Query 048777
Match_columns 547
No_of_seqs 66 out of 68
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 13:05:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048777.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048777hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10250 O-FucT: GDP-fucose pr 99.6 7.2E-17 1.6E-21 157.0 3.5 244 256-535 8-329 (351)
2 PF01531 Glyco_transf_11: Glyc 85.8 1.9 4E-05 43.4 6.3 30 254-283 37-66 (298)
3 KOG3849 GDP-fucose protein O-f 58.0 6.2 0.00013 41.8 1.9 66 254-326 34-105 (386)
4 PF05830 NodZ: Nodulation prot 50.6 7.8 0.00017 41.1 1.3 239 254-530 9-279 (321)
5 PF01320 Colicin_Pyocin: Colic 35.2 30 0.00064 30.5 2.3 30 419-452 46-75 (85)
6 PF06900 DUF1270: Protein of u 34.0 12 0.00026 30.7 -0.3 20 20-39 5-24 (53)
7 PF14399 Transpep_BrtH: NlpC/p 30.5 67 0.0015 31.6 4.1 54 402-473 53-106 (317)
8 PRK15367 type III secretion sy 29.3 62 0.0013 35.4 3.9 54 20-74 115-172 (395)
9 PF03610 EIIA-man: PTS system 28.3 1.7E+02 0.0036 25.4 5.8 61 395-470 9-72 (116)
10 PF05620 DUF788: Protein of un 27.8 75 0.0016 30.1 3.8 29 51-79 62-90 (170)
11 PF10917 DUF2708: Protein of u 27.3 24 0.00052 27.9 0.3 15 20-34 4-18 (43)
12 PF14642 FAM47: FAM47 family 26.5 45 0.00098 34.7 2.2 29 430-459 132-160 (258)
13 cd03002 PDI_a_MPD1_like PDI fa 24.5 59 0.0013 26.7 2.2 34 111-144 54-87 (109)
14 PF10294 Methyltransf_16: Puta 23.0 61 0.0013 30.2 2.2 52 414-476 119-173 (173)
15 PF09580 Spore_YhcN_YlaJ: Spor 22.4 2.1E+02 0.0046 26.5 5.6 74 399-475 75-150 (177)
16 PF12841 YvrJ: YvrJ protein fa 21.8 46 0.001 25.5 1.0 18 13-30 1-18 (38)
17 PF02602 HEM4: Uroporphyrinoge 21.3 75 0.0016 29.7 2.5 49 439-487 102-151 (231)
18 cd03007 PDI_a_ERp29_N PDIa fam 21.3 79 0.0017 28.8 2.5 33 109-141 53-90 (116)
19 cd02992 PDI_a_QSOX PDIa family 21.2 62 0.0013 28.1 1.8 34 111-144 58-91 (114)
20 PF05830 NodZ: Nodulation prot 21.2 1.2E+02 0.0025 32.7 4.0 14 441-454 223-236 (321)
21 cd06592 GH31_glucosidase_KIAA1 20.9 1.6E+02 0.0034 30.0 4.8 48 396-450 28-81 (303)
22 PF00085 Thioredoxin: Thioredo 20.8 58 0.0013 25.9 1.4 35 109-145 51-85 (103)
23 PF06245 DUF1015: Protein of u 20.4 1E+02 0.0022 33.1 3.5 54 397-465 152-210 (416)
No 1
>PF10250 O-FucT: GDP-fucose protein O-fucosyltransferase; InterPro: IPR019378 This is a family of conserved proteins representing the enzyme responsible for adding O-fucose to EGF (epidermal growth factor-like) repeats. Six highly conserved cysteines are present as well as a DXD-like motif (ERD), conserved in mammals, Drosophila, and Caenorhabditis elegans. Both features are characteristic of several glycosyltransferase families. The enzyme is a membrane-bound protein released by proteolysis and, as for most glycosyltransferases, is strongly activated by manganese []. ; PDB: 3ZY6_A 3ZY3_A 3ZY5_A 3ZY2_A 3ZY4_A.
Probab=99.64 E-value=7.2e-17 Score=156.98 Aligned_cols=244 Identities=23% Similarity=0.293 Sum_probs=123.5
Q ss_pred CCcchhHHHHHhhcccccccceeeeeecccccccccCCCCCCCCCccceeecchhcccccc-ceeechhhhhhhhHHhHh
Q 048777 256 KGMNHFAWSFLCGLGEAMYLKRTFVMDLSMCLAAKYNPSNQDVDGKDFRYYFDFEHLKDVA-SVVEEGEFLREWKKWDQK 334 (547)
Q Consensus 256 kgm~H~~~SllCAL~EA~yLNRTfVMdl~mCLs~~yn~~g~~eegkd~r~yfD~ehl~~~v-~VIe~~qF~~dw~~W~~~ 334 (547)
.|.|.|.-+|+-|+-=|+.||||||||- .+.....+... ....-.|..+||++||++.+ +||+-.+|+. +.|...
T Consensus 8 GGfnNQr~~~~~a~~~A~~LnRTLVLPp-~~~~~~~~~~~-~~~~ipf~~~fD~~~l~~~~~~vi~~~ef~~--~~~~~~ 83 (351)
T PF10250_consen 8 GGFNNQRMGFENAVVFAKALNRTLVLPP-FIKHYHWKDQS-KQRHIPFSDFFDVEHLRKFLRPVITMEEFLP--KHWDEV 83 (351)
T ss_dssp SSHHHHHHHHHHHHHHHHHHT-EEE--E-EEEESSSS-----EEEEEHHHHB-HHHHTTTS--EE-HHHHHH--HHS-GG
T ss_pred CCHHHHHHHHHHHHHHHHHhCCEEEcCC-ccccccccccc-cccccChhhhccHHHHHHHhhCceehheecc--chhccc
Confidence 4899999999999999999999999987 33332222111 12234578899999999999 9999998983 223332
Q ss_pred hc---------------------------ccccceEEEEe-eecccc-ccc------------cccceEEeccCCCCCCC
Q 048777 335 HE---------------------------KKVSVKKVVSY-KVKPKN-LKK------------DNSTIIWRQFDAPSPGN 373 (547)
Q Consensus 335 ~~---------------------------~kL~~r~v~~~-~Vtp~~-Lk~------------~~~~li~rkf~~~ep~n 373 (547)
.. ++......... ...+.- +.+ ....+.+..+...=+.+
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~ 163 (351)
T PF10250_consen 84 FRLQYCWSPWESGSWDDNMKDGNPFGPFWDKFPIKFDPCEFWSSPSLYLEDVLPELREWNENSEHPVIAFTGFESRLPDN 163 (351)
T ss_dssp G-EEEESS-B--------TTSSTTHHHHHHHTT---SEEE-E-TTSTTTT-STTHHHHHHHHTT-SEEEESS-SS-SS--
T ss_pred cchhhcccccccccchhhccccccccccccccceeeccccccCCchhhHHHhhhHHhhhccccccccceeccccccchhc
Confidence 00 01111111110 111111 111 01233333333332222
Q ss_pred eeeeeecccccccccccchhhhhhHHHHHHHHHHhcccC---CCCceEEEecC-cc------------------------
Q 048777 374 FWFMVCDREAAKYIERPWHALLKSKILLNIVAEIGGRMD---YEYDAIHVVRG-ER------------------------ 425 (547)
Q Consensus 374 yWy~vCege~~s~i~~P~~~l~kskrLm~iv~~I~~rm~---~DfDavHVrRG-Dk------------------------ 425 (547)
++ ...+++ .|..++.|+++|+++..++- +.|-|||+|+| |+
T Consensus 164 ~~--------~~~~~r---~l~~~~~i~~~a~~~i~~~~~~~~~yiavHlR~~~D~~~~C~~~~~~~~~~~~~~~~~~~~ 232 (351)
T PF10250_consen 164 YL--------DRDLQR---YLRFSPEIRELADKFIKRLLAGGGPYIAVHLRRGKDWFSACEFKGERHLLASPRCWGKKSI 232 (351)
T ss_dssp GG--------GGGGGG---G--B-HHHHHHHHHHHHHH----SSEEEEEE--SHHHHHHHCT-T----TTTHHHH-GGGT
T ss_pred cc--------CccceE---EEecCHHHHHHHHHHHHHhhcccCceEEEeecccCchHhhcccCCchHHHHHhHhhccccc
Confidence 11 122333 77888999999999998877 99999999999 88
Q ss_pred ---cc-ccccCCCCCCCCChHHHHHHhhhhcC--CCcEEEEeeCCCC--CcchhhhhcceeEeeccchhHHhccCChhhh
Q 048777 426 ---VK-NKKLWPNLDSDTSPGALLEKLEEVVH--PWTNLYIATNEPS--YNYFDTLRSEYKVHLLDDYRDLWNSTSEWYH 497 (547)
Q Consensus 426 ---~~-nk~l~PnLd~DTspE~i~~~i~~~i~--~GR~LYIATnE~~--~~fFdpLk~kY~vhfLdDFk~Lw~~~sewy~ 497 (547)
.. .....| +.+.++..|++.+. ..++||||||+.. ...+++|++.|.-.+ .++.+. ...
T Consensus 233 ~~~~~~~~~~~p------~~~~~~~~i~~~~~~~~~~~vYiAtd~~~~~~~~l~~l~~~~~~~~---~~~~~~----~~~ 299 (351)
T PF10250_consen 233 NPEKKRRNGCCP------STPQEAKQILRALGKNNTTVVYIATDEIYGGERRLDPLKNMFPNVV---TKDDLL----SHE 299 (351)
T ss_dssp T-----HHHHS--------HHHHHHHHHHHHHHHT-SEEEEEESS-----------HHHHHHHH---GGGT------EE-
T ss_pred cchhhhhcCCCC------ChHHHHHHHHHHhccCCCCEEEEecCcccccchhHHHHHHHhhhhE---eccccC----CHH
Confidence 10 111233 23455566666554 4599999999943 356788888877444 111111 011
Q ss_pred hhhhccCCCccccCChhhhhhhHhhhccCceeEeeccc
Q 048777 498 WMTRLTRGRPVEFDGYMRAIVDTEVFYRGKIRLETFNN 535 (547)
Q Consensus 498 Et~~Ln~G~PV~fdgYmr~mVDteVf~rGK~~VeTf~~ 535 (547)
|. ..+++.+..|||++|.+++..||+|..+
T Consensus 300 ~~--------~~~~~~~~a~vD~~i~~~s~~Figt~~S 329 (351)
T PF10250_consen 300 EL--------EPLNDDQLAMVDQEICSRSDVFIGTCGS 329 (351)
T ss_dssp -S-------------S--HHHHHHHHHHSSEEEE-TT-
T ss_pred Hh--------hhccccchhHHHHHHHhcCCEEEecCcc
Confidence 22 2344477899999999999999999876
No 2
>PF01531 Glyco_transf_11: Glycosyl transferase family 11; InterPro: IPR002516 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 11 GT11 from CAZY comprises enzymes with only one known activity; galactoside 2-L-fucosyltransferase (2.4.1.69 from EC). Some of the proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Galactoside 2-L-fucosyltransferase 1 (2.4.1.69 from EC) and Galactoside 2-L-fucosyltransferase 2 (2.4.1.69 from EC) belong to the Hh blood group system and are associated with H/h and Se/se antigens.; GO: 0008107 galactoside 2-alpha-L-fucosyltransferase activity, 0005975 carbohydrate metabolic process, 0016020 membrane
Probab=85.85 E-value=1.9 Score=43.40 Aligned_cols=30 Identities=13% Similarity=0.123 Sum_probs=25.0
Q ss_pred cCCCcchhHHHHHhhcccccccceeeeeec
Q 048777 254 YCKGMNHFAWSFLCGLGEAMYLKRTFVMDL 283 (547)
Q Consensus 254 ~Ckgm~H~~~SllCAL~EA~yLNRTfVMdl 283 (547)
...++|-|++-+-..++.|+.++|+.+++.
T Consensus 37 ~~g~LGNqmfqya~l~~lak~~~~~~~i~~ 66 (298)
T PF01531_consen 37 LNGRLGNQMFQYASLYGLAKLNGRTAFIPI 66 (298)
T ss_pred EcchHHHHHhHHHHHHHHHHhcCCccccch
Confidence 466799999999888999998888877654
No 3
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=57.97 E-value=6.2 Score=41.78 Aligned_cols=66 Identities=30% Similarity=0.486 Sum_probs=47.3
Q ss_pred cCCCcc---hhHHHHHhhcccccccceeeeeecccccccccCCCCCCCC---Cccceeecchhccccccceeechhhhh
Q 048777 254 YCKGMN---HFAWSFLCGLGEAMYLKRTFVMDLSMCLAAKYNPSNQDVD---GKDFRYYFDFEHLKDVASVVEEGEFLR 326 (547)
Q Consensus 254 ~Ckgm~---H~~~SllCAL~EA~yLNRTfVMdl~mCLs~~yn~~g~~ee---gkd~r~yfD~ehl~~~v~VIe~~qF~~ 326 (547)
+|--|| .|.--||=.|+=|.-||||||+|-=+ .|- .+|- --.|++||-.|-|++---||.-.+|.+
T Consensus 34 yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwi----Ey~---~pe~~n~~vpf~~yF~vepl~~YhRVitm~dFm~ 105 (386)
T KOG3849|consen 34 YCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWI----EYK---HPETKNLMVPFEFYFQVEPLAKYHRVITMQDFMK 105 (386)
T ss_pred EccccccccchHHHHHHHHHHHHHhcccccCCcch----hcc---CCcccccccchhheeecccHhhhhhheeHHHHHH
Confidence 466664 45566777788899999999998644 222 1111 135899999999999999997777754
No 4
>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.
Probab=50.63 E-value=7.8 Score=41.08 Aligned_cols=239 Identities=15% Similarity=0.257 Sum_probs=104.3
Q ss_pred cCCCcchhHHHHHhhcccccccceeeeeecc-cccccccCCCCCCCCCccceeecchhcccccccee-ec--hh------
Q 048777 254 YCKGMNHFAWSFLCGLGEAMYLKRTFVMDLS-MCLAAKYNPSNQDVDGKDFRYYFDFEHLKDVASVV-EE--GE------ 323 (547)
Q Consensus 254 ~Ckgm~H~~~SllCAL~EA~yLNRTfVMdl~-mCLs~~yn~~g~~eegkd~r~yfD~ehl~~~v~VI-e~--~q------ 323 (547)
+|.|||--+|||--|-.=|+-+|||||+|-+ -|....-. --+|.-+|+.-.=-..|+|| +. .|
T Consensus 9 ~r~g~gd~l~~la~aw~~a~~~~r~l~idw~~s~~~~~~f-------~n~f~~ffepv~~i~~~~~~~~d~i~~~~~~g~ 81 (321)
T PF05830_consen 9 RRTGLGDCLWSLAAAWRYAKRTGRTLVIDWRGSCYLDQPF-------TNAFPVFFEPVEDIAGVRVICDDRINQFSFPGP 81 (321)
T ss_dssp --S-HHHHHHHHHHHHHHHHHHT-EEEEE-BT-TT-SSTT-------SBSHHHHB---SEETTEEEE-SGGGGT----SS
T ss_pred ccCCchhHHHHHHHHHHHHHHhCCeEEEEcCCceecCCcc-------cccCCcccchhhhhcCceeEecchhhhhcCCCC
Confidence 6999999999999999999999999999965 33321111 13455555433322457777 22 12
Q ss_pred hhhhhhHHhHhhcccccceEEEEeee--ccc------ccccc--ccceEEeccCCCCCCCeeeeeecccccccccccchh
Q 048777 324 FLREWKKWDQKHEKKVSVKKVVSYKV--KPK------NLKKD--NSTIIWRQFDAPSPGNFWFMVCDREAAKYIERPWHA 393 (547)
Q Consensus 324 F~~dw~~W~~~~~~kL~~r~v~~~~V--tp~------~Lk~~--~~~li~rkf~~~ep~nyWy~vCege~~s~i~~P~~~ 393 (547)
|.. ..|.+-. ..--.| .|.-| .+- ++.++ .+|+|--+-.-. -|+-++|+-| |..
T Consensus 82 ~fp--~~w~~p~-~~~~~~--pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~c~~~--------~c~~~aeR~i---f~s 145 (321)
T PF05830_consen 82 FFP--AWWNKPS-IDCVYR--PDEQIFRERDELRQLFQSQEDHEANTVVCDACLMW--------RCDEEAEREI---FSS 145 (321)
T ss_dssp EES--GGGGS-G-GGGS-----HHHHHHHHHHHHHHHHSSS--S-SEEEE-S--TT--------SS-HHHHHHH---HHH
T ss_pred cCh--hHHhCCC-cceecC--ChHHHhhhhHHHHHHhhcccccccchhhhHhhcCC--------cchhHHHHHH---HHh
Confidence 222 2244410 000001 11000 011 22232 245554443333 4777777655 445
Q ss_pred hhhhHHHHHHHHHHhcccCCCCc--eEEEecCccccccccCCCCCCCCChHHHH----HHhh--hhcCCC--cEEEEeeC
Q 048777 394 LLKSKILLNIVAEIGGRMDYEYD--AIHVVRGERVKNKKLWPNLDSDTSPGALL----EKLE--EVVHPW--TNLYIATN 463 (547)
Q Consensus 394 l~kskrLm~iv~~I~~rm~~DfD--avHVrRGDk~~nk~l~PnLd~DTspE~i~----~~i~--~~i~~G--R~LYIATn 463 (547)
|-..+....-+++|..+.-.++. +||||+|.-. ..+-|-..=+.++--+ ..+. +...++ -.||+|||
T Consensus 146 lkpR~eIqarID~iy~ehf~g~~~IGVHVRhGnge---D~~~h~~~~~D~e~~L~~V~~ai~~ak~~~~~k~~~IFLATD 222 (321)
T PF05830_consen 146 LKPRPEIQARIDAIYREHFAGYSVIGVHVRHGNGE---DIMDHAPYWADEERALRQVCTAIDKAKALAPPKPVRIFLATD 222 (321)
T ss_dssp S-B-HHHHHHHHHHHHHHTTTSEEEEEEE------------------HHHHHHHHHHHHHHHHHHTS--SS-EEEEEEES
T ss_pred CCCCHHHHHHHHHHHHHHcCCCceEEEEEeccCCc---chhccCccccCchHHHHHHHHHHHHHHhccCCCCeeEEEecC
Confidence 56667777888887766544664 6899999441 0111100012233222 2232 223444 45999999
Q ss_pred CCCCcchhhhhccee--EeeccchhHHhccCChhhhhhhhccCCCccccCChhhhhhhHhhhccCceeE
Q 048777 464 EPSYNYFDTLRSEYK--VHLLDDYRDLWNSTSEWYHWMTRLTRGRPVEFDGYMRAIVDTEVFYRGKIRL 530 (547)
Q Consensus 464 E~~~~fFdpLk~kY~--vhfLdDFk~Lw~~~sewy~Et~~Ln~G~PV~fdgYmr~mVDteVf~rGK~~V 530 (547)
+.. .-+.||++|- ++--++|..- + ...+.+--..++ |=..++||-..++|-.+-|
T Consensus 223 Sae--Vid~fr~~FPdiiti~k~F~~~-~-~g~Lhs~~~g~~--------gg~~ALIDM~LLSrCD~LI 279 (321)
T PF05830_consen 223 SAE--VIDQFRKKFPDIITIPKQFPAS-Q-AGPLHSAAVGIE--------GGESALIDMYLLSRCDYLI 279 (321)
T ss_dssp -HH--HHHHHHHHSTTEE------------------HHHHHH--------HHHHHHHHHHHHTTSSEEE
T ss_pred cHH--HHHHHHHHCCCeEEcccccCCC-C-CCcCcccccccc--------hHHHHHHHHHHHHhCCeEE
Confidence 875 4677777775 2223344311 1 112222111233 2334788888888877776
No 5
>PF01320 Colicin_Pyocin: Colicin immunity protein / pyocin immunity protein; InterPro: IPR023802 Bacterial colicin and pyocin immunity proteins [, ] can bind specifically to the DNase-type colicins and pyocins and inhibit their bactericidal activity. The 1.8-angstrom crystal structure of the ImmE7 protein consists of four antiparallel alpha-helices []. Sequence similarities between colicins E2, A and E1 [] are less striking. The colicin E2 (pyocin) immunity protein does not share similarity with either the colicin E3 or cloacin DF13 [] immunity proteins. Pyocin protects a cell that harbours the plasmid ColE2 encoding colicin E2 against colicin E2; it is thus essential both for autonomous replication and colicin E2 immunity []. This entry represents the structural domain of colicin and pyocin immunity proteins.; GO: 0015643 toxin binding, 0030153 bacteriocin immunity; PDB: 1GXH_A 1GXG_A 1MZ8_C 2ERH_A 1ZNV_C 1AYI_A 1UNK_A 2JBG_A 7CEI_A 1CEI_A ....
Probab=35.19 E-value=30 Score=30.50 Aligned_cols=30 Identities=17% Similarity=0.401 Sum_probs=23.3
Q ss_pred EEecCccccccccCCCCCCCCChHHHHHHhhhhc
Q 048777 419 HVVRGERVKNKKLWPNLDSDTSPGALLEKLEEVV 452 (547)
Q Consensus 419 HVrRGDk~~nk~l~PnLd~DTspE~i~~~i~~~i 452 (547)
|-...|.+ -||.-++|-|||.|++.|++|=
T Consensus 46 HP~gSDLI----fYP~~~~edsPegIv~~vKeWR 75 (85)
T PF01320_consen 46 HPDGSDLI----FYPEDGREDSPEGIVKEVKEWR 75 (85)
T ss_dssp -TTTTHHH----HS-STTSTSSHHHHHHHHHHHH
T ss_pred CCCCCcee----eeCCCCCCCCHHHHHHHHHHHH
Confidence 55566665 4788899999999999999984
No 6
>PF06900 DUF1270: Protein of unknown function (DUF1270); InterPro: IPR009682 This entry is represented by Bacteriophage 92, Orf86. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Staphylococcus aureus and phage proteins of 53 residues in length. The function of this family is unknown.
Probab=33.96 E-value=12 Score=30.69 Aligned_cols=20 Identities=30% Similarity=0.698 Sum_probs=14.7
Q ss_pred HHHHHHHHHHhhheeeeccC
Q 048777 20 FSVFVFSVLIFTVIAITYQP 39 (547)
Q Consensus 20 fs~fV~~vl~fTviA~tyqP 39 (547)
|--|++|+|.|||+|+.-+|
T Consensus 5 ykSylIA~l~ftvlsi~L~~ 24 (53)
T PF06900_consen 5 YKSYLIANLCFTVLSIALMP 24 (53)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34478888888888887663
No 7
>PF14399 Transpep_BrtH: NlpC/p60-like transpeptidase
Probab=30.51 E-value=67 Score=31.65 Aligned_cols=54 Identities=15% Similarity=0.180 Sum_probs=43.1
Q ss_pred HHHHHHhcccCCCCceEEEecCccccccccCCCCCCCCChHHHHHHhhhhcCCCcEEEEeeCCCCCcchhhh
Q 048777 402 NIVAEIGGRMDYEYDAIHVVRGERVKNKKLWPNLDSDTSPGALLEKLEEVVHPWTNLYIATNEPSYNYFDTL 473 (547)
Q Consensus 402 ~iv~~I~~rm~~DfDavHVrRGDk~~nk~l~PnLd~DTspE~i~~~i~~~i~~GR~LYIATnE~~~~fFdpL 473 (547)
++.+.+..++|+.+. +... .+++++++.|++.|..|+-|.|.+|.-.-.|+...
T Consensus 53 ~~~~~~~~~lG~~~~---~~~~---------------~~~~~~~~~l~~~l~~g~pv~~~~D~~~lpy~~~~ 106 (317)
T PF14399_consen 53 DFEENLLERLGIKYE---WREF---------------SSPDEAWEELKEALDAGRPVIVWVDMYYLPYRPNY 106 (317)
T ss_pred HHHHHHHHHCCceEE---EEec---------------CCHHHHHHHHHHHHhCCCceEEEeccccCCCCccc
Confidence 788888888996554 2211 36999999999999999999999998877777664
No 8
>PRK15367 type III secretion system protein SsaD; Provisional
Probab=29.33 E-value=62 Score=35.44 Aligned_cols=54 Identities=15% Similarity=0.168 Sum_probs=40.1
Q ss_pred HHHHHHHHHHhhheeeeccCCCCCccchhhhhhhhccCC----CCccccCCceeecccc
Q 048777 20 FSVFVFSVLIFTVIAITYQPPDPWLESTSALTKFFSKTE----NPTLEDGNSILKSGEV 74 (547)
Q Consensus 20 fs~fV~~vl~fTviA~tyqP~DP~l~~s~~~t~~~t~~~----NaTf~~d~svl~TGEd 74 (547)
+.++++.+|+|+++..+=+| .|.......+..+|.... +++..+|++|+.+|--
T Consensus 115 ~~~li~l~ll~~~~~ls~~~-~~~~~~~~~l~~~L~~p~l~~V~~~W~~dg~l~LsGyC 172 (395)
T PRK15367 115 GVFLIFIGGMGVLLSISGQP-ETVNDLPLRVKFLLDKSNIHYVRAQWKEDGSLQLSGYC 172 (395)
T ss_pred HHHHHHHHHHHHHeeccCCC-CCCCChHHHHHHHhhcccccceEEEECCCCcEEEEEEE
Confidence 46778888888888888888 444555677777776533 5677789999999953
No 9
>PF03610 EIIA-man: PTS system fructose IIA component; InterPro: IPR004701 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for IIA and IIB components.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane; PDB: 3GDW_B 2JZN_A 1VSQ_A 2JZO_B 1VRC_A 1PDO_A 3GX1_A 3B48_B 3BED_B 3IPR_C ....
Probab=28.31 E-value=1.7e+02 Score=25.41 Aligned_cols=61 Identities=30% Similarity=0.235 Sum_probs=43.4
Q ss_pred hhhHHHHHHHHHHhcccCCCCceEEEecCccccccccCCCCCCCCChHHHHHHhhhhc---CCCcEEEEeeCCCCCcch
Q 048777 395 LKSKILLNIVAEIGGRMDYEYDAIHVVRGERVKNKKLWPNLDSDTSPGALLEKLEEVV---HPWTNLYIATNEPSYNYF 470 (547)
Q Consensus 395 ~kskrLm~iv~~I~~rm~~DfDavHVrRGDk~~nk~l~PnLd~DTspE~i~~~i~~~i---~~GR~LYIATnE~~~~fF 470 (547)
.-|+-+.+.++.|.+.. .+.+|.. .+..|.+++++.+++++.| +++..+.|-||=..-+-|
T Consensus 9 ~~A~g~~~~~~~i~G~~---~~~i~~~------------~~~~~~~~~~~~~~l~~~i~~~~~~~~vlil~Dl~ggsp~ 72 (116)
T PF03610_consen 9 SLAEGLLESAEMILGED---QDNIEAV------------DLYPDESIEDFEEKLEEAIEELDEGDGVLILTDLGGGSPF 72 (116)
T ss_dssp THHHHHHHHHHHHHTST---CSSEEEE------------EETTTSCHHHHHHHHHHHHHHCCTTSEEEEEESSTTSHHH
T ss_pred HHHHHHHHHHHHHcCCC---cccEEEE------------ECcCCCCHHHHHHHHHHHHHhccCCCcEEEEeeCCCCccc
Confidence 34778889999988752 3455555 1234577998888888888 778999998886655443
No 10
>PF05620 DUF788: Protein of unknown function (DUF788); InterPro: IPR008506 This family consists of several eukaryotic proteins of unknown function.
Probab=27.85 E-value=75 Score=30.14 Aligned_cols=29 Identities=17% Similarity=0.408 Sum_probs=24.8
Q ss_pred hhhhccCCCCccccCCceeeccccccCCC
Q 048777 51 TKFFSKTENPTLEDGNSILKSGEVFRSAP 79 (547)
Q Consensus 51 t~~~t~~~NaTf~~d~svl~TGEd~~~~~ 79 (547)
-.++...+.++|..++.++..|+|++.+.
T Consensus 62 ~~~l~~~~rp~~~~~g~Lv~~G~DL~~~G 90 (170)
T PF05620_consen 62 YYFLEKMARPKYDETGELVDAGEDLNQPG 90 (170)
T ss_pred HHHHHHhCCCCcCCCCCeecCcccccCCc
Confidence 44667789999999999999999998655
No 11
>PF10917 DUF2708: Protein of unknown function (DUF2708); InterPro: IPR024415 This entry represents fungus-induced proteins which may have role in hypoxia response[].
Probab=27.27 E-value=24 Score=27.95 Aligned_cols=15 Identities=40% Similarity=0.915 Sum_probs=11.9
Q ss_pred HHHHHHHHHHhhhee
Q 048777 20 FSVFVFSVLIFTVIA 34 (547)
Q Consensus 20 fs~fV~~vl~fTviA 34 (547)
+|+|||++|+++-..
T Consensus 4 YsvfvFaiLaissvs 18 (43)
T PF10917_consen 4 YSVFVFAILAISSVS 18 (43)
T ss_pred eeehHHHHhhhhccc
Confidence 689999999887554
No 12
>PF14642 FAM47: FAM47 family
Probab=26.46 E-value=45 Score=34.67 Aligned_cols=29 Identities=41% Similarity=0.660 Sum_probs=23.8
Q ss_pred ccCCCCCCCCChHHHHHHhhhhcCCCcEEE
Q 048777 430 KLWPNLDSDTSPGALLEKLEEVVHPWTNLY 459 (547)
Q Consensus 430 ~l~PnLd~DTspE~i~~~i~~~i~~GR~LY 459 (547)
-+||||..|++|| |+.++-+.|.|.|.|=
T Consensus 132 AlyP~LeE~mPpd-Lll~VLevLDPerkLe 160 (258)
T PF14642_consen 132 ALYPHLEEDMPPD-LLLKVLEVLDPERKLE 160 (258)
T ss_pred ccCCCccccCCHH-HHHHHHhccCcccchh
Confidence 5999999999997 6677777778888773
No 13
>cd03002 PDI_a_MPD1_like PDI family, MPD1-like subfamily; composed of eukaryotic proteins similar to Saccharomyces cerevisiae MPD1 protein, which contains a single redox active TRX domain located at the N-terminus, and an ER retention signal at the C-terminus indicative of an ER-resident protein. MPD1 has been shown to suppress the maturation defect of carboxypeptidase Y caused by deletion of the yeast PDI1 gene. Other characterized members of this subfamily include the Aspergillus niger prpA protein and Giardia PDI-1. PrpA is non-essential to strain viability, however, its transcript level is induced by heterologous protein expression suggesting a possible role in oxidative protein folding during high protein production. Giardia PDI-1 has the ability to refold scrambled RNase and exhibits transglutaminase activity.
Probab=24.48 E-value=59 Score=26.66 Aligned_cols=34 Identities=9% Similarity=0.275 Sum_probs=26.7
Q ss_pred ccccCCChHHHHHHHHHhhhcCcceeeeeecccc
Q 048777 111 REVNCSDPRVLLAVERFNLKQFKSVLFLEYLTPV 144 (547)
Q Consensus 111 ~p~~CsDp~v~~~~~r~~~~~F~~i~f~~~g~PV 144 (547)
.-+||.+.+.-.+..+++++.+|.+.||.-|.++
T Consensus 54 ~~v~~~~~~~~~~~~~~~i~~~Pt~~~~~~~~~~ 87 (109)
T cd03002 54 AAVDCDEDKNKPLCGKYGVQGFPTLKVFRPPKKA 87 (109)
T ss_pred EEEecCccccHHHHHHcCCCcCCEEEEEeCCCcc
Confidence 4467776555567889999999999999988743
No 14
>PF10294 Methyltransf_16: Putative methyltransferase; InterPro: IPR019410 There are a number of unidentified genes that have a high probability of coding for methyltransferases. They make up approximately 0.6-1.6% of the genes in the yeast, human, mouse, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, and Escherichia coli genomes []. This entry represents putative nicotinamide N-methyltransferases involved in rDNA silencing and in lifespan determination. ; PDB: 3BZB_A.
Probab=22.95 E-value=61 Score=30.22 Aligned_cols=52 Identities=19% Similarity=0.420 Sum_probs=35.2
Q ss_pred CCceEEEecCccccccccCCCCCCCCChHHHHHHhhhhcCCCcEEEEeeCCCC---Ccchhhhhcc
Q 048777 414 EYDAIHVVRGERVKNKKLWPNLDSDTSPGALLEKLEEVVHPWTNLYIATNEPS---YNYFDTLRSE 476 (547)
Q Consensus 414 DfDavHVrRGDk~~nk~l~PnLd~DTspE~i~~~i~~~i~~GR~LYIATnE~~---~~fFdpLk~k 476 (547)
.||-|-. -|-.|+.++ .+.|++.++..+.++..+|||.-.|. ..||+.+++|
T Consensus 119 ~~D~Ila--sDv~Y~~~~---------~~~L~~tl~~ll~~~~~vl~~~~~R~~~~~~F~~~~~k~ 173 (173)
T PF10294_consen 119 SFDVILA--SDVLYDEEL---------FEPLVRTLKRLLKPNGKVLLAYKRRRKSEQEFFDRLKKH 173 (173)
T ss_dssp SBSEEEE--ES--S-GGG---------HHHHHHHHHHHBTT-TTEEEEEE-S-TGGCHHHHHH---
T ss_pred cCCEEEE--ecccchHHH---------HHHHHHHHHHHhCCCCEEEEEeCEecHHHHHHHHHhhhC
Confidence 6886544 588887655 68999999999999999999998773 4688888765
No 15
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=22.37 E-value=2.1e+02 Score=26.48 Aligned_cols=74 Identities=16% Similarity=0.174 Sum_probs=40.8
Q ss_pred HHHHHHHHHhcccCCCCceEEEecCccccccccCC--CCCCCCChHHHHHHhhhhcCCCcEEEEeeCCCCCcchhhhhc
Q 048777 399 ILLNIVAEIGGRMDYEYDAIHVVRGERVKNKKLWP--NLDSDTSPGALLEKLEEVVHPWTNLYIATNEPSYNYFDTLRS 475 (547)
Q Consensus 399 rLm~iv~~I~~rm~~DfDavHVrRGDk~~nk~l~P--nLd~DTspE~i~~~i~~~i~~GR~LYIATnE~~~~fFdpLk~ 475 (547)
.+.+-+..+..+|.+==||.=|+-|+-++--..-. ....+.-...|.+++++..+..++|||.||. .+|.-|+.
T Consensus 75 ~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~~~~~~~~~i~~~V~~~v~~~~p~~~~V~Vs~D~---~~~~ri~~ 150 (177)
T PF09580_consen 75 QLADRIANRVKKVPGVEDATVVVTDDNAYVAVDLDFNRFNTKKIKKKVEKAVKSADPRIYNVYVSTDP---DIFDRIRN 150 (177)
T ss_pred HHHHHHHHHHhcCCCceEEEEEEECCEEEEEEEecccccchhHHHHHHHHHHHHhCCCccEEEEEcCH---HHHHHHHH
Confidence 34444444445577555666667777665543322 1221122234445555555566999999974 56666553
No 16
>PF12841 YvrJ: YvrJ protein family; InterPro: IPR024419 This entry is represents a family of uncharacterised protein. The function of the Bacillus subtilis YvrJ protein is not known, but its expression is regulated by the cell envelope stress-inducible sigma factor YvrI [].
Probab=21.78 E-value=46 Score=25.48 Aligned_cols=18 Identities=39% Similarity=0.530 Sum_probs=15.5
Q ss_pred HHHhhhhHHHHHHHHHHh
Q 048777 13 RLISNLCFSVFVFSVLIF 30 (547)
Q Consensus 13 ~~i~n~cfs~fV~~vl~f 30 (547)
++|||+.|..+|..-|++
T Consensus 1 ~~I~n~GFPi~va~yLL~ 18 (38)
T PF12841_consen 1 QLISNVGFPIAVAIYLLV 18 (38)
T ss_pred CchhhcCcHHHHHHHHHH
Confidence 369999999999988875
No 17
>PF02602 HEM4: Uroporphyrinogen-III synthase HemD; InterPro: IPR003754 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents uroporphyrinogen III synthase (4.2.1.75 from EC) which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the inversion of the final pyrrole unit (ring D) of the linear tetrapyrrole molecule, linking it to the first pyrrole unit (ring A), thereby generating a large macrocyclic structure called uroporphyrinogen III []. The enzyme folds into two alpha/beta domains connected by a beta-ladder, the active site being located between the two domains []. Congenital erythropoietic porphyria (CEP) is an autosomal recessive inborn error of metabolism that results from the markedly deficient activity of uroporphyrinogen III synthase []. ; GO: 0004852 uroporphyrinogen-III synthase activity, 0033014 tetrapyrrole biosynthetic process; PDB: 1WD7_B 1WCX_A 1WCW_A 3D8R_A 3D8T_B 3D8S_A 3D8N_A 3RE1_A 3MW8_A 3P9Z_A ....
Probab=21.28 E-value=75 Score=29.69 Aligned_cols=49 Identities=20% Similarity=0.148 Sum_probs=42.0
Q ss_pred CChHHHHHHhhhhcCCCcEEEEeeCCCCCcchhhhhcc-eeEeeccchhH
Q 048777 439 TSPGALLEKLEEVVHPWTNLYIATNEPSYNYFDTLRSE-YKVHLLDDYRD 487 (547)
Q Consensus 439 TspE~i~~~i~~~i~~GR~LYIATnE~~~~fFdpLk~k-Y~vhfLdDFk~ 487 (547)
-+.|.|++.+++.+.++|.||+.++.....+-+.|+++ ++|..+.=|+.
T Consensus 102 ~~s~~L~~~l~~~~~~~~vl~~~g~~~~~~l~~~L~~~g~~v~~~~vY~~ 151 (231)
T PF02602_consen 102 GSSEGLAELLKEQLRGKRVLILRGEGGRPDLPEKLREAGIEVTEVIVYET 151 (231)
T ss_dssp SSHHHHHGGHHHCCTTEEEEEEESSSSCHHHHHHHHHTTEEEEEEECEEE
T ss_pred CCHHHHHHHHHhhCCCCeEEEEcCCCccHHHHHHHHHCCCeEEEEEEeec
Confidence 46899999999988899999999999999999999544 57877777776
No 18
>cd03007 PDI_a_ERp29_N PDIa family, endoplasmic reticulum protein 29 (ERp29) subfamily; ERp29 is a ubiquitous ER-resident protein expressed in high levels in secretory cells. It forms homodimers and higher oligomers in vitro and in vivo. It contains a redox inactive TRX-like domain at the N-terminus, which is homologous to the redox active TRX (a) domains of PDI, and a C-terminal helical domain similar to the C-terminal domain of P5. The expression profile of ERp29 suggests a role in secretory protein production distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase.
Probab=21.27 E-value=79 Score=28.81 Aligned_cols=33 Identities=18% Similarity=0.219 Sum_probs=27.6
Q ss_pred CCccccCCC---hHHHHHHHHHhhh--cCcceeeeeec
Q 048777 109 ELREVNCSD---PRVLLAVERFNLK--QFKSVLFLEYL 141 (547)
Q Consensus 109 ~~~p~~CsD---p~v~~~~~r~~~~--~F~~i~f~~~g 141 (547)
..+-|||.| .+=-.+.+|++|+ .||-|.||+=|
T Consensus 53 ~lakVd~~d~~~~~~~~L~~~y~I~~~gyPTl~lF~~g 90 (116)
T cd03007 53 LVAEVGIKDYGEKLNMELGERYKLDKESYPVIYLFHGG 90 (116)
T ss_pred EEEEEecccccchhhHHHHHHhCCCcCCCCEEEEEeCC
Confidence 567888976 5556799999999 99999999966
No 19
>cd02992 PDI_a_QSOX PDIa family, Quiescin-sulfhydryl oxidase (QSOX) subfamily; QSOX is a eukaryotic protein containing an N-terminal redox active TRX domain, similar to that of PDI, and a small C-terminal flavin adenine dinucleotide (FAD)-binding domain homologous to the yeast ERV1p protein. QSOX oxidizes thiol groups to disulfides like PDI, however, unlike PDI, this oxidation is accompanied by the reduction of oxygen to hydrogen peroxide. QSOX is localized in high concentrations in cells with heavy secretory load and prefers peptides and proteins as substrates, not monothiols like glutathione. Inside the cell, QSOX is found in the endoplasmic reticulum and Golgi. The flow of reducing equivalents in a QSOX-catalyzed reaction goes from the dithiol substrate - dithiol of the QSOX TRX domain - dithiols of the QSOX ERV1p domain - FAD - oxygen.
Probab=21.23 E-value=62 Score=28.05 Aligned_cols=34 Identities=12% Similarity=0.373 Sum_probs=27.6
Q ss_pred ccccCCChHHHHHHHHHhhhcCcceeeeeecccc
Q 048777 111 REVNCSDPRVLLAVERFNLKQFKSVLFLEYLTPV 144 (547)
Q Consensus 111 ~p~~CsDp~v~~~~~r~~~~~F~~i~f~~~g~PV 144 (547)
+-+||+......+..++.++.+|.+.||+-|.+.
T Consensus 58 ~~vd~~~~~~~~~~~~~~i~~~Pt~~lf~~~~~~ 91 (114)
T cd02992 58 AAVDCADEENVALCRDFGVTGYPTLRYFPPFSKE 91 (114)
T ss_pred EEEeccchhhHHHHHhCCCCCCCEEEEECCCCcc
Confidence 5678876556677889999999999999998843
No 20
>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.
Probab=21.21 E-value=1.2e+02 Score=32.70 Aligned_cols=14 Identities=0% Similarity=0.238 Sum_probs=10.0
Q ss_pred hHHHHHHhhhhcCC
Q 048777 441 PGALLEKLEEVVHP 454 (547)
Q Consensus 441 pE~i~~~i~~~i~~ 454 (547)
-.++++.+++.++.
T Consensus 223 SaeVid~fr~~FPd 236 (321)
T PF05830_consen 223 SAEVIDQFRKKFPD 236 (321)
T ss_dssp -HHHHHHHHHHSTT
T ss_pred cHHHHHHHHHHCCC
Confidence 45778888888873
No 21
>cd06592 GH31_glucosidase_KIAA1161 KIAA1161 is an uncharacterized Homo sapiens protein with a glycosyl hydrolase family 31 (GH31) domain that is homologous to the Escherichia coli YihQ glucosidase. Orthologs of KIA1161 are found in eukaryotes and prokaryotes. In bacteria, YihQ (along with YihO) is important for bacterial O-antigen capsule assembly and translocation. Enzymes of the GH31 family possess a wide range of different hydrolytic activities including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein.
Probab=20.86 E-value=1.6e+02 Score=30.01 Aligned_cols=48 Identities=19% Similarity=0.378 Sum_probs=39.2
Q ss_pred hhHHHHHHHHHHhcccCCCCceEEEe------cCccccccccCCCCCCCCChHHHHHHhhh
Q 048777 396 KSKILLNIVAEIGGRMDYEYDAIHVV------RGERVKNKKLWPNLDSDTSPGALLEKLEE 450 (547)
Q Consensus 396 kskrLm~iv~~I~~rm~~DfDavHVr------RGDk~~nk~l~PnLd~DTspE~i~~~i~~ 450 (547)
....|+++|+++.+ .+--+|.||+- .||+.-+++.||+ |.++++.|++
T Consensus 28 s~~~v~~~~~~~~~-~~iP~d~i~iD~~w~~~~g~f~~d~~~FPd------p~~mi~~l~~ 81 (303)
T cd06592 28 NQETVLNYAQEIID-NGFPNGQIEIDDNWETCYGDFDFDPTKFPD------PKGMIDQLHD 81 (303)
T ss_pred CHHHHHHHHHHHHH-cCCCCCeEEeCCCccccCCccccChhhCCC------HHHHHHHHHH
Confidence 45678999999888 46678999985 6889889999994 7888888886
No 22
>PF00085 Thioredoxin: Thioredoxin; InterPro: IPR013766 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of two cysteine thiol groups to a disulphide, accompanied by the transfer of two electrons and two protons. The net result is the covalent interconversion of a disulphide and a dithiol. In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses the reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide; reduced thioredoxin then directly reduces the disulphide in the substrate protein []. Thioredoxin is present in prokaryotes and eukaryotes and the sequence around the redox-active disulphide bond is well conserved. All thioredoxins contain a cis-proline located in a loop preceding beta-strand 4, which makes contact with the active site cysteines, and is important for stability and function []. Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase []. Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins. A number of eukaryotic proteins contain domains evolutionary related to thioredoxin, most of them are protein disulphide isomerases (PDI). PDI (5.3.4.1 from EC) [, , ] is an endoplasmic reticulum multi-functional enzyme that catalyses the formation and rearrangement of disulphide bonds during protein folding []. All PDI contains two or three (ERp72) copies of the thioredoxin domain, each of which contributes to disulphide isomerase activity, but which are functionally non-equivalent []. Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity []. The various forms of PDI which are currently known are: PDI major isozyme; a multifunctional protein that also function as the beta subunit of prolyl 4-hydroxylase (1.14.11.2 from EC), as a component of oligosaccharyl transferase (2.4.1.119 from EC), as thyroxine deiodinase (3.8.1.4 from EC), as glutathione-insulin transhydrogenase (1.8.4.2 from EC) and as a thyroid hormone-binding protein ERp60 (ER-60; 58 Kd microsomal protein). ERp60 was originally thought to be a phosphoinositide-specific phospholipase C isozyme and later to be a protease. ERp72. ERp5. Bacterial proteins that act as thiol:disulphide interchange proteins that allows disulphide bond formation in some periplasmic proteins also contain a thioredoxin domain. These proteins include: Escherichia coli DsbA (or PrfA) and its orthologs in Vibrio cholerae (TtcpG) and Haemophilus influenzae (Por). E. coli DsbC (or XpRA) and its orthologues in Erwinia chrysanthemi and H. influenzae. E. coli DsbD (or DipZ) and its H. influenzae orthologue. E. coli DsbE (or CcmG) and orthologues in H. influenzae. Rhodobacter capsulatus (Rhodopseudomonas capsulata) (HelX), Rhiziobiacae (CycY and TlpA). This entry represents the thioredoxin domain.; GO: 0045454 cell redox homeostasis; PDB: 3ED3_B 1EP7_A 1EP8_B 1TOF_A 2OE3_B 2OE1_B 2OE0_B 1V98_A 3H79_A 3CXG_A ....
Probab=20.76 E-value=58 Score=25.87 Aligned_cols=35 Identities=14% Similarity=0.447 Sum_probs=28.0
Q ss_pred CCccccCCChHHHHHHHHHhhhcCcceeeeeeccccC
Q 048777 109 ELREVNCSDPRVLLAVERFNLKQFKSVLFLEYLTPVN 145 (547)
Q Consensus 109 ~~~p~~CsDp~v~~~~~r~~~~~F~~i~f~~~g~PV~ 145 (547)
.-.-|||.+- ..+..+++++.+|.+.||+-|..+.
T Consensus 51 ~~~~vd~~~~--~~l~~~~~v~~~Pt~~~~~~g~~~~ 85 (103)
T PF00085_consen 51 KFAKVDCDEN--KELCKKYGVKSVPTIIFFKNGKEVK 85 (103)
T ss_dssp EEEEEETTTS--HHHHHHTTCSSSSEEEEEETTEEEE
T ss_pred ccchhhhhcc--chhhhccCCCCCCEEEEEECCcEEE
Confidence 4466788733 4577999999999999999998773
No 23
>PF06245 DUF1015: Protein of unknown function (DUF1015); InterPro: IPR008323 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.42 E-value=1e+02 Score=33.11 Aligned_cols=54 Identities=22% Similarity=0.365 Sum_probs=39.4
Q ss_pred hHHHHHHHHHHhcccCCCCce-----EEEecCccccccccCCCCCCCCChHHHHHHhhhhcCCCcEEEEeeCCC
Q 048777 397 SKILLNIVAEIGGRMDYEYDA-----IHVVRGERVKNKKLWPNLDSDTSPGALLEKLEEVVHPWTNLYIATNEP 465 (547)
Q Consensus 397 skrLm~iv~~I~~rm~~DfDa-----vHVrRGDk~~nk~l~PnLd~DTspE~i~~~i~~~i~~GR~LYIATnE~ 465 (547)
...|..+++++.......||. +|.+ +|. .+.++.+++|++.+...+.|||| |+.
T Consensus 152 ~~~i~~~i~~~~~~~~p~~~~~~~~G~~H~---------lW~-----v~d~~~i~~i~~~~~~~~~lyIA-DGH 210 (416)
T PF06245_consen 152 DNEIDELIDEAKEKGEPLYDFTDMDGVRHR---------LWR-----VTDPAVIAKIQEAFEADKPLYIA-DGH 210 (416)
T ss_pred chHHHHHHHHHHhcCCCeEEEEcCCCCEEE---------EEE-----eCCHHHHHHHHHHHhhcCceEEe-cCc
Confidence 577888888888444444443 4443 564 45678999999999889999999 664
Done!