Query 032447
Match_columns 140
No_of_seqs 92 out of 94
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 14:13:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032447.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032447hhsearch_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 4.4E-92 9.6E-97 542.2 10.1 130 11-140 1-135 (137)
2 KOG1632 Uncharacterized PHD Zn 100.0 1.7E-30 3.7E-35 219.3 -0.3 131 8-138 35-179 (345)
3 PF00319 SRF-TF: SRF-type tran 61.3 11 0.00023 24.8 2.9 36 18-59 11-46 (51)
4 cd04120 Rab12 Rab12 subfamily. 56.7 6.3 0.00014 30.6 1.3 14 64-77 184-197 (202)
5 PF05402 PqqD: Coenzyme PQQ sy 56.4 18 0.00039 22.9 3.2 32 10-41 29-60 (68)
6 PHA03099 epidermal growth fact 44.6 6.3 0.00014 31.5 -0.4 23 30-53 34-56 (139)
7 smart00432 MADS MADS domain. 43.7 35 0.00077 22.8 3.2 38 19-61 19-56 (59)
8 PF06452 DUF1083: Domain of un 37.6 6.1 0.00013 28.7 -1.3 43 58-101 123-170 (185)
9 PF11351 DUF3154: Protein of u 36.9 20 0.00042 26.8 1.2 14 101-114 100-115 (123)
10 PF15643 Tox-PL-2: Papain fold 36.3 17 0.00037 27.6 0.8 14 80-93 83-96 (100)
11 PF13880 Acetyltransf_13: ESCO 34.8 5.8 0.00013 27.8 -1.7 52 21-92 16-68 (70)
12 TIGR03859 PQQ_PqqD coenzyme PQ 30.3 63 0.0014 22.1 2.8 31 10-41 43-73 (81)
13 TIGR03019 pepcterm_femAB FemAB 29.4 55 0.0012 26.7 2.8 39 10-48 126-173 (330)
14 PF01361 Tautomerase: Tautomer 28.8 1.4E+02 0.003 18.6 4.0 39 22-61 14-52 (60)
15 PF11385 DUF3189: Protein of u 28.4 24 0.00052 27.5 0.5 47 90-136 93-145 (148)
16 KOG0014 MADS box transcription 27.2 92 0.002 23.3 3.5 23 19-45 20-42 (195)
17 PF09447 Cnl2_NKP2: Cnl2/NKP2 27.2 1.1E+02 0.0024 21.4 3.6 29 12-40 38-66 (67)
18 PRK03598 putative efflux pump 27.1 19 0.00041 29.4 -0.3 27 86-112 1-27 (331)
19 cd04301 NAT_SF N-Acyltransfera 25.4 70 0.0015 17.2 2.0 27 21-49 36-62 (65)
20 cd00266 MADS_SRF_like SRF-like 25.3 1.1E+02 0.0024 21.3 3.3 38 19-61 19-56 (83)
21 PF06426 SATase_N: Serine acet 25.1 94 0.002 22.5 3.1 32 10-41 52-83 (105)
22 cd00120 MADS MADS: MCM1, Agamo 24.8 71 0.0015 21.3 2.2 24 19-46 19-42 (59)
23 PF08479 POTRA_2: POTRA domain 24.6 82 0.0018 20.6 2.5 34 8-41 14-49 (76)
24 PF04068 RLI: Possible Fer4-li 24.4 27 0.00059 21.4 0.1 10 39-48 8-17 (35)
25 PRK05988 formate dehydrogenase 24.3 71 0.0015 24.7 2.4 27 12-39 10-36 (156)
26 PF13527 Acetyltransf_9: Acety 24.1 70 0.0015 21.4 2.1 33 19-53 81-113 (127)
27 COG1484 DnaC DNA replication p 22.8 84 0.0018 25.6 2.7 22 34-56 94-115 (254)
28 KOG4148 Uncharacterized conser 22.7 33 0.00071 26.4 0.3 28 24-51 13-47 (106)
29 PF13673 Acetyltransf_10: Acet 22.2 73 0.0016 20.7 1.9 29 21-52 75-103 (117)
30 KOG0721 Molecular chaperone (D 21.9 50 0.0011 28.3 1.3 24 25-57 146-169 (230)
31 PF09065 Haemadin: Haemadin; 21.4 33 0.00071 20.7 0.1 9 47-55 5-13 (27)
32 PRK01964 4-oxalocrotonate taut 21.0 1.5E+02 0.0032 18.7 3.1 37 24-61 17-53 (64)
33 PF01257 2Fe-2S_thioredx: Thio 20.8 1E+02 0.0022 23.2 2.6 21 13-33 1-21 (145)
34 PF12221 HflK_N: Bacterial mem 20.5 86 0.0019 20.1 1.9 19 9-27 19-37 (42)
35 PRK02220 4-oxalocrotonate taut 20.3 1.6E+02 0.0035 18.1 3.1 37 24-61 17-53 (61)
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=4.4e-92 Score=542.19 Aligned_cols=130 Identities=78% Similarity=1.323 Sum_probs=128.2
Q ss_pred CCHHHHHHhhhhhHhHHHHhhhhhHHHHhhcCCcCCcceeeeeCCCCceeeeCCCCCCCCCCCCCccCccccCCCCcchh
Q 032447 11 RTVEEVFRDFKGRRAGMIKALTTDVEEFYQQCDPEKENLCLYGFPSEQWEVNLPAEEVPPELPEPALGINFARDGMQDKD 90 (140)
Q Consensus 11 rtvE~iF~Df~~RR~giirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV~lPaeevPpeLPEPalGINfaRDgM~rkd 90 (140)
||||+||+||++||+|||||||+|||+||+||||+||||||||+|||+|||+||+||||||||||+||||||||||+|||
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 hhhhhhhhhhhHHHHHHHHhhhccccCcccc-----ccccchhhhhhhhcccccC
Q 032447 91 WLSLVAVHSDAWLLAVAFYFGARFGFDKADR-----YINSLEILLLVKCSFNLRQ 140 (140)
Q Consensus 91 WLslVAvHSDsWLlsvAfy~gar~gfd~~~R-----miN~lpTv~Evv~~~~~~~ 140 (140)
|||||||||||||||||||||||||||+++| |||+||||||||+|..-||
T Consensus 81 WLslVAvHsDsWLlsvAfy~gar~~~~~~~R~rLF~mIN~lpTv~Evv~g~~~~q 135 (137)
T PF12165_consen 81 WLSLVAVHSDSWLLSVAFYFGARFGFDKNERKRLFSMINDLPTVFEVVTGRAKKQ 135 (137)
T ss_pred HHHHHHHhccHHHHHHHHHHHHhhccChHHHHHHHHHHhcCchHHHHHhcccccc
Confidence 9999999999999999999999999999999 9999999999999988776
No 2
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=99.96 E-value=1.7e-30 Score=219.32 Aligned_cols=131 Identities=37% Similarity=0.532 Sum_probs=125.9
Q ss_pred CCCCCHHHHHHhhhhhHhHHHHhhhhhHHHHhhcCCc----CCcceeeeeCCCCceeeeCCCCCCCCCCCCCccCccccC
Q 032447 8 NNPRTVEEVFRDFKGRRAGMIKALTTDVEEFYQQCDP----EKENLCLYGFPSEQWEVNLPAEEVPPELPEPALGINFAR 83 (140)
Q Consensus 8 ~~prtvE~iF~Df~~RR~giirALT~Dve~Fy~~CDP----~kenLcLYG~p~~~WeV~lPaeevPpeLPEPalGINfaR 83 (140)
+.+++++++|.+|++||+++++|+++++.+||.+||| .++++|+|+++++.|+|++|.+|+|+++++++.|+|+++
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 7889999999999999999999999999999999999 689999999999999999999999999999999999999
Q ss_pred CCCcchhhhhhhhhhhhhHHHHHHHHhhhcc-----ccCcccc-----ccccchhhhhhhhcccc
Q 032447 84 DGMQDKDWLSLVAVHSDAWLLAVAFYFGARF-----GFDKADR-----YINSLEILLLVKCSFNL 138 (140)
Q Consensus 84 DgM~rkdWLslVAvHSDsWLlsvAfy~gar~-----gfd~~~R-----miN~lpTv~Evv~~~~~ 138 (140)
|||+.+|||+++++|+|+|+.+++||||+++ ++.+.+| ++|++|||++++++...
T Consensus 115 ~~~~~~~~l~~~~~~~~~~~~s~s~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~t~~~~~~~~~~ 179 (345)
T KOG1632|consen 115 DGMSESDGLSCVCRQDDSELLSPSFYFGKRGCQFWVKLQKLGRVRLEAEKNDDPTVFEVVSGTAT 179 (345)
T ss_pred hhhhhhccceeecccccccccccccccCCccccccccchhhhhhhhhhhhcccchhhhccccccc
Confidence 9999999999999999999999999999998 7777777 99999999999998653
No 3
>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=61.34 E-value=11 Score=24.81 Aligned_cols=36 Identities=19% Similarity=0.488 Sum_probs=25.2
Q ss_pred HhhhhhHhHHHHhhhhhHHHHhhcCCcCCcceeeeeCCCCce
Q 032447 18 RDFKGRRAGMIKALTTDVEEFYQQCDPEKENLCLYGFPSEQW 59 (140)
Q Consensus 18 ~Df~~RR~giirALT~Dve~Fy~~CDP~kenLcLYG~p~~~W 59 (140)
.-|+.||.||.|= +.|+..+||-+-.-+ +|+ |+|..
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 567889998876533 477 66654
No 4
>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=56.72 E-value=6.3 Score=30.56 Aligned_cols=14 Identities=57% Similarity=1.151 Sum_probs=12.1
Q ss_pred CCCCCCCCCCCCcc
Q 032447 64 PAEEVPPELPEPAL 77 (140)
Q Consensus 64 PaeevPpeLPEPal 77 (140)
|..|+|||||.|-.
T Consensus 184 ~~~~~~~~~~~~~~ 197 (202)
T cd04120 184 PEPEIPPELPPPRP 197 (202)
T ss_pred CCCCCCcCCCCCCC
Confidence 78899999998864
No 5
>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=56.39 E-value=18 Score=22.91 Aligned_cols=32 Identities=38% Similarity=0.467 Sum_probs=23.2
Q ss_pred CCCHHHHHHhhhhhHhHHHHhhhhhHHHHhhc
Q 032447 10 PRTVEEVFRDFKGRRAGMIKALTTDVEEFYQQ 41 (140)
Q Consensus 10 prtvE~iF~Df~~RR~giirALT~Dve~Fy~~ 41 (140)
++|+++|-+.+..+=..=-..+..||.+|.++
T Consensus 29 ~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~ 60 (68)
T PF05402_consen 29 PRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQ 60 (68)
T ss_dssp SS-HHHHHHHHHHHTT--HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 69999999888877655555578899999765
No 6
>PHA03099 epidermal growth factor-like protein (EGF-like protein); Provisional
Probab=44.57 E-value=6.3 Score=31.46 Aligned_cols=23 Identities=39% Similarity=0.793 Sum_probs=20.2
Q ss_pred hhhhhHHHHhhcCCcCCcceeeee
Q 032447 30 ALTTDVEEFYQQCDPEKENLCLYG 53 (140)
Q Consensus 30 ALT~Dve~Fy~~CDP~kenLcLYG 53 (140)
--|+|+-+ ++.|.+++++.||.|
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 7
>smart00432 MADS MADS domain.
Probab=43.70 E-value=35 Score=22.83 Aligned_cols=38 Identities=26% Similarity=0.507 Sum_probs=24.4
Q ss_pred hhhhhHhHHHHhhhhhHHHHhhcCCcCCcceeeeeCCCCceee
Q 032447 19 DFKGRRAGMIKALTTDVEEFYQQCDPEKENLCLYGFPSEQWEV 61 (140)
Q Consensus 19 Df~~RR~giirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV 61 (140)
-|+.||+||.|-- .++.-+||-+---+ +|+..+..+++
T Consensus 19 tf~kRk~gl~kKa----~Els~Lc~~~v~~i-v~sp~g~~~~~ 56 (59)
T smart00432 19 TFSKRRNGLFKKA----HELSVLCDAEVALI-VFSPTGKLYEF 56 (59)
T ss_pred hhHhhhhhHHHHH----HHHhhccCCeEEEE-EECCCCCeeec
Confidence 3899999999864 56888999754322 25544444433
No 8
>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=37.60 E-value=6.1 Score=28.69 Aligned_cols=43 Identities=28% Similarity=0.594 Sum_probs=25.1
Q ss_pred ceeeeCCCCCC-CCCCCCCccCcccc----CCCCcchhhhhhhhhhhhh
Q 032447 58 QWEVNLPAEEV-PPELPEPALGINFA----RDGMQDKDWLSLVAVHSDA 101 (140)
Q Consensus 58 ~WeV~lPaeev-PpeLPEPalGINfa----RDgM~rkdWLslVAvHSDs 101 (140)
+.|+.+|-+.+ +|+.... +|+||. .++=.|+.|++......++
T Consensus 123 ~~E~~IP~~~l~~~~~g~~-~g~~~~~~d~~~~~~r~~~~~w~~~~~~~ 170 (185)
T PF06452_consen 123 TVEIAIPWSALFPPQPGDK-FGFNFAVNDNDDGGKREGWISWSDPSGPS 170 (185)
T ss_dssp EEEEEEE-SS-----TTEE-EEEEEEEEEE-TTS-EEEEEESS-SSS-T
T ss_pred EEEEEechHHcCCCCCCCE-EEEEEEEEECCCCCcceEEEEEcCCCCcC
Confidence 68999999998 4444433 888888 4555677788776666555
No 9
>PF11351 DUF3154: Protein of unknown function (DUF3154); InterPro: IPR021497 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=36.92 E-value=20 Score=26.80 Aligned_cols=14 Identities=64% Similarity=0.994 Sum_probs=11.7
Q ss_pred hHHH--HHHHHhhhcc
Q 032447 101 AWLL--AVAFYFGARF 114 (140)
Q Consensus 101 sWLl--svAfy~gar~ 114 (140)
.||| .|.||+|+|-
T Consensus 100 w~Llg~~vlgy~~~Rs 115 (123)
T PF11351_consen 100 WWLLGAGVLGYFGARS 115 (123)
T ss_pred HHHHHHHHhhhHHHhh
Confidence 4777 8999999994
No 10
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=36.29 E-value=17 Score=27.55 Aligned_cols=14 Identities=43% Similarity=0.987 Sum_probs=12.9
Q ss_pred cccCCCCcchhhhh
Q 032447 80 NFARDGMQDKDWLS 93 (140)
Q Consensus 80 NfaRDgM~rkdWLs 93 (140)
|+-+.||.|.|||.
T Consensus 83 Nl~p~G~~r~dWl~ 96 (100)
T PF15643_consen 83 NLHPEGMSREDWLR 96 (100)
T ss_pred ccCcccCCHHHHHH
Confidence 88899999999985
No 11
>PF13880 Acetyltransf_13: ESCO1/2 acetyl-transferase
Probab=34.81 E-value=5.8 Score=27.83 Aligned_cols=52 Identities=29% Similarity=0.506 Sum_probs=36.1
Q ss_pred hhhHhHHHHhhhhhHHHHhhcCCcCCcceeeeeCCCCceeeeCCCCCCCCCCCCCc-cCccccCCCCcchhhh
Q 032447 21 KGRRAGMIKALTTDVEEFYQQCDPEKENLCLYGFPSEQWEVNLPAEEVPPELPEPA-LGINFARDGMQDKDWL 92 (140)
Q Consensus 21 ~~RR~giirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV~lPaeevPpeLPEPa-lGINfaRDgM~rkdWL 92 (140)
+-||.||...|..=+- ++ .+||..-...||.. -+|+ -|..||+.-..+.+||
T Consensus 16 ~~RR~GIAt~Lld~ar----------~~-~iyG~~l~~~~iAF---------SqPT~~G~~fA~~y~~~~~fl 68 (70)
T PF13880_consen 16 SHRRKGIATRLLDAAR----------EN-FIYGCVLPKNEIAF---------SQPTESGKKFAKKYFGTDDFL 68 (70)
T ss_pred hhhhhhHHHHHHHHHH----------Hh-ccCceEechhheEe---------cCCCHhHHHHHHHHcCCCCEE
Confidence 5699999999987432 23 35887666655553 2344 6888888887777776
No 12
>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=30.27 E-value=63 Score=22.12 Aligned_cols=31 Identities=19% Similarity=0.388 Sum_probs=24.0
Q ss_pred CCCHHHHHHhhhhhHhHHHHhhhhhHHHHhhc
Q 032447 10 PRTVEEVFRDFKGRRAGMIKALTTDVEEFYQQ 41 (140)
Q Consensus 10 prtvE~iF~Df~~RR~giirALT~Dve~Fy~~ 41 (140)
++||++|-+....+=.. -.-...||.+|.++
T Consensus 43 ~~tv~eI~~~L~~~Y~~-~e~~~~dV~~fL~~ 73 (81)
T TIGR03859 43 KRSLAEIIQELAQRFPA-AEEIEDDVIAFLAV 73 (81)
T ss_pred CCcHHHHHHHHHHHcCC-hhhHHHHHHHHHHH
Confidence 68999998888777666 55567899888764
No 13
>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=29.44 E-value=55 Score=26.71 Aligned_cols=39 Identities=21% Similarity=0.365 Sum_probs=28.2
Q ss_pred CCCHHHHHHhhhhh-HhHHHHhh--------hhhHHHHhhcCCcCCcc
Q 032447 10 PRTVEEVFRDFKGR-RAGMIKAL--------TTDVEEFYQQCDPEKEN 48 (140)
Q Consensus 10 prtvE~iF~Df~~R-R~giirAL--------T~Dve~Fy~~CDP~ken 48 (140)
+.+.|++++.|+.+ |..|=||. .+|+++||+.....++.
T Consensus 126 ~~~~e~~~~~~~~k~R~~IRka~k~Gv~v~~~~~l~~F~~l~~~t~~r 173 (330)
T TIGR03019 126 PADPEANWLAIPRKQRAMVRKGIKAGLTVTVDGDLDRFYDVYAENMRD 173 (330)
T ss_pred CCCHHHHHHhcCHHHHHHHHHHHHCCeEEEECCcHHHHHHHHHHHHhc
Confidence 45889999999887 55555654 24789999987655544
No 14
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=28.79 E-value=1.4e+02 Score=18.56 Aligned_cols=39 Identities=23% Similarity=0.482 Sum_probs=28.7
Q ss_pred hhHhHHHHhhhhhHHHHhhcCCcCCcceeeeeCCCCceee
Q 032447 22 GRRAGMIKALTTDVEEFYQQCDPEKENLCLYGFPSEQWEV 61 (140)
Q Consensus 22 ~RR~giirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV 61 (140)
..++.|++++|.=+.+-+.. +++.-..-+.-+|.+.|-+
T Consensus 14 e~K~~l~~~it~~~~~~lg~-~~~~i~V~i~E~~~~~w~~ 52 (60)
T PF01361_consen 14 EQKRELAEAITDAVVEVLGI-PPERISVVIEEVPPENWGI 52 (60)
T ss_dssp HHHHHHHHHHHHHHHHHHTS--GGGEEEEEEEE-CCCEEE
T ss_pred HHHHHHHHHHHHHHHHHhCc-CCCeEEEEEEEEChhheEE
Confidence 45788999999988887755 7777666777788888865
No 15
>PF11385 DUF3189: Protein of unknown function (DUF3189); InterPro: IPR021525 This family of proteins with unknown function appears to be restricted to Firmicutes
Probab=28.38 E-value=24 Score=27.48 Aligned_cols=47 Identities=11% Similarity=0.142 Sum_probs=36.4
Q ss_pred hhhhhhhhhhhhHHHHHHHHhhhccccCcccc------ccccchhhhhhhhcc
Q 032447 90 DWLSLVAVHSDAWLLAVAFYFGARFGFDKADR------YINSLEILLLVKCSF 136 (140)
Q Consensus 90 dWLslVAvHSDsWLlsvAfy~gar~gfd~~~R------miN~lpTv~Evv~~~ 136 (140)
+++=.=+.+..-|+|.+..|+.-|+|+.+=+| .....+.+.+.|..+
T Consensus 93 ~i~~vdt~~~vn~~m~iGg~lsrrl~l~~iGrpl~~~g~~k~y~~i~~lV~~v 145 (148)
T PF11385_consen 93 EIILVDTSPYVNLLMKIGGFLSRRLGLVKIGRPLVVWGIQKAYPNIVELVEEV 145 (148)
T ss_pred cEEEEeccccchHHHHHHHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333345667899999999999999999999 667778888887643
No 16
>KOG0014 consensus MADS box transcription factor [Transcription]
Probab=27.23 E-value=92 Score=23.27 Aligned_cols=23 Identities=39% Similarity=0.715 Sum_probs=17.6
Q ss_pred hhhhhHhHHHHhhhhhHHHHhhcCCcC
Q 032447 19 DFKGRRAGMIKALTTDVEEFYQQCDPE 45 (140)
Q Consensus 19 Df~~RR~giirALT~Dve~Fy~~CDP~ 45 (140)
-|+.||.||.|= ..++--+||-+
T Consensus 20 TFsKRr~GL~KK----A~ELsvLCd~e 42 (195)
T KOG0014|consen 20 TFSKRRNGLFKK----ASELSVLCDAE 42 (195)
T ss_pred hhHHHHhhHHHH----HHHHHHhcCCe
Confidence 389999999874 45677789654
No 17
>PF09447 Cnl2_NKP2: Cnl2/NKP2 family protein; InterPro: IPR018565 This entry includes the Cnl2 kinetochore protein [].
Probab=27.18 E-value=1.1e+02 Score=21.38 Aligned_cols=29 Identities=10% Similarity=0.548 Sum_probs=26.5
Q ss_pred CHHHHHHhhhhhHhHHHHhhhhhHHHHhh
Q 032447 12 TVEEVFRDFKGRRAGMIKALTTDVEEFYQ 40 (140)
Q Consensus 12 tvE~iF~Df~~RR~giirALT~Dve~Fy~ 40 (140)
.|..+|++....|+..+-.....++.+++
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 67999999999999999999999998875
No 18
>PRK03598 putative efflux pump membrane fusion protein; Provisional
Probab=27.09 E-value=19 Score=29.40 Aligned_cols=27 Identities=19% Similarity=0.203 Sum_probs=18.0
Q ss_pred CcchhhhhhhhhhhhhHHHHHHHHhhh
Q 032447 86 MQDKDWLSLVAVHSDAWLLAVAFYFGA 112 (140)
Q Consensus 86 M~rkdWLslVAvHSDsWLlsvAfy~ga 112 (140)
|.+|+|++|.|+-.=.=+..+.+.||.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 27 (331)
T PRK03598 1 MKKKVVIGLAVVVLAAAVAGGWWWYQS 27 (331)
T ss_pred CCceEEEEhHHHHHHHHHHHheeEeee
Confidence 889999999998764443334444443
No 19
>cd04301 NAT_SF N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate. NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransfera
Probab=25.35 E-value=70 Score=17.18 Aligned_cols=27 Identities=26% Similarity=0.220 Sum_probs=19.6
Q ss_pred hhhHhHHHHhhhhhHHHHhhcCCcCCcce
Q 032447 21 KGRRAGMIKALTTDVEEFYQQCDPEKENL 49 (140)
Q Consensus 21 ~~RR~giirALT~Dve~Fy~~CDP~kenL 49 (140)
.-|+.|+-+.|...+.++..+ ++.+.+
T Consensus 36 ~~~~~g~~~~~~~~~~~~~~~--~~~~~v 62 (65)
T cd04301 36 EYRGKGIGSALLEAAEEEARE--RGAKRL 62 (65)
T ss_pred HHcCcCHHHHHHHHHHHHHHH--cCCcEE
Confidence 345679999999998888886 444444
No 20
>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=25.35 E-value=1.1e+02 Score=21.28 Aligned_cols=38 Identities=24% Similarity=0.464 Sum_probs=25.3
Q ss_pred hhhhhHhHHHHhhhhhHHHHhhcCCcCCcceeeeeCCCCceee
Q 032447 19 DFKGRRAGMIKALTTDVEEFYQQCDPEKENLCLYGFPSEQWEV 61 (140)
Q Consensus 19 Df~~RR~giirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV 61 (140)
-|+.||.||.|-- .++--+||-+---+ +|+-.+...++
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 66888998765433 25544444333
No 21
>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=25.05 E-value=94 Score=22.51 Aligned_cols=32 Identities=19% Similarity=0.461 Sum_probs=28.8
Q ss_pred CCCHHHHHHhhhhhHhHHHHhhhhhHHHHhhc
Q 032447 10 PRTVEEVFRDFKGRRAGMIKALTTDVEEFYQQ 41 (140)
Q Consensus 10 prtvE~iF~Df~~RR~giirALT~Dve~Fy~~ 41 (140)
..++.++|.++-.....|++++..|+...|..
T Consensus 52 ~~~l~~~~~~~~~~~p~i~~~~~~Dl~Av~~R 83 (105)
T PF06426_consen 52 ADQLRDLFRDALEADPEIVEAARADLQAVYER 83 (105)
T ss_dssp HHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCHHHHHHHHHHHHHHHhC
Confidence 35778999999999999999999999999875
No 22
>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=24.77 E-value=71 Score=21.31 Aligned_cols=24 Identities=38% Similarity=0.643 Sum_probs=18.2
Q ss_pred hhhhhHhHHHHhhhhhHHHHhhcCCcCC
Q 032447 19 DFKGRRAGMIKALTTDVEEFYQQCDPEK 46 (140)
Q Consensus 19 Df~~RR~giirALT~Dve~Fy~~CDP~k 46 (140)
-|+.||+||.|-- .++--+||-+-
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 56777888553
No 23
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=24.62 E-value=82 Score=20.64 Aligned_cols=34 Identities=12% Similarity=0.365 Sum_probs=27.3
Q ss_pred CCCCCHHHHHHhhhhhHhH--HHHhhhhhHHHHhhc
Q 032447 8 NNPRTVEEVFRDFKGRRAG--MIKALTTDVEEFYQQ 41 (140)
Q Consensus 8 ~~prtvE~iF~Df~~RR~g--iirALT~Dve~Fy~~ 41 (140)
..+..++++++.|.+|.-+ =++++...+.++|..
T Consensus 14 ~~~~~l~~~~~~~~g~~l~~~~l~~~~~~l~~~y~~ 49 (76)
T PF08479_consen 14 LPEEELQAILAPYIGRCLTLADLQQLADALTNYYRE 49 (76)
T ss_dssp SSCCHHHHHHGGGTTSBB-HHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHH
Confidence 4556889999999999854 478889999999975
No 24
>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=24.39 E-value=27 Score=21.41 Aligned_cols=10 Identities=50% Similarity=1.145 Sum_probs=6.0
Q ss_pred hhcCCcCCcc
Q 032447 39 YQQCDPEKEN 48 (140)
Q Consensus 39 y~~CDP~ken 48 (140)
|.||||.|-+
T Consensus 8 ~~~CdPkKCt 17 (35)
T PF04068_consen 8 FDQCDPKKCT 17 (35)
T ss_dssp CCC--CCCCS
T ss_pred cCCCCccccC
Confidence 5799999854
No 25
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=24.26 E-value=71 Score=24.75 Aligned_cols=27 Identities=7% Similarity=0.326 Sum_probs=21.1
Q ss_pred CHHHHHHhhhhhHhHHHHhhhhhHHHHh
Q 032447 12 TVEEVFRDFKGRRAGMIKALTTDVEEFY 39 (140)
Q Consensus 12 tvE~iF~Df~~RR~giirALT~Dve~Fy 39 (140)
.+++|++.|..+|+++|-+| +++.+-|
T Consensus 10 ~i~~ii~~y~~~~~~li~~L-~~vQ~~~ 36 (156)
T PRK05988 10 RIAAIIAEHKHLEGALLPIL-HAIQDEF 36 (156)
T ss_pred HHHHHHHHcCCCHHHHHHHH-HHHHHHc
Confidence 36899999999999999888 4555444
No 26
>PF13527 Acetyltransf_9: Acetyltransferase (GNAT) domain; PDB: 3SXN_C 2I00_D 1M4D_B 1M44_A 1M4G_B 1M4I_A 2OZG_A 2HV2_F 3N7Z_A 3RYO_B ....
Probab=24.06 E-value=70 Score=21.35 Aligned_cols=33 Identities=18% Similarity=0.134 Sum_probs=21.2
Q ss_pred hhhhhHhHHHHhhhhhHHHHhhcCCcCCcceeeee
Q 032447 19 DFKGRRAGMIKALTTDVEEFYQQCDPEKENLCLYG 53 (140)
Q Consensus 19 Df~~RR~giirALT~Dve~Fy~~CDP~kenLcLYG 53 (140)
+=.-||.|+.++|...+.+-.+.. +..-.+||+
T Consensus 81 ~p~~R~~Gl~~~L~~~~~~~~~~~--g~~~~~l~~ 113 (127)
T PF13527_consen 81 DPEYRGRGLGRQLMRALLERARER--GVPFIFLFP 113 (127)
T ss_dssp -GGGTTSSHHHHHHHHHHHHHHHT--T-SEEEEE-
T ss_pred CHHHcCCCHHHHHHHHHHHHHHhC--CCCEEEEec
Confidence 334588999999999887777654 333345554
No 27
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=22.83 E-value=84 Score=25.64 Aligned_cols=22 Identities=32% Similarity=0.517 Sum_probs=15.4
Q ss_pred hHHHHhhcCCcCCcceeeeeCCC
Q 032447 34 DVEEFYQQCDPEKENLCLYGFPS 56 (140)
Q Consensus 34 Dve~Fy~~CDP~kenLcLYG~p~ 56 (140)
+...|.+.++ ..+|++|||.|.
T Consensus 94 ~~~~~~~~~~-~~~nl~l~G~~G 115 (254)
T COG1484 94 DLASLVEFFE-RGENLVLLGPPG 115 (254)
T ss_pred HHHHHHHHhc-cCCcEEEECCCC
Confidence 3444444555 779999999885
No 28
>KOG4148 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.74 E-value=33 Score=26.40 Aligned_cols=28 Identities=32% Similarity=0.712 Sum_probs=22.6
Q ss_pred HhHHHHhhhh-----hHHHHhhcCCcCCcce--ee
Q 032447 24 RAGMIKALTT-----DVEEFYQQCDPEKENL--CL 51 (140)
Q Consensus 24 R~giirALT~-----Dve~Fy~~CDP~kenL--cL 51 (140)
..-+|+||-. -..+||..|+..|..| ||
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 6789999999998655 66
No 29
>PF13673 Acetyltransf_10: Acetyltransferase (GNAT) domain; PDB: 2FIW_A 1BOB_A 3FNC_B 3EXN_A.
Probab=22.23 E-value=73 Score=20.69 Aligned_cols=29 Identities=21% Similarity=0.163 Sum_probs=22.4
Q ss_pred hhhHhHHHHhhhhhHHHHhhcCCcCCcceeee
Q 032447 21 KGRRAGMIKALTTDVEEFYQQCDPEKENLCLY 52 (140)
Q Consensus 21 ~~RR~giirALT~Dve~Fy~~CDP~kenLcLY 52 (140)
.-||.||-++|...+++-.+. ++..+++-
T Consensus 75 ~~r~~Gig~~Ll~~~~~~~~~---~~~~l~~~ 103 (117)
T PF13673_consen 75 EYRGRGIGRALLDAAEKEAKD---GIRRLTVE 103 (117)
T ss_dssp GGTTSSHHHHHHHHHHHHHTT---TCEEEEEE
T ss_pred hhcCCcHHHHHHHHHHHHHHc---CCcEEEEE
Confidence 458999999999999997766 55555554
No 30
>KOG0721 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=21.86 E-value=50 Score=28.27 Aligned_cols=24 Identities=38% Similarity=0.448 Sum_probs=17.4
Q ss_pred hHHHHhhhhhHHHHhhcCCcCCcceeeeeCCCC
Q 032447 25 AGMIKALTTDVEEFYQQCDPEKENLCLYGFPSE 57 (140)
Q Consensus 25 ~giirALT~Dve~Fy~~CDP~kenLcLYG~p~~ 57 (140)
+-.-+|||.++ .+||.-.||+|||
T Consensus 146 ~KAY~aLTD~~---------sreN~ekYG~PDG 169 (230)
T KOG0721|consen 146 AKAYQALTDKK---------SRENWEKYGNPDG 169 (230)
T ss_pred HHHHHHhcchh---------hHHHHHHhCCCCC
Confidence 33445666644 4599999999999
No 31
>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=21.38 E-value=33 Score=20.69 Aligned_cols=9 Identities=56% Similarity=1.291 Sum_probs=6.1
Q ss_pred cceeeeeCC
Q 032447 47 ENLCLYGFP 55 (140)
Q Consensus 47 enLcLYG~p 55 (140)
|.+||||..
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 32
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=20.97 E-value=1.5e+02 Score=18.75 Aligned_cols=37 Identities=19% Similarity=0.405 Sum_probs=26.8
Q ss_pred HhHHHHhhhhhHHHHhhcCCcCCcceeeeeCCCCceee
Q 032447 24 RAGMIKALTTDVEEFYQQCDPEKENLCLYGFPSEQWEV 61 (140)
Q Consensus 24 R~giirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV 61 (140)
+..|++++|.-+.+-+ .|+|+.--.-+--+|.+.|.+
T Consensus 17 k~~l~~~it~~l~~~l-g~p~~~v~V~i~e~~~~~w~~ 53 (64)
T PRK01964 17 IKNLIREVTEAISATL-DVPKERVRVIVNEVPSSHWGV 53 (64)
T ss_pred HHHHHHHHHHHHHHHh-CcChhhEEEEEEEcChHHeeE
Confidence 6778999998887765 566666555667777777765
No 33
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 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 []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=20.84 E-value=1e+02 Score=23.16 Aligned_cols=21 Identities=19% Similarity=0.559 Sum_probs=16.0
Q ss_pred HHHHHHhhhhhHhHHHHhhhh
Q 032447 13 VEEVFRDFKGRRAGMIKALTT 33 (140)
Q Consensus 13 vE~iF~Df~~RR~giirALT~ 33 (140)
+|+|.+.|..+|++||-+|-.
T Consensus 1 i~~i~~~~~~~~~~ll~~L~~ 21 (145)
T PF01257_consen 1 IEEIIARYPSKRSALLPILHE 21 (145)
T ss_dssp -HHHHHTS--GGGGHHHHHHH
T ss_pred ChHHHHHCCCCHHHHHHHHHH
Confidence 589999999999999998854
No 34
>PF12221 HflK_N: Bacterial membrane protein N terminal; InterPro: IPR020980 HflK is a bacterial membrane protein which is thought, together with the HflC protein, to form a membrane protease complex whose activity is modulated by the GTPase HflX []. This entry represents the N-terminal, membrane-spanning, region of of HflK responsible for anchoring the protein in the bacterial membrane. It is often found in association with PF01145 from PFAM.
Probab=20.52 E-value=86 Score=20.12 Aligned_cols=19 Identities=26% Similarity=0.758 Sum_probs=16.0
Q ss_pred CCCCHHHHHHhhhhhHhHH
Q 032447 9 NPRTVEEVFRDFKGRRAGM 27 (140)
Q Consensus 9 ~prtvE~iF~Df~~RR~gi 27 (140)
.|-..||||+++..|=.++
T Consensus 19 gPPDLdel~r~l~~kl~~~ 37 (42)
T PF12221_consen 19 GPPDLDELFRKLQDKLGGL 37 (42)
T ss_pred CCCCHHHHHHHHHHHHhcc
Confidence 4788999999999986665
No 35
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=20.27 E-value=1.6e+02 Score=18.15 Aligned_cols=37 Identities=14% Similarity=0.235 Sum_probs=24.6
Q ss_pred HhHHHHhhhhhHHHHhhcCCcCCcceeeeeCCCCceee
Q 032447 24 RAGMIKALTTDVEEFYQQCDPEKENLCLYGFPSEQWEV 61 (140)
Q Consensus 24 R~giirALT~Dve~Fy~~CDP~kenLcLYG~p~~~WeV 61 (140)
+..|+++||..+.+-+. |+|+--...+=-+|.+.|.+
T Consensus 17 k~~l~~~it~~l~~~~~-~p~~~v~V~i~e~~~~~~~~ 53 (61)
T PRK02220 17 LKALVKDVTAAVSKNTG-APAEHIHVIINEMSKNHYAV 53 (61)
T ss_pred HHHHHHHHHHHHHHHhC-cChhhEEEEEEEeChhHeEE
Confidence 67899999998877665 44554444555566666654
Done!