22 Score=164.82 Aligned_cols=65 Identities=35% Similarity=0.603 Sum_probs=63.3
Q ss_pred ccchhhhhhCC---CCCCCCHHHHhhcccCCCCCCcccCHHHHHHHHHHHhhccCChhhHHHHHHhcC
Q psy7641 21 NLRLHSILRQS---MGLAFSLRERQQLGIHGLMPPTIKNQDQQIEVCRESVRRFQEDLNKFTYLSELQ 85 (85)
Q Consensus 21 ~~~g~~~l~~p---KGtaFt~eER~~lgl~GLLPp~v~tle~Q~~R~~~~l~~~~t~L~Ky~yL~~L~ 85 (85)
..+|.++|+|| ||||||.+||++|||+|||||+|+|+|+|++|||.||+++++||+||+||++||
T Consensus 39 ~~~G~~ll~~p~~NKgtaFt~~ER~~lgl~GLlP~~v~t~e~Q~~R~~~~~~~~~~~l~ky~~L~~L~ 106 (581)
T PLN03129 39 VASGYDLLRDPRYNKGLAFTETERDRLGLRGLLPPAVLSQELQVKRFMENLRALESPLAKYRALMDLQ 106 (581)
T ss_pred CCcchhhhcCcccccccCCCHHHHhhcCCccCCCCCcCCHHHHHHHHHHHHhccCCcHHHHHHHHHHH
Confidence 56899999999 999999999999999999999999999999999999999999999999999986
No 4
>KOG1257|consensus
Probab=99.86 E-value=4.9e-22 Score=159.90 Aligned_cols=68 Identities=44% Similarity=0.780 Sum_probs=66.0
Q ss_pred eecccchhhhhhCC---CCCCCCHHHHhhcccCCCCCCcccCHHHHHHHHHHHhhccCChhhHHHHHHhcC
Q psy7641 18 SQVNLRLHSILRQS---MGLAFSLRERQQLGIHGLMPPTIKNQDQQIEVCRESVRRFQEDLNKFTYLSELQ 85 (85)
Q Consensus 18 ~~~~~~g~~~l~~p---KGtaFt~eER~~lgl~GLLPp~v~tle~Q~~R~~~~l~~~~t~L~Ky~yL~~L~ 85 (85)
..++.+|+++++|| ||+|||.+||++|||||||||+|.|+|+|++||+.+|++.++||+||+||++||
T Consensus 25 ~~~~~~g~~ll~~p~~NKglAFTl~ERq~l~i~GLLPp~v~t~d~Q~~r~~~~l~~~~~~l~ky~~L~~L~ 95 (582)
T KOG1257|consen 25 VESKKRGYDLLRDPRYNKGLAFTLEERQRLGIHGLLPPVVRTQDEQALRCMNNLRSLTSPLAKYIYLMDLQ 95 (582)
T ss_pred cccccCChhhccCCCcccccccCHHHHHhhCccccCCccccCHHHHHHHHHHHHHhccchHHHHHHHHHHH
Confidence 56789999999999 999999999999999999999999999999999999999999999999999985
No 5
>COG0281 SfcA Malic enzyme [Energy production and conversion]
Probab=71.76 E-value=2.4 Score=34.48 Aligned_cols=27 Identities=26% Similarity=0.452 Sum_probs=24.4
Q ss_pred ccCHHHHHHHHHHHhhccCC-hhhHHHHH
Q psy7641 54 IKNQDQQIEVCRESVRRFQE-DLNKFTYL 81 (85)
Q Consensus 54 v~tle~Q~~R~~~~l~~~~t-~L~Ky~yL 81 (85)
++|+| |.+|++.++....+ +|++|.|+
T Consensus 1 v~t~~-q~~~~~~~~~~~~~~aL~~h~~~ 28 (432)
T COG0281 1 VETIE-QAERAYEQYEQLKTEALDKHEYL 28 (432)
T ss_pred CccHH-HHHHHHHHHhhhhhhhHHHhccC
Confidence 56889 99999999998887 99999986
No 6
>PF09036 Bcr-Abl_Oligo: Bcr-Abl oncoprotein oligomerisation domain; InterPro: IPR015123 This entry represents the oligomerisation domain of the breakpoint cluster region oncoprotein Bcr, and the Bcr/Abl (Abelson-leukemia-virus) fusion protein created by a reciprocal (9;22) fusion []. Brc displays serine/threonine protein kinase activity (2.7.11.1 from EC), acting as a GTPase-activating protein for RAC1 and CDC42. Brc promotes the exchange of RAC or CDC42-bound GDP by GTP, thereby activating them []. The Bcr/Abl fusion protein loses some of the regulatory function of Bcr with regards to small Rho-like GTPases with negative consequences on cell motility, in particular on the capacity to adhere to endothelial cells []. The Bcr, Bcr/Abl oncoprotein oligomerisation domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerisation domain is essential for the oncogenicity of the Bcr-Abl protein []. ; GO: 0004674 protein serine/threonine kinase activity, 0005096 GTPase activator activity, 0006468 protein phosphorylation, 0007165 signal transduction; PDB: 1K1F_C.
Probab=65.38 E-value=3.4 Score=26.24 Aligned_cols=32 Identities=34% Similarity=0.812 Sum_probs=24.7
Q ss_pred cccCHHHHHHHHHHHhhccCChhhH----HHHHHhc
Q psy7641 53 TIKNQDQQIEVCRESVRRFQEDLNK----FTYLSEL 84 (85)
Q Consensus 53 ~v~tle~Q~~R~~~~l~~~~t~L~K----y~yL~~L 84 (85)
.|.++|+.++||...++..+-.+.| -|||..|
T Consensus 27 svgd~e~eLerCK~sirrLeqevnkERFrmiYLQTl 62 (79)
T PF09036_consen 27 SVGDIEQELERCKASIRRLEQEVNKERFRMIYLQTL 62 (79)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667999999999999998876643 3577654
No 7
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=53.42 E-value=18 Score=22.32 Aligned_cols=31 Identities=23% Similarity=0.446 Sum_probs=21.7
Q ss_pred CCcccCHHHHHHHHHHHhhccCChhhHHHHHHhc
Q psy7641 51 PPTIKNQDQQIEVCRESVRRFQEDLNKFTYLSEL 84 (85)
Q Consensus 51 Pp~v~tle~Q~~R~~~~l~~~~t~L~Ky~yL~~L 84 (85)
|+.-.| -.|-+|.|..+... +-++|-||.++
T Consensus 1 p~~P~~-~~eF~~~w~~~~~~--~~~~~~yL~~i 31 (94)
T PF13877_consen 1 PPAPKN-SYEFERDWRRLKKD--PEERYEYLKSI 31 (94)
T ss_pred CcCCCC-HHHHHHHHHHHcCC--HHHHHHHHHhC
Confidence 444444 56788889988743 33999999876
No 8
>PF04697 Pinin_SDK_N: pinin/SDK conserved region; InterPro: IPR006787 This conserved region is found at the N-terminal of the member proteins. It is located adjacent and N-terminal to the pinin/SKD/memA domain IPR006786 from INTERPRO. Members of this family have very varied localisations within the eukaryotic cell. Pinin is known to localise at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque [, ]. SDK2/3 is a dynamically localised nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing []. MemA is a tumour marker preferentially expressed in human melanoma cell lines. A common feature of the members of this family is that they may all participate in regulating protein-protein interactions [].
Probab=49.58 E-value=9.7 Score=26.45 Aligned_cols=27 Identities=22% Similarity=0.507 Sum_probs=24.0
Q ss_pred CcccCHHHHHHHHHHHhhccCChhhHH
Q psy7641 52 PTIKNQDQQIEVCRESVRRFQEDLNKF 78 (85)
Q Consensus 52 p~v~tle~Q~~R~~~~l~~~~t~L~Ky 78 (85)
-+|.+++.|++.+.+.|+..+.+|-|-
T Consensus 3 vav~~Lq~qlE~Ake~Lk~vDenIkKl 29 (134)
T PF04697_consen 3 VAVRTLQAQLEKAKESLKNVDENIKKL 29 (134)
T ss_pred hhHHHHHHHHHHHHHHhhhhhHHHHHH
Confidence 468899999999999999999888774
No 9
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=47.21 E-value=8.8 Score=23.13 Aligned_cols=17 Identities=29% Similarity=0.470 Sum_probs=10.7
Q ss_pred CCCCCCHHHHhhcccCC
Q psy7641 32 MGLAFSLRERQQLGIHG 48 (85)
Q Consensus 32 KGtaFt~eER~~lgl~G 48 (85)
=|++||+++|+.+-..|
T Consensus 25 iGsG~td~~R~~~~~iG 41 (66)
T PF14743_consen 25 IGSGFTDEEREEPPYIG 41 (66)
T ss_dssp E-SS--HHHHHHHHHTT
T ss_pred ECCCCCHHHHhcCCCCC
Confidence 47999999999876444
No 10
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=44.73 E-value=28 Score=19.30 Aligned_cols=23 Identities=13% Similarity=0.317 Sum_probs=16.6
Q ss_pred HHHHHHhhccCChhhHHHHHHhc
Q psy7641 62 EVCRESVRRFQEDLNKFTYLSEL 84 (85)
Q Consensus 62 ~R~~~~l~~~~t~L~Ky~yL~~L 84 (85)
.++...+...++++.|..|+..|
T Consensus 26 ~~~~~~i~~i~~~i~r~~y~~~l 48 (59)
T PF10410_consen 26 REAAPLIAQIPDPIERELYIREL 48 (59)
T ss_dssp HHHHHHHTT--SHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCHHHHHHHHHHH
Confidence 45566678889999999998865
No 11
>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]
Probab=38.60 E-value=45 Score=25.74 Aligned_cols=33 Identities=15% Similarity=0.274 Sum_probs=30.0
Q ss_pred CCCcccCHHHHHHHHHHHhhccCChhhHHHHHH
Q psy7641 50 MPPTIKNQDQQIEVCRESVRRFQEDLNKFTYLS 82 (85)
Q Consensus 50 LPp~v~tle~Q~~R~~~~l~~~~t~L~Ky~yL~ 82 (85)
=||.-+++|.++.+.-..++..|+|.+.|.+|-
T Consensus 131 ~~~~~~~~~~l~a~Le~~L~~nP~d~egW~~Lg 163 (287)
T COG4235 131 QPPAEQEMEALIARLETHLQQNPGDAEGWDLLG 163 (287)
T ss_pred cCCCcccHHHHHHHHHHHHHhCCCCchhHHHHH
Confidence 578888999999999999999999999999774
No 12
>PF09006 Surfac_D-trimer: Lung surfactant protein D coiled-coil trimerisation; InterPro: IPR015097 This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein []. ; PDB: 4DN8_A 3G84_A 2RIE_C 3IKR_B 1B08_A 2GGX_B 2OS9_C 2ORK_B 1PWB_A 2RIA_C ....
Probab=38.37 E-value=15 Score=21.16 Aligned_cols=25 Identities=24% Similarity=0.452 Sum_probs=18.0
Q ss_pred cCHHHHHHHHHHHhhccCChhhHHH
Q psy7641 55 KNQDQQIEVCRESVRRFQEDLNKFT 79 (85)
Q Consensus 55 ~tle~Q~~R~~~~l~~~~t~L~Ky~ 79 (85)
.++.+|++..-.+++...+.+.+|-
T Consensus 2 ~aLrqQv~aL~~qv~~Lq~~fs~yK 26 (46)
T PF09006_consen 2 NALRQQVEALQGQVQRLQAAFSQYK 26 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777777777777777777664
No 13
>cd06150 YjgF_YER057c_UK114_like_2 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=36.55 E-value=40 Score=21.12 Aligned_cols=25 Identities=8% Similarity=0.088 Sum_probs=17.9
Q ss_pred cCCCCCCc-ccCHHHHHHHHHHHhhc
Q psy7641 46 IHGLMPPT-IKNQDQQIEVCRESVRR 70 (85)
Q Consensus 46 l~GLLPp~-v~tle~Q~~R~~~~l~~ 70 (85)
+.|.+|.. -.++++|.+.++.+++.
T Consensus 15 iSGq~~~~~~~~~~~Q~~~~~~nl~~ 40 (105)
T cd06150 15 LAGQVADDTSADITGQTRQVLAKIDA 40 (105)
T ss_pred EeCcCCcCCCCCHHHHHHHHHHHHHH
Confidence 44444432 27899999999999864
No 14
>COG0669 CoaD Phosphopantetheine adenylyltransferase [Coenzyme metabolism]
Probab=36.20 E-value=19 Score=25.63 Aligned_cols=19 Identities=32% Similarity=0.384 Sum_probs=16.2
Q ss_pred hhhhCC-CCCCCCHHHHhhc
Q psy7641 26 SILRQS-MGLAFSLRERQQL 44 (85)
Q Consensus 26 ~~l~~p-KGtaFt~eER~~l 44 (85)
.+..|| |..=||.+||.++
T Consensus 35 aV~~np~K~plFsleER~~l 54 (159)
T COG0669 35 AVAINPSKKPLFSLEERVEL 54 (159)
T ss_pred EEEeCCCcCCCcCHHHHHHH
Confidence 456788 9999999999876
No 15
>PF06737 Transglycosylas: Transglycosylase-like domain; InterPro: IPR010618 This family of proteins is very likely to act as transglycosylase enzymes related to IPR001916 from INTERPRO and IPR008258 from INTERPRO. These other families are weakly matched by this family, and include the known active site residues.; GO: 0005576 extracellular region; PDB: 1XSF_A 3EO5_A.
Probab=34.89 E-value=72 Score=20.08 Aligned_cols=39 Identities=31% Similarity=0.441 Sum_probs=32.2
Q ss_pred CCCCCCHHHHhhcccCCCCC-CcccCHHHHHHHHHHHhhc
Q psy7641 32 MGLAFSLRERQQLGIHGLMP-PTIKNQDQQIEVCRESVRR 70 (85)
Q Consensus 32 KGtaFt~eER~~lgl~GLLP-p~v~tle~Q~~R~~~~l~~ 70 (85)
-|.-|+...=+.+|=.|.-| |.--|-++|+.++.+-+..
T Consensus 29 Gg~Qf~~sTW~a~Gg~~yap~~~~As~~eQi~~A~~l~~~ 68 (77)
T PF06737_consen 29 GGLQFSQSTWRAYGGSGYAPRPDQASRAEQIAVAEKLYAR 68 (77)
T ss_dssp TTTTBBHHHHHHTTGGGT-SSCCCS-HHHHHHHHHHHHHH
T ss_pred ceeccCHHHHHHhCCCcCCCChhhCCHHHHHHHHHHHHHH
Confidence 68899999999999888887 8888999999999887754
No 16
>TIGR00004 endoribonuclease L-PSP, putative. This protein was described initially as an inhibitor of protein synthesis intiation but is now viewed as an endoribonuclease active on single-stranded mRNA. The cleavage of mRNA is responsible for the inhibition of protein synthesis. A role in purine regulation has also been suggested.
Probab=34.52 E-value=45 Score=21.36 Aligned_cols=16 Identities=19% Similarity=0.227 Sum_probs=13.9
Q ss_pred cCHHHHHHHHHHHhhc
Q psy7641 55 KNQDQQIEVCRESVRR 70 (85)
Q Consensus 55 ~tle~Q~~R~~~~l~~ 70 (85)
.++++|++.|+.+++.
T Consensus 44 ~d~~~Q~~~~~~ni~~ 59 (124)
T TIGR00004 44 GDIAEQAEQVLENLKA 59 (124)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 6899999999999854
No 17
>TIGR03391 FeS_syn_CsdE cysteine desulfurase, sulfur acceptor subunit CsdE. Members of this protein family are CsdE, formerly called YgdK. This protein, found as a paralog to SufE in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE), in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair, although involved in FeS cluster biosynthesis, is not found next to other such genes as are its paralogs from the Suf or Isc systems.
Probab=33.79 E-value=63 Score=22.10 Aligned_cols=27 Identities=7% Similarity=-0.004 Sum_probs=22.0
Q ss_pred HHHHHHHHHHhhccCChhhHHHHHHhc
Q psy7641 58 DQQIEVCRESVRRFQEDLNKFTYLSEL 84 (85)
Q Consensus 58 e~Q~~R~~~~l~~~~t~L~Ky~yL~~L 84 (85)
+.-.+.+.++|...++.-+||.||-.|
T Consensus 9 ~~~~~~i~~~f~~~~dwe~ry~~lI~l 35 (138)
T TIGR03391 9 EITAADLIATFAACRQWEDRYRQLILL 35 (138)
T ss_pred chHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 344567889999999999999999754
No 18
>PF00373 FERM_M: FERM central domain; InterPro: IPR019748 The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 4DXA_B 2EMS_A 2ZPY_A 1J19_A 2D10_B 2D11_B 1GC6_A 2D2Q_A 2EMT_A 2YVC_A ....
Probab=33.75 E-value=43 Score=20.83 Aligned_cols=33 Identities=15% Similarity=0.188 Sum_probs=24.5
Q ss_pred CcccCHHHHHHHHHHHhhccCChhhHHHHHHhc
Q psy7641 52 PTIKNQDQQIEVCRESVRRFQEDLNKFTYLSEL 84 (85)
Q Consensus 52 p~v~tle~Q~~R~~~~l~~~~t~L~Ky~yL~~L 84 (85)
.....++.++.+.+++++..+..-.|..||.-+
T Consensus 83 ~~~~~~~~~I~~~~~~l~~~s~~~a~~~fl~~~ 115 (126)
T PF00373_consen 83 MKQKEWEKRILEQHKKLRGMSPEEAKLQFLQIC 115 (126)
T ss_dssp STHHHHHHHHHHHHHHTTT--HHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHH
Confidence 455567788888999999888888999998754
No 19
>PF02731 SKIP_SNW: SKIP/SNW domain; InterPro: IPR004015 SKIP (SKI-interacting protein) is an essential spliceosomal component and transcriptional coregulator, which may provide regulatory coupling of transcription initiation and splicing []. SKIP was identified in a yeast 2-hybrid screen, where it was shown to interact with both the cellular and viral forms of SKI through the highly conserved region on SKIP known as the SNW domain []. SKIP is now known to interact with a number of other proteins as well. SKIP potentiates the activity of important transcription factors, such as vitamin D receptor, CBF1 (RBP-Jkappa), Smad2/3, and MyoD. It works with Ski in overcoming pRb-mediated cell cycle arrest, and it is targeted by the viral transactivators EBNA2 and E7 []. This entry represents the SNW domain.; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=33.65 E-value=30 Score=24.61 Aligned_cols=42 Identities=21% Similarity=0.353 Sum_probs=29.1
Q ss_pred hhhhhCC-CCCCCCHHHHhhcccCCCCCCcccCHHHHHHHHHHHhhccCChhhHHHH
Q psy7641 25 HSILRQS-MGLAFSLRERQQLGIHGLMPPTIKNQDQQIEVCRESVRRFQEDLNKFTY 80 (85)
Q Consensus 25 ~~~l~~p-KGtaFt~eER~~lgl~GLLPp~v~tle~Q~~R~~~~l~~~~t~L~Ky~y 80 (85)
..|+++| +- .|.+|++... +||+|.+ |.+=..+.-||||-+-
T Consensus 50 ~PVlhsp~rK--lT~eeq~~Wk----IPp~ISN--------WKN~kGytIpLDKRla 92 (158)
T PF02731_consen 50 APVLHSPPRK--LTKEEQQKWK----IPPCISN--------WKNPKGYTIPLDKRLA 92 (158)
T ss_pred CccccCCccc--CCHHHHhccc----CCCcccc--------ccCCCCCccCHHHHHh
Confidence 4556666 43 3788888754 6999988 7777777777776553
No 20
>cd08041 OBF_kDNA_ligase_like The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. The mitochondrial DNA of parasitic protozoan is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-de
Probab=32.35 E-value=29 Score=20.90 Aligned_cols=14 Identities=29% Similarity=0.425 Sum_probs=12.3
Q ss_pred CCCCCCHHHHhhcc
Q psy7641 32 MGLAFSLRERQQLG 45 (85)
Q Consensus 32 KGtaFt~eER~~lg 45 (85)
=|++||.++|+++.
T Consensus 36 vgtG~t~~~r~~~~ 49 (77)
T cd08041 36 IGSGFSDEQRRNPP 49 (77)
T ss_pred EcCCCCHHHHhcCC
Confidence 48999999999875
No 21
>cd06156 eu_AANH_C_2 A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the second of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=30.00 E-value=65 Score=20.94 Aligned_cols=16 Identities=13% Similarity=0.084 Sum_probs=14.0
Q ss_pred cCHHHHHHHHHHHhhc
Q psy7641 55 KNQDQQIEVCRESVRR 70 (85)
Q Consensus 55 ~tle~Q~~R~~~~l~~ 70 (85)
.+++.|.++|++++..
T Consensus 29 ~~~~~Q~~qal~Ni~~ 44 (118)
T cd06156 29 GGITLQAVLSLQHLER 44 (118)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 5899999999999864
No 22
>cd07971 OBF_DNA_ligase_LigD The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Mycobacterium tuberculosis LigD and similar ba
Probab=29.95 E-value=31 Score=22.14 Aligned_cols=13 Identities=31% Similarity=0.506 Sum_probs=11.6
Q ss_pred CCCCCCHHHHhhc
Q psy7641 32 MGLAFSLRERQQL 44 (85)
Q Consensus 32 KGtaFt~eER~~l 44 (85)
=|++||.+++++|
T Consensus 39 vgtG~s~~~~~~l 51 (115)
T cd07971 39 VGTGFSAATLREL 51 (115)
T ss_pred EcCCCCHHHHHHH
Confidence 5899999999876
No 23
>PF15225 IL32: Interleukin 32
Probab=29.26 E-value=50 Score=21.78 Aligned_cols=37 Identities=14% Similarity=0.242 Sum_probs=26.1
Q ss_pred CCCHHHHhhcccCCCCC--CcccCHHHH--------HHHHHHHhhcc
Q psy7641 35 AFSLRERQQLGIHGLMP--PTIKNQDQQ--------IEVCRESVRRF 71 (85)
Q Consensus 35 aFt~eER~~lgl~GLLP--p~v~tle~Q--------~~R~~~~l~~~ 71 (85)
..-.+||+.|..+|-=| |.+++-+.+ ..+++..|.+.
T Consensus 4 PLLeeeRd~LR~RgnRspvp~~EDp~te~~eP~Esf~dkvmR~Fqam 50 (104)
T PF15225_consen 4 PLLEEERDELRCRGNRSPVPDVEDPATEVWEPGESFCDKVMRWFQAM 50 (104)
T ss_pred cccHHHHHHHHhccCCCCCCCCCCcccccCCcchhHHHHHHHHHHHH
Confidence 44578999999999887 455655555 56777766554
No 24
>cd08040 OBF_DNA_ligase_family The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV,
Probab=28.88 E-value=34 Score=21.66 Aligned_cols=13 Identities=46% Similarity=0.764 Sum_probs=11.7
Q ss_pred CCCCCCHHHHhhc
Q psy7641 32 MGLAFSLRERQQL 44 (85)
Q Consensus 32 KGtaFt~eER~~l 44 (85)
-|++||.+++++|
T Consensus 40 vgtGf~~~~~~~l 52 (108)
T cd08040 40 VGTGFSADERRDL 52 (108)
T ss_pred EcCCCCHHHHHHH
Confidence 6899999999886
No 25
>cd06155 eu_AANH_C_1 A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the first of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=27.61 E-value=81 Score=19.64 Aligned_cols=17 Identities=18% Similarity=0.227 Sum_probs=14.5
Q ss_pred ccCHHHHHHHHHHHhhc
Q psy7641 54 IKNQDQQIEVCRESVRR 70 (85)
Q Consensus 54 v~tle~Q~~R~~~~l~~ 70 (85)
-.++++|.++++++++.
T Consensus 21 ~~d~~~Q~~~v~~ni~~ 37 (101)
T cd06155 21 DETVEEQMESIFSKLRE 37 (101)
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 36899999999999864
No 26
>cd00448 YjgF_YER057c_UK114_family YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=27.24 E-value=86 Score=18.84 Aligned_cols=17 Identities=12% Similarity=0.091 Sum_probs=14.2
Q ss_pred ccCHHHHHHHHHHHhhc
Q psy7641 54 IKNQDQQIEVCRESVRR 70 (85)
Q Consensus 54 v~tle~Q~~R~~~~l~~ 70 (85)
..++++|++.++.++..
T Consensus 27 ~~~~~~Q~~~~~~ni~~ 43 (107)
T cd00448 27 PGDIEAQTRQALENLEA 43 (107)
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 47899999999988754
No 27
>KOG4117|consensus
Probab=26.75 E-value=44 Score=20.76 Aligned_cols=28 Identities=18% Similarity=0.121 Sum_probs=23.5
Q ss_pred CcccCHHHHHHHHHHHhhccCChhhHHH
Q psy7641 52 PTIKNQDQQIEVCRESVRRFQEDLNKFT 79 (85)
Q Consensus 52 p~v~tle~Q~~R~~~~l~~~~t~L~Ky~ 79 (85)
.++.|+..|+-+-...+.+.-+||+|.+
T Consensus 30 DkFQtMSDQII~RiDDM~~riDDLEKnI 57 (73)
T KOG4117|consen 30 DKFQTMSDQIIGRIDDMSSRIDDLEKNI 57 (73)
T ss_pred HHHHHHHHHHHHHHhhhhhhhHHHHHHH
Confidence 3567788888888888889999999987
No 28
>cd06154 YjgF_YER057c_UK114_like_6 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=24.65 E-value=78 Score=20.27 Aligned_cols=16 Identities=19% Similarity=0.310 Sum_probs=14.0
Q ss_pred cCHHHHHHHHHHHhhc
Q psy7641 55 KNQDQQIEVCRESVRR 70 (85)
Q Consensus 55 ~tle~Q~~R~~~~l~~ 70 (85)
.++++|++.++.++..
T Consensus 40 ~d~~~Q~~~~~~ni~~ 55 (119)
T cd06154 40 GDAYEQTRQCLEIIEA 55 (119)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 5899999999999864
No 29
>PF09776 Mitoc_L55: Mitochondrial ribosomal protein L55; InterPro: IPR018615 Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
Probab=23.55 E-value=90 Score=21.13 Aligned_cols=47 Identities=15% Similarity=0.096 Sum_probs=34.3
Q ss_pred eeecccCCCCCcceecccchhhhhhCC-CCCCCCHHHHhhcccCCCCCC
Q psy7641 5 YQLGIEDEQGFPSSQVNLRLHSILRQS-MGLAFSLRERQQLGIHGLMPP 52 (85)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~g~~~l~~p-KGtaFt~eER~~lgl~GLLPp 52 (85)
|..-.+.+||..+.+.-.-...++.-| .=...|+|||++. +.-.-|.
T Consensus 45 Ypv~lV~pDGSTI~Iry~EPR~ii~mPlDl~~LSeeERk~r-l~kR~pk 92 (116)
T PF09776_consen 45 YPVLLVRPDGSTINIRYHEPRRIIKMPLDLDTLSEEERKAR-LRKRKPK 92 (116)
T ss_pred ccEEEEecCCCEEEEeccChHHHhccccCcccCCHHHHHHH-HHHhCCc
Confidence 566677888988888777777888888 6667889998764 4444553
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=23.03 E-value=44 Score=20.73 Aligned_cols=13 Identities=38% Similarity=0.554 Sum_probs=8.2
Q ss_pred CCCCCCHHHHhhc
Q psy7641 32 MGLAFSLRERQQL 44 (85)
Q Consensus 32 KGtaFt~eER~~l 44 (85)
=|++||.+++++|
T Consensus 26 vgtG~~~~~~~~l 38 (97)
T PF04679_consen 26 VGTGFSDEELREL 38 (97)
T ss_dssp E-SS--HHHHHHH
T ss_pred ECCCCCHHHHHHH
Confidence 5889999998876
No 31
>cd06152 YjgF_YER057c_UK114_like_4 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=21.97 E-value=1.1e+02 Score=19.65 Aligned_cols=16 Identities=13% Similarity=0.327 Sum_probs=13.8
Q ss_pred cCHHHHHHHHHHHhhc
Q psy7641 55 KNQDQQIEVCRESVRR 70 (85)
Q Consensus 55 ~tle~Q~~R~~~~l~~ 70 (85)
.++++|++.|+++++.
T Consensus 30 ~d~~~Q~~~~~~Nl~~ 45 (114)
T cd06152 30 EDLEEEIDQAFDNVEL 45 (114)
T ss_pred cCHHHHHHHHHHHHHH
Confidence 4899999999999864
No 32
>KOG0969|consensus
Probab=21.52 E-value=55 Score=29.30 Aligned_cols=48 Identities=15% Similarity=0.298 Sum_probs=40.9
Q ss_pred hhCCCCCCCCHHHHhhcccCCCCCCcccCHHHHHHHHHHHhhccCChhhHHH
Q psy7641 28 LRQSMGLAFSLRERQQLGIHGLMPPTIKNQDQQIEVCRESVRRFQEDLNKFT 79 (85)
Q Consensus 28 l~~pKGtaFt~eER~~lgl~GLLPp~v~tle~Q~~R~~~~l~~~~t~L~Ky~ 79 (85)
.+.|.|--|-..++++ ||||...+++=.--+|+.+.++...+|+.|-+
T Consensus 602 ~~TP~g~yFv~~~~rk----GlLP~ILe~ll~aRKraK~dlk~ekDp~kr~v 649 (1066)
T KOG0969|consen 602 TRTPTGDYFVKTEVRK----GLLPEILEDLLTARKRAKADLKKEKDPFKRAV 649 (1066)
T ss_pred eECCCCCeeeehhhhc----cccHHHHHHHHHHHHHHHHHHHhccCHHHHhh
Confidence 4455788888888875 99999999999999999999999999987754
No 33
>cd06151 YjgF_YER057c_UK114_like_3 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=20.39 E-value=87 Score=20.30 Aligned_cols=16 Identities=6% Similarity=0.092 Sum_probs=14.0
Q ss_pred cCHHHHHHHHHHHhhc
Q psy7641 55 KNQDQQIEVCRESVRR 70 (85)
Q Consensus 55 ~tle~Q~~R~~~~l~~ 70 (85)
.++++|+.+|+++++.
T Consensus 37 ~d~~~Q~~~~l~ni~~ 52 (126)
T cd06151 37 GDTETQTISVLKRIET 52 (126)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 5899999999999864
Done!