Query 040608
Match_columns 314
No_of_seqs 85 out of 87
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 10:02:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040608.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040608hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11303 DUF3105: Protein of u 88.4 0.17 3.6E-06 43.8 0.5 39 15-53 44-85 (130)
2 PF02070 NMU: Neuromedin U; I 77.8 1.2 2.6E-05 28.9 1.0 16 13-30 9-24 (25)
3 smart00084 NMU Neuromedin U. N 74.7 1.6 3.5E-05 28.5 1.0 16 13-30 9-24 (26)
4 TIGR02609 doc_partner putative 18.5 1.3E+02 0.0029 23.2 2.9 28 183-215 9-36 (74)
5 KOG0227 Splicing factor 3a, su 17.5 1.1E+02 0.0025 28.9 2.8 103 141-270 64-174 (222)
6 PF11284 DUF3085: Protein of u 15.2 1.7E+02 0.0037 24.1 3.0 25 164-188 9-36 (90)
7 cd01771 Faf1_UBX Faf1 UBX doma 14.6 2E+02 0.0044 22.6 3.2 70 112-213 10-79 (80)
8 PF07370 DUF1489: Protein of u 13.9 1.2E+02 0.0026 27.0 1.8 39 15-53 42-87 (137)
9 TIGR01439 lp_hng_hel_AbrB loop 13.6 1.8E+02 0.0039 19.2 2.3 25 184-213 7-31 (43)
10 cd05879 Ig_P0 Immunoglobulin ( 13.5 1.2E+02 0.0026 25.2 1.7 18 201-218 87-104 (116)
No 1
>PF11303 DUF3105: Protein of unknown function (DUF3105); InterPro: IPR021454 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.
Probab=88.44 E-value=0.17 Score=43.80 Aligned_cols=39 Identities=21% Similarity=0.451 Sum_probs=34.8
Q ss_pred ccceeeceEEEEeccCCCCCCCCChhhhhee---eEEEeecC
Q 040608 15 VEIQERGEIFFFYRPKVGKEEAHSSDDVQRL---YLVLRPES 53 (314)
Q Consensus 15 ~~IlEKG~IYFFyRpkV~~ee~~s~dDVqR~---yivLrP~~ 53 (314)
+--||.|-|.|+|+|.+.-++-..+.++++. |+||.|.+
T Consensus 44 VH~LEHGaV~i~Y~p~~~~~~v~~L~~l~~~~~~~~visP~~ 85 (130)
T PF11303_consen 44 VHNLEHGAVWITYDPCLPPDQVAKLKALAKSCLPYVVISPYP 85 (130)
T ss_pred HHhhhcCcEEEEECCCCCHHHHHHHHHHHhccCCcEEEecCC
Confidence 6779999999999999988888899998877 89999964
No 2
>PF02070 NMU: Neuromedin U; InterPro: IPR008199 Neuromedin U (NmU) [, ] is a vertebrate peptide which stimulates uterine smooth muscle contraction and causes selective vasoconstriction. Like most other active peptides, it is proteolytically processed from a larger precursor protein. The mature peptides are 8 (NmU-8) to 25 (NmU-25) residues long and C-terminally amidated. The sequence of the C-terminal extremity of NmU is extremely well conserved.; GO: 0006940 regulation of smooth muscle contraction
Probab=77.79 E-value=1.2 Score=28.87 Aligned_cols=16 Identities=44% Similarity=1.010 Sum_probs=12.5
Q ss_pred CCccceeeceEEEEeccC
Q 040608 13 SQVEIQERGEIFFFYRPK 30 (314)
Q Consensus 13 ~~~~IlEKG~IYFFyRpk 30 (314)
-|..|+-+| ||+||||
T Consensus 9 gP~~~qsrg--yFlfRPR 24 (25)
T PF02070_consen 9 GPGGIQSRG--YFLFRPR 24 (25)
T ss_pred CCccccccc--EEEeccC
Confidence 455677777 9999998
No 3
>smart00084 NMU Neuromedin U. Neuromedin U (NmU) is a vertebrate peptide which stimulates uterine smooth muscle contraction and causes selective vasoconstriction. Like most other active peptides, it is proteolytically processed from a larger precursor protein. The mature peptides are 8 (NmU-8) to 25 (NmU-25) residues long and C- terminally amidated. The sequence of the C-terminal extremity of NmU is extremely well conserved in mammals, birds and amphibians.
Probab=74.69 E-value=1.6 Score=28.53 Aligned_cols=16 Identities=38% Similarity=1.039 Sum_probs=11.5
Q ss_pred CCccceeeceEEEEeccC
Q 040608 13 SQVEIQERGEIFFFYRPK 30 (314)
Q Consensus 13 ~~~~IlEKG~IYFFyRpk 30 (314)
-|..|+-+| ||+||||
T Consensus 9 gp~~~qsrg--yFLfRPR 24 (26)
T smart00084 9 GPIASQSRG--YFLFRPR 24 (26)
T ss_pred CccccccCc--eEEeccC
Confidence 345555555 9999998
No 4
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=18.50 E-value=1.3e+02 Score=23.23 Aligned_cols=28 Identities=18% Similarity=0.362 Sum_probs=21.2
Q ss_pred EEEeeCCCCCCchhhhhhhCCCccccEEEEeeC
Q 040608 183 IYKLEFPPEDMENETQESLNIEHEGSFLIQIKK 215 (314)
Q Consensus 183 ~Y~Lt~P~~~e~GevQ~~lgi~~~gSFIiqvKN 215 (314)
+|.++||. ++-++|||+.-..+.|.+.|
T Consensus 9 S~~vtIPk-----~i~~~lgl~~Gd~v~v~~~~ 36 (74)
T TIGR02609 9 SLVVTLPK-----EVLESLGLKEGDTLYVDEEE 36 (74)
T ss_pred eeEEEECH-----HHHHHcCcCCCCEEEEEEEC
Confidence 37899996 89999999966665555554
No 5
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=17.52 E-value=1.1e+02 Score=28.91 Aligned_cols=103 Identities=19% Similarity=0.370 Sum_probs=72.1
Q ss_pred hcCCcccccCCccccCC--CcccccceeEEEEecCCCCccceeeEEEeeCCCC-CCchhhhhhhCCCccccEEEEeeCCC
Q 040608 141 LAGEEYDTSTRGHRRNL--PARAVGEGVYRILRHSPGKKMHTHLIYKLEFPPE-DMENETQESLNIEHEGSFLIQIKKPD 217 (314)
Q Consensus 141 L~~~~YeTkTrG~Rh~p--~Arp~gEGvYaI~~~~~~~~~~tHL~Y~Lt~P~~-~e~GevQ~~lgi~~~gSFIiqvKNP~ 217 (314)
+.+.-|.+-|.|.+|.- +-|++-|--=++ ++|.. .-.-+||+--+|-.-|-=|..+|||+
T Consensus 64 ~ne~Syl~HtqGKKHq~Nlarraa~e~k~s~-----------------~~~~~~k~~v~vk~~vkigrpgykvtk~r~~~ 126 (222)
T KOG0227|consen 64 NNEGSYLAHTQGKKHQTNLARRAAKEAKESP-----------------DLPQPQKIIVEVKKFVKIGRPGYKVTKQRDPE 126 (222)
T ss_pred cchhhhhhhhccchhhHHHHHHHHHHhhcCc-----------------cccccccchhhhhhhhhcCCCcceeeeeecCc
Confidence 34677899999999977 555554433222 33331 12468999889999999999999999
Q ss_pred CCCCCcccCCccccCCCCchhHHHhhCCCCccCC-----CCCCCCCCCCceEEEEecc
Q 040608 218 QHGTSQFRGLQNKRKAVFPAHLQGQFGQKRYCPA-----DPPDFLNYEGCEFLLISAS 270 (314)
Q Consensus 218 ~~~~~~~~gl~~~r~p~yP~ei~~~Fg~~Rw~p~-----~pP~~LDY~gaqlLLIga~ 270 (314)
.+.- | +-=.-+||+..-+.---+||+.+ +||+ .+-|+|||++.
T Consensus 127 ~gq~----~--L~fQv~Yp~i~~~~~Pr~rfmssyeq~ve~~d----k~~qyLvfaae 174 (222)
T KOG0227|consen 127 NGQQ----G--LLFQVNYPEIEEGIMPRHRFMSSYEQKVEPPD----KSWQYLVFAAE 174 (222)
T ss_pred cCce----e--eEEEecchhhhhccCCcchhhhhhHhhcCCcc----ccceEEEEEec
Confidence 4221 2 22357899888777777899875 4443 47899999986
No 6
>PF11284 DUF3085: Protein of unknown function (DUF3085); InterPro: IPR021436 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=15.23 E-value=1.7e+02 Score=24.07 Aligned_cols=25 Identities=16% Similarity=0.199 Sum_probs=18.1
Q ss_pred ceeEEEEecCC---CCccceeeEEEeeC
Q 040608 164 EGVYRILRHSP---GKKMHTHLIYKLEF 188 (314)
Q Consensus 164 EGvYaI~~~~~---~~~~~tHL~Y~Lt~ 188 (314)
.|||-+++..+ ..+|-.++||-..-
T Consensus 9 ~GVYlmsn~~~~~~~G~r~~~vaYA~gC 36 (90)
T PF11284_consen 9 HGVYLMSNGGERLPDGERPKLVAYAEGC 36 (90)
T ss_pred CeEEEEeCCCccCCCCccceEEEEeecc
Confidence 69999998863 22234699998764
No 7
>cd01771 Faf1_UBX Faf1 UBX domain. Faf1 (fas-associated factor1) is a nucleolar protein that was first identified as an interaction partner of the death receptor Fas. Faf1 contains N-terminal UAS (ubiquitin-associated) and C-terminal UBX (ubiquitin-like) domains and is closely related to other UBA/UBX-containing proteins like p47, Rep8 and SAKS1. Faf1 is thought to be involved in 18S rRNA synthesis and/or 40S ribosomal subunit assembly. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=14.61 E-value=2e+02 Score=22.60 Aligned_cols=70 Identities=16% Similarity=0.149 Sum_probs=44.3
Q ss_pred CCCCCCCCCCCeeEEEecccCCHHHHHHhhcCCcccccCCccccCCCcccccceeEEEEecCCCCccceeeEEEeeCCCC
Q 040608 112 SLPDPREKSRPYWGFVEMVTTKVEDVKVALAGEEYDTSTRGHRRNLPARAVGEGVYRILRHSPGKKMHTHLIYKLEFPPE 191 (314)
Q Consensus 112 ~LP~~~~~~~rf~gfVe~~~~~~~~lk~~L~~~~YeTkTrG~Rh~p~Arp~gEGvYaI~~~~~~~~~~tHL~Y~Lt~P~~ 191 (314)
+||+-.+-.+|| .++.++++|-+++....|+ ...|.|.++= +++--+ .
T Consensus 10 RlP~G~r~~rrF-----~~t~~L~~l~~fv~~~~~~----------------~~~f~L~t~f-PRk~~~---------~- 57 (80)
T cd01771 10 RTPSGDFLERRF-----LGDTPLQVLLNFVASKGYP----------------IDEYKLLSSW-PRRDLT---------Q- 57 (80)
T ss_pred ECCCCCEEEEEe-----CCCCcHHHHHHHHHhcCCC----------------CCCEEEecCC-CCCCCc---------C-
Confidence 688865434444 4679999999988533321 2368888765 443221 1
Q ss_pred CCchhhhhhhCCCccccEEEEe
Q 040608 192 DMENETQESLNIEHEGSFLIQI 213 (314)
Q Consensus 192 ~e~GevQ~~lgi~~~gSFIiqv 213 (314)
.+.+.-=+++||.+.+..+|+-
T Consensus 58 ~d~~~TL~e~gL~p~~~L~Vee 79 (80)
T cd01771 58 LDPNFTLLELKLYPQETLILEE 79 (80)
T ss_pred CCCCCcHHHcCCCCCcEEEEEc
Confidence 1233455788999999888863
No 8
>PF07370 DUF1489: Protein of unknown function (DUF1489); InterPro: IPR008320 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=13.92 E-value=1.2e+02 Score=27.05 Aligned_cols=39 Identities=26% Similarity=0.524 Sum_probs=34.0
Q ss_pred ccceeeceEEEEeccCCC-------CCCCCChhhhheeeEEEeecC
Q 040608 15 VEIQERGEIFFFYRPKVG-------KEEAHSSDDVQRLYLVLRPES 53 (314)
Q Consensus 15 ~~IlEKG~IYFFyRpkV~-------~ee~~s~dDVqR~yivLrP~~ 53 (314)
.+||.-|-||..++..|. +++...-|-+.|--|||-|.-
T Consensus 42 ~Ell~GGSlYWVikg~i~~RQ~Il~i~~~~~~dG~~rc~ivL~P~l 87 (137)
T PF07370_consen 42 DELLDGGSLYWVIKGQIQCRQRILDIEEVTDGDGIRRCAIVLDPEL 87 (137)
T ss_pred HHhccCCcEEEEECCEEEEeeeeeeeeEecCCCCcccEEEEECCcE
Confidence 789999999999998765 677788888999999999864
No 9
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=13.56 E-value=1.8e+02 Score=19.18 Aligned_cols=25 Identities=16% Similarity=0.275 Sum_probs=21.3
Q ss_pred EEeeCCCCCCchhhhhhhCCCccccEEEEe
Q 040608 184 YKLEFPPEDMENETQESLNIEHEGSFLIQI 213 (314)
Q Consensus 184 Y~Lt~P~~~e~GevQ~~lgi~~~gSFIiqv 213 (314)
+.+++|. ++-+.||++.-..|.|..
T Consensus 7 gri~iP~-----~~r~~l~~~~gd~~~i~~ 31 (43)
T TIGR01439 7 GQIVIPK-----EIREKLGLKEGDRLEVIR 31 (43)
T ss_pred CeEEecH-----HHHHHcCcCCCCEEEEEE
Confidence 5688995 899999999888888884
No 10
>cd05879 Ig_P0 Immunoglobulin (Ig)-like domain of Protein zero (P0). Ig_P0ex: immunoglobulin (Ig) domain of Protein zero (P0). P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin.
Probab=13.51 E-value=1.2e+02 Score=25.20 Aligned_cols=18 Identities=28% Similarity=0.652 Sum_probs=14.6
Q ss_pred hCCCccccEEEEeeCCCC
Q 040608 201 LNIEHEGSFLIQIKKPDQ 218 (314)
Q Consensus 201 lgi~~~gSFIiqvKNP~~ 218 (314)
+-+.+.|-|++++|||--
T Consensus 87 v~~sD~G~Y~C~v~n~p~ 104 (116)
T cd05879 87 LDYTDNGTFTCDVKNPPD 104 (116)
T ss_pred CCcccCEEEEEEEEcCCC
Confidence 345678999999999983
Done!