Query 013187
Match_columns 448
No_of_seqs 194 out of 607
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 01:17:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013187.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013187hhsearch_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 99.9 6.4E-28 1.4E-32 252.7 9.4 210 108-319 308-530 (564)
2 PRK10343 RNA-binding protein Y 99.9 5.1E-27 1.1E-31 198.9 12.8 89 172-261 1-89 (97)
3 TIGR00253 RNA_bind_YhbY putati 99.9 6E-27 1.3E-31 197.5 12.6 87 174-261 1-87 (95)
4 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 1.4E-26 3E-31 189.1 11.0 84 174-258 1-84 (84)
5 COG1534 Predicted RNA-binding 99.9 3.4E-25 7.4E-30 188.3 12.4 91 173-265 1-91 (97)
6 KOG1990 Poly(A)-specific exori 97.8 1.1E-05 2.4E-10 86.3 2.9 152 113-265 114-268 (564)
7 PRK13482 DNA integrity scannin 47.4 46 0.00099 35.1 6.2 50 226-279 97-147 (352)
8 COG1623 Predicted nucleic-acid 45.4 93 0.002 32.8 7.9 72 227-310 104-176 (349)
9 PF04472 DUF552: Protein of un 44.2 1.1E+02 0.0024 24.5 6.7 56 205-262 12-70 (73)
10 PF07412 Geminin: Geminin; In 38.9 75 0.0016 31.3 5.8 33 277-311 115-147 (200)
11 PF03641 Lysine_decarbox: Poss 34.5 45 0.00098 29.4 3.4 35 180-214 74-109 (133)
12 PF13604 AAA_30: AAA domain; P 34.5 2.2E+02 0.0047 26.5 8.0 69 173-246 1-71 (196)
13 PF04931 DNA_pol_phi: DNA poly 31.6 1.2E+02 0.0027 34.3 6.9 37 275-313 597-633 (784)
14 PF12207 DUF3600: Domain of un 23.4 10 0.00023 35.9 -2.7 97 136-232 27-138 (162)
15 PF02609 Exonuc_VII_S: Exonucl 22.5 95 0.0021 23.7 2.8 38 403-445 1-38 (53)
16 TIGR00730 conserved hypothetic 21.9 1.8E+02 0.004 27.3 5.2 36 179-214 116-151 (178)
17 TIGR01223 Pmev_kin_anim phosph 21.9 50 0.0011 32.0 1.5 28 384-411 146-175 (182)
18 PRK09423 gldA glycerol dehydro 20.8 3.5E+02 0.0077 27.5 7.3 21 425-445 341-361 (366)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.95 E-value=6.4e-28 Score=252.72 Aligned_cols=210 Identities=41% Similarity=0.590 Sum_probs=189.6
Q ss_pred hhhhhhhhhhhhhhhhhh-----hHHhhccChH---HHHHHHHHHHHHHHHHHHHhhcccCCC-CCCCCCCCCCCCCHHH
Q 013187 108 LKGKRAVVRWLKHFRYKK-----KKEYERMTAE---EKILYKLRKARKKEERIVEGLKKIEPK-ESSEMTHDPEILTPEE 178 (448)
Q Consensus 108 ~k~k~a~~~~~~~~r~~~-----kke~~~~~~e---~ri~~KL~~A~kK~er~~e~L~K~E~~-~paEp~~DpE~LT~EE 178 (448)
..-..+..+|.+.+.+.. +.+.+.+..+ +.+.+++..+++|++++...|++++.+ .|++..++++.+|.++
T Consensus 308 ~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee 387 (564)
T KOG1990|consen 308 LELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEE 387 (564)
T ss_pred HHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHH
Confidence 344556677776666554 6666666555 788999999999999999999999987 8899999999999999
Q ss_pred HHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCH-HHHHHHHHHHHHHhCCEEEEEe---eCcEE
Q 013187 179 HFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA-EEVKEIAAELARLTGGIVLEIH---EENTI 254 (448)
Q Consensus 179 Rk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~-ed~keIAeeLee~SGGeLVQVi---IG~tI 254 (448)
+.+++++|.+|++++.+|++|+++||+.++|.||++||++||+|+.... .++++.|..++..+|+++|++. .|..|
T Consensus 388 ~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai 467 (564)
T KOG1990|consen 388 RLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAI 467 (564)
T ss_pred HHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhH
Confidence 9999999999999999999999999999999999999999999999765 9999999999999999999975 46669
Q ss_pred EEEeCCCCCCCCCccCCCCcccchHHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHhhhcccc
Q 013187 255 IMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSENR 319 (448)
Q Consensus 255 ILYRGKNY~rP~~~i~~P~~lLtKrkAL~rS~e~Qr~eslk~~I~~le~~ie~l~~~~~~~~~~~ 319 (448)
+.|||+||++|.+ |+|.++|+||+|+.+++++|+.+|+++||..+++++++++.++.......
T Consensus 468 ~~yr~k~y~~p~~--l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~~~~~~~ 530 (564)
T KOG1990|consen 468 IAYRGKNYDRPTS--LRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQASVEAMPAIN 530 (564)
T ss_pred HHhhhhhccCCcc--cCchhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchhcccccc
Confidence 9999999999975 99999999999999999999999999999999999999999987765444
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.94 E-value=5.1e-27 Score=198.92 Aligned_cols=89 Identities=21% Similarity=0.340 Sum_probs=86.3
Q ss_pred CCCCHHHHHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeC
Q 013187 172 EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 251 (448)
Q Consensus 172 E~LT~EERk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLVQViIG 251 (448)
++||++||++||++||+|+|+|+||++||||+|+.+|+.+|++||||||++.+++.+++++++++|++.|||++||+ ||
T Consensus 1 m~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~-IG 79 (97)
T PRK10343 1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQV-IG 79 (97)
T ss_pred CCCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEee-eC
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999999997 69
Q ss_pred cEEEEEeCCC
Q 013187 252 NTIIMYRGKN 261 (448)
Q Consensus 252 ~tIILYRGKN 261 (448)
+++||||++.
T Consensus 80 ~~~vlYR~~~ 89 (97)
T PRK10343 80 KTLVLYRPTK 89 (97)
T ss_pred cEEEEEecCC
Confidence 9999999864
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=99.94 E-value=6e-27 Score=197.51 Aligned_cols=87 Identities=28% Similarity=0.369 Sum_probs=84.8
Q ss_pred CCHHHHHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCcE
Q 013187 174 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT 253 (448)
Q Consensus 174 LT~EERk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLVQViIG~t 253 (448)
||++||++||++||+|+|+|+||++|||++||++|+.+|++||||||++.+++.++++++|++|++.|||++||+ +|++
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~-iG~~ 79 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQV-IGKT 79 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEE-EccE
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999997 6999
Q ss_pred EEEEeCCC
Q 013187 254 IIMYRGKN 261 (448)
Q Consensus 254 IILYRGKN 261 (448)
+||||++.
T Consensus 80 ~vlYR~~~ 87 (95)
T TIGR00253 80 IVLYRPTK 87 (95)
T ss_pred EEEEecCC
Confidence 99999864
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=99.94 E-value=1.4e-26 Score=189.12 Aligned_cols=84 Identities=36% Similarity=0.522 Sum_probs=74.9
Q ss_pred CCHHHHHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCcE
Q 013187 174 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT 253 (448)
Q Consensus 174 LT~EERk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLVQViIG~t 253 (448)
||++|+++||++||+|+|+|+||++|||++|+++|+.+|++||||||+|.+++.++++++|+.|++.|||++|++ +|++
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~-iG~~ 79 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQV-IGRT 79 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEE-ETTE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEE-ECCE
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999986 7999
Q ss_pred EEEEe
Q 013187 254 IIMYR 258 (448)
Q Consensus 254 IILYR 258 (448)
+||||
T Consensus 80 ~vlyR 84 (84)
T PF01985_consen 80 IVLYR 84 (84)
T ss_dssp EEEEE
T ss_pred EEEEC
Confidence 99998
No 5
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=3.4e-25 Score=188.27 Aligned_cols=91 Identities=26% Similarity=0.429 Sum_probs=86.4
Q ss_pred CCCHHHHHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 013187 173 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN 252 (448)
Q Consensus 173 ~LT~EERk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLVQViIG~ 252 (448)
+||++|+++||+.||+++|+|+||++|||++||.+|+.+|++||||||++.+++.++.+++|+.|++.+||.+||+ +|+
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqv-iG~ 79 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQV-IGK 79 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeee-eee
Confidence 5999999999999999999999999999999999999999999999999999999999999999999999999998 699
Q ss_pred EEEEEeCCCCCCC
Q 013187 253 TIIMYRGKNYAQP 265 (448)
Q Consensus 253 tIILYRGKNY~rP 265 (448)
++|||| .+...+
T Consensus 80 ~~vlyr-~~~e~~ 91 (97)
T COG1534 80 TLVLYR-ESKEKR 91 (97)
T ss_pred EEEEEe-cCcccc
Confidence 999999 444444
No 6
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=97.80 E-value=1.1e-05 Score=86.26 Aligned_cols=152 Identities=21% Similarity=0.288 Sum_probs=125.6
Q ss_pred hhhhhhhhhhhhhhHHhhccChHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCCCHHHHHHHHhhhccCCce
Q 013187 113 AVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNY 192 (448)
Q Consensus 113 a~~~~~~~~r~~~kke~~~~~~e~ri~~KL~~A~kK~er~~e~L~K~E~~~paEp~~DpE~LT~EERk~LRKlGhkLKPV 192 (448)
+...|+..++..++.-...|.++..--|-..........+.+.+..+..|...-+...+..||..+.-++|.+|-...|+
T Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~ 193 (564)
T KOG1990|consen 114 QAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPH 193 (564)
T ss_pred hhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhccccccc
Confidence 45557777777778888888888544444444555666778888888888777788889999999999999999999999
Q ss_pred eeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCC-CHHHHHHHHHHH--HHHhCCEEEEEeeCcEEEEEeCCCCCCC
Q 013187 193 VPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTF-SAEEVKEIAAEL--ARLTGGIVLEIHEENTIIMYRGKNYAQP 265 (448)
Q Consensus 193 V~IGKrGVTDgVIeeIh~AwK~HELVKVKvk~~-s~ed~keIAeeL--ee~SGGeLVQViIG~tIILYRGKNY~rP 265 (448)
+.+|.++.-.++...|..+|..|+..|+-+... .......++..+ -..+|+.||.. -|..+|+||++||-.|
T Consensus 194 ~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~h-N~~~dv~y~~~~Fl~~ 268 (564)
T KOG1990|consen 194 FALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLH-NKLLDVMYRYKNFLSP 268 (564)
T ss_pred ceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEee-ccceeeeeehhhcccc
Confidence 999999999999999999999999999877654 344456778888 88999999964 6889999999999774
No 7
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=47.41 E-value=46 Score=35.14 Aligned_cols=50 Identities=24% Similarity=0.314 Sum_probs=34.3
Q ss_pred CHHHHHHHHHHHHHHhCCEEEEEe-eCcEEEEEeCCCCCCCCCccCCCCcccchH
Q 013187 226 SAEEVKEIAAELARLTGGIVLEIH-EENTIIMYRGKNYAQPPTEIMSPRITLSRK 279 (448)
Q Consensus 226 s~ed~keIAeeLee~SGGeLVQVi-IG~tIILYRGKNY~rP~~~i~~P~~lLtKr 279 (448)
....++.+|.-+++.||+.+|.|. .-++|-+|.+. .... +..|..+++|-
T Consensus 97 e~GtRHRaA~gise~Tda~vIvVSee~g~Isl~~~g-~~~~---~~d~~~l~~~a 147 (352)
T PRK13482 97 ETGTRHRTAERVAKQTGVPVIAVSQRRNIITLYVGG-LRYV---LEDIGVILSRA 147 (352)
T ss_pred cCcHHHHHhhHHHHhcCCEEEEEecccCeEEEEECC-EEEe---cCCHHHHHHHH
Confidence 345789999999999999999764 23577777753 2332 34466666654
No 8
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=45.37 E-value=93 Score=32.79 Aligned_cols=72 Identities=26% Similarity=0.402 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHHHHhCCEEEEEe-eCcEEEEEeCCCCCCCCCccCCCCcccchHHHHHHHHHHhhhHHHHhhHHHHHHHH
Q 013187 227 AEEVKEIAAELARLTGGIVLEIH-EENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQEL 305 (448)
Q Consensus 227 ~ed~keIAeeLee~SGGeLVQVi-IG~tIILYRGKNY~rP~~~i~~P~~lLtKrkAL~rS~e~Qr~eslk~~I~~le~~i 305 (448)
...++..|+-.|..||..||+|. --|+|.||.+ |++.- +-.+-.+|+| .-|-++.|..|-..|.+.+
T Consensus 104 tGtRHRTAER~AkqTG~~VIaiS~rrNvITlY~~-~~ky~---L~d~~~il~r--------anQAi~TLEkYk~~Ld~~~ 171 (349)
T COG1623 104 TGTRHRTAERVAKQTGNPVIAISERRNVITLYVG-NLKYV---LKDSAFILSR--------ANQAIQTLEKYKTVLDRVL 171 (349)
T ss_pred CccccchHHHHHHHhCCeEEEEecccceEEEEec-Ceeee---ecChHHHHHH--------HHHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999974 3579999987 66552 1223334554 4566666666666666666
Q ss_pred HHHHH
Q 013187 306 ELLRA 310 (448)
Q Consensus 306 e~l~~ 310 (448)
..|..
T Consensus 172 ~~L~~ 176 (349)
T COG1623 172 NQLNL 176 (349)
T ss_pred hhhhh
Confidence 65543
No 9
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=44.23 E-value=1.1e+02 Score=24.49 Aligned_cols=56 Identities=14% Similarity=0.181 Sum_probs=39.3
Q ss_pred HHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHH---HhCCEEEEEeeCcEEEEEeCCCC
Q 013187 205 ILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELAR---LTGGIVLEIHEENTIIMYRGKNY 262 (448)
Q Consensus 205 IeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee---~SGGeLVQViIG~tIILYRGKNY 262 (448)
+.++-++++....|=|.+.....++.+++...|.. ..+|.+..+ |..++++=++|.
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~i--~~~~~l~~P~~V 70 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQKI--SEKVFLLTPKGV 70 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEEE--ETTEEEEE----
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEEE--cCCEEEEECCCc
Confidence 35588999999999999999998889999988876 679999964 777888877654
No 10
>PF07412 Geminin: Geminin; InterPro: IPR022786 This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle []. ; GO: 0008156 negative regulation of DNA replication; PDB: 1T6F_B 2LP0_B 1UII_B 2WVR_B 2ZXX_B.
Probab=38.87 E-value=75 Score=31.28 Aligned_cols=33 Identities=24% Similarity=0.405 Sum_probs=21.7
Q ss_pred chHHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHH
Q 013187 277 SRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQ 311 (448)
Q Consensus 277 tKrkAL~rS~e~Qr~eslk~~I~~le~~ie~l~~~ 311 (448)
-||+||.-++++-.. |..-|..++.+|..|+.+
T Consensus 115 ~RR~AL~eaL~ENe~--Lh~~ie~~~eEi~~lk~e 147 (200)
T PF07412_consen 115 ERRKALEEALEENEK--LHKEIEQKDEEIAKLKEE 147 (200)
T ss_dssp HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
Confidence 367888888876433 555566666666666654
No 11
>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=34.54 E-value=45 Score=29.42 Aligned_cols=35 Identities=11% Similarity=0.299 Sum_probs=29.1
Q ss_pred HHHHhhhccCC-ceeeeCCCCCcHHHHHHHHHHHHh
Q 013187 180 FYFLKMGRKCK-NYVPVGRRGIYQGVILNMHLHWKK 214 (448)
Q Consensus 180 k~LRKlGhkLK-PVV~IGKrGVTDgVIeeIh~AwK~ 214 (448)
-.+.++|.+-+ |++.++.+|.++.+++.++..+..
T Consensus 74 ~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~ 109 (133)
T PF03641_consen 74 LTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEE 109 (133)
T ss_dssp HHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHT
T ss_pred HHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHC
Confidence 44677888888 999999999999999999755544
No 12
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=34.46 E-value=2.2e+02 Score=26.50 Aligned_cols=69 Identities=16% Similarity=0.058 Sum_probs=47.6
Q ss_pred CCCHHHHHHHHhhhccCCceeee-CCCCCcHH-HHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEE
Q 013187 173 ILTPEEHFYFLKMGRKCKNYVPV-GRRGIYQG-VILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVL 246 (448)
Q Consensus 173 ~LT~EERk~LRKlGhkLKPVV~I-GKrGVTDg-VIeeIh~AwK~HELVKVKvk~~s~ed~keIAeeLee~SGGeLV 246 (448)
.||++|+..++.+-..-+.++.| |..|---. ++..+..+|..+. .+|.+...+ ..++..|...+|....
T Consensus 1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~g-~~v~~~apT----~~Aa~~L~~~~~~~a~ 71 (196)
T PF13604_consen 1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEAAG-KRVIGLAPT----NKAAKELREKTGIEAQ 71 (196)
T ss_dssp -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHHTT---EEEEESS----HHHHHHHHHHHTS-EE
T ss_pred CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHhCC-CeEEEECCc----HHHHHHHHHhhCcchh
Confidence 48999999999997666655555 99886554 4667899999987 777776665 3456667777775554
No 13
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=31.58 E-value=1.2e+02 Score=34.28 Aligned_cols=37 Identities=24% Similarity=0.199 Sum_probs=27.5
Q ss_pred ccchHHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHh
Q 013187 275 TLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAE 313 (448)
Q Consensus 275 lLtKrkAL~rS~e~Qr~eslk~~I~~le~~ie~l~~~~~ 313 (448)
+|++..+|=|.+-.|=-+++-.||. +..|+.|-..+.
T Consensus 597 lls~~s~llR~~~~~vf~~~~~~~t--~~~l~~ll~vl~ 633 (784)
T PF04931_consen 597 LLSQPSALLRKVSEQVFEAFCPHLT--ESGLQLLLDVLD 633 (784)
T ss_pred HHhCcchHHHHHHHHHHHHHHhhcC--HHHHHHHHHHhc
Confidence 6899999999999987777766654 345666666665
No 14
>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=23.40 E-value=10 Score=35.93 Aligned_cols=97 Identities=22% Similarity=0.162 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHHH-----HHHHHHhhcccCCC----CCCCCCCCCCCCCHHHHHHHHhhhccCCceee------eCCCCC
Q 013187 136 EKILYKLRKARKK-----EERIVEGLKKIEPK----ESSEMTHDPEILTPEEHFYFLKMGRKCKNYVP------VGRRGI 200 (448)
Q Consensus 136 ~ri~~KL~~A~kK-----~er~~e~L~K~E~~----~paEp~~DpE~LT~EERk~LRKlGhkLKPVV~------IGKrGV 200 (448)
.|+.-||..|+-. -+...+.|+++-.. .-+.-..|.+.|+..++..++++...|.|++- --|.=+
T Consensus 27 ~~~eaKLqqAK~~lgeeEfeef~~lLK~lt~~kLkygD~NGnidye~ls~~eqee~k~~~~eLqPYFdKLN~~~SsK~vl 106 (162)
T PF12207_consen 27 LRLEAKLQQAKGELGEEEFEEFKELLKKLTNAKLKYGDKNGNIDYEKLSKEEQEEYKKLTMELQPYFDKLNGHKSSKEVL 106 (162)
T ss_dssp HHHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHB-TTS-B-GGGS-HHHHHHHHHHHHHHHHHHHHHTT---HHHHS
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhHHhhcccCCCcCHHhCCHHHHHHHHHHHHhcchHHHHhcCCcchhhhc
Confidence 3666777766532 23334445544331 34556789999999999999999999999862 223445
Q ss_pred cHHHHHHHHHHHHhCCeeeEEecCCCHHHHHH
Q 013187 201 YQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 232 (448)
Q Consensus 201 TDgVIeeIh~AwK~HELVKVKvk~~s~ed~ke 232 (448)
|+.-.+.--.||-.+|.|+|+.....+..+.+
T Consensus 107 t~~E~d~y~eALm~~e~v~vk~~~~~~~~ve~ 138 (162)
T PF12207_consen 107 TQEEYDQYIEALMTYETVRVKTKSSGGITVEE 138 (162)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHCT-SS---GGG
T ss_pred CHHHHHHHHHHHhhhheeeeeccCCCCCcHHh
Confidence 66667777889999999999987654444433
No 15
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=22.48 E-value=95 Score=23.71 Aligned_cols=38 Identities=29% Similarity=0.406 Sum_probs=28.7
Q ss_pred HHHHHHhhhhcccccccCCCCCCCCCchhHHHHHHHHHHhhhh
Q 013187 403 FEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKK 445 (448)
Q Consensus 403 f~~~~~~~~~~~~~~~~~~~~~~~~~~de~d~~flra~s~lkk 445 (448)
||+.+.++-.-..+.++ .++| +|+.=++|-+|..|+++
T Consensus 1 fEe~~~~Le~Iv~~Le~----~~~s-Ldes~~lyeeg~~l~~~ 38 (53)
T PF02609_consen 1 FEEAMERLEEIVEKLES----GELS-LDESLKLYEEGMELIKK 38 (53)
T ss_dssp HHHHHHHHHHHHHHHHT----T-S--HHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHc----CCCC-HHHHHHHHHHHHHHHHH
Confidence 77777777776666654 3444 99999999999999886
No 16
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=21.93 E-value=1.8e+02 Score=27.33 Aligned_cols=36 Identities=11% Similarity=0.261 Sum_probs=29.3
Q ss_pred HHHHHhhhccCCceeeeCCCCCcHHHHHHHHHHHHh
Q 013187 179 HFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKK 214 (448)
Q Consensus 179 Rk~LRKlGhkLKPVV~IGKrGVTDgVIeeIh~AwK~ 214 (448)
--.+.++|.+-||++.++-+|.++.+++-++.....
T Consensus 116 ~~~~~qlg~~~kPiil~n~~g~~~~l~~~l~~~~~~ 151 (178)
T TIGR00730 116 VLTWAQLGIHQKPIILFNVNGHFDGLVEWLKYSIQE 151 (178)
T ss_pred HHHHHHcCCCCCCEEEECCcchHHHHHHHHHHHHHC
Confidence 345677888999999999999999999988844443
No 17
>TIGR01223 Pmev_kin_anim phosphomevalonate kinase, animal type. This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found. One is this type, found in animals. The other is the ERG8 type, found in plants and fungi (TIGR01219) and in Gram-positive bacteria (TIGR01220).
Probab=21.88 E-value=50 Score=32.02 Aligned_cols=28 Identities=29% Similarity=0.506 Sum_probs=24.3
Q ss_pred cchhhhcCCC--CCCCCCcchHHHHHHhhh
Q 013187 384 LYLDQFDKFP--VQNDEEHEDFEEHLRQIS 411 (448)
Q Consensus 384 l~l~~~~~f~--~~~~~~~~df~~~~~~~~ 411 (448)
..||.|..|- ++||+..+.+++||.+|-
T Consensus 146 c~lDd~~~~D~vi~Nd~~~~~l~~~l~~l~ 175 (182)
T TIGR01223 146 CGLDNFGDFDWVIENHGVEQRLEEQLENLI 175 (182)
T ss_pred cCCCcccceeEEEecCCChHHHHHHHHHHH
Confidence 6899997777 999999999999998874
No 18
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=20.81 E-value=3.5e+02 Score=27.54 Aligned_cols=21 Identities=14% Similarity=0.086 Sum_probs=15.4
Q ss_pred CCCCchhHHHHHHHHHHhhhh
Q 013187 425 DSSHFDEVDKMFLRAASLLKK 445 (448)
Q Consensus 425 ~~~~~de~d~~flra~s~lkk 445 (448)
.....++|-+|+.++=..-+|
T Consensus 341 ~~~t~~~i~~il~~~~~~~~~ 361 (366)
T PRK09423 341 FKVTPEDVAAAILAADAYGQR 361 (366)
T ss_pred CCCCHHHHHHHHHHHHHHHHH
Confidence 445778899999888776544
Done!