Query psy8046
Match_columns 214
No_of_seqs 192 out of 406
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 17:02:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8046.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8046hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3149|consensus 100.0 2E-36 4.3E-41 267.1 13.0 181 2-183 23-242 (249)
2 PF03366 YEATS: YEATS family; 100.0 1.5E-36 3.3E-41 228.8 9.3 82 16-97 1-83 (84)
3 COG5033 TFG3 Transcription ini 100.0 7E-34 1.5E-38 245.2 8.4 188 2-195 20-225 (225)
4 PF14723 SSFA2_C: Sperm-specif 57.6 24 0.00052 30.5 5.1 36 149-184 139-174 (179)
5 PLN00172 ubiquitin conjugating 53.7 37 0.0008 27.7 5.5 35 13-47 27-61 (147)
6 PF09154 DUF1939: Domain of un 52.0 7.7 0.00017 27.3 1.1 13 59-71 37-49 (57)
7 smart00212 UBCc Ubiquitin-conj 42.4 93 0.002 24.7 6.1 36 12-47 24-59 (145)
8 PF05524 PEP-utilisers_N: PEP- 40.6 58 0.0013 25.1 4.5 29 154-182 34-62 (123)
9 KOG0930|consensus 40.2 59 0.0013 30.7 5.1 37 148-184 10-46 (395)
10 PF07278 DUF1441: Protein of u 37.9 41 0.0009 28.3 3.5 27 162-188 126-152 (152)
11 TIGR02449 conserved hypothetic 36.3 44 0.00096 24.4 3.0 22 155-176 39-60 (65)
12 PF13028 DUF3889: Protein of u 35.6 1.7E+02 0.0036 23.0 6.3 23 64-86 70-92 (97)
13 PF09340 NuA4: Histone acetylt 34.9 70 0.0015 23.9 4.0 36 155-190 2-37 (80)
14 PF04568 IATP: Mitochondrial A 34.8 1E+02 0.0022 24.3 5.0 23 157-179 71-93 (100)
15 PF04201 TPD52: Tumour protein 31.2 1E+02 0.0023 26.3 4.9 32 155-186 29-60 (162)
16 PF07820 TraC: TraC-like prote 30.5 61 0.0013 25.3 3.1 21 164-184 4-24 (92)
17 PRK13848 conjugal transfer pro 28.5 64 0.0014 25.4 2.9 20 165-184 6-25 (98)
18 KOG0417|consensus 26.3 2.4E+02 0.0053 23.8 6.2 40 7-46 20-60 (148)
19 KOG4010|consensus 25.0 1.3E+02 0.0029 26.5 4.5 37 149-185 38-74 (208)
20 PRK02220 4-oxalocrotonate taut 24.1 45 0.00097 22.4 1.2 29 172-200 14-42 (61)
21 PF14193 DUF4315: Domain of un 22.7 1.7E+02 0.0037 22.2 4.3 27 157-183 3-29 (83)
22 PF01361 Tautomerase: Tautomer 22.6 44 0.00095 22.5 0.9 29 172-200 13-41 (60)
23 PF10458 Val_tRNA-synt_C: Valy 22.0 2E+02 0.0043 20.2 4.3 26 155-180 4-29 (66)
24 cd00195 UBCc Ubiquitin-conjuga 21.5 3.1E+02 0.0067 21.5 5.8 33 15-47 27-59 (141)
25 PF04822 Takusan: Takusan; In 21.1 2.3E+02 0.005 21.6 4.7 30 151-180 15-44 (84)
26 COG5509 Uncharacterized small 20.9 1.9E+02 0.0041 21.2 3.9 25 158-182 28-52 (65)
27 PF07798 DUF1640: Protein of u 20.4 2.2E+02 0.0048 23.7 4.9 29 154-182 72-100 (177)
28 KOG1465|consensus 20.3 2.8E+02 0.0061 26.4 6.0 62 118-187 100-161 (353)
No 1
>KOG3149|consensus
Probab=100.00 E-value=2e-36 Score=267.12 Aligned_cols=181 Identities=35% Similarity=0.558 Sum_probs=147.0
Q ss_pred CCccccccCCCCCCeeeEEEEEecCCCcCcccceeeEEEEeCCCCCCceeeeecCCcEEEEeeEeeEEEEEEEEEeC-CC
Q psy8046 2 EPLQMGKKRESDGHTHEWKVYIKPYYKEDLAKYIKKVSFKLHESYPVNVRILTKPPFEISETGWGEFELVIKIYFHD-PN 80 (214)
Q Consensus 2 ~~~~lgkK~~~~~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~nP~Rvv~~PPFeVtE~GWGEF~I~I~I~F~d-~~ 80 (214)
+|+++|+ +.++++||.|+|||||.++||++.||+||+|+||+||+||+|+|++|||+|+|+|||+|+|.|+|||.| .+
T Consensus 23 ~a~~~~~-~~~~~~th~w~v~v~~~~~ed~~~~V~KV~f~LH~sf~~P~Rvv~~pPf~i~EtGwgeF~i~i~i~f~d~~~ 101 (249)
T KOG3149|consen 23 RAAILGK-RLPDGFTHIWEVYVRGPGKEDISAFVDKVVFKLHESFPNPRRVVESPPFEITETGWGEFEIQIEIFFTDDAN 101 (249)
T ss_pred cccccCC-CCCcccceeeEEEecCcCccccceeeeeeeeecccccccccccccCCCceEEeeccccceEEEEEEeccCCC
Confidence 5788888 667889999999999999999999999999999999999999999999999999999999999999996 78
Q ss_pred CCcEEEEEeecccCCCcc--------------cccCCCCceeEEEEE-EEEecCCCHHHHHHHhcCCCCCCCchhh----
Q psy8046 81 ERPVTLYHMLKLFKTKDA--------------ACDATNSLLYNEFYE-EIIFNEPTLTMYKTLSSTVPHTPASASL---- 141 (214)
Q Consensus 81 ekpv~i~H~L~L~~~~~~--------------~~~~~~~~v~se~yd-eIvF~nPte~f~~~L~~~~~~~~~~~~~---- 141 (214)
++++.++|.|.|+.++.. .....+.+|+++.|+ +++|++|++.++..+.+.+..+....+.
T Consensus 102 ~~~v~~~~~l~l~~~~~p~~~~~~~~~~~~~~~~~~~r~~v~~~~~~~e~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 181 (249)
T KOG3149|consen 102 EKKVTLYHDLKLHSYGAPPVPHEESTKKTFVNPTISLRIPVVREGVDVEIVFPDPTESTSIEASSRPVGPGSNLAAVTDL 181 (249)
T ss_pred CceeeeeeeEEeeccCCCCccchhhhcccccccchhcccccccccccceeecCCCCcccccccCCCCCcCCccccccccc
Confidence 899999999999987421 113457799999999 9999999999999998775322111000
Q ss_pred -----------hhccC-----C---ChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy8046 142 -----------IAAHS-----V---NFESAKASTLRGIIEAKKRLEREIGVYKDKISTKLF 183 (214)
Q Consensus 142 -----------~~~~~-----~---~~~~~e~~el~~i~~a~~~v~~eI~~lk~~l~~~~~ 183 (214)
..+.. + .+.-.+..+.+++..+.+.++.++.++++++.....
T Consensus 182 ~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~e~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~ 242 (249)
T KOG3149|consen 182 KQVKSKTLPSLLSKESSKDVKTEKSSERPNEIDEVDRLEKKIKELKKEINKVRKDIEKLEG 242 (249)
T ss_pred cccccccCcccccccccccccccccccccccchhhhhhhhhhhhhhhHHHHHHHhhhhccc
Confidence 00000 0 112235678899888899999999999998876653
No 2
>PF03366 YEATS: YEATS family; InterPro: IPR005033 Named the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit', this family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activity.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3QRL_A 2L7E_A 3FK3_C 3RLS_A.
Probab=100.00 E-value=1.5e-36 Score=228.85 Aligned_cols=82 Identities=60% Similarity=1.071 Sum_probs=70.1
Q ss_pred eeeEEEEEecCCCcCcccceeeEEEEeCCCCCCceeeeecCCcEEEEeeEeeEEEEEEEEEeCC-CCCcEEEEEeecccC
Q psy8046 16 THEWKVYIKPYYKEDLAKYIKKVSFKLHESYPVNVRILTKPPFEISETGWGEFELVIKIYFHDP-NERPVTLYHMLKLFK 94 (214)
Q Consensus 16 tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~nP~Rvv~~PPFeVtE~GWGEF~I~I~I~F~d~-~ekpv~i~H~L~L~~ 94 (214)
||+|+||||+++++|++++|+||+|+|||||+||+|++++|||+|+|+|||||+|.|+|+|++. +++|+++.|+|+|++
T Consensus 1 th~W~v~Vr~~~~~d~~~~i~kV~f~LHpsF~~p~r~v~~pPFevte~GWGeF~i~I~i~f~~~~~~~~~~~~h~L~l~~ 80 (84)
T PF03366_consen 1 THKWTVYVRGLDNEDLSYFIKKVTFKLHPSFPNPVRVVTKPPFEVTETGWGEFEIPIKIHFKDPSNEKPVTIQHDLKLHQ 80 (84)
T ss_dssp -EEEEEEEEECCCT--TTTEEEEEEES-TTSSS-EEECSSTTEEEEEEESS--EEEEEEECCCGGCTCEEEEEEE--SSS
T ss_pred CcEEEEEEEeCCCCCccceEEEEEEECCCCCCCCceEecCCCCEEEEeEeccEEEEEEEEEeCCCCCCcEEEEEEEEcCC
Confidence 7999999999999999999999999999999999999999999999999999999999999994 889999999999998
Q ss_pred CCc
Q psy8046 95 TKD 97 (214)
Q Consensus 95 ~~~ 97 (214)
+++
T Consensus 81 ~~~ 83 (84)
T PF03366_consen 81 DGY 83 (84)
T ss_dssp CEE
T ss_pred CCC
Confidence 763
No 3
>COG5033 TFG3 Transcription initiation factor IIF, auxiliary subunit [Transcription]
Probab=100.00 E-value=7e-34 Score=245.23 Aligned_cols=188 Identities=29% Similarity=0.427 Sum_probs=140.1
Q ss_pred CCcccccc-CCCCCCeeeEEEEEecCCCcCcccceeeEEEEeCCCCCCceeeeecCCcEEEEeeEeeEEEEEEEEEeC-C
Q psy8046 2 EPLQMGKK-RESDGHTHEWKVYIKPYYKEDLAKYIKKVSFKLHESYPVNVRILTKPPFEISETGWGEFELVIKIYFHD-P 79 (214)
Q Consensus 2 ~~~~lgkK-~~~~~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~nP~Rvv~~PPFeVtE~GWGEF~I~I~I~F~d-~ 79 (214)
||--+|.- +-+-.+||-|.|||||.++||++.||+||+|+|||||+||+|++++|||+|.|+|||||+|.|+|||.+ +
T Consensus 20 ea~~~~~e~~~P~r~th~w~v~v~~~g~E~~~~iv~KVifkLH~Tf~NP~Rti~~pPFeI~EtGWGEF~i~I~iff~~~a 99 (225)
T COG5033 20 EAKPLGNEERFPVRHTHIWLVFVRAPGKEDIATIVKKVIFKLHPTFSNPTRTIESPPFEIKETGWGEFDIQIKIFFAEKA 99 (225)
T ss_pred ccccCCccccCCchhhEEEEEEEeCCCCcchhhhhheeeEEeccccCCCcccccCCCcEEEecccccceEEEEEEEecCC
Confidence 45556643 356679999999999999999999999999999999999999999999999999999999999999998 5
Q ss_pred CCCcEEEEEeecccCCCcc-------------cccCCCCceeEEEEEEEEecCCCHHHHHHHhcCCCCCCCchhhhhccC
Q psy8046 80 NERPVTLYHMLKLFKTKDA-------------ACDATNSLLYNEFYEEIIFNEPTLTMYKTLSSTVPHTPASASLIAAHS 146 (214)
Q Consensus 80 ~ekpv~i~H~L~L~~~~~~-------------~~~~~~~~v~se~ydeIvF~nPte~f~~~L~~~~~~~~~~~~~~~~~~ 146 (214)
+++.+..+|.+.++++... ...+....|-++.+++++|++|....+++|+..+.. ++- .+....+
T Consensus 100 ge~~~~fyl~f~~~~Y~v~~~v~~~~~~~~l~~elsk~geve~~~~~~~~~nep~i~~~k~~~~~~~~-~a~-gl~~~~e 177 (225)
T COG5033 100 GEKTIHFYLHFGDEPYAVDEPVDIPVNRPDLTSELSKSGEVESVYKREKRFNEPNIQALKLLNGAKMK-LAI-GLHKLRE 177 (225)
T ss_pred CceEeehhhhcccccccccccccccccccchhhhhhhcCcccceeeeeecccCchhHHHHhhhcCccc-ccc-cCccccc
Confidence 6655554444444433210 011223456678899999999999999999887631 111 0111223
Q ss_pred CC--h-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccceeeecCC
Q psy8046 147 VN--F-ESAKASTLRGIIEAKKRLEREIGVYKDKISTKLFTHCDSYVLCPKN 195 (214)
Q Consensus 147 ~~--~-~~~e~~el~~i~~a~~~v~~eI~~lk~~l~~~~~~~~~~~~~~~~~ 195 (214)
.| | .|+++++.+++..+.+++...|+.++.......+ .+--|++|
T Consensus 178 dd~~~v~Ql~~d~~~~v~~~ie~~~~~id~y~~~~~~L~~----~~~~~~~~ 225 (225)
T COG5033 178 DDLVFVVQLVQDPIMAVLNLIEKGEFKIDLYKLPSDLLHK----LESVKAKN 225 (225)
T ss_pred ccceeeEecCcCHHHHHHhccccCceEeeehhCchhhhhh----ccccccCC
Confidence 33 4 5899999999999999999999988766554432 34445554
No 4
>PF14723 SSFA2_C: Sperm-specific antigen 2 C-terminus
Probab=57.58 E-value=24 Score=30.54 Aligned_cols=36 Identities=6% Similarity=0.188 Sum_probs=31.2
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy8046 149 FESAKASTLRGIIEAKKRLEREIGVYKDKISTKLFT 184 (214)
Q Consensus 149 ~~~~e~~el~~i~~a~~~v~~eI~~lk~~l~~~~~~ 184 (214)
.++.|+.|.+.|..-|+.|+.|.++|..+|..++.+
T Consensus 139 MSeeER~EaeQLQsLR~avRqElqELE~QL~DRl~~ 174 (179)
T PF14723_consen 139 MSEEEREEAEQLQSLRSAVRQELQELEFQLEDRLLQ 174 (179)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456678899999999999999999999999988743
No 5
>PLN00172 ubiquitin conjugating enzyme; Provisional
Probab=53.68 E-value=37 Score=27.71 Aligned_cols=35 Identities=20% Similarity=0.239 Sum_probs=24.3
Q ss_pred CCCeeeEEEEEecCCCcCcccceeeEEEEeCCCCC
Q psy8046 13 DGHTHEWKVYIKPYYKEDLAKYIKKVSFKLHESYP 47 (214)
Q Consensus 13 ~~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~ 47 (214)
++..+.|.+.+.|+.+..-..-+=++.+.+.+.|+
T Consensus 27 ~~nl~~w~~~i~GP~~tpyegg~f~~~i~fp~~YP 61 (147)
T PLN00172 27 DENLFRWTASIIGPSDSPYAGGVFFLSILFPPDYP 61 (147)
T ss_pred CCChheEEEEEECCCCCCCCCCEEEEEEECCcccC
Confidence 35789999999998654433334467777777775
No 6
>PF09154 DUF1939: Domain of unknown function (DUF1939); InterPro: IPR015237 This entry represents a C-terminal domain associated with prokaryotic alpha-amylases. It adopts a secondary structure consisting of an eight-stranded antiparallel beta-sheet containing a Greek key motif. Its exact function has not, as yet, been determined []. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds; PDB: 1MXD_A 1MWO_A 1MXG_A 1W9X_A 2DIE_A 1VJS_A 1BPL_B 1BLI_A 1OB0_A 1E3Z_A ....
Probab=52.03 E-value=7.7 Score=27.34 Aligned_cols=13 Identities=54% Similarity=1.165 Sum_probs=9.8
Q ss_pred EEEEeeEeeEEEE
Q psy8046 59 EISETGWGEFELV 71 (214)
Q Consensus 59 eVtE~GWGEF~I~ 71 (214)
.+.|.|||+|.++
T Consensus 37 tid~dG~~~f~v~ 49 (57)
T PF09154_consen 37 TIDEDGWGEFPVP 49 (57)
T ss_dssp EE-TTSEEEEEE-
T ss_pred EECCCeEEEEEEC
Confidence 5789999999986
No 7
>smart00212 UBCc Ubiquitin-conjugating enzyme E2, catalytic domain homologues. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine.
Probab=42.41 E-value=93 Score=24.67 Aligned_cols=36 Identities=19% Similarity=0.254 Sum_probs=23.5
Q ss_pred CCCCeeeEEEEEecCCCcCcccceeeEEEEeCCCCC
Q psy8046 12 SDGHTHEWKVYIKPYYKEDLAKYIKKVSFKLHESYP 47 (214)
Q Consensus 12 ~~~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~ 47 (214)
+++....|.+-+.|+.+..-..-+=++++.+.+.|+
T Consensus 24 ~~~~~~~w~~~i~gp~~~~y~g~~f~~~l~~p~~yP 59 (145)
T smart00212 24 DEDNLLEWTGTIVGPPGTPYEGGIFKLTIEFPPDYP 59 (145)
T ss_pred CCCChheEEEEEEcCCCCCcCCcEEEEEEECCcccC
Confidence 344788999988876543322223377778888886
No 8
>PF05524 PEP-utilisers_N: PEP-utilising enzyme, N-terminal; InterPro: IPR008731 This sequence identifies proteins which are a component of the phosphoenolpyruvate:sugar phosphotransferase system (PTS), a major carbohydrate active transport system. The PTS system is found throughout the bacterial kingdom, and is responsible for the coupled phosphorylation and translocation of numerous sugars across the cytoplasmic membrane []. This entry represents the N-terminal domain of enzyme I (EIN) which transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr) which in turn phosphorylates a group of membrane-associated proteins, known as enzyme II. The N-terminal domain of EI (EIN) extends from residues 1 to 259 and can be phosphorylated in a fully reversible manner by phosphorylated HPr. EIN, however, cannot be autophosphorylated by PEP [, ].; GO: 0005351 sugar:hydrogen symporter activity, 0008965 phosphoenolpyruvate-protein phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 2WQD_A 2XDF_B 2HWG_A 3EZB_A 2L5H_A 3EZA_A 1EZB_A 2EZA_A 1EZA_A 1EZC_A ....
Probab=40.63 E-value=58 Score=25.10 Aligned_cols=29 Identities=14% Similarity=0.300 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy8046 154 ASTLRGIIEAKKRLEREIGVYKDKISTKL 182 (214)
Q Consensus 154 ~~el~~i~~a~~~v~~eI~~lk~~l~~~~ 182 (214)
..|+.|+..|..++.+++..+.+++..+.
T Consensus 34 ~~E~~rl~~Al~~~~~eL~~l~~~~~~~~ 62 (123)
T PF05524_consen 34 EAEIERLEQALEKAREELEQLAERAESKL 62 (123)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 46999999999999999999999976654
No 9
>KOG0930|consensus
Probab=40.21 E-value=59 Score=30.68 Aligned_cols=37 Identities=24% Similarity=0.287 Sum_probs=32.0
Q ss_pred ChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy8046 148 NFESAKASTLRGIIEAKKRLEREIGVYKDKISTKLFT 184 (214)
Q Consensus 148 ~~~~~e~~el~~i~~a~~~v~~eI~~lk~~l~~~~~~ 184 (214)
+.+..|+.||.+|..-++++-.+|+.||+.+.+-..+
T Consensus 10 ~Ls~~E~~eL~~ir~rk~qL~deIq~Lk~Ei~ev~~e 46 (395)
T KOG0930|consen 10 DLSEEERMELENIRRRKQELLDEIQRLKDEIAEVMEE 46 (395)
T ss_pred CCCHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5567788999999999999999999999998876644
No 10
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=37.85 E-value=41 Score=28.33 Aligned_cols=27 Identities=19% Similarity=0.433 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcccc
Q psy8046 162 EAKKRLEREIGVYKDKISTKLFTHCDS 188 (214)
Q Consensus 162 ~a~~~v~~eI~~lk~~l~~~~~~~~~~ 188 (214)
.+..+|+..|.++|++|..++.++|+.
T Consensus 126 ~~v~~vQ~~iD~lR~~l~~~i~~~~~~ 152 (152)
T PF07278_consen 126 EQVARVQSVIDDLRDQLAERIQEACAD 152 (152)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 366799999999999999999999973
No 11
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=36.30 E-value=44 Score=24.39 Aligned_cols=22 Identities=23% Similarity=0.218 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q psy8046 155 STLRGIIEAKKRLEREIGVYKD 176 (214)
Q Consensus 155 ~el~~i~~a~~~v~~eI~~lk~ 176 (214)
.=+++...|+++|.+.|+.|+.
T Consensus 39 ~L~ekne~Ar~rvEamI~RLk~ 60 (65)
T TIGR02449 39 QLLEKNEQARQKVEAMITRLKA 60 (65)
T ss_pred HHHHHHHHHHHHHHHHHHhhhh
Confidence 4578889999999999998873
No 12
>PF13028 DUF3889: Protein of unknown function (DUF3889)
Probab=35.56 E-value=1.7e+02 Score=22.98 Aligned_cols=23 Identities=22% Similarity=0.524 Sum_probs=17.6
Q ss_pred eEeeEEEEEEEEEeCCCCCcEEE
Q psy8046 64 GWGEFELVIKIYFHDPNERPVTL 86 (214)
Q Consensus 64 GWGEF~I~I~I~F~d~~ekpv~i 86 (214)
|=-||.+.++|+|.+..++-++|
T Consensus 70 ~~kefgV~v~V~f~p~T~ki~~I 92 (97)
T PF13028_consen 70 GGKEFGVFVTVSFNPKTEKIISI 92 (97)
T ss_pred CCeEEEEEEEEEEeCCCCcEEEE
Confidence 33589999999999977765554
No 13
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=34.92 E-value=70 Score=23.88 Aligned_cols=36 Identities=19% Similarity=0.371 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccee
Q psy8046 155 STLRGIIEAKKRLEREIGVYKDKISTKLFTHCDSYV 190 (214)
Q Consensus 155 ~el~~i~~a~~~v~~eI~~lk~~l~~~~~~~~~~~~ 190 (214)
.+|..+.+.++++.++++.+.+++=.++++-.+.+.
T Consensus 2 ~~L~~l~~~k~~Le~~L~~lE~qIy~~Et~YL~~~~ 37 (80)
T PF09340_consen 2 KELKELLQKKKKLEKDLAALEKQIYDKETSYLEDTS 37 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccC
Confidence 578889999999999999999999999988777443
No 14
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=34.79 E-value=1e+02 Score=24.25 Aligned_cols=23 Identities=22% Similarity=0.323 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy8046 157 LRGIIEAKKRLEREIGVYKDKIS 179 (214)
Q Consensus 157 l~~i~~a~~~v~~eI~~lk~~l~ 179 (214)
.++|.+-++++.++|...+++|+
T Consensus 71 kEqL~~Lk~kl~~e~~~~~k~i~ 93 (100)
T PF04568_consen 71 KEQLKKLKEKLKEEIEHHRKEID 93 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444444444444444443
No 15
>PF04201 TPD52: Tumour protein D52 family; InterPro: IPR007327 The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family []. These proteins have an N-terminal coiled-coil that allows members to form homo- and heterodimers with each other [].
Probab=31.16 E-value=1e+02 Score=26.28 Aligned_cols=32 Identities=13% Similarity=0.140 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcc
Q psy8046 155 STLRGIIEAKKRLEREIGVYKDKISTKLFTHC 186 (214)
Q Consensus 155 ~el~~i~~a~~~v~~eI~~lk~~l~~~~~~~~ 186 (214)
+|-+.|..--.+|.+||..||+-|..|++.+-
T Consensus 29 eE~eeLr~EL~KvEeEI~TLrqvL~aKer~~~ 60 (162)
T PF04201_consen 29 EEREELRSELAKVEEEIQTLRQVLAAKERHCA 60 (162)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 34444555677899999999998888876543
No 16
>PF07820 TraC: TraC-like protein; InterPro: IPR012930 The members of this family are sequences that are similar to TraC (Q84HT8 from SWISSPROT) from Rhizobium etli. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli (strain CFN 42/ATCC 51251) that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42d, the symbiotic plasmid which carries most of the genes required for nodulation and nitrogen fixation by this symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 []. ; GO: 0000746 conjugation
Probab=30.48 E-value=61 Score=25.31 Aligned_cols=21 Identities=10% Similarity=0.238 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHhhhh
Q psy8046 164 KKRLEREIGVYKDKISTKLFT 184 (214)
Q Consensus 164 ~~~v~~eI~~lk~~l~~~~~~ 184 (214)
..+|.++|+.|+++|+..++.
T Consensus 4 ~s~I~~eIekLqe~lk~~e~k 24 (92)
T PF07820_consen 4 SSKIREEIEKLQEQLKQAETK 24 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 467888888888888776643
No 17
>PRK13848 conjugal transfer protein TraC; Provisional
Probab=28.52 E-value=64 Score=25.40 Aligned_cols=20 Identities=10% Similarity=0.265 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHhhhh
Q psy8046 165 KRLEREIGVYKDKISTKLFT 184 (214)
Q Consensus 165 ~~v~~eI~~lk~~l~~~~~~ 184 (214)
.+|.+||+.|+++|+..++.
T Consensus 6 s~I~~eI~kLqe~lk~~e~k 25 (98)
T PRK13848 6 SKIREEIAKLQEQLKQAETR 25 (98)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 57888888888888876654
No 18
>KOG0417|consensus
Probab=26.26 E-value=2.4e+02 Score=23.77 Aligned_cols=40 Identities=13% Similarity=0.136 Sum_probs=24.6
Q ss_pred cccCC-CCCCeeeEEEEEecCCCcCcccceeeEEEEeCCCC
Q psy8046 7 GKKRE-SDGHTHEWKVYIKPYYKEDLAKYIKKVSFKLHESY 46 (214)
Q Consensus 7 gkK~~-~~~~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF 46 (214)
|+.+. .++++.+|++.+.|+.+..-..=+=++...+++.|
T Consensus 20 ~~~~~~~~dnl~~w~a~I~GP~~SpYEgG~F~l~I~~p~~Y 60 (148)
T KOG0417|consen 20 GCSAGPVGDNLFHWQATILGPPGSPYEGGVFFLEIHFPEDY 60 (148)
T ss_pred CCccCCCCCceeeEEEEEECCCCCCcCCCEEEEEEECCCCC
Confidence 45554 25688889999999865433333344555555555
No 19
>KOG4010|consensus
Probab=25.01 E-value=1.3e+02 Score=26.52 Aligned_cols=37 Identities=16% Similarity=0.194 Sum_probs=25.4
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q psy8046 149 FESAKASTLRGIIEAKKRLEREIGVYKDKISTKLFTH 185 (214)
Q Consensus 149 ~~~~e~~el~~i~~a~~~v~~eI~~lk~~l~~~~~~~ 185 (214)
|..+-.+|-+.|..--.+|.+||..||+-|..+.+-+
T Consensus 38 ~~~LSe~Ekeelr~EL~kvEeEI~TLrqVLaAKerH~ 74 (208)
T KOG4010|consen 38 FEALSEEEKEELRTELAKVEEEIVTLRQVLAAKERHA 74 (208)
T ss_pred HhhhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4333344445556666789999999999888877543
No 20
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=24.07 E-value=45 Score=22.41 Aligned_cols=29 Identities=7% Similarity=0.034 Sum_probs=21.6
Q ss_pred HHHHHHHHHhhhhcccceeeecCCcceee
Q psy8046 172 GVYKDKISTKLFTHCDSYVLCPKNNFWQI 200 (214)
Q Consensus 172 ~~lk~~l~~~~~~~~~~~~~~~~~~~~~~ 200 (214)
.+.|++|...+++++.....||.++.+.+
T Consensus 14 ~eqk~~l~~~it~~l~~~~~~p~~~v~V~ 42 (61)
T PRK02220 14 EEQLKALVKDVTAAVSKNTGAPAEHIHVI 42 (61)
T ss_pred HHHHHHHHHHHHHHHHHHhCcChhhEEEE
Confidence 35566777777777778888888887764
No 21
>PF14193 DUF4315: Domain of unknown function (DUF4315)
Probab=22.75 E-value=1.7e+02 Score=22.18 Aligned_cols=27 Identities=11% Similarity=0.129 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy8046 157 LRGIIEAKKRLEREIGVYKDKISTKLF 183 (214)
Q Consensus 157 l~~i~~a~~~v~~eI~~lk~~l~~~~~ 183 (214)
++||.+=..|+++.|+++..+|+....
T Consensus 3 leKi~~eieK~k~Kiae~Q~rlK~Le~ 29 (83)
T PF14193_consen 3 LEKIRAEIEKTKEKIAELQARLKELEA 29 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666666666677777666665543
No 22
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=22.55 E-value=44 Score=22.49 Aligned_cols=29 Identities=7% Similarity=0.051 Sum_probs=21.6
Q ss_pred HHHHHHHHHhhhhcccceeeecCCcceee
Q psy8046 172 GVYKDKISTKLFTHCDSYVLCPKNNFWQI 200 (214)
Q Consensus 172 ~~lk~~l~~~~~~~~~~~~~~~~~~~~~~ 200 (214)
.+.|++|..++++++.....||.+.+|-+
T Consensus 13 ~e~K~~l~~~it~~~~~~lg~~~~~i~V~ 41 (60)
T PF01361_consen 13 AEQKRELAEAITDAVVEVLGIPPERISVV 41 (60)
T ss_dssp HHHHHHHHHHHHHHHHHHHTS-GGGEEEE
T ss_pred HHHHHHHHHHHHHHHHHHhCcCCCeEEEE
Confidence 45677888888888888888888887754
No 23
>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.
Probab=22.02 E-value=2e+02 Score=20.21 Aligned_cols=26 Identities=23% Similarity=0.409 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8046 155 STLRGIIEAKKRLEREIGVYKDKIST 180 (214)
Q Consensus 155 ~el~~i~~a~~~v~~eI~~lk~~l~~ 180 (214)
.|+.||..-..+++.+|+.+..+|..
T Consensus 4 ~E~~rL~Kel~kl~~~i~~~~~kL~n 29 (66)
T PF10458_consen 4 AEIERLEKELEKLEKEIERLEKKLSN 29 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 57888888888899999988888764
No 24
>cd00195 UBCc Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
Probab=21.47 E-value=3.1e+02 Score=21.51 Aligned_cols=33 Identities=24% Similarity=0.340 Sum_probs=18.6
Q ss_pred CeeeEEEEEecCCCcCcccceeeEEEEeCCCCC
Q psy8046 15 HTHEWKVYIKPYYKEDLAKYIKKVSFKLHESYP 47 (214)
Q Consensus 15 ~tH~WtVyVr~~~~edls~~IkKV~F~LHpSF~ 47 (214)
....|.+-+.|..+..-..=+=++.+.+.+.|+
T Consensus 27 ~~~~w~~~i~g~~~t~y~g~~~~~~~~~p~~yP 59 (141)
T cd00195 27 NLLEWHGTIRGPPDTPYEGGIFKLDIEFPEDYP 59 (141)
T ss_pred ChhEEEEEEecCCCCCccCCEEEEEEECCCccC
Confidence 567788888876332222223345555666665
No 25
>PF04822 Takusan: Takusan; InterPro: IPR006907 This family includes several uncharacterised muridae (mouse and rat) proteins.
Probab=21.14 E-value=2.3e+02 Score=21.57 Aligned_cols=30 Identities=13% Similarity=0.197 Sum_probs=25.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy8046 151 SAKASTLRGIIEAKKRLEREIGVYKDKIST 180 (214)
Q Consensus 151 ~~e~~el~~i~~a~~~v~~eI~~lk~~l~~ 180 (214)
+..-+++++|..+-++|..|-.+|++.|..
T Consensus 15 e~~~k~lE~L~~eL~~it~ERnELr~~L~~ 44 (84)
T PF04822_consen 15 EKKMKELERLKFELQKITKERNELRDILAL 44 (84)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333378999999999999999999999874
No 26
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=20.88 E-value=1.9e+02 Score=21.15 Aligned_cols=25 Identities=24% Similarity=0.216 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q psy8046 158 RGIIEAKKRLEREIGVYKDKISTKL 182 (214)
Q Consensus 158 ~~i~~a~~~v~~eI~~lk~~l~~~~ 182 (214)
..|.+-..-++.||+.|+.++..|-
T Consensus 28 ~El~eRIalLq~EIeRlkAe~~kK~ 52 (65)
T COG5509 28 AELEERIALLQAEIERLKAELAKKK 52 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3444455567899999999887764
No 27
>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins.
Probab=20.41 E-value=2.2e+02 Score=23.70 Aligned_cols=29 Identities=17% Similarity=0.397 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy8046 154 ASTLRGIIEAKKRLEREIGVYKDKISTKL 182 (214)
Q Consensus 154 ~~el~~i~~a~~~v~~eI~~lk~~l~~~~ 182 (214)
+.+...+.....+++.+|+.++++|+..+
T Consensus 72 k~~~~~lr~~~e~L~~eie~l~~~L~~ei 100 (177)
T PF07798_consen 72 KSEFAELRSENEKLQREIEKLRQELREEI 100 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566666677777888888777777654
No 28
>KOG1465|consensus
Probab=20.33 E-value=2.8e+02 Score=26.38 Aligned_cols=62 Identities=23% Similarity=0.237 Sum_probs=39.0
Q ss_pred cCCCHHHHHHHhcCCCCCCCchhhhhccCCChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccc
Q psy8046 118 NEPTLTMYKTLSSTVPHTPASASLIAAHSVNFESAKASTLRGIIEAKKRLEREIGVYKDKISTKLFTHCD 187 (214)
Q Consensus 118 ~nPte~f~~~L~~~~~~~~~~~~~~~~~~~~~~~~e~~el~~i~~a~~~v~~eI~~lk~~l~~~~~~~~~ 187 (214)
.+|++.++++|+++++..... +..+.... +--.-+.++.+.+..||+.-++.+...-.+||-
T Consensus 100 s~~~~Sl~kLl~~~~e~~~~~-----~~S~~~~~---~lr~~~i~~I~eli~Eie~~~E~Ia~Qa~ehih 161 (353)
T KOG1465|consen 100 SSPSESLHKLLQSTEESHTNK-----KLSSADAK---KLRKDLIEGIKELITEIEGSRENIAVQAIEHIH 161 (353)
T ss_pred CchHHHHHHHHhCCCcccccc-----ccccccHH---HHHHHHHHHHHHHHHHHhhhhHhHHHHHHHHhc
Confidence 357778999999886532211 11111111 233445667778888888888888888777764
Done!