Query 040293
Match_columns 327
No_of_seqs 82 out of 101
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 06:58:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040293.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040293hhsearch_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 7.7E-78 1.7E-82 522.8 5.9 131 108-260 2-153 (154)
2 TIGR01624 LRP1_Cterm LRP1 C-te 100.0 8.4E-33 1.8E-37 202.8 5.3 47 212-258 1-50 (50)
3 TIGR01623 put_zinc_LRP1 putati 100.0 5.7E-32 1.2E-36 193.5 0.8 43 112-154 1-43 (43)
4 PF02150 RNA_POL_M_15KD: RNA p 79.2 0.67 1.5E-05 31.9 0.2 20 112-132 3-26 (35)
5 PLN03158 methionine aminopepti 71.6 1.8 4E-05 43.2 1.1 35 109-148 8-48 (396)
6 PF10977 DUF2797: Protein of u 43.0 13 0.00027 35.3 1.3 42 109-151 10-51 (235)
7 PRK00564 hypA hydrogenase nick 38.9 14 0.0003 31.1 0.8 25 109-133 70-95 (117)
8 PF13975 gag-asp_proteas: gag- 34.2 51 0.0011 24.9 3.2 28 235-263 6-33 (72)
9 PF10419 TFIIIC_sub6: TFIIIC s 30.1 37 0.00081 23.6 1.7 14 241-254 12-25 (35)
10 PRK03824 hypA hydrogenase nick 29.9 24 0.00053 30.4 0.9 25 109-133 69-114 (135)
11 PHA00626 hypothetical protein 28.8 28 0.00061 27.3 1.0 26 111-141 1-27 (59)
12 PRK11823 DNA repair protein Ra 28.6 24 0.00051 35.7 0.7 20 111-132 8-27 (446)
13 PRK12380 hydrogenase nickel in 28.5 27 0.00059 29.2 0.9 25 109-133 69-93 (113)
14 PF05294 Toxin_5: Scorpion sho 27.1 15 0.00033 25.8 -0.7 10 128-137 14-23 (32)
15 PLN02189 cellulose synthase 26.9 60 0.0013 37.1 3.4 45 108-152 32-98 (1040)
16 TIGR00416 sms DNA repair prote 26.0 27 0.00059 35.4 0.6 21 111-133 8-28 (454)
17 TIGR00100 hypA hydrogenase nic 24.8 35 0.00076 28.6 0.9 24 109-132 69-92 (115)
18 PLN02436 cellulose synthase A 23.6 76 0.0016 36.5 3.4 45 108-152 34-100 (1094)
19 PF04658 TAFII55_N: TAFII55 pr 23.3 58 0.0013 29.2 2.1 18 240-257 43-60 (162)
20 PF09272 Hepsin-SRCR: Hepsin, 22.8 28 0.0006 30.3 -0.0 10 110-119 98-107 (110)
21 PLN02638 cellulose synthase A 22.6 48 0.001 38.0 1.7 41 109-152 16-81 (1079)
22 cd01121 Sms Sms (bacterial rad 22.2 37 0.00081 33.7 0.7 21 112-134 2-22 (372)
23 COG3357 Predicted transcriptio 21.0 45 0.00098 28.4 0.8 29 111-151 59-89 (97)
24 PLN02915 cellulose synthase A 21.0 55 0.0012 37.4 1.7 41 109-152 14-79 (1044)
25 COG5082 AIR1 Arginine methyltr 20.9 39 0.00086 31.6 0.6 23 110-132 60-84 (190)
26 PRK03681 hypA hydrogenase nick 20.5 46 0.001 27.9 0.8 25 109-133 69-94 (114)
27 PRK04023 DNA polymerase II lar 20.3 62 0.0013 37.2 2.0 29 109-137 625-662 (1121)
28 PRK00398 rpoP DNA-directed RNA 20.1 49 0.0011 23.3 0.8 21 112-132 5-27 (46)
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=7.7e-78 Score=522.83 Aligned_cols=131 Identities=73% Similarity=1.269 Sum_probs=111.0
Q ss_pred CCCcccccccccccccCCCccccccccCCCccccCcccceeecchhhhHHHHHHHHHHhhhHHHHHHhhhcccccCCCCC
Q 040293 108 GGGMNCQDCGNQAKKDCPHMRCRTCCKSRGFQCQTHVKSTWVPAAKRRERQQQLAALQRHQQQQEQQQLNQQDSQHHHHH 187 (327)
Q Consensus 108 ~gg~~CQDCGNQAKKDC~h~RCRTCCKSRGFdC~THVKSTWVPAarRRERqq~~~a~~~~~~~~~~~~~~~~~~~~~~~~ 187 (327)
+|+++||||||||||||+|||||||||||||||+||||||||||+||||||+++++++..++....
T Consensus 2 ~gg~~CqdCGNqAkk~C~~~rCRtCCk~rg~~C~tHvksTWVPA~~rRer~~~~~~~~~~~~~~~~-------------- 67 (154)
T PF05142_consen 2 SGGISCQDCGNQAKKDCSHRRCRTCCKSRGFDCPTHVKSTWVPAARRRERQQQLAAAQQQQQGSQG-------------- 67 (154)
T ss_pred CCCcchhhhcchhhcCCCcchhhhhhccCCCCCccceeccccchhhhchhhhcccccccccccCcc--------------
Confidence 578999999999999999999999999999999999999999999999999998876542211110
Q ss_pred ccccccccCCCCCCccc-------------------CCCccccCCCcccccceeeeeee--ccCCCCcceeEEeeeeecc
Q 040293 188 HHQQQQFRGENPKRQRE-------------------NQGLEVSQFPSELSSSAVFRCVR--AIDDPDEEFAYQTAVHIGG 246 (327)
Q Consensus 188 ~~~~~~~~~~~pkr~~~-------------------sSg~~~~~fP~eV~spAVFRCVR--siddge~E~AYQt~V~IgG 246 (327)
...+||+|+ ..+++.++||+|||||||||||| +|||+||||||||+|+|||
T Consensus 68 --------~~~~kr~r~~~~~~~~~~~~t~~~~~~~~~~~~~~~fP~eV~spAvFRCVRVssiDdgedE~AYQTaV~IGG 139 (154)
T PF05142_consen 68 --------SSGPKRPRELSNSTQSSTSCTSTSNGTSPSSLETGSFPAEVSSPAVFRCVRVSSIDDGEDEYAYQTAVNIGG 139 (154)
T ss_pred --------cCCcCCcccccccCCCCccccccCCCcccccchhccCChhhcccceEEEEEEecccCcccceeeEEeEEECC
Confidence 112222221 12566679999999999999999 9999999999999999999
Q ss_pred eeeeeeeeccCCCc
Q 040293 247 HVFKGILYDQGPEN 260 (327)
Q Consensus 247 HVFKGiLYDqG~e~ 260 (327)
|||||||||||||.
T Consensus 140 HVFKGiLYDqG~~~ 153 (154)
T PF05142_consen 140 HVFKGILYDQGPES 153 (154)
T ss_pred EEeeeeeeccCCCC
Confidence 99999999999986
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=99.97 E-value=8.4e-33 Score=202.79 Aligned_cols=47 Identities=66% Similarity=1.138 Sum_probs=45.9
Q ss_pred CCCcccccceeeeeee--ccCCCCc-ceeEEeeeeecceeeeeeeeccCC
Q 040293 212 QFPSELSSSAVFRCVR--AIDDPDE-EFAYQTAVHIGGHVFKGILYDQGP 258 (327)
Q Consensus 212 ~fP~eV~spAVFRCVR--siddge~-E~AYQt~V~IgGHVFKGiLYDqG~ 258 (327)
.||+||+||||||||| +|||+|+ ||||||+|+|||||||||||||||
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 5999999999999999 9999999 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=99.97 E-value=5.7e-32 Score=193.47 Aligned_cols=43 Identities=79% Similarity=1.533 Sum_probs=42.1
Q ss_pred ccccccccccccCCCccccccccCCCccccCcccceeecchhh
Q 040293 112 NCQDCGNQAKKDCPHMRCRTCCKSRGFQCQTHVKSTWVPAAKR 154 (327)
Q Consensus 112 ~CQDCGNQAKKDC~h~RCRTCCKSRGFdC~THVKSTWVPAarR 154 (327)
+|+||||||||+|.|+|||||||+|||||+||||||||||+||
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=79.20 E-value=0.67 Score=31.90 Aligned_cols=20 Identities=45% Similarity=1.076 Sum_probs=14.0
Q ss_pred ccccccc----cccccCCCcccccc
Q 040293 112 NCQDCGN----QAKKDCPHMRCRTC 132 (327)
Q Consensus 112 ~CQDCGN----QAKKDC~h~RCRTC 132 (327)
-|.+||| +..|+-.. +||||
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 34444444 69999
No 5
>PLN03158 methionine aminopeptidase; Provisional
Probab=71.60 E-value=1.8 Score=43.24 Aligned_cols=35 Identities=23% Similarity=0.720 Sum_probs=25.3
Q ss_pred CCcccccccccccccCCCccccccccC-----CCccccC-ccccee
Q 040293 109 GGMNCQDCGNQAKKDCPHMRCRTCCKS-----RGFQCQT-HVKSTW 148 (327)
Q Consensus 109 gg~~CQDCGNQAKKDC~h~RCRTCCKS-----RGFdC~T-HVKSTW 148 (327)
+-..|.+||++|+ +.|-+|.|. +.|.|.- =-|.-|
T Consensus 8 ~~~~c~~c~~~a~-----l~Cp~C~k~~~~~~~s~fCsq~CFk~~w 48 (396)
T PLN03158 8 SPLACARCSKPAH-----LQCPKCLELKLPREGASFCSQDCFKAAW 48 (396)
T ss_pred CcccccCCCCccc-----ccCccchhcCCCCCCceeECHHHHHHHH
Confidence 3557999999986 889999994 4788853 234444
No 6
>PF10977 DUF2797: Protein of unknown function (DUF2797); InterPro: IPR021246 This family of proteins has no known function.
Probab=42.99 E-value=13 Score=35.29 Aligned_cols=42 Identities=24% Similarity=0.543 Sum_probs=35.6
Q ss_pred CCcccccccccccccCCCccccccccCCCccccCcccceeecc
Q 040293 109 GGMNCQDCGNQAKKDCPHMRCRTCCKSRGFQCQTHVKSTWVPA 151 (327)
Q Consensus 109 gg~~CQDCGNQAKKDC~h~RCRTCCKSRGFdC~THVKSTWVPA 151 (327)
|.+.|-.||..-||-=...+|--|-+. .-+|..|+.+.|.-.
T Consensus 10 g~i~c~~cG~~~~~s~~qg~C~~C~~~-~aqC~~Ci~~pe~c~ 51 (235)
T PF10977_consen 10 GEIQCLNCGRKTKKSFRQGYCYPCFQT-LAQCDECIMRPELCH 51 (235)
T ss_pred CcEEEecCCccccccCCCCceeCCCCc-CccChhHhCCcchhh
Confidence 466899999999999999999888765 559999999999543
No 7
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=38.93 E-value=14 Score=31.14 Aligned_cols=25 Identities=24% Similarity=0.610 Sum_probs=19.1
Q ss_pred CCcccccccccccccC-CCccccccc
Q 040293 109 GGMNCQDCGNQAKKDC-PHMRCRTCC 133 (327)
Q Consensus 109 gg~~CQDCGNQAKKDC-~h~RCRTCC 133 (327)
.-..|.|||+.-..+- .+.||..|-
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cg 95 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCH 95 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCC
Confidence 3569999999877765 466799883
No 8
>PF13975 gag-asp_proteas: gag-polyprotein putative aspartyl protease
Probab=34.15 E-value=51 Score=24.88 Aligned_cols=28 Identities=29% Similarity=0.374 Sum_probs=23.4
Q ss_pred ceeEEeeeeecceeeeeeeeccCCCcccc
Q 040293 235 EFAYQTAVHIGGHVFKGILYDQGPENRYT 263 (327)
Q Consensus 235 E~AYQt~V~IgGHVFKGiLYDqG~e~~~~ 263 (327)
+=.+...|.|+||.++ .|=|-|....+.
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 3457889999999999 999999887654
No 9
>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=30.11 E-value=37 Score=23.63 Aligned_cols=14 Identities=36% Similarity=0.631 Sum_probs=11.6
Q ss_pred eeeecceeeeeeee
Q 040293 241 AVHIGGHVFKGILY 254 (327)
Q Consensus 241 ~V~IgGHVFKGiLY 254 (327)
.|+||++||+|---
T Consensus 12 il~i~~~vf~G~~~ 25 (35)
T PF10419_consen 12 ILQIGNQVFEGEWE 25 (35)
T ss_pred EEEECCEEEEEEEh
Confidence 58999999999643
No 10
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.86 E-value=24 Score=30.37 Aligned_cols=25 Identities=24% Similarity=0.788 Sum_probs=19.4
Q ss_pred CCccccccccccccc---------------------CCCccccccc
Q 040293 109 GGMNCQDCGNQAKKD---------------------CPHMRCRTCC 133 (327)
Q Consensus 109 gg~~CQDCGNQAKKD---------------------C~h~RCRTCC 133 (327)
.-..|.|||..-..+ -.+.+|..|-
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cg 114 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCG 114 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCC
Confidence 356999999877665 6778898884
No 11
>PHA00626 hypothetical protein
Probab=28.83 E-value=28 Score=27.35 Aligned_cols=26 Identities=27% Similarity=0.598 Sum_probs=17.4
Q ss_pred cccccccccccccCCCcccccccc-CCCcccc
Q 040293 111 MNCQDCGNQAKKDCPHMRCRTCCK-SRGFQCQ 141 (327)
Q Consensus 111 ~~CQDCGNQAKKDC~h~RCRTCCK-SRGFdC~ 141 (327)
+.|.+||.. .+.||-+|.+ |--|.|.
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 6667774
No 12
>PRK11823 DNA repair protein RadA; Provisional
Probab=28.55 E-value=24 Score=35.65 Aligned_cols=20 Identities=40% Similarity=0.896 Sum_probs=17.5
Q ss_pred cccccccccccccCCCcccccc
Q 040293 111 MNCQDCGNQAKKDCPHMRCRTC 132 (327)
Q Consensus 111 ~~CQDCGNQAKKDC~h~RCRTC 132 (327)
-.|+.||.+..|- +-||..|
T Consensus 8 y~C~~Cg~~~~~~--~g~Cp~C 27 (446)
T PRK11823 8 YVCQECGAESPKW--LGRCPEC 27 (446)
T ss_pred EECCcCCCCCccc--CeeCcCC
Confidence 4799999999884 7789999
No 13
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=28.53 E-value=27 Score=29.24 Aligned_cols=25 Identities=20% Similarity=0.502 Sum_probs=19.1
Q ss_pred CCcccccccccccccCCCccccccc
Q 040293 109 GGMNCQDCGNQAKKDCPHMRCRTCC 133 (327)
Q Consensus 109 gg~~CQDCGNQAKKDC~h~RCRTCC 133 (327)
+-..|.+||..-..+=.+.+|..|-
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cg 93 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQHDAQCPHCH 93 (113)
T ss_pred cEEEcccCCCEEecCCcCccCcCCC
Confidence 4569999998776665667788884
No 14
>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=27.07 E-value=15 Score=25.77 Aligned_cols=10 Identities=60% Similarity=1.747 Sum_probs=8.4
Q ss_pred cccccccCCC
Q 040293 128 RCRTCCKSRG 137 (327)
Q Consensus 128 RCRTCCKSRG 137 (327)
.||.||.+||
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 15
>PLN02189 cellulose synthase
Probab=26.88 E-value=60 Score=37.13 Aligned_cols=45 Identities=33% Similarity=0.636 Sum_probs=33.0
Q ss_pred CCCccccccccc-----------ccccCCCccccccc-------cCCCccccCccc----ceeecch
Q 040293 108 GGGMNCQDCGNQ-----------AKKDCPHMRCRTCC-------KSRGFQCQTHVK----STWVPAA 152 (327)
Q Consensus 108 ~gg~~CQDCGNQ-----------AKKDC~h~RCRTCC-------KSRGFdC~THVK----STWVPAa 152 (327)
.++-.||-||-. |=-+|.+--||.|- ...==+|-|+-| |-||+.+
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cyeyer~eg~q~CpqCkt~Y~r~kgs~~v~gd 98 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYEYERREGTQNCPQCKTRYKRLKGSPRVEGD 98 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhccCCCCcCCc
Confidence 456699999987 44569999999992 001124899988 8888875
No 16
>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=26.03 E-value=27 Score=35.44 Aligned_cols=21 Identities=33% Similarity=0.844 Sum_probs=17.9
Q ss_pred cccccccccccccCCCccccccc
Q 040293 111 MNCQDCGNQAKKDCPHMRCRTCC 133 (327)
Q Consensus 111 ~~CQDCGNQAKKDC~h~RCRTCC 133 (327)
-.|++||.+..| -+-||..|-
T Consensus 8 y~C~~Cg~~~~~--~~g~Cp~C~ 28 (454)
T TIGR00416 8 FVCQHCGADSPK--WQGKCPACH 28 (454)
T ss_pred EECCcCCCCCcc--ccEECcCCC
Confidence 479999999998 478899993
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=24.81 E-value=35 Score=28.60 Aligned_cols=24 Identities=25% Similarity=0.744 Sum_probs=18.5
Q ss_pred CCcccccccccccccCCCcccccc
Q 040293 109 GGMNCQDCGNQAKKDCPHMRCRTC 132 (327)
Q Consensus 109 gg~~CQDCGNQAKKDC~h~RCRTC 132 (327)
.-..|.+||+.-..+=.+.+|..|
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~C 92 (115)
T TIGR00100 69 VECECEDCSEEVSPEIDLYRCPKC 92 (115)
T ss_pred cEEEcccCCCEEecCCcCccCcCC
Confidence 356999999977765557778887
No 18
>PLN02436 cellulose synthase A
Probab=23.61 E-value=76 Score=36.55 Aligned_cols=45 Identities=36% Similarity=0.681 Sum_probs=32.8
Q ss_pred CCCccccccccc-----------ccccCCCcccccccc-------CCCccccCccc----ceeecch
Q 040293 108 GGGMNCQDCGNQ-----------AKKDCPHMRCRTCCK-------SRGFQCQTHVK----STWVPAA 152 (327)
Q Consensus 108 ~gg~~CQDCGNQ-----------AKKDC~h~RCRTCCK-------SRGFdC~THVK----STWVPAa 152 (327)
..+-.||=||-. |=-+|.+--||.|-- ..==+|-|+-| |-||+..
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cyeyer~eg~~~Cpqckt~Y~r~kgs~~~~~d 100 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYEYERREGNQACPQCKTRYKRIKGSPRVEGD 100 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchhhhhhhcCCccCcccCCchhhccCCCCcCCc
Confidence 456699999987 455799999999930 01124889888 7888875
No 19
>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=23.31 E-value=58 Score=29.23 Aligned_cols=18 Identities=33% Similarity=0.634 Sum_probs=17.0
Q ss_pred eeeeecceeeeeeeeccC
Q 040293 240 TAVHIGGHVFKGILYDQG 257 (327)
Q Consensus 240 t~V~IgGHVFKGiLYDqG 257 (327)
++|+|+|.+|.|.|.|.=
T Consensus 43 ~~v~i~~~~y~a~LvDLP 60 (162)
T PF04658_consen 43 AVVRIGGQIYSAKLVDLP 60 (162)
T ss_pred EEEEECCEEcceEEeecC
Confidence 899999999999999985
No 20
>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=22.80 E-value=28 Score=30.26 Aligned_cols=10 Identities=50% Similarity=1.195 Sum_probs=3.7
Q ss_pred Cccccccccc
Q 040293 110 GMNCQDCGNQ 119 (327)
Q Consensus 110 g~~CQDCGNQ 119 (327)
...|||||.+
T Consensus 98 at~CQDCGRR 107 (110)
T PF09272_consen 98 ATICQDCGRR 107 (110)
T ss_dssp EEEE---S--
T ss_pred ehhhhhhCcc
Confidence 3589999964
No 21
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=22.60 E-value=48 Score=37.99 Aligned_cols=41 Identities=39% Similarity=0.748 Sum_probs=33.1
Q ss_pred CCccccccccc-----------ccccCCCcccccc----------ccCCCccccCccc----ceeecch
Q 040293 109 GGMNCQDCGNQ-----------AKKDCPHMRCRTC----------CKSRGFQCQTHVK----STWVPAA 152 (327)
Q Consensus 109 gg~~CQDCGNQ-----------AKKDC~h~RCRTC----------CKSRGFdC~THVK----STWVPAa 152 (327)
.+-.||=||-. |=-+|.+--||.| ||- +|-|+-| |-||+.+
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 35699999987 6678999999999 333 4999988 8888885
No 22
>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=22.23 E-value=37 Score=33.70 Aligned_cols=21 Identities=29% Similarity=0.708 Sum_probs=17.5
Q ss_pred ccccccccccccCCCcccccccc
Q 040293 112 NCQDCGNQAKKDCPHMRCRTCCK 134 (327)
Q Consensus 112 ~CQDCGNQAKKDC~h~RCRTCCK 134 (327)
.||+||.+..| -+-||..|-.
T Consensus 2 ~c~~cg~~~~~--~~g~cp~c~~ 22 (372)
T cd01121 2 VCSECGYVSPK--WLGKCPECGE 22 (372)
T ss_pred CCCCCCCCCCC--ccEECcCCCC
Confidence 69999999888 4778999944
No 23
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=20.98 E-value=45 Score=28.44 Aligned_cols=29 Identities=34% Similarity=0.902 Sum_probs=21.0
Q ss_pred cccccccccccccC--CCccccccccCCCccccCcccceeecc
Q 040293 111 MNCQDCGNQAKKDC--PHMRCRTCCKSRGFQCQTHVKSTWVPA 151 (327)
Q Consensus 111 ~~CQDCGNQAKKDC--~h~RCRTCCKSRGFdC~THVKSTWVPA 151 (327)
..|.+||---+.|= .-.||.-| ||-||--
T Consensus 59 a~CkkCGfef~~~~ik~pSRCP~C------------KSE~Ie~ 89 (97)
T COG3357 59 ARCKKCGFEFRDDKIKKPSRCPKC------------KSEWIEE 89 (97)
T ss_pred hhhcccCccccccccCCcccCCcc------------hhhcccC
Confidence 38999997554432 35899988 8888844
No 24
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=20.96 E-value=55 Score=37.42 Aligned_cols=41 Identities=29% Similarity=0.644 Sum_probs=31.9
Q ss_pred CCccccccccc-----------ccccCCCccccccc----------cCCCccccCccc----ceeecch
Q 040293 109 GGMNCQDCGNQ-----------AKKDCPHMRCRTCC----------KSRGFQCQTHVK----STWVPAA 152 (327)
Q Consensus 109 gg~~CQDCGNQ-----------AKKDC~h~RCRTCC----------KSRGFdC~THVK----STWVPAa 152 (327)
++-.||-||-. |=-+|.+--||.|- |- +|-||-| |-||+.+
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cyeye~~~g~~~cp---~c~t~y~~~~~~~~~~~d 79 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERSEGNQCCP---QCNTRYKRHKGCPRVEGD 79 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCccccchhhhhhhcCCccCC---ccCCchhhhcCCCCccCC
Confidence 35689999987 66789999999992 22 4888888 7777775
No 25
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=20.94 E-value=39 Score=31.60 Aligned_cols=23 Identities=39% Similarity=1.133 Sum_probs=20.0
Q ss_pred Cccccccccc--ccccCCCcccccc
Q 040293 110 GMNCQDCGNQ--AKKDCPHMRCRTC 132 (327)
Q Consensus 110 g~~CQDCGNQ--AKKDC~h~RCRTC 132 (327)
...|+-||++ -++||+|.-|-+|
T Consensus 60 ~~~C~nCg~~GH~~~DCP~~iC~~C 84 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCPHSICYNC 84 (190)
T ss_pred ccccchhcccCcccccCChhHhhhc
Confidence 5699999995 7899999888777
No 26
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=20.54 E-value=46 Score=27.91 Aligned_cols=25 Identities=20% Similarity=0.442 Sum_probs=17.9
Q ss_pred CCcccccccccccccCC-Cccccccc
Q 040293 109 GGMNCQDCGNQAKKDCP-HMRCRTCC 133 (327)
Q Consensus 109 gg~~CQDCGNQAKKDC~-h~RCRTCC 133 (327)
+-..|.|||+....+=. +.+|..|-
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cg 94 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCH 94 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcC
Confidence 45699999987766433 36788884
No 27
>PRK04023 DNA polymerase II large subunit; Validated
Probab=20.29 E-value=62 Score=37.20 Aligned_cols=29 Identities=31% Similarity=0.826 Sum_probs=18.5
Q ss_pred CCccccccccc-ccccCC--------CccccccccCCC
Q 040293 109 GGMNCQDCGNQ-AKKDCP--------HMRCRTCCKSRG 137 (327)
Q Consensus 109 gg~~CQDCGNQ-AKKDC~--------h~RCRTCCKSRG 137 (327)
+...|.+||.. .++-|+ ..||..|++.-+
T Consensus 625 g~RfCpsCG~~t~~frCP~CG~~Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 625 GRRKCPSCGKETFYRRCPFCGTHTEPVYRCPRCGIEVE 662 (1121)
T ss_pred cCccCCCCCCcCCcccCCCCCCCCCcceeCccccCcCC
Confidence 34578888875 555565 457777766554
No 28
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=20.11 E-value=49 Score=23.30 Aligned_cols=21 Identities=33% Similarity=0.869 Sum_probs=11.4
Q ss_pred ccccccccccccCC--Ccccccc
Q 040293 112 NCQDCGNQAKKDCP--HMRCRTC 132 (327)
Q Consensus 112 ~CQDCGNQAKKDC~--h~RCRTC 132 (327)
.|.+||.+..-|=. -.+|..|
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~C 27 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPYC 27 (46)
T ss_pred ECCCCCCEEEECCCCCceECCCC
Confidence 57777776533211 3566666
Done!