Query 032675
Match_columns 136
No_of_seqs 114 out of 216
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 04:30:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032675.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032675hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03998 Utp11: Utp11 protein; 100.0 5.5E-51 1.2E-55 332.8 9.8 113 10-122 1-115 (243)
2 KOG3237 Uncharacterized conser 100.0 4.1E-51 8.8E-56 336.5 8.2 126 1-126 1-128 (250)
3 COG5223 Uncharacterized conser 100.0 5.4E-37 1.2E-41 249.9 7.5 123 1-123 1-124 (240)
4 PF06290 PsiB: Plasmid SOS inh 70.8 6.5 0.00014 31.1 3.8 47 84-130 3-70 (143)
5 PRK13701 psiB plasmid SOS inhi 67.1 8.2 0.00018 30.6 3.6 46 84-129 3-69 (144)
6 PF10241 KxDL: Uncharacterized 55.5 18 0.00038 25.6 3.4 24 40-63 65-88 (88)
7 PF09391 DUF2000: Protein of u 45.9 1.3 2.7E-05 33.9 -4.0 69 44-123 62-132 (133)
8 PF04998 RNA_pol_Rpb1_5: RNA p 42.2 5.3 0.00011 31.3 -1.1 51 59-127 3-53 (277)
9 cd07605 I-BAR_IMD Inverse (I)- 42.1 34 0.00074 28.2 3.5 31 32-62 119-149 (223)
10 PF07774 DUF1620: Protein of u 41.8 13 0.00029 30.3 1.1 14 122-135 168-181 (217)
11 PF02202 Tachykinin: Tachykini 27.1 11 0.00023 18.2 -1.0 6 59-64 3-8 (11)
12 PF10258 RNA_GG_bind: PHAX RNA 22.0 1.3E+02 0.0027 21.6 3.2 69 26-94 9-79 (87)
13 TIGR02390 RNA_pol_rpoA1 DNA-di 20.6 41 0.00089 32.8 0.6 51 58-126 786-836 (868)
No 1
>PF03998 Utp11: Utp11 protein; InterPro: IPR007144 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. This entry contains Utp11, a large ribonuclear protein that associates with snoRNA U3 [].; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=100.00 E-value=5.5e-51 Score=332.76 Aligned_cols=113 Identities=51% Similarity=0.770 Sum_probs=108.9
Q ss_pred cccccccCCcchhhccccccccccHHHHHHHHHHHHHHHHHHHHHHhhhCCCchhhhhhhceecC-Cccccccc-cCCCC
Q 032675 10 RRAHKERAQPQSRKKFGLLEKHKDYVVRAKAYRKKEETIRRLKEKAAFRNPDEFYLKMIKTKIVD-GVHRLESE-ANKYT 87 (136)
Q Consensus 10 rr~HrER~Qp~~R~~lGlLEKkKDY~~RA~dy~~K~~~lk~Lr~KA~~rNpDEFyf~M~~~k~~~-Gvh~~~~~-~~~~t 87 (136)
||+|+|||||++|++||+|||||||++||+|||+|+++|+.|++||++||||||||+|+|+++.+ |+|+...+ ++.+|
T Consensus 1 rr~HrERsQP~~R~~lGlLEKkKDY~lRA~dy~~K~~~Lk~Lr~KA~~RNpDEFyf~M~~sk~~~~G~h~~~~~~~~~~~ 80 (243)
T PF03998_consen 1 RRNHRERSQPASRKKLGLLEKKKDYKLRAKDYHKKEAKLKRLREKAANRNPDEFYFGMINSKTDDDGVHVEKREENEELS 80 (243)
T ss_pred CCcccccCChHHhhhcCcccccccHHHHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHhcccCCCCeeccCccccccCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999 99999887 78999
Q ss_pred HHHHHHhhhccHHHHHHHHHHHhhhhhhhhhceee
Q 032675 88 QEELILMKTQDIGYILQKLQSERNVRNCFYIVFMV 122 (136)
Q Consensus 88 ~eq~klmkTQDl~Yv~~kr~~e~kKie~~~~~~~~ 122 (136)
+|+++||+|||++||++++++|.+||++|.....+
T Consensus 81 ~e~~~llkTQD~~Yv~~~~~~e~kKIekL~~~l~~ 115 (243)
T PF03998_consen 81 KEQVKLLKTQDLNYVRTKRQIERKKIEKLQSELHL 115 (243)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 99999999999999999999999999999887643
No 2
>KOG3237 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=4.1e-51 Score=336.49 Aligned_cols=126 Identities=48% Similarity=0.669 Sum_probs=122.7
Q ss_pred CCccccccc--cccccccCCcchhhccccccccccHHHHHHHHHHHHHHHHHHHHHHhhhCCCchhhhhhhceecCCccc
Q 032675 1 MSSRRNAIP--RRAHKERAQPQSRKKFGLLEKHKDYVVRAKAYRKKEETIRRLKEKAAFRNPDEFYLKMIKTKIVDGVHR 78 (136)
Q Consensus 1 MSSlrnavk--rr~HrER~Qp~~R~~lGlLEKkKDY~~RA~dy~~K~~~lk~Lr~KA~~rNpDEFyf~M~~~k~~~Gvh~ 78 (136)
||||+||++ +++|||||||.+|++||+|||||||++||.|||+||++|+.|+++|+++|||||||+|+|+++.||+|+
T Consensus 1 mss~~~a~ks~rk~HRERsQP~~Rrk~G~LEKkKDY~~RA~dy~kKq~tLK~LrekA~eKNpDEfyh~M~~~K~~dG~hi 80 (250)
T KOG3237|consen 1 MSSFVNASKSRRKVHRERSQPEARRKYGFLEKKKDYKKRAQDYHKKQDTLKKLREKALEKNPDEFYHKMHNSKTKDGRHI 80 (250)
T ss_pred CcchhhcchhhhhHHHhhcChhHHHhhhhHHhhhHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHhhccccCCccc
Confidence 999999999 899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCHHHHHHhhhccHHHHHHHHHHHhhhhhhhhhceeeeeee
Q 032675 79 LESEANKYTQEELILMKTQDIGYILQKLQSERNVRNCFYIVFMVHIRI 126 (136)
Q Consensus 79 ~~~~~~~~t~eq~klmkTQDl~Yv~~kr~~e~kKie~~~~~~~~~~~~ 126 (136)
+..+.+++|+|||+||+|||++||.+++++|++|||.|.+..+.+-++
T Consensus 81 ~k~e~~e~t~eqlklmktQDi~YV~~kr~~ErkKIerlka~L~~~~~~ 128 (250)
T KOG3237|consen 81 EKDEVDEPTMEQLKLMKTQDIGYVRMKRQRERKKIERLKAQLHCVDRN 128 (250)
T ss_pred cccccccCCHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhccccccccc
Confidence 998889999999999999999999999999999999999999887744
No 3
>COG5223 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=5.4e-37 Score=249.93 Aligned_cols=123 Identities=35% Similarity=0.451 Sum_probs=114.6
Q ss_pred CCc-cccccccccccccCCcchhhccccccccccHHHHHHHHHHHHHHHHHHHHHHhhhCCCchhhhhhhceecCCcccc
Q 032675 1 MSS-RRNAIPRRAHKERAQPQSRKKFGLLEKHKDYVVRAKAYRKKEETIRRLKEKAAFRNPDEFYLKMIKTKIVDGVHRL 79 (136)
Q Consensus 1 MSS-lrnavkrr~HrER~Qp~~R~~lGlLEKkKDY~~RA~dy~~K~~~lk~Lr~KA~~rNpDEFyf~M~~~k~~~Gvh~~ 79 (136)
||+ |.++-+|++|+||+||.+|++||+|||+|||++||.|||+||.+|+.||++|..||||||||+|.+.++.+|+..+
T Consensus 1 Ms~~f~~v~qrK~hrERtQp~~RrkyG~LEK~KDyvkRaqd~~~kq~~lk~lrEka~ernpdEyyh~mhs~Ktd~gv~~~ 80 (240)
T COG5223 1 MSLGFTKVPQRKVHRERTQPKDRRKYGKLEKKKDYVKRAQDINKKQDELKKLREKARERNPDEYYHGMHSVKTDGGVSSI 80 (240)
T ss_pred CCcccccchHhhhHHHhcCcchhhhhhhHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcChHHHHHHhhhhcccCCccce
Confidence 775 5555588999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred ccccCCCCHHHHHHhhhccHHHHHHHHHHHhhhhhhhhhceeee
Q 032675 80 ESEANKYTQEELILMKTQDIGYILQKLQSERNVRNCFYIVFMVH 123 (136)
Q Consensus 80 ~~~~~~~t~eq~klmkTQDl~Yv~~kr~~e~kKie~~~~~~~~~ 123 (136)
.++.+.++.|++++++|||.+|++..++.|..|++.++.-.+..
T Consensus 81 ~ReDe~~~md~~KmlktqD~~~~R~~r~lEr~k~~~~~~qi~f~ 124 (240)
T COG5223 81 YREDEPTIMDLAKMLKTQDNEIQRCRRKLERYKPMPCGTQIKFE 124 (240)
T ss_pred eccccchHHHHHHHHHhhhhHHHHHHHHHHHhCCcchhceeeee
Confidence 88888999999999999999999999999999999887665554
No 4
>PF06290 PsiB: Plasmid SOS inhibition protein (PsiB); InterPro: IPR009385 This family consists of several plasmid SOS inhibition protein (PsiB) sequences [].; PDB: 3NCT_B.
Probab=70.79 E-value=6.5 Score=31.14 Aligned_cols=47 Identities=26% Similarity=0.142 Sum_probs=29.2
Q ss_pred CCCCHHHHHHhhhccHHHHHHHHHHHhhh---------------------hhhhhhceeeeeeeecce
Q 032675 84 NKYTQEELILMKTQDIGYILQKLQSERNV---------------------RNCFYIVFMVHIRIAFSI 130 (136)
Q Consensus 84 ~~~t~eq~klmkTQDl~Yv~~kr~~e~kK---------------------ie~~~~~~~~~~~~~~~~ 130 (136)
..+|.++|+-|.+||+.-++..-.--++. -..|+-.|||+.||.|+=
T Consensus 3 ~~ltl~~L~tm~a~elE~~R~~Ged~RR~L~~aVm~~L~~P~gW~~n~Ey~~EFgGffPVq~Rftp~~ 70 (143)
T PF06290_consen 3 TELTLEVLKTMSAQELEDYRAAGEDFRRELTHAVMRELTLPEGWRVNAEYRSEFGGFFPVQCRFTPSH 70 (143)
T ss_dssp ----HHHHHH--HHHHHHHHHH-HHHHHHHHHHHHHT----TTEEEEE-SSSTT-S-SSSEEEEEETT
T ss_pred ceehHHHHhhcCHHHHHHHHHhhHHHHHHhHHHHHHhccCCccceeeceeccccccEeeEEEEecCCC
Confidence 36899999999999998887654433332 246888999999999974
No 5
>PRK13701 psiB plasmid SOS inhibition protein B; Provisional
Probab=67.08 E-value=8.2 Score=30.62 Aligned_cols=46 Identities=24% Similarity=0.182 Sum_probs=35.0
Q ss_pred CCCCHHHHHHhhhccHHHHHHHHHHHhh---------------------hhhhhhhceeeeeeeecc
Q 032675 84 NKYTQEELILMKTQDIGYILQKLQSERN---------------------VRNCFYIVFMVHIRIAFS 129 (136)
Q Consensus 84 ~~~t~eq~klmkTQDl~Yv~~kr~~e~k---------------------Kie~~~~~~~~~~~~~~~ 129 (136)
..+|.++|+-|.+|++.-++..-.--++ -...|+--|||..||+|+
T Consensus 3 ~~ltl~~l~tM~a~ElEd~R~~G~d~RR~Lt~aVm~~L~~P~gW~~naEy~sEFgGffPVq~Rfsp~ 69 (144)
T PRK13701 3 TELTLNVLQTMSAQEYEDIRAAGSDERRELTHAVMRELDAPDGWTMNGEYGSEFGGFFPVQVRFTPA 69 (144)
T ss_pred cEEcHHHHhccCHHHHHHHHHHhHHHHHHhHHHHHhccCCCccceeehhhhccccCeeeEEEEecCC
Confidence 4688999999999999888755433332 235688899999999995
No 6
>PF10241 KxDL: Uncharacterized conserved protein; InterPro: IPR019371 This entry represents a conserved region of 80 residues which defines a family of short proteins. There is a characteristic KxDL motif towards the C terminus. The function is unknown.
Probab=55.50 E-value=18 Score=25.56 Aligned_cols=24 Identities=33% Similarity=0.393 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHhhhCCCch
Q 032675 40 AYRKKEETIRRLKEKAAFRNPDEF 63 (136)
Q Consensus 40 dy~~K~~~lk~Lr~KA~~rNpDEF 63 (136)
|-.--..+|..|+.++....|+||
T Consensus 65 DLd~i~krir~lk~kl~~~yP~~y 88 (88)
T PF10241_consen 65 DLDYIFKRIRSLKAKLAKQYPEEY 88 (88)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCcC
Confidence 334456789999999999999998
No 7
>PF09391 DUF2000: Protein of unknown function (DUF2000); InterPro: IPR018988 This is a family of proteins of unknown function. The structure of one of the proteins in this family has been shown to adopt an alpha beta fold. ; PDB: 2GAX_A.
Probab=45.93 E-value=1.3 Score=33.86 Aligned_cols=69 Identities=19% Similarity=0.197 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHhhhCCC--chhhhhhhceecCCccccccccCCCCHHHHHHhhhccHHHHHHHHHHHhhhhhhhhhcee
Q 032675 44 KEETIRRLKEKAAFRNPD--EFYLKMIKTKIVDGVHRLESEANKYTQEELILMKTQDIGYILQKLQSERNVRNCFYIVFM 121 (136)
Q Consensus 44 K~~~lk~Lr~KA~~rNpD--EFyf~M~~~k~~~Gvh~~~~~~~~~t~eq~klmkTQDl~Yv~~kr~~e~kKie~~~~~~~ 121 (136)
..++|+.|+++|+.+.=. -|---|..++ +... -.+.+....++|+.|+-.-.--+++.|++|+.+||
T Consensus 62 ~~~~L~~l~~~a~~~~i~~~~F~~~aq~~~-----~y~e------~~~~~~~~~~~~l~y~Gi~L~G~kk~V~kltg~l~ 130 (133)
T PF09391_consen 62 NSEQLRELRQKALEREITVVDFTDEAQSTG-----HYEE------YRAAVAATPEEDLEYVGIALFGPKKAVDKLTGSLP 130 (133)
T ss_dssp -HHHHHHHHHHHHHTT---EEEEGGGGG--------HHH------HHHHHTT--TTT--EEEEEEEEEHHHHHHHCTT-E
T ss_pred CHHHHHHHHHHHHHCCCeEEeChHHHhhCC-----CHHH------HHHHHhcCChhhccEEEEEEECCHHHHHHHhcCCC
Confidence 467899999999988100 0222222222 1111 01224456678999999888889999999999999
Q ss_pred ee
Q 032675 122 VH 123 (136)
Q Consensus 122 ~~ 123 (136)
++
T Consensus 131 L~ 132 (133)
T PF09391_consen 131 LL 132 (133)
T ss_dssp E-
T ss_pred CC
Confidence 85
No 8
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=42.23 E-value=5.3 Score=31.28 Aligned_cols=51 Identities=20% Similarity=0.449 Sum_probs=36.2
Q ss_pred CCCchhhhhhhceecCCccccccccCCCCHHHHHHhhhccHHHHHHHHHHHhhhhhhhhhceeeeeeee
Q 032675 59 NPDEFYLKMIKTKIVDGVHRLESEANKYTQEELILMKTQDIGYILQKLQSERNVRNCFYIVFMVHIRIA 127 (136)
Q Consensus 59 NpDEFyf~M~~~k~~~Gvh~~~~~~~~~t~eq~klmkTQDl~Yv~~kr~~e~kKie~~~~~~~~~~~~~ 127 (136)
||-||||+.+.+| .|. + + --+||-|-+|+.-++..- .+-+.+.+.-|.|.+
T Consensus 3 ~~~e~f~~~~~~R--~gl-~-d-----------ta~kTa~sGyl~R~lv~~---~~~~~v~~~~~~~~~ 53 (277)
T PF04998_consen 3 TPTEYFFHCMGGR--EGL-I-D-----------TAVKTADSGYLQRRLVKV---LEDLIVRYDDCVRNS 53 (277)
T ss_dssp THHHHHHHHHHHH--HHH-H-H-----------HHHCHHHHHHHHHHHHHH---HTTHEEETTSEEEST
T ss_pred CHHHHHHHHhccc--ccc-c-c-----------cceeeeccccchhhhhhc---cceEEEEEcCccccc
Confidence 7899999999888 452 1 1 127999999998776543 356666666677665
No 9
>cd07605 I-BAR_IMD Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), a dimerization module that binds and bends membranes. Inverse (I)-BAR (or IMD) is a member of the Bin/Amphiphysin/Rvs (BAR) domain family. It is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. IMD domains are found in Insulin Receptor tyrosine kinase Substrate p53 (IRSp53), Missing in Metastasis (MIM), and Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-like (BAIAP2L) proteins. These are multi-domain proteins that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. Most members contain an N-terminal IMD, an SH3 domain, and a WASP homology 2 (WH2) actin-binding motif at the C-terminus, exccept for MIM which does not carry an SH3 domain. Some me
Probab=42.05 E-value=34 Score=28.24 Aligned_cols=31 Identities=16% Similarity=0.365 Sum_probs=26.7
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHhhhCCCc
Q 032675 32 KDYVVRAKAYRKKEETIRRLKEKAAFRNPDE 62 (136)
Q Consensus 32 KDY~~RA~dy~~K~~~lk~Lr~KA~~rNpDE 62 (136)
++|+.+..++.+.+..++.|+.|+...||+.
T Consensus 119 ~E~K~~~~~l~K~~sel~Kl~KKs~~~~~~k 149 (223)
T cd07605 119 KEYKQKREDLDKARSELKKLQKKSQKSGTGK 149 (223)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcccCCCc
Confidence 5788888899999999999999999777653
No 10
>PF07774 DUF1620: Protein of unknown function (DUF1620); InterPro: IPR011678 These sequences are mainly derived from predicted eukaryotic proteins. The region in question lies towards the C terminus of these large proteins and is approximately 300 amino acid residues long.
Probab=41.80 E-value=13 Score=30.34 Aligned_cols=14 Identities=43% Similarity=0.558 Sum_probs=12.6
Q ss_pred eeeeeecceeeeec
Q 032675 122 VHIRIAFSITFDIV 135 (136)
Q Consensus 122 ~~~~~~~~~~~~~~ 135 (136)
.|-||+||-+||+.
T Consensus 168 F~Tri~PS~~FD~L 181 (217)
T PF07774_consen 168 FCTRIAPSKSFDLL 181 (217)
T ss_pred EEEEecCCcccccc
Confidence 49999999999985
No 11
>PF02202 Tachykinin: Tachykinin family; InterPro: IPR002040 This family includes peptides, which belong to the tachykinin family. Tachykinins [, , ] are a group of biologically active peptides which excite neurons, evoke behavioral responses, are potent vasodilatators and contract (directly or indirectly) many smooth muscles. Tachykinins, like most other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. Tachykinins are from ten to twelve residues long.; GO: 0007217 tachykinin receptor signaling pathway, 0007268 synaptic transmission; PDB: 1MYU_A 1N6T_A 2GFR_A.
Probab=27.09 E-value=11 Score=18.17 Aligned_cols=6 Identities=67% Similarity=1.641 Sum_probs=4.6
Q ss_pred CCCchh
Q 032675 59 NPDEFY 64 (136)
Q Consensus 59 NpDEFy 64 (136)
+||+||
T Consensus 3 ~pd~F~ 8 (11)
T PF02202_consen 3 KPDQFY 8 (11)
T ss_dssp CHHHHC
T ss_pred Ccccce
Confidence 688886
No 12
>PF10258 RNA_GG_bind: PHAX RNA-binding domain; InterPro: IPR019385 The phosphorylated adaptor for RNA export (PHAX) protein transports U3 snoRNA from the nucleus after transcription []. This entry represents the highly conserved U3 snoRNA-binding domain of PHAX, which is characterised by having two pairs of adjacent glycines with the sequence motif GGx12GG.; PDB: 2XC7_A 2W4S_B.
Probab=22.00 E-value=1.3e+02 Score=21.57 Aligned_cols=69 Identities=17% Similarity=0.126 Sum_probs=46.9
Q ss_pred ccccccccHHHHHHHHHHHHHHHHHHHHH-HhhhCCCchhhhhhhceecCCccccc-cccCCCCHHHHHHh
Q 032675 26 GLLEKHKDYVVRAKAYRKKEETIRRLKEK-AAFRNPDEFYLKMIKTKIVDGVHRLE-SEANKYTQEELILM 94 (136)
Q Consensus 26 GlLEKkKDY~~RA~dy~~K~~~lk~Lr~K-A~~rNpDEFyf~M~~~k~~~Gvh~~~-~~~~~~t~eq~klm 94 (136)
.|-|++.|...|+=..-=.+..+..+.+- +-+.|...+.-.-...||.+||-..- ...+..|+++.+.+
T Consensus 9 ~L~E~k~~li~rvV~~lG~~~~~~l~~et~~Ie~~GG~~~~dG~RrRTpGGVF~~LlK~~~~i~~e~~k~I 79 (87)
T PF10258_consen 9 RLKEPKKDLIERVVKRLGVEKALELLNETMKIEKNGGMMTADGSRRRTPGGVFFNLLKNDDDISPEDKKEI 79 (87)
T ss_dssp HCT-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT-EE-TTSSCE-SHHHHHHHHHHHTTSS-HHHHHHH
T ss_pred HhCCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHcCCeEeecCccCcCCCcchhHhhccCccCCHHHHHHH
Confidence 47799999999999999898888888874 45778877766666667888875421 12456788887654
No 13
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=20.64 E-value=41 Score=32.79 Aligned_cols=51 Identities=18% Similarity=0.421 Sum_probs=30.9
Q ss_pred hCCCchhhhhhhceecCCccccccccCCCCHHHHHHhhhccHHHHHHHHHHHhhhhhhhhhceeeeeee
Q 032675 58 RNPDEFYLKMIKTKIVDGVHRLESEANKYTQEELILMKTQDIGYILQKLQSERNVRNCFYIVFMVHIRI 126 (136)
Q Consensus 58 rNpDEFyf~M~~~k~~~Gvh~~~~~~~~~t~eq~klmkTQDl~Yv~~kr~~e~kKie~~~~~~~~~~~~ 126 (136)
-||.||||+.+.+| +|.- .. -+||-|-+|++-+... -.|-+.+.|---.|-
T Consensus 786 L~p~EfFfH~m~gR--eGLi-DT------------AvKTa~sGYLqRrLvk---~lEdl~v~yD~tVR~ 836 (868)
T TIGR02390 786 LDPTEYFFHAAGGR--EGLV-DT------------AVRTSQSGYMQRRLIN---ALQDLYVEYDGTVRD 836 (868)
T ss_pred CCHHHHHHHHhhhc--cccc-cc------------cccccccchhHHHHHH---HHhheEEecCCeEEe
Confidence 47999999988777 4521 11 1578888888766543 234544444444443
Done!