Query psy16397
Match_columns 60
No_of_seqs 93 out of 95
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 20:16:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16397.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16397hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10255 Paf67: RNA polymerase 99.8 2.9E-19 6.2E-24 132.0 4.1 48 2-49 354-404 (404)
2 KOG3677|consensus 99.5 1.3E-14 2.7E-19 109.7 2.5 57 3-59 464-523 (525)
3 PF06565 DUF1126: Repeat of un 70.1 4 8.7E-05 20.7 1.7 17 17-33 2-18 (33)
4 cd05403 NT_KNTase_like Nucleot 68.4 3 6.6E-05 23.0 1.1 17 6-22 25-43 (93)
5 cd05397 NT_Pol-beta-like Nucle 59.3 8 0.00017 20.5 1.7 17 6-22 24-42 (49)
6 COG4446 Uncharacterized protei 58.5 7.9 0.00017 25.7 1.8 19 14-32 95-115 (141)
7 cd05402 NT_PAP_TUTase Nucleoti 57.1 14 0.0003 21.8 2.6 19 6-24 26-46 (114)
8 PF04004 Leo1: Leo1-like prote 56.0 4.2 9.2E-05 26.9 0.2 9 1-9 70-78 (171)
9 PF10772 DUF2597: Protein of u 54.5 11 0.00023 25.0 1.9 18 16-33 2-19 (134)
10 PF01909 NTP_transf_2: Nucleot 50.6 3.8 8.3E-05 23.0 -0.6 17 6-22 21-39 (93)
11 PF09088 MIF4G_like: MIF4G lik 50.5 6.2 0.00013 27.1 0.4 18 32-49 128-145 (191)
12 TIGR02609 doc_partner putative 49.9 48 0.001 18.9 6.1 40 17-56 30-73 (74)
13 PF12163 HobA: DNA replication 40.3 29 0.00063 23.9 2.4 34 15-48 35-68 (180)
14 PF07599 DUF1563: Protein of u 39.6 21 0.00046 19.3 1.3 11 35-45 19-29 (43)
15 PF01267 F-actin_cap_A: F-acti 39.5 42 0.0009 23.8 3.2 48 5-52 173-228 (271)
16 PF07386 DUF1499: Protein of u 39.1 75 0.0016 19.4 3.9 41 14-56 76-118 (118)
17 PF06868 DUF1257: Protein of u 37.7 39 0.00085 20.8 2.5 44 15-58 37-84 (105)
18 cd06867 PX_SNX41_42 The phosph 37.6 18 0.00039 21.9 0.9 17 26-42 23-39 (112)
19 PF02787 CPSase_L_D3: Carbamoy 37.1 44 0.00096 21.0 2.7 21 37-57 35-55 (123)
20 PF14956 DUF4505: Domain of un 35.9 39 0.00085 23.3 2.5 31 17-47 17-56 (183)
21 KOG2477|consensus 32.5 43 0.00093 27.0 2.5 32 13-46 555-586 (628)
22 COG1669 Predicted nucleotidylt 31.2 26 0.00057 21.8 0.9 18 6-23 31-50 (97)
23 PRK13746 aminoglycoside resist 31.1 30 0.00066 24.6 1.4 17 6-22 35-53 (262)
24 PF04149 DUF397: Domain of unk 30.4 83 0.0018 17.3 2.8 33 2-34 3-35 (56)
25 smart00676 DM10 Domains in hyp 30.1 80 0.0017 19.3 3.0 31 3-33 11-42 (104)
26 PF08154 NLE: NLE (NUC135) dom 29.4 29 0.00064 19.4 0.9 20 7-26 37-57 (65)
27 PHA02771 hypothetical protein; 29.2 63 0.0014 20.0 2.4 16 16-31 69-84 (90)
28 PF14025 DUF4241: Protein of u 29.1 87 0.0019 21.0 3.3 31 17-47 85-115 (185)
29 COG1708 Predicted nucleotidylt 29.0 38 0.00082 19.5 1.4 17 6-22 33-51 (128)
30 COG0536 Obg Predicted GTPase [ 28.4 31 0.00067 26.2 1.1 21 31-51 221-241 (369)
31 PF08346 AntA: AntA/AntB antir 28.1 42 0.0009 19.5 1.4 16 32-47 11-26 (71)
32 PF08148 DSHCT: DSHCT (NUC185) 27.1 70 0.0015 20.9 2.5 23 36-58 126-148 (180)
33 PF08750 CNP1: CNP1-like famil 27.0 39 0.00083 22.1 1.2 22 14-35 32-53 (139)
34 PF03586 Herpes_UL36: Herpesvi 26.1 83 0.0018 22.8 2.9 24 35-58 157-180 (253)
35 COG1665 Predicted nucleotidylt 25.2 33 0.00073 25.5 0.8 19 6-24 128-148 (315)
36 PF08902 DUF1848: Domain of un 24.5 41 0.0009 24.2 1.1 12 35-46 12-23 (266)
37 PRK06789 flagellar motor switc 24.2 62 0.0013 19.1 1.7 26 1-26 26-53 (74)
38 KOG2527|consensus 24.1 23 0.0005 23.7 -0.2 14 27-40 50-63 (144)
39 PF01043 SecA_PP_bind: SecA pr 22.7 74 0.0016 19.8 1.9 22 14-35 76-97 (113)
40 COG1098 VacB Predicted RNA bin 22.3 61 0.0013 21.3 1.5 38 4-47 4-48 (129)
41 cd00707 Pancreat_lipase_like P 21.8 53 0.0011 22.7 1.2 22 4-25 172-194 (275)
42 PF14521 Aspzincin_M35: Lysine 21.6 94 0.002 19.8 2.3 25 34-58 11-41 (148)
43 PF14792 DNA_pol_B_palm: DNA p 21.5 37 0.00081 20.8 0.4 17 6-22 31-48 (112)
44 PHA02417 hypothetical protein 20.7 92 0.002 18.9 1.9 31 20-50 16-46 (83)
45 PF00773 RNB: RNB domain CAUTI 20.5 78 0.0017 21.9 1.8 20 29-48 302-321 (325)
No 1
>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 [].
Probab=99.76 E-value=2.9e-19 Score=132.01 Aligned_cols=48 Identities=63% Similarity=1.036 Sum_probs=46.1
Q ss_pred ccccC-cccCCee--ecceeEEeeCCEEEEeeccchhhhhhHHHHHHHHHH
Q psy16397 2 RVKNQ-GLTEGTL--TAMLDFYIDNEMIHIADTKVAHRYGDFFIRKIIKFE 49 (60)
Q Consensus 2 r~~~g-~LleG~~--~sDldF~id~dmIhI~e~k~~rry~d~Flr~i~K~~ 49 (60)
+|+.| |+|+|+. ++|+|||||+|||||+|+|++|||+|||+|||+|++
T Consensus 354 ~w~~g~sll~G~~~~~~dlDf~Id~D~IhI~e~k~~r~~~d~F~r~i~k~e 404 (404)
T PF10255_consen 354 RWSGGASLLDGEFQSSSDLDFYIDGDMIHIAETKVARRYGDFFIRQINKFE 404 (404)
T ss_pred hccCCCcccccceeecCceEEEEeCCEEEEeeccccchhHHHHHHHHHhcC
Confidence 79999 9999996 799999999999999999999999999999999985
No 2
>KOG3677|consensus
Probab=99.48 E-value=1.3e-14 Score=109.70 Aligned_cols=57 Identities=54% Similarity=0.860 Sum_probs=52.0
Q ss_pred cccC-cccCCee--ecceeEEeeCCEEEEeeccchhhhhhHHHHHHHHHHHHHHHHhhcc
Q psy16397 3 VKNQ-GLTEGTL--TAMLDFYIDNEMIHIADTKVAHRYGDFFIRKIIKFEELNKKLQAIK 59 (60)
Q Consensus 3 ~~~g-~LleG~~--~sDldF~id~dmIhI~e~k~~rry~d~Flr~i~K~~~~~~~l~~~~ 59 (60)
|+-| |-++|.. .+++|||||.|||||+++|+.|||||+|+|||+||+|+.+.|+.+.
T Consensus 464 ~~sg~s~~d~~f~~~s~idfyid~dmi~iaDtkv~r~~gd~fir~i~kf~El~~vLK~i~ 523 (525)
T KOG3677|consen 464 WTSGPSDLDDAFFSRSEIDFYIDKDMIHIADTKVARRYGDIFIRQIHKFEELNRVLKLIT 523 (525)
T ss_pred HhcCCccccccccCcceeeEEechhHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 6666 6677774 8999999999999999999999999999999999999999998764
No 3
>PF06565 DUF1126: Repeat of unknown function (DUF1126); InterPro: IPR010554 This group contains several eukaryote specific repeats of around 35 residues in length. The function of this family is unknown.; PDB: 2Z14_A 2Z13_A.
Probab=70.10 E-value=4 Score=20.65 Aligned_cols=17 Identities=24% Similarity=0.669 Sum_probs=12.0
Q ss_pred eeEEeeCCEEEEeeccc
Q psy16397 17 LDFYIDNEMIHIADTKV 33 (60)
Q Consensus 17 ldF~id~dmIhI~e~k~ 33 (60)
+.||+.+|+|.|.|..+
T Consensus 2 i~y~L~DdTi~I~E~~~ 18 (33)
T PF06565_consen 2 ISYYLADDTISIFEPPV 18 (33)
T ss_dssp EEEETTTTEEEEE----
T ss_pred EEEEccCCCEEEEEecc
Confidence 57999999999999665
No 4
>cd05403 NT_KNTase_like Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is
Probab=68.38 E-value=3 Score=23.01 Aligned_cols=17 Identities=12% Similarity=0.251 Sum_probs=14.1
Q ss_pred CcccCCee--ecceeEEee
Q psy16397 6 QGLTEGTL--TAMLDFYID 22 (60)
Q Consensus 6 g~LleG~~--~sDldF~id 22 (60)
||...|+. .||+|+.|-
T Consensus 25 GS~arg~~~~~SDiDl~vi 43 (93)
T cd05403 25 GSYARGDARPDSDIDLLVI 43 (93)
T ss_pred eeeecCCCCCCCCeeEEEE
Confidence 78888886 899999864
No 5
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=59.28 E-value=8 Score=20.47 Aligned_cols=17 Identities=24% Similarity=0.315 Sum_probs=14.0
Q ss_pred CcccCCee--ecceeEEee
Q psy16397 6 QGLTEGTL--TAMLDFYID 22 (60)
Q Consensus 6 g~LleG~~--~sDldF~id 22 (60)
||...|+. .||+|..+.
T Consensus 24 GS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 24 GSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred CCcCCCCCCCCCCEEEEEE
Confidence 77778875 799999987
No 6
>COG4446 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.47 E-value=7.9 Score=25.73 Aligned_cols=19 Identities=21% Similarity=0.515 Sum_probs=15.4
Q ss_pred ecceeEEeeCCE--EEEeecc
Q psy16397 14 TAMLDFYIDNEM--IHIADTK 32 (60)
Q Consensus 14 ~sDldF~id~dm--IhI~e~k 32 (60)
+.|++||++.|- |+|+.++
T Consensus 95 VDDlEfyl~~d~~vi~vRSaS 115 (141)
T COG4446 95 VDDLEFYLPQDHNVIWVRSAS 115 (141)
T ss_pred ccceEEecCCCCceEEEeecc
Confidence 679999999776 8887654
No 7
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
Probab=57.11 E-value=14 Score=21.76 Aligned_cols=19 Identities=11% Similarity=0.088 Sum_probs=14.7
Q ss_pred CcccCCee--ecceeEEeeCC
Q psy16397 6 QGLTEGTL--TAMLDFYIDNE 24 (60)
Q Consensus 6 g~LleG~~--~sDldF~id~d 24 (60)
||...|.. .||+|+.|..+
T Consensus 26 GS~~~g~~~~~SDiDl~i~~~ 46 (114)
T cd05402 26 GSYVTGLGLPGSDIDLCLLGP 46 (114)
T ss_pred cccccCCCCCCCCeeEEEEeC
Confidence 67777763 89999998755
No 8
>PF04004 Leo1: Leo1-like protein; InterPro: IPR007149 Members of this family are part of the Paf1/RNA polymerase II complex [, ]. The Paf1 complex probably functions during the elongation phase of transcription [].
Probab=55.98 E-value=4.2 Score=26.89 Aligned_cols=9 Identities=22% Similarity=0.405 Sum_probs=6.9
Q ss_pred CccccCccc
Q psy16397 1 MRVKNQGLT 9 (60)
Q Consensus 1 ~r~~~g~Ll 9 (60)
.||+|||+.
T Consensus 70 VrWsDGS~s 78 (171)
T PF04004_consen 70 VRWSDGSLS 78 (171)
T ss_pred EEEcCCceE
Confidence 389999654
No 9
>PF10772 DUF2597: Protein of unknown function (DUF2597); InterPro: IPR019708 This entry is represented by Bacteriophage HP1, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents proteins with unknown function and is restricted to Proteobacteria. One of the proteins is annotated to a predictive tail tube protein.
Probab=54.47 E-value=11 Score=25.02 Aligned_cols=18 Identities=22% Similarity=0.468 Sum_probs=15.2
Q ss_pred ceeEEeeCCEEEEeeccc
Q psy16397 16 MLDFYIDNEMIHIADTKV 33 (60)
Q Consensus 16 DldF~id~dmIhI~e~k~ 33 (60)
++|++|.+.+|||...+.
T Consensus 2 ~fD~~ig~~~vhve~~tl 19 (134)
T PF10772_consen 2 SFDVNIGGLMVHVEKATL 19 (134)
T ss_pred ceeEEeCCEEEEEEEEEE
Confidence 689999999999987543
No 10
>PF01909 NTP_transf_2: Nucleotidyltransferase domain A subset of this Pfam family; InterPro: IPR002934 A small region that overlaps with a nuclear localization signal and binds to the RNA primer contains three aspartates that are essential for catalysis. Sequence and secondary structure comparisons of regions surrounding these aspartates with sequences of other polymerases revealed a significant homology to the palm structure of DNA polymerase beta, terminal deoxynucleotidyltransferase and DNA polymerase IV of Saccharomyces cerevisiae, all members of the family X of polymerases. This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor [, ]. Proteins containing this domain include kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase inactivates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. In experiments, Mn2+ strongly stimulated this reaction due to a 50-fold lower Ki for 8-azido-ATP in the presence of Mn2+. Mutations of the highly conserved Asp residues 113, 115, and 167, critical for metal binding in the catalytic domain of bovine poly(A) polymerase, led to a strong reduction of cross-linking efficiency, and Mn2+ no longer stimulated the reaction. Mutations in the region of the "helical turn motif" (a domain binding the triphosphate moiety of the nucleotide) and in the suspected nucleotide-binding helix of bovine poly(A) polymerase impaired ATP binding and catalysis. The results indicate that ATP is bound in part by the helical turn motif and in part by a region that may be a structural analogue of the fingers domain found in many polymerases.; GO: 0016779 nucleotidyltransferase activity; PDB: 4EBK_B 4EBJ_A 1KNY_A 2B4V_A 2B56_A 2B51_A 1NO5_B 1Q79_A 1Q78_A 1F5A_A ....
Probab=50.64 E-value=3.8 Score=22.95 Aligned_cols=17 Identities=18% Similarity=0.268 Sum_probs=12.5
Q ss_pred CcccCCee--ecceeEEee
Q psy16397 6 QGLTEGTL--TAMLDFYID 22 (60)
Q Consensus 6 g~LleG~~--~sDldF~id 22 (60)
||...|+. .||+|+.|-
T Consensus 21 GS~a~g~~~~~SDIDl~i~ 39 (93)
T PF01909_consen 21 GSYARGDATPDSDIDLLII 39 (93)
T ss_dssp HHHHHTSSCTTSCEEEEEE
T ss_pred CCcccCcCCCCCCEEEEEE
Confidence 56666774 799999865
No 11
>PF09088 MIF4G_like: MIF4G like; InterPro: IPR015172 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 1", and is found in nuclear cap-binding proteins and eIF4G. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA.; GO: 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A.
Probab=50.52 E-value=6.2 Score=27.14 Aligned_cols=18 Identities=22% Similarity=0.593 Sum_probs=15.0
Q ss_pred cchhhhhhHHHHHHHHHH
Q psy16397 32 KVAHRYGDFFIRKIIKFE 49 (60)
Q Consensus 32 k~~rry~d~Flr~i~K~~ 49 (60)
...+||.|||..|+..|+
T Consensus 128 e~~~Rf~dWfS~hLSNF~ 145 (191)
T PF09088_consen 128 ELRDRFVDWFSHHLSNFG 145 (191)
T ss_dssp HHHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHhcCC
Confidence 457899999999998764
No 12
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=49.93 E-value=48 Score=18.94 Aligned_cols=40 Identities=13% Similarity=0.101 Sum_probs=26.6
Q ss_pred eeEEeeCCEEEEeeccchhhhhhHHHH----HHHHHHHHHHHHh
Q psy16397 17 LDFYIDNEMIHIADTKVAHRYGDFFIR----KIIKFEELNKKLQ 56 (60)
Q Consensus 17 ldF~id~dmIhI~e~k~~rry~d~Flr----~i~K~~~~~~~l~ 56 (60)
|++.++++-|.|...+..+-|...|.. -+.+..+.++.|.
T Consensus 30 v~v~~~~~~iii~~~~~~~~~~~~~~~~~~~~~~~y~~~l~~La 73 (74)
T TIGR02609 30 LYVDEEEGGLKLKRFDEGKELEKKMQMAVERAMSKYDEALKELA 73 (74)
T ss_pred EEEEEECCEEEEEECCCCccHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 588899999999888875556666553 3344555555553
No 13
>PF12163 HobA: DNA replication regulator; InterPro: IPR021011 This family of proteins is found exclusively in epsilon-proteobacteria. Proteins in this family are approximately 180 amino acids in length. The crystal structure of HobA from Helicobacter pylori has been reported at 1.7A resolution; HobA represents a modified Rossmann fold consisting of a five-stranded parallel beta-sheet (beta1-5) flanked on one side by alpha-2, alpha-3 and alpha-6 helices and alpha-4 and alpha-5 on the other. The alpha-1 helix is extended away from and has minimal interaction with the globular part of the protein. Four monomers interact to form a tetrameric molecule. Four calcium atoms bind to the tetramer and these binding sites may have functional relevance. The closest structural homologue of HobA is a sugar isomerase (SIS) domain containing protein, the phosphoheptose isomerase from Pseudomonas aeruginosa. The SIS proteins share strong sequence homology with DiaA from Escherichia coli; yet, HobA and DiaA share no sequence homology []. HobA is a novel protein essential for initiation of H. pylori chromosome replication. It interacts specifically via DnaA with the oriC-DnaA complex. It is possible that HobA is essential for the correct formation and stabilisation of the orisome by facilitating the spatial positioning of DnaA at oriC [].; PDB: 2UVP_D 2WP0_A.
Probab=40.27 E-value=29 Score=23.90 Aligned_cols=34 Identities=6% Similarity=0.211 Sum_probs=24.8
Q ss_pred cceeEEeeCCEEEEeeccchhhhhhHHHHHHHHH
Q psy16397 15 AMLDFYIDNEMIHIADTKVAHRYGDFFIRKIIKF 48 (60)
Q Consensus 15 sDldF~id~dmIhI~e~k~~rry~d~Flr~i~K~ 48 (60)
+-+.+.++|..+-|..-....+|.+|++.+|.+.
T Consensus 35 ~~l~~il~G~s~iliTD~~R~WF~~Yil~~IN~~ 68 (180)
T PF12163_consen 35 SALSHILNGGSFILITDEEREWFEEYILSNINNS 68 (180)
T ss_dssp HHHHHHHTT-EEEEEE-GGGHHHHHHHHHHHS-S
T ss_pred HHHHHHhCCCeEEEEeCchhHHHHHHHHHhcCcc
Confidence 4466777877777777777889999999999853
No 14
>PF07599 DUF1563: Protein of unknown function (DUF1563); InterPro: IPR011457 This is a small family of short hypothetical proteins in Leptospira interrogans.
Probab=39.60 E-value=21 Score=19.29 Aligned_cols=11 Identities=18% Similarity=0.748 Sum_probs=8.9
Q ss_pred hhhhhHHHHHH
Q psy16397 35 HRYGDFFIRKI 45 (60)
Q Consensus 35 rry~d~Flr~i 45 (60)
..|++||++|+
T Consensus 19 atyve~~lkq~ 29 (43)
T PF07599_consen 19 ATYVEYFLKQT 29 (43)
T ss_pred HHHHHHHHHHH
Confidence 35899999986
No 15
>PF01267 F-actin_cap_A: F-actin capping protein alpha subunit; InterPro: IPR002189 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. The actin filament system, a prominent part of the cytoskeleton in eukaryotic cells, is both a static structure and a dynamic network that can undergo rearrangements: it is thought to be involved in processes such as cell movement and phagocytosis [], as well as muscle contraction. The F-actin capping protein binds in a calcium-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike gelsolin and severin this protein does not sever actin filaments. The F-actin capping protein is a heterodimer composed of two unrelated subunits: alpha and beta (see IPR001698 from INTERPRO). Neither of the subunits shows sequence similarity to other filament-capping proteins []. The alpha subunit is a protein of about 268 to 286 amino acid residues whose sequence is well conserved in eukaryotic species [].; GO: 0003779 actin binding, 0030036 actin cytoskeleton organization, 0008290 F-actin capping protein complex; PDB: 1MQ1_D 1MWN_X 2KBM_Y 2KZ7_A 3AAE_C 3AA6_A 3LK4_G 1IZN_A 3AA7_A 3AAA_A ....
Probab=39.53 E-value=42 Score=23.85 Aligned_cols=48 Identities=15% Similarity=0.324 Sum_probs=34.6
Q ss_pred cCcccCCeeecceeEEeeCCEEEEeeccchh--------hhhhHHHHHHHHHHHHH
Q psy16397 5 NQGLTEGTLTAMLDFYIDNEMIHIADTKVAH--------RYGDFFIRKIIKFEELN 52 (60)
Q Consensus 5 ~g~LleG~~~sDldF~id~dmIhI~e~k~~r--------ry~d~Flr~i~K~~~~~ 52 (60)
+.+.+.|++.-+++||=|||+-.....++.. -.+.-+++.|.+++.-+
T Consensus 173 ~~~~l~G~I~V~vHYyEdGNVqL~~~k~~~~~~~~~~~~~~a~~iv~~I~~~E~~~ 228 (271)
T PF01267_consen 173 SSGTLSGKIKVQVHYYEDGNVQLNSSKEVSETVSVSNDEQFASDIVKAIKEAENKY 228 (271)
T ss_dssp TTEEEEEEEEEEEEE-TTEEEEEEEEEEEEEEEE--SHHHHHHHHHHHHHHHHHHH
T ss_pred CCceEEEEEEeeEEEEeecEEEEEEccccceeeccCChhhhHHHHHHHHHHHHHHH
Confidence 4467889999999999888865544444333 57899999999887643
No 16
>PF07386 DUF1499: Protein of unknown function (DUF1499); InterPro: IPR010865 This family consists of several hypothetical bacterial and plant proteins of around 125 residues in length. The function of this family is unknown.
Probab=39.06 E-value=75 Score=19.42 Aligned_cols=41 Identities=15% Similarity=0.238 Sum_probs=29.6
Q ss_pred ecceeEEeeCC--EEEEeeccchhhhhhHHHHHHHHHHHHHHHHh
Q psy16397 14 TAMLDFYIDNE--MIHIADTKVAHRYGDFFIRKIIKFEELNKKLQ 56 (60)
Q Consensus 14 ~sDldF~id~d--mIhI~e~k~~rry~d~Flr~i~K~~~~~~~l~ 56 (60)
..|+.|+++.+ .|+|....-.- |.| |..|-.+.+++++.|+
T Consensus 76 ~DDv~i~~~~~~~~v~vRS~SR~G-~~D-lG~Nr~Ri~~~~~~L~ 118 (118)
T PF07386_consen 76 PDDVEIRVRPEEGRVDVRSASRVG-YSD-LGVNRRRIEALRAALE 118 (118)
T ss_pred CcEEEEEEeCCCCEEEEEEeccCC-CCc-cchhHHHHHHHHHHhC
Confidence 57899999977 99998765431 233 5677788888877764
No 17
>PF06868 DUF1257: Protein of unknown function (DUF1257); InterPro: IPR009666 This family represents Ycf35, which is encoded in algal chloroplast and in cyanobacteria. The function of these proteins are unknown. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=37.74 E-value=39 Score=20.83 Aligned_cols=44 Identities=16% Similarity=0.069 Sum_probs=26.7
Q ss_pred cceeEEeeCCE--EEEee--ccchhhhhhHHHHHHHHHHHHHHHHhhc
Q psy16397 15 AMLDFYIDNEM--IHIAD--TKVAHRYGDFFIRKIIKFEELNKKLQAI 58 (60)
Q Consensus 15 sDldF~id~dm--IhI~e--~k~~rry~d~Flr~i~K~~~~~~~l~~~ 58 (60)
.||-|--+++. =-|++ -=..+.-.+-|+.+|...+....-|+..
T Consensus 37 ~DIGF~wn~~~sYeLVaDl~~W~q~~~~e~fl~kl~Q~YA~~~vl~~a 84 (105)
T PF06868_consen 37 YDIGFRWNGDGSYELVADLQFWQQPYSVERFLNKLTQRYAYNTVLAEA 84 (105)
T ss_pred ccEEEEECCCccEEEEeehhhhcccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555443 22334 1125667889999999988877666544
No 18
>cd06867 PX_SNX41_42 The phosphoinositide binding Phox Homology domain of fungal Sorting Nexins 41 and 42. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX41 and SNX42 (also called Atg20p) form dimers with SNX4, and are required in protein recycling from the sorting endosome (post-Golgi endosome) back
Probab=37.63 E-value=18 Score=21.89 Aligned_cols=17 Identities=29% Similarity=0.612 Sum_probs=13.3
Q ss_pred EEEeeccchhhhhhHHH
Q psy16397 26 IHIADTKVAHRYGDFFI 42 (60)
Q Consensus 26 IhI~e~k~~rry~d~Fl 42 (60)
|++....+.|||.||-.
T Consensus 23 I~~~~~~V~RRYsdF~~ 39 (112)
T cd06867 23 IRLGGSEVKRRYSEFES 39 (112)
T ss_pred EEeeeEEEEeccHHHHH
Confidence 55666788999999854
No 19
>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=37.09 E-value=44 Score=21.03 Aligned_cols=21 Identities=19% Similarity=0.510 Sum_probs=16.3
Q ss_pred hhhHHHHHHHHHHHHHHHHhh
Q psy16397 37 YGDFFIRKIIKFEELNKKLQA 57 (60)
Q Consensus 37 y~d~Flr~i~K~~~~~~~l~~ 57 (60)
...|||.++...-++-+.|+.
T Consensus 35 ID~wFL~~i~~Iv~~e~~L~~ 55 (123)
T PF02787_consen 35 IDPWFLEQIKNIVDMEKELKE 55 (123)
T ss_dssp --HHHHHHHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHHHHHHH
Confidence 567999999998888887765
No 20
>PF14956 DUF4505: Domain of unknown function (DUF4505)
Probab=35.88 E-value=39 Score=23.34 Aligned_cols=31 Identities=26% Similarity=0.623 Sum_probs=25.2
Q ss_pred eeEEee-CCEEEEeeccc--------hhhhhhHHHHHHHH
Q psy16397 17 LDFYID-NEMIHIADTKV--------AHRYGDFFIRKIIK 47 (60)
Q Consensus 17 ldF~id-~dmIhI~e~k~--------~rry~d~Flr~i~K 47 (60)
-=|||| ..+....++|+ .+.|=+||-+++..
T Consensus 17 YFYyid~~G~LFlddsk~KNftscfKd~~FL~FFF~rlr~ 56 (183)
T PF14956_consen 17 YFYYIDHQGQLFLDDSKMKNFTSCFKDKKFLDFFFSRLRP 56 (183)
T ss_pred EEEEECCCCcEEeccccccchhhhccchHHHHHHHHHhcc
Confidence 347788 67999999994 68899999998764
No 21
>KOG2477|consensus
Probab=32.51 E-value=43 Score=27.01 Aligned_cols=32 Identities=19% Similarity=0.286 Sum_probs=25.4
Q ss_pred eecceeEEeeCCEEEEeeccchhhhhhHHHHHHH
Q psy16397 13 LTAMLDFYIDNEMIHIADTKVAHRYGDFFIRKII 46 (60)
Q Consensus 13 ~~sDldF~id~dmIhI~e~k~~rry~d~Flr~i~ 46 (60)
+---++|.||+.-+||.| ...+|..-|.++|.
T Consensus 555 pYfhV~Fgld~GfaHVIE--ded~fpsnfa~eVi 586 (628)
T KOG2477|consen 555 PYFHVWFGLDGGFAHVIE--DEDGFPSNFAREVI 586 (628)
T ss_pred CeEEEEEeccCceeeeec--ccccCcchHHHHHH
Confidence 355699999999999999 45567777877764
No 22
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=31.17 E-value=26 Score=21.84 Aligned_cols=18 Identities=11% Similarity=0.259 Sum_probs=13.9
Q ss_pred CcccCCe--eecceeEEeeC
Q psy16397 6 QGLTEGT--LTAMLDFYIDN 23 (60)
Q Consensus 6 g~LleG~--~~sDldF~id~ 23 (60)
||..-|+ +.||+|..++-
T Consensus 31 GS~aRgE~~~~SDIDILVef 50 (97)
T COG1669 31 GSYARGEQKPDSDIDILVEF 50 (97)
T ss_pred eeeecCCCCCCCCceeEEee
Confidence 6777777 59999998763
No 23
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=31.13 E-value=30 Score=24.59 Aligned_cols=17 Identities=12% Similarity=0.286 Sum_probs=13.2
Q ss_pred CcccCCe--eecceeEEee
Q psy16397 6 QGLTEGT--LTAMLDFYID 22 (60)
Q Consensus 6 g~LleG~--~~sDldF~id 22 (60)
||...|. +.||+|+.+-
T Consensus 35 GS~~~G~~~p~SDIDllvv 53 (262)
T PRK13746 35 GSAVDGGLKPHSDIDLLVT 53 (262)
T ss_pred CCcccCCCCCCCceeEEEE
Confidence 7788886 4899999853
No 24
>PF04149 DUF397: Domain of unknown function (DUF397); InterPro: IPR007278 The function of this family is unknown. It has been suggested that some members of this family are regulators of transcription.
Probab=30.35 E-value=83 Score=17.26 Aligned_cols=33 Identities=12% Similarity=0.084 Sum_probs=21.8
Q ss_pred ccccCcccCCeeecceeEEeeCCEEEEeeccch
Q psy16397 2 RVKNQGLTEGTLTAMLDFYIDNEMIHIADTKVA 34 (60)
Q Consensus 2 r~~~g~LleG~~~sDldF~id~dmIhI~e~k~~ 34 (60)
+|.-.+...|.-..=++.....+-|+|.++|..
T Consensus 3 ~W~KSs~S~~~~~~CVEva~~~~~v~vRDSk~p 35 (56)
T PF04149_consen 3 RWRKSSYSGGGGGNCVEVARLPGGVAVRDSKDP 35 (56)
T ss_pred ceeeCCCCCCCCCCcEEEEeecceEEEecCCCC
Confidence 577777775443334555555556999999964
No 25
>smart00676 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases.
Probab=30.07 E-value=80 Score=19.28 Aligned_cols=31 Identities=10% Similarity=0.215 Sum_probs=21.3
Q ss_pred cccCcccCCee-ecceeEEeeCCEEEEeeccc
Q psy16397 3 VKNQGLTEGTL-TAMLDFYIDNEMIHIADTKV 33 (60)
Q Consensus 3 ~~~g~LleG~~-~sDldF~id~dmIhI~e~k~ 33 (60)
|.|-....|.. .-=|.||+.+++|.|.|..+
T Consensus 11 ~~d~~~~~~~~R~~~i~yyl~D~Tvei~E~~~ 42 (104)
T smart00676 11 WEDPVAMFYLIRRFKIYYYLEDDTIEVFEPDV 42 (104)
T ss_pred EecCCCCcCcEEEEEEEEECCCCeEEEEEccc
Confidence 44443333444 44489999999999998754
No 26
>PF08154 NLE: NLE (NUC135) domain; InterPro: IPR012972 This domain is located N-terminal to WD40 repeats(IPR001680 from INTERPRO). It is found in the microtubule-associated protein Q12024 from SWISSPROT [].
Probab=29.42 E-value=29 Score=19.37 Aligned_cols=20 Identities=25% Similarity=0.388 Sum_probs=13.9
Q ss_pred ccc-CCeeecceeEEeeCCEE
Q psy16397 7 GLT-EGTLTAMLDFYIDNEMI 26 (60)
Q Consensus 7 ~Ll-eG~~~sDldF~id~dmI 26 (60)
.|| +++-.-.+||+|++.-|
T Consensus 37 ~LL~~~~~~vpfdF~i~~~~l 57 (65)
T PF08154_consen 37 QLLDDEEEPVPFDFLINGEEL 57 (65)
T ss_pred HHhccCCCCCcEEEEECCEEe
Confidence 355 44446679999999755
No 27
>PHA02771 hypothetical protein; Provisional
Probab=29.18 E-value=63 Score=20.04 Aligned_cols=16 Identities=19% Similarity=0.596 Sum_probs=14.0
Q ss_pred ceeEEeeCCEEEEeec
Q psy16397 16 MLDFYIDNEMIHIADT 31 (60)
Q Consensus 16 DldF~id~dmIhI~e~ 31 (60)
=++||-+.|-|||-|-
T Consensus 69 iI~Yyk~ddkI~I~EI 84 (90)
T PHA02771 69 IIDYFWKDNKICIIEI 84 (90)
T ss_pred EEEEEecCCEEEEEEE
Confidence 4899999999999874
No 28
>PF14025 DUF4241: Protein of unknown function (DUF4241)
Probab=29.08 E-value=87 Score=20.96 Aligned_cols=31 Identities=19% Similarity=0.217 Sum_probs=27.0
Q ss_pred eeEEeeCCEEEEeeccchhhhhhHHHHHHHH
Q psy16397 17 LDFYIDNEMIHIADTKVAHRYGDFFIRKIIK 47 (60)
Q Consensus 17 ldF~id~dmIhI~e~k~~rry~d~Flr~i~K 47 (60)
+-|.+|-.|.++.+.++.+-|.+|.-+...+
T Consensus 85 fGf~VDaG~~~f~D~~~~~~~~~~~~~~~~~ 115 (185)
T PF14025_consen 85 FGFGVDAGLGCFCDAEAFEAYCDFEEEWYEE 115 (185)
T ss_pred eEEEecCccEEEEcHHHHHHHHHHHHHhhhh
Confidence 7799999999999999999988888776555
No 29
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=28.99 E-value=38 Score=19.45 Aligned_cols=17 Identities=12% Similarity=0.329 Sum_probs=13.6
Q ss_pred CcccCCee--ecceeEEee
Q psy16397 6 QGLTEGTL--TAMLDFYID 22 (60)
Q Consensus 6 g~LleG~~--~sDldF~id 22 (60)
||...|+. .||+|..|-
T Consensus 33 GS~arG~~~~~SDiDv~vv 51 (128)
T COG1708 33 GSYARGDFVKESDIDLLVV 51 (128)
T ss_pred ccCcccccccCCCeeEEEE
Confidence 78888886 789998865
No 30
>COG0536 Obg Predicted GTPase [General function prediction only]
Probab=28.45 E-value=31 Score=26.23 Aligned_cols=21 Identities=24% Similarity=0.241 Sum_probs=17.1
Q ss_pred ccchhhhhhHHHHHHHHHHHH
Q psy16397 31 TKVAHRYGDFFIRKIIKFEEL 51 (60)
Q Consensus 31 ~k~~rry~d~Flr~i~K~~~~ 51 (60)
+.-++-.|.-|||||+||+=+
T Consensus 221 As~G~GLG~~FLrHIERt~vL 241 (369)
T COG0536 221 ASEGVGLGLRFLRHIERTRVL 241 (369)
T ss_pred cccCCCccHHHHHHHHhhhee
Confidence 455677999999999998754
No 31
>PF08346 AntA: AntA/AntB antirepressor; InterPro: IPR013557 In Escherichia coli the two proteins AntA and AntB have 62% amino acid identities near their N termini. AntA appears to be encoded by a truncated and divergent copy of AntB. The two proteins are homologous to putative antirepressors found in numerous bacteriophages, such as the hypothetical antirepressor protein encoded by the gene LO142 of the Bacteriophage 933W.
Probab=28.10 E-value=42 Score=19.50 Aligned_cols=16 Identities=25% Similarity=0.571 Sum_probs=13.7
Q ss_pred cchhhhhhHHHHHHHH
Q psy16397 32 KVAHRYGDFFIRKIIK 47 (60)
Q Consensus 32 k~~rry~d~Flr~i~K 47 (60)
.+.++|.+||=++|.+
T Consensus 11 ~v~~~Fs~Wik~ri~~ 26 (71)
T PF08346_consen 11 EVKKRFSTWIKRRIEE 26 (71)
T ss_pred cCCCcHHHHHHHHhhh
Confidence 3578999999999987
No 32
>PF08148 DSHCT: DSHCT (NUC185) domain; InterPro: IPR012961 This C-terminal domain is found in DOB1/SK12/helY-like DEAD box helicases [].; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 4A4Z_A 2XGJ_B 3L9O_A.
Probab=27.09 E-value=70 Score=20.92 Aligned_cols=23 Identities=17% Similarity=0.251 Sum_probs=18.9
Q ss_pred hhhhHHHHHHHHHHHHHHHHhhc
Q psy16397 36 RYGDFFIRKIIKFEELNKKLQAI 58 (60)
Q Consensus 36 ry~d~Flr~i~K~~~~~~~l~~~ 58 (60)
-+..-|+|-+.|..+++++|..+
T Consensus 126 l~EGdiVR~~rRl~dlLrql~~a 148 (180)
T PF08148_consen 126 LFEGDIVRWIRRLIDLLRQLANA 148 (180)
T ss_dssp S-HHHHHHHHHHHHHHHHHHHHH
T ss_pred CCchHHHHHHHHHHHHHHHHHHH
Confidence 35677899999999999999875
No 33
>PF08750 CNP1: CNP1-like family; InterPro: IPR014861 This group of proteins are likely to be lipoproteins. CNP1 (cryptic neisserial protein) has been expressed in Escherichia coli and shown to be localised periplasmicly [].
Probab=26.96 E-value=39 Score=22.08 Aligned_cols=22 Identities=32% Similarity=0.533 Sum_probs=18.6
Q ss_pred ecceeEEeeCCEEEEeeccchh
Q psy16397 14 TAMLDFYIDNEMIHIADTKVAH 35 (60)
Q Consensus 14 ~sDldF~id~dmIhI~e~k~~r 35 (60)
++.+.|+||...|.|.+-.+.|
T Consensus 32 ~~~~~f~ID~~Sisvg~DgvVR 53 (139)
T PF08750_consen 32 TSPLKFFIDPKSISVGPDGVVR 53 (139)
T ss_pred CCCceEEEchhheEECCCCcEE
Confidence 7889999999999998776654
No 34
>PF03586 Herpes_UL36: Herpesvirus UL36 tegument protein; InterPro: IPR005210 The UL36 open reading frame (ORF) encodes the largest Human herpesvirus 1 (HHV-1) protein, a 270 kDa polypeptide designated VP1/2, which is also a component of the virion tegument. A null mutation in the UL36 gene of herpes simplex virus type 1 results in accumulation of unenveloped DNA-filled capsids in the cytoplasm of infected cells []. The region which defines these sequences only covers a small central part of this large protein.; GO: 0004197 cysteine-type endopeptidase activity, 0008242 omega peptidase activity
Probab=26.10 E-value=83 Score=22.79 Aligned_cols=24 Identities=38% Similarity=0.634 Sum_probs=21.5
Q ss_pred hhhhhHHHHHHHHHHHHHHHHhhc
Q psy16397 35 HRYGDFFIRKIIKFEELNKKLQAI 58 (60)
Q Consensus 35 rry~d~Flr~i~K~~~~~~~l~~~ 58 (60)
.+|+|||-|--.+|.+....|+.+
T Consensus 157 ~kYVdFYrrgy~~F~~~~~~L~~l 180 (253)
T PF03586_consen 157 AKYVDFYRRGYEEFEEERARLSAL 180 (253)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHH
Confidence 679999999999999999888765
No 35
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=25.23 E-value=33 Score=25.53 Aligned_cols=19 Identities=16% Similarity=0.314 Sum_probs=14.7
Q ss_pred CcccCCee--ecceeEEeeCC
Q psy16397 6 QGLTEGTL--TAMLDFYIDNE 24 (60)
Q Consensus 6 g~LleG~~--~sDldF~id~d 24 (60)
||+|-|-. .||+||.|=|.
T Consensus 128 GSiL~gl~~~nSDIDfVVYG~ 148 (315)
T COG1665 128 GSILLGLYDENSDIDFVVYGQ 148 (315)
T ss_pred ccccccccCCCCCceEEEEcH
Confidence 67777775 89999997553
No 36
>PF08902 DUF1848: Domain of unknown function (DUF1848); InterPro: IPR014998 This group of proteins are functionally uncharacterised. The C terminus contains a cluster of cysteines that are similar to the iron-sulphur cluster found at the N terminus of IPR007197 from INTERPRO.
Probab=24.49 E-value=41 Score=24.21 Aligned_cols=12 Identities=25% Similarity=0.706 Sum_probs=9.6
Q ss_pred hhhhhHHHHHHH
Q psy16397 35 HRYGDFFIRKII 46 (60)
Q Consensus 35 rry~d~Flr~i~ 46 (60)
.-|++||+..+.
T Consensus 12 AfY~~Wf~nRl~ 23 (266)
T PF08902_consen 12 AFYSDWFMNRLR 23 (266)
T ss_pred cchHHHHHHHhh
Confidence 449999998765
No 37
>PRK06789 flagellar motor switch protein; Validated
Probab=24.24 E-value=62 Score=19.13 Aligned_cols=26 Identities=19% Similarity=0.323 Sum_probs=16.9
Q ss_pred CccccCcccC-Ceeec-ceeEEeeCCEE
Q psy16397 1 MRVKNQGLTE-GTLTA-MLDFYIDNEMI 26 (60)
Q Consensus 1 ~r~~~g~Lle-G~~~s-DldF~id~dmI 26 (60)
+.|++||.++ .+..+ -+|.++++-.|
T Consensus 26 l~L~~Gsvi~Ldk~~~epvdI~vNg~li 53 (74)
T PRK06789 26 LHITKGTLYRLENSTKNTVRLMLENEEI 53 (74)
T ss_pred hcCCCCCEEEeCCcCCCCEEEEECCEEE
Confidence 3577788777 33333 39999986543
No 38
>KOG2527|consensus
Probab=24.08 E-value=23 Score=23.72 Aligned_cols=14 Identities=36% Similarity=0.655 Sum_probs=11.7
Q ss_pred EEeeccchhhhhhH
Q psy16397 27 HIADTKVAHRYGDF 40 (60)
Q Consensus 27 hI~e~k~~rry~d~ 40 (60)
+..+++|-|||.||
T Consensus 50 ~~k~S~VRRRYsdF 63 (144)
T KOG2527|consen 50 KKKESCVRRRYSDF 63 (144)
T ss_pred hhhhHHHHHHHHHH
Confidence 45688999999997
No 39
>PF01043 SecA_PP_bind: SecA preprotein cross-linking domain; InterPro: IPR011130 The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domain is comprised of two sub domains that are inserted within the ATPase domain [].; GO: 0017038 protein import, 0016020 membrane; PDB: 3DIN_B 3JUX_A 3IQY_A 2IBM_A 3DL8_A 3JV2_B 3IQM_A 1TF2_A 1TF5_A 1M74_A ....
Probab=22.67 E-value=74 Score=19.82 Aligned_cols=22 Identities=14% Similarity=0.262 Sum_probs=18.2
Q ss_pred ecceeEEeeCCEEEEeeccchh
Q psy16397 14 TAMLDFYIDNEMIHIADTKVAH 35 (60)
Q Consensus 14 ~sDldF~id~dmIhI~e~k~~r 35 (60)
.-|.||.|.++-|-|.+.-.||
T Consensus 76 ~rd~dYiV~dg~V~IVDe~TGR 97 (113)
T PF01043_consen 76 KRDVDYIVRDGEVVIVDEFTGR 97 (113)
T ss_dssp TTTTSEEEETTEEEEBCTTTTS
T ss_pred hCCcceEEEcCEEEEEECCCCC
Confidence 4689999999988888877764
No 40
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=22.25 E-value=61 Score=21.32 Aligned_cols=38 Identities=21% Similarity=0.533 Sum_probs=23.8
Q ss_pred ccCcccCCeeecceeE--Eee-----CCEEEEeeccchhhhhhHHHHHHHH
Q psy16397 4 KNQGLTEGTLTAMLDF--YID-----NEMIHIADTKVAHRYGDFFIRKIIK 47 (60)
Q Consensus 4 ~~g~LleG~~~sDldF--~id-----~dmIhI~e~k~~rry~d~Flr~i~K 47 (60)
.=|+.++|+++.=-+| +++ ..+|||+|-. +=|+++|+.
T Consensus 4 kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa------~~fVkdI~d 48 (129)
T COG1098 4 KVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIA------DGFVKDIHD 48 (129)
T ss_pred cccceEEEEEEeeEecceEEEecCCCcceEEehHhh------hhhHHhHHH
Confidence 4488999998433222 333 4699999864 346666654
No 41
>cd00707 Pancreat_lipase_like Pancreatic lipase-like enzymes. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is "interfacial activation," the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure. A "lid" or "flap" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site.
Probab=21.77 E-value=53 Score=22.66 Aligned_cols=22 Identities=23% Similarity=0.339 Sum_probs=15.4
Q ss_pred ccCcccC-CeeecceeEEeeCCE
Q psy16397 4 KNQGLTE-GTLTAMLDFYIDNEM 25 (60)
Q Consensus 4 ~~g~Lle-G~~~sDldF~id~dm 25 (60)
|+++++. .++.+++|||.++..
T Consensus 172 T~~~~~G~~~~~gh~dfypngg~ 194 (275)
T cd00707 172 TDGGLLGFSQPIGHADFYPNGGR 194 (275)
T ss_pred eCCCCCCccccccceEeccCCCC
Confidence 4555542 335899999999765
No 42
>PF14521 Aspzincin_M35: Lysine-specific metallo-endopeptidase ; PDB: 2X3C_A 2X3A_A 2X3B_A 1GE7_B 1GE6_A 1GE5_A 1G12_A.
Probab=21.62 E-value=94 Score=19.81 Aligned_cols=25 Identities=16% Similarity=0.356 Sum_probs=14.1
Q ss_pred hhhhhhHHHH-HHH-----HHHHHHHHHhhc
Q psy16397 34 AHRYGDFFIR-KII-----KFEELNKKLQAI 58 (60)
Q Consensus 34 ~rry~d~Flr-~i~-----K~~~~~~~l~~~ 58 (60)
..+|..||.+ ... |...+.+.++.+
T Consensus 11 ~~~y~~WFG~~~~~~~~~~r~~~v~~~~~~~ 41 (148)
T PF14521_consen 11 RARYKTWFGAYDSETNRITRYNTVKDVYKKI 41 (148)
T ss_dssp -HHHHHHH-S--HH-----HHHHHHHHHHHH
T ss_pred chhhhhhcCCCCchhhHHHHHHHHHHHHHHH
Confidence 4678999988 333 555666655543
No 43
>PF14792 DNA_pol_B_palm: DNA polymerase beta palm ; PDB: 1RZT_A 3PML_A 2PFN_A 3HX0_K 3HWT_A 2GWS_E 2BCQ_A 3UPQ_A 2BCS_A 3UQ2_A ....
Probab=21.48 E-value=37 Score=20.77 Aligned_cols=17 Identities=18% Similarity=0.296 Sum_probs=12.0
Q ss_pred CcccCCee-ecceeEEee
Q psy16397 6 QGLTEGTL-TAMLDFYID 22 (60)
Q Consensus 6 g~LleG~~-~sDldF~id 22 (60)
||+--|+. ++|+|+-|-
T Consensus 31 GSyRRGK~~~gDiDiLIt 48 (112)
T PF14792_consen 31 GSYRRGKETSGDIDILIT 48 (112)
T ss_dssp HHHHTT-SEESSEEEEEE
T ss_pred cccccCCCcCCCeEEEEe
Confidence 56666885 999999853
No 44
>PHA02417 hypothetical protein
Probab=20.71 E-value=92 Score=18.95 Aligned_cols=31 Identities=13% Similarity=0.207 Sum_probs=27.5
Q ss_pred EeeCCEEEEeeccchhhhhhHHHHHHHHHHH
Q psy16397 20 YIDNEMIHIADTKVAHRYGDFFIRKIIKFEE 50 (60)
Q Consensus 20 ~id~dmIhI~e~k~~rry~d~Flr~i~K~~~ 50 (60)
.+|+-.+|-++-.+++|-+--|-+.|+-|.+
T Consensus 16 V~~gr~~~A~~~QVQrRvAgLFW~EIA~Csd 46 (83)
T PHA02417 16 VRGGKLFCAGACQVQQRVAGLFWLEIAYCSD 46 (83)
T ss_pred ccCCceeeechhHHHHHHHHHHHHHHHHHcC
Confidence 5788899999999999999999999988765
No 45
>PF00773 RNB: RNB domain CAUTION: The Prosite pattern does not correspond to this Pfam.; InterPro: IPR001900 This entry represents the catalytic domain of ribonuclease II []. It includes characterised and related sequences to exoribonuclease II (RNase II) and ribonuclease R, a bacterial 3' --> 5' exoribonuclease homologous to RNase II [,,].; GO: 0003723 RNA binding, 0004540 ribonuclease activity; PDB: 2R7D_A 2R7F_A 2ID0_D 2IX1_A 2IX0_A 2VNU_D 2WP8_J.
Probab=20.50 E-value=78 Score=21.94 Aligned_cols=20 Identities=25% Similarity=0.383 Sum_probs=13.7
Q ss_pred eeccchhhhhhHHHHHHHHH
Q psy16397 29 ADTKVAHRYGDFFIRKIIKF 48 (60)
Q Consensus 29 ~e~k~~rry~d~Flr~i~K~ 48 (60)
.=|.+-|||+|.+.+.+.+.
T Consensus 302 ~~TSPlRRY~Dl~~hrql~~ 321 (325)
T PF00773_consen 302 HFTSPLRRYADLVVHRQLKA 321 (325)
T ss_dssp --S-TTTBHHHHHHHHHHHH
T ss_pred cccChhhhhHHHHHHHHHHH
Confidence 34677899999999887653
Done!