Query 031559
Match_columns 157
No_of_seqs 90 out of 119
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 15:50:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031559.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031559hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12165 DUF3594: Domain of un 100.0 4.1E-95 9E-100 567.3 9.5 129 8-136 1-131 (137)
2 KOG1632 Uncharacterized PHD Zn 100.0 1.2E-33 2.7E-38 242.6 1.8 152 5-156 35-201 (345)
3 cd04120 Rab12 Rab12 subfamily. 55.6 6.7 0.00014 31.0 1.3 14 61-74 184-197 (202)
4 PF07775 PaRep2b: PaRep2b prot 55.0 13 0.00028 35.5 3.3 74 18-132 119-197 (512)
5 PF00319 SRF-TF: SRF-type tran 51.3 11 0.00024 25.2 1.7 36 15-56 11-46 (51)
6 PF05402 PqqD: Coenzyme PQQ sy 51.3 20 0.00043 23.2 2.9 33 6-38 28-60 (68)
7 PF06452 DUF1083: Domain of un 42.8 6.3 0.00014 29.2 -0.6 44 55-99 123-171 (185)
8 PHA03099 epidermal growth fact 42.1 9 0.0002 31.1 0.2 23 27-50 34-56 (139)
9 smart00432 MADS MADS domain. 38.7 36 0.00079 23.2 2.7 38 16-58 19-56 (59)
10 PF11351 DUF3154: Protein of u 37.9 18 0.00039 27.5 1.2 14 98-111 100-115 (123)
11 PF09483 HpaP: Type III secret 33.7 37 0.0008 28.3 2.5 48 23-81 95-142 (185)
12 PF13880 Acetyltransf_13: ESCO 32.2 7.7 0.00017 27.7 -1.5 52 18-89 16-68 (70)
13 PF13111 DUF3962: Protein of u 30.9 26 0.00057 30.3 1.2 33 86-125 24-56 (216)
14 PF15643 Tox-PL-2: Papain fold 28.5 24 0.00052 27.2 0.5 14 77-90 83-96 (100)
15 PTZ00211 ribonucleoside-diphos 26.8 36 0.00079 29.3 1.4 39 89-130 108-146 (330)
16 KOG0736 Peroxisome assembly fa 26.0 58 0.0012 33.4 2.8 26 20-45 848-881 (953)
17 COG1993 PII-like signaling pro 25.8 35 0.00077 26.6 1.0 20 116-135 57-76 (109)
18 PF09065 Haemadin: Haemadin; 25.6 29 0.00064 21.2 0.5 9 44-52 5-13 (27)
19 TIGR03859 PQQ_PqqD coenzyme PQ 24.2 71 0.0015 22.3 2.3 32 6-38 42-73 (81)
20 PF09447 Cnl2_NKP2: Cnl2/NKP2 23.4 1.3E+02 0.0028 21.4 3.4 29 9-37 38-66 (67)
21 TIGR03019 pepcterm_femAB FemAB 23.2 78 0.0017 26.4 2.7 40 7-46 126-174 (330)
22 PRK05988 formate dehydrogenase 22.6 72 0.0016 25.2 2.2 27 10-37 11-37 (156)
23 KOG0721 Molecular chaperone (D 22.5 42 0.0009 29.3 1.0 23 23-54 147-169 (230)
24 PF14367 DUF4411: Domain of un 22.5 1E+02 0.0022 23.9 3.1 16 94-109 103-118 (162)
25 KOG4148 Uncharacterized conser 22.4 29 0.00063 27.1 0.0 28 21-48 13-47 (106)
26 PF04068 RLI: Possible Fer4-li 22.3 37 0.0008 21.2 0.5 10 36-45 8-17 (35)
27 PRK03598 putative efflux pump 21.3 25 0.00053 29.3 -0.6 27 83-109 1-27 (331)
28 PF06426 SATase_N: Serine acet 21.2 1.1E+02 0.0024 22.5 2.9 31 8-38 53-83 (105)
29 cd00266 MADS_SRF_like SRF-like 21.0 1.2E+02 0.0027 21.4 3.0 38 16-58 19-56 (83)
30 PF08040 NADH_oxidored: MNLL s 20.8 63 0.0014 23.0 1.4 31 91-121 4-37 (59)
31 cd00120 MADS MADS: MCM1, Agamo 20.1 90 0.002 21.2 2.0 24 16-43 19-42 (59)
No 1
>PF12165 DUF3594: Domain of unknown function (DUF3594); InterPro: IPR021998 This presumed domain is functionally uncharacterised.This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF00628 from PFAM.
Probab=100.00 E-value=4.1e-95 Score=567.28 Aligned_cols=129 Identities=82% Similarity=1.410 Sum_probs=127.9
Q ss_pred CCHHHHHHHHhhhHHHHHHHhhhcHHHhhhcCCCCCCcceeccCCCCceeeeCCCCCCCCCCCCCccCccccCCCccccc
Q 031559 8 RTVEEIYKDFCARRAGVVRALTNDVDEFYGLCDPDKENLCLYGHPNESWEVTLPAEEVPPELPEPALGINFARDGMNRKD 87 (157)
Q Consensus 8 rTvE~iF~Df~~RR~glirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV~lPaeevPpeLPEPalGINfaRDgM~rkd 87 (157)
||||+||+||++||+|||||||+|||+||+||||+||||||||+|||+|||+||+||||||||||+||||||||||+|+|
T Consensus 1 rtve~if~df~~RR~g~v~ALT~dve~Fy~~CDP~kenLCLYG~p~~~WeV~lP~eevPpeLPEPaLGINfaRDgM~r~d 80 (137)
T PF12165_consen 1 RTVEEIFRDFSGRRAGIVRALTTDVEEFYQQCDPEKENLCLYGHPDGTWEVNLPAEEVPPELPEPALGINFARDGMQRKD 80 (137)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccceEEecCCCCCeEEeCChHhCCCCCCCcccCcccccCCccHHH
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhccchHHHHHHHHhhhc--CCchhhhHHHHhhhcCCceeeeeccc
Q 031559 88 WLSLVAVHTDSWLLSVAFYLGAR--LNRNERKRLFSLINDQPTVFEVVTER 136 (157)
Q Consensus 88 WLslVAvHSDsWLlsVAfy~gar--~~~~~R~rLF~mIN~lPTv~Evv~g~ 136 (157)
||||||||||||||||||||||| ||+++|+|||+|||+||||||+|+|+
T Consensus 81 WLslVAvHsDsWLlsvAfy~gar~~~~~~~R~rLF~mIN~lpTv~Evv~g~ 131 (137)
T PF12165_consen 81 WLSLVAVHSDSWLLSVAFYFGARFGFDKNERKRLFSMINDLPTVFEVVTGR 131 (137)
T ss_pred HHHHHHHhccHHHHHHHHHHHHhhccChHHHHHHHHHHhcCchHHHHHhcc
Confidence 99999999999999999999999 79999999999999999999999994
No 2
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=99.97 E-value=1.2e-33 Score=242.62 Aligned_cols=152 Identities=40% Similarity=0.555 Sum_probs=140.6
Q ss_pred CCCCCHHHHHHHHhhhHHHHHHHhhhcHHHhhhcCCC----CCCcceeccCCCCceeeeCCCCCCCCCCCCCccCccccC
Q 031559 5 SSPRTVEEIYKDFCARRAGVVRALTNDVDEFYGLCDP----DKENLCLYGHPNESWEVTLPAEEVPPELPEPALGINFAR 80 (157)
Q Consensus 5 ~~prTvE~iF~Df~~RR~glirALT~Dve~Fy~~CDP----~kenLcLYG~p~~~WeV~lPaeevPpeLPEPalGINfaR 80 (157)
+.+++|+++|.+|++||++++.|+++++.+||.+||| .++++|+|+++++.|+|++|++|+|+++++++.|||+++
T Consensus 35 ~~~~~~~~~~~~~k~~~~~~~~a~~~~~~~~~~~~~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~ 114 (345)
T KOG1632|consen 35 PIERPVPDVFRGRKGRRGGLLKALTQRYCKCYKPCDPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQ 114 (345)
T ss_pred CCCCCCcccccccccccccccHhhhhchhhcccccCchhhhhccccccccccccccccCchhhcCCccccccccccchhh
Confidence 6789999999999999999999999999999999999 689999999999999999999999999999999999999
Q ss_pred CCccccchhhhhhhccchHHHHHHHHhhhcC-------CchhhhHHHHhhhcCCceeeeecccc----cCCCCCCCCCCC
Q 031559 81 DGMNRKDWLSLVAVHTDSWLLSVAFYLGARL-------NRNERKRLFSLINDQPTVFEVVTERK----PIKDKPSVDSSS 149 (157)
Q Consensus 81 DgM~rkdWLslVAvHSDsWLlsVAfy~gar~-------~~~~R~rLF~mIN~lPTv~Evv~g~k----~~k~~~~~~~~~ 149 (157)
|||+.+|||+++++|+|+|+.+++||||+++ .+.+|+|++.++|++|||+++++|.. +.|.++++++++
T Consensus 115 ~~~~~~~~l~~~~~~~~~~~~s~s~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~t~~~~~~~~~~~~~~~k~~~~~~~~~ 194 (345)
T KOG1632|consen 115 DGMSESDGLSCVCRQDDSELLSPSFYFGKRGCQFWVKLQKLGRVRLEAEKNDDPTVFEVVSGTATGELPSKDKSSNDRGS 194 (345)
T ss_pred hhhhhhccceeecccccccccccccccCCccccccccchhhhhhhhhhhhcccchhhhcccccccccccccccccccccc
Confidence 9999999999999999999999999999995 89999999999999999999999933 556666666666
Q ss_pred CCCCCCC
Q 031559 150 KSRGSTK 156 (157)
Q Consensus 150 ~~k~~~k 156 (157)
+++.+.+
T Consensus 195 ~~~~~~~ 201 (345)
T KOG1632|consen 195 KSKTRKK 201 (345)
T ss_pred eecccCc
Confidence 6555443
No 3
>cd04120 Rab12 Rab12 subfamily. Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic
Probab=55.63 E-value=6.7 Score=31.04 Aligned_cols=14 Identities=57% Similarity=1.151 Sum_probs=12.2
Q ss_pred CCCCCCCCCCCCcc
Q 031559 61 PAEEVPPELPEPAL 74 (157)
Q Consensus 61 PaeevPpeLPEPal 74 (157)
|..|+|||||.|-.
T Consensus 184 ~~~~~~~~~~~~~~ 197 (202)
T cd04120 184 PEPEIPPELPPPRP 197 (202)
T ss_pred CCCCCCcCCCCCCC
Confidence 78899999999864
No 4
>PF07775 PaRep2b: PaRep2b protein; InterPro: IPR011689 This is a group of proteins, expressed in the crenarchaeon Pyrobaculum aerophilum, whose members are variable in length and level of conservation. The presence of numerous frameshifts and internal stop codons in multiple alignments are thought to indicate that most family members are no longer functional [].
Probab=54.97 E-value=13 Score=35.46 Aligned_cols=74 Identities=28% Similarity=0.583 Sum_probs=58.4
Q ss_pred hhhHHHHHHHhhhcHHHhhhcCCCCCCcceeccCCCCceeeeCCCCCCCCCCCCCccCccccCCCccccchhhhhhhccc
Q 031559 18 CARRAGVVRALTNDVDEFYGLCDPDKENLCLYGHPNESWEVTLPAEEVPPELPEPALGINFARDGMNRKDWLSLVAVHTD 97 (157)
Q Consensus 18 ~~RR~glirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV~lPaeevPpeLPEPalGINfaRDgM~rkdWLslVAvHSD 97 (157)
..|++.|++||--++|. |+ | ++.|-|.|-.+ |+-|+-.+
T Consensus 119 AErlAsILrAlG~~aEv--------k~----~---g~~W~V~l~Td--------------------------~IaAirh~ 157 (512)
T PF07775_consen 119 AERLASILRALGAEAEV--------KK----Y---GGEWRVVLTTD--------------------------SIAAIRHP 157 (512)
T ss_pred HHHHHHHHHhcCCeeEE--------EE----c---CCeEEEEEEeC--------------------------cchhcccH
Confidence 46899999999876653 11 1 67899998655 34777889
Q ss_pred hHHHHHHHHhhhc-----CCchhhhHHHHhhhcCCceeee
Q 031559 98 SWLLSVAFYLGAR-----LNRNERKRLFSLINDQPTVFEV 132 (157)
Q Consensus 98 sWLlsVAfy~gar-----~~~~~R~rLF~mIN~lPTv~Ev 132 (157)
.||=+|.-|.-.. ++.+.|.||..-|..=|.+-|+
T Consensus 158 ewl~AV~~fVeel~~~G~I~~~~~~~L~~~ieaGPN~ve~ 197 (512)
T PF07775_consen 158 EWLEAVRAFVEELHEKGVISEEQYERLLKKIEAGPNVVEI 197 (512)
T ss_pred HHHHHHHHHHHHHhhcccccHHHHHHHHHHHhcCCCCCcc
Confidence 9999998887654 5999999999999998888654
No 5
>PF00319 SRF-TF: SRF-type transcription factor (DNA-binding and dimerisation domain); InterPro: IPR002100 Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation []. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see IPR002487 from INTERPRO ; GO: 0003677 DNA binding, 0046983 protein dimerization activity; PDB: 1MNM_B 1N6J_A 1TQE_S 3MU6_D 3P57_I 1EGW_A 1C7U_B 3KOV_A 1HBX_A 1K6O_C ....
Probab=51.34 E-value=11 Score=25.22 Aligned_cols=36 Identities=22% Similarity=0.540 Sum_probs=24.8
Q ss_pred HHHhhhHHHHHHHhhhcHHHhhhcCCCCCCcceeccCCCCce
Q 031559 15 KDFCARRAGVVRALTNDVDEFYGLCDPDKENLCLYGHPNESW 56 (157)
Q Consensus 15 ~Df~~RR~glirALT~Dve~Fy~~CDP~kenLcLYG~p~~~W 56 (157)
.-|+.||.||.|= +.++--+||-+-.-+ +|| |+|..
T Consensus 11 ~tf~KRk~gL~KK----a~ELs~LC~~~v~~i-v~~-~~g~~ 46 (51)
T PF00319_consen 11 VTFSKRKKGLFKK----ASELSTLCGVDVALI-VFS-PDGKL 46 (51)
T ss_dssp HHHHHHHHHHHHH----HHHHHHHHT-EEEEE-EEE-TTSEE
T ss_pred hHHHHHHhhhhhc----cceeeeecCCeEEEE-EEC-CCCCE
Confidence 3588999999874 567888998875543 366 66653
No 6
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=51.29 E-value=20 Score=23.17 Aligned_cols=33 Identities=33% Similarity=0.412 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHHhhhHHHHHHHhhhcHHHhhhc
Q 031559 6 SPRTVEEIYKDFCARRAGVVRALTNDVDEFYGL 38 (157)
Q Consensus 6 ~prTvE~iF~Df~~RR~glirALT~Dve~Fy~~ 38 (157)
.++|+++|-+.+..+=..=...+..||.+|.++
T Consensus 28 g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~ 60 (68)
T PF05402_consen 28 GPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQ 60 (68)
T ss_dssp SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 579999999988887655555578899999764
No 7
>PF06452 DUF1083: Domain of unknown function (DUF1083); InterPro: IPR010502 This entry represents the family 9 carbohydrate-binding module (CBD9), which exhibit an immunoglobulin-like beta-sandwich fold, with an additional beta-strand at the N terminus []. Bacterial extracellular cellulases and hemicellulases are involved in the hydrolysis of the major structural polysaccharides of plant cell walls. These are usually modular enzymes that contain catalytic and non-catalytic domains. The CBD9 domain binds to cellulose, xylan, as well as to a range of soluble di- and mono-saccharides, and is found in cellulose- and xylan-degrading enzymes, such as endo-1,4-beta-xylanase (3.2.1.8 from EC) [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0016052 carbohydrate catabolic process; PDB: 1I82_A 1I8A_A 1I8U_A.
Probab=42.85 E-value=6.3 Score=29.21 Aligned_cols=44 Identities=32% Similarity=0.642 Sum_probs=26.2
Q ss_pred ceeeeCCCCCC-CCCCCCCccCccccC----CCccccchhhhhhhccchH
Q 031559 55 SWEVTLPAEEV-PPELPEPALGINFAR----DGMNRKDWLSLVAVHTDSW 99 (157)
Q Consensus 55 ~WeV~lPaeev-PpeLPEPalGINfaR----DgM~rkdWLslVAvHSDsW 99 (157)
+.|+.+|-+.+ +|+.... +|+||.+ ++=.|..|++......+.|
T Consensus 123 ~~E~~IP~~~l~~~~~g~~-~g~~~~~~d~~~~~~r~~~~~w~~~~~~~~ 171 (185)
T PF06452_consen 123 TVEIAIPWSALFPPQPGDK-FGFNFAVNDNDDGGKREGWISWSDPSGPSF 171 (185)
T ss_dssp EEEEEEE-SS-----TTEE-EEEEEEEEEE-TTS-EEEEEESS-SSS-TT
T ss_pred EEEEEechHHcCCCCCCCE-EEEEEEEEECCCCCcceEEEEEcCCCCcCc
Confidence 57999999998 4444433 8888884 4556788888777666554
No 8
>PHA03099 epidermal growth factor-like protein (EGF-like protein); Provisional
Probab=42.05 E-value=9 Score=31.10 Aligned_cols=23 Identities=35% Similarity=0.793 Sum_probs=20.1
Q ss_pred HhhhcHHHhhhcCCCCCCcceecc
Q 031559 27 ALTNDVDEFYGLCDPDKENLCLYG 50 (157)
Q Consensus 27 ALT~Dve~Fy~~CDP~kenLcLYG 50 (157)
--|+|+-+ ++.|.+++.+.||+|
T Consensus 34 ~~~~~~~~-i~~Cp~ey~~YClHG 56 (139)
T PHA03099 34 NATTDIPA-IRLCGPEGDGYCLHG 56 (139)
T ss_pred cCccCCcc-cccCChhhCCEeECC
Confidence 34778888 899999999999998
No 9
>smart00432 MADS MADS domain.
Probab=38.73 E-value=36 Score=23.19 Aligned_cols=38 Identities=24% Similarity=0.521 Sum_probs=24.3
Q ss_pred HHhhhHHHHHHHhhhcHHHhhhcCCCCCCcceeccCCCCceee
Q 031559 16 DFCARRAGVVRALTNDVDEFYGLCDPDKENLCLYGHPNESWEV 58 (157)
Q Consensus 16 Df~~RR~glirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV 58 (157)
-|+.||.||.+-- .++.-+||-+---++ |+..+..+++
T Consensus 19 tf~kRk~gl~kKa----~Els~Lc~~~v~~iv-~sp~g~~~~~ 56 (59)
T smart00432 19 TFSKRRNGLFKKA----HELSVLCDAEVALIV-FSPTGKLYEF 56 (59)
T ss_pred hhHhhhhhHHHHH----HHHhhccCCeEEEEE-ECCCCCeeec
Confidence 3899999999865 557779987543222 5544444433
No 10
>PF11351 DUF3154: Protein of unknown function (DUF3154); InterPro: IPR021497 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=37.95 E-value=18 Score=27.51 Aligned_cols=14 Identities=57% Similarity=0.897 Sum_probs=11.7
Q ss_pred hHHH--HHHHHhhhcC
Q 031559 98 SWLL--SVAFYLGARL 111 (157)
Q Consensus 98 sWLl--sVAfy~gar~ 111 (157)
-||| .|.||+|+|-
T Consensus 100 w~Llg~~vlgy~~~Rs 115 (123)
T PF11351_consen 100 WWLLGAGVLGYFGARS 115 (123)
T ss_pred HHHHHHHHhhhHHHhh
Confidence 4777 8999999983
No 11
>PF09483 HpaP: Type III secretion protein (HpaP); InterPro: IPR013390 This entry represents proteins encoded by genes which are always found in type III secretion operons, although their function in the processes of secretion and virulence is unclear []. Hpa stands for Hrp-associated gene, where Hrp stands for hypersensitivity response and virulence.
Probab=33.70 E-value=37 Score=28.31 Aligned_cols=48 Identities=25% Similarity=0.464 Sum_probs=35.0
Q ss_pred HHHHHhhhcHHHhhhcCCCCCCcceeccCCCCceeeeCCCCCCCCCCCCCccCccccCC
Q 031559 23 GVVRALTNDVDEFYGLCDPDKENLCLYGHPNESWEVTLPAEEVPPELPEPALGINFARD 81 (157)
Q Consensus 23 glirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV~lPaeevPpeLPEPalGINfaRD 81 (157)
.+|..|+..|-.|...=.= ...|+|||.||-+ |.-||+=+|..-..+.
T Consensus 95 ~~~~~la~eIA~FC~~~aI---------~~aG~We~~l~LD--paiLp~TtL~L~LS~f 142 (185)
T PF09483_consen 95 RVAEHLAREIAAFCADPAI---------REAGNWEAQLPLD--PAILPETTLNLRLSPF 142 (185)
T ss_pred HHHHHHHHHHHHHhCCccc---------ccCCcceEeeeCC--hhhccCceEEEEeccc
Confidence 4678888888888653221 1368899999754 6778999999888765
No 12
>PF13880 Acetyltransf_13: ESCO1/2 acetyl-transferase
Probab=32.17 E-value=7.7 Score=27.71 Aligned_cols=52 Identities=29% Similarity=0.523 Sum_probs=36.4
Q ss_pred hhhHHHHHHHhhhcHHHhhhcCCCCCCcceeccCCCCceeeeCCCCCCCCCCCCCc-cCccccCCCccccchh
Q 031559 18 CARRAGVVRALTNDVDEFYGLCDPDKENLCLYGHPNESWEVTLPAEEVPPELPEPA-LGINFARDGMNRKDWL 89 (157)
Q Consensus 18 ~~RR~glirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV~lPaeevPpeLPEPa-lGINfaRDgM~rkdWL 89 (157)
+-||.||...|.+=+-+ + .+||..-...||.. -+|+ -|..||+.-..+.+||
T Consensus 16 ~~RR~GIAt~Lld~ar~----------~-~iyG~~l~~~~iAF---------SqPT~~G~~fA~~y~~~~~fl 68 (70)
T PF13880_consen 16 SHRRKGIATRLLDAARE----------N-FIYGCVLPKNEIAF---------SQPTESGKKFAKKYFGTDDFL 68 (70)
T ss_pred hhhhhhHHHHHHHHHHH----------h-ccCceEechhheEe---------cCCCHhHHHHHHHHcCCCCEE
Confidence 56999999999874332 2 35887666666653 3444 6888888888877776
No 13
>PF13111 DUF3962: Protein of unknown function (DUF3962)
Probab=30.93 E-value=26 Score=30.26 Aligned_cols=33 Identities=27% Similarity=0.741 Sum_probs=26.0
Q ss_pred cchhhhhhhccchHHHHHHHHhhhcCCchhhhHHHHhhhc
Q 031559 86 KDWLSLVAVHTDSWLLSVAFYLGARLNRNERKRLFSLIND 125 (157)
Q Consensus 86 kdWLslVAvHSDsWLlsVAfy~gar~~~~~R~rLF~mIN~ 125 (157)
.+|+.||-.|-|-|++-+-+ +.-++||+.|.-+
T Consensus 24 ~~W~~ll~~~~~~~~l~~Kl-------~~l~erL~~mFsd 56 (216)
T PF13111_consen 24 IEWLDLLEIHYKTFLLTSKL-------KRLNERLYDMFSD 56 (216)
T ss_pred HHHHHHHHHhccccccHHHH-------HHHHHHHHHHHHH
Confidence 68999999999999998765 3345778877654
No 14
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=28.51 E-value=24 Score=27.20 Aligned_cols=14 Identities=50% Similarity=1.123 Sum_probs=12.8
Q ss_pred cccCCCccccchhh
Q 031559 77 NFARDGMNRKDWLS 90 (157)
Q Consensus 77 NfaRDgM~rkdWLs 90 (157)
|+-+.||.|.|||.
T Consensus 83 Nl~p~G~~r~dWl~ 96 (100)
T PF15643_consen 83 NLHPEGMSREDWLR 96 (100)
T ss_pred ccCcccCCHHHHHH
Confidence 78899999999985
No 15
>PTZ00211 ribonucleoside-diphosphate reductase small subunit; Provisional
Probab=26.81 E-value=36 Score=29.27 Aligned_cols=39 Identities=23% Similarity=0.588 Sum_probs=28.5
Q ss_pred hhhhhhccchHHHHHHHHhhhcCCchhhhHHHHhhhcCCcee
Q 031559 89 LSLVAVHTDSWLLSVAFYLGARLNRNERKRLFSLINDQPTVF 130 (157)
Q Consensus 89 LslVAvHSDsWLlsVAfy~gar~~~~~R~rLF~mIN~lPTv~ 130 (157)
...=+||+++.-.-+--|. .|..+|.++|..+.++|+|-
T Consensus 108 ~~~E~iHs~sYs~il~tl~---~~~~~~~~~f~~~~~~p~i~ 146 (330)
T PTZ00211 108 IAMENIHSETYSLLIDTYI---TDEEEKDRLFHAIETIPAIK 146 (330)
T ss_pred HHHHHHHHHHHHHHHHHcC---CCHHHHHHHHHHHHhCHHHH
Confidence 3344799999876544332 26789999999999999864
No 16
>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]
Probab=26.01 E-value=58 Score=33.38 Aligned_cols=26 Identities=31% Similarity=0.480 Sum_probs=20.8
Q ss_pred hHHHHHHHhhh--------cHHHhhhcCCCCCCc
Q 031559 20 RRAGVVRALTN--------DVDEFYGLCDPDKEN 45 (157)
Q Consensus 20 RR~glirALT~--------Dve~Fy~~CDP~ken 45 (157)
-++.+++|||. |..+--+.|+|.+..
T Consensus 848 sk~~vL~AlTrkFkLdedVdL~eiAk~cp~~~TG 881 (953)
T KOG0736|consen 848 SKLRVLEALTRKFKLDEDVDLVEIAKKCPPNMTG 881 (953)
T ss_pred HHHHHHHHHHHHccCCCCcCHHHHHhhCCcCCch
Confidence 36789999998 677888889887753
No 17
>COG1993 PII-like signaling protein [Signal transduction mechanisms]
Probab=25.76 E-value=35 Score=26.65 Aligned_cols=20 Identities=45% Similarity=0.705 Sum_probs=17.9
Q ss_pred hhHHHHhhhcCCceeeeecc
Q 031559 116 RKRLFSLINDQPTVFEVVTE 135 (157)
Q Consensus 116 R~rLF~mIN~lPTv~Evv~g 135 (157)
.-++|++-++||.|.|+|-.
T Consensus 57 ~~~if~Ls~~LPVviEvVD~ 76 (109)
T COG1993 57 GSKIFRLSTDLPVVVEVVDE 76 (109)
T ss_pred ccchhhccCCCCEEEEEeCC
Confidence 46799999999999999975
No 18
>PF09065 Haemadin: Haemadin; InterPro: IPR015150 Members of this family adopt a secondary structure consisting of five short beta-strands (beta1-beta5), which are arranged in two antiparallel distorted sheets formed by strands beta1-beta4-beta5 and beta2-beta3 facing each other. This beta-sandwich is stabilised by six enclosed cysteines arranged in a [1-2, 3-5, 4-6] disulphide pairing resulting in a disulphide-rich hydrophobic core that is largely inaccessible to bulk solvent. The close proximity of disulphide bonds [3-5] and [4-6] organises haemadin into four distinct loops. The N-terminal segment of this domain binds to the active site of thrombin, inhibiting it []. ; PDB: 1E0F_K.
Probab=25.62 E-value=29 Score=21.22 Aligned_cols=9 Identities=56% Similarity=1.431 Sum_probs=6.1
Q ss_pred CcceeccCC
Q 031559 44 ENLCLYGHP 52 (157)
Q Consensus 44 enLcLYG~p 52 (157)
|.+||||..
T Consensus 5 ekiclygqs 13 (27)
T PF09065_consen 5 EKICLYGQS 13 (27)
T ss_dssp SSEE-TTEE
T ss_pred ceeeEeccc
Confidence 569999973
No 19
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=24.23 E-value=71 Score=22.28 Aligned_cols=32 Identities=22% Similarity=0.444 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHHhhhHHHHHHHhhhcHHHhhhc
Q 031559 6 SPRTVEEIYKDFCARRAGVVRALTNDVDEFYGL 38 (157)
Q Consensus 6 ~prTvE~iF~Df~~RR~glirALT~Dve~Fy~~ 38 (157)
.++||++|-+....+=.. -.-...||.+|.++
T Consensus 42 g~~tv~eI~~~L~~~Y~~-~e~~~~dV~~fL~~ 73 (81)
T TIGR03859 42 GKRSLAEIIQELAQRFPA-AEEIEDDVIAFLAV 73 (81)
T ss_pred CCCcHHHHHHHHHHHcCC-hhhHHHHHHHHHHH
Confidence 478999998888777666 55567888888764
No 20
>PF09447 Cnl2_NKP2: Cnl2/NKP2 family protein; InterPro: IPR018565 This entry includes the Cnl2 kinetochore protein [].
Probab=23.37 E-value=1.3e+02 Score=21.40 Aligned_cols=29 Identities=21% Similarity=0.549 Sum_probs=26.2
Q ss_pred CHHHHHHHHhhhHHHHHHHhhhcHHHhhh
Q 031559 9 TVEEIYKDFCARRAGVVRALTNDVDEFYG 37 (157)
Q Consensus 9 TvE~iF~Df~~RR~glirALT~Dve~Fy~ 37 (157)
.|..+|++....|+..+-.+....+.+++
T Consensus 38 ~ir~LYr~Lq~qR~~~~d~V~~nI~~e~~ 66 (67)
T PF09447_consen 38 QIRSLYRDLQAQREQVLDKVRENIDQEFK 66 (67)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 57899999999999999999999988764
No 21
>TIGR03019 pepcterm_femAB FemAB-related protein, PEP-CTERM system-associated. Members of this protein family are found always as part of extended exopolysaccharide biosynthesis loci in bacteria. In nearly every case, these loci contain determinants for the processing of the PEP-CTERM proposed C-terminal protein sorting signal. This family shows remote, local sequence similarity to the FemAB protein family (see pfam02388), whose members
Probab=23.23 E-value=78 Score=26.37 Aligned_cols=40 Identities=25% Similarity=0.447 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHhhh-HHHHHHHh--------hhcHHHhhhcCCCCCCcc
Q 031559 7 PRTVEEIYKDFCAR-RAGVVRAL--------TNDVDEFYGLCDPDKENL 46 (157)
Q Consensus 7 prTvE~iF~Df~~R-R~glirAL--------T~Dve~Fy~~CDP~kenL 46 (157)
+.+.|+++..|+.+ |..|=||. .+|+++||+.+...++.+
T Consensus 126 ~~~~e~~~~~~~~k~R~~IRka~k~Gv~v~~~~~l~~F~~l~~~t~~r~ 174 (330)
T TIGR03019 126 PADPEANWLAIPRKQRAMVRKGIKAGLTVTVDGDLDRFYDVYAENMRDL 174 (330)
T ss_pred CCCHHHHHHhcCHHHHHHHHHHHHCCeEEEECCcHHHHHHHHHHHHhcC
Confidence 45889999999887 55555664 247899999877555543
No 22
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=22.58 E-value=72 Score=25.18 Aligned_cols=27 Identities=11% Similarity=0.316 Sum_probs=21.6
Q ss_pred HHHHHHHHhhhHHHHHHHhhhcHHHhhh
Q 031559 10 VEEIYKDFCARRAGVVRALTNDVDEFYG 37 (157)
Q Consensus 10 vE~iF~Df~~RR~glirALT~Dve~Fy~ 37 (157)
+++|+..|..+|++||-+| +++.+-|.
T Consensus 11 i~~ii~~y~~~~~~li~~L-~~vQ~~~G 37 (156)
T PRK05988 11 IAAIIAEHKHLEGALLPIL-HAIQDEFG 37 (156)
T ss_pred HHHHHHHcCCCHHHHHHHH-HHHHHHcC
Confidence 6899999999999999888 55665543
No 23
>KOG0721 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=22.51 E-value=42 Score=29.25 Aligned_cols=23 Identities=35% Similarity=0.562 Sum_probs=16.9
Q ss_pred HHHHHhhhcHHHhhhcCCCCCCcceeccCCCC
Q 031559 23 GVVRALTNDVDEFYGLCDPDKENLCLYGHPNE 54 (157)
Q Consensus 23 glirALT~Dve~Fy~~CDP~kenLcLYG~p~~ 54 (157)
-.-+|||.++ .+||.-.||+|||
T Consensus 147 KAY~aLTD~~---------sreN~ekYG~PDG 169 (230)
T KOG0721|consen 147 KAYQALTDKK---------SRENWEKYGNPDG 169 (230)
T ss_pred HHHHHhcchh---------hHHHHHHhCCCCC
Confidence 3445666643 4599999999999
No 24
>PF14367 DUF4411: Domain of unknown function (DUF4411)
Probab=22.49 E-value=1e+02 Score=23.90 Aligned_cols=16 Identities=38% Similarity=0.617 Sum_probs=14.1
Q ss_pred hccchHHHHHHHHhhh
Q 031559 94 VHTDSWLLSVAFYLGA 109 (157)
Q Consensus 94 vHSDsWLlsVAfy~ga 109 (157)
-..|.||+|.|--.|+
T Consensus 103 ~~ADp~LIA~A~~~~~ 118 (162)
T PF14367_consen 103 SVADPWLIAYAKAYGA 118 (162)
T ss_pred ccCCHHHHHHHHhcCC
Confidence 7789999999988776
No 25
>KOG4148 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.40 E-value=29 Score=27.09 Aligned_cols=28 Identities=32% Similarity=0.780 Sum_probs=22.7
Q ss_pred HHHHHHHhhh-----cHHHhhhcCCCCCCcc--ee
Q 031559 21 RAGVVRALTN-----DVDEFYGLCDPDKENL--CL 48 (157)
Q Consensus 21 R~glirALT~-----Dve~Fy~~CDP~kenL--cL 48 (157)
..-+|+||-+ -.-+||..|+..+..| ||
T Consensus 13 C~dlInaL~eCH~~~~~~kfFG~CN~~k~eL~kCL 47 (106)
T KOG4148|consen 13 CNDLINALKECHKNHNILKFFGYCNDVKRELRKCL 47 (106)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHhhccHHHHHHHHH
Confidence 4678999974 6789999999998766 76
No 26
>PF04068 RLI: Possible Fer4-like domain in RNase L inhibitor, RLI; InterPro: IPR007209 This is a possible metal-binding domain in endoribonuclease RNase L inhibitor. It is found at the N-terminal end of RNase L inhibitor proteins, adjacent to the 4Fe-4S binding domain, fer4, IPR001450 from INTERPRO. Also often found adjacent to IPR007177 from INTERPRO in uncharacterised proteins. The RNase L system plays a major role in the anti-viral and anti-proliferative activities of interferons [], and could possibly play a more general role in the regulation of RNA stability in mammalian cells. Inhibitory activity requires concentration-dependent association of RLI with RNase L [].; PDB: 3J16_B 3BK7_A.
Probab=22.35 E-value=37 Score=21.20 Aligned_cols=10 Identities=40% Similarity=0.953 Sum_probs=6.1
Q ss_pred hhcCCCCCCc
Q 031559 36 YGLCDPDKEN 45 (157)
Q Consensus 36 y~~CDP~ken 45 (157)
|.||||.|-+
T Consensus 8 ~~~CdPkKCt 17 (35)
T PF04068_consen 8 FDQCDPKKCT 17 (35)
T ss_dssp CCC--CCCCS
T ss_pred cCCCCccccC
Confidence 6799999854
No 27
>PRK03598 putative efflux pump membrane fusion protein; Provisional
Probab=21.35 E-value=25 Score=29.30 Aligned_cols=27 Identities=15% Similarity=0.151 Sum_probs=17.5
Q ss_pred ccccchhhhhhhccchHHHHHHHHhhh
Q 031559 83 MNRKDWLSLVAVHTDSWLLSVAFYLGA 109 (157)
Q Consensus 83 M~rkdWLslVAvHSDsWLlsVAfy~ga 109 (157)
|.+++||+|.|+-.=.=+..+.+.||.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 27 (331)
T PRK03598 1 MKKKVVIGLAVVVLAAAVAGGWWWYQS 27 (331)
T ss_pred CCceEEEEhHHHHHHHHHHHheeEeee
Confidence 789999999998664433333334443
No 28
>PF06426 SATase_N: Serine acetyltransferase, N-terminal ; InterPro: IPR010493 The N-terminal domain of serine acetyltransferase has a sequence that is conserved in plants [] and bacteria [].; GO: 0009001 serine O-acetyltransferase activity, 0006535 cysteine biosynthetic process from serine, 0005737 cytoplasm; PDB: 1T3D_C 3MC4_B 3P47_A 3P1B_A 3Q1X_A 1SSM_A 1S80_C 1SSQ_D 1SST_A 3GVD_L ....
Probab=21.24 E-value=1.1e+02 Score=22.54 Aligned_cols=31 Identities=16% Similarity=0.373 Sum_probs=28.1
Q ss_pred CCHHHHHHHHhhhHHHHHHHhhhcHHHhhhc
Q 031559 8 RTVEEIYKDFCARRAGVVRALTNDVDEFYGL 38 (157)
Q Consensus 8 rTvE~iF~Df~~RR~glirALT~Dve~Fy~~ 38 (157)
.++.++|.++-.....|++++..|+...|.-
T Consensus 53 ~~l~~~~~~~~~~~p~i~~~~~~Dl~Av~~R 83 (105)
T PF06426_consen 53 DQLRDLFRDALEADPEIVEAARADLQAVYER 83 (105)
T ss_dssp HHHHHHHHHHHHHHTHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCHHHHHHHHHHHHHHHhC
Confidence 4678999999999999999999999999873
No 29
>cd00266 MADS_SRF_like SRF-like/Type I subfamily of MADS (MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero- and homo-dimers. Differs from the MEF-like/Type II subgroup mainly in position of the alpha 2 helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=20.95 E-value=1.2e+02 Score=21.38 Aligned_cols=38 Identities=21% Similarity=0.503 Sum_probs=24.9
Q ss_pred HHhhhHHHHHHHhhhcHHHhhhcCCCCCCcceeccCCCCceee
Q 031559 16 DFCARRAGVVRALTNDVDEFYGLCDPDKENLCLYGHPNESWEV 58 (157)
Q Consensus 16 Df~~RR~glirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV 58 (157)
-|+.||.||.|-- .++--+||-+---+ +|+-.+...++
T Consensus 19 tf~KRk~gl~kKa----~ELs~Lc~~~v~~i-v~sp~~~~~~~ 56 (83)
T cd00266 19 TFSKRRQGLFKKA----SELSTLCGAEVAVI-VYSPSGKLYVF 56 (83)
T ss_pred hHHHhhhhHHHHH----HHHHHhhCCcEEEE-EECCCCCccee
Confidence 4899999999865 56778898764433 25544443333
No 30
>PF08040 NADH_oxidored: MNLL subunit; InterPro: IPR012575 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of the MNLL subunits of NADH:ubiquinone oxidoreductase complex []. MNLL subunit is one of the many subunits found in the complex and it contains a mitochondrial import sequence. However, the role of MNLL subunit is unclear [].; GO: 0003954 NADH dehydrogenase activity, 0005739 mitochondrion
Probab=20.77 E-value=63 Score=22.99 Aligned_cols=31 Identities=32% Similarity=0.710 Sum_probs=23.6
Q ss_pred hhhhccchHHHH---HHHHhhhcCCchhhhHHHH
Q 031559 91 LVAVHTDSWLLS---VAFYLGARLNRNERKRLFS 121 (157)
Q Consensus 91 lVAvHSDsWLls---VAfy~gar~~~~~R~rLF~ 121 (157)
++++|-|-|+-. +.|.+|-.||+.+-.||-.
T Consensus 4 ~~~~vr~~~~~~~vPlgf~iG~yLDr~~~erlT~ 37 (59)
T PF08040_consen 4 LIQIVRDHWVWILVPLGFVIGCYLDRKETERLTA 37 (59)
T ss_pred HHHHHHHHHHHHHHhhHhhheeeecccchHHHHh
Confidence 567777888644 5799999999988777643
No 31
>cd00120 MADS MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi.
Probab=20.13 E-value=90 Score=21.21 Aligned_cols=24 Identities=33% Similarity=0.664 Sum_probs=18.0
Q ss_pred HHhhhHHHHHHHhhhcHHHhhhcCCCCC
Q 031559 16 DFCARRAGVVRALTNDVDEFYGLCDPDK 43 (157)
Q Consensus 16 Df~~RR~glirALT~Dve~Fy~~CDP~k 43 (157)
-|+.||.||.+-- .++--+||-+-
T Consensus 19 tf~kR~~gl~kKa----~Els~Lc~~~v 42 (59)
T cd00120 19 TFSKRRNGLFKKA----SELSVLCDAEV 42 (59)
T ss_pred hHHHHhchHHHhh----hhheeccCCcE
Confidence 4899999999864 55677888543
Done!