Query 028918
Match_columns 202
No_of_seqs 153 out of 1124
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 04:36:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028918.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028918hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0432 Uncharacterized conser 100.0 2.2E-56 4.8E-61 360.7 16.8 135 61-201 1-137 (137)
2 TIGR00149 TIGR00149_YbjQ secon 100.0 1.2E-53 2.6E-58 342.9 16.3 130 67-202 2-132 (132)
3 PF01894 UPF0047: Uncharacteri 100.0 7.3E-52 1.6E-56 327.0 13.9 118 78-200 1-118 (118)
4 KOG3267 Uncharacterized conser 100.0 3E-47 6.5E-52 300.2 11.0 138 65-202 1-138 (138)
5 COG3292 Predicted periplasmic 25.8 34 0.00073 34.7 1.2 18 170-187 216-233 (671)
6 PF03460 NIR_SIR_ferr: Nitrite 21.2 69 0.0015 21.9 1.7 17 170-186 38-54 (69)
7 KOG0482 DNA replication licens 20.9 1.8E+02 0.0039 29.7 5.0 65 117-188 382-449 (721)
8 PF14438 SM-ATX: Ataxin 2 SM d 18.9 1.3E+02 0.0027 21.4 2.7 28 153-184 4-31 (77)
9 KOG1166 Mitotic checkpoint ser 16.1 1.3E+02 0.0028 32.1 3.0 57 68-127 727-786 (974)
10 PF15054 DUF4535: Domain of un 14.8 4.1E+02 0.0088 18.0 4.3 29 100-128 3-32 (46)
No 1
>COG0432 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.2e-56 Score=360.71 Aligned_cols=135 Identities=45% Similarity=0.770 Sum_probs=130.1
Q ss_pred CeEEEEEEEecCCCC-eEEeccHHHHHHHHhhccCcceeEEEEEecccceEEEEeecCCchhHHHHHHHHhhhCCCCCCC
Q 028918 61 PRWAQKTVTLPPLRR-GCHLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPEGRSA 139 (202)
Q Consensus 61 m~~~~~titv~T~~r-~~~dIT~eV~~~V~~~~Sgi~~Glv~Vf~~HTTAsLtinEn~DP~v~~Dl~~~L~rLvP~~~~~ 139 (202)
|++++++|+|+|++| +++|||++|+++|++ |||++|+|+||++||||||+||| +||+|++||+++|++|+|++.
T Consensus 1 m~~~~~~l~v~T~~r~~~vdIT~ev~~~v~e--sgv~~Gl~~vf~~HtTaal~inE-~ep~l~~Di~~~l~~lvP~~~-- 75 (137)
T COG0432 1 MKVYQKELTVSTKRRIEFVDITDEVEKFVRE--SGVKNGLLLVFVPHTTAALTINE-AEPGLKEDIERFLEKLVPEGA-- 75 (137)
T ss_pred CceEEEEEEEeccCccceEEchHHHHHHHHH--cCCccceEEEEecCcceEEEEec-CCCcHHHHHHHHHHHhCCCCC--
Confidence 889999999999998 999999999999999 99999999999999999999999 799999999999999999984
Q ss_pred CcccCCCCCCCchhhhhhhhcCceEEEEEeCCeeecCCcceEEEEEecCCCCC-eEEEEEEec
Q 028918 140 SWKHTLEGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGIWLCEHRDAPTP-RKVVITLNG 201 (202)
Q Consensus 140 ~Y~H~~eG~dn~~AHlkssLlG~SltIPV~dG~L~LGtWQ~I~l~E~~dgpr~-R~V~v~v~G 201 (202)
.|+|+.+|+|||+|||||+|+|+|++|||.||+|.|||||+|||+|| ||||. |+|+++++|
T Consensus 76 ~Y~H~~~~~Dn~~aHlkasllG~S~~iPv~~GrL~LGTWQ~I~~~E~-dg~r~~R~v~v~i~g 137 (137)
T COG0432 76 GYRHDEEGPDNAPAHLKASLLGPSLTIPVINGRLVLGTWQGIFLVEF-DGPRHRRRVVVKIIG 137 (137)
T ss_pred CcccccCCCCchHHHHHHHhcCceEEEEEeCCeEceecccEEEEEEe-cCCCCccEEEEEEcC
Confidence 79999999999999999999999999999999999999999999999 56665 999999987
No 2
>TIGR00149 TIGR00149_YbjQ secondary thiamine-phosphate synthase enzyme. Members of this protein family have been studied extensively by crystallography. Members from several different species have been shown to have sufficient thiamin phosphate synthase activity (EC 2.5.1.3) to complement thiE mutants. However, it is presumed that this is a secondary activity, and the primary function of this enzyme remains unknown.
Probab=100.00 E-value=1.2e-53 Score=342.91 Aligned_cols=130 Identities=41% Similarity=0.731 Sum_probs=123.5
Q ss_pred EEEecCCCC-eEEeccHHHHHHHHhhccCcceeEEEEEecccceEEEEeecCCchhHHHHHHHHhhhCCCCCCCCcccCC
Q 028918 67 TVTLPPLRR-GCHLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPEGRSASWKHTL 145 (202)
Q Consensus 67 titv~T~~r-~~~dIT~eV~~~V~~~~Sgi~~Glv~Vf~~HTTAsLtinEn~DP~v~~Dl~~~L~rLvP~~~~~~Y~H~~ 145 (202)
++++.|.++ +++|||++|+++|++ ||+++|+|+||++||||||++|||+||+++.||+++|++|+|++. +|+|+
T Consensus 2 ~~~~~t~~~~~~~dIT~~V~~~v~~--s~i~~G~~~v~~~HTTa~l~inE~~dp~l~~Dl~~~l~~lvP~~~--~y~H~- 76 (132)
T TIGR00149 2 ELLLKTTKRVELIDITSEIEAVLQS--SGVKDGLLLVYVPHTTASLTINENADPDVLHDIERFFERLVPDDG--NYEHD- 76 (132)
T ss_pred EEEEEcCCCCeEEEChHHHHHHHHH--cCCcccEEEEEeCCCcEEEEEecCCCccHHHHHHHHHHHHCCCCC--Ccccc-
Confidence 467777655 999999999999999 999999999999999999999999999999999999999999874 69998
Q ss_pred CCCCCchhhhhhhhcCceEEEEEeCCeeecCCcceEEEEEecCCCCCeEEEEEEecC
Q 028918 146 EGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGIWLCEHRDAPTPRKVVITLNGI 202 (202)
Q Consensus 146 eG~dn~~AHlkssLlG~SltIPV~dG~L~LGtWQ~I~l~E~~dgpr~R~V~v~v~Ge 202 (202)
+++|||+|||||+|+|+|++|||.||+|.||+||+|||||| ||||+|+|+|+++||
T Consensus 77 ~~~~n~~aHlka~L~G~s~tipi~dG~L~LGtwQ~I~l~E~-Dg~r~R~v~v~i~Ge 132 (132)
T TIGR00149 77 EGDDNMDAHIKSSLLGTSQHVPVENGRLQLGTWQGIFFAEF-DGPRTRRIIVKVQGE 132 (132)
T ss_pred CCCCCHHHHHHHHhcCccEEEEEeCCEEcccCccEEEEEEC-CCCCCcEEEEEEEeC
Confidence 89999999999999999999999999999999999999999 699999999999997
No 3
>PF01894 UPF0047: Uncharacterised protein family UPF0047; InterPro: IPR001602 This family contains small uncharacterised proteins of 14 to 16 kDa mainly from bacteria although the signatures also occur in a hypothetical protein from archaea and from yeast.; PDB: 1VPH_E 2P6C_A 2CU5_A 1VMJ_A 1XBF_B 1VMH_A 1VE0_A 2P6H_B 1VMF_C.
Probab=100.00 E-value=7.3e-52 Score=326.99 Aligned_cols=118 Identities=47% Similarity=0.833 Sum_probs=105.2
Q ss_pred EeccHHHHHHHHhhccCcceeEEEEEecccceEEEEeecCCchhHHHHHHHHhhhCCCCCCCCcccCCCCCCCchhhhhh
Q 028918 78 HLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPEGRSASWKHTLEGPDDMPAHIKS 157 (202)
Q Consensus 78 ~dIT~eV~~~V~~~~Sgi~~Glv~Vf~~HTTAsLtinEn~DP~v~~Dl~~~L~rLvP~~~~~~Y~H~~eG~dn~~AHlks 157 (202)
||||++|+++|++ ||+++|+|+||++||||||++|||+||++++||+++|++|+|++. +|+|+.+|++||+||+||
T Consensus 1 idIT~~V~~~v~~--s~i~~Gl~~v~~~HTTaal~inE~~dp~v~~Dl~~~l~~lvP~~~--~y~H~~~~~~n~~aHlks 76 (118)
T PF01894_consen 1 IDITEEVREAVEE--SGIRNGLVHVFVPHTTAALTINENADPDVRRDLLEALERLVPEDD--PYRHNEEGPDNAPAHLKS 76 (118)
T ss_dssp EE-HHHHHHHHHH--HT-SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHS-TTS--T-GGGCTT-STHHHHHHH
T ss_pred CcchHHHHHHHHH--hCCcceEEEEEeCCCeEEEEEeecCChhHHHhHHHHHHHhCCCCC--ceEeCCccccCccHHHHH
Confidence 7999999999999 999999999999999999999999999999999999999999984 899999999999999999
Q ss_pred hhcCceEEEEEeCCeeecCCcceEEEEEecCCCCCeEEEEEEe
Q 028918 158 SMFGCTLTIPITDGQLNMGTWQGIWLCEHRDAPTPRKVVITLN 200 (202)
Q Consensus 158 sLlG~SltIPV~dG~L~LGtWQ~I~l~E~~dgpr~R~V~v~v~ 200 (202)
+|+|+|++|||.||+|.||+||+|||+|| ||||+|+|+|+||
T Consensus 77 ~l~G~S~~vpv~~G~L~LGtwQ~I~l~E~-dgpr~R~v~v~i~ 118 (118)
T PF01894_consen 77 SLIGPSLTVPVHDGKLALGTWQGIYLVEF-DGPRERTVVVQIM 118 (118)
T ss_dssp HHH-SEEEEEEETTEE---TTEEEEEEES-S-SSEEEEEEEEE
T ss_pred HhcCCeEEEEEECCEEccCCcCEEEEEEC-CCCCeEEEEEEEC
Confidence 99999999999999999999999999998 6799999999986
No 4
>KOG3267 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3e-47 Score=300.16 Aligned_cols=138 Identities=66% Similarity=1.141 Sum_probs=133.5
Q ss_pred EEEEEecCCCCeEEeccHHHHHHHHhhccCcceeEEEEEecccceEEEEeecCCchhHHHHHHHHhhhCCCCCCCCcccC
Q 028918 65 QKTVTLPPLRRGCHLITPKIVKEIAQDLSEFKCGLAHLFLLHTSASLTINENYDSDVRDDTETFLNKIVPEGRSASWKHT 144 (202)
Q Consensus 65 ~~titv~T~~r~~~dIT~eV~~~V~~~~Sgi~~Glv~Vf~~HTTAsLtinEn~DP~v~~Dl~~~L~rLvP~~~~~~Y~H~ 144 (202)
|++|++...++|||.||+++.+.+++.++....|++|+|.+||+|+|+||||+||+++.|++++|+++||++.+.+|+|.
T Consensus 1 qk~itl~~~~kg~~iit~~ilkeir~dl~~fn~g~~~~fiqhtsaaltinen~d~d~qad~~~~ldkivpe~nsa~~rht 80 (138)
T KOG3267|consen 1 QKIITLDPLRKGCHIITNDILKEIREDLKDFNCGLAHFFIQHTSAALTINENWDADTQADMEDFLDKIVPEGNSAGWRHT 80 (138)
T ss_pred CceEecCcccCccEEecHHHHHHHHHHHhhccccceeeeeeccceeeEecccCCcchhhhHHHHHHhhCcCCCCcccccc
Confidence 57899999888999999999999988889999999999999999999999999999999999999999999977899999
Q ss_pred CCCCCCchhhhhhhhcCceEEEEEeCCeeecCCcceEEEEEecCCCCCeEEEEEEecC
Q 028918 145 LEGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGIWLCEHRDAPTPRKVVITLNGI 202 (202)
Q Consensus 145 ~eG~dn~~AHlkssLlG~SltIPV~dG~L~LGtWQ~I~l~E~~dgpr~R~V~v~v~Ge 202 (202)
.||.||||||+||+|+|+++||||.+|+|.|||||+|+|+|||+.|+.|+|+++++|.
T Consensus 81 ~eg~ddmpahikssl~g~qltipit~gklslgtwq~i~l~e~r~~p~ar~iv~ti~gi 138 (138)
T KOG3267|consen 81 AEGLDDMPAHIKSSLFGCQLTIPITKGKLSLGTWQDIQLAEFRDAPHARRIVCTIIGI 138 (138)
T ss_pred ccCcccchhhhhhccccceEEEEeccCeecccccccchhhhhhcCCcccEEEEEEecC
Confidence 9999999999999999999999999999999999999999999999999999999984
No 5
>COG3292 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=25.76 E-value=34 Score=34.66 Aligned_cols=18 Identities=44% Similarity=0.671 Sum_probs=16.3
Q ss_pred CCeeecCCcceEEEEEec
Q 028918 170 DGQLNMGTWQGIWLCEHR 187 (202)
Q Consensus 170 dG~L~LGtWQ~I~l~E~~ 187 (202)
+|+|-.|||||||+.|-+
T Consensus 216 qg~LWVGTdqGv~~~e~~ 233 (671)
T COG3292 216 QGRLWVGTDQGVYLQEAE 233 (671)
T ss_pred cCcEEEEeccceEEEchh
Confidence 699999999999999963
No 6
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=21.23 E-value=69 Score=21.89 Aligned_cols=17 Identities=29% Similarity=0.411 Sum_probs=14.5
Q ss_pred CCeeecCCcceEEEEEe
Q 028918 170 DGQLNMGTWQGIWLCEH 186 (202)
Q Consensus 170 dG~L~LGtWQ~I~l~E~ 186 (202)
+|.+.|.+||+|+|...
T Consensus 38 ~~~irlT~~Q~l~l~~v 54 (69)
T PF03460_consen 38 DGEIRLTTRQNLQLRGV 54 (69)
T ss_dssp TSEEEEETTSCEEEEEE
T ss_pred CCeEEECCCCeEEEeCC
Confidence 58899999999998765
No 7
>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]
Probab=20.90 E-value=1.8e+02 Score=29.68 Aligned_cols=65 Identities=20% Similarity=0.342 Sum_probs=45.0
Q ss_pred CCchhHH-HHHHHHhhhCCCCCCCCcccCC--CCCCCchhhhhhhhcCceEEEEEeCCeeecCCcceEEEEEecC
Q 028918 117 YDSDVRD-DTETFLNKIVPEGRSASWKHTL--EGPDDMPAHIKSSMFGCTLTIPITDGQLNMGTWQGIWLCEHRD 188 (202)
Q Consensus 117 ~DP~v~~-Dl~~~L~rLvP~~~~~~Y~H~~--eG~dn~~AHlkssLlG~SltIPV~dG~L~LGtWQ~I~l~E~~d 188 (202)
+||+|.+ -|+.++.||+|++ .|.-.. .|-+=..|-.|-.++|- .-.++|.|.|-. |||.-+|-+|
T Consensus 382 GDPGVAKSQLLkyi~rlapRg---vYTTGrGSSGVGLTAAVmkDpvTgE---M~LEGGALVLAD-~GICCIDEfD 449 (721)
T KOG0482|consen 382 GDPGVAKSQLLKYISRLAPRG---VYTTGRGSSGVGLTAAVMKDPVTGE---MVLEGGALVLAD-GGICCIDEFD 449 (721)
T ss_pred CCCchhHHHHHHHHHhcCccc---ceecCCCCCccccchhhhcCCCCCe---eEeccceEEEcc-CceEeehhhh
Confidence 6999954 8999999999987 465332 12223445555555553 456899999966 8898876544
No 8
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=18.86 E-value=1.3e+02 Score=21.40 Aligned_cols=28 Identities=18% Similarity=0.525 Sum_probs=22.8
Q ss_pred hhhhhhhcCceEEEEEeCCeeecCCcceEEEE
Q 028918 153 AHIKSSMFGCTLTIPITDGQLNMGTWQGIWLC 184 (202)
Q Consensus 153 AHlkssLlG~SltIPV~dG~L~LGtWQ~I~l~ 184 (202)
.|+-+.|+|..+.|=+.||.. ++|||-.
T Consensus 4 ~~l~~~lvG~~V~V~~~~G~~----yeGif~s 31 (77)
T PF14438_consen 4 VYLLTNLVGQTVEVTTKNGSV----YEGIFHS 31 (77)
T ss_dssp HHHHHTTTTSEEEEEETTS-E----EEEEEEE
T ss_pred HHHHHhCcCCEEEEEECCCCE----EEEEEEe
Confidence 578899999999999999986 6777643
No 9
>KOG1166 consensus Mitotic checkpoint serine/threonine protein kinase [Cell cycle control, cell division, chromosome partitioning]
Probab=16.06 E-value=1.3e+02 Score=32.13 Aligned_cols=57 Identities=12% Similarity=0.099 Sum_probs=43.8
Q ss_pred EEecCCCC-eEEeccHHHHHHHHhhccCcceeEEEEEecc--cceEEEEeecCCchhHHHHHH
Q 028918 68 VTLPPLRR-GCHLITPKIVKEIAQDLSEFKCGLAHLFLLH--TSASLTINENYDSDVRDDTET 127 (202)
Q Consensus 68 itv~T~~r-~~~dIT~eV~~~V~~~~Sgi~~Glv~Vf~~H--TTAsLtinEn~DP~v~~Dl~~ 127 (202)
|+|+...- =-+-|..||+.-++ ..+..++.++...| -.+|+.++|+.+=+-+.|+.+
T Consensus 727 lK~e~P~~~WEfYI~~q~~~RLk---~~~~~~~~~~~~a~~~~~~S~lv~ey~~~Gtlld~~N 786 (974)
T KOG1166|consen 727 LKVEKPPNPWEFYICLQVMERLK---PQMLPSIMHISSAHVFQNASVLVSEYSPYGTLLDLIN 786 (974)
T ss_pred EEeecCCCceeeeehHHHHHhhc---hhhhcchHHHHHHHccCCcceeeeeccccccHHHhhc
Confidence 55555322 12349999999988 46789999998887 489999999988888888877
No 10
>PF15054 DUF4535: Domain of unknown function (DUF4535)
Probab=14.82 E-value=4.1e+02 Score=18.02 Aligned_cols=29 Identities=24% Similarity=0.284 Sum_probs=20.8
Q ss_pred EEEEecccceEEEEeecCC-chhHHHHHHH
Q 028918 100 AHLFLLHTSASLTINENYD-SDVRDDTETF 128 (202)
Q Consensus 100 v~Vf~~HTTAsLtinEn~D-P~v~~Dl~~~ 128 (202)
+.-|..+|-|+|.+.-|++ |++.+=+..+
T Consensus 3 ~fsF~~G~~~GiY~AQNY~VPnv~kl~~~~ 32 (46)
T PF15054_consen 3 LFSFGAGTYTGIYVAQNYEVPNVKKLAETG 32 (46)
T ss_pred eEEEeeccEEEEEeeecccCCchHHHHHHH
Confidence 4568899999999998866 7764433333
Done!