Query 024352
Match_columns 269
No_of_seqs 104 out of 121
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 03:55:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024352.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024352hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05212 DUF707: Protein of un 100.0 2.1E-94 4.6E-99 662.1 16.5 194 68-268 3-196 (294)
2 PF14538 Raptor_N: Raptor N-te 71.5 2 4.2E-05 37.0 1.1 47 137-195 90-144 (154)
3 PF12996 DUF3880: DUF based on 69.1 4.6 0.0001 30.5 2.6 26 180-215 13-38 (79)
4 PRK05325 hypothetical protein; 45.3 14 0.0003 36.8 2.0 28 123-152 296-325 (401)
5 PF04285 DUF444: Protein of un 41.4 18 0.00038 36.3 2.1 28 124-153 321-350 (421)
6 PHA03165 hypothetical protein; 38.2 25 0.00054 26.3 1.9 32 30-70 23-54 (57)
7 PF07862 Nif11: Nitrogen fixat 37.5 27 0.00058 24.0 1.9 20 202-221 28-47 (49)
8 TIGR02877 spore_yhbH sporulati 37.5 24 0.00051 35.0 2.3 28 124-153 277-306 (371)
9 PRK13863 type IV secretion sys 37.4 39 0.00084 34.4 3.7 82 109-217 83-178 (446)
10 PF12621 DUF3779: Phosphate me 36.3 53 0.0012 26.0 3.7 53 174-231 33-87 (95)
11 PF15018 InaF-motif: TRP-inter 31.6 17 0.00038 25.4 0.2 8 188-195 28-35 (38)
12 cd08910 START_STARD2-like Lipi 31.4 67 0.0014 28.2 3.9 41 200-248 4-44 (207)
13 KOG1517 Guanine nucleotide bin 30.9 23 0.00051 39.9 1.1 48 137-196 186-241 (1387)
14 PF13778 DUF4174: Domain of un 30.1 33 0.00072 27.9 1.7 39 122-160 63-103 (118)
15 PF11057 Cortexin: Cortexin of 26.5 70 0.0015 25.9 2.8 49 1-49 1-52 (81)
16 PRK05637 anthranilate synthase 26.0 71 0.0015 28.3 3.1 49 135-184 136-190 (208)
17 PF07172 GRP: Glycine rich pro 25.8 79 0.0017 25.5 3.1 13 26-38 4-16 (95)
18 TIGR03798 ocin_TIGR03798 bacte 25.8 53 0.0011 24.0 1.9 23 202-224 26-48 (64)
19 PF06679 DUF1180: Protein of u 25.8 1.1E+02 0.0024 27.1 4.3 24 24-47 95-118 (163)
20 PF09665 RE_Alw26IDE: Type II 24.7 39 0.00084 34.9 1.4 28 175-203 362-393 (511)
21 TIGR02876 spore_yqfD sporulati 23.9 2.4E+02 0.0051 27.6 6.5 60 190-250 104-175 (382)
22 PF12849 PBP_like_2: PBP super 21.9 53 0.0011 28.7 1.5 25 144-168 121-146 (281)
23 PF07976 Phe_hydrox_dim: Pheno 21.5 2E+02 0.0043 24.7 4.9 74 75-158 33-125 (169)
24 CHL00123 rps6 ribosomal protei 21.2 59 0.0013 25.8 1.5 56 183-239 5-62 (97)
25 PF07745 Glyco_hydro_53: Glyco 21.2 52 0.0011 31.8 1.4 41 88-144 39-80 (332)
26 KOG2431 1, 2-alpha-mannosidase 20.1 1E+02 0.0022 32.0 3.3 93 28-132 13-106 (546)
No 1
>PF05212 DUF707: Protein of unknown function (DUF707); InterPro: IPR007877 This family consists of uncharacterised proteins from Arabidopsis thaliana.
Probab=100.00 E-value=2.1e-94 Score=662.14 Aligned_cols=194 Identities=59% Similarity=1.092 Sum_probs=187.7
Q ss_pred cccCCCCcCCCCCCceecCCCcceecCCCCCCCCcccCCCCCccEEEEeecccccccHHHHHhhhCCCCeEEEEEeeeCc
Q 024352 68 SRFSSGRLKSLPRGIVQARSDLELRPLWSTSSSRKKFGVYSNRNLLAIPAGIKQKDNVDAIVRKFLPENFTVILFHYDGD 147 (269)
Q Consensus 68 ~~~~p~g~e~LP~GIV~~~Sdl~lr~Lwg~p~~~~~~~~~~~k~LlamaVGikQK~~Vd~~V~KF~~~nF~vmLFHYDG~ 147 (269)
.+++|+|+|+||+|||+++||||||||||+|+++. +.++|||||||||||||++||++|+|| ++||+||||||||+
T Consensus 3 ~~~~p~g~e~Lp~giv~~~sd~~~r~lw~~p~~~~---~~~~k~Lla~~VG~kqk~~vd~~v~Kf-~~nF~i~LfhYDg~ 78 (294)
T PF05212_consen 3 VPCNPRGAERLPPGIVVRESDLELRPLWGNPSEDL---PKKPKYLLAMTVGIKQKDNVDAIVKKF-SDNFDIMLFHYDGR 78 (294)
T ss_pred cCCCCCccccCCCCccccCCCceeeecCCCccccc---cCCCceEEEEEecHHHHhhhhHHHhhh-ccCceEEEEEecCC
Confidence 46899999999999999999999999999999887 358899999999999999999999999 99999999999999
Q ss_pred cccccccccCCceEEEEEecccceeeecccCCCccccccceEEEeeccccCCCCChhHHHHHHHHhCCccccCccCCCCC
Q 024352 148 VNAWRGLDWSNKAIHIAAQNQTKWWFAKRFLHPDVVSNYDYIFLWDEDLGVENFDPRRYLEIVKSEGFEISQPALDPNST 227 (269)
Q Consensus 148 vd~W~dleWS~~aIHVsa~~QTKWWfAKRFLHPdiVa~YdYIFlWDEDLgVe~F~~~rYl~Ivk~~gLEISQPaLd~~~s 227 (269)
||+|+|||||++||||+++|||||||||||||||||++||||||||||||||||||+||++|||+|||||||||||++++
T Consensus 79 vd~w~~~~ws~~aiHv~~~kqtKww~akrfLHPdiv~~YdYiflwDeDL~vd~f~~~ry~~Ivk~~gLeISQPALd~~~~ 158 (294)
T PF05212_consen 79 VDEWDDFEWSDRAIHVSARKQTKWWFAKRFLHPDIVAPYDYIFLWDEDLGVDHFDINRYFEIVKKEGLEISQPALDPDSS 158 (294)
T ss_pred cCchhhcccccceEEEEeccceEEeehhhhcChhhhccceeEEecCCccCcCcCCHHHHHHHHHHhCCcccCcccCCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeeeeeeccCcceeeeEeeccCCccCCCCCCCCCcccee
Q 024352 228 EIHHKFTIRARTKKFHRRVYDLRGSVKCTNISEGPPCTGYV 268 (269)
Q Consensus 228 ~ihh~iT~R~~~~~vHrr~~~~~g~~~C~~~s~~PPC~g~V 268 (269)
++||+||+|+++.+||| ++++++.|.+++++|||||||
T Consensus 159 ~~~~~iT~R~~~~~vhr---~~~~~~~~~~~~~~ppct~fV 196 (294)
T PF05212_consen 159 EIHHPITKRRPDSEVHR---KTRGGPRCCDDSTGPPCTGFV 196 (294)
T ss_pred eeeeeEEeecCCceeEe---ccCCCCCcCCCCCCCCcceEE
Confidence 99999999999999999 456788888899999999998
No 2
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=71.50 E-value=2 Score=37.02 Aligned_cols=47 Identities=32% Similarity=0.613 Sum_probs=29.6
Q ss_pred eEEEEEeeeCccccccccccCCceEEEEEecccceeeecccCCCccccccc--------eEEEeecc
Q 024352 137 FTVILFHYDGDVNAWRGLDWSNKAIHIAAQNQTKWWFAKRFLHPDVVSNYD--------YIFLWDED 195 (269)
Q Consensus 137 F~vmLFHYDG~vd~W~dleWS~~aIHVsa~~QTKWWfAKRFLHPdiVa~Yd--------YIFlWDED 195 (269)
-.=+||||-|. .++. -..+..=|-|.|.+-.-.-+.-|| -||+||++
T Consensus 90 ~~RvLFHYnGh-----GvP~-------Pt~~GeIw~f~~~~tqyip~si~dL~~~lg~Psi~V~DC~ 144 (154)
T PF14538_consen 90 DERVLFHYNGH-----GVPR-------PTENGEIWVFNKNYTQYIPLSIYDLQSWLGSPSIYVFDCS 144 (154)
T ss_pred CceEEEEECCC-----CCCC-------CCCCCeEEEEcCCCCcceEEEHHHHHHhcCCCEEEEEECC
Confidence 37899999993 2222 122334477777775555555555 48999987
No 3
>PF12996 DUF3880: DUF based on E. rectale Gene description (DUF3880); InterPro: IPR024542 This entry represents proteins of unknown function. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=69.13 E-value=4.6 Score=30.50 Aligned_cols=26 Identities=31% Similarity=0.685 Sum_probs=19.6
Q ss_pred CccccccceEEEeeccccCCCCChhHHHHHHHHhCC
Q 024352 180 PDVVSNYDYIFLWDEDLGVENFDPRRYLEIVKSEGF 215 (269)
Q Consensus 180 PdiVa~YdYIFlWDEDLgVe~F~~~rYl~Ivk~~gL 215 (269)
..+...|||||+||++ .++-.|+.|.
T Consensus 13 ~~i~~~~~~iFt~D~~----------~~~~~~~~G~ 38 (79)
T PF12996_consen 13 YSIANSYDYIFTFDRS----------FVEEYRNLGA 38 (79)
T ss_pred hhhCCCCCEEEEECHH----------HHHHHHHcCC
Confidence 3677899999999974 4566667773
No 4
>PRK05325 hypothetical protein; Provisional
Probab=45.32 E-value=14 Score=36.80 Aligned_cols=28 Identities=21% Similarity=0.621 Sum_probs=24.0
Q ss_pred ccHHHHHhh-hCCCCeEEEEEee-eCcccccc
Q 024352 123 DNVDAIVRK-FLPENFTVILFHY-DGDVNAWR 152 (269)
Q Consensus 123 ~~Vd~~V~K-F~~~nF~vmLFHY-DG~vd~W~ 152 (269)
+.++.||++ |+++++.|..||. || |.|.
T Consensus 296 ~l~~eIi~~rYpp~~wNIY~f~aSDG--DNw~ 325 (401)
T PRK05325 296 KLALEIIEERYPPAEWNIYAFQASDG--DNWS 325 (401)
T ss_pred HHHHHHHHhhCCHhHCeeEEEEcccC--CCcC
Confidence 346788885 9999999999997 89 8887
No 5
>PF04285 DUF444: Protein of unknown function (DUF444); InterPro: IPR006698 This entry is represented by Thermus phage phiYS40, Orf56. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches [].
Probab=41.41 E-value=18 Score=36.26 Aligned_cols=28 Identities=25% Similarity=0.730 Sum_probs=23.8
Q ss_pred cHHHHHhh-hCCCCeEEEEEee-eCccccccc
Q 024352 124 NVDAIVRK-FLPENFTVILFHY-DGDVNAWRG 153 (269)
Q Consensus 124 ~Vd~~V~K-F~~~nF~vmLFHY-DG~vd~W~d 153 (269)
.++.||++ |+++++.|..||. || |.|.+
T Consensus 321 l~~~ii~erypp~~wNiY~~~~SDG--DN~~~ 350 (421)
T PF04285_consen 321 LALEIIEERYPPSDWNIYVFHASDG--DNWSS 350 (421)
T ss_pred HHHHHHHhhCChhhceeeeEEcccC--ccccC
Confidence 36788886 9999999999997 89 88864
No 6
>PHA03165 hypothetical protein; Provisional
Probab=38.17 E-value=25 Score=26.29 Aligned_cols=32 Identities=25% Similarity=0.491 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHhhhcchhhhhhhhhhhccCCCcccccccc
Q 024352 30 FMAIMCTVMLFVVYRTTYYQYKQTEMEAKFSPFDISKGSRF 70 (269)
Q Consensus 30 ~~~~~c~~~~f~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~ 70 (269)
...+++.+++|++|.++- ...+||++.-.++|
T Consensus 23 yilvvafvlaflvysdfl---------snlspfgeilsspc 54 (57)
T PHA03165 23 YILVVAFVLAFLVYSDFL---------SNLSPFGEILSSPC 54 (57)
T ss_pred ehhHHHHHHHHHHHHHHH---------hccCchhhhhcCcc
Confidence 366788889999999887 66788887665554
No 7
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=37.53 E-value=27 Score=24.05 Aligned_cols=20 Identities=10% Similarity=0.587 Sum_probs=17.8
Q ss_pred ChhHHHHHHHHhCCccccCc
Q 024352 202 DPRRYLEIVKSEGFEISQPA 221 (269)
Q Consensus 202 ~~~rYl~Ivk~~gLEISQPa 221 (269)
+++..++|++++|.++|.--
T Consensus 28 ~~~e~~~lA~~~Gy~ft~~e 47 (49)
T PF07862_consen 28 NPEEVVALAREAGYDFTEEE 47 (49)
T ss_pred CHHHHHHHHHHcCCCCCHHH
Confidence 89999999999999998643
No 8
>TIGR02877 spore_yhbH sporulation protein YhbH. This protein family, typified by YhbH in Bacillus subtilis, is found in nearly every endospore-forming bacterium and in no other genome (but note that the trusted cutoff score is set high to exclude a single high-scoring sequence from Nitrosococcus oceani ATCC 19707, which is classified in the Gammaproteobacteria). The gene in Bacillus subtilis was shown to be in the regulon of the sporulation sigma factor, sigma-E, and its mutation was shown to create a sporulation defect.
Probab=37.48 E-value=24 Score=35.03 Aligned_cols=28 Identities=21% Similarity=0.643 Sum_probs=23.2
Q ss_pred cHHHHHh-hhCCCCeEEEEEee-eCccccccc
Q 024352 124 NVDAIVR-KFLPENFTVILFHY-DGDVNAWRG 153 (269)
Q Consensus 124 ~Vd~~V~-KF~~~nF~vmLFHY-DG~vd~W~d 153 (269)
..+.||+ +|+++++.|..||. || |.|.+
T Consensus 277 l~~eII~~rYpp~~wNIY~f~aSDG--DNw~~ 306 (371)
T TIGR02877 277 KALEIIDERYNPARYNIYAFHFSDG--DNLTS 306 (371)
T ss_pred HHHHHHHhhCChhhCeeEEEEcccC--CCccC
Confidence 3566777 69999999999997 89 88873
No 9
>PRK13863 type IV secretion system T-DNA border endonuclease VirD2; Provisional
Probab=37.38 E-value=39 Score=34.40 Aligned_cols=82 Identities=20% Similarity=0.341 Sum_probs=51.3
Q ss_pred CccEEEEeecccccccHHH----HHhhhCCC----Ce-EEEEEeeeCccccccccccCCceEEEEEe---cccceeeecc
Q 024352 109 NRNLLAIPAGIKQKDNVDA----IVRKFLPE----NF-TVILFHYDGDVNAWRGLDWSNKAIHIAAQ---NQTKWWFAKR 176 (269)
Q Consensus 109 ~k~LlamaVGikQK~~Vd~----~V~KF~~~----nF-~vmLFHYDG~vd~W~dleWS~~aIHVsa~---~QTKWWfAKR 176 (269)
..-+|.|+.|-.+.+..++ +-++|++. +| -||-||-|-. .--+||++. +--|=|
T Consensus 83 ~NIVLSMPaGTd~eAVrdAARefA~E~FgsG~~G~~~dYV~AlH~D~d----------HPHVHLvVnrRd~~G~~~---- 148 (446)
T PRK13863 83 THIIVSFPAGTSQVAAYAASREWAAEMFGSGAGGGRYNYLTAFHIDRD----------HPHLHVVVNRRELLGHGW---- 148 (446)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHhCCCCCCCceeEEEEEecCCC----------CCeEEEEEEeecCCCCce----
Confidence 3468999999777665552 33566542 33 4788998761 456899988 555533
Q ss_pred cCCCccccccceEEEe--eccccCCCCChhHHHHHHHHhCCcc
Q 024352 177 FLHPDVVSNYDYIFLW--DEDLGVENFDPRRYLEIVKSEGFEI 217 (269)
Q Consensus 177 FLHPdiVa~YdYIFlW--DEDLgVe~F~~~rYl~Ivk~~gLEI 217 (269)
++|+ ..|+.++++ -+.|-++.+++|++.
T Consensus 149 ------------lri~~rk~dlNld~~-Re~FAE~LRe~GIea 178 (446)
T PRK13863 149 ------------LKISRRHPQLNYDAL-RIKMAEISLRHGIVL 178 (446)
T ss_pred ------------eeecCCCccccHHHH-HHHHHHHHHhcCcee
Confidence 2333 233333222 257999999999985
No 10
>PF12621 DUF3779: Phosphate metabolism protein ; InterPro: IPR022257 This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with PF02714 from PFAM. There are two completely conserved residues (W and D) that may be functionally important. This family is likely to be involved in phosphate metabolism however there is little accompanying literature to confirm this.
Probab=36.34 E-value=53 Score=26.00 Aligned_cols=53 Identities=26% Similarity=0.453 Sum_probs=42.2
Q ss_pred ecccCCCccccccceEEEeeccccCCCCChhHHHHHHHHhCCccccCc--cCCCCCceee
Q 024352 174 AKRFLHPDVVSNYDYIFLWDEDLGVENFDPRRYLEIVKSEGFEISQPA--LDPNSTEIHH 231 (269)
Q Consensus 174 AKRFLHPdiVa~YdYIFlWDEDLgVe~F~~~rYl~Ivk~~gLEISQPa--Ld~~~s~ihh 231 (269)
..-|+||.+-++--.|-|=-.++|| .+.=++-.++.|++||.-+ ||. +|.+.+
T Consensus 33 ~~ay~~Pa~~~~~P~lWIP~D~~Gv----S~~ei~~~~~~~v~~Sd~gA~lde-kgkv~~ 87 (95)
T PF12621_consen 33 KHAYLHPAVSAPQPILWIPRDPLGV----SRQEIEETRKVGVPISDEGATLDE-KGKVVW 87 (95)
T ss_pred HhccCCHhHcCCCCeEEeecCCCCC----CHHHHHHhhcCCeEEECCCeEEcc-CCCEEE
Confidence 4579999999998888888889999 4567788889999999876 566 455555
No 11
>PF15018 InaF-motif: TRP-interacting helix
Probab=31.61 E-value=17 Score=25.43 Aligned_cols=8 Identities=75% Similarity=1.825 Sum_probs=5.2
Q ss_pred eEEEeecc
Q 024352 188 YIFLWDED 195 (269)
Q Consensus 188 YIFlWDED 195 (269)
|+|+||.+
T Consensus 28 Y~f~W~p~ 35 (38)
T PF15018_consen 28 YIFFWDPD 35 (38)
T ss_pred HheeeCCC
Confidence 66777654
No 12
>cd08910 START_STARD2-like Lipid-binding START domain of mammalian STARD2 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD2 (also known as phosphatidylcholine transfer protein/PC-TP) and related proteins. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD2 is a cytosolic phosphatidycholine (PtdCho) transfer protein, which traffics PtdCho, the most common class of phospholipids in eukaryotes, between membranes. It represents a minimal START domain structure. STARD2 plays roles in hepatic cholesterol metabolism, in the development of atherosclerosis, and may have a mitochondrial function.
Probab=31.45 E-value=67 Score=28.19 Aligned_cols=41 Identities=22% Similarity=0.370 Sum_probs=33.3
Q ss_pred CCChhHHHHHHHHhCCccccCccCCCCCceeeeeeeeccCcceeeeEee
Q 024352 200 NFDPRRYLEIVKSEGFEISQPALDPNSTEIHHKFTIRARTKKFHRRVYD 248 (269)
Q Consensus 200 ~F~~~rYl~Ivk~~gLEISQPaLd~~~s~ihh~iT~R~~~~~vHrr~~~ 248 (269)
.|.-+.++... .|++||.+|... |++..-+++.+|++|-.+
T Consensus 4 ~~~~~~~~~~~----~~~~~~~~~~~~----W~l~~~~~~i~Vy~r~~~ 44 (207)
T cd08910 4 TFSEEQFREAC----AELQQPALDGAA----WELLVESSGISIYRLLDE 44 (207)
T ss_pred ccCHHHHHHHH----HHhcCCCCCCCC----eEEEEecCCeEEEEeccC
Confidence 46777777776 689999999864 899999999999998544
No 13
>KOG1517 consensus Guanine nucleotide binding protein MIP1 [Cell cycle control, cell division, chromosome partitioning]
Probab=30.86 E-value=23 Score=39.92 Aligned_cols=48 Identities=29% Similarity=0.532 Sum_probs=29.4
Q ss_pred eEEEEEeeeCccccccccccCCceEEEEEecccceeeecccCCCccccccc--------eEEEeeccc
Q 024352 137 FTVILFHYDGDVNAWRGLDWSNKAIHIAAQNQTKWWFAKRFLHPDVVSNYD--------YIFLWDEDL 196 (269)
Q Consensus 137 F~vmLFHYDG~vd~W~dleWS~~aIHVsa~~QTKWWfAKRFLHPdiVa~Yd--------YIFlWDEDL 196 (269)
=.=+||||.|. -|---..|.-=|=|.|-|--===+.-|| -|++||+--
T Consensus 186 ~eRvLFHYNGH------------GVPkPT~nGEIWVFNK~fTQYIPlsi~dLqsWl~aP~IyVydcss 241 (1387)
T KOG1517|consen 186 EERVLFHYNGH------------GVPKPTANGEIWVFNKSFTQYIPLSIFDLQSWLGAPTIYVYDCSS 241 (1387)
T ss_pred CceEEEEecCC------------CCCCCCCCCcEEEEecCcceeecccHHHHHhhhcCCeEEEEeccc
Confidence 34589999992 1111133445588999985433333343 589999754
No 14
>PF13778 DUF4174: Domain of unknown function (DUF4174)
Probab=30.06 E-value=33 Score=27.85 Aligned_cols=39 Identities=23% Similarity=0.399 Sum_probs=31.3
Q ss_pred cccHHHHHhhhC--CCCeEEEEEeeeCccccccccccCCce
Q 024352 122 KDNVDAIVRKFL--PENFTVILFHYDGDVNAWRGLDWSNKA 160 (269)
Q Consensus 122 K~~Vd~~V~KF~--~~nF~vmLFHYDG~vd~W~dleWS~~a 160 (269)
...+..+-++|. .++|+++|.-.||.|-.+..-+|+-++
T Consensus 63 ~~~~~~lr~~l~~~~~~f~~vLiGKDG~vK~r~~~p~~~~~ 103 (118)
T PF13778_consen 63 PEDIQALRKRLRIPPGGFTVVLIGKDGGVKLRWPEPIDPEE 103 (118)
T ss_pred HHHHHHHHHHhCCCCCceEEEEEeCCCcEEEecCCCCCHHH
Confidence 345678888887 789999999999999888777766443
No 15
>PF11057 Cortexin: Cortexin of kidney; InterPro: IPR020066 Cortexin is a neuron-specific, 82-residue membrane protein which is found especially in vertebrate brain cortex tissue. It may mediate extracellular or intracellular signalling of cortical neurons during forebrain development. Cortexin is present at significant levels in the foetal brain, suggesting that it may be important to neurons of both the developing and adult cerebral cortex. Cortexin has a conserved single membrane-spanning region in the middle of each sequence []. In humans, there is selective expression of Cortexin 3 (CTXN3) in the kidney as well as the brain []. This entry contains Cortexins 1, 2 and 3.; GO: 0031224 intrinsic to membrane
Probab=26.50 E-value=70 Score=25.85 Aligned_cols=49 Identities=12% Similarity=0.112 Sum_probs=28.9
Q ss_pred CcchhhhhhhhhcCCCcccccceeee---hhhHHHHHHHHHHHHhhhcchhh
Q 024352 1 MKSIKTWRLLKRNSFSDGVKFGVKMK---QLQFMAIMCTVMLFVVYRTTYYQ 49 (269)
Q Consensus 1 m~s~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~c~~~~f~~~~~~~~q 49 (269)
|.|+-.+-+.-..+-.....+++... .+-|+.++|+.+++++.|.+.+-
T Consensus 1 M~s~~~~~s~~~~s~~~~~~~~~~~eqkt~faFV~~L~~fL~~liVRCfrIl 52 (81)
T PF11057_consen 1 MSSTYCLPSPLPMSGNPLSASSLDLEQKTAFAFVGLLCLFLGLLIVRCFRIL 52 (81)
T ss_pred CCCcccCCCCcccCCCCCcccccccccceeehHHHHHHHHHHHHHHHHHHHH
Confidence 34444443332222233344444332 35678999999999999999854
No 16
>PRK05637 anthranilate synthase component II; Provisional
Probab=26.03 E-value=71 Score=28.31 Aligned_cols=49 Identities=20% Similarity=0.306 Sum_probs=34.5
Q ss_pred CCeEEEEEeeeCcc---ccccccccCCc---eEEEEEecccceeeecccCCCcccc
Q 024352 135 ENFTVILFHYDGDV---NAWRGLDWSNK---AIHIAAQNQTKWWFAKRFLHPDVVS 184 (269)
Q Consensus 135 ~nF~vmLFHYDG~v---d~W~dleWS~~---aIHVsa~~QTKWWfAKRFLHPdiVa 184 (269)
+.|.|..+|-|.++ ++..-+.||+. .+-.++.+..+..|+=.| ||+++-
T Consensus 136 ~~~~V~~~H~~~v~~lp~~~~vlA~s~~~~~~v~~a~~~~~~~~~GvQf-HPE~~~ 190 (208)
T PRK05637 136 RKVPIARYHSLGCVVAPDGMESLGTCSSEIGPVIMAAETTDGKAIGLQF-HPESVL 190 (208)
T ss_pred CceEEEEechhhhhcCCCCeEEEEEecCCCCCEEEEEEECCCCEEEEEe-CCccCc
Confidence 45889999998864 34555667654 354555677888888888 998764
No 17
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=25.85 E-value=79 Score=25.49 Aligned_cols=13 Identities=8% Similarity=0.419 Sum_probs=5.2
Q ss_pred ehhhHHHHHHHHH
Q 024352 26 KQLQFMAIMCTVM 38 (269)
Q Consensus 26 ~~~~~~~~~c~~~ 38 (269)
|.|.+++|+-+++
T Consensus 4 K~~llL~l~LA~l 16 (95)
T PF07172_consen 4 KAFLLLGLLLAAL 16 (95)
T ss_pred hHHHHHHHHHHHH
Confidence 4344444433333
No 18
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=25.82 E-value=53 Score=23.98 Aligned_cols=23 Identities=35% Similarity=0.606 Sum_probs=20.5
Q ss_pred ChhHHHHHHHHhCCccccCccCC
Q 024352 202 DPRRYLEIVKSEGFEISQPALDP 224 (269)
Q Consensus 202 ~~~rYl~Ivk~~gLEISQPaLd~ 224 (269)
+++..++|++++|.+||.--|+.
T Consensus 26 ~~e~~~~lA~~~Gf~ft~~el~~ 48 (64)
T TIGR03798 26 DPEDRVAIAKEAGFEFTGEDLKE 48 (64)
T ss_pred CHHHHHHHHHHcCCCCCHHHHHH
Confidence 58999999999999999887764
No 19
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=25.80 E-value=1.1e+02 Score=27.07 Aligned_cols=24 Identities=21% Similarity=0.285 Sum_probs=16.9
Q ss_pred eeehhhHHHHHHHHHHHHhhhcch
Q 024352 24 KMKQLQFMAIMCTVMLFVVYRTTY 47 (269)
Q Consensus 24 ~~~~~~~~~~~c~~~~f~~~~~~~ 47 (269)
+.-++-++++.++++++||.+++-
T Consensus 95 ~R~~~Vl~g~s~l~i~yfvir~~R 118 (163)
T PF06679_consen 95 KRALYVLVGLSALAILYFVIRTFR 118 (163)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHh
Confidence 444455677778888888888765
No 20
>PF09665 RE_Alw26IDE: Type II restriction endonuclease (RE_Alw26IDE); InterPro: IPR014328 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
Probab=24.75 E-value=39 Score=34.92 Aligned_cols=28 Identities=32% Similarity=0.561 Sum_probs=20.9
Q ss_pred cccCCCccccccceEE--Eeecc--ccCCCCCh
Q 024352 175 KRFLHPDVVSNYDYIF--LWDED--LGVENFDP 203 (269)
Q Consensus 175 KRFLHPdiVa~YdYIF--lWDED--LgVe~F~~ 203 (269)
.-||||.. |.|+|.| +|-++ +...++.+
T Consensus 362 ~t~L~~~Y-a~y~y~Fe~~~~~~~~~~~~~i~~ 393 (511)
T PF09665_consen 362 ATFLKPEY-ANYDYTFEGLNISNHLTQYKSIYK 393 (511)
T ss_pred HHHhchhh-hhccceeccccccccccccccccc
Confidence 46899998 9999999 56555 55555655
No 21
>TIGR02876 spore_yqfD sporulation protein YqfD. YqfD is part of the sigma-E regulon in the sporulation program of endospore-forming Gram-positive bacteria. Mutation results in a sporulation defect in Bacillus subtilis. Members are found in all currently known endospore-forming bacteria, including the genera Bacillus, Symbiobacterium, Carboxydothermus, Clostridium, and Thermoanaerobacter.
Probab=23.93 E-value=2.4e+02 Score=27.55 Aligned_cols=60 Identities=23% Similarity=0.383 Sum_probs=48.1
Q ss_pred EEeecc-ccCCCCChhHHHHHHHHhCCc--cccCccCC---------CCCceeeeeeeeccCcceeeeEeecc
Q 024352 190 FLWDED-LGVENFDPRRYLEIVKSEGFE--ISQPALDP---------NSTEIHHKFTIRARTKKFHRRVYDLR 250 (269)
Q Consensus 190 FlWDED-LgVe~F~~~rYl~Ivk~~gLE--ISQPaLd~---------~~s~ihh~iT~R~~~~~vHrr~~~~~ 250 (269)
|+|+=| .|-++-.+++=++..++.|+. ..|..+|+ .-.+|.| +.++.+++++|=.+-++.
T Consensus 104 fIW~IeI~Gn~~~t~~~i~~~L~e~Gi~~G~~k~~id~~~ie~~l~~~~~~i~W-V~v~i~GTrl~i~v~Ek~ 175 (382)
T TIGR02876 104 FIWKIDITGVKGETPYEIRKQLKEMGIKPGVWKFSVDVYKLERKLLDRVPEIMW-AGVRVRGTTLVIKVVEKQ 175 (382)
T ss_pred eEEEEEEECCCCCCHHHHHHHHHHcCCCcCeeeCCCCHHHHHHHHHhhCCCcEE-EEEEEEeEEEEEEEEecC
Confidence 799866 466777888889999999998 66777776 3457888 889999999998877764
No 22
>PF12849 PBP_like_2: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.; PDB: 1QUL_A 1OIB_A 1A54_A 1IXH_A 1A40_A 1QUJ_A 1A55_A 1IXI_A 2ABH_A 1QUK_A ....
Probab=21.92 E-value=53 Score=28.68 Aligned_cols=25 Identities=16% Similarity=0.662 Sum_probs=18.6
Q ss_pred eeCcccccccc-ccCCceEEEEEecc
Q 024352 144 YDGDVNAWRGL-DWSNKAIHIAAQNQ 168 (269)
Q Consensus 144 YDG~vd~W~dl-eWS~~aIHVsa~~Q 168 (269)
|.|.++.|+|+ .|.++.|++..+..
T Consensus 121 ~~G~It~W~~~~~~~~~~I~~~~r~~ 146 (281)
T PF12849_consen 121 FSGEITNWSDLGGGPDRPIKVVGRSD 146 (281)
T ss_dssp HCTS--BGGGTTTCHSSB-EEEEESS
T ss_pred HhhhhhcccccccCCCCceEEEeCCC
Confidence 35789999999 89999999998764
No 23
>PF07976 Phe_hydrox_dim: Phenol hydroxylase, C-terminal dimerisation domain ; InterPro: IPR012941 Phenol hydroxylase is a homodimer which hydroxylates phenol to catechol, or similar products. The enzyme is comprised of three domains. The first two domains form the active site. The third domain, this domain, is involved in forming the dimerisation interface. The domain adopts a thioredoxin-like fold [].; PDB: 2DKH_A 2DKI_A 1PN0_A 1FOH_D.
Probab=21.54 E-value=2e+02 Score=24.71 Aligned_cols=74 Identities=19% Similarity=0.295 Sum_probs=42.5
Q ss_pred cCCCCCCceecCCCcceecCCCCCCCCcccCCCCCccEEEEeecccccc---cHH----------HHHhhhCC------C
Q 024352 75 LKSLPRGIVQARSDLELRPLWSTSSSRKKFGVYSNRNLLAIPAGIKQKD---NVD----------AIVRKFLP------E 135 (269)
Q Consensus 75 ~e~LP~GIV~~~Sdl~lr~Lwg~p~~~~~~~~~~~k~LlamaVGikQK~---~Vd----------~~V~KF~~------~ 135 (269)
-++||+.-|.+-+|-....|-..=..+ -.=.++.++=-+.+-+ .++ .++++|.. +
T Consensus 33 G~Rlp~~~v~r~aD~~p~~l~~~l~sd------Grfri~vFagd~~~~~~~~~l~~l~~~L~~~~s~~~r~~~~~~~~~s 106 (169)
T PF07976_consen 33 GRRLPSAKVVRHADGNPVHLQDDLPSD------GRFRILVFAGDISLPEQLSRLSALADYLESPSSFLSRFTPKDRDPDS 106 (169)
T ss_dssp TCB----EEEETTTTEEEEGGGG--SS------S-EEEEEEEETTTTCHCCCHHHHHHHHHHSTTSHHHHHSBTTS-TTS
T ss_pred ccccCCceEEEEcCCCChhHhhhcccC------CCEEEEEEeCCCccchhHHHHHHHHHHHHhcchHHHhcCCCCCCCCC
Confidence 358999999999998888884321111 1225667765554433 233 35667765 3
Q ss_pred CeEEEEEeeeCccccccccccCC
Q 024352 136 NFTVILFHYDGDVNAWRGLDWSN 158 (269)
Q Consensus 136 nF~vmLFHYDG~vd~W~dleWS~ 158 (269)
-|+++|.| =..++++||.+
T Consensus 107 ~~~~~~I~----~~~~~~~e~~d 125 (169)
T PF07976_consen 107 VFDVLLIH----SSPRDEVELFD 125 (169)
T ss_dssp SEEEEEEE----SS-CCCS-GGG
T ss_pred eeEEEEEe----cCCCCceeHHH
Confidence 39999999 45688888875
No 24
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=21.18 E-value=59 Score=25.80 Aligned_cols=56 Identities=14% Similarity=0.297 Sum_probs=41.6
Q ss_pred ccccceEEEeeccccCCCCCh--hHHHHHHHHhCCccccCccCCCCCceeeeeeeeccC
Q 024352 183 VSNYDYIFLWDEDLGVENFDP--RRYLEIVKSEGFEISQPALDPNSTEIHHKFTIRART 239 (269)
Q Consensus 183 Va~YdYIFlWDEDLgVe~F~~--~rYl~Ivk~~gLEISQPaLd~~~s~ihh~iT~R~~~ 239 (269)
+..||-+||.+.|+.=|.... ++|-+++.++|-+|-. .-+...-..-++|-+..++
T Consensus 5 mr~YE~~~Il~p~l~e~~~~~~~~~~~~~i~~~gg~i~~-~~~wG~r~LAY~I~k~~~G 62 (97)
T CHL00123 5 LNKYETMYLLKPDLNEEELLKWIENYKKLLRKRGAKNIS-VQNRGKRKLSYKINKYEDG 62 (97)
T ss_pred ccceeEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEE-EEeecCeeeeEEcCCCCEE
Confidence 356999999999998887774 8899999999988754 2234444566777655444
No 25
>PF07745 Glyco_hydro_53: Glycosyl hydrolase family 53; InterPro: IPR011683 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This domain is found in family 53 of the glycosyl hydrolase classification []. These enzymes are endo-1,4- beta-galactanases (3.2.1.89 from EC). The structure of this domain is known [] and has a TIM barrel fold.; GO: 0015926 glucosidase activity; PDB: 1HJQ_A 1HJS_A 1HJU_B 1FHL_A 1FOB_A 2GFT_A 1UR4_B 1UR0_A 1R8L_B 2CCR_A ....
Probab=21.17 E-value=52 Score=31.82 Aligned_cols=41 Identities=22% Similarity=0.477 Sum_probs=29.6
Q ss_pred CcceecCCCCCCCCcccCCCCCccEEEEeecccccccHHHHHhhhCCCCeEEEE-Eee
Q 024352 88 DLELRPLWSTSSSRKKFGVYSNRNLLAIPAGIKQKDNVDAIVRKFLPENFTVIL-FHY 144 (269)
Q Consensus 88 dl~lr~Lwg~p~~~~~~~~~~~k~LlamaVGikQK~~Vd~~V~KF~~~nF~vmL-FHY 144 (269)
|.-.-|+|-+|.. -|....+.|-++.|+--...+.||| |||
T Consensus 39 N~vRlRvwv~P~~----------------~g~~~~~~~~~~akrak~~Gm~vlldfHY 80 (332)
T PF07745_consen 39 NAVRLRVWVNPYD----------------GGYNDLEDVIALAKRAKAAGMKVLLDFHY 80 (332)
T ss_dssp -EEEEEE-SS-TT----------------TTTTSHHHHHHHHHHHHHTT-EEEEEE-S
T ss_pred CeEEEEeccCCcc----------------cccCCHHHHHHHHHHHHHCCCeEEEeecc
Confidence 3334488998865 5888899999999998778899998 999
No 26
>KOG2431 consensus 1, 2-alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=20.14 E-value=1e+02 Score=31.98 Aligned_cols=93 Identities=16% Similarity=0.126 Sum_probs=46.2
Q ss_pred hhHHHHHHHHHHHHhhhcchhhhhhhhhhhccCCCccccccccCCCCcCCCCCCceecCCCcceecC-CCCCCCCcccCC
Q 024352 28 LQFMAIMCTVMLFVVYRTTYYQYKQTEMEAKFSPFDISKGSRFSSGRLKSLPRGIVQARSDLELRPL-WSTSSSRKKFGV 106 (269)
Q Consensus 28 ~~~~~~~c~~~~f~~~~~~~~q~~~~~~~~~~~~~~~~~~~~~~p~g~e~LP~GIV~~~Sdl~lr~L-wg~p~~~~~~~~ 106 (269)
+.|.+.+|+.+++.+|...+ ..+ +-..|-...+.....-+++|.|||++-+..+.-++..- -+.+..-.....
T Consensus 13 ilf~~~~~~~v~l~~~~~~~----~p~--~~~~~~~~~~t~~~~~~sa~~l~p~~~~~~~~~~~~~p~~~~~~~~~i~~~ 86 (546)
T KOG2431|consen 13 ILFILAFLLFVLLLLYINPA----NPA--ELPNPQSGQKTKRGGQRSAENLPPDLPQQSATDEQEAPKEGDPNRTVISFR 86 (546)
T ss_pred HHHHHHHHHHHHHHHhcCCC----Chh--hcCCccccchhhhhcccCcccCCCCcchhhchhhccCCccCCCCCcceeec
Confidence 56677777776665555422 111 11111111122234567888899988877776665432 111111111000
Q ss_pred CCCccEEEEeecccccccHHHHHhhh
Q 024352 107 YSNRNLLAIPAGIKQKDNVDAIVRKF 132 (269)
Q Consensus 107 ~~~k~LlamaVGikQK~~Vd~~V~KF 132 (269)
-| | -.+-.||+.|++..+-|
T Consensus 87 -~P----t-g~nerq~avv~aF~haW 106 (546)
T KOG2431|consen 87 -GP----T-GLNERQKAVVDAFLHAW 106 (546)
T ss_pred -CC----C-chhHHHHHHHHHHHHHH
Confidence 11 1 13667888888877766
Done!