Query 029049
Match_columns 200
No_of_seqs 124 out of 131
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 06:40:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029049.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029049hhsearch_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 4E-96 9E-101 590.1 9.7 137 10-146 1-137 (137)
2 KOG1632 Uncharacterized PHD Zn 100.0 4.5E-35 9.7E-40 260.2 2.4 160 7-168 35-205 (345)
3 PF00319 SRF-TF: SRF-type tran 50.8 17 0.00036 25.3 2.5 35 18-58 12-46 (51)
4 COG1993 PII-like signaling pro 46.9 11 0.00023 30.5 1.3 27 113-139 47-76 (109)
5 cd04120 Rab12 Rab12 subfamily. 42.0 14 0.00031 30.3 1.3 14 63-76 184-197 (202)
6 PF05402 PqqD: Coenzyme PQQ sy 41.3 38 0.00083 22.7 3.1 32 9-40 29-60 (68)
7 PF11351 DUF3154: Protein of u 37.4 18 0.0004 28.5 1.2 14 100-113 100-115 (123)
8 smart00432 MADS MADS domain. 36.0 50 0.0011 23.4 3.1 38 18-60 19-56 (59)
9 PF06452 DUF1083: Domain of un 34.8 8.8 0.00019 29.6 -0.9 44 57-101 123-171 (185)
10 PHA03099 epidermal growth fact 33.5 12 0.00025 31.5 -0.4 23 29-52 34-56 (139)
11 PF13111 DUF3962: Protein of u 27.6 36 0.00077 30.5 1.5 33 88-129 24-56 (216)
12 PRK03598 putative efflux pump 25.4 21 0.00046 30.8 -0.2 15 85-99 1-15 (331)
13 PF13880 Acetyltransf_13: ESCO 25.2 12 0.00026 27.7 -1.6 52 20-91 16-68 (70)
14 TIGR03859 PQQ_PqqD coenzyme PQ 24.9 81 0.0018 22.8 2.7 31 9-40 43-73 (81)
15 PTZ00211 ribonucleoside-diphos 23.5 59 0.0013 29.1 2.2 40 90-134 107-146 (330)
16 cd01182 INT_REC_C DNA breaking 22.6 73 0.0016 22.2 2.1 17 97-113 15-31 (162)
17 cd05036 PTKc_ALK_LTK Catalytic 22.4 90 0.002 24.9 2.8 34 95-128 199-235 (277)
18 cd00120 MADS MADS: MCM1, Agamo 22.3 88 0.0019 22.1 2.4 32 18-54 19-50 (59)
19 cd05112 PTKc_Itk Catalytic dom 22.2 92 0.002 24.2 2.7 34 95-128 179-215 (256)
20 PF09065 Haemadin: Haemadin; 22.2 34 0.00073 21.7 0.3 9 46-54 5-13 (27)
21 PF08479 POTRA_2: POTRA domain 22.0 1.1E+02 0.0023 21.3 2.8 34 7-40 14-49 (76)
22 cd05060 PTKc_Syk_like Catalyti 21.6 1.1E+02 0.0023 24.1 3.0 36 95-130 176-214 (257)
23 PF15643 Tox-PL-2: Papain fold 21.5 40 0.00087 26.9 0.6 14 79-92 83-96 (100)
24 COG1484 DnaC DNA replication p 21.1 92 0.002 26.9 2.8 22 33-55 94-115 (254)
25 KOG4148 Uncharacterized conser 20.9 38 0.00082 27.4 0.4 28 23-50 13-47 (106)
26 smart00464 LON Found in ATP-de 20.5 75 0.0016 22.7 1.8 25 103-127 56-80 (92)
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=4e-96 Score=590.13 Aligned_cols=137 Identities=84% Similarity=1.432 Sum_probs=135.6
Q ss_pred CCHHHHHhhhhhhhhHHHHHHhHHHHHhhhcCCcCCcceeeecCCCCceeeeCCCCCCCCCCCCCcCCccccCCCccccc
Q 029049 10 RTVEEVFGDFKGRRAGMIKALTTEVEEFYHQCDPEKENLCLYGFPSEQWEVNLPAEEVPPELPEPALGINFARDGMQEKD 89 (200)
Q Consensus 10 rTvE~iF~Df~~RR~glirALT~Dve~Fy~~CDPekenLcLYG~p~~~WeV~lPaeevPpelPEPalGINfaRDgM~rkd 89 (200)
||||+||+||++||+|||||||+||++||+||||+||||||||+|||+|||+||+||||||||||+||||||||||+|+|
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 hhhhhhhhcchHHHHHHHHhhhccCCChhhhHHHHHhhccCCceeeeeeCccccccc
Q 029049 90 WLSLVAVHSDAWLLSVAFYFGARFGFDKSDRKRLFNMINELPTIFEVVTGTTKKQAK 146 (200)
Q Consensus 90 WLslVAvHSDsWLlsvAfy~gar~gF~~~~R~rLf~mIN~lpTv~Evv~g~~kkq~k 146 (200)
|||||||||||||||||||||||||||+++|+|||+|||+||||||||+|+++||+|
T Consensus 81 WLslVAvHsDsWLlsvAfy~gar~~~~~~~R~rLF~mIN~lpTv~Evv~g~~~~q~k 137 (137)
T PF12165_consen 81 WLSLVAVHSDSWLLSVAFYFGARFGFDKNERKRLFSMINDLPTVFEVVTGRAKKQSK 137 (137)
T ss_pred HHHHHHHhccHHHHHHHHHHHHhhccChHHHHHHHHHHhcCchHHHHHhccccccCC
Confidence 999999999999999999999999999999999999999999999999999999865
No 2
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=100.00 E-value=4.5e-35 Score=260.24 Aligned_cols=160 Identities=44% Similarity=0.611 Sum_probs=146.1
Q ss_pred CCCCCHHHHHhhhhhhhhHHHHHHhHHHHHhhhcCCc----CCcceeeecCCCCceeeeCCCCCCCCCCCCCcCCccccC
Q 029049 7 YNPRTVEEVFGDFKGRRAGMIKALTTEVEEFYHQCDP----EKENLCLYGFPSEQWEVNLPAEEVPPELPEPALGINFAR 82 (200)
Q Consensus 7 ~~prTvE~iF~Df~~RR~glirALT~Dve~Fy~~CDP----ekenLcLYG~p~~~WeV~lPaeevPpelPEPalGINfaR 82 (200)
+.+++|+++|.+|++||++++.|+++++..||.+||| .++|+|+|+++++.|+|++|++++|+++++++.|||+++
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 789999999999999999999999999999999999999
Q ss_pred CCccccchhhhhhhhcchHHHHHHHHhhhcc-----CCChhhhHHHHHhhccCCceeeeeeCcccc--cccccCCcCCCC
Q 029049 83 DGMQEKDWLSLVAVHSDAWLLSVAFYFGARF-----GFDKSDRKRLFNMINELPTIFEVVTGTTKK--QAKEKSSVSNHS 155 (200)
Q Consensus 83 DgM~rkdWLslVAvHSDsWLlsvAfy~gar~-----gF~~~~R~rLf~mIN~lpTv~Evv~g~~kk--q~kek~~~~~~~ 155 (200)
|||+.+|||++|++|+++|+++++||||+++ ++.+.+|+|++.++|++|||+++++|.+.. +.|.++ .+++
T Consensus 115 ~~~~~~~~l~~~~~~~~~~~~s~s~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~t~~~~~~~~~~~~~~~k~~~--~~~~ 192 (345)
T KOG1632|consen 115 DGMSESDGLSCVCRQDDSELLSPSFYFGKRGCQFWVKLQKLGRVRLEAEKNDDPTVFEVVSGTATGELPSKDKS--SNDR 192 (345)
T ss_pred hhhhhhccceeecccccccccccccccCCccccccccchhhhhhhhhhhhcccchhhhcccccccccccccccc--cccc
Confidence 9999999999999999999999999999998 899999999999999999999999997754 344444 4466
Q ss_pred CCCCCCCCCCCCC
Q 029049 156 SSKSKSNSKRGSE 168 (200)
Q Consensus 156 ~~k~ks~~kr~~~ 168 (200)
+++++++.++..+
T Consensus 193 ~~~~~~~~~~~~~ 205 (345)
T KOG1632|consen 193 GSKSKTRKKRNRE 205 (345)
T ss_pred cceecccCccccc
Confidence 6777666664333
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=50.83 E-value=17 Score=25.26 Aligned_cols=35 Identities=20% Similarity=0.481 Sum_probs=24.9
Q ss_pred hhhhhhhHHHHHHhHHHHHhhhcCCcCCcceeeecCCCCce
Q 029049 18 DFKGRRAGMIKALTTEVEEFYHQCDPEKENLCLYGFPSEQW 58 (200)
Q Consensus 18 Df~~RR~glirALT~Dve~Fy~~CDPekenLcLYG~p~~~W 58 (200)
-|+.||.||.|= +.++.-+||-+--- -+|+ |+|..
T Consensus 12 tf~KRk~gL~KK----a~ELs~LC~~~v~~-iv~~-~~g~~ 46 (51)
T PF00319_consen 12 TFSKRKKGLFKK----ASELSTLCGVDVAL-IVFS-PDGKL 46 (51)
T ss_dssp HHHHHHHHHHHH----HHHHHHHHT-EEEE-EEEE-TTSEE
T ss_pred HHHHHHhhhhhc----cceeeeecCCeEEE-EEEC-CCCCE
Confidence 588999999874 56788899887654 3477 66654
No 4
>COG1993 PII-like signaling protein [Signal transduction mechanisms]
Probab=46.87 E-value=11 Score=30.49 Aligned_cols=27 Identities=33% Similarity=0.688 Sum_probs=22.4
Q ss_pred cCCChhh---hHHHHHhhccCCceeeeeeC
Q 029049 113 FGFDKSD---RKRLFNMINELPTIFEVVTG 139 (200)
Q Consensus 113 ~gF~~~~---R~rLf~mIN~lpTv~Evv~g 139 (200)
.||.+.. .-++|.+-++||.|.|||--
T Consensus 47 ~GfG~~~~~h~~~if~Ls~~LPVviEvVD~ 76 (109)
T COG1993 47 AGFGKDGKIHGSKIFRLSTDLPVVVEVVDE 76 (109)
T ss_pred eccCCCCcccccchhhccCCCCEEEEEeCC
Confidence 4666655 56899999999999999976
No 5
>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=41.97 E-value=14 Score=30.27 Aligned_cols=14 Identities=57% Similarity=1.151 Sum_probs=12.1
Q ss_pred CCCCCCCCCCCCcC
Q 029049 63 PAEEVPPELPEPAL 76 (200)
Q Consensus 63 PaeevPpelPEPal 76 (200)
|..|+|||||.|-.
T Consensus 184 ~~~~~~~~~~~~~~ 197 (202)
T cd04120 184 PEPEIPPELPPPRP 197 (202)
T ss_pred CCCCCCcCCCCCCC
Confidence 78899999999864
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=41.31 E-value=38 Score=22.69 Aligned_cols=32 Identities=34% Similarity=0.437 Sum_probs=23.2
Q ss_pred CCCHHHHHhhhhhhhhHHHHHHhHHHHHhhhc
Q 029049 9 PRTVEEVFGDFKGRRAGMIKALTTEVEEFYHQ 40 (200)
Q Consensus 9 prTvE~iF~Df~~RR~glirALT~Dve~Fy~~ 40 (200)
++|+++|-+.+..+=..=...+..||..|.++
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 69999999888877655555578899999764
No 7
>PF11351 DUF3154: Protein of unknown function (DUF3154); InterPro: IPR021497 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=37.41 E-value=18 Score=28.48 Aligned_cols=14 Identities=64% Similarity=0.992 Sum_probs=11.7
Q ss_pred hHHH--HHHHHhhhcc
Q 029049 100 AWLL--SVAFYFGARF 113 (200)
Q Consensus 100 sWLl--svAfy~gar~ 113 (200)
-||| .|.||||+|-
T Consensus 100 w~Llg~~vlgy~~~Rs 115 (123)
T PF11351_consen 100 WWLLGAGVLGYFGARS 115 (123)
T ss_pred HHHHHHHHhhhHHHhh
Confidence 4777 8999999994
No 8
>smart00432 MADS MADS domain.
Probab=36.03 E-value=50 Score=23.37 Aligned_cols=38 Identities=26% Similarity=0.503 Sum_probs=24.9
Q ss_pred hhhhhhhHHHHHHhHHHHHhhhcCCcCCcceeeecCCCCceee
Q 029049 18 DFKGRRAGMIKALTTEVEEFYHQCDPEKENLCLYGFPSEQWEV 60 (200)
Q Consensus 18 Df~~RR~glirALT~Dve~Fy~~CDPekenLcLYG~p~~~WeV 60 (200)
-|+.||+||.+-- .++.-+||-+---+ +|+..+..+.+
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 3899999999865 56778999754332 35554444443
No 9
>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=34.77 E-value=8.8 Score=29.58 Aligned_cols=44 Identities=27% Similarity=0.613 Sum_probs=26.1
Q ss_pred ceeeeCCCCCC-CCCCCCCcCCcccc----CCCccccchhhhhhhhcchH
Q 029049 57 QWEVNLPAEEV-PPELPEPALGINFA----RDGMQEKDWLSLVAVHSDAW 101 (200)
Q Consensus 57 ~WeV~lPaeev-PpelPEPalGINfa----RDgM~rkdWLslVAvHSDsW 101 (200)
++|+.+|-..+ +|+.... +|+||. .++=.|.-|++...+....|
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 888888 45566888888777766663
No 10
>PHA03099 epidermal growth factor-like protein (EGF-like protein); Provisional
Probab=33.47 E-value=12 Score=31.51 Aligned_cols=23 Identities=35% Similarity=0.751 Sum_probs=20.1
Q ss_pred HHhHHHHHhhhcCCcCCcceeeec
Q 029049 29 ALTTEVEEFYHQCDPEKENLCLYG 52 (200)
Q Consensus 29 ALT~Dve~Fy~~CDPekenLcLYG 52 (200)
--|+|+-+ ++.|.+++.+.||+|
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 11
>PF13111 DUF3962: Protein of unknown function (DUF3962)
Probab=27.59 E-value=36 Score=30.47 Aligned_cols=33 Identities=30% Similarity=0.732 Sum_probs=25.0
Q ss_pred cchhhhhhhhcchHHHHHHHHhhhccCCChhhhHHHHHhhcc
Q 029049 88 KDWLSLVAVHSDAWLLSVAFYFGARFGFDKSDRKRLFNMINE 129 (200)
Q Consensus 88 kdWLslVAvHSDsWLlsvAfy~gar~gF~~~~R~rLf~mIN~ 129 (200)
.+|+.||-.|-|.|++-+-+ +.-++||+.|.-+
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 68999999999999998754 2235677776543
No 12
>PRK03598 putative efflux pump membrane fusion protein; Provisional
Probab=25.42 E-value=21 Score=30.83 Aligned_cols=15 Identities=27% Similarity=0.248 Sum_probs=12.7
Q ss_pred ccccchhhhhhhhcc
Q 029049 85 MQEKDWLSLVAVHSD 99 (200)
Q Consensus 85 M~rkdWLslVAvHSD 99 (200)
|.+++||+|.|+-+=
T Consensus 1 ~~~~~~~~~~~~~~~ 15 (331)
T PRK03598 1 MKKKVVIGLAVVVLA 15 (331)
T ss_pred CCceEEEEhHHHHHH
Confidence 889999999998653
No 13
>PF13880 Acetyltransf_13: ESCO1/2 acetyl-transferase
Probab=25.23 E-value=12 Score=27.74 Aligned_cols=52 Identities=29% Similarity=0.507 Sum_probs=36.6
Q ss_pred hhhhhHHHHHHhHHHHHhhhcCCcCCcceeeecCCCCceeeeCCCCCCCCCCCCCc-CCccccCCCccccchh
Q 029049 20 KGRRAGMIKALTTEVEEFYHQCDPEKENLCLYGFPSEQWEVNLPAEEVPPELPEPA-LGINFARDGMQEKDWL 91 (200)
Q Consensus 20 ~~RR~glirALT~Dve~Fy~~CDPekenLcLYG~p~~~WeV~lPaeevPpelPEPa-lGINfaRDgM~rkdWL 91 (200)
+-||.||...|..=+- +| .+||..-..++|.. -+|+ -|..||+.-....+||
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 5699999999987443 23 35888766666653 2344 6888888877777776
No 14
>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=24.89 E-value=81 Score=22.84 Aligned_cols=31 Identities=16% Similarity=0.334 Sum_probs=23.7
Q ss_pred CCCHHHHHhhhhhhhhHHHHHHhHHHHHhhhc
Q 029049 9 PRTVEEVFGDFKGRRAGMIKALTTEVEEFYHQ 40 (200)
Q Consensus 9 prTvE~iF~Df~~RR~glirALT~Dve~Fy~~ 40 (200)
++||++|-.....+=.. -.-+..||..|..+
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 68999998887776666 55567899888764
No 15
>PTZ00211 ribonucleoside-diphosphate reductase small subunit; Provisional
Probab=23.54 E-value=59 Score=29.06 Aligned_cols=40 Identities=25% Similarity=0.534 Sum_probs=30.0
Q ss_pred hhhhhhhhcchHHHHHHHHhhhccCCChhhhHHHHHhhccCCcee
Q 029049 90 WLSLVAVHSDAWLLSVAFYFGARFGFDKSDRKRLFNMINELPTIF 134 (200)
Q Consensus 90 WLslVAvHSDsWLlsvAfy~gar~gF~~~~R~rLf~mIN~lpTv~ 134 (200)
|...=+||+++.-.-+-- ++-+..+|.++|..|.++|+|.
T Consensus 107 q~~~E~iHs~sYs~il~t-----l~~~~~~~~~~f~~~~~~p~i~ 146 (330)
T PTZ00211 107 QIAMENIHSETYSLLIDT-----YITDEEEKDRLFHAIETIPAIK 146 (330)
T ss_pred HHHHHHHHHHHHHHHHHH-----cCCCHHHHHHHHHHHHhCHHHH
Confidence 444557999998765543 4447889999999999999864
No 16
>cd01182 INT_REC_C DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family include the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many intergrase/recombinases also have N-terminal domains, which show little sequence or structure similarity.
Probab=22.65 E-value=73 Score=22.17 Aligned_cols=17 Identities=29% Similarity=0.438 Sum_probs=14.6
Q ss_pred hcchHHHHHHHHhhhcc
Q 029049 97 HSDAWLLSVAFYFGARF 113 (200)
Q Consensus 97 HSDsWLlsvAfy~gar~ 113 (200)
....|.+.++++.|.|.
T Consensus 15 ~~~~~~~~l~~~~G~R~ 31 (162)
T cd01182 15 PRDRALILLLLYTGLRV 31 (162)
T ss_pred HHHHHHHHHHHHhCCCH
Confidence 45688899999999998
No 17
>cd05036 PTKc_ALK_LTK Catalytic domain of the Protein Tyrosine Kinases, Anaplastic Lymphoma Kinase and Leukocyte Tyrosine Kinase. Protein Tyrosine Kinase (PTK) family; Anaplastic Lymphoma Kinase (ALK) and Leukocyte Tyrosine (tyr) Kinase (LTK); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyr residues in protein substrates. ALK and LTK are orphan receptor tyr kinases (RTKs) whose ligands are not yet well-defined. RTKs contain an extracellular ligand-binding domain, a transmembrane region, and an intracellular tyr kinase domain. They are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain. ALK appears to play an important role in mammalian neural development as well
Probab=22.42 E-value=90 Score=24.94 Aligned_cols=34 Identities=9% Similarity=0.340 Sum_probs=24.1
Q ss_pred hhhcchHHHHHHHHh---hhccCCChhhhHHHHHhhc
Q 029049 95 AVHSDAWLLSVAFYF---GARFGFDKSDRKRLFNMIN 128 (200)
Q Consensus 95 AvHSDsWLlsvAfy~---gar~gF~~~~R~rLf~mIN 128 (200)
.-.||.|-++|.+|. +.++-|.......+..+|.
T Consensus 199 ~~~~DiwslG~il~el~~~g~~pf~~~~~~~~~~~~~ 235 (277)
T cd05036 199 TSKTDVWSFGVLLWEIFSLGYMPYPGRTNQEVMEFVT 235 (277)
T ss_pred CchhHHHHHHHHHHHHHcCCCCCCCCCCHHHHHHHHH
Confidence 357999999999885 3555566666666666654
No 18
>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=22.27 E-value=88 Score=22.08 Aligned_cols=32 Identities=28% Similarity=0.526 Sum_probs=21.8
Q ss_pred hhhhhhhHHHHHHhHHHHHhhhcCCcCCcceeeecCC
Q 029049 18 DFKGRRAGMIKALTTEVEEFYHQCDPEKENLCLYGFP 54 (200)
Q Consensus 18 Df~~RR~glirALT~Dve~Fy~~CDPekenLcLYG~p 54 (200)
-|+.||+||.|-. .++--+||-+-- +.+|+..
T Consensus 19 tf~kR~~gl~kKa----~Els~Lc~~~v~-~iv~sp~ 50 (59)
T cd00120 19 TFSKRRNGLFKKA----SELSVLCDAEVA-VIVFSPS 50 (59)
T ss_pred hHHHHhchHHHhh----hhheeccCCcEE-EEEECCC
Confidence 4899999999864 567778986543 3345433
No 19
>cd05112 PTKc_Itk Catalytic domain of the Protein Tyrosine Kinase, Interleukin-2-inducible T-cell Kinase. Protein Tyrosine Kinase (PTK) family; Interleukin-2 (IL-2)-inducible T-cell kinase (Itk); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Itk (also known as Tsk or Emt) is a member of the Tec subfamily of proteins, which are cytoplasmic (or nonreceptor) tyr kinases with similarity to Src kinases in that they contain Src homology protein interaction domains (SH3, SH2) N-terminal to the catalytic tyr kinase domain. Unlike Src kinases, most Tec subfamily members (except Rlk) also contain an N-terminal pleckstrin homology (PH) domain, which binds the products of PI3K and allows membrane recruitment and activ
Probab=22.16 E-value=92 Score=24.21 Aligned_cols=34 Identities=18% Similarity=0.413 Sum_probs=23.6
Q ss_pred hhhcchHHHHHHHHhh---hccCCChhhhHHHHHhhc
Q 029049 95 AVHSDAWLLSVAFYFG---ARFGFDKSDRKRLFNMIN 128 (200)
Q Consensus 95 AvHSDsWLlsvAfy~g---ar~gF~~~~R~rLf~mIN 128 (200)
.-.+|.|-++|.+|.- .+.-|+......+...|+
T Consensus 179 ~~~~Dv~slG~~l~el~~~g~~p~~~~~~~~~~~~~~ 215 (256)
T cd05112 179 SSKSDVWSFGVLMWEVFSEGKTPYENRSNSEVVETIN 215 (256)
T ss_pred ChHHHHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHHh
Confidence 3469999999999862 455567666666666553
No 20
>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=22.16 E-value=34 Score=21.67 Aligned_cols=9 Identities=56% Similarity=1.291 Sum_probs=6.0
Q ss_pred cceeeecCC
Q 029049 46 ENLCLYGFP 54 (200)
Q Consensus 46 enLcLYG~p 54 (200)
|.+||||..
T Consensus 5 ekiclygqs 13 (27)
T PF09065_consen 5 EKICLYGQS 13 (27)
T ss_dssp SSEE-TTEE
T ss_pred ceeeEeccc
Confidence 568999963
No 21
>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=21.96 E-value=1.1e+02 Score=21.30 Aligned_cols=34 Identities=12% Similarity=0.399 Sum_probs=27.4
Q ss_pred CCCCCHHHHHhhhhhhhhH--HHHHHhHHHHHhhhc
Q 029049 7 YNPRTVEEVFGDFKGRRAG--MIKALTTEVEEFYHQ 40 (200)
Q Consensus 7 ~~prTvE~iF~Df~~RR~g--lirALT~Dve~Fy~~ 40 (200)
..+..++.+++.|.||.-+ =+.+|+..+.++|..
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 4567889999999999854 478889999999874
No 22
>cd05060 PTKc_Syk_like Catalytic domain of Spleen Tyrosine Kinase-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Spleen Tyrosine Kinase (Syk) subfamily; catalytic (c) domain. The Syk subfamily is composed of Syk, ZAP-70, Shark, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Syk subfamily kinases are cytoplasmic (or nonreceptor) tyr kinases containing two Src homology 2 (SH2) domains N-terminal to the catalytic tyr kinase domain. They are involved in the signaling downstream of activated receptors (including B-cell, T-cell, and Fc receptors) that contain ITAMs (immunoreceptor tyr activation motifs), leading to processes such as cell proliferation, differentiation, survival, adhesion, mi
Probab=21.62 E-value=1.1e+02 Score=24.07 Aligned_cols=36 Identities=14% Similarity=0.278 Sum_probs=23.8
Q ss_pred hhhcchHHHHHHHHhhh---ccCCChhhhHHHHHhhccC
Q 029049 95 AVHSDAWLLSVAFYFGA---RFGFDKSDRKRLFNMINEL 130 (200)
Q Consensus 95 AvHSDsWLlsvAfy~ga---r~gF~~~~R~rLf~mIN~l 130 (200)
-.++|.|-+.+.+|.-. +.-|+......+...|+..
T Consensus 176 ~~~~Di~slG~~l~~~~~~g~~p~~~~~~~~~~~~~~~~ 214 (257)
T cd05060 176 SSKSDVWSYGVTLWEAFSYGAKPYGEMKGAEVIAMLESG 214 (257)
T ss_pred CccchHHHHHHHHHHHHcCCCCCcccCCHHHHHHHHHcC
Confidence 34699999999998654 3335555555666665543
No 23
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=21.46 E-value=40 Score=26.93 Aligned_cols=14 Identities=43% Similarity=1.004 Sum_probs=12.8
Q ss_pred cccCCCccccchhh
Q 029049 79 NFARDGMQEKDWLS 92 (200)
Q Consensus 79 NfaRDgM~rkdWLs 92 (200)
|+-+.||.|.|||.
T Consensus 83 Nl~p~G~~r~dWl~ 96 (100)
T PF15643_consen 83 NLHPEGMSREDWLR 96 (100)
T ss_pred ccCcccCCHHHHHH
Confidence 88899999999985
No 24
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=21.09 E-value=92 Score=26.91 Aligned_cols=22 Identities=27% Similarity=0.468 Sum_probs=15.3
Q ss_pred HHHHhhhcCCcCCcceeeecCCC
Q 029049 33 EVEEFYHQCDPEKENLCLYGFPS 55 (200)
Q Consensus 33 Dve~Fy~~CDPekenLcLYG~p~ 55 (200)
+...|.+.++ ..+||+|||.|.
T Consensus 94 ~~~~~~~~~~-~~~nl~l~G~~G 115 (254)
T COG1484 94 DLASLVEFFE-RGENLVLLGPPG 115 (254)
T ss_pred HHHHHHHHhc-cCCcEEEECCCC
Confidence 3444444455 779999999885
No 25
>KOG4148 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.86 E-value=38 Score=27.39 Aligned_cols=28 Identities=32% Similarity=0.692 Sum_probs=22.4
Q ss_pred hhHHHHHHhH-----HHHHhhhcCCcCCcce--ee
Q 029049 23 RAGMIKALTT-----EVEEFYHQCDPEKENL--CL 50 (200)
Q Consensus 23 R~glirALT~-----Dve~Fy~~CDPekenL--cL 50 (200)
-.-+|+||-. -.-+||..|+..|..| ||
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 6789999999998666 76
No 26
>smart00464 LON Found in ATP-dependent protease La (LON). N-terminal domain of the ATP-dependent protease La (LON), present also in other bacterial ORFs.
Probab=20.48 E-value=75 Score=22.66 Aligned_cols=25 Identities=8% Similarity=0.169 Sum_probs=21.6
Q ss_pred HHHHHHhhhccCCChhhhHHHHHhh
Q 029049 103 LSVAFYFGARFGFDKSDRKRLFNMI 127 (200)
Q Consensus 103 lsvAfy~gar~gF~~~~R~rLf~mI 127 (200)
.-+|+..+++++++..++++|..|-
T Consensus 56 ~~~~~~~a~~~~~~~~~~q~lL~~~ 80 (92)
T smart00464 56 EPLSDTIAALMPLELHEKQELLELE 80 (92)
T ss_pred hhhhHHHhhcccccHHHHHHHHhcc
Confidence 3578889999999999999999874
Done!