Query psy5912
Match_columns 122
No_of_seqs 26 out of 28
Neff 2.0
Searched_HMMs 46136
Date Fri Aug 16 21:38:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5912.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5912hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA00451 protein kinase 71.1 2 4.4E-05 37.6 1.1 13 53-65 204-216 (362)
2 PF08271 TF_Zn_Ribbon: TFIIB z 56.4 6.9 0.00015 23.3 1.2 17 57-73 10-27 (43)
3 TIGR03054 photo_alph_chp1 puta 54.6 7.5 0.00016 29.5 1.4 17 52-68 102-118 (135)
4 cd04095 CysN_NoDQ_III TCysN_No 34.1 21 0.00046 23.7 1.0 16 54-69 84-99 (103)
5 PRK12495 hypothetical protein; 31.9 26 0.00056 29.2 1.3 25 48-74 42-67 (226)
6 PRK00423 tfb transcription ini 30.6 34 0.00073 27.8 1.7 25 50-74 13-39 (310)
7 TIGR02596 Verrucomicrobium spi 26.3 35 0.00075 27.2 1.1 16 53-68 178-193 (195)
8 PF07846 Metallothio_Cad: Meta 20.7 66 0.0014 18.3 1.2 13 53-65 5-17 (21)
9 smart00250 PLEC Plectin repeat 20.4 50 0.0011 19.1 0.7 10 58-67 12-21 (38)
10 PF08265 YL1_C: YL1 nuclear pr 19.5 72 0.0016 18.8 1.3 16 51-66 3-19 (30)
No 1
>PHA00451 protein kinase
Probab=71.15 E-value=2 Score=37.58 Aligned_cols=13 Identities=46% Similarity=0.726 Sum_probs=11.5
Q ss_pred CCCCceecCCCCC
Q psy5912 53 DTGRPIFTDPISG 65 (122)
Q Consensus 53 e~GRPi~TDPvtG 65 (122)
++|+|+|||||+=
T Consensus 204 ~~g~p~ITDPVSF 216 (362)
T PHA00451 204 QDGVPYITDPVSF 216 (362)
T ss_pred CCCCeEecCCccc
Confidence 6899999999974
No 2
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=56.41 E-value=6.9 Score=23.31 Aligned_cols=17 Identities=35% Similarity=0.849 Sum_probs=13.5
Q ss_pred ceecCCCCCceeec-ccc
Q psy5912 57 PIFTDPISGQTICS-CQY 73 (122)
Q Consensus 57 Pi~TDPvtGQTVCS-CQY 73 (122)
.|+.|+.+|+.||. |-+
T Consensus 10 ~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 10 EIVFDPERGELVCPNCGL 27 (43)
T ss_dssp EEEEETTTTEEEETTT-B
T ss_pred ceEEcCCCCeEECCCCCC
Confidence 39999999999995 443
No 3
>TIGR03054 photo_alph_chp1 putative photosynthetic complex assembly protein. In twenty or so anoxygenic photosynthetic alpha-Proteobacteria known so far, a gene for a member of this protein family is present and is found in the vicinity of puhA, which encodes a component of the photosynthetic reaction center, and other genes associated with photosynthesis. This protein family is suggested, consequently, as a probable assembly factor for the photosynthetic reaction center, but its seems its actual function has not yet been demonstrated.
Probab=54.61 E-value=7.5 Score=29.55 Aligned_cols=17 Identities=47% Similarity=0.784 Sum_probs=15.6
Q ss_pred CCCCCceecCCCCCcee
Q psy5912 52 CDTGRPIFTDPISGQTI 68 (122)
Q Consensus 52 Ce~GRPi~TDPvtGQTV 68 (122)
=||||=.++||.||+.+
T Consensus 102 ~~dGrltL~Dp~Tg~~i 118 (135)
T TIGR03054 102 YDNGRLTLTDPATGWSI 118 (135)
T ss_pred EeCCcEEEEcCCCCcEE
Confidence 48999999999999986
No 4
>cd04095 CysN_NoDQ_III TCysN_NoDQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which s
Probab=34.10 E-value=21 Score=23.75 Aligned_cols=16 Identities=31% Similarity=0.468 Sum_probs=14.3
Q ss_pred CCCceecCCCCCceee
Q psy5912 54 TGRPIFTDPISGQTIC 69 (122)
Q Consensus 54 ~GRPi~TDPvtGQTVC 69 (122)
.||=|+-|+.+|.||.
T Consensus 84 ~GrfiliD~~~~~tva 99 (103)
T cd04095 84 TGSFILIDRLTNATVG 99 (103)
T ss_pred cceEEEEECCCCcEEE
Confidence 3999999999999985
No 5
>PRK12495 hypothetical protein; Provisional
Probab=31.93 E-value=26 Score=29.18 Aligned_cols=25 Identities=40% Similarity=0.931 Sum_probs=21.1
Q ss_pred CCCCCCCCCceecCCCCCceee-ccccc
Q psy5912 48 GSRCCDTGRPIFTDPISGQTIC-SCQYD 74 (122)
Q Consensus 48 ~~~CCe~GRPi~TDPvtGQTVC-SCQYD 74 (122)
...|.+=|-||+ =+.|.++| .||-.
T Consensus 42 a~hC~~CG~PIp--a~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 42 NAHCDECGDPIF--RHDGQEFCPTCQQP 67 (226)
T ss_pred hhhcccccCccc--CCCCeeECCCCCCc
Confidence 347889999999 47999999 79965
No 6
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=30.59 E-value=34 Score=27.81 Aligned_cols=25 Identities=24% Similarity=0.614 Sum_probs=19.0
Q ss_pred CCCCCCC-ceecCCCCCceeec-cccc
Q psy5912 50 RCCDTGR-PIFTDPISGQTICS-CQYD 74 (122)
Q Consensus 50 ~CCe~GR-Pi~TDPvtGQTVCS-CQYD 74 (122)
.|-+-|. .|+.|..+|+.||. |.+-
T Consensus 13 ~Cp~Cg~~~iv~d~~~Ge~vC~~CG~V 39 (310)
T PRK00423 13 VCPECGSDKLIYDYERGEIVCADCGLV 39 (310)
T ss_pred cCcCCCCCCeeEECCCCeEeecccCCc
Confidence 4544444 89999999999995 8773
No 7
>TIGR02596 Verrucomicrobium spinosum paralogous family TIGR02596. This model describes a nearly twenty member protein family unique to Verrucomicrobium spinosum. All members share a type IV pilin-like N-terminal leader sequence (TIGR02532). Sequences are from 207 to 248 in length. The function is unknown.
Probab=26.27 E-value=35 Score=27.15 Aligned_cols=16 Identities=25% Similarity=0.596 Sum_probs=13.6
Q ss_pred CCCCceecCCCCCcee
Q psy5912 53 DTGRPIFTDPISGQTI 68 (122)
Q Consensus 53 e~GRPi~TDPvtGQTV 68 (122)
+|=|-|+.|||||+.+
T Consensus 178 ~n~~t~~~~pvtg~~~ 193 (195)
T TIGR02596 178 PNYRTLVLDPVTGAVV 193 (195)
T ss_pred CceeEEEEccccceeE
Confidence 4668899999999865
No 8
>PF07846 Metallothio_Cad: Metallothionein family; InterPro: IPR012484 The sequence making up family 7 of the metallothionein superfamily are found repeated in metallothionein proteins expressed by two Tetrahymena species. Metallothioneins are low molecular mass, cysteine-rich metal-binding proteins that are thought to be involved in the regulation of levels of trace metals, and detoxification of these metals when present in excess []. Some of the metallothioneins found in this family (for example, Q8T6B3 from SWISSPROT) are known to be induced by cadmium and are thought to be involved in the cellular sequestration of toxic metal ions. The high proportion of cysteine residues allows the metal ions to be bound by the formation of clusters of metal-thiolate complexes []. Tetrahymena spp. metallothioneins differ from other eukaryotic metallothioneins mainly in the length of their sequences and in the cysteine-containing motifs they exhibit. ; GO: 0046870 cadmium ion binding
Probab=20.74 E-value=66 Score=18.26 Aligned_cols=13 Identities=46% Similarity=0.700 Sum_probs=11.1
Q ss_pred CCCCceecCCCCC
Q psy5912 53 DTGRPIFTDPISG 65 (122)
Q Consensus 53 e~GRPi~TDPvtG 65 (122)
+|-++--+||.+|
T Consensus 5 ~naK~cC~DPnsG 17 (21)
T PF07846_consen 5 VNAKPCCTDPNSG 17 (21)
T ss_pred CCCcccccCCCCc
Confidence 6778888999998
No 9
>smart00250 PLEC Plectin repeat.
Probab=20.36 E-value=50 Score=19.11 Aligned_cols=10 Identities=40% Similarity=0.547 Sum_probs=8.0
Q ss_pred eecCCCCCce
Q psy5912 58 IFTDPISGQT 67 (122)
Q Consensus 58 i~TDPvtGQT 67 (122)
-|.||.|||.
T Consensus 12 Giidp~t~~~ 21 (38)
T smart00250 12 GIIDPETGQK 21 (38)
T ss_pred EEEcCCCCCC
Confidence 3789999985
No 10
>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []. These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.
Probab=19.48 E-value=72 Score=18.77 Aligned_cols=16 Identities=44% Similarity=0.796 Sum_probs=11.8
Q ss_pred CCCCCCc-eecCCCCCc
Q psy5912 51 CCDTGRP-IFTDPISGQ 66 (122)
Q Consensus 51 CCe~GRP-i~TDPvtGQ 66 (122)
|--+|.| -.+||+||.
T Consensus 3 C~iTglpA~Y~DP~T~l 19 (30)
T PF08265_consen 3 CDITGLPARYRDPKTGL 19 (30)
T ss_pred ccccCCCccccCCCCCC
Confidence 5567776 478999985
Done!