Query 031631
Match_columns 156
No_of_seqs 78 out of 80
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 03:13:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031631.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031631hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10674 Ycf54: Protein of unk 100.0 1.2E-43 2.5E-48 263.3 3.6 74 82-156 1-76 (93)
2 PRK05728 DNA polymerase III su 52.3 13 0.00029 28.4 2.5 29 96-124 111-139 (142)
3 PF06440 DNA_pol3_theta: DNA p 52.2 8.9 0.00019 28.3 1.4 20 98-117 45-64 (75)
4 PRK10969 DNA polymerase III su 45.3 12 0.00027 27.5 1.3 19 99-117 46-64 (75)
5 cd00377 ICL_PEPM Members of th 40.1 90 0.002 25.8 5.7 66 84-152 142-207 (243)
6 PF09664 DUF2399: Protein of u 38.8 27 0.00059 27.4 2.4 30 121-153 21-50 (152)
7 KOG4113 Guanine nucleotide exc 37.0 18 0.00038 28.0 1.0 38 100-137 23-66 (99)
8 PF05774 Herpes_heli_pri: Herp 34.6 65 0.0014 25.6 3.9 52 101-153 18-72 (128)
9 PF10962 DUF2764: Protein of u 34.5 21 0.00045 31.1 1.2 12 81-92 1-12 (271)
10 TIGR01212 radical SAM protein, 31.6 1.1E+02 0.0024 25.9 5.0 34 98-131 59-92 (302)
11 PF03721 UDPG_MGDP_dh_N: UDP-g 29.0 1.4E+02 0.003 23.6 4.9 36 100-137 126-161 (185)
12 PRK05365 malonic semialdehyde 28.7 61 0.0013 25.1 2.8 37 117-153 49-91 (195)
13 PF11455 DUF3018: Protein of 28.7 24 0.00051 25.2 0.5 27 106-132 2-35 (65)
14 PF04364 DNA_pol3_chi: DNA pol 26.3 55 0.0012 24.9 2.2 24 97-120 113-136 (137)
15 PF02171 Piwi: Piwi domain; I 26.2 1.1E+02 0.0025 24.9 4.1 54 99-152 126-196 (302)
16 TIGR02562 cas3_yersinia CRISPR 26.0 48 0.001 34.4 2.3 37 115-151 850-895 (1110)
17 PF06721 DUF1204: Protein of u 21.2 35 0.00075 29.6 0.2 37 116-152 97-139 (228)
18 PHA02360 hypothetical protein 21.1 45 0.00098 24.4 0.8 34 86-123 15-48 (70)
19 PRK01732 rnpA ribonuclease P; 21.1 1.2E+02 0.0025 22.7 3.0 42 99-140 63-105 (114)
20 PF02410 Oligomerisation: Olig 20.8 1.1E+02 0.0023 22.1 2.6 44 83-127 29-78 (100)
21 KOG1543 Cysteine proteinase Ca 20.7 51 0.0011 28.7 1.1 9 118-126 283-291 (325)
22 TIGR00188 rnpA ribonuclease P 20.4 1.3E+02 0.0028 21.8 3.0 57 84-140 42-100 (105)
23 cd01425 RPS2 Ribosomal protein 20.0 2E+02 0.0044 22.9 4.3 39 112-152 121-161 (193)
No 1
>PF10674 Ycf54: Protein of unknown function (DUF2488); InterPro: IPR019616 This entry represents proteins annotated as Ycf54. It is found encoded in the chloroplast genomes of algae, it is also found in plants and in the cyanobacteria. The function is unknown. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.; PDB: 3JSR_A 3HZE_D.
Probab=100.00 E-value=1.2e-43 Score=263.26 Aligned_cols=74 Identities=58% Similarity=1.007 Sum_probs=64.9
Q ss_pred ceEEEEeecccccCcccchhHHHHHHHHHhhhccCceecEEEeeCccccc--cChhhHhhcCCCcEEEEecCCCCCC
Q 031631 82 NKYYFVVANAKFMLDEEEHFQELLFERLRNYGERSKEQDFWLVIEPKFLD--KFPNITKRLRRPAVALVSTNGPWIT 156 (156)
Q Consensus 82 ttYYfvvAS~kFLl~eEEplEEVLrER~R~Y~E~~KeiDFWLV~~PaFLe--efp~ik~klpqPaaAIVSTd~~FIT 156 (156)
|||||+|||++||+ +|||||||||||+|||+|+||+||||||++|+||| +|+++++|||+||+||||||++|||
T Consensus 1 ttYyf~~As~~Fl~-~eEpleEvLrER~r~y~e~~k~iDFWlv~~PaFLe~p~~~~~~~k~~~p~~AiVSTd~~fIt 76 (93)
T PF10674_consen 1 TTYYFVLASAKFLL-EEEPLEEVLRERTRHYKEKNKEIDFWLVKEPAFLEAPEFPEIKKKLPQPAAAIVSTDKQFIT 76 (93)
T ss_dssp EEEEEEEEEHHHHH-CTS-HHHHHHHHHHHHHHCT----EEEEESBGGGGSGGGHHHHHHS-SSEEEEEES-HHHHH
T ss_pred CeEEEEEechhhhc-cCccHHHHHHHHHHHHHhcCCCccEEEecChhhcCccccHHHHHhCCCCcEEEEecChHHHH
Confidence 69999999999998 77999999999999999999999999999999999 5999999999999999999999996
No 2
>PRK05728 DNA polymerase III subunit chi; Validated
Probab=52.30 E-value=13 Score=28.44 Aligned_cols=29 Identities=17% Similarity=0.315 Sum_probs=24.7
Q ss_pred cccchhHHHHHHHHHhhhccCceecEEEe
Q 031631 96 DEEEHFQELLFERLRNYGERSKEQDFWLV 124 (156)
Q Consensus 96 ~eEEplEEVLrER~R~Y~E~~KeiDFWLV 124 (156)
.++|..-+.-|+|-|+|+++|-++.+|=+
T Consensus 111 ~~d~~~~~~aR~r~r~Yr~~G~~l~~~~~ 139 (142)
T PRK05728 111 GYDEAAKQAARERWKAYRAAGYALTYWQQ 139 (142)
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCceEecC
Confidence 34567788999999999999999999854
No 3
>PF06440 DNA_pol3_theta: DNA polymerase III, theta subunit; InterPro: IPR009052 This entry represents the theta subunit of DNA polymerase III from bacteria, whose core structure consists of an irregular array of three helices []. DNA polymerase III (Pol III) is the primary enzyme responsible for replication of Escherichia coli chromosomal DNA. The holoenzyme consists of 17 proteins and contains two core polymerases. The Pol III catalytic core has three tightly associated subunits: alpha, epsilon and theta. The alpha subunit is responsible for the DNA polymerase activity, while the epsilon subunit is the 3'-5' proofreading exonuclease. The epsilon subunit binds to both the alpha and theta subunits in the linear order alpha-epsilon-theta. The theta subunit is the smallest, and may act to enhance the proofreading activity of epsilon, especially under extreme conditions []. This entry also includes a homologue of polymerase III theta called HOT (homologue of theta) from Bacteriophage P1. HOT contains three alpha-helices, as reported for theta, but the folding topology of the two is different, which could account for the suggested greater heat stability of HOT as compared to theta [].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1SE7_A 2IDO_D 2AE9_A 1DU2_A 2XY8_B 2AXD_S.
Probab=52.22 E-value=8.9 Score=28.33 Aligned_cols=20 Identities=45% Similarity=0.629 Sum_probs=17.1
Q ss_pred cchhHHHHHHHHHhhhccCc
Q 031631 98 EEHFQELLFERLRNYGERSK 117 (156)
Q Consensus 98 EEplEEVLrER~R~Y~E~~K 117 (156)
-|+|.+-++||+.||....+
T Consensus 45 Pe~LR~YFreRL~~YR~~s~ 64 (75)
T PF06440_consen 45 PEHLREYFRERLNYYRQISK 64 (75)
T ss_dssp -GGGHHHHHHHHHHHHHHHC
T ss_pred cHHHHHHHHHHHHHHHHHHH
Confidence 38999999999999998754
No 4
>PRK10969 DNA polymerase III subunit theta; Reviewed
Probab=45.31 E-value=12 Score=27.53 Aligned_cols=19 Identities=37% Similarity=0.450 Sum_probs=16.7
Q ss_pred chhHHHHHHHHHhhhccCc
Q 031631 99 EHFQELLFERLRNYGERSK 117 (156)
Q Consensus 99 EplEEVLrER~R~Y~E~~K 117 (156)
|++.|-+|||+.||.+..+
T Consensus 46 e~lR~yFreRL~~yR~~s~ 64 (75)
T PRK10969 46 EHLRSYFRERLIAYRLASV 64 (75)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 7899999999999997654
No 5
>cd00377 ICL_PEPM Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate lyase (ICL), and 2-methylisocitrate lyase (MICL). Isocitrate lyase (ICL) catalyzes the conversion of isocitrate to succinate and glyoxylate, the first committed step in the glyoxylate pathway. This carbon-conserving pathway is present in most prokaryotes, lower eukaryotes and plants, but has not been observed in vertebrates. PEP mutase (PEPM) turns phosphoenolpyruvate (PEP) into phosphonopyruvate (P-pyr), an important intermediate in the formation of organophosphonates, which function as antibiotics or play a role in pathogenesis or signaling. P-pyr can be hydrolyzed by phosphonopyruvate hydrolase (PPH) to from pyruvate and phosphate. Oxaloacetate acetylhydrolase (OAH) catalyzes the hydrolytic cleavage of oxaloacetate to
Probab=40.07 E-value=90 Score=25.80 Aligned_cols=66 Identities=21% Similarity=0.289 Sum_probs=49.8
Q ss_pred EEEEeecccccCcccchhHHHHHHHHHhhhccCceecEEEeeCccccccChhhHhhcCCCcEEEEecCC
Q 031631 84 YYFVVANAKFMLDEEEHFQELLFERLRNYGERSKEQDFWLVIEPKFLDKFPNITKRLRRPAVALVSTNG 152 (156)
Q Consensus 84 YYfvvAS~kFLl~eEEplEEVLrER~R~Y~E~~KeiDFWLV~~PaFLeefp~ik~klpqPaaAIVSTd~ 152 (156)
=.+|+|.-+-+...++.++|.+ ||.+.|.+-+- |-=+|.-|.=.+++..+.+.++-|.+...+-+.
T Consensus 142 ~~~IiARTDa~~~~~~~~~eai-~Ra~ay~~AGA--D~v~v~~~~~~~~~~~~~~~~~~Pl~~~~~~~~ 207 (243)
T cd00377 142 DFVIIARTDALLAGEEGLDEAI-ERAKAYAEAGA--DGIFVEGLKDPEEIRAFAEAPDVPLNVNMTPGG 207 (243)
T ss_pred CeEEEEEcCchhccCCCHHHHH-HHHHHHHHcCC--CEEEeCCCCCHHHHHHHHhcCCCCEEEEecCCC
Confidence 5788888775543446888877 69999999984 777777776555788888999999887766554
No 6
>PF09664 DUF2399: Protein of unknown function C-terminus (DUF2399); InterPro: IPR024465 This domain is found in archaeal, bacterial and eukaryotic proteins. Its function is unknown.
Probab=38.84 E-value=27 Score=27.45 Aligned_cols=30 Identities=23% Similarity=0.441 Sum_probs=24.3
Q ss_pred EEEeeCccccccChhhHhhcCCCcEEEEecCCC
Q 031631 121 FWLVIEPKFLDKFPNITKRLRRPAVALVSTNGP 153 (156)
Q Consensus 121 FWLV~~PaFLeefp~ik~klpqPaaAIVSTd~~ 153 (156)
.|+|.||+-++.+ .+++..++..+|+|+++
T Consensus 21 V~VvENp~Vf~~~---~~~~~~~~~pLVCt~G~ 50 (152)
T PF09664_consen 21 VYVVENPAVFSAL---ADELGASCPPLVCTSGQ 50 (152)
T ss_pred EEEEecHHHHHHH---HHhcCCCCCeEEEcCCc
Confidence 9999999987653 44466689999999986
No 7
>KOG4113 consensus Guanine nucleotide exchange factor [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=37.04 E-value=18 Score=27.98 Aligned_cols=38 Identities=18% Similarity=0.244 Sum_probs=24.6
Q ss_pred hhHHHHHHHHHhhhccCceecEEEeeCccccc------cChhhH
Q 031631 100 HFQELLFERLRNYGERSKEQDFWLVIEPKFLD------KFPNIT 137 (156)
Q Consensus 100 plEEVLrER~R~Y~E~~KeiDFWLV~~PaFLe------efp~ik 137 (156)
|++-...|++-+=....-..|||||+.+=-.| +.+++|
T Consensus 23 p~~rkk~~~~~d~~~te~~~dF~lVkDmf~FeNVgfSr~v~~~K 66 (99)
T KOG4113|consen 23 PSMRKKLEARTDSDNTEPLSDFFLVKDMFAFENVGFSREVPNLK 66 (99)
T ss_pred ccchhhhhhhccccCCCcccceEeeccceeeecceeccccCCee
Confidence 45555555666655566689999999873333 456655
No 8
>PF05774 Herpes_heli_pri: Herpesvirus helicase-primase complex component; InterPro: IPR008650 This family consists of several helicase-primase complex components from the Gammaherpesviruses.
Probab=34.59 E-value=65 Score=25.60 Aligned_cols=52 Identities=21% Similarity=0.466 Sum_probs=38.9
Q ss_pred hHHHHHHHHHhhhccCceecEEEeeCcccccc---ChhhHhhcCCCcEEEEecCCC
Q 031631 101 FQELLFERLRNYGERSKEQDFWLVIEPKFLDK---FPNITKRLRRPAVALVSTNGP 153 (156)
Q Consensus 101 lEEVLrER~R~Y~E~~KeiDFWLV~~PaFLee---fp~ik~klpqPaaAIVSTd~~ 153 (156)
-+++|.+=+.-|-.+...-.|||++ =+|.+. =|.+-.-|-.|.-=|+.+|+.
T Consensus 18 p~~il~~il~~~f~nr~~t~FWLlP-~~f~~~~~~~P~~p~dcl~P~~fi~T~~G~ 72 (128)
T PF05774_consen 18 PEDILETILPLYFANRRNTNFWLLP-RSFVESAPIKPPLPSDCLAPKFFIFTKDGP 72 (128)
T ss_pred HHHHHHHHHHHHHHccccCceeecc-cccccCCCCCCCCCccccCcceEEEeCCCc
Confidence 4678888889999999999999998 577772 355555555566668887763
No 9
>PF10962 DUF2764: Protein of unknown function (DUF2764); InterPro: IPR024492 This bacterial family of proteins has no known function.
Probab=34.51 E-value=21 Score=31.10 Aligned_cols=12 Identities=42% Similarity=0.830 Sum_probs=10.2
Q ss_pred cceEEEEeeccc
Q 031631 81 ANKYYFVVANAK 92 (156)
Q Consensus 81 ~ttYYfvvAS~k 92 (156)
|++|||++|.--
T Consensus 1 M~~YY~lvagLP 12 (271)
T PF10962_consen 1 MTKYYYLVAGLP 12 (271)
T ss_pred CCceeEEeecCC
Confidence 889999999754
No 10
>TIGR01212 radical SAM protein, TIGR01212 family. This uncharacterized protein family shows significant similarity to TIGR01211, a longer protein that is a histone acetyltransferase at its C-terminus and is a subunit of RNA polymerase II (in yeast). This family lacks the GNAT acetyltransferase domain.
Probab=31.64 E-value=1.1e+02 Score=25.93 Aligned_cols=34 Identities=9% Similarity=0.229 Sum_probs=18.6
Q ss_pred cchhHHHHHHHHHhhhccCceecEEEeeCccccc
Q 031631 98 EEHFQELLFERLRNYGERSKEQDFWLVIEPKFLD 131 (156)
Q Consensus 98 EEplEEVLrER~R~Y~E~~KeiDFWLV~~PaFLe 131 (156)
.++++|+|++-+++|.+.++.+=||---.|.++.
T Consensus 59 ~~~i~~qi~~~~~~~~~~~~~~iyf~ggt~t~l~ 92 (302)
T TIGR01212 59 RIPIKEQIKKQMKKYKKDKKFIAYFQAYTNTYAP 92 (302)
T ss_pred CCCHHHHHHHHHHHhhccCEEEEEEECCCcCCCC
Confidence 4556666666666665554444455555555554
No 11
>PF03721 UDPG_MGDP_dh_N: UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain; InterPro: IPR001732 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents the N-terminal NAD(+)-binding domain. Structural studies indicate that this domain forms an alpha-beta structure containing the six-stranded parallel beta sheet characteristic of the dinucleotide binding Rossman fold [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 3OJO_A 3OJL_A 1MV8_B 1MUU_A 1MFZ_C 3GG2_D 1DLJ_A 1DLI_A 3G79_B 2Y0E_D ....
Probab=29.00 E-value=1.4e+02 Score=23.62 Aligned_cols=36 Identities=28% Similarity=0.322 Sum_probs=20.0
Q ss_pred hhHHHHHHHHHhhhccCceecEEEeeCccccccChhhH
Q 031631 100 HFQELLFERLRNYGERSKEQDFWLVIEPKFLDKFPNIT 137 (156)
Q Consensus 100 plEEVLrER~R~Y~E~~KeiDFWLV~~PaFLeefp~ik 137 (156)
--+++++..++.+..+. .||-++-+|+|+.+=..+.
T Consensus 126 tt~~~~~~ile~~~~~~--~~f~la~~PErl~~G~a~~ 161 (185)
T PF03721_consen 126 TTEELLKPILEKRSGKK--EDFHLAYSPERLREGRAIE 161 (185)
T ss_dssp HHHHHHHHHHHHHCCTT--TCEEEEE------TTSHHH
T ss_pred eehHhhhhhhhhhcccc--cCCeEEECCCccCCCCcch
Confidence 45566666666666655 9999999999999533333
No 12
>PRK05365 malonic semialdehyde reductase; Provisional
Probab=28.69 E-value=61 Score=25.06 Aligned_cols=37 Identities=16% Similarity=0.263 Sum_probs=23.4
Q ss_pred ceecEEEeeCccccccChhhHh-----h-cCCCcEEEEecCCC
Q 031631 117 KEQDFWLVIEPKFLDKFPNITK-----R-LRRPAVALVSTNGP 153 (156)
Q Consensus 117 KeiDFWLV~~PaFLeefp~ik~-----k-lpqPaaAIVSTd~~ 153 (156)
..-.|-+|.+|+-++++.+... + ..-|++.+|+.|..
T Consensus 49 QPw~fvvv~~~e~~~~l~~~~~~~~~~~~~~Ap~~i~v~~~~~ 91 (195)
T PRK05365 49 SPARFVFVRSAEAKERLRPALSEGNLAKTLAAPVTAIVAYDTE 91 (195)
T ss_pred CCeEEEEEeCHHHHHHHHHHHHhcCcchhcCCCEEEEEeeCcc
Confidence 3456888888887776554321 1 23477777888754
No 13
>PF11455 DUF3018: Protein of unknown function (DUF3018); InterPro: IPR021558 This is a bacterial family of uncharacterised proteins.
Probab=28.69 E-value=24 Score=25.24 Aligned_cols=27 Identities=30% Similarity=0.587 Sum_probs=20.1
Q ss_pred HHHHHhhhcc-----CceecEEE--eeCcccccc
Q 031631 106 FERLRNYGER-----SKEQDFWL--VIEPKFLDK 132 (156)
Q Consensus 106 rER~R~Y~E~-----~KeiDFWL--V~~PaFLee 132 (156)
+||++.|.++ =|.+-+|+ +.+|.|.++
T Consensus 2 ~~RV~khR~~lRa~GLRPVqiWVPDtr~p~F~~E 35 (65)
T PF11455_consen 2 RERVRKHRERLRAAGLRPVQIWVPDTRRPEFAAE 35 (65)
T ss_pred hHHHHHHHHHHHHcCCCcceeeCCCCCChHHHHH
Confidence 5788888877 56799998 456777664
No 14
>PF04364 DNA_pol3_chi: DNA polymerase III chi subunit, HolC; InterPro: IPR007459 The DNA polymerase III holoenzyme (2.7.7.7 from EC) is the polymerase responsible for the replication of the Escherichia coli chromosome. The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either the tau or gamma product of gene dnax, complexed to delta.delta and to chi psi. Chi forms a 1:1 heterodimer with psi. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta allowing a functional clamp-loading complex to form at physiological subunit concentrations. Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi [].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3SXU_A 1EM8_C.
Probab=26.31 E-value=55 Score=24.88 Aligned_cols=24 Identities=25% Similarity=0.390 Sum_probs=19.2
Q ss_pred ccchhHHHHHHHHHhhhccCceec
Q 031631 97 EEEHFQELLFERLRNYGERSKEQD 120 (156)
Q Consensus 97 eEEplEEVLrER~R~Y~E~~KeiD 120 (156)
.+|..-+.-|||-|+|+++|-++.
T Consensus 113 ~~~~~~~~aR~r~r~Yk~~G~~l~ 136 (137)
T PF04364_consen 113 QDDEAKQAARERYRFYKDRGYELQ 136 (137)
T ss_dssp SSHHHHHHHHHHHHHHHHTTEEEE
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCc
Confidence 444577888999999999997764
No 15
>PF02171 Piwi: Piwi domain; InterPro: IPR003165 This domain is found in the stem cell self-renewal protein Piwi and its relatives in Drosophila melanogaster []. It has been found in the C-terminal of a number of proteins which also contain the PAZ domain (IPR003100 from INTERPRO) in their central region, for example the Argonaute proteins. Several of these proteins have been implicated in the development and maintenance of stem cells through the RNA-mediated gene-quelling mechanisms associated with the protein DICER. ; GO: 0005515 protein binding; PDB: 4F1N_B 3LUH_B 4EI1_A 3QX8_A 3LUC_C 3LUJ_B 3LUD_B 3QX9_A 3LUG_B 3LUK_B ....
Probab=26.19 E-value=1.1e+02 Score=24.86 Aligned_cols=54 Identities=13% Similarity=0.395 Sum_probs=32.8
Q ss_pred chhHHHHHHHHHhhhccCce--ecEEEeeCc--------cccc-cChhhHhhc---C---CCcEEEEecCC
Q 031631 99 EHFQELLFERLRNYGERSKE--QDFWLVIEP--------KFLD-KFPNITKRL---R---RPAVALVSTNG 152 (156)
Q Consensus 99 EplEEVLrER~R~Y~E~~Ke--iDFWLV~~P--------aFLe-efp~ik~kl---p---qPaaAIVSTd~ 152 (156)
+.|+|.++|.++.|.+.++. -+==+|-.. ..++ |++.|++-| . +|.+++|..++
T Consensus 126 ~~l~~~~~~~L~~~~~~~~~~~P~~IiiyRdGvse~~~~~v~~~Ei~~i~~a~~~~~~~~~p~~~~i~v~K 196 (302)
T PF02171_consen 126 DNLEEIIKEALKEFKKNNGKWLPERIIIYRDGVSEGQFKKVLEEEIEAIKEAIKELGEDYNPKITYIVVQK 196 (302)
T ss_dssp HHHHHHHHHHHHHHHHTTTT-TTSEEEEEEES--GGGHHHHHHHHHHHHHHHHHHHTHTTCTEEEEEEEES
T ss_pred cchhhHHHHHHHHHHHHcCCCCCceEEEEEcccCHHhhcccHHHHHHHHHHHHhhcccCCCCcEEEEEeec
Confidence 45999999999999888664 222222211 3344 666666333 2 37777766544
No 16
>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3. The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.
Probab=26.05 E-value=48 Score=34.40 Aligned_cols=37 Identities=19% Similarity=0.620 Sum_probs=27.9
Q ss_pred cCceecE-EEeeCccccccChhhHhhcCC--------CcEEEEecC
Q 031631 115 RSKEQDF-WLVIEPKFLDKFPNITKRLRR--------PAVALVSTN 151 (156)
Q Consensus 115 ~~KeiDF-WLV~~PaFLeefp~ik~klpq--------PaaAIVSTd 151 (156)
.+.++|| |++.+|+=++.+-....+|.+ |-+.|..+|
T Consensus 850 ~g~D~dfd~~~~~~~~~~sliQ~aGR~~R~~~~~~~~~N~~i~~~N 895 (1110)
T TIGR02562 850 VGRDHDYDWAIADPSSMRSIIQLAGRVNRHRLEKVQQPNIVILQWN 895 (1110)
T ss_pred EEecccCCeeeeccCcHHHHHHHhhcccccccCCCCCCcEEEeHhH
Confidence 3667899 999999999977777766643 667776655
No 17
>PF06721 DUF1204: Protein of unknown function (DUF1204); InterPro: IPR009596 This family represents the C terminus of a number of Arabidopsis thaliana hypothetical proteins of unknown function. Family members contain a conserved DFD motif.
Probab=21.22 E-value=35 Score=29.60 Aligned_cols=37 Identities=22% Similarity=0.280 Sum_probs=29.1
Q ss_pred CceecEEEeeCccccc------cChhhHhhcCCCcEEEEecCC
Q 031631 116 SKEQDFWLVIEPKFLD------KFPNITKRLRRPAVALVSTNG 152 (156)
Q Consensus 116 ~KeiDFWLV~~PaFLe------efp~ik~klpqPaaAIVSTd~ 152 (156)
.+.||==+-.+|+||+ ....+.+.+-.-.+-|+||+-
T Consensus 97 K~HiDdkia~ePkFle~nQV~GniKlLd~lIe~G~~E~KSte~ 139 (228)
T PF06721_consen 97 KAHIDDKIADEPKFLEFNQVKGNIKLLDNLIENGEMEMKSTER 139 (228)
T ss_pred HHHhhhhhhcchHHHHHHHhhchHHHHHHHhhcCceeecccch
Confidence 4567888889999999 266777888888888888863
No 18
>PHA02360 hypothetical protein
Probab=21.12 E-value=45 Score=24.39 Aligned_cols=34 Identities=32% Similarity=0.498 Sum_probs=21.9
Q ss_pred EEeecccccCcccchhHHHHHHHHHhhhccCceecEEE
Q 031631 86 FVVANAKFMLDEEEHFQELLFERLRNYGERSKEQDFWL 123 (156)
Q Consensus 86 fvvAS~kFLl~eEEplEEVLrER~R~Y~E~~KeiDFWL 123 (156)
+.+||.+-+||-|-| .|-.|+|.|-| .+.|||.=
T Consensus 15 ~~A~~r~l~LDveyP---klY~~i~k~YE-e~gidFyG 48 (70)
T PHA02360 15 RAAANRELFLDVEYP---KLYKKIRKYYE-EEGIDFYG 48 (70)
T ss_pred HHHhcchheeecccH---HHHHHHHHHHH-HcCCcccC
Confidence 346777877777766 45556555555 66789863
No 19
>PRK01732 rnpA ribonuclease P; Reviewed
Probab=21.08 E-value=1.2e+02 Score=22.68 Aligned_cols=42 Identities=17% Similarity=0.178 Sum_probs=32.7
Q ss_pred chhHHHHHHHHHhhhccCceecEEEeeCccccc-cChhhHhhc
Q 031631 99 EHFQELLFERLRNYGERSKEQDFWLVIEPKFLD-KFPNITKRL 140 (156)
Q Consensus 99 EplEEVLrER~R~Y~E~~KeiDFWLV~~PaFLe-efp~ik~kl 140 (156)
--+.-+|||=.|.+...-...|+=+|..|...+ .++++.+.|
T Consensus 63 NriKR~lRe~~R~~~~~l~~~diVviar~~~~~~~~~~l~~~l 105 (114)
T PRK01732 63 NRIKRLTRESFRLHQHELPAMDFVVIAKKGVADLDNRELFELL 105 (114)
T ss_pred HHHHHHHHHHHHHhhhcCCCCeEEEEeCCCcccCCHHHHHHHH
Confidence 467778888888877666678999999999888 677777654
No 20
>PF02410 Oligomerisation: Oligomerisation domain; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear [, ]. This entry contains the bacterial protein YbeB (P0AAT6 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2O5A_A 2ID1_B 3UPS_A.
Probab=20.85 E-value=1.1e+02 Score=22.12 Aligned_cols=44 Identities=14% Similarity=0.289 Sum_probs=24.2
Q ss_pred eEEEEeecccccCcccchhHHHHHHHH------HhhhccCceecEEEeeCc
Q 031631 83 KYYFVVANAKFMLDEEEHFQELLFERL------RNYGERSKEQDFWLVIEP 127 (156)
Q Consensus 83 tYYfvvAS~kFLl~eEEplEEVLrER~------R~Y~E~~KeiDFWLV~~P 127 (156)
+=|||+|+.+--- +-..+.+-+++.+ +.+.-.+++-+-|.+..-
T Consensus 29 ~dy~II~T~~S~r-h~~aia~~v~~~~~k~~~~~~~~~eG~~~~~W~lvD~ 78 (100)
T PF02410_consen 29 ADYFIIATGRSER-HVRAIADEVEKALKKEYGERPLRIEGLDESDWVLVDY 78 (100)
T ss_dssp -SEEEEEEESSHH-HHHHHHHHHHHHH-HHTT----EEESTTTTSEEEEEE
T ss_pred cCEEEEEEcCCHH-HHHHHHHHHHHHHHHHcCCcccccCCCCCCCEEEEcc
Confidence 4589999987542 2233444444444 333444667788988753
No 21
>KOG1543 consensus Cysteine proteinase Cathepsin L [Posttranslational modification, protein turnover, chaperones]
Probab=20.72 E-value=51 Score=28.67 Aligned_cols=9 Identities=33% Similarity=0.988 Sum_probs=7.8
Q ss_pred eecEEEeeC
Q 031631 118 EQDFWLVIE 126 (156)
Q Consensus 118 eiDFWLV~~ 126 (156)
..|||||+|
T Consensus 283 ~~~YWivkN 291 (325)
T KOG1543|consen 283 GVDYWIVKN 291 (325)
T ss_pred CceeEEEEc
Confidence 479999997
No 22
>TIGR00188 rnpA ribonuclease P protein component, eubacterial. The yeast mitochondrial RNase P protein component gene RPM2 has no obvious sequence similarity to rnpA, but resembles eukaryotic nuclear RNase P instead.
Probab=20.37 E-value=1.3e+02 Score=21.79 Aligned_cols=57 Identities=19% Similarity=0.217 Sum_probs=37.6
Q ss_pred EEEEeecccccCc-ccchhHHHHHHHHHhhhccCceecEEEeeCccccc-cChhhHhhc
Q 031631 84 YYFVVANAKFMLD-EEEHFQELLFERLRNYGERSKEQDFWLVIEPKFLD-KFPNITKRL 140 (156)
Q Consensus 84 YYfvvAS~kFLl~-eEEplEEVLrER~R~Y~E~~KeiDFWLV~~PaFLe-efp~ik~kl 140 (156)
=.-++.|.++=-- +---+.-+|||=.|.....-+..|+=++..|.+.+ .+.++.+.+
T Consensus 42 RlGi~vsKK~g~AV~RNriKR~lRe~~R~~~~~l~~~d~v~i~r~~~~~~~~~~l~~~l 100 (105)
T TIGR00188 42 RVGLSVSKKVKNAVERNRIKRLIREVFRERQELLKALDVVVIVRKGFSELTYEAFLKLL 100 (105)
T ss_pred EEEEEEecccCchhHHHHHHHHHHHHHHHhhcccCCccEEEEECCCcCcCCHHHHHHHH
Confidence 3456667772110 01355667777777776665578998899999888 678877655
No 23
>cd01425 RPS2 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the protein also functions as the 67 kDa laminin receptor (LAMR1 or 67LR), which is formed from a 37 kDa precursor, and is overexpressed in many tumors. 67LR is a cell surface receptor which interacts with a variety of ligands, laminin-1 and others. It is assumed that the ligand interactions are mediated via the conserved C-terminus, which becomes extracellular as the protein undergoes conformational changes which are not well understood. Specifically, a conserved palindromic motif, LMWWML, may participate in the interactions. 67LR plays essential roles in the adhesion of cells to the basement membrane an
Probab=20.04 E-value=2e+02 Score=22.93 Aligned_cols=39 Identities=26% Similarity=0.475 Sum_probs=28.2
Q ss_pred hhccCceecEEEeeCccccccChhh--HhhcCCCcEEEEecCC
Q 031631 112 YGERSKEQDFWLVIEPKFLDKFPNI--TKRLRRPAVALVSTNG 152 (156)
Q Consensus 112 Y~E~~KeiDFWLV~~PaFLeefp~i--k~klpqPaaAIVSTd~ 152 (156)
++...++.|.=+|.+|. ++-.-+ ..++.=|.++||.||.
T Consensus 121 ~~~~~~~Pdlviv~~~~--~~~~ai~Ea~~l~IP~I~i~Dtn~ 161 (193)
T cd01425 121 IKDMFRLPDLVIVLDPR--KEHQAIREASKLGIPVIAIVDTNC 161 (193)
T ss_pred ccccccCCCEEEEeCCc--cchHHHHHHHHcCCCEEEEecCCC
Confidence 33467889999999883 222222 3788999999999984
Done!