Query 015483
Match_columns 406
No_of_seqs 252 out of 518
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 06:44:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015483.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015483hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04784 DUF547: Protein of un 100.0 1.9E-40 4E-45 286.6 10.6 112 185-322 1-117 (117)
2 PF13107 DUF3964: Protein of u 33.9 19 0.0004 30.6 0.8 16 186-202 89-104 (109)
3 PF15147 DUF4578: Domain of un 28.6 25 0.00053 30.9 0.7 11 292-302 5-16 (127)
4 cd03742 SOCS_Rab40 SOCS (suppr 23.3 64 0.0014 23.5 1.9 35 314-348 6-40 (43)
5 PRK05097 Ter macrodomain organ 21.6 1.2E+02 0.0027 27.5 3.7 30 350-379 51-80 (150)
6 PF06303 MatP: Organiser of ma 18.3 1.5E+02 0.0033 27.1 3.6 30 350-379 51-80 (148)
7 KOG3749 Phosphoenolpyruvate ca 17.7 47 0.001 35.9 0.4 31 333-363 523-564 (640)
8 smart00253 SOCS suppressors of 15.6 1.6E+02 0.0034 21.0 2.5 34 314-347 10-43 (43)
9 PLN03052 acetate--CoA ligase; 12.6 4E+02 0.0086 29.9 5.9 24 229-252 611-634 (728)
10 PF08004 DUF1699: Protein of u 12.0 4.2E+02 0.0092 23.8 4.7 46 280-325 14-67 (131)
No 1
>PF04784 DUF547: Protein of unknown function, DUF547; InterPro: IPR006869 This is a conserved region found in uncharacterised proteins from Caenorhabditis elegans and Arabidopsis thaliana (Mouse-ear cress).
Probab=100.00 E-value=1.9e-40 Score=286.58 Aligned_cols=112 Identities=46% Similarity=0.756 Sum_probs=105.2
Q ss_pred ccCCCCCCcchhHHHHHHHHHHHHHHHHHHhCCCCCchhh---hccccceeEEECCEEeeHHHHHHhhccCCCCCCChhH
Q 015483 185 KVNPVHLSSNEKLAFWINLYNALIMHAYLAYGVPRNDLKL---FSLMQKAAYTVGGHSYNAAAIEYMILKMKPPLHRPQI 261 (406)
Q Consensus 185 ~Vdl~~Ls~~EKLAFWINiYNalvmHa~L~~G~P~s~~k~---~~~~~ka~Y~VGG~~~SL~dIEh~ILR~~~p~~rp~~ 261 (406)
+||++.|+++||+|||||+||+|+||+++++|+|.+..++ ..+|.+..|+|||+.+||+||||+|||++.+
T Consensus 1 ~v~~~~l~~~e~lAFwIN~yNal~~h~~l~~~~~~s~~~~~~~~~~~~~~~y~Igg~~~SL~dIe~~ILR~~~~------ 74 (117)
T PF04784_consen 1 RVDLSSLSREEKLAFWINLYNALVLHAILENGPPKSILDRKLGGSFFSKVRYNIGGQRFSLDDIEHGILRGNRP------ 74 (117)
T ss_pred CcChHHCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHhhcccccccceEEEECCEEecHHHHHHhhccCCCC------
Confidence 5899999999999999999999999999999999888765 6899999999999999999999999998642
Q ss_pred HHHHHHhhccchHHHhhhccCCCCCeeEEEeccCCCCCCCce--eeccchHHHHHHHHHHHHH
Q 015483 262 ALLLALQKLKVTEEQRKCAIDEYEPLVAFALSCGMYSSPAIS--IYTAKNVREELQEAQRDFI 322 (406)
Q Consensus 262 ~~l~~~~~~~~~d~r~~~~L~~~ePrIhFAL~cGs~SsP~lR--vYta~~v~~qLe~A~~eFL 322 (406)
.++||||||||+||++|||+|| +|||++|++||++|+++||
T Consensus 75 --------------------~~~DprihFaL~cgs~s~P~lr~~~yt~~~l~~qL~~a~~~fi 117 (117)
T PF04784_consen 75 --------------------PWPDPRIHFALNCGSKSCPPLRREAYTAENLDEQLEEAAREFI 117 (117)
T ss_pred --------------------CCCCCceeeeeecCCCCChhhhhhccCHHHHHHHHHHHHHhhC
Confidence 0589999999999999999999 9999999999999999996
No 2
>PF13107 DUF3964: Protein of unknown function (DUF3964)
Probab=33.94 E-value=19 Score=30.64 Aligned_cols=16 Identities=44% Similarity=0.931 Sum_probs=11.8
Q ss_pred cCCCCCCcchhHHHHHH
Q 015483 186 VNPVHLSSNEKLAFWIN 202 (406)
Q Consensus 186 Vdl~~Ls~~EKLAFWIN 202 (406)
|++..+ .+|++|||+|
T Consensus 89 v~Lp~i-~~~~~AFW~N 104 (109)
T PF13107_consen 89 VNLPEI-ENQQMAFWFN 104 (109)
T ss_pred eeCchh-hHHHHHHHhh
Confidence 455544 4789999998
No 3
>PF15147 DUF4578: Domain of unknown function (DUF4578)
Probab=28.64 E-value=25 Score=30.87 Aligned_cols=11 Identities=45% Similarity=1.069 Sum_probs=8.7
Q ss_pred eccC-CCCCCCc
Q 015483 292 LSCG-MYSSPAI 302 (406)
Q Consensus 292 L~cG-s~SsP~l 302 (406)
|||| +||||.-
T Consensus 5 lCCggSWScPst 16 (127)
T PF15147_consen 5 LCCGGSWSCPST 16 (127)
T ss_pred cccCCCcCCchh
Confidence 6776 7999984
No 4
>cd03742 SOCS_Rab40 SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as membrane-associated molecular switches. Rab40 is characterized by a SOCS box c-terminal to the GTPase domain. The SOCS boxes interact with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions.
Probab=23.34 E-value=64 Score=23.54 Aligned_cols=35 Identities=20% Similarity=0.104 Sum_probs=28.2
Q ss_pred HHHHHHHHHHhccccccCCeEEechhhHhhhcccC
Q 015483 314 LQEAQRDFIRASVGFSSKGKLLVPKMLHCFCKGSV 348 (406)
Q Consensus 314 Le~A~~eFL~a~v~V~~~~kv~LpKi~~wY~~DF~ 348 (406)
|+...|.-|++.+.++.=.++-||+-++-|.++|.
T Consensus 6 LQ~LCR~~I~~~t~~~~I~~LPLP~~Lk~yLkey~ 40 (43)
T cd03742 6 LQDLCCRAIVSCTPVYLIDKLPLPVSIKSHLKSFA 40 (43)
T ss_pred HHHHHHHHHHHhCCcchhhhCCCCHHHHHHHHhcc
Confidence 77788888888776543357999999999999986
No 5
>PRK05097 Ter macrodomain organizer matS-binding protein; Provisional
Probab=21.58 E-value=1.2e+02 Score=27.54 Aligned_cols=30 Identities=23% Similarity=0.412 Sum_probs=25.8
Q ss_pred ChhHHHHHHhcCCHHHHHHHHHHHHhhhhc
Q 015483 350 DANLAVWISHYLPPLQAAFVEQCISQRRQS 379 (406)
Q Consensus 350 ~~~Ll~wI~~~Lp~~~~~~i~~~l~~~~~~ 379 (406)
+..+++||.+++.+++...+.+.+++++.|
T Consensus 51 P~~v~~WI~~hm~p~l~nklkQaIRArRKR 80 (150)
T PRK05097 51 PVKVLEWIDKHMNPELVNRMKQTIRARRKR 80 (150)
T ss_pred cHHHHHHHHHhcCHHHHHHHHHHHHHHHHc
Confidence 467999999999999999999988877554
No 6
>PF06303 MatP: Organiser of macrodomain of Terminus of chromosome; InterPro: IPR009390 Many bacteria have circular genomes that are large in comparison to their cellular dimensions; this imposes the necessity for compaction of the chromosome during cellular growth, replication, transcription, and segregation. Compaction of chromosomes results in the formation of structures called nucleoids. Nucleoids can be generated by a number of different processes: they include unrestrained DNA supercoiling, formation of a chromatin-like structure through the interaction of DNA binding proteins, condensation by structural maintenance of chromosomes (SMC)-like proteins, and macromolecular crowding []. Chromosome replication and segregation are intimately linked and tightly controlled to ensure that daughter cells each receive a complete copy of the genome. Chromosomes have replication origin (Ori) and termination (Ter) regions that are diametrically opposed. During the process of chromosome replication and cell division the Ori and Ter regions form two macrodomains (MDs), the Ori MD is centred on migS, a 25 bp sequence, that acts as the cis-acting site for the bipolar positioning of oriC []. The Ter MD is centred on dif (deletion-induced filamentation), which is a resolvase site that reduces chromosome multimers to monomers []. The Ori and Ter MDs are insulated from one and other by non-structural regions and other nucleoids. Chromosome replication initiates bidirectionally from oriC. Within the Ori MD with sister chromatids being located in separate cell halves and with the Ter macrodomain anchored to the cell pole. Cell division occurs with the completion of replication of the Ter region and the subsequent separation of the two sister chromatids [, ]. This entry contains MatP (YcbG), which is a component of the MatP/MatS site-specific system that organises the Ter macrodomain (MD) in Escherichia coli (strain K12) and related enterobacteria during replication of the chromosome. In E. coli there are 23 matS sequences, located in the Ter region which is centred on dif. The matS consensus is a palindromic sequence 5'-GTGAC[AG][CT]GTCAC, which is the recognition sequence for MatP. MatP binds to the matS sequences; and is critical for Ter MD formation. Inactivation of matP causes severe defects in chromosome segregation and cell division revealing its role as a major organiser of the Ter MD [].
Probab=18.27 E-value=1.5e+02 Score=27.11 Aligned_cols=30 Identities=23% Similarity=0.389 Sum_probs=25.6
Q ss_pred ChhHHHHHHhcCCHHHHHHHHHHHHhhhhc
Q 015483 350 DANLAVWISHYLPPLQAAFVEQCISQRRQS 379 (406)
Q Consensus 350 ~~~Ll~wI~~~Lp~~~~~~i~~~l~~~~~~ 379 (406)
+..+.+||.++|.+++...+.+.++.++.|
T Consensus 51 P~~v~~WI~~~m~~~l~nklkQaIRArRkR 80 (148)
T PF06303_consen 51 PVKVNEWIKKHMNPELWNKLKQAIRARRKR 80 (148)
T ss_pred hHHHHHHHHHHCCHHHHHHHHHHHHHHHHh
Confidence 468999999999999999999988876544
No 7
>KOG3749 consensus Phosphoenolpyruvate carboxykinase [Energy production and conversion]
Probab=17.68 E-value=47 Score=35.91 Aligned_cols=31 Identities=29% Similarity=0.516 Sum_probs=24.9
Q ss_pred eEEechhhH--hhhccc---------CCChhHHHHHHhcCCH
Q 015483 333 KLLVPKMLH--CFCKGS---------VDDANLAVWISHYLPP 363 (406)
Q Consensus 333 kv~LpKi~~--wY~~DF---------~~~~~Ll~wI~~~Lp~ 363 (406)
+-.+||||+ ||++|- |++..+++||++.+..
T Consensus 523 ~~~~PkIFhvNwfrk~~~gKfLWPGfgeN~RVlewI~rR~~g 564 (640)
T KOG3749|consen 523 KAKLPKIFHVNWFRKDKEGKFLWPGFGENARVLEWIFRRVAG 564 (640)
T ss_pred CCCCCcEEEeeeeeeccCCCccCCCCcchhHHHHHHHHHhcc
Confidence 367899987 999884 3456899999998876
No 8
>smart00253 SOCS suppressors of cytokine signalling. suppressors of cytokine signalling
Probab=15.63 E-value=1.6e+02 Score=21.04 Aligned_cols=34 Identities=24% Similarity=0.124 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhccccccCCeEEechhhHhhhccc
Q 015483 314 LQEAQRDFIRASVGFSSKGKLLVPKMLHCFCKGS 347 (406)
Q Consensus 314 Le~A~~eFL~a~v~V~~~~kv~LpKi~~wY~~DF 347 (406)
|+.-.|.-|++.++.+.=.++-||..+++|..+|
T Consensus 10 LqhLCR~~I~~~~~~~~i~~LpLP~~lk~yL~~y 43 (43)
T smart00253 10 LQHLCRFTIRRCTRTDQIKTLPLPPKLKDYLSYY 43 (43)
T ss_pred HHHHHHHHHHHHcCCcCcccCCCCHHHHHHHHhC
Confidence 4556777777776653225789999999998765
No 9
>PLN03052 acetate--CoA ligase; Provisional
Probab=12.58 E-value=4e+02 Score=29.88 Aligned_cols=24 Identities=17% Similarity=0.238 Sum_probs=20.5
Q ss_pred cceeEEECCEEeeHHHHHHhhccC
Q 015483 229 QKAAYTVGGHSYNAAAIEYMILKM 252 (406)
Q Consensus 229 ~ka~Y~VGG~~~SL~dIEh~ILR~ 252 (406)
.+..+++||++++..+||..+++.
T Consensus 611 ~Dd~I~~~G~rI~~~EIE~~l~~~ 634 (728)
T PLN03052 611 ADDTMNLGGIKVSSVEIERVCNAA 634 (728)
T ss_pred CCCEEeeCCEEeCHHHHHHHHHhc
Confidence 356789999999999999998753
No 10
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=12.05 E-value=4.2e+02 Score=23.79 Aligned_cols=46 Identities=15% Similarity=0.258 Sum_probs=38.1
Q ss_pred ccCCCCCeeEEEeccCC-------CCCCCce-eeccchHHHHHHHHHHHHHHhc
Q 015483 280 AIDEYEPLVAFALSCGM-------YSSPAIS-IYTAKNVREELQEAQRDFIRAS 325 (406)
Q Consensus 280 ~L~~~ePrIhFAL~cGs-------~SsP~lR-vYta~~v~~qLe~A~~eFL~a~ 325 (406)
.|...|-.||+|+---. ..||.|+ +.-|..-..-+-.+++-||.-.
T Consensus 14 ~Ln~nE~~VHlAFRPSN~Dif~Lv~~CP~lk~iqiP~SY~~t~Sksi~mfL~mq 67 (131)
T PF08004_consen 14 TLNPNEEIVHLAFRPSNKDIFSLVERCPNLKAIQIPPSYYKTLSKSIKMFLEMQ 67 (131)
T ss_pred hcCCCceEEEEEecCcchHHHHHHHhCCCCeEEeCChHHHHHHhHHHHHHHHhc
Confidence 45667888999985443 4699997 7889999999999999999865
Done!