Query 002316
Match_columns 936
No_of_seqs 352 out of 1007
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 21:20:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002316.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002316hhsearch_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 1.9E-77 4E-82 684.1 22.9 533 242-848 3-540 (564)
2 PRK10343 RNA-binding protein Y 99.9 7.4E-25 1.6E-29 202.0 12.7 89 252-340 1-89 (97)
3 PRK10343 RNA-binding protein Y 99.9 9E-25 1.9E-29 201.5 13.2 88 691-782 2-89 (97)
4 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 1.1E-24 2.3E-29 195.3 10.8 84 254-337 1-84 (84)
5 TIGR00253 RNA_bind_YhbY putati 99.9 2E-24 4.3E-29 198.6 12.9 87 692-782 1-87 (95)
6 TIGR00253 RNA_bind_YhbY putati 99.9 3E-24 6.4E-29 197.4 12.6 87 254-340 1-87 (95)
7 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 7.6E-24 1.6E-28 189.8 10.5 84 692-779 1-84 (84)
8 COG1534 Predicted RNA-binding 99.9 2.2E-23 4.8E-28 191.8 12.1 96 691-791 1-96 (97)
9 COG1534 Predicted RNA-binding 99.9 2.6E-22 5.7E-27 184.7 11.7 85 253-337 1-85 (97)
10 KOG1990 Poly(A)-specific exori 99.8 5.7E-21 1.2E-25 220.4 6.3 324 246-603 167-510 (564)
11 PF10446 DUF2457: Protein of u 38.0 40 0.00086 40.0 4.5 11 910-920 119-129 (458)
12 PF15237 PTRF_SDPR: PTRF/SDPR 30.7 1.2E+02 0.0025 33.8 6.3 69 503-573 50-120 (246)
13 PF07412 Geminin: Geminin; In 30.5 38 0.00083 36.4 2.6 39 797-837 116-154 (200)
14 PF15249 GLTSCR1: Glioma tumor 28.9 22 0.00047 34.2 0.5 20 462-481 15-42 (109)
15 COG0488 Uup ATPase components 28.3 1.2E+03 0.026 28.7 14.6 101 667-785 133-237 (530)
16 PRK14472 F0F1 ATP synthase sub 27.7 90 0.002 31.9 4.7 41 559-599 30-70 (175)
17 PF12207 DUF3600: Domain of un 23.3 17 0.00037 37.5 -1.4 92 654-747 28-135 (162)
18 PF04472 DUF552: Protein of un 22.3 3.2E+02 0.0069 24.4 6.5 55 723-782 12-69 (73)
19 PF04472 DUF552: Protein of un 21.8 5.1E+02 0.011 23.1 7.7 54 285-339 12-68 (73)
20 TIGR03321 alt_F1F0_F0_B altern 20.3 1.1E+03 0.024 25.5 15.1 33 565-597 23-55 (246)
21 PTZ00399 cysteinyl-tRNA-synthe 20.1 2.9E+02 0.0063 34.5 7.7 19 685-703 615-633 (651)
No 1
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=100.00 E-value=1.9e-77 Score=684.14 Aligned_cols=533 Identities=46% Similarity=0.674 Sum_probs=496.8
Q ss_pred ccccccccccCCCCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHh
Q 002316 242 RRSSRTSLAELTLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKT 321 (936)
Q Consensus 242 kk~~~pslae~tLt~kErr~LR~lAh~LkPvV~IGK~GLTd~VVeeI~~awekhELVKVKv~~~~~~dmk~~ae~LeekT 321 (936)
++.+ +.+|++++.+.++.+||..|..+.-.+ +++|+|+.+++.|+..|+.+|+++++|....+.+|.+++++++..|
T Consensus 3 ~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~--~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~ 79 (564)
T KOG1990|consen 3 NFES-LSLAELTVDEADLRRLRLVATGMTSAP--WKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMST 79 (564)
T ss_pred cccc-hhHHHhhcCHHHHHHHhhhhccceecc--cccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccC
Confidence 3456 999999999999999999999987777 9999999999999999999999999999999999999999999999
Q ss_pred CC-eEEEEECcEEEEecCCCCCCcchhhhHHHhhhcCCCcccccchhhhhhhhhcccccCccccccccccCCCCCCCCcc
Q 002316 322 GG-LVIWRSGTAVSLYRGVSYEVPSVQLNKRIYKRNELPASSVSQATDKQIHKQISMSGNSLSAAADKTAQDPSNFDSYN 400 (936)
Q Consensus 322 Gg-eVVqrIG~viVLYRg~nY~~P~v~~~~~~~~~~E~~~~~l~~~~~~~~~~~~~~~~~s~~~a~~~~~~~p~~~~~~~ 400 (936)
|| -+||+.|..+..|++..|..|.+-.+ +.+| .+
T Consensus 80 ~~n~~~~~~g~~~s~~~~~~~~~~~~~~~----~~~~-----------~~------------------------------ 114 (564)
T KOG1990|consen 80 GGNFVVWSRGDSISSPEFLCQRSPVDFVA----RQQE-----------NQ------------------------------ 114 (564)
T ss_pred CCceeeeecCccccCCccceeecchhhhh----hhch-----------hh------------------------------
Confidence 99 99999999999998888888754321 1000 00
Q ss_pred cccccchhccccccccchhhhhhhccHHHHHHHhhccCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCcccc
Q 002316 401 NVHATQVNLETASEEQETDFVREVKYEDEVEKLLDGLGPRYTDWPGCDPLPVDADMLPGIVPGYQPPFRVLPYGVRSTLA 480 (936)
Q Consensus 401 ~~~~~~l~~~~ts~~~~~~~~~ev~~E~E~nkLLD~LGPRf~dW~g~~PlPVDADLLPa~VPgyk~PfRllP~gvre~LT 480 (936)
... -..+++++++.+++++||+|.+||+.+|+|||+||+|++||+|.+|||.+|+|+++.||
T Consensus 115 ----------------~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~ 176 (564)
T KOG1990|consen 115 ----------------AGK--WPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLT 176 (564)
T ss_pred ----------------hhh--hHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhh
Confidence 000 02356889999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccCCCeEEecccchhHHHHHHHHHhhccccceeEeeccCCCCchHHHHHHHH--HhhhCCeEeeecCce
Q 002316 481 RKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDI--KKLTGGTLLSRNKDF 558 (936)
Q Consensus 481 deE~t~lRrLar~lpphfaLGRnrvlqGLA~aI~klWEkseIaKIavKrGvqnT~~e~MAeeL--K~LTGGvLLSRnK~~ 558 (936)
..|++++|+||.+.||||+||+++.+||++.+|+++|++++++||++++|++++.++.||.+| ..+|||+||++|+++
T Consensus 177 ~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~hN~~~ 256 (564)
T KOG1990|consen 177 SIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVLHNKLL 256 (564)
T ss_pred hHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEeeccce
Confidence 999999999999999999999999999999999999999999999999999999999999999 999999999999999
Q ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHHhhHHHHHHhhhhcccccccccccccCccchhHHHHHhhhccccCCChhHH-H
Q 002316 559 LVFYRGKNFLSPDVTEALQERERLAKSLQDEEEQARLRASAFVLPSIETIEKSGTAGTLKETLDANSRWGKRLDDSHK-E 637 (936)
Q Consensus 559 II~YRGKDFlpp~V~~~L~eRe~l~rs~q~~Ee~aR~~a~~~~~~~~~~~~~~~~aGtl~e~~~a~~~~g~~~~~~~~-~ 637 (936)
+|+||||+|++ .|..+|.+++++...+++.++.+|+.+.... .....++|+.|+..+.++|+..+.-... .
T Consensus 257 dv~y~~~~Fl~-~lp~~l~~f~~~~~~fp~~~~~~~~~~~~~~-------~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~ 328 (564)
T KOG1990|consen 257 DVMYRYKNFLS-PLPSTLEEFTDSSSMFPNIEDTKRLAKLSEY-------QKLNLKATLLELARAKAKKEKEIERRSISS 328 (564)
T ss_pred eeeeehhhccc-ccchhHHHhhhhhhhhhhhHHHHHhhccccc-------cchhhhhhHHHHHHHhcccccCcccccccc
Confidence 99999999999 9999999999998899999999999983311 1246899999999999999999975543 4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCCCCCCCCHHHHHHHHhcccCCCceEEeCCCC
Q 002316 638 NLVREAEVRRHAYLVQKLEKKLARAERKLLRAERALSKVEESLKPAERQADPESITDEERFMFRKLGLRMKAFLLLGRRG 717 (936)
Q Consensus 638 ~~~~e~~~~r~~~~vk~~e~kL~~a~~K~~rae~~L~k~e~~~~p~~~~~d~E~LT~eER~~LRklghkLKpvV~IGKrG 717 (936)
.+..+.++..+++..+.+.++++.+++|+.++++.|++++....|++..+|++.+|.+++.+++++|.+|++++.+|++|
T Consensus 329 ~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg 408 (564)
T KOG1990|consen 329 RLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEERLMLRKVGLKMKRRLLSGRRG 408 (564)
T ss_pred hhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHHHHHHHHHHHhhccccccCCcc
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHhcCeEeEEEcCCCH-HHHHHHHHHHHHHhCCEEEeccccccccEEEEEecCCCCCCCcCCCCcccc
Q 002316 718 VFDGTVENMHLHWKYRELVKIIVKVKTF-DQAKKIALALEAESGGVLVSVDKISKGYAMVVYRGKDYQRPSTLRPKNLLT 796 (936)
Q Consensus 718 VtdgVIeeIh~aLk~hELVKVkv~~~~~-~d~keiA~~Le~~SGg~lVqV~k~~IG~tiILYRgkNY~rP~~l~P~nlLT 796 (936)
+++|+|.+||.||++||++||+|+.... .+++..|..++..+|+++|.|+++..|+.|+.||++||++|..++|.++|+
T Consensus 409 ~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~ 488 (564)
T KOG1990|consen 409 VFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLS 488 (564)
T ss_pred cccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhHHHhhhhhccCCcccCchhhhc
Confidence 9999999999999999999999998776 999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCcHHHHHh
Q 002316 797 KRKALARSIELQRQEALLKHVATLESNAGRLRSEIEQMNSVKGTGDEQLYDK 848 (936)
Q Consensus 797 KrkAl~rs~~~qr~~~l~~~i~~l~~~i~~l~~~l~~~~~~~~~~~~~l~~~ 848 (936)
||+|+.+++++|++++++.||..++.++++++.+++.|.......|.+.|++
T Consensus 489 ~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~~~~~~~~~~d~~~en~ 540 (564)
T KOG1990|consen 489 RRKALERSLEEQRKEALKSHISDLEQEIEQLQASVEAMPAINKKDDLEEENS 540 (564)
T ss_pred ccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchhcccccccccchHHHhh
Confidence 9999999999999999999999999999999999999999888999999998
No 2
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.92 E-value=7.4e-25 Score=202.03 Aligned_cols=89 Identities=22% Similarity=0.349 Sum_probs=87.1
Q ss_pred CCCCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECc
Q 002316 252 LTLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGT 331 (936)
Q Consensus 252 ~tLt~kErr~LR~lAh~LkPvV~IGK~GLTd~VVeeI~~awekhELVKVKv~~~~~~dmk~~ae~LeekTGgeVVqrIG~ 331 (936)
|+||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||++++++.++.++++++|+++||+++||+||+
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 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCCC
Q 002316 332 AVSLYRGVS 340 (936)
Q Consensus 332 viVLYRg~n 340 (936)
++||||+++
T Consensus 81 ~~vlYR~~~ 89 (97)
T PRK10343 81 TLVLYRPTK 89 (97)
T ss_pred EEEEEecCC
Confidence 999999985
No 3
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.92 E-value=9e-25 Score=201.47 Aligned_cols=88 Identities=22% Similarity=0.406 Sum_probs=86.2
Q ss_pred CCCHHHHHHHHhcccCCCceEEeCCCCCCHHHHHHHHHHHHhcCeEeEEEcCCCHHHHHHHHHHHHHHhCCEEEeccccc
Q 002316 691 SITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKIS 770 (936)
Q Consensus 691 ~LT~eER~~LRklghkLKpvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~lVqV~k~~ 770 (936)
+||++||++||++||+|+|+|+||++||||+||++|+.+|++||||||++.+++.++++++|++||+.+||++|| +
T Consensus 2 ~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq----~ 77 (97)
T PRK10343 2 NLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQ----V 77 (97)
T ss_pred CCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEe----e
Confidence 699999999999999999999999999999999999999999999999999999999999999999999999999 6
Q ss_pred cccEEEEEecCC
Q 002316 771 KGYAMVVYRGKD 782 (936)
Q Consensus 771 IG~tiILYRgkN 782 (936)
||+++||||++.
T Consensus 78 IG~~~vlYR~~~ 89 (97)
T PRK10343 78 IGKTLVLYRPTK 89 (97)
T ss_pred eCcEEEEEecCC
Confidence 999999999874
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=99.91 E-value=1.1e-24 Score=195.28 Aligned_cols=84 Identities=32% Similarity=0.466 Sum_probs=75.7
Q ss_pred CCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEE
Q 002316 254 LPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGTAV 333 (936)
Q Consensus 254 Lt~kErr~LR~lAh~LkPvV~IGK~GLTd~VVeeI~~awekhELVKVKv~~~~~~dmk~~ae~LeekTGgeVVqrIG~vi 333 (936)
||++|+++||++||+++|+|+|||+|+|++|+++|+++|++||||||+|.+++..+++++|+.|+++|||++||++|+++
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 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEec
Q 002316 334 SLYR 337 (936)
Q Consensus 334 VLYR 337 (936)
||||
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
>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=2e-24 Score=198.55 Aligned_cols=87 Identities=26% Similarity=0.445 Sum_probs=85.1
Q ss_pred CCHHHHHHHHhcccCCCceEEeCCCCCCHHHHHHHHHHHHhcCeEeEEEcCCCHHHHHHHHHHHHHHhCCEEEecccccc
Q 002316 692 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKISK 771 (936)
Q Consensus 692 LT~eER~~LRklghkLKpvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~lVqV~k~~I 771 (936)
||++||++||++||+|+|+|+||++||||+||++|+.+|++||||||++++++.++++++|++||+.|||++|| .|
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 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQ----VI 76 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEE----EE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999 69
Q ss_pred ccEEEEEecCC
Q 002316 772 GYAMVVYRGKD 782 (936)
Q Consensus 772 G~tiILYRgkN 782 (936)
|+++||||++.
T Consensus 77 G~~~vlYR~~~ 87 (95)
T TIGR00253 77 GKTIVLYRPTK 87 (95)
T ss_pred ccEEEEEecCC
Confidence 99999999864
No 6
>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=3e-24 Score=197.39 Aligned_cols=87 Identities=23% Similarity=0.356 Sum_probs=85.4
Q ss_pred CCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcEE
Q 002316 254 LPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGTAV 333 (936)
Q Consensus 254 Lt~kErr~LR~lAh~LkPvV~IGK~GLTd~VVeeI~~awekhELVKVKv~~~~~~dmk~~ae~LeekTGgeVVqrIG~vi 333 (936)
||++|+++||++||+|+|+|+|||+|||++|+++|+++|++||||||+++.++..+.+++|++|+++||+++||.||+++
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 EEecCCC
Q 002316 334 SLYRGVS 340 (936)
Q Consensus 334 VLYRg~n 340 (936)
||||+++
T Consensus 81 vlYR~~~ 87 (95)
T TIGR00253 81 VLYRPTK 87 (95)
T ss_pred EEEecCC
Confidence 9999974
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=99.90 E-value=7.6e-24 Score=189.78 Aligned_cols=84 Identities=32% Similarity=0.512 Sum_probs=75.4
Q ss_pred CCHHHHHHHHhcccCCCceEEeCCCCCCHHHHHHHHHHHHhcCeEeEEEcCCCHHHHHHHHHHHHHHhCCEEEecccccc
Q 002316 692 ITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKISK 771 (936)
Q Consensus 692 LT~eER~~LRklghkLKpvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~lVqV~k~~I 771 (936)
||++||++||++||+|+|+|+|||+|||++|+++|+.+|++||||||+|.+++.++++++|+.|++.|||++|+ .|
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 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQ----VI 76 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEE----EE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEE----EE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999 79
Q ss_pred ccEEEEEe
Q 002316 772 GYAMVVYR 779 (936)
Q Consensus 772 G~tiILYR 779 (936)
|+++||||
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
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=2.2e-23 Score=191.77 Aligned_cols=96 Identities=26% Similarity=0.460 Sum_probs=89.2
Q ss_pred CCCHHHHHHHHhcccCCCceEEeCCCCCCHHHHHHHHHHHHhcCeEeEEEcCCCHHHHHHHHHHHHHHhCCEEEeccccc
Q 002316 691 SITDEERFMFRKLGLRMKAFLLLGRRGVFDGTVENMHLHWKYRELVKIIVKVKTFDQAKKIALALEAESGGVLVSVDKIS 770 (936)
Q Consensus 691 ~LT~eER~~LRklghkLKpvV~IGKrGVtdgVIeeIh~aLk~hELVKVkv~~~~~~d~keiA~~Le~~SGg~lVqV~k~~ 770 (936)
+||++|+++||+.||+++|+|+||++|||++||.+|+.+|++||||||++.+++.++++++|+.|++++||.+|| +
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVq----v 76 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQ----V 76 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEee----e
Confidence 699999999999999999999999999999999999999999999999999999999999999999999999999 6
Q ss_pred cccEEEEEecCCCCCCCcCCC
Q 002316 771 KGYAMVVYRGKDYQRPSTLRP 791 (936)
Q Consensus 771 IG~tiILYRgkNY~rP~~l~P 791 (936)
||+++|||| .+..++....|
T Consensus 77 iG~~~vlyr-~~~e~~~i~l~ 96 (97)
T COG1534 77 IGKTLVLYR-ESKEKRKISLP 96 (97)
T ss_pred eeeEEEEEe-cCcccccccCC
Confidence 999999999 44455444444
No 9
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=2.6e-22 Score=184.74 Aligned_cols=85 Identities=26% Similarity=0.388 Sum_probs=84.2
Q ss_pred CCCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHHHhCCeEEEEECcE
Q 002316 253 TLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILERKTGGLVIWRSGTA 332 (936)
Q Consensus 253 tLt~kErr~LR~lAh~LkPvV~IGK~GLTd~VVeeI~~awekhELVKVKv~~~~~~dmk~~ae~LeekTGgeVVqrIG~v 332 (936)
+||++|+++||+.||+++|+|+|||+|||++|+++|+++|++||||||++.+++.++.+.+|+.|++.||+.+||+||++
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 EEEec
Q 002316 333 VSLYR 337 (936)
Q Consensus 333 iVLYR 337 (936)
+||||
T Consensus 81 ~vlyr 85 (97)
T COG1534 81 LVLYR 85 (97)
T ss_pred EEEEe
Confidence 99999
No 10
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.82 E-value=5.7e-21 Score=220.39 Aligned_cols=324 Identities=18% Similarity=0.227 Sum_probs=223.1
Q ss_pred ccccccCCCCHHHHHHHHhhhcCCCCeEEeCCCCCCHHHHHHHHHHHHhCCeEEEEec-CCChhhHHHHHHHH--HHHhC
Q 002316 246 RTSLAELTLPESELRRLRNLTFQTKSKTRIKGAGLTQAVVDIIHEKWKTSEIVRLKIE-GAPALNMKRMHEIL--ERKTG 322 (936)
Q Consensus 246 ~pslae~tLt~kErr~LR~lAh~LkPvV~IGK~GLTd~VVeeI~~awekhELVKVKv~-~~~~~dmk~~ae~L--eekTG 322 (936)
.|.--...|+..+...+|.++..++++|.+|..+.-+++.-.+...|.+|+.+|+.+. +.+......++.++ ...||
T Consensus 167 l~~~~~~~l~~~~~~~~r~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg 246 (564)
T KOG1990|consen 167 LPVGSPPLLTSIESTLLRRLGYKLPPHFALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTG 246 (564)
T ss_pred CCCCChhhhhhHHHHHHHHhcccccccceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcC
Confidence 3444555699999999999999999999999999999999999999999999999888 77788888899999 89999
Q ss_pred CeEEEEECcEEEEecCCCCCCcchhhhHHHhhhcCCCcccccchhhhhhhhhcccccC-cc-------ccccccccCCCC
Q 002316 323 GLVIWRSGTAVSLYRGVSYEVPSVQLNKRIYKRNELPASSVSQATDKQIHKQISMSGN-SL-------SAAADKTAQDPS 394 (936)
Q Consensus 323 geVVqrIG~viVLYRg~nY~~P~v~~~~~~~~~~E~~~~~l~~~~~~~~~~~~~~~~~-s~-------~~a~~~~~~~p~ 394 (936)
+.||.++|-..|+||+++|.. ++..+.. . ........++..+...-.++....+ .. ..+...|...+.
T Consensus 247 ~~lv~hN~~~dv~y~~~~Fl~-~lp~~l~--~-f~~~~~~fp~~~~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~ 322 (564)
T KOG1990|consen 247 KVLVLHNKLLDVMYRYKNFLS-PLPSTLE--E-FTDSSSMFPNIEDTKRLAKLSEYQKLNLKATLLELARAKAKKEKEIE 322 (564)
T ss_pred CeEEeeccceeeeeehhhccc-ccchhHH--H-hhhhhhhhhhhHHHHHhhccccccchhhhhhHHHHHHHhcccccCcc
Confidence 999999999999999999998 5654322 1 1221233344332211111111111 00 011122221111
Q ss_pred CCCCcccccccchhccccccccchhhhhhhccHHHHHHHhhcc--CCCcCCCCCCCCCCCCCCCCCCCCCCCCCCcccCC
Q 002316 395 NFDSYNNVHATQVNLETASEEQETDFVREVKYEDEVEKLLDGL--GPRYTDWPGCDPLPVDADMLPGIVPGYQPPFRVLP 472 (936)
Q Consensus 395 ~~~~~~~~~~~~l~~~~ts~~~~~~~~~ev~~E~E~nkLLD~L--GPRf~dW~g~~PlPVDADLLPa~VPgyk~PfRllP 472 (936)
....... . .+.....+ -+.-.+.+-+.| |-++..|.-...--+....-|+.-
T Consensus 323 ~~~~~~~--~-~~e~~~~~------------~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~----------- 376 (564)
T KOG1990|consen 323 RRSISSR--L-KLEFEKAS------------SEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAEL----------- 376 (564)
T ss_pred cccccch--h-hhhhhccc------------hhhHHHHHHHHHhhhhhhccchhhhhhccccccccccc-----------
Confidence 0000000 0 00000000 000111111111 222222222211122222223331
Q ss_pred CCCCccccHHHHHHHHHhhccCCCeEEecccchhHHHHHHHHHhhccccceeEeeccCCCCchHHHHHHHHHhhhCCeEe
Q 002316 473 YGVRSTLARKEATNLQRLARVLPPHFALGRSRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKLTGGTLL 552 (936)
Q Consensus 473 ~gvre~LTdeE~t~lRrLar~lpphfaLGRnrvlqGLA~aI~klWEkseIaKIavKrGvqnT~~e~MAeeLK~LTGGvLL 552 (936)
+-.++.+|++|+.+++++|.+|...+.+||+++|.||+.+||.||++++.+|+++|....-...+..|.+|+.++||++|
T Consensus 377 ~~~~e~~t~ee~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v 456 (564)
T KOG1990|consen 377 RYDPESITEEERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILV 456 (564)
T ss_pred ccchhhcChHHHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCcee
Confidence 12578999999999999999999999999999999999999999999999999999876669999999999999999999
Q ss_pred eecC----ceEEEEecCCCCCHHH---HHHHHHHHHHHHHHhhHHHHHHhhhhccccc
Q 002316 553 SRNK----DFLVFYRGKNFLSPDV---TEALQERERLAKSLQDEEEQARLRASAFVLP 603 (936)
Q Consensus 553 SRnK----~~II~YRGKDFlpp~V---~~~L~eRe~l~rs~q~~Ee~aR~~a~~~~~~ 603 (936)
+.++ |+|++||||+|-.|.. .+.|++|.++.+++... +.+|-...++
T Consensus 457 ~~~~~~~~~ai~~yr~k~y~~p~~l~P~~~l~~~k~~~~~~~~~----~~~a~~~~i~ 510 (564)
T KOG1990|consen 457 SIDKNPKGYAIIAYRGKNYDRPTSLRPRNLLSRRKALERSLEEQ----RKEALKSHIS 510 (564)
T ss_pred eeccCCchhhHHHhhhhhccCCcccCchhhhcccCCccccHHHH----HHHHHhhhcc
Confidence 9888 7799999999988875 38999999999887654 4455444443
No 11
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=37.98 E-value=40 Score=40.03 Aligned_cols=11 Identities=27% Similarity=0.271 Sum_probs=7.1
Q ss_pred ccceeeeeeee
Q 002316 910 DSESEAYTVHS 920 (936)
Q Consensus 910 ~~~~~~~~~~~ 920 (936)
.|.|..||--.
T Consensus 119 ~sd~~~WtP~~ 129 (458)
T PF10446_consen 119 GSDYEFWTPGA 129 (458)
T ss_pred cccceeecccc
Confidence 46777777543
No 12
>PF15237 PTRF_SDPR: PTRF/SDPR family
Probab=30.70 E-value=1.2e+02 Score=33.76 Aligned_cols=69 Identities=26% Similarity=0.343 Sum_probs=55.5
Q ss_pred cchhHHHHHHHHHhhccccceeEeeccCCCCchHHHHHHHHHhh--hCCeEeeecCceEEEEecCCCCCHHHH
Q 002316 503 SRQLQGLAVAMIKLWEKSSIAKIALKRGVQLTTSERMVEDIKKL--TGGTLLSRNKDFLVFYRGKNFLSPDVT 573 (936)
Q Consensus 503 nrvlqGLA~aI~klWEkseIaKIavKrGvqnT~~e~MAeeLK~L--TGGvLLSRnK~~II~YRGKDFlpp~V~ 573 (936)
.+.+.+++..+-||.+|+.=|-+.||. |. ...++=|--+|+| +-+-||-||++.++||.+..=+|..+.
T Consensus 50 sk~H~~TsnTV~KLLeK~RKVS~~vk~-Vr-~r~ekQ~~qVkklE~n~~eLL~Rn~FkVlI~Qee~eiPa~~~ 120 (246)
T PF15237_consen 50 SKSHSTTSNTVNKLLEKTRKVSVNVKE-VR-ERLEKQAAQVKKLEANHAELLKRNKFKVLIFQEENEIPASVF 120 (246)
T ss_pred HHhcccHHHHHHHHHHHHHHhhhhHHH-HH-HHHHHHHHHHhhhhccHHHHhhccCceEEeccccccCCCccc
Confidence 456778999999999999988888883 43 5666666666654 557799999999999999999998754
No 13
>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=30.50 E-value=38 Score=36.39 Aligned_cols=39 Identities=26% Similarity=0.481 Sum_probs=26.0
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 002316 797 KRKALARSIELQRQEALLKHVATLESNAGRLRSEIEQMNSV 837 (936)
Q Consensus 797 KrkAl~rs~~~qr~~~l~~~i~~l~~~i~~l~~~l~~~~~~ 837 (936)
||+||.-+++.-+. |..-|..++.+|..|+.+...+..+
T Consensus 116 RR~AL~eaL~ENe~--Lh~~ie~~~eEi~~lk~en~~L~el 154 (200)
T PF07412_consen 116 RRKALEEALEENEK--LHKEIEQKDEEIAKLKEENEELKEL 154 (200)
T ss_dssp HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHCCHHH
T ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78888877765443 5555777777777777766555443
No 14
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=28.88 E-value=22 Score=34.21 Aligned_cols=20 Identities=45% Similarity=0.909 Sum_probs=14.3
Q ss_pred CCCCCCc--------ccCCCCCCccccH
Q 002316 462 PGYQPPF--------RVLPYGVRSTLAR 481 (936)
Q Consensus 462 Pgyk~Pf--------RllP~gvre~LTd 481 (936)
|.|++|| |||||.|-.....
T Consensus 15 PD~~tPF~s~~DA~~RLLPYHv~~~~~~ 42 (109)
T PF15249_consen 15 PDYKTPFRSLEDAVERLLPYHVFQEPEE 42 (109)
T ss_pred CCcCCCCCCHHHHHHHhcchhhhcCCCC
Confidence 6788998 6888877555443
No 15
>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
Probab=28.25 E-value=1.2e+03 Score=28.66 Aligned_cols=101 Identities=21% Similarity=0.113 Sum_probs=73.9
Q ss_pred HHHHHHHHhhhccCCCCCCCCCCCCCCHHHHHHH-HhcccCCCceEEe---CCCCCCHHHHHHHHHHHHhcCeEeEEEcC
Q 002316 667 LRAERALSKVEESLKPAERQADPESITDEERFMF-RKLGLRMKAFLLL---GRRGVFDGTVENMHLHWKYRELVKIIVKV 742 (936)
Q Consensus 667 ~rae~~L~k~e~~~~p~~~~~d~E~LT~eER~~L-RklghkLKpvV~I---GKrGVtdgVIeeIh~aLk~hELVKVkv~~ 742 (936)
.+++..|..|.-.. + +.....|++-||..+ =+.++-.+|-+++ --+-|--..|+=+...|+.++= -|++-.
T Consensus 133 ~~~~~~L~gLg~~~---~-~~~~~~LSGG~r~Rv~LA~aL~~~pDlLLLDEPTNHLD~~~i~WLe~~L~~~~g-tviiVS 207 (530)
T COG0488 133 ARAEEALLGLGFPD---E-DRPVSSLSGGWRRRVALARALLEEPDLLLLDEPTNHLDLESIEWLEDYLKRYPG-TVIVVS 207 (530)
T ss_pred HHHHHHHhcCCCCc---c-cCchhhcCHHHHHHHHHHHHHhcCCCEEEEcCCCcccCHHHHHHHHHHHHhCCC-cEEEEe
Confidence 56677777776642 2 666778999877654 6777888888887 6778888999999999988776 555555
Q ss_pred CCHHHHHHHHHHHHHHhCCEEEeccccccccEEEEEecCCCCC
Q 002316 743 KTFDQAKKIALALEAESGGVLVSVDKISKGYAMVVYRGKDYQR 785 (936)
Q Consensus 743 ~~~~d~keiA~~Le~~SGg~lVqV~k~~IG~tiILYRgkNY~r 785 (936)
.++...+++|..|.....+ .+..|.| ||..
T Consensus 208 HDR~FLd~V~t~I~~ld~g------------~l~~y~G-ny~~ 237 (530)
T COG0488 208 HDRYFLDNVATHILELDRG------------KLTPYKG-NYSS 237 (530)
T ss_pred CCHHHHHHHhhheEEecCC------------ceeEecC-CHHH
Confidence 6788888888876554444 5566888 7765
No 16
>PRK14472 F0F1 ATP synthase subunit B; Provisional
Probab=27.69 E-value=90 Score=31.94 Aligned_cols=41 Identities=29% Similarity=0.254 Sum_probs=28.8
Q ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHHhhHHHHHHhhhhc
Q 002316 559 LVFYRGKNFLSPDVTEALQERERLAKSLQDEEEQARLRASA 599 (936)
Q Consensus 559 II~YRGKDFlpp~V~~~L~eRe~l~rs~q~~Ee~aR~~a~~ 599 (936)
|+++=-+-|+.+.+.+.|.+|+.....-.++-++++..|-.
T Consensus 30 il~~lL~~~l~kpi~~~l~~R~~~I~~~l~~Ae~~~~eA~~ 70 (175)
T PRK14472 30 IVLLILKKIAWGPILSALEEREKGIQSSIDRAHSAKDEAEA 70 (175)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444456788889999999999877666666666665543
No 17
>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=23.29 E-value=17 Score=37.52 Aligned_cols=92 Identities=20% Similarity=0.223 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHHHHHH-----HHHHh-----hhccCCCCCCCCCCCCCCHHHHHHHHhcccCCCceE------EeCCCC
Q 002316 654 KLEKKLARAERKLLRAE-----RALSK-----VEESLKPAERQADPESITDEERFMFRKLGLRMKAFL------LLGRRG 717 (936)
Q Consensus 654 ~~e~kL~~a~~K~~rae-----~~L~k-----~e~~~~p~~~~~d~E~LT~eER~~LRklghkLKpvV------~IGKrG 717 (936)
+++.||+.|+.++-..| +.|.+ |.-. -+.-..|.+.|+..++..++++...|.|++ +--|.=
T Consensus 28 ~~eaKLqqAK~~lgeeEfeef~~lLK~lt~~kLkyg--D~NGnidye~ls~~eqee~k~~~~eLqPYFdKLN~~~SsK~v 105 (162)
T PF12207_consen 28 RLEAKLQQAKGELGEEEFEEFKELLKKLTNAKLKYG--DKNGNIDYEKLSKEEQEEYKKLTMELQPYFDKLNGHKSSKEV 105 (162)
T ss_dssp HHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHB---TTS-B-GGGS-HHHHHHHHHHHHHHHHHHHHHTT---HHHH
T ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhHHhhc--ccCCCcCHHhCCHHHHHHHHHHHHhcchHHHHhcCCcchhhh
Confidence 57778888765433222 23333 3332 345688999999999999999999999986 334445
Q ss_pred CCHHHHHHHHHHHHhcCeEeEEEcCCCHHH
Q 002316 718 VFDGTVENMHLHWKYRELVKIIVKVKTFDQ 747 (936)
Q Consensus 718 VtdgVIeeIh~aLk~hELVKVkv~~~~~~d 747 (936)
+++.-.+.--.||-..|.|+|+........
T Consensus 106 lt~~E~d~y~eALm~~e~v~vk~~~~~~~~ 135 (162)
T PF12207_consen 106 LTQEEYDQYIEALMTYETVRVKTKSSGGIT 135 (162)
T ss_dssp S-HHHHHHHHHHHHHHHHHHHHCT-SS---
T ss_pred cCHHHHHHHHHHHhhhheeeeeccCCCCCc
Confidence 677777777789999999999987544433
No 18
>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=22.31 E-value=3.2e+02 Score=24.39 Aligned_cols=55 Identities=11% Similarity=0.067 Sum_probs=38.9
Q ss_pred HHHHHHHHHhcCeEeEEEcCCCHHHHHHHHHHHHH---HhCCEEEeccccccccEEEEEecCC
Q 002316 723 VENMHLHWKYRELVKIIVKVKTFDQAKKIALALEA---ESGGVLVSVDKISKGYAMVVYRGKD 782 (936)
Q Consensus 723 IeeIh~aLk~hELVKVkv~~~~~~d~keiA~~Le~---~SGg~lVqV~k~~IG~tiILYRgkN 782 (936)
+.+|-.+++....|=|.+..-..+..+.+.+.|.. ..+|.+.. +|..++++=+++
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~-----i~~~~~l~~P~~ 69 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQK-----ISEKVFLLTPKG 69 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEE-----EETTEEEEE---
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEE-----EcCCEEEEECCC
Confidence 34588899999999999988888888888887765 77999999 688888887665
No 19
>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=21.75 E-value=5.1e+02 Score=23.10 Aligned_cols=54 Identities=19% Similarity=0.169 Sum_probs=37.1
Q ss_pred HHHHHHHHHhCCeEEEEecCCChhhHHHHHHHHHH---HhCCeEEEEECcEEEEecCC
Q 002316 285 VDIIHEKWKTSEIVRLKIEGAPALNMKRMHEILER---KTGGLVIWRSGTAVSLYRGV 339 (936)
Q Consensus 285 VeeI~~awekhELVKVKv~~~~~~dmk~~ae~Lee---kTGgeVVqrIG~viVLYRg~ 339 (936)
+.+|-++++...+|=|.+........+++.+.|.. ..+|.+.+...+ ++|+=++
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~i~~~-~~l~~P~ 68 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQKISEK-VFLLTPK 68 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEEEETT-EEEEE--
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEEEcCC-EEEEECC
Confidence 45688999999999999999888889999888875 668998877555 5555443
No 20
>TIGR03321 alt_F1F0_F0_B alternate F1F0 ATPase, F0 subunit B. CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
Probab=20.31 E-value=1.1e+03 Score=25.54 Aligned_cols=33 Identities=21% Similarity=0.338 Sum_probs=22.2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhhHHHHHHhhh
Q 002316 565 KNFLSPDVTEALQERERLAKSLQDEEEQARLRA 597 (936)
Q Consensus 565 KDFlpp~V~~~L~eRe~l~rs~q~~Ee~aR~~a 597 (936)
+-|+-+.+.+.|.+|++....-...-|+++..|
T Consensus 23 ~kfl~kPi~~~l~~R~~~I~~~l~~Ae~~~~eA 55 (246)
T TIGR03321 23 KRFLYRPILDAMDAREKKIAGELADADTKKREA 55 (246)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667799999999986665555555555444
No 21
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=20.06 E-value=2.9e+02 Score=34.47 Aligned_cols=19 Identities=37% Similarity=0.419 Sum_probs=16.4
Q ss_pred CCCCCCCCCHHHHHHHHhc
Q 002316 685 RQADPESITDEERFMFRKL 703 (936)
Q Consensus 685 ~~~d~E~LT~eER~~LRkl 703 (936)
.+.+++.||..|++-|+|.
T Consensus 615 ~d~~G~~~sk~~~kkl~K~ 633 (651)
T PTZ00399 615 HDADGEEISKKERKKLSKE 633 (651)
T ss_pred CCCCCCCCCHHHHHHHHHH
Confidence 3788899999999999875
Done!