Query 001786
Match_columns 1013
No_of_seqs 355 out of 1137
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 09:17:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001786.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001786hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1990 Poly(A)-specific exori 100.0 1.2E-63 2.5E-68 575.1 18.6 512 169-741 4-531 (564)
2 PRK10343 RNA-binding protein Y 99.9 3E-24 6.5E-29 199.5 12.9 89 593-685 2-90 (97)
3 TIGR00253 RNA_bind_YhbY putati 99.9 3.3E-24 7.2E-29 198.6 12.2 88 594-685 1-88 (95)
4 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 8.7E-24 1.9E-28 190.9 10.9 84 180-263 1-84 (84)
5 PRK10343 RNA-binding protein Y 99.9 5.2E-23 1.1E-27 191.3 12.8 89 178-266 1-89 (97)
6 COG1534 Predicted RNA-binding 99.9 4E-23 8.6E-28 191.5 11.9 96 593-693 1-96 (97)
7 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 2.8E-23 6.1E-28 187.7 10.2 84 594-681 1-84 (84)
8 TIGR00253 RNA_bind_YhbY putati 99.9 9.7E-23 2.1E-27 188.9 13.0 88 180-267 1-88 (95)
9 COG1534 Predicted RNA-binding 99.8 4.7E-21 1E-25 177.8 12.0 87 179-265 1-87 (97)
10 KOG1990 Poly(A)-specific exori 99.8 8.5E-20 1.8E-24 212.3 4.7 304 167-503 162-494 (564)
11 PF15337 Vasculin: Vascular pr 37.1 18 0.00039 35.1 1.3 41 399-440 34-74 (97)
12 PF12207 DUF3600: Domain of un 26.5 12 0.00027 38.7 -1.7 101 553-653 24-139 (162)
13 PF03641 Lysine_decarbox: Poss 22.1 1.4E+02 0.003 29.7 4.6 37 598-634 72-109 (133)
14 TIGR02398 gluc_glyc_Psyn gluco 20.6 1.2E+02 0.0025 36.9 4.5 72 937-1010 273-354 (487)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=100.00 E-value=1.2e-63 Score=575.14 Aligned_cols=512 Identities=44% Similarity=0.642 Sum_probs=445.2
Q ss_pred ccCCCchhhccCCHHHHHHHHhcccCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCchhhHHHHHHHHHHHhC
Q 001786 169 EKEVPTLAELKLSGKELRRLRTLGIGLRKKLKIGKAGITEGIVNGIHERWRHAEVVKIVCEDLCRLNMKRTHDSLERKTG 248 (1013)
Q Consensus 169 ~~~~PtlAEltLt~kErr~LRklA~~Lkp~V~IGK~GLTd~VVeeI~~aWkk~ELVKIKv~~~~~~dmk~~aE~LE~kTG 248 (1013)
... |++|++++...++.+||..|..+.-.+ +++|+|+.+++.|+..|+.+|+++++|......+|.+++++++..||
T Consensus 4 ~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~~ 80 (564)
T KOG1990|consen 4 FES-LSLAELTVDEADLRRLRLVATGMTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMSTG 80 (564)
T ss_pred ccc-hhHHHhhcCHHHHHHHhhhhccceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccCC
Confidence 445 999999999999999999999998877 99999999999999999999999999998888999999999999999
Q ss_pred C-EEEEEECcEEEEEecCCCCCCccccCCCCCCCCCCCCCCCcccccccccccccccCCCCCCCCCCCCCCchhhhhhhc
Q 001786 249 G-LVVWRSGSKIILYRGADYKYPYFLADESSTDGASSDDLPNQLVDDEGLDETKTHSSGADSAKPSGQSPTNKKVQQTLI 327 (1013)
Q Consensus 249 G-~VVqriG~tiVLYRGknY~~P~~~~~~~~~~e~~~~~~~~~~~d~e~~~~~~~~~ss~~~~~~~g~~~e~~~~~~~l~ 327 (1013)
| -+||+.|.....|++..|..|..-.... ++ .....|
T Consensus 81 ~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~--------------~~---------------------------~~~~~~- 118 (564)
T KOG1990|consen 81 GNFVVWSRGDSISSPEFLCQRSPVDFVARQ--------------QE---------------------------NQAGKW- 118 (564)
T ss_pred CceeeeecCccccCCccceeecchhhhhhh--------------ch---------------------------hhhhhh-
Confidence 9 9999999999999888887764322210 00 000000
Q ss_pred cccCCCCccccCCcchhhhHHHHHHhhcccCCCccCCCCCCCCccCCCCCCcccCCCCCCcccCCCCCCCCCCHHHHHHH
Q 001786 328 HSVGSPDKLRYQLPGEAELVEEADRLLDGLGPRFTDWWGYDPQPVDADLLPATVPGYRRPFRLLPYGVQPKLTNDEMTTL 407 (1013)
Q Consensus 328 ~~~~~~~~~~~~~p~E~~~e~E~~~LLd~LGPRF~dW~g~~PlPVDAdLLP~~Vpgyk~PfR~lP~gvr~~LT~eErt~L 407 (1013)
...++.+.+.+++++||+|.+||+.+|+|+|+|++|++||+|.+|||.+|+|++++||..|.+++
T Consensus 119 ---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~ 183 (564)
T KOG1990|consen 119 ---------------PSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLL 183 (564)
T ss_pred ---------------HHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHH
Confidence 13456789999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCCceEEeccCcchHHHHHHHHHHhhcCcceEEEecCCCCCchHHHHHHHH--HhhhCCEEEEeeCCEEEEEcCC
Q 001786 408 RRLGRPLPCHFALGRNRNLQGLAAAIVKLWEKCEIAKIAVKRGAQNTNSEMMAQEL--KRLTGGTLLSRDREFIVFYRGK 485 (1013)
Q Consensus 408 Rklar~lpph~~LGRnGv~~GLa~aI~k~Wkk~ELVKI~~K~gv~~td~e~ma~eL--k~lTGGvLVsr~~~~IIlYRGK 485 (1013)
|++|..+||||++|+++..+|++.+|+.+|++|+.+++.+++|+..+..+.+|..| ...||++||++|+.++|+|||+
T Consensus 184 r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~dv~y~~~ 263 (564)
T KOG1990|consen 184 RRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLLDVMYRYK 263 (564)
T ss_pred HHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccceeeeeehh
Confidence 99999999999999999999999999999999999999999999999999999999 9999999999999999999999
Q ss_pred CCCChhhhhHHHHHhhhhccccCCCCCccccCCC--CCCCCCCCccccc---ccccc----cc--chhhHHHHHHhHHHH
Q 001786 486 DFLPPAASSAIEERRKHEFSTSNDSKEEPELGNR--HDNSGDNTQDEFG---CTNDQ----KS--TMHSEQKERRSAEVA 554 (1013)
Q Consensus 486 df~p~~V~~~L~eR~~l~~s~~~~~~~~~e~~~~--~~~s~~~t~~~~~---~~~~~----~~--~~~~~~~~~~~~~~~ 554 (1013)
+|++ .+..+|.++++.....+.+.......... ++....+|..++. +.++. .. .....+.+....++.
T Consensus 264 ~Fl~-~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ 342 (564)
T KOG1990|consen 264 NFLS-PLPSTLEEFTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIERRSISSRLKLEFEKASSEKL 342 (564)
T ss_pred hccc-ccchhHHHhhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCcccccccchhhhhhhccchhhH
Confidence 9999 89999999988622222211100011111 1112334444332 11111 01 011223344566788
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcc-cCCCCcccCcCCCCHHHHHHHHhcccCCCceEEeccCCCCHHHHHHHHHHHh
Q 001786 555 IRRTNIRLSRVLEKKAEAEKLLAELEE-ERPEQYEVDKEGITEEERYMLRKVGLRMKAFLLMGRRGVFDGTVENMHLHWK 633 (1013)
Q Consensus 555 ~k~~e~kL~~~~~K~~kae~ll~kle~-~~P~~~~~d~E~LT~eERk~LRkiGhkmkPvV~IGK~GVtdgVIe~Ih~Alk 633 (1013)
.+.+..++..+..|...++..+++++. ..|.+..+|+|.+|.+++.+++++|.+|++++.+|++|+|+|++.+||+||+
T Consensus 343 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk 422 (564)
T KOG1990|consen 343 TEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWK 422 (564)
T ss_pred HHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhh
Confidence 899999999999999999999999998 8999998999999999999999999999999999999999999999999999
Q ss_pred ccceEEEEecCCCH-HHHHHHHHHHHHHhCCEEEeeeecccCcEEEEEccCCCCCCCcCCCcccccHHHHHHHhHHHHHH
Q 001786 634 HRELVKIISKQRKI-EAALQEARTLEVESGGILVAVERVNKGYAIILYRGKNYERPACLRPKTLLTKREAMKRSLEAQRR 712 (1013)
Q Consensus 634 ~rELIKVk~~~n~~-ed~keiA~~Lee~Sgg~LVqv~kv~IG~tIILYRgKNY~rP~~l~P~~lLtKrkAl~rs~e~qr~ 712 (1013)
+||++|++|+.... .++++.|..++.++|+++|+++++..|++|+.|||+||++|..++|.++|+||+|+.+|+++|++
T Consensus 423 ~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~~~~~~~ 502 (564)
T KOG1990|consen 423 SRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERSLEEQRK 502 (564)
T ss_pred hcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhcccCCccccHHHHHH
Confidence 99999999999877 99999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhcc
Q 001786 713 QSLKLHVLELTRNIEKLKLQLVKDKEANS 741 (1013)
Q Consensus 713 ~sl~~~i~~l~~~i~~l~~~l~~~~~~~~ 741 (1013)
++++.||..+..++++++.++..+...+.
T Consensus 503 ~a~~~~i~~~~~~~e~~~~~~~~~~~~~~ 531 (564)
T KOG1990|consen 503 EALKSHISDLEQEIEQLQASVEAMPAINK 531 (564)
T ss_pred HHHhhhcchhhhhHHHhhcchhccccccc
Confidence 99999999999999999999877655554
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.91 E-value=3e-24 Score=199.53 Aligned_cols=89 Identities=21% Similarity=0.398 Sum_probs=86.9
Q ss_pred CCCHHHHHHHHhcccCCCceEEeccCCCCHHHHHHHHHHHhccceEEEEecCCCHHHHHHHHHHHHHHhCCEEEeeeecc
Q 001786 593 GITEEERYMLRKVGLRMKAFLLMGRRGVFDGTVENMHLHWKHRELVKIISKQRKIEAALQEARTLEVESGGILVAVERVN 672 (1013)
Q Consensus 593 ~LT~eERk~LRkiGhkmkPvV~IGK~GVtdgVIe~Ih~Alk~rELIKVk~~~n~~ed~keiA~~Lee~Sgg~LVqv~kv~ 672 (1013)
+||++||+|||++||+++|+|+||++|||++|+.++++||++||||||++++++.++++++|++|++.+||++||+
T Consensus 2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~---- 77 (97)
T PRK10343 2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQV---- 77 (97)
T ss_pred CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEee----
Confidence 4999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcEEEEEccCCC
Q 001786 673 KGYAIILYRGKNY 685 (1013)
Q Consensus 673 IG~tIILYRgKNY 685 (1013)
||+++||||+++.
T Consensus 78 IG~~~vlYR~~~~ 90 (97)
T PRK10343 78 IGKTLVLYRPTKE 90 (97)
T ss_pred eCcEEEEEecCCC
Confidence 9999999999863
No 3
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=99.91 E-value=3.3e-24 Score=198.62 Aligned_cols=88 Identities=28% Similarity=0.451 Sum_probs=86.1
Q ss_pred CCHHHHHHHHhcccCCCceEEeccCCCCHHHHHHHHHHHhccceEEEEecCCCHHHHHHHHHHHHHHhCCEEEeeeeccc
Q 001786 594 ITEEERYMLRKVGLRMKAFLLMGRRGVFDGTVENMHLHWKHRELVKIISKQRKIEAALQEARTLEVESGGILVAVERVNK 673 (1013)
Q Consensus 594 LT~eERk~LRkiGhkmkPvV~IGK~GVtdgVIe~Ih~Alk~rELIKVk~~~n~~ed~keiA~~Lee~Sgg~LVqv~kv~I 673 (1013)
||++||+|||++||+|+|+|+||++|||++||+++++||++||||||+++++++++++++|.+|++.+||++||+ |
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~----i 76 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQV----I 76 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEE----E
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred CcEEEEEccCCC
Q 001786 674 GYAIILYRGKNY 685 (1013)
Q Consensus 674 G~tIILYRgKNY 685 (1013)
|+++||||+++.
T Consensus 77 G~~~vlYR~~~~ 88 (95)
T TIGR00253 77 GKTIVLYRPTKE 88 (95)
T ss_pred ccEEEEEecCCc
Confidence 999999999754
No 4
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.90 E-value=8.7e-24 Score=190.94 Aligned_cols=84 Identities=37% Similarity=0.580 Sum_probs=75.7
Q ss_pred CCHHHHHHHHhcccCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCchhhHHHHHHHHHHHhCCEEEEEECcEE
Q 001786 180 LSGKELRRLRTLGIGLRKKLKIGKAGITEGIVNGIHERWRHAEVVKIVCEDLCRLNMKRTHDSLERKTGGLVVWRSGSKI 259 (1013)
Q Consensus 180 Lt~kErr~LRklA~~Lkp~V~IGK~GLTd~VVeeI~~aWkk~ELVKIKv~~~~~~dmk~~aE~LE~kTGG~VVqriG~ti 259 (1013)
||++|+++||+.||+|+|+|+|||+|+|++|+++|+++|++||||||+|.+++..|++++|++|+++|||++||++|+++
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG~~~ 80 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIGRTI 80 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEETTEE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEECCEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEe
Q 001786 260 ILYR 263 (1013)
Q Consensus 260 VLYR 263 (1013)
||||
T Consensus 81 vlyR 84 (84)
T PF01985_consen 81 VLYR 84 (84)
T ss_dssp EEEE
T ss_pred EEEC
Confidence 9998
No 5
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.89 E-value=5.2e-23 Score=191.32 Aligned_cols=89 Identities=27% Similarity=0.428 Sum_probs=87.0
Q ss_pred ccCCHHHHHHHHhcccCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCchhhHHHHHHHHHHHhCCEEEEEECc
Q 001786 178 LKLSGKELRRLRTLGIGLRKKLKIGKAGITEGIVNGIHERWRHAEVVKIVCEDLCRLNMKRTHDSLERKTGGLVVWRSGS 257 (1013)
Q Consensus 178 ltLt~kErr~LRklA~~Lkp~V~IGK~GLTd~VVeeI~~aWkk~ELVKIKv~~~~~~dmk~~aE~LE~kTGG~VVqriG~ 257 (1013)
|+||++|+++||++||+|+|+|+|||+|||++|+++|.++|++||||||++.+++.++.++++++|++.||+++||+||+
T Consensus 1 m~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~IG~ 80 (97)
T PRK10343 1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQVIGK 80 (97)
T ss_pred CCCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEeeeCc
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEecCC
Q 001786 258 KIILYRGAD 266 (1013)
Q Consensus 258 tiVLYRGkn 266 (1013)
++||||.+.
T Consensus 81 ~~vlYR~~~ 89 (97)
T PRK10343 81 TLVLYRPTK 89 (97)
T ss_pred EEEEEecCC
Confidence 999999975
No 6
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=4e-23 Score=191.54 Aligned_cols=96 Identities=27% Similarity=0.443 Sum_probs=89.6
Q ss_pred CCCHHHHHHHHhcccCCCceEEeccCCCCHHHHHHHHHHHhccceEEEEecCCCHHHHHHHHHHHHHHhCCEEEeeeecc
Q 001786 593 GITEEERYMLRKVGLRMKAFLLMGRRGVFDGTVENMHLHWKHRELVKIISKQRKIEAALQEARTLEVESGGILVAVERVN 672 (1013)
Q Consensus 593 ~LT~eERk~LRkiGhkmkPvV~IGK~GVtdgVIe~Ih~Alk~rELIKVk~~~n~~ed~keiA~~Lee~Sgg~LVqv~kv~ 672 (1013)
+||++|++|||+.||+++|+|+||++|||++||.+|+++|++||||||++.+++.++.+++|+.|++.+||.+||+
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqv---- 76 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQV---- 76 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeee----
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcEEEEEccCCCCCCCcCCC
Q 001786 673 KGYAIILYRGKNYERPACLRP 693 (1013)
Q Consensus 673 IG~tIILYRgKNY~rP~~l~P 693 (1013)
||+++|||| .+..+++..+|
T Consensus 77 iG~~~vlyr-~~~e~~~i~l~ 96 (97)
T COG1534 77 IGKTLVLYR-ESKEKRKISLP 96 (97)
T ss_pred eeeEEEEEe-cCcccccccCC
Confidence 999999999 44445554444
No 7
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.89 E-value=2.8e-23 Score=187.65 Aligned_cols=84 Identities=32% Similarity=0.493 Sum_probs=75.6
Q ss_pred CCHHHHHHHHhcccCCCceEEeccCCCCHHHHHHHHHHHhccceEEEEecCCCHHHHHHHHHHHHHHhCCEEEeeeeccc
Q 001786 594 ITEEERYMLRKVGLRMKAFLLMGRRGVFDGTVENMHLHWKHRELVKIISKQRKIEAALQEARTLEVESGGILVAVERVNK 673 (1013)
Q Consensus 594 LT~eERk~LRkiGhkmkPvV~IGK~GVtdgVIe~Ih~Alk~rELIKVk~~~n~~ed~keiA~~Lee~Sgg~LVqv~kv~I 673 (1013)
||++||++||++||+|+|+|+|||+|||++|+++|++||++||||||+|.+++.++++++|..|++.+||++|++ +
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~----i 76 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQV----I 76 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEE----E
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEE----E
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999998 9
Q ss_pred CcEEEEEc
Q 001786 674 GYAIILYR 681 (1013)
Q Consensus 674 G~tIILYR 681 (1013)
|+++||||
T Consensus 77 G~~~vlyR 84 (84)
T PF01985_consen 77 GRTIVLYR 84 (84)
T ss_dssp TTEEEEEE
T ss_pred CCEEEEEC
Confidence 99999998
No 8
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=99.89 E-value=9.7e-23 Score=188.89 Aligned_cols=88 Identities=31% Similarity=0.472 Sum_probs=85.9
Q ss_pred CCHHHHHHHHhcccCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCchhhHHHHHHHHHHHhCCEEEEEECcEE
Q 001786 180 LSGKELRRLRTLGIGLRKKLKIGKAGITEGIVNGIHERWRHAEVVKIVCEDLCRLNMKRTHDSLERKTGGLVVWRSGSKI 259 (1013)
Q Consensus 180 Lt~kErr~LRklA~~Lkp~V~IGK~GLTd~VVeeI~~aWkk~ELVKIKv~~~~~~dmk~~aE~LE~kTGG~VVqriG~ti 259 (1013)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||++.+++..+.+++|++|+++||+++|+.+|+++
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG~~~ 80 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIGKTI 80 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEccEE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCC
Q 001786 260 ILYRGADY 267 (1013)
Q Consensus 260 VLYRGknY 267 (1013)
||||++..
T Consensus 81 vlYR~~~~ 88 (95)
T TIGR00253 81 VLYRPTKE 88 (95)
T ss_pred EEEecCCc
Confidence 99999754
No 9
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=4.7e-21 Score=177.83 Aligned_cols=87 Identities=31% Similarity=0.497 Sum_probs=84.9
Q ss_pred cCCHHHHHHHHhcccCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEcCCchhhHHHHHHHHHHHhCCEEEEEECcE
Q 001786 179 KLSGKELRRLRTLGIGLRKKLKIGKAGITEGIVNGIHERWRHAEVVKIVCEDLCRLNMKRTHDSLERKTGGLVVWRSGSK 258 (1013)
Q Consensus 179 tLt~kErr~LRklA~~Lkp~V~IGK~GLTd~VVeeI~~aWkk~ELVKIKv~~~~~~dmk~~aE~LE~kTGG~VVqriG~t 258 (1013)
+||++|+++||+.||+++|+|+|||+|||++|+.+|.++|++||||||++.+++..|.+++|+.|++++|+.+|+++|++
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqviG~~ 80 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVIGKT 80 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeeeeeE
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecC
Q 001786 259 IILYRGA 265 (1013)
Q Consensus 259 iVLYRGk 265 (1013)
+||||.+
T Consensus 81 ~vlyr~~ 87 (97)
T COG1534 81 LVLYRES 87 (97)
T ss_pred EEEEecC
Confidence 9999943
No 10
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.78 E-value=8.5e-20 Score=212.35 Aligned_cols=304 Identities=21% Similarity=0.284 Sum_probs=218.3
Q ss_pred ccccCCCchhhccCCHHHHHHHHhcccCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEEc-CCchhhHHHHHHHH--
Q 001786 167 EKEKEVPTLAELKLSGKELRRLRTLGIGLRKKLKIGKAGITEGIVNGIHERWRHAEVVKIVCE-DLCRLNMKRTHDSL-- 243 (1013)
Q Consensus 167 ~k~~~~PtlAEltLt~kErr~LRklA~~Lkp~V~IGK~GLTd~VVeeI~~aWkk~ELVKIKv~-~~~~~dmk~~aE~L-- 243 (1013)
.-.+.+|.+.+..|+..+...+|+++...+++|.+|..+.-+++.-.+...|.+|+.+|+.+. +.+......++.++
T Consensus 162 ~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~ 241 (564)
T KOG1990|consen 162 RPFRTLPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQE 241 (564)
T ss_pred ChhccCCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHH
Confidence 346788999999999999999999999999999999999999999999999999999998886 77778888999999
Q ss_pred HHHhCCEEEEEECcEEEEEecCCCCCCccccCCCCCCCCCCCCCCCcccccccccccccccCCCCCCCCCCCCCCchhhh
Q 001786 244 ERKTGGLVVWRSGSKIILYRGADYKYPYFLADESSTDGASSDDLPNQLVDDEGLDETKTHSSGADSAKPSGQSPTNKKVQ 323 (1013)
Q Consensus 244 E~kTGG~VVqriG~tiVLYRGknY~~P~~~~~~~~~~e~~~~~~~~~~~d~e~~~~~~~~~ss~~~~~~~g~~~e~~~~~ 323 (1013)
-..||+.||.++|...|+||+++|.. ............ ... ..+...........+ .......++..+...+.
T Consensus 242 ~~~tg~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~~f~~~-~~~----fp~~~~~~~~~~~~~-~~~~~~~~t~~e~~~~~ 314 (564)
T KOG1990|consen 242 LLLTGKVLVLHNKLLDVMYRYKNFLS-PLPSTLEEFTDS-SSM----FPNIEDTKRLAKLSE-YQKLNLKATLLELARAK 314 (564)
T ss_pred HHhcCCeEEeeccceeeeeehhhccc-ccchhHHHhhhh-hhh----hhhhHHHHHhhcccc-ccchhhhhhHHHHHHHh
Confidence 89999999999999999999999966 333222100000 001 111111111111111 11112334444444555
Q ss_pred hhhccccCCCCcc-ccCCcchh----hh--------------HHHHHHhhcccCCCccCCCCCCCCccCCCCCCcccCCC
Q 001786 324 QTLIHSVGSPDKL-RYQLPGEA----EL--------------VEEADRLLDGLGPRFTDWWGYDPQPVDADLLPATVPGY 384 (1013)
Q Consensus 324 ~~l~~~~~~~~~~-~~~~p~E~----~~--------------e~E~~~LLd~LGPRF~dW~g~~PlPVDAdLLP~~Vpgy 384 (1013)
..|...+...+.. +..++.+. +. +..++..|++++ ....|+.
T Consensus 315 ~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~---------------~~~~~~~---- 375 (564)
T KOG1990|consen 315 AKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLE---------------DPKIPAE---- 375 (564)
T ss_pred cccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhccc---------------ccccccc----
Confidence 5554444333211 11111111 11 112344444432 1112221
Q ss_pred CCCcccCCCCCCCCCCHHHHHHHHHcCCCCCceEEeccCcchHHHHHHHHHHhhcCcceEEEecCCCCCchHHHHHHHHH
Q 001786 385 RRPFRLLPYGVQPKLTNDEMTTLRRLGRPLPCHFALGRNRNLQGLAAAIVKLWEKCEIAKIAVKRGAQNTNSEMMAQELK 464 (1013)
Q Consensus 385 k~PfR~lP~gvr~~LT~eErt~LRklar~lpph~~LGRnGv~~GLa~aI~k~Wkk~ELVKI~~K~gv~~td~e~ma~eLk 464 (1013)
++.+.+.+|++|+.++++.|..+...+.+||.|+|+|++.++|.||++++++++.||........+..|..++
T Consensus 376 -------~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le 448 (564)
T KOG1990|consen 376 -------LRYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALE 448 (564)
T ss_pred -------cccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHH
Confidence 2245567999999999999999999999999999999999999999999999999998877799999999999
Q ss_pred hhhCCEEEEeeC----CEEEEEcCCCCCChhh---hhHHHHHhhhh
Q 001786 465 RLTGGTLLSRDR----EFIVFYRGKDFLPPAA---SSAIEERRKHE 503 (1013)
Q Consensus 465 ~lTGGvLVsr~~----~~IIlYRGKdf~p~~V---~~~L~eR~~l~ 503 (1013)
.+.||++|+.+. +.|++|||++|..|.. .+.|.+|.++.
T Consensus 449 ~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~ 494 (564)
T KOG1990|consen 449 RESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALE 494 (564)
T ss_pred HHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhcccCCcc
Confidence 999999999977 5589999999999976 24455554443
No 11
>PF15337 Vasculin: Vascular protein family Vasculin-like 1
Probab=37.15 E-value=18 Score=35.09 Aligned_cols=41 Identities=24% Similarity=0.419 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHcCCCCCceEEeccCcchHHHHHHHHHHhhcC
Q 001786 399 LTNDEMTTLRRLGRPLPCHFALGRNRNLQGLAAAIVKLWEKC 440 (1013)
Q Consensus 399 LT~eErt~LRklar~lpph~~LGRnGv~~GLa~aI~k~Wkk~ 440 (1013)
||.+|+++|--+.-.|. ---+||||++++..-++-..|...
T Consensus 34 lTEDElkEF~~kseQlr-rNGf~kngfl~~rs~slf~pWr~t 74 (97)
T PF15337_consen 34 LTEDELKEFQVKSEQLR-RNGFGKNGFLQSRSLSLFSPWRST 74 (97)
T ss_pred CcHHHHHHHHHHHHHHH-Hccccccchhhhhhhhcccccccc
Confidence 99999999987775554 356899999999888877778654
No 12
>PF12207 DUF3600: Domain of unknown function (DUF3600); InterPro: IPR022019 This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. This domain is the C-terminal of the putative ecf-type sigma factor negative effector. ; PDB: 3FGG_A 3FH3_A.
Probab=26.52 E-value=12 Score=38.75 Aligned_cols=101 Identities=14% Similarity=0.147 Sum_probs=68.2
Q ss_pred HHHHHHHHHHHHHHHHH---H--HHHHHHHhhcc----cCCCCcccCcCCCCHHHHHHHHhcccCCCceEE------ecc
Q 001786 553 VAIRRTNIRLSRVLEKK---A--EAEKLLAELEE----ERPEQYEVDKEGITEEERYMLRKVGLRMKAFLL------MGR 617 (1013)
Q Consensus 553 ~~~k~~e~kL~~~~~K~---~--kae~ll~kle~----~~P~~~~~d~E~LT~eERk~LRkiGhkmkPvV~------IGK 617 (1013)
..--+++.||+.|+-.. + .=..+|++|-. ..-+.-..|.|-|+..++..++++...+.|+|- --|
T Consensus 24 e~Y~~~eaKLqqAK~~lgeeEfeef~~lLK~lt~~kLkygD~NGnidye~ls~~eqee~k~~~~eLqPYFdKLN~~~SsK 103 (162)
T PF12207_consen 24 EDYLRLEAKLQQAKGELGEEEFEEFKELLKKLTNAKLKYGDKNGNIDYEKLSKEEQEEYKKLTMELQPYFDKLNGHKSSK 103 (162)
T ss_dssp HHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHB-TTS-B-GGGS-HHHHHHHHHHHHHHHHHHHHHTT---HH
T ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhHHhhcccCCCcCHHhCCHHHHHHHHHHHHhcchHHHHhcCCcchh
Confidence 34567899999998543 2 22246666654 345677889999999999999999999999873 344
Q ss_pred CCCCHHHHHHHHHHHhccceEEEEecCCCHHHHHHH
Q 001786 618 RGVFDGTVENMHLHWKHRELVKIISKQRKIEAALQE 653 (1013)
Q Consensus 618 ~GVtdgVIe~Ih~Alk~rELIKVk~~~n~~ed~kei 653 (1013)
.=+++.=.+.--.||-..|.|+|+........+.++
T Consensus 104 ~vlt~~E~d~y~eALm~~e~v~vk~~~~~~~~ve~v 139 (162)
T PF12207_consen 104 EVLTQEEYDQYIEALMTYETVRVKTKSSGGITVEEV 139 (162)
T ss_dssp HHS-HHHHHHHHHHHHHHHHHHHHCT-SS---GGGS
T ss_pred hhcCHHHHHHHHHHHhhhheeeeeccCCCCCcHHhc
Confidence 556777777888899999999998886554444443
No 13
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=22.14 E-value=1.4e+02 Score=29.70 Aligned_cols=37 Identities=22% Similarity=0.330 Sum_probs=31.2
Q ss_pred HHHHHHhcccCCC-ceEEeccCCCCHHHHHHHHHHHhc
Q 001786 598 ERYMLRKVGLRMK-AFLLMGRRGVFDGTVENMHLHWKH 634 (1013)
Q Consensus 598 ERk~LRkiGhkmk-PvV~IGK~GVtdgVIe~Ih~Alk~ 634 (1013)
+--.+.++|.+-+ |++.++.+|.|+.+++.++.....
T Consensus 72 ~~~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~ 109 (133)
T PF03641_consen 72 EALTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEE 109 (133)
T ss_dssp HHHHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHT
T ss_pred HHHHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHC
Confidence 5566788998888 999999999999999999755543
No 14
>TIGR02398 gluc_glyc_Psyn glucosylglycerol-phosphate synthase. Glucosylglycerol-phosphate synthase catalyzes the key step in the biosynthesis of the osmolyte glucosylglycerol. It is known in several cyanobacteria and in Pseudomonas anguilliseptica. The enzyme is closely related to the alpha,alpha-trehalose-phosphate synthase, likewise involved in osmolyte biosynthesis, of E. coli and many other bacteria. A close homolog from Xanthomonas campestris is excluded from this model and scores between trusted and noise.
Probab=20.64 E-value=1.2e+02 Score=36.86 Aligned_cols=72 Identities=19% Similarity=0.244 Sum_probs=55.2
Q ss_pred hHHHHHHHHHHhhcCCCeecccchhHHHHHHHHHHHh---hhcCC-------eEEEeeccCCCCCcHHHHHHHHHHhcCc
Q 001786 937 RDRLLLRKQALRMKKRPVLAVGRSNIVTGVAKAIKAH---FEKYP-------LAIVNVKGRAKGTSVQEVVAKLEVCMPK 1006 (1013)
Q Consensus 937 r~rl~lrkqal~mk~rp~~~igr~n~vtg~ak~ik~h---f~k~p-------~~~v~vk~ra~gt~v~~~~~~le~~t~~ 1006 (1013)
..+..||++ +. .++-+|.|||=--..|+-.-|.|+ +++|| |.+|.+.-|.....-+++..+|++..|.
T Consensus 273 ~~~~~lr~~-~~-~~kiIl~VDRLDy~KGI~~kl~Afe~~L~~~Pe~~gkv~Lvqi~~psr~~v~~y~~l~~~v~~~v~~ 350 (487)
T TIGR02398 273 EMMERIRSE-LA-GVKLILSAERVDYTKGILEKLNAYERLLERRPELLGKVTLVTACVPAASGMTIYDELQGQIEQAVGR 350 (487)
T ss_pred HHHHHHHHH-cC-CceEEEEecccccccCHHHHHHHHHHHHHhCccccCceEEEEEeCCCcccchHHHHHHHHHHHHHHH
Confidence 344556664 33 234589999988888888777665 68999 8899999898888889999999998888
Q ss_pred ceee
Q 001786 1007 YNFV 1010 (1013)
Q Consensus 1007 ~~~~ 1010 (1013)
+|--
T Consensus 351 IN~~ 354 (487)
T TIGR02398 351 INGR 354 (487)
T ss_pred Hhhc
Confidence 7543
Done!