Query 019213
Match_columns 344
No_of_seqs 96 out of 98
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 07:38:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019213.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019213hhsearch_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 1.8E-82 3.8E-87 554.3 8.8 149 114-263 1-154 (154)
2 TIGR01624 LRP1_Cterm LRP1 C-te 100.0 1.2E-34 2.6E-39 213.7 5.9 49 212-260 1-50 (50)
3 TIGR01623 put_zinc_LRP1 putati 100.0 3.2E-31 6.9E-36 190.8 0.9 43 119-161 1-43 (43)
4 PF02150 RNA_POL_M_15KD: RNA p 78.8 0.73 1.6E-05 31.9 0.3 20 119-139 3-26 (35)
5 PLN03158 methionine aminopepti 69.2 2.1 4.6E-05 43.0 1.0 27 117-148 9-40 (396)
6 PF10977 DUF2797: Protein of u 42.5 13 0.00027 35.5 1.2 43 116-159 10-52 (235)
7 PRK00564 hypA hydrogenase nick 39.6 13 0.00027 31.6 0.7 25 116-140 70-95 (117)
8 PLN02436 cellulose synthase A 38.1 28 0.00062 39.9 3.2 44 116-159 35-100 (1094)
9 PF13975 gag-asp_proteas: gag- 36.2 41 0.0009 25.5 3.0 28 237-265 6-33 (72)
10 PHA00626 hypothetical protein 33.0 21 0.00045 28.2 0.9 26 118-148 1-27 (59)
11 PRK03824 hypA hydrogenase nick 32.0 20 0.00044 31.0 0.8 24 117-140 70-114 (135)
12 PRK12380 hydrogenase nickel in 30.8 22 0.00048 29.9 0.8 25 116-140 69-93 (113)
13 PLN02189 cellulose synthase 30.2 45 0.00097 38.3 3.2 44 116-159 33-98 (1040)
14 PRK11823 DNA repair protein Ra 29.3 22 0.00048 36.0 0.6 20 118-139 8-27 (446)
15 TIGR00416 sms DNA repair prote 27.3 25 0.00054 35.9 0.6 21 118-140 8-28 (454)
16 PF05294 Toxin_5: Scorpion sho 27.0 15 0.00033 26.0 -0.7 10 135-144 14-23 (32)
17 TIGR00100 hypA hydrogenase nic 26.4 30 0.00064 29.2 0.8 24 117-140 70-93 (115)
18 PF10419 TFIIIC_sub6: TFIIIC s 25.6 51 0.0011 23.1 1.7 15 243-257 12-26 (35)
19 PLN02400 cellulose synthase 24.7 52 0.0011 37.9 2.5 24 116-139 35-69 (1085)
20 cd01121 Sms Sms (bacterial rad 22.9 35 0.00075 34.1 0.6 21 119-141 2-22 (372)
21 PF01155 HypA: Hydrogenase exp 22.8 22 0.00048 29.7 -0.6 24 117-140 70-93 (113)
22 PRK03681 hypA hydrogenase nick 22.6 38 0.00082 28.6 0.7 25 116-140 69-94 (114)
23 PLN02638 cellulose synthase A 22.4 47 0.001 38.2 1.6 40 117-159 17-81 (1079)
24 PF09272 Hepsin-SRCR: Hepsin, 22.3 29 0.00063 30.3 -0.0 10 117-126 98-107 (110)
25 PRK00398 rpoP DNA-directed RNA 22.3 41 0.0009 23.8 0.8 21 119-139 5-27 (46)
26 TIGR01384 TFS_arch transcripti 20.6 46 0.00099 26.8 0.8 22 119-140 2-23 (104)
27 COG5082 AIR1 Arginine methyltr 20.2 41 0.00089 31.7 0.5 23 117-139 60-84 (190)
28 PLN02915 cellulose synthase A 20.0 57 0.0012 37.5 1.6 40 117-159 15-79 (1044)
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=1.8e-82 Score=554.34 Aligned_cols=149 Identities=66% Similarity=1.116 Sum_probs=129.5
Q ss_pred CCCCcccccccccccccCCCccccccccCCCCccCCCccceeeecchhhHHHHHHHHHHHhhh--hcCCCCCCCCCCC-C
Q 019213 114 IGGGMSCQDCGNQAKKDCAHMRCRTCCKSRGFDCQTHVKSTWVAASKRREKQQQLALQQQRLQ--LRGETNKRPREAN-P 190 (344)
Q Consensus 114 ~~gg~~CQDCGNQAKKDC~h~RCRTCCKSRGFdC~THVKSTWVPAarRRERqq~~~~~~~~~~--~~g~~~Kr~r~~~-~ 190 (344)
++|+++||||||||||||+|||||||||||||||+||||||||||+|||||||++++++++++ .....+||||++. .
T Consensus 1 ~~gg~~CqdCGNqAkk~C~~~rCRtCCk~rg~~C~tHvksTWVPA~~rRer~~~~~~~~~~~~~~~~~~~~kr~r~~~~~ 80 (154)
T PF05142_consen 1 GSGGISCQDCGNQAKKDCSHRRCRTCCKSRGFDCPTHVKSTWVPAARRRERQQQLAAAQQQQQGSQGSSGPKRPRELSNS 80 (154)
T ss_pred CCCCcchhhhcchhhcCCCcchhhhhhccCCCCCccceeccccchhhhchhhhcccccccccccCcccCCcCCccccccc
Confidence 357899999999999999999999999999999999999999999999999999988765442 2455699999863 3
Q ss_pred CCCcccccCCCCC--CCcchhhccCCccccccceeeEEEeeccCCCccceeEEEEEeecceeeeeeecccCCCCC
Q 019213 191 ISSSLACSRLPAN--ASGFEVAENLPGEVSTQAVFRCVKVSGIDDSEDQFAYQTSVNIGGHLFKGILYDQGPEST 263 (344)
Q Consensus 191 ~~ss~~~t~~~~t--sSg~e~~e~fP~eV~s~AvFRCVRVssvdd~e~E~AYQt~V~IgGHVFKGiLYDqG~e~~ 263 (344)
..+++++|+++++ +++++.. +||+|||||||||||||++|||+||||||||+|+||||||||||||||||+.
T Consensus 81 ~~~~~~~t~~~~~~~~~~~~~~-~fP~eV~spAvFRCVRVssiDdgedE~AYQTaV~IGGHVFKGiLYDqG~~~~ 154 (154)
T PF05142_consen 81 TQSSTSCTSTSNGTSPSSLETG-SFPAEVSSPAVFRCVRVSSIDDGEDEYAYQTAVNIGGHVFKGILYDQGPESQ 154 (154)
T ss_pred CCCCccccccCCCcccccchhc-cCChhhcccceEEEEEEecccCcccceeeEEeEEECCEEeeeeeeccCCCCC
Confidence 4445555554443 4477766 8999999999999999999999999999999999999999999999999863
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=1.2e-34 Score=213.75 Aligned_cols=49 Identities=61% Similarity=1.121 Sum_probs=47.9
Q ss_pred cCCccccccceeeEEEeeccCCCcc-ceeEEEEEeecceeeeeeecccCC
Q 019213 212 NLPGEVSTQAVFRCVKVSGIDDSED-QFAYQTSVNIGGHLFKGILYDQGP 260 (344)
Q Consensus 212 ~fP~eV~s~AvFRCVRVssvdd~e~-E~AYQt~V~IgGHVFKGiLYDqG~ 260 (344)
+||+||++|||||||||++|||+|+ ||||||+|+|||||||||||||||
T Consensus 1 ~fP~ev~s~AvFrcvRvs~idd~~~~e~aYQt~V~IgGHvFkGiLyDqG~ 50 (50)
T TIGR01624 1 GFPGEVSAPAVFKCVRVTAIDDGEQAEYAYQATVTIGGHVFKGFLHDQGL 50 (50)
T ss_pred CCccccccceEEEEEEEeccCCCCCceEEEEEEEEECceEEeeEEeccCC
Confidence 4999999999999999999999999 999999999999999999999997
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=99.96 E-value=3.2e-31 Score=190.76 Aligned_cols=43 Identities=74% Similarity=1.478 Sum_probs=42.1
Q ss_pred ccccccccccccCCCccccccccCCCCccCCCccceeeecchh
Q 019213 119 SCQDCGNQAKKDCAHMRCRTCCKSRGFDCQTHVKSTWVAASKR 161 (344)
Q Consensus 119 ~CQDCGNQAKKDC~h~RCRTCCKSRGFdC~THVKSTWVPAarR 161 (344)
+||||||||||+|.|+|||||||+|+|||+||||||||||+||
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 5999999999999999999999999999999999999999997
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=78.83 E-value=0.73 Score=31.92 Aligned_cols=20 Identities=45% Similarity=1.032 Sum_probs=13.6
Q ss_pred ccccccc--c--ccccCCCcccccc
Q 019213 119 SCQDCGN--Q--AKKDCAHMRCRTC 139 (344)
Q Consensus 119 ~CQDCGN--Q--AKKDC~h~RCRTC 139 (344)
-|.+||| . ..|+-.. +||||
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 5899999 3 3344444 69998
No 5
>PLN03158 methionine aminopeptidase; Provisional
Probab=69.24 E-value=2.1 Score=43.02 Aligned_cols=27 Identities=22% Similarity=0.701 Sum_probs=21.9
Q ss_pred CcccccccccccccCCCccccccccC-----CCCccC
Q 019213 117 GMSCQDCGNQAKKDCAHMRCRTCCKS-----RGFDCQ 148 (344)
Q Consensus 117 g~~CQDCGNQAKKDC~h~RCRTCCKS-----RGFdC~ 148 (344)
-..|.+||++|+ +.|-+|.|. +.|.|.
T Consensus 9 ~~~c~~c~~~a~-----l~Cp~C~k~~~~~~~s~fCs 40 (396)
T PLN03158 9 PLACARCSKPAH-----LQCPKCLELKLPREGASFCS 40 (396)
T ss_pred cccccCCCCccc-----ccCccchhcCCCCCCceeEC
Confidence 447999999886 889999994 478885
No 6
>PF10977 DUF2797: Protein of unknown function (DUF2797); InterPro: IPR021246 This family of proteins has no known function.
Probab=42.47 E-value=13 Score=35.47 Aligned_cols=43 Identities=21% Similarity=0.529 Sum_probs=36.1
Q ss_pred CCcccccccccccccCCCccccccccCCCCccCCCccceeeecc
Q 019213 116 GGMSCQDCGNQAKKDCAHMRCRTCCKSRGFDCQTHVKSTWVAAS 159 (344)
Q Consensus 116 gg~~CQDCGNQAKKDC~h~RCRTCCKSRGFdC~THVKSTWVPAa 159 (344)
|.+.|-.||..-||-=...+|--|-+. .-.|..|+.+.|.-..
T Consensus 10 g~i~c~~cG~~~~~s~~qg~C~~C~~~-~aqC~~Ci~~pe~c~~ 52 (235)
T PF10977_consen 10 GEIQCLNCGRKTKKSFRQGYCYPCFQT-LAQCDECIMRPELCHY 52 (235)
T ss_pred CcEEEecCCccccccCCCCceeCCCCc-CccChhHhCCcchhhe
Confidence 366999999999999999999887765 5599999999995533
No 7
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.65 E-value=13 Score=31.55 Aligned_cols=25 Identities=24% Similarity=0.606 Sum_probs=19.0
Q ss_pred CCcccccccccccccC-CCccccccc
Q 019213 116 GGMSCQDCGNQAKKDC-AHMRCRTCC 140 (344)
Q Consensus 116 gg~~CQDCGNQAKKDC-~h~RCRTCC 140 (344)
.-..|.|||+.-..+- .+.||..|-
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cg 95 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCH 95 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCC
Confidence 3569999999877765 466799884
No 8
>PLN02436 cellulose synthase A
Probab=38.10 E-value=28 Score=39.95 Aligned_cols=44 Identities=36% Similarity=0.749 Sum_probs=32.1
Q ss_pred CCccccccccc-----------ccccCCCcccccccc-------CCCCccCCCcc----ceeeecc
Q 019213 116 GGMSCQDCGNQ-----------AKKDCAHMRCRTCCK-------SRGFDCQTHVK----STWVAAS 159 (344)
Q Consensus 116 gg~~CQDCGNQ-----------AKKDC~h~RCRTCCK-------SRGFdC~THVK----STWVPAa 159 (344)
++-.||=||-. |=-+|.+--||.|-- ..=-+|-|+-| |-||+..
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r~kgs~~~~~d 100 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYKRIKGSPRVEGD 100 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhccCCCCcCCc
Confidence 34599999987 455799999999930 01124889888 8888874
No 9
>PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease
Probab=36.15 E-value=41 Score=25.53 Aligned_cols=28 Identities=29% Similarity=0.376 Sum_probs=23.7
Q ss_pred ceeEEEEEeecceeeeeeecccCCCCCCC
Q 019213 237 QFAYQTSVNIGGHLFKGILYDQGPESTYT 265 (344)
Q Consensus 237 E~AYQt~V~IgGHVFKGiLYDqG~e~~~~ 265 (344)
+=.+...|.|+||.++ .|-|-|....|.
T Consensus 6 ~g~~~v~~~I~g~~~~-alvDtGat~~fi 33 (72)
T PF13975_consen 6 PGLMYVPVSIGGVQVK-ALVDTGATHNFI 33 (72)
T ss_pred CCEEEEEEEECCEEEE-EEEeCCCcceec
Confidence 3457789999999999 899999987765
No 10
>PHA00626 hypothetical protein
Probab=33.04 E-value=21 Score=28.23 Aligned_cols=26 Identities=31% Similarity=0.604 Sum_probs=17.5
Q ss_pred cccccccccccccCCCcccccccc-CCCCccC
Q 019213 118 MSCQDCGNQAKKDCAHMRCRTCCK-SRGFDCQ 148 (344)
Q Consensus 118 ~~CQDCGNQAKKDC~h~RCRTCCK-SRGFdC~ 148 (344)
+.|.+||.. .+.||-+|.+ |--|.|.
T Consensus 1 m~CP~CGS~-----~Ivrcg~cr~~snrYkCk 27 (59)
T PHA00626 1 MSCPKCGSG-----NIAKEKTMRGWSDDYVCC 27 (59)
T ss_pred CCCCCCCCc-----eeeeeceecccCcceEcC
Confidence 468888872 1346778877 6667775
No 11
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.00 E-value=20 Score=31.02 Aligned_cols=24 Identities=29% Similarity=0.833 Sum_probs=19.1
Q ss_pred Cccccccccccccc---------------------CCCccccccc
Q 019213 117 GMSCQDCGNQAKKD---------------------CAHMRCRTCC 140 (344)
Q Consensus 117 g~~CQDCGNQAKKD---------------------C~h~RCRTCC 140 (344)
-..|.|||..-..+ -.+.+|..|-
T Consensus 70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cg 114 (135)
T PRK03824 70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCG 114 (135)
T ss_pred EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCC
Confidence 45999999877665 6778898884
No 12
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.81 E-value=22 Score=29.92 Aligned_cols=25 Identities=20% Similarity=0.510 Sum_probs=19.3
Q ss_pred CCcccccccccccccCCCccccccc
Q 019213 116 GGMSCQDCGNQAKKDCAHMRCRTCC 140 (344)
Q Consensus 116 gg~~CQDCGNQAKKDC~h~RCRTCC 140 (344)
.-..|.+||..-..+=.+.+|..|-
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cg 93 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQHDAQCPHCH 93 (113)
T ss_pred cEEEcccCCCEEecCCcCccCcCCC
Confidence 4569999998776665677798884
No 13
>PLN02189 cellulose synthase
Probab=30.19 E-value=45 Score=38.27 Aligned_cols=44 Identities=32% Similarity=0.705 Sum_probs=32.1
Q ss_pred CCccccccccc-----------ccccCCCccccccc-------cCCCCccCCCcc----ceeeecc
Q 019213 116 GGMSCQDCGNQ-----------AKKDCAHMRCRTCC-------KSRGFDCQTHVK----STWVAAS 159 (344)
Q Consensus 116 gg~~CQDCGNQ-----------AKKDC~h~RCRTCC-------KSRGFdC~THVK----STWVPAa 159 (344)
++-.||-||-. |-.+|.+--||.|- ...==+|-|+-| |-||+.+
T Consensus 33 ~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~r~kgs~~v~gd 98 (1040)
T PLN02189 33 DGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYKRLKGSPRVEGD 98 (1040)
T ss_pred cCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhccCCCCcCCc
Confidence 35599999987 34569999999993 011124899988 8888875
No 14
>PRK11823 DNA repair protein RadA; Provisional
Probab=29.30 E-value=22 Score=36.03 Aligned_cols=20 Identities=40% Similarity=0.916 Sum_probs=17.6
Q ss_pred cccccccccccccCCCcccccc
Q 019213 118 MSCQDCGNQAKKDCAHMRCRTC 139 (344)
Q Consensus 118 ~~CQDCGNQAKKDC~h~RCRTC 139 (344)
-.|+.||.+..|- +-||..|
T Consensus 8 y~C~~Cg~~~~~~--~g~Cp~C 27 (446)
T PRK11823 8 YVCQECGAESPKW--LGRCPEC 27 (446)
T ss_pred EECCcCCCCCccc--CeeCcCC
Confidence 4899999999884 7889999
No 15
>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=27.31 E-value=25 Score=35.89 Aligned_cols=21 Identities=33% Similarity=0.885 Sum_probs=18.0
Q ss_pred cccccccccccccCCCccccccc
Q 019213 118 MSCQDCGNQAKKDCAHMRCRTCC 140 (344)
Q Consensus 118 ~~CQDCGNQAKKDC~h~RCRTCC 140 (344)
-.||+||.+..| -+-||..|-
T Consensus 8 y~C~~Cg~~~~~--~~g~Cp~C~ 28 (454)
T TIGR00416 8 FVCQHCGADSPK--WQGKCPACH 28 (454)
T ss_pred EECCcCCCCCcc--ccEECcCCC
Confidence 489999999998 478899993
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=27.00 E-value=15 Score=25.97 Aligned_cols=10 Identities=60% Similarity=1.747 Sum_probs=8.4
Q ss_pred cccccccCCC
Q 019213 135 RCRTCCKSRG 144 (344)
Q Consensus 135 RCRTCCKSRG 144 (344)
.||.||.+||
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=26.42 E-value=30 Score=29.19 Aligned_cols=24 Identities=25% Similarity=0.768 Sum_probs=18.6
Q ss_pred CcccccccccccccCCCccccccc
Q 019213 117 GMSCQDCGNQAKKDCAHMRCRTCC 140 (344)
Q Consensus 117 g~~CQDCGNQAKKDC~h~RCRTCC 140 (344)
-..|.|||+.-..+=.+.+|..|-
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cg 93 (115)
T TIGR00100 70 ECECEDCSEEVSPEIDLYRCPKCH 93 (115)
T ss_pred EEEcccCCCEEecCCcCccCcCCc
Confidence 569999999777655677788873
No 18
>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=25.61 E-value=51 Score=23.13 Aligned_cols=15 Identities=33% Similarity=0.625 Sum_probs=12.1
Q ss_pred EEeecceeeeeeecc
Q 019213 243 SVNIGGHLFKGILYD 257 (344)
Q Consensus 243 ~V~IgGHVFKGiLYD 257 (344)
.|+||++||+|---|
T Consensus 12 il~i~~~vf~G~~~~ 26 (35)
T PF10419_consen 12 ILQIGNQVFEGEWED 26 (35)
T ss_pred EEEECCEEEEEEEhh
Confidence 589999999997543
No 19
>PLN02400 cellulose synthase
Probab=24.70 E-value=52 Score=37.94 Aligned_cols=24 Identities=46% Similarity=1.056 Sum_probs=20.7
Q ss_pred CCccccccccc-----------ccccCCCcccccc
Q 019213 116 GGMSCQDCGNQ-----------AKKDCAHMRCRTC 139 (344)
Q Consensus 116 gg~~CQDCGNQ-----------AKKDC~h~RCRTC 139 (344)
.+-.||=||-. |=-+|.+--||.|
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpC 69 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPC 69 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccch
Confidence 35599999987 6678999999999
No 20
>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=22.93 E-value=35 Score=34.10 Aligned_cols=21 Identities=29% Similarity=0.749 Sum_probs=17.6
Q ss_pred ccccccccccccCCCcccccccc
Q 019213 119 SCQDCGNQAKKDCAHMRCRTCCK 141 (344)
Q Consensus 119 ~CQDCGNQAKKDC~h~RCRTCCK 141 (344)
.||+||.+..| -+-||..|-.
T Consensus 2 ~c~~cg~~~~~--~~g~cp~c~~ 22 (372)
T cd01121 2 VCSECGYVSPK--WLGKCPECGE 22 (372)
T ss_pred CCCCCCCCCCC--ccEECcCCCC
Confidence 69999999888 4788999944
No 21
>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=22.80 E-value=22 Score=29.74 Aligned_cols=24 Identities=29% Similarity=0.780 Sum_probs=17.4
Q ss_pred CcccccccccccccCCCccccccc
Q 019213 117 GMSCQDCGNQAKKDCAHMRCRTCC 140 (344)
Q Consensus 117 g~~CQDCGNQAKKDC~h~RCRTCC 140 (344)
-..|.+||..-.-+=.+.+|..|-
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~CP~Cg 93 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEFDFSCPRCG 93 (113)
T ss_dssp EEEETTTS-EEECHHCCHH-SSSS
T ss_pred cEECCCCCCEEecCCCCCCCcCCc
Confidence 559999999887777778888874
No 22
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=22.56 E-value=38 Score=28.59 Aligned_cols=25 Identities=20% Similarity=0.446 Sum_probs=18.1
Q ss_pred CCcccccccccccccCC-Cccccccc
Q 019213 116 GGMSCQDCGNQAKKDCA-HMRCRTCC 140 (344)
Q Consensus 116 gg~~CQDCGNQAKKDC~-h~RCRTCC 140 (344)
+-..|.|||+....+=. +.+|..|-
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cg 94 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCH 94 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcC
Confidence 45699999987766433 37788884
No 23
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=22.37 E-value=47 Score=38.23 Aligned_cols=40 Identities=38% Similarity=0.740 Sum_probs=32.7
Q ss_pred Cccccccccc-----------ccccCCCcccccc----------ccCCCCccCCCcc----ceeeecc
Q 019213 117 GMSCQDCGNQ-----------AKKDCAHMRCRTC----------CKSRGFDCQTHVK----STWVAAS 159 (344)
Q Consensus 117 g~~CQDCGNQ-----------AKKDC~h~RCRTC----------CKSRGFdC~THVK----STWVPAa 159 (344)
+-.||-||-. |=.+|.+--||.| ||- +|-|+-| |-||+.+
T Consensus 17 ~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYEYEr~eG~q~CP---qCktrYkr~kgsprv~gD 81 (1079)
T PLN02638 17 GQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDGNQSCP---QCKTKYKRHKGSPAILGD 81 (1079)
T ss_pred CceeeecccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCC---ccCCchhhhcCCCCcCcc
Confidence 4599999987 6678999999999 333 4999988 8888875
No 24
>PF09272 Hepsin-SRCR: Hepsin, SRCR; InterPro: IPR015352 This entry represents the extracellular domain of the serine protease hepsin. The domain is formed primarily by three elements of regular secondary structure: a 12-residue alpha helix, a twisted five-stranded antiparallel beta sheet, and a second, two-stranded, antiparallel sheet. The two beta-sheets lie at roughly right angles to each other, with the helix nestled between the two, adopting an SRCR fold. The exact function of this domain has not been identified, though it probably may serve to orient the protease domain or place it in the vicinity of its substrate []. ; GO: 0004252 serine-type endopeptidase activity, 0070008 serine-type exopeptidase activity; PDB: 3T2N_B 1Z8G_A 1P57_A 1O5E_L 1O5F_L.
Probab=22.29 E-value=29 Score=30.33 Aligned_cols=10 Identities=50% Similarity=1.228 Sum_probs=3.8
Q ss_pred Cccccccccc
Q 019213 117 GMSCQDCGNQ 126 (344)
Q Consensus 117 g~~CQDCGNQ 126 (344)
...|||||.+
T Consensus 98 at~CQDCGRR 107 (110)
T PF09272_consen 98 ATICQDCGRR 107 (110)
T ss_dssp EEEE---S--
T ss_pred ehhhhhhCcc
Confidence 4589999964
No 25
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=22.29 E-value=41 Score=23.80 Aligned_cols=21 Identities=33% Similarity=0.873 Sum_probs=11.8
Q ss_pred ccccccccccccCC--Ccccccc
Q 019213 119 SCQDCGNQAKKDCA--HMRCRTC 139 (344)
Q Consensus 119 ~CQDCGNQAKKDC~--h~RCRTC 139 (344)
.|.+||.+...|=. -.+|..|
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~C 27 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPYC 27 (46)
T ss_pred ECCCCCCEEEECCCCCceECCCC
Confidence 57777776533322 3566666
No 26
>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=20.59 E-value=46 Score=26.80 Aligned_cols=22 Identities=23% Similarity=0.634 Sum_probs=16.8
Q ss_pred ccccccccccccCCCccccccc
Q 019213 119 SCQDCGNQAKKDCAHMRCRTCC 140 (344)
Q Consensus 119 ~CQDCGNQAKKDC~h~RCRTCC 140 (344)
.|.+|||--.+.=..+.|++|-
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~ 23 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCG 23 (104)
T ss_pred CCcccCcccccCCCeEECcCCC
Confidence 6999999665544588899984
No 27
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=20.22 E-value=41 Score=31.66 Aligned_cols=23 Identities=35% Similarity=1.045 Sum_probs=20.2
Q ss_pred Cccccccccc--ccccCCCcccccc
Q 019213 117 GMSCQDCGNQ--AKKDCAHMRCRTC 139 (344)
Q Consensus 117 g~~CQDCGNQ--AKKDC~h~RCRTC 139 (344)
...|+-||++ -++||+|.-|-+|
T Consensus 60 ~~~C~nCg~~GH~~~DCP~~iC~~C 84 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCPHSICYNC 84 (190)
T ss_pred ccccchhcccCcccccCChhHhhhc
Confidence 5699999995 7899999888887
No 28
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=20.01 E-value=57 Score=37.49 Aligned_cols=40 Identities=28% Similarity=0.681 Sum_probs=31.8
Q ss_pred Cccccccccc-----------ccccCCCccccccc----------cCCCCccCCCcc----ceeeecc
Q 019213 117 GMSCQDCGNQ-----------AKKDCAHMRCRTCC----------KSRGFDCQTHVK----STWVAAS 159 (344)
Q Consensus 117 g~~CQDCGNQ-----------AKKDC~h~RCRTCC----------KSRGFdC~THVK----STWVPAa 159 (344)
+-.||-||-. |=.+|.+--||.|- |- +|-||-| |-||..+
T Consensus 15 ~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp---~c~t~y~~~~~~~~~~~d 79 (1044)
T PLN02915 15 AKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCP---QCNTRYKRHKGCPRVEGD 79 (1044)
T ss_pred cchhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCC---ccCCchhhhcCCCCccCC
Confidence 5589999987 66789999999993 32 4889888 7788775
Done!