Query 029719
Match_columns 189
No_of_seqs 123 out of 147
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 02:35:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029719.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029719hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0347 RNA helicase [RNA proc 99.9 2.1E-24 4.5E-29 205.0 6.9 114 1-131 598-715 (731)
2 KOG4055 Uncharacterized conser 38.7 89 0.0019 27.3 5.7 96 69-184 33-142 (213)
3 COG3492 Uncharacterized protei 33.8 40 0.00087 26.4 2.5 35 13-47 34-68 (104)
4 PF10410 DnaB_bind: DnaB-helic 32.7 99 0.0022 20.1 4.1 40 4-43 18-57 (59)
5 PF06844 DUF1244: Protein of u 25.9 55 0.0012 24.1 2.0 33 14-46 4-36 (68)
6 PF04748 Polysacc_deac_2: Dive 21.5 92 0.002 26.5 2.9 52 82-142 143-194 (213)
7 PRK11151 DNA-binding transcrip 18.1 1.5E+02 0.0033 25.0 3.5 29 70-98 37-65 (305)
8 PRK09791 putative DNA-binding 18.1 1.3E+02 0.0029 25.2 3.1 49 30-98 21-69 (302)
9 PF01817 CM_2: Chorismate muta 17.8 3.2E+02 0.0069 19.0 4.6 40 2-41 13-59 (81)
10 PF13093 FTA4: Kinetochore com 15.6 1.5E+02 0.0033 25.5 2.9 40 68-108 14-54 (213)
No 1
>KOG0347 consensus RNA helicase [RNA processing and modification]
Probab=99.90 E-value=2.1e-24 Score=204.98 Aligned_cols=114 Identities=29% Similarity=0.504 Sum_probs=96.9
Q ss_pred ChhHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHhcCccccCCcchHHHHHH----HHHhHHhHHHHHHHHHHHHHHh
Q 029719 1 MPEVMKRMSLARQIDKIMRKDSQEKAKKTWFERNAEAVELVVDNYDSEEEVVKN----RKQKKATSMQLKKLQQELNAML 76 (189)
Q Consensus 1 m~~IKeRV~LArqIdk~e~~~~k~k~e~sWlkkAAEeLgIdlDsDd~e~e~~~~----~Kq~k~~k~~lk~LraeLk~LL 76 (189)
|++||+||+||++|+++++++.+.+.+++||++||++||||+|+|++++..... .=+.+..+.+++.||+||+.||
T Consensus 598 m~~lkeRvrLA~ei~~~e~k~~~v~~~~sWlkkaA~el~id~d~d~d~~~~~~~e~~~~me~~~nk~qv~~lRaeL~~lL 677 (731)
T KOG0347|consen 598 MDALKERVRLAREIDKLEIKSKRVRKEESWLKKAADELGIDVDEDEDDIGKSNSETFLKMEKRRNKKQVKALRAELNELL 677 (731)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHhCCccccccccccccccchhHHHHHHHHHHHHHHHHHHHHhhc
Confidence 789999999999999999999999999999999999999999998864322111 1234466888999999999999
Q ss_pred CCCCCCCCCccccccCCCCchhhHHhHHHHHHhhcCCcchhhhhcccCceeeccc
Q 029719 77 SRPLQPKTFSRHYLAGAGVSPLLQRQLEEIAKEKLPDSKSAIENKRRKLVVIGQD 131 (189)
Q Consensus 77 SqPL~~kg~S~kYlT~ggv~~l~~~~~~~L~~~~v~~~~~~~~~k~~~~~viGq~ 131 (189)
++||++.|||++|||+|+|+++ ++++. +++|.++||+|
T Consensus 678 ~~pi~t~~~~~KY~T~~~v~~a-----~~~~~------------~~v~~~~~~id 715 (731)
T KOG0347|consen 678 SQPIRTDGFSTKYLTSGLVNLA-----DSLAK------------SAVHNSIIGID 715 (731)
T ss_pred ccccccccccccccChhhhhHH-----HHhhh------------hhhhHHHHHHH
Confidence 9999988999999999999443 34444 68999999997
No 2
>KOG4055 consensus Uncharacterized conserved protein [Function unknown]
Probab=38.72 E-value=89 Score=27.33 Aligned_cols=96 Identities=20% Similarity=0.170 Sum_probs=62.5
Q ss_pred HHHHHHHhCCCCCCCCC-----ccccccCCCCchhhHHhHHHHHHhhcCCcchhhhhcccCceeecccccchhHHHHhcC
Q 029719 69 QQELNAMLSRPLQPKTF-----SRHYLAGAGVSPLLQRQLEEIAKEKLPDSKSAIENKRRKLVVIGQDCVEPLQALRNAG 143 (189)
Q Consensus 69 raeLk~LLSqPL~~kg~-----S~kYlT~ggv~~l~~~~~~~L~~~~v~~~~~~~~~k~~~~~viGq~~Ve~L~~Lr~~~ 143 (189)
+..|-.|...|..|... +-+-|-.+ +. .++++.+.++.++| -|.|.|.-| ||..-
T Consensus 33 rlkl~rl~knpdkp~~ip~~k~~lr~~~e~---vp------~fVrnv~GSSAgaG---SgeFHvYR~--------lRRrE 92 (213)
T KOG4055|consen 33 RLKLERLMKNPDKPVPIPDEKVKLRAPLEN---VP------EFVRNVMGSSAGAG---SGEFHVYRH--------LRRRE 92 (213)
T ss_pred hhHHHHHhcCCCcCCCCchHHHHHhccccc---cc------HHHHhcccccccCC---CchhHHHHH--------HHHHH
Confidence 34466777777554433 33333222 22 78888888666666 666666666 88888
Q ss_pred cccccchhHHHHHhhhhHHHHHhhH------H---HHHHhHHHHHHHHhh
Q 029719 144 HEVHMDGKEMAEKRRNLDSLRRKRK------E---EKKRLRDQCRKQRKK 184 (189)
Q Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~------~---~~~~~~~~~~~~~~~ 184 (189)
+-..-.++-.+.|+-.++.++-+.- | -|+|...|++||+.+
T Consensus 93 q~Rl~~md~~a~Ke~~daefq~r~ek~~kaaEeKTaKKRaKRqk~Kq~ak 142 (213)
T KOG4055|consen 93 QDRLDYMDADANKELLDAEFQIRLEKNQKAAEEKTAKKRAKRQKKKQKAK 142 (213)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8777788888999988888775542 2 256777788877443
No 3
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.76 E-value=40 Score=26.42 Aligned_cols=35 Identities=17% Similarity=0.261 Sum_probs=26.8
Q ss_pred HHHHHHHHhhhhhhhhhHHHHHHHhcCccccCCcc
Q 029719 13 QIDKIMRKDSQEKAKKTWFERNAEAVELVVDNYDS 47 (189)
Q Consensus 13 qIdk~e~~~~k~k~e~sWlkkAAEeLgIdlDsDd~ 47 (189)
-||=+.++..=-+-=.+|++.||++.||++.-|..
T Consensus 34 NIDLMnLAgFCRNCLs~Wy~eaae~~gv~lskd~a 68 (104)
T COG3492 34 NIDLMNLAGFCRNCLSNWYREAAEAQGVDLSKDQA 68 (104)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhccCCCccHHHH
Confidence 35555666555566679999999999999987764
No 4
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=32.68 E-value=99 Score=20.08 Aligned_cols=40 Identities=10% Similarity=0.156 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHhcCcccc
Q 029719 4 VMKRMSLARQIDKIMRKDSQEKAKKTWFERNAEAVELVVD 43 (189)
Q Consensus 4 IKeRV~LArqIdk~e~~~~k~k~e~sWlkkAAEeLgIdlD 43 (189)
.-.|+.++.++...-..-...---+.++++.|+.+||+.+
T Consensus 18 ~egk~~~~~~~~~~i~~i~~~i~r~~y~~~la~~~~i~~~ 57 (59)
T PF10410_consen 18 PEGKAEAVREAAPLIAQIPDPIERELYIRELAERLGISED 57 (59)
T ss_dssp HHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHCT-SST
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhCcCcc
Confidence 4467777777777776666777778999999999999765
No 5
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=25.91 E-value=55 Score=24.05 Aligned_cols=33 Identities=18% Similarity=0.304 Sum_probs=18.4
Q ss_pred HHHHHHHhhhhhhhhhHHHHHHHhcCccccCCc
Q 029719 14 IDKIMRKDSQEKAKKTWFERNAEAVELVVDNYD 46 (189)
Q Consensus 14 Idk~e~~~~k~k~e~sWlkkAAEeLgIdlDsDd 46 (189)
||=..++..=-+==..|+..||++.||+++.|+
T Consensus 4 IDLMnLAgFCRNCLskWy~~aA~~~g~~~~~d~ 36 (68)
T PF06844_consen 4 IDLMNLAGFCRNCLSKWYREAAEERGIEMDKDE 36 (68)
T ss_dssp HHHHHHHS--HHHHHHHHHHHHHHCT----HHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCcCCHHH
Confidence 333444444444445899999999999998775
No 6
>PF04748 Polysacc_deac_2: Divergent polysaccharide deacetylase; InterPro: IPR006837 This is a family of uncharacterised proteins that includes YibQ.; PDB: 2QV5_A 2NLY_A.
Probab=21.53 E-value=92 Score=26.53 Aligned_cols=52 Identities=27% Similarity=0.395 Sum_probs=36.3
Q ss_pred CCCCccccccCCCCchhhHHhHHHHHHhhcCCcchhhhhcccCceeecccccchhHHHHhc
Q 029719 82 PKTFSRHYLAGAGVSPLLQRQLEEIAKEKLPDSKSAIENKRRKLVVIGQDCVEPLQALRNA 142 (189)
Q Consensus 82 ~kg~S~kYlT~ggv~~l~~~~~~~L~~~~v~~~~~~~~~k~~~~~viGq~~Ve~L~~Lr~~ 142 (189)
|...+..||....-...+..||+.++. -+.+.|+-.+|||-.-+-|++|+.-
T Consensus 143 p~~~rdvfLD~~~~~~~I~~ql~~~~~---------~A~~~G~aI~Igh~~p~Tl~~L~~~ 194 (213)
T PF04748_consen 143 PAARRDVFLDNDQDEAAIRRQLDQAAR---------IARKQGSAIAIGHPRPETLEALEEW 194 (213)
T ss_dssp -EEE-SEETTST-SHHHHHHHHHHHHH---------HHHCCSEEEEEEE-SCCHHHHHHHH
T ss_pred CEEeeceecCCCCCHHHHHHHHHHHHH---------hhhhcCcEEEEEcCCHHHHHHHHHH
Confidence 345567778776666677888888877 3336899999999888888888753
No 7
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=18.12 E-value=1.5e+02 Score=24.95 Aligned_cols=29 Identities=21% Similarity=0.230 Sum_probs=22.8
Q ss_pred HHHHHHhCCCCCCCCCccccccCCCCchh
Q 029719 70 QELNAMLSRPLQPKTFSRHYLAGAGVSPL 98 (189)
Q Consensus 70 aeLk~LLSqPL~~kg~S~kYlT~ggv~~l 98 (189)
.+|.+.|.-|||-++-++=.||..|...+
T Consensus 37 ~~LE~~lg~~LF~R~~r~~~lT~~G~~l~ 65 (305)
T PRK11151 37 RKLEDELGVMLLERTSRKVLFTQAGLLLV 65 (305)
T ss_pred HHHHHHhCchheeeCCCceeECccHHHHH
Confidence 46777789999988888888999886443
No 8
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=18.05 E-value=1.3e+02 Score=25.21 Aligned_cols=49 Identities=24% Similarity=0.154 Sum_probs=34.2
Q ss_pred HHHHHHHhcCccccCCcchHHHHHHHHHhHHhHHHHHHHHHHHHHHhCCCCCCCCCccccccCCCCchh
Q 029719 30 WFERNAEAVELVVDNYDSEEEVVKNRKQKKATSMQLKKLQQELNAMLSRPLQPKTFSRHYLAGAGVSPL 98 (189)
Q Consensus 30 WlkkAAEeLgIdlDsDd~e~e~~~~~Kq~k~~k~~lk~LraeLk~LLSqPL~~kg~S~kYlT~ggv~~l 98 (189)
=|.+||++|+| .. --+-.-=++|.+.|..|||-++-+.=.||..|...+
T Consensus 21 s~s~AA~~L~i------sQ--------------~avS~~i~~LE~~lG~~LF~R~~r~~~lT~~G~~l~ 69 (302)
T PRK09791 21 SIRGASRMLNM------SQ--------------PALTKSIQELEEGLAAQLFFRRSKGVTLTDAGESFY 69 (302)
T ss_pred CHHHHHHHhCC------Ch--------------HHHHHHHHHHHHHhCCeEEEEcCCCceECccHHHHH
Confidence 37788998887 21 111112356778899999988888889999887543
No 9
>PF01817 CM_2: Chorismate mutase type II; InterPro: IPR020822 Chorismate mutase, 5.4.99.5 from EC, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [, ]. Prephenate dehydratase (IPR001086 from INTERPRO, 4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate into phenylpyruvate. In microorganisms PDT is involved in the terminal pathway of the biosynthesis of phenylalanine. In some bacteria, such as Escherichia coli, PDT is part of a bifunctional enzyme (P-protein) that also catalyzes the transformation of chorismate into prephenate (chorismate mutase) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional chorismate mutase aligns well with the N-terminal part of P-proteins [].; GO: 0046417 chorismate metabolic process; PDB: 1YBZ_A 2GTV_X 2FP1_B 2F6L_B 2FP2_B 2AO2_A 3HGW_C 3HGX_B 2H9C_A 3RET_B ....
Probab=17.77 E-value=3.2e+02 Score=19.02 Aligned_cols=40 Identities=23% Similarity=0.264 Sum_probs=26.2
Q ss_pred hhHHHHHHHHHHHHHHHHHhh-------hhhhhhhHHHHHHHhcCcc
Q 029719 2 PEVMKRMSLARQIDKIMRKDS-------QEKAKKTWFERNAEAVELV 41 (189)
Q Consensus 2 ~~IKeRV~LArqIdk~e~~~~-------k~k~e~sWlkkAAEeLgId 41 (189)
.-|-+|..||.+|...-..+. ++..--+++...|.+.|++
T Consensus 13 ~Ll~~R~~l~~~i~~~K~~~~~~i~d~~RE~~v~~~~~~~~~~~~l~ 59 (81)
T PF01817_consen 13 DLLAERMDLVRKIAEYKKENGLPIFDPDREEEVLERLRELAEEGGLD 59 (81)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTCCSSTHHHHHHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCCcHHHHHHHHHHHHHhHhCCCC
Confidence 357899999999998877773 3333344555555555553
No 10
>PF13093 FTA4: Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
Probab=15.59 E-value=1.5e+02 Score=25.54 Aligned_cols=40 Identities=23% Similarity=0.434 Sum_probs=28.4
Q ss_pred HHHHHHHHhCCCCCCCCCccccccC-CCCchhhHHhHHHHHH
Q 029719 68 LQQELNAMLSRPLQPKTFSRHYLAG-AGVSPLLQRQLEEIAK 108 (189)
Q Consensus 68 LraeLk~LLSqPL~~kg~S~kYlT~-ggv~~l~~~~~~~L~~ 108 (189)
+..|. .+||+||.|.--=+.|++. ...++++.++++..+.
T Consensus 14 I~~Qv-riLsqPL~ps~~wr~~~~~~~~~~~l~~k~v~~vL~ 54 (213)
T PF13093_consen 14 IRAQV-RILSQPLAPSRDWRSINSEPASEDPLSDKVVQDVLQ 54 (213)
T ss_pred HHHHH-HHcCCCCCCCHHHHHhcccccccCCCCHHHHHHHHH
Confidence 44454 7899999988877888864 3355677777776654
Done!