Query 039064
Match_columns 224
No_of_seqs 90 out of 92
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 05:58:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039064.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039064hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05142 DUF702: Domain of unk 100.0 1.9E-81 4E-86 521.2 9.3 136 5-144 1-153 (154)
2 TIGR01624 LRP1_Cterm LRP1 C-te 100.0 4.1E-35 8.9E-40 206.3 5.9 49 92-142 1-50 (50)
3 TIGR01623 put_zinc_LRP1 putati 100.0 3E-32 6.5E-37 187.0 1.0 43 10-52 1-43 (43)
4 PF02150 RNA_POL_M_15KD: RNA p 80.0 0.54 1.2E-05 30.7 -0.1 20 10-30 3-26 (35)
5 PLN03158 methionine aminopepti 73.2 1.7 3.7E-05 41.1 1.3 29 6-39 7-40 (396)
6 PF10419 TFIIIC_sub6: TFIIIC s 58.1 11 0.00024 24.9 2.4 14 125-138 12-25 (35)
7 PF10977 DUF2797: Protein of u 49.2 8.6 0.00019 34.5 1.2 44 6-50 9-52 (235)
8 PF13975 gag-asp_proteas: gag- 43.6 32 0.0007 24.5 3.2 23 121-144 8-30 (72)
9 PRK00564 hypA hydrogenase nick 42.8 10 0.00022 30.2 0.5 24 8-31 71-95 (117)
10 PRK11823 DNA repair protein Ra 34.3 16 0.00034 34.8 0.5 20 9-30 8-27 (446)
11 PRK03824 hypA hydrogenase nick 32.9 17 0.00037 29.6 0.4 24 8-31 70-114 (135)
12 PRK12380 hydrogenase nickel in 32.9 17 0.00038 28.7 0.4 24 8-31 70-93 (113)
13 TIGR00416 sms DNA repair prote 31.9 18 0.00039 34.7 0.4 21 9-31 8-28 (454)
14 PF04658 TAFII55_N: TAFII55 pr 29.6 42 0.00091 28.5 2.2 20 123-142 42-61 (162)
15 PHA00626 hypothetical protein 29.4 25 0.00055 26.3 0.8 26 9-39 1-27 (59)
16 PF05294 Toxin_5: Scorpion sho 29.1 14 0.0003 24.7 -0.6 10 26-35 14-23 (32)
17 TIGR00100 hypA hydrogenase nic 28.6 23 0.0005 28.1 0.5 23 8-30 70-92 (115)
18 cd01121 Sms Sms (bacterial rad 26.4 26 0.00056 32.9 0.5 22 10-33 2-23 (372)
19 PLN02638 cellulose synthase A 26.0 36 0.00077 37.0 1.4 41 7-50 16-81 (1079)
20 cd08047 TAF7 TATA Binding Prot 25.0 59 0.0013 27.1 2.3 20 123-142 40-59 (162)
21 PRK00398 rpoP DNA-directed RNA 24.4 29 0.00063 23.0 0.3 22 9-30 4-27 (46)
22 TIGR01384 TFS_arch transcripti 24.4 32 0.00069 26.0 0.5 22 10-31 2-23 (104)
23 COG3357 Predicted transcriptio 24.0 33 0.00072 27.8 0.6 30 9-50 59-90 (97)
24 PLN02915 cellulose synthase A 23.9 43 0.00092 36.4 1.5 43 5-50 12-79 (1044)
25 PF01155 HypA: Hydrogenase exp 23.7 17 0.00038 28.5 -1.0 23 9-31 71-93 (113)
26 PRK03681 hypA hydrogenase nick 23.4 32 0.00069 27.3 0.4 24 8-31 70-94 (114)
27 COG5082 AIR1 Arginine methyltr 22.3 33 0.00072 30.4 0.4 23 8-30 60-84 (190)
28 smart00661 RPOL9 RNA polymeras 21.3 38 0.00082 22.3 0.4 21 10-30 2-26 (52)
29 PRK09289 riboflavin synthase s 21.0 49 0.0011 28.6 1.1 23 120-142 85-107 (194)
No 1
>PF05142 DUF702: Domain of unknown function (DUF702) ; InterPro: IPR007818 This is a family of plant proteins of unknown function.
Probab=100.00 E-value=1.9e-81 Score=521.17 Aligned_cols=136 Identities=57% Similarity=1.014 Sum_probs=120.2
Q ss_pred CCCCcccccccchhhhcCCCcccccccccCCcccccccccceeccchhchhhhccccccccccc-ccccCCCCCCCccC-
Q 039064 5 ELGVTRCQDCGNQAKKNCAYMRCRTCCKRRGYECETHIKSTWIPAYRRHQRYHHQHLVPVHEQH-LQLQGHSPKRLREN- 82 (224)
Q Consensus 5 ~~gg~~CQDCGNQAKKdC~h~RCRTCCKsRGf~C~THVKSTWVPAarRRERq~~q~~~~~~~~~-~~~~~~~~kr~r~~- 82 (224)
|+|+++||||||||||||+|||||||||||||||+||||||||||+|||||| |++.++++++ .......+||+|++
T Consensus 1 ~~gg~~CqdCGNqAkk~C~~~rCRtCCk~rg~~C~tHvksTWVPA~~rRer~--~~~~~~~~~~~~~~~~~~~kr~r~~~ 78 (154)
T PF05142_consen 1 GSGGISCQDCGNQAKKDCSHRRCRTCCKSRGFDCPTHVKSTWVPAARRRERQ--QQLAAAQQQQQGSQGSSGPKRPRELS 78 (154)
T ss_pred CCCCcchhhhcchhhcCCCcchhhhhhccCCCCCccceeccccchhhhchhh--hcccccccccccCcccCCcCCccccc
Confidence 5899999999999999999999999999999999999999999999999999 6666654432 22356789999984
Q ss_pred ---CC------------CCCccccCCCccccCcceeeEEEeeccccccccceeEEEEEEEecceeeeeeeeccCCCC
Q 039064 83 ---PS------------SPGLQIGNFPAEITSEATFRCVKVSSIDDAIDRTTLAYKTSISVGGHIFKGILYYQGCES 144 (224)
Q Consensus 83 ---~s------------ssg~~~~~fP~eV~s~AvFRCVRVssidd~e~e~~~AYQt~V~IgGHVFKGiLYDqG~e~ 144 (224)
.+ ..+++.++||+|||||||||||||++|||+||| |||||+|+||||||||||||||||+
T Consensus 79 ~~~~~~~~~t~~~~~~~~~~~~~~~fP~eV~spAvFRCVRVssiDdgedE--~AYQTaV~IGGHVFKGiLYDqG~~~ 153 (154)
T PF05142_consen 79 NSTQSSTSCTSTSNGTSPSSLETGSFPAEVSSPAVFRCVRVSSIDDGEDE--YAYQTAVNIGGHVFKGILYDQGPES 153 (154)
T ss_pred ccCCCCccccccCCCcccccchhccCChhhcccceEEEEEEecccCcccc--eeeEEeEEECCEEeeeeeeccCCCC
Confidence 00 025677899999999999999999999999999 9999999999999999999999995
No 2
>TIGR01624 LRP1_Cterm LRP1 C-terminal domain. This model represents a tightly conserved small domain found in LRP1 and related plant proteins. This family also contains a well-conserved putative zinc finger domain (TIGR01623). The rest of the sequence of most members consists of highly divergent, low-complexity sequence.
Probab=100.00 E-value=4.1e-35 Score=206.31 Aligned_cols=49 Identities=45% Similarity=0.958 Sum_probs=47.5
Q ss_pred CCCccccCcceeeEEEeeccccccc-cceeEEEEEEEecceeeeeeeeccCC
Q 039064 92 NFPAEITSEATFRCVKVSSIDDAID-RTTLAYKTSISVGGHIFKGILYYQGC 142 (224)
Q Consensus 92 ~fP~eV~s~AvFRCVRVssidd~e~-e~~~AYQt~V~IgGHVFKGiLYDqG~ 142 (224)
+||+|||||||||||||++|||+|+ | |||||+|+|||||||||||||||
T Consensus 1 ~fP~ev~s~AvFrcvRvs~idd~~~~e--~aYQt~V~IgGHvFkGiLyDqG~ 50 (50)
T TIGR01624 1 GFPGEVSAPAVFKCVRVTAIDDGEQAE--YAYQATVTIGGHVFKGFLHDQGL 50 (50)
T ss_pred CCccccccceEEEEEEEeccCCCCCce--EEEEEEEEECceEEeeEEeccCC
Confidence 5999999999999999999999998 7 99999999999999999999997
No 3
>TIGR01623 put_zinc_LRP1 putative zinc finger domain, LRP1 type. This model represents a putative zinc finger domain found in plants. Arabidopsis thaliana has at least 10 distinct members. Proteins containing this domain, including LRP1, generally share the same size, about 300 amino acids, and architecture. This 43-residue domain, and a more C-terminal companion domain of similar size, appear as tightly conserved islands of sequence similarity. The remainder consists largely of low-complexity sequence. Several animal proteins have regions with matching patterns of Cys, Gly, and His residues. These are not included in the model but score between trusted and noise cutoffs.
Probab=99.97 E-value=3e-32 Score=187.02 Aligned_cols=43 Identities=74% Similarity=1.511 Sum_probs=42.1
Q ss_pred ccccccchhhhcCCCcccccccccCCcccccccccceeccchh
Q 039064 10 RCQDCGNQAKKNCAYMRCRTCCKRRGYECETHIKSTWIPAYRR 52 (224)
Q Consensus 10 ~CQDCGNQAKKdC~h~RCRTCCKsRGf~C~THVKSTWVPAarR 52 (224)
+||||||||||+|.|+|||||||+|||||+||||||||||+||
T Consensus 1 ~C~~CgNpa~k~C~~~~CRtCCK~r~~DC~tHv~stw~p~~~r 43 (43)
T TIGR01623 1 VCQDCGNQAKKECLFERCRTCCKSRGFHCVTHVKSTWIPAARR 43 (43)
T ss_pred ChhhccchhhCCCchhhhhHHhcccCcCCcchhcccccccccC
Confidence 5999999999999999999999999999999999999999987
No 4
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=80.04 E-value=0.54 Score=30.72 Aligned_cols=20 Identities=45% Similarity=1.064 Sum_probs=14.0
Q ss_pred ccccccc----hhhhcCCCcccccc
Q 039064 10 RCQDCGN----QAKKNCAYMRCRTC 30 (224)
Q Consensus 10 ~CQDCGN----QAKKdC~h~RCRTC 30 (224)
-|.+||| +..++-.. +||+|
T Consensus 3 FCp~C~nlL~p~~~~~~~~-~C~~C 26 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRV-ACRTC 26 (35)
T ss_dssp BETTTTSBEEEEEETTTTE-EESSS
T ss_pred eCCCCCccceEcCCCccCc-CCCCC
Confidence 5999999 33444444 69999
No 5
>PLN03158 methionine aminopeptidase; Provisional
Probab=73.25 E-value=1.7 Score=41.10 Aligned_cols=29 Identities=21% Similarity=0.590 Sum_probs=23.2
Q ss_pred CCCcccccccchhhhcCCCccccccccc-----CCcccc
Q 039064 6 LGVTRCQDCGNQAKKNCAYMRCRTCCKR-----RGYECE 39 (224)
Q Consensus 6 ~gg~~CQDCGNQAKKdC~h~RCRTCCKs-----RGf~C~ 39 (224)
.+...|.+||++|+ +.|-+|.|. +.|.|.
T Consensus 7 ~~~~~c~~c~~~a~-----l~Cp~C~k~~~~~~~s~fCs 40 (396)
T PLN03158 7 TSPLACARCSKPAH-----LQCPKCLELKLPREGASFCS 40 (396)
T ss_pred CCcccccCCCCccc-----ccCccchhcCCCCCCceeEC
Confidence 34567999999886 889999994 478885
No 6
>PF10419 TFIIIC_sub6: TFIIIC subunit; InterPro: IPR019481 This conserved domain is found in a family of proteins that function as subunits of transcription factor IIIC (TFIIIC) []. TFIIIC in yeast and humans is required for transcription of tRNA and 5 S RNA genes by RNA polymerase III. The yeast proteins in this entry are fused to phosphoglycerate mutase domain.
Probab=58.09 E-value=11 Score=24.91 Aligned_cols=14 Identities=21% Similarity=0.579 Sum_probs=11.7
Q ss_pred EEEecceeeeeeee
Q 039064 125 SISVGGHIFKGILY 138 (224)
Q Consensus 125 ~V~IgGHVFKGiLY 138 (224)
.|.||++||+|---
T Consensus 12 il~i~~~vf~G~~~ 25 (35)
T PF10419_consen 12 ILQIGNQVFEGEWE 25 (35)
T ss_pred EEEECCEEEEEEEh
Confidence 48999999999643
No 7
>PF10977 DUF2797: Protein of unknown function (DUF2797); InterPro: IPR021246 This family of proteins has no known function.
Probab=49.24 E-value=8.6 Score=34.46 Aligned_cols=44 Identities=25% Similarity=0.534 Sum_probs=36.7
Q ss_pred CCCcccccccchhhhcCCCcccccccccCCcccccccccceeccc
Q 039064 6 LGVTRCQDCGNQAKKNCAYMRCRTCCKRRGYECETHIKSTWIPAY 50 (224)
Q Consensus 6 ~gg~~CQDCGNQAKKdC~h~RCRTCCKsRGf~C~THVKSTWVPAa 50 (224)
.|.+.|-.||..-||-=...+|--|-+. .-.|..|+.+.|.-..
T Consensus 9 ~g~i~c~~cG~~~~~s~~qg~C~~C~~~-~aqC~~Ci~~pe~c~~ 52 (235)
T PF10977_consen 9 TGEIQCLNCGRKTKKSFRQGYCYPCFQT-LAQCDECIMRPELCHY 52 (235)
T ss_pred CCcEEEecCCccccccCCCCceeCCCCc-CccChhHhCCcchhhe
Confidence 3566899999999999999999888765 5599999999996543
No 8
>PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease
Probab=43.58 E-value=32 Score=24.47 Aligned_cols=23 Identities=26% Similarity=0.349 Sum_probs=20.2
Q ss_pred EEEEEEEecceeeeeeeeccCCCC
Q 039064 121 AYKTSISVGGHIFKGILYYQGCES 144 (224)
Q Consensus 121 AYQt~V~IgGHVFKGiLYDqG~e~ 144 (224)
.+...|.|+||.++ .|=|-|...
T Consensus 8 ~~~v~~~I~g~~~~-alvDtGat~ 30 (72)
T PF13975_consen 8 LMYVPVSIGGVQVK-ALVDTGATH 30 (72)
T ss_pred EEEEEEEECCEEEE-EEEeCCCcc
Confidence 57789999999999 899999873
No 9
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.77 E-value=10 Score=30.21 Aligned_cols=24 Identities=33% Similarity=0.768 Sum_probs=18.1
Q ss_pred CcccccccchhhhcC-CCccccccc
Q 039064 8 VTRCQDCGNQAKKNC-AYMRCRTCC 31 (224)
Q Consensus 8 g~~CQDCGNQAKKdC-~h~RCRTCC 31 (224)
-..|.|||+.-..+- .+.||..|-
T Consensus 71 ~~~C~~Cg~~~~~~~~~~~~CP~Cg 95 (117)
T PRK00564 71 ELECKDCSHVFKPNALDYGVCEKCH 95 (117)
T ss_pred EEEhhhCCCccccCCccCCcCcCCC
Confidence 358999999877764 466799883
No 10
>PRK11823 DNA repair protein RadA; Provisional
Probab=34.32 E-value=16 Score=34.84 Aligned_cols=20 Identities=40% Similarity=0.929 Sum_probs=17.5
Q ss_pred cccccccchhhhcCCCcccccc
Q 039064 9 TRCQDCGNQAKKNCAYMRCRTC 30 (224)
Q Consensus 9 ~~CQDCGNQAKKdC~h~RCRTC 30 (224)
-.|+.||.+..| -+-||..|
T Consensus 8 y~C~~Cg~~~~~--~~g~Cp~C 27 (446)
T PRK11823 8 YVCQECGAESPK--WLGRCPEC 27 (446)
T ss_pred EECCcCCCCCcc--cCeeCcCC
Confidence 379999999988 47889999
No 11
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.88 E-value=17 Score=29.62 Aligned_cols=24 Identities=33% Similarity=0.981 Sum_probs=18.5
Q ss_pred Ccccccccchhhhc---------------------CCCccccccc
Q 039064 8 VTRCQDCGNQAKKN---------------------CAYMRCRTCC 31 (224)
Q Consensus 8 g~~CQDCGNQAKKd---------------------C~h~RCRTCC 31 (224)
-..|.|||..-.-+ =.+.+|..|-
T Consensus 70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cg 114 (135)
T PRK03824 70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCG 114 (135)
T ss_pred EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCC
Confidence 35899999877665 6778888883
No 12
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=32.86 E-value=17 Score=28.71 Aligned_cols=24 Identities=21% Similarity=0.526 Sum_probs=18.1
Q ss_pred CcccccccchhhhcCCCccccccc
Q 039064 8 VTRCQDCGNQAKKNCAYMRCRTCC 31 (224)
Q Consensus 8 g~~CQDCGNQAKKdC~h~RCRTCC 31 (224)
-..|.+||..-..+=.+.+|..|-
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cg 93 (113)
T PRK12380 70 QAWCWDCSQVVEIHQHDAQCPHCH 93 (113)
T ss_pred EEEcccCCCEEecCCcCccCcCCC
Confidence 458999998766655667788884
No 13
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=31.90 E-value=18 Score=34.67 Aligned_cols=21 Identities=33% Similarity=0.763 Sum_probs=18.0
Q ss_pred cccccccchhhhcCCCccccccc
Q 039064 9 TRCQDCGNQAKKNCAYMRCRTCC 31 (224)
Q Consensus 9 ~~CQDCGNQAKKdC~h~RCRTCC 31 (224)
-.||+||.+..| -+-||..|-
T Consensus 8 y~C~~Cg~~~~~--~~g~Cp~C~ 28 (454)
T TIGR00416 8 FVCQHCGADSPK--WQGKCPACH 28 (454)
T ss_pred EECCcCCCCCcc--ccEECcCCC
Confidence 379999999998 488899993
No 14
>PF04658 TAFII55_N: TAFII55 protein conserved region; InterPro: IPR006751 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. TAFII55 binds to TAFII250 and inhibits its acetyltransferase activity. The exact role of TAFII55 is currently unknown. The conserved region is situated towards the N-terminal of the protein [].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005669 transcription factor TFIID complex
Probab=29.59 E-value=42 Score=28.47 Aligned_cols=20 Identities=25% Similarity=0.645 Sum_probs=18.0
Q ss_pred EEEEEecceeeeeeeeccCC
Q 039064 123 KTSISVGGHIFKGILYYQGC 142 (224)
Q Consensus 123 Qt~V~IgGHVFKGiLYDqG~ 142 (224)
.+.|+|+|+.|.|.|.|.=.
T Consensus 42 ~~~v~i~~~~y~a~LvDLP~ 61 (162)
T PF04658_consen 42 RAVVRIGGQIYSAKLVDLPC 61 (162)
T ss_pred EEEEEECCEEcceEEeecCc
Confidence 48999999999999999863
No 15
>PHA00626 hypothetical protein
Probab=29.35 E-value=25 Score=26.27 Aligned_cols=26 Identities=23% Similarity=0.539 Sum_probs=19.1
Q ss_pred cccccccchhhhcCCCcccccccc-cCCcccc
Q 039064 9 TRCQDCGNQAKKNCAYMRCRTCCK-RRGYECE 39 (224)
Q Consensus 9 ~~CQDCGNQAKKdC~h~RCRTCCK-sRGf~C~ 39 (224)
+.|.+||.. .+.||-+|.+ |--|.|.
T Consensus 1 m~CP~CGS~-----~Ivrcg~cr~~snrYkCk 27 (59)
T PHA00626 1 MSCPKCGSG-----NIAKEKTMRGWSDDYVCC 27 (59)
T ss_pred CCCCCCCCc-----eeeeeceecccCcceEcC
Confidence 579999973 1457888888 7777775
No 16
>PF05294 Toxin_5: Scorpion short toxin; InterPro: IPR007958 This family contains various secreted scorpion short toxins which seem to be unrelated to those described in IPR001947 from INTERPRO.; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1SIS_A 1CHL_A.
Probab=29.13 E-value=14 Score=24.73 Aligned_cols=10 Identities=60% Similarity=1.700 Sum_probs=8.4
Q ss_pred ccccccccCC
Q 039064 26 RCRTCCKRRG 35 (224)
Q Consensus 26 RCRTCCKsRG 35 (224)
.||.||.+||
T Consensus 14 kC~~CCgg~G 23 (32)
T PF05294_consen 14 KCRDCCGGRG 23 (32)
T ss_dssp HHHHHCTTSE
T ss_pred HHHHHhCCCC
Confidence 4999999885
No 17
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=28.55 E-value=23 Score=28.06 Aligned_cols=23 Identities=26% Similarity=0.814 Sum_probs=17.5
Q ss_pred CcccccccchhhhcCCCcccccc
Q 039064 8 VTRCQDCGNQAKKNCAYMRCRTC 30 (224)
Q Consensus 8 g~~CQDCGNQAKKdC~h~RCRTC 30 (224)
-..|.+||+.-..+=.+.+|..|
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~C 92 (115)
T TIGR00100 70 ECECEDCSEEVSPEIDLYRCPKC 92 (115)
T ss_pred EEEcccCCCEEecCCcCccCcCC
Confidence 35899999877665457778887
No 18
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=26.40 E-value=26 Score=32.86 Aligned_cols=22 Identities=27% Similarity=0.705 Sum_probs=18.1
Q ss_pred ccccccchhhhcCCCccccccccc
Q 039064 10 RCQDCGNQAKKNCAYMRCRTCCKR 33 (224)
Q Consensus 10 ~CQDCGNQAKKdC~h~RCRTCCKs 33 (224)
.||+||.+..| -+-||..|-.=
T Consensus 2 ~c~~cg~~~~~--~~g~cp~c~~w 23 (372)
T cd01121 2 VCSECGYVSPK--WLGKCPECGEW 23 (372)
T ss_pred CCCCCCCCCCC--ccEECcCCCCc
Confidence 69999999888 47889999443
No 19
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.97 E-value=36 Score=37.04 Aligned_cols=41 Identities=39% Similarity=0.711 Sum_probs=32.7
Q ss_pred CCcccccccch-----------hhhcCCCcccccc----------cccCCcccccccc----cceeccc
Q 039064 7 GVTRCQDCGNQ-----------AKKNCAYMRCRTC----------CKRRGYECETHIK----STWIPAY 50 (224)
Q Consensus 7 gg~~CQDCGNQ-----------AKKdC~h~RCRTC----------CKsRGf~C~THVK----STWVPAa 50 (224)
.+..||-||-. |=.+|.+--||.| ||- +|-|+-| |-||+.+
T Consensus 16 ~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CP---qCktrYkr~kgsprv~gD 81 (1079)
T PLN02638 16 GGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCP---QCKTKYKRHKGSPAILGD 81 (1079)
T ss_pred CCceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCC---ccCCchhhhcCCCCcCcc
Confidence 45699999987 6678999999999 232 4888888 7788875
No 20
>cd08047 TAF7 TATA Binding Protein (TBP) Associated Factor 7 (TAF7) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 7 (TAF7) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving
Probab=25.02 E-value=59 Score=27.14 Aligned_cols=20 Identities=10% Similarity=0.230 Sum_probs=18.2
Q ss_pred EEEEEecceeeeeeeeccCC
Q 039064 123 KTSISVGGHIFKGILYYQGC 142 (224)
Q Consensus 123 Qt~V~IgGHVFKGiLYDqG~ 142 (224)
.+.|+|+|+.|.|+|.|.=.
T Consensus 40 ~~~v~v~~~~y~a~LvdLPt 59 (162)
T cd08047 40 RAVVRINGQKYPAKLVDLPT 59 (162)
T ss_pred EEEEEECCEEcceEEeecCc
Confidence 68999999999999999864
No 21
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=24.41 E-value=29 Score=23.05 Aligned_cols=22 Identities=27% Similarity=0.767 Sum_probs=14.2
Q ss_pred cccccccchhhhcCC--Ccccccc
Q 039064 9 TRCQDCGNQAKKNCA--YMRCRTC 30 (224)
Q Consensus 9 ~~CQDCGNQAKKdC~--h~RCRTC 30 (224)
..|.+||.+..-|=. -.+|..|
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~C 27 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYC 27 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCC
Confidence 468999987633322 4677777
No 22
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=24.36 E-value=32 Score=25.97 Aligned_cols=22 Identities=23% Similarity=0.646 Sum_probs=17.1
Q ss_pred ccccccchhhhcCCCccccccc
Q 039064 10 RCQDCGNQAKKNCAYMRCRTCC 31 (224)
Q Consensus 10 ~CQDCGNQAKKdC~h~RCRTCC 31 (224)
.|.+|||--...=..+.|++|-
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~ 23 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCG 23 (104)
T ss_pred CCcccCcccccCCCeEECcCCC
Confidence 6999999665544588999984
No 23
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=24.03 E-value=33 Score=27.82 Aligned_cols=30 Identities=37% Similarity=0.863 Sum_probs=20.9
Q ss_pred cccccccchhhhcC--CCcccccccccCCcccccccccceeccc
Q 039064 9 TRCQDCGNQAKKNC--AYMRCRTCCKRRGYECETHIKSTWIPAY 50 (224)
Q Consensus 9 ~~CQDCGNQAKKdC--~h~RCRTCCKsRGf~C~THVKSTWVPAa 50 (224)
..|.+||---+.|= .-.||.-| ||-||--.
T Consensus 59 a~CkkCGfef~~~~ik~pSRCP~C------------KSE~Ie~p 90 (97)
T COG3357 59 ARCKKCGFEFRDDKIKKPSRCPKC------------KSEWIEEP 90 (97)
T ss_pred hhhcccCccccccccCCcccCCcc------------hhhcccCC
Confidence 47999997544432 35789888 88898543
No 24
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=23.94 E-value=43 Score=36.36 Aligned_cols=43 Identities=23% Similarity=0.637 Sum_probs=33.4
Q ss_pred CCCCcccccccch-----------hhhcCCCccccccc----------ccCCcccccccc----cceeccc
Q 039064 5 ELGVTRCQDCGNQ-----------AKKNCAYMRCRTCC----------KRRGYECETHIK----STWIPAY 50 (224)
Q Consensus 5 ~~gg~~CQDCGNQ-----------AKKdC~h~RCRTCC----------KsRGf~C~THVK----STWVPAa 50 (224)
+.++..||-||-. |=.+|.+--||.|- |- +|-||-| |-||..+
T Consensus 12 ~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp---~c~t~y~~~~~~~~~~~d 79 (1044)
T PLN02915 12 SADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCP---QCNTRYKRHKGCPRVEGD 79 (1044)
T ss_pred CCCcchhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCC---ccCCchhhhcCCCCccCC
Confidence 3467789999987 66789999999993 22 4888888 7777775
No 25
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=23.65 E-value=17 Score=28.50 Aligned_cols=23 Identities=30% Similarity=0.836 Sum_probs=15.8
Q ss_pred cccccccchhhhcCCCccccccc
Q 039064 9 TRCQDCGNQAKKNCAYMRCRTCC 31 (224)
Q Consensus 9 ~~CQDCGNQAKKdC~h~RCRTCC 31 (224)
..|.+||..-.-+=.+.+|..|-
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cg 93 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFDFSCPRCG 93 (113)
T ss_dssp EEETTTS-EEECHHCCHH-SSSS
T ss_pred EECCCCCCEEecCCCCCCCcCCc
Confidence 58999999776666667788773
No 26
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.42 E-value=32 Score=27.27 Aligned_cols=24 Identities=21% Similarity=0.498 Sum_probs=16.8
Q ss_pred CcccccccchhhhcCC-Cccccccc
Q 039064 8 VTRCQDCGNQAKKNCA-YMRCRTCC 31 (224)
Q Consensus 8 g~~CQDCGNQAKKdC~-h~RCRTCC 31 (224)
-..|.|||+....+=. +.+|..|-
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~~CP~Cg 94 (114)
T PRK03681 70 ECWCETCQQYVTLLTQRVRRCPQCH 94 (114)
T ss_pred EEEcccCCCeeecCCccCCcCcCcC
Confidence 4589999987665433 36788884
No 27
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=22.34 E-value=33 Score=30.43 Aligned_cols=23 Identities=26% Similarity=0.875 Sum_probs=19.6
Q ss_pred Ccccccccch--hhhcCCCcccccc
Q 039064 8 VTRCQDCGNQ--AKKNCAYMRCRTC 30 (224)
Q Consensus 8 g~~CQDCGNQ--AKKdC~h~RCRTC 30 (224)
...|+-||++ -++||+|.-|-.|
T Consensus 60 ~~~C~nCg~~GH~~~DCP~~iC~~C 84 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCPHSICYNC 84 (190)
T ss_pred ccccchhcccCcccccCChhHhhhc
Confidence 4689999995 6899999888777
No 28
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.27 E-value=38 Score=22.30 Aligned_cols=21 Identities=33% Similarity=0.771 Sum_probs=14.1
Q ss_pred ccccccchhhhc----CCCcccccc
Q 039064 10 RCQDCGNQAKKN----CAYMRCRTC 30 (224)
Q Consensus 10 ~CQDCGNQAKKd----C~h~RCRTC 30 (224)
-|.+|||-.... -.+..|+.|
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~C 26 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKC 26 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcC
Confidence 489999954222 236778888
No 29
>PRK09289 riboflavin synthase subunit alpha; Provisional
Probab=21.01 E-value=49 Score=28.56 Aligned_cols=23 Identities=30% Similarity=0.381 Sum_probs=17.3
Q ss_pred eEEEEEEEecceeeeeeeeccCC
Q 039064 120 LAYKTSISVGGHIFKGILYYQGC 142 (224)
Q Consensus 120 ~AYQt~V~IgGHVFKGiLYDqG~ 142 (224)
-|-...=.+|||+|.|+.=..|.
T Consensus 85 ra~~~~~~~gGHm~tGhVd~~g~ 107 (194)
T PRK09289 85 RALRLGDRLGGHIVSGHVDGTGE 107 (194)
T ss_pred EcccCCCcccceeEEEEEEEEEE
Confidence 34444445899999999988885
Done!