Query 004540
Match_columns 746
No_of_seqs 101 out of 114
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 01:07:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004540.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004540hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07227 DUF1423: Protein of u 100.0 1.6E-52 3.4E-57 451.7 6.4 152 144-303 91-256 (446)
2 PF00041 fn3: Fibronectin type 98.6 3.5E-07 7.5E-12 75.4 8.7 82 355-438 2-83 (85)
3 cd00063 FN3 Fibronectin type 3 98.0 8.4E-05 1.8E-09 59.3 9.9 72 359-434 7-81 (93)
4 smart00060 FN3 Fibronectin typ 97.0 0.0063 1.4E-07 46.9 9.1 74 359-434 7-81 (83)
5 KOG4221 Receptor mediating net 95.6 0.02 4.3E-07 70.6 6.5 76 357-435 620-699 (1381)
6 PF09294 Interfer-bind: Interf 95.5 0.034 7.3E-07 49.3 6.1 85 356-444 5-103 (106)
7 KOG4221 Receptor mediating net 94.2 0.18 4E-06 62.6 9.4 88 359-450 527-615 (1381)
8 KOG3513 Neural cell adhesion m 94.1 0.21 4.4E-06 61.7 9.6 88 351-439 818-905 (1051)
9 smart00249 PHD PHD zinc finger 93.8 0.065 1.4E-06 40.1 3.1 46 174-238 2-47 (47)
10 KOG0196 Tyrosine kinase, EPH ( 93.1 0.31 6.6E-06 58.9 8.6 88 357-446 447-537 (996)
11 KOG3513 Neural cell adhesion m 84.9 2.5 5.4E-05 52.7 7.9 85 348-436 611-700 (1051)
12 PF00628 PHD: PHD-finger; Int 84.2 0.19 4.1E-06 39.8 -1.3 48 174-239 2-49 (51)
13 PF07498 Rho_N: Rho terminatio 82.5 2.1 4.6E-05 33.9 4.0 39 54-94 2-40 (43)
14 PF11781 RRN7: RNA polymerase 67.7 2.4 5.2E-05 32.8 0.8 16 228-243 21-36 (36)
15 PF11793 FANCL_C: FANCL C-term 56.3 4.8 0.0001 34.8 0.7 62 173-242 4-65 (70)
16 PF01807 zf-CHC2: CHC2 zinc fi 50.3 13 0.00027 34.0 2.4 18 231-248 53-70 (97)
17 KOG4222 Axon guidance receptor 50.2 34 0.00074 43.6 6.7 71 363-435 759-832 (1281)
18 KOG4222 Axon guidance receptor 47.6 21 0.00046 45.3 4.4 69 363-432 652-723 (1281)
19 PHA02739 hypothetical protein; 39.9 30 0.00065 33.5 3.3 27 357-396 40-66 (116)
20 PF09423 PhoD: PhoD-like phosp 34.8 36 0.00078 38.3 3.5 34 411-446 65-98 (453)
21 KOG4802 Adhesion-type protein 33.9 4.6E+02 0.01 30.8 11.7 95 354-450 254-356 (516)
22 PLN02533 probable purple acid 32.7 29 0.00064 39.3 2.4 80 358-447 46-135 (427)
23 KOG0196 Tyrosine kinase, EPH ( 29.5 2.8E+02 0.0061 35.0 9.6 87 354-440 332-428 (996)
24 KOG0955 PHD finger protein BR1 27.9 43 0.00094 42.5 2.8 53 161-239 214-267 (1051)
25 PF07353 Uroplakin_II: Uroplak 25.6 1.2E+02 0.0026 31.3 4.9 45 406-450 98-142 (184)
26 KOG4258 Insulin/growth factor 25.4 4.1E+02 0.0088 33.8 10.0 110 324-433 451-589 (1025)
27 smart00109 C1 Protein kinase C 25.3 43 0.00094 25.4 1.5 31 174-214 14-44 (49)
28 cd00029 C1 Protein kinase C co 24.4 44 0.00096 25.7 1.4 33 174-215 14-46 (50)
29 PF01108 Tissue_fac: Tissue fa 23.2 4.8E+02 0.01 23.7 8.0 81 350-433 19-102 (107)
30 PF13248 zf-ribbon_3: zinc-rib 22.3 40 0.00086 24.1 0.7 16 157-172 7-22 (26)
31 KOG1948 Metalloproteinase-rela 22.1 1.4E+02 0.0031 37.6 5.5 68 359-432 879-968 (1165)
32 PF07649 C1_3: C1-like domain; 21.9 48 0.0011 24.1 1.1 18 187-212 13-30 (30)
33 KOG4802 Adhesion-type protein 20.5 1.4E+02 0.003 34.8 4.7 80 352-440 145-239 (516)
No 1
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=100.00 E-value=1.6e-52 Score=451.75 Aligned_cols=152 Identities=39% Similarity=0.770 Sum_probs=143.1
Q ss_pred CCCCCccccccCccccccccCCc----------CCcCCceeeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhh
Q 004540 144 GSDLVNAIYCKNSACRATLRKED----------VFCKRCSCCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECAL 213 (746)
Q Consensus 144 ~~~~~~~~~C~N~aCra~L~~ed----------~FCr~CsC~IC~kfD~nkdp~~Wl~C~s~~~~~~~~CghscHleCAL 213 (746)
=.++|.+.+|||+||||+||++| |||++||||||+|||+|+|||+||+|| +||||||+||||
T Consensus 91 LveiFl~~rCrN~aC~s~LP~ddc~C~iC~~~~gFC~~C~C~iC~kfD~~~n~~~Wi~Cd--------~CgH~cH~dCAL 162 (446)
T PF07227_consen 91 LVEIFLYKRCRNLACRSQLPVDDCDCKICCSEPGFCRRCMCCICSKFDDNKNTCSWIGCD--------VCGHWCHLDCAL 162 (446)
T ss_pred HHHHHHHHhcCCHHhhccCCccccCcchhcCCCCccccCCccccCCcccCCCCeeEEecc--------CCCceehhhhhc
Confidence 35689999999999999999976 999999999999999999999999998 999999999999
Q ss_pred hccccccccC--CCccccceeEEeccCCCccchhHHHHHHHHHhhccccchhhhhhhhchhhhccccHH--HHHHHHHHH
Q 004540 214 KNERSGIGKD--RCYSGLDGSFYCISCRKVNDLLGCWKKQLVVAKNTRRVDILCYRLSLGQKLVNATEK--YKNLSKIVD 289 (746)
Q Consensus 214 r~~~~G~~~~--g~~~~lD~~f~C~~Cgk~sdLlg~w~Kql~~ake~rrvD~Lc~rL~l~~kll~GS~r--~k~L~~~ve 289 (746)
|+++||+|.+ |+.+++||+|||++|||+|||||||+++|.+|+++||+|+||+||++++|||+||++ ||+||++++
T Consensus 163 r~~~i~~G~s~~g~~g~~d~~f~C~~C~~~seLlG~vk~vf~~ca~~~~~d~L~~eL~l~~rIf~GSed~rgk~L~~~~e 242 (446)
T PF07227_consen 163 RHELIGTGPSVKGSIGTLDMQFHCRACGKTSELLGFVKKVFQTCAKAWRVDVLCKELDLVRRIFRGSEDYRGKELHEKVE 242 (446)
T ss_pred ccccccCCccCCCCCccCceEEEccCCCChhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhCccchhHHHHHHHHH
Confidence 9999977654 666889999999999999999999999999999999999999999999999999994 799999999
Q ss_pred HHHHHhhhccCCCC
Q 004540 290 DAVKMLEDEVGPLT 303 (746)
Q Consensus 290 ~Al~KLe~evgpl~ 303 (746)
+|++|||++++++.
T Consensus 243 ~al~KL~~~~~~~~ 256 (446)
T PF07227_consen 243 EALAKLENGVIDSS 256 (446)
T ss_pred HHHHHHhCCCCCHH
Confidence 99999999997663
No 2
>PF00041 fn3: Fibronectin type III domain; InterPro: IPR003961 Fibronectins are multi-domain glycoproteins found in a soluble form in plasma, and in an insoluble form in loose connective tissue and basement membranes []. They contain multiple copies of 3 repeat regions (types I, II and III), which bind to a variety of substances including heparin, collagen, DNA, actin, fibrin and fibronectin receptors on cell surfaces. The wide variety of these substances means that fibronectins are involved in a number of important functions: e.g., wound healing; cell adhesion; blood coagulation; cell differentiation and migration; maintenance of the cellular cytoskeleton; and tumour metastasis []. The role of fibronectin in cell differentiation is demonstrated by the marked reduction in the expression of its gene when neoplastic transformation occurs. Cell attachment has been found to be mediated by the binding of the tetrapeptide RGDS to integrins on the cell surface [], although related sequences can also display cell adhesion activity. Plasma fibronectin occurs as a dimer of 2 different subunits, linked together by 2 disulphide bonds near the C terminus. The difference in the 2 chains occurs in the type III repeat region and is caused by alternative splicing of the mRNA from one gene []. The observation that, in a given protein, an individual repeat of one of the 3 types (e.g., the first FnIII repeat) shows much less similarity to its subsequent tandem repeats within that protein than to its equivalent repeat between fibronectins from other species, has suggested that the repeating structure of fibronectin arose at an early stage of evolution. It also seems to suggest that the structure is subject to high selective pressure []. The fibronectin type III repeat region is an approximately 100 amino acid domain, different tandem repeats of which contain binding sites for DNA, heparin and the cell surface []. The superfamily of sequences believed to contain FnIII repeats represents 45 different families, the majority of which are involved in cell surface binding in some manner, or are receptor protein tyrosine kinases, or cytokine receptors.; GO: 0005515 protein binding; PDB: 1UEM_A 1TDQ_A 1X5I_A 2IC2_B 2IBG_C 2IBB_A 3R8Q_A 2FNB_A 1FNH_A 2EDB_A ....
Probab=98.56 E-value=3.5e-07 Score=75.35 Aligned_cols=82 Identities=26% Similarity=0.403 Sum_probs=67.9
Q ss_pred cCceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecCCceeEeecCCcceeeeEEEEeccCCc
Q 004540 355 VPNMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNGTT 434 (746)
Q Consensus 355 ~~~~~rFEevt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ePt~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~~~ 434 (746)
++..+++.+++++||+|-+.........+.||.|.++..... .......+....+.++|.||.|.|+|.|||.+++..|
T Consensus 2 ~P~~l~v~~~~~~sv~v~W~~~~~~~~~~~~y~v~~~~~~~~-~~~~~~~~~~~~~~~~i~~L~p~t~Y~~~v~a~~~~g 80 (85)
T PF00041_consen 2 APENLSVSNISPTSVTVSWKPPSSGNGPITGYRVEYRSVNST-SDWQEVTVPGNETSYTITGLQPGTTYEFRVRAVNSDG 80 (85)
T ss_dssp SSEEEEEEEECSSEEEEEEEESSSTSSSESEEEEEEEETTSS-SEEEEEEEETTSSEEEEESCCTTSEEEEEEEEEETTE
T ss_pred cCcCeEEEECCCCEEEEEEECCCCCCCCeeEEEEEEEecccc-eeeeeeeeeeeeeeeeeccCCCCCEEEEEEEEEeCCc
Confidence 456799999999999999998875678899999999887664 1233445677777999999999999999999999888
Q ss_pred cCcc
Q 004540 435 ELGR 438 (746)
Q Consensus 435 elg~ 438 (746)
.|.
T Consensus 81 -~g~ 83 (85)
T PF00041_consen 81 -EGP 83 (85)
T ss_dssp -EEE
T ss_pred -CcC
Confidence 444
No 3
>cd00063 FN3 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
Probab=97.96 E-value=8.4e-05 Score=59.29 Aligned_cols=72 Identities=31% Similarity=0.465 Sum_probs=57.0
Q ss_pred EEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeee---cCCceeEeecCCcceeeeEEEEeccCCc
Q 004540 359 VKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLF---APNTRFVVTGLCPATEYQFKVVSSNGTT 434 (746)
Q Consensus 359 ~rFEevt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ePt~~~~---~p~~r~~vs~L~P~TEY~fkvvsF~~~~ 434 (746)
|++....+.++.|.+.........+.+|.|++++..+. ....+. ....++.|.+|.|.|.|.|+|.++...+
T Consensus 7 ~~~~~~~~~~~~v~W~~~~~~~~~~~~y~v~~~~~~~~----~~~~~~~~~~~~~~~~i~~l~p~~~Y~~~v~a~~~~~ 81 (93)
T cd00063 7 LRVTDVTSTSVTLSWTPPEDDGGPITGYVVEYREKGSG----DWKEVEVTPGSETSYTLTGLKPGTEYEFRVRAVNGGG 81 (93)
T ss_pred cEEEEecCCEEEEEECCCCCCCCcceeEEEEEeeCCCC----CCEEeeccCCcccEEEEccccCCCEEEEEEEEECCCc
Confidence 67888889999999988875446789999999987521 121222 3778999999999999999999998744
No 4
>smart00060 FN3 Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
Probab=97.04 E-value=0.0063 Score=46.90 Aligned_cols=74 Identities=28% Similarity=0.385 Sum_probs=52.3
Q ss_pred EEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecC-CceeEeecCCcceeeeEEEEeccCCc
Q 004540 359 VKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAP-NTRFVVTGLCPATEYQFKVVSSNGTT 434 (746)
Q Consensus 359 ~rFEevt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ePt~~~~~p-~~r~~vs~L~P~TEY~fkvvsF~~~~ 434 (746)
+..+.+.+.++.|-.+..... .. .+|.+++.........+-..+...+ +.++.|.+|.|.|-|.|+|.+++..|
T Consensus 7 ~~~~~~~~~~~~v~W~~~~~~-~~-~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~~~~Y~v~v~a~~~~g 81 (83)
T smart00060 7 LRVTDVTSTSVTLSWEPPPDD-GI-TGYIVGYRVEYREEGSSWKEVNVTPSSTSYTLTGLKPGTEYEFRVRAVNGAG 81 (83)
T ss_pred EEEEEEeCCEEEEEECCCCCC-CC-CccEEEEEEEEecCCCccEEEEecCCccEEEEeCcCCCCEEEEEEEEEcccC
Confidence 778888888999888733222 22 8999998877554211222222223 58999999999999999999988643
No 5
>KOG4221 consensus Receptor mediating netrin-dependent axon guidance [Signal transduction mechanisms]
Probab=95.61 E-value=0.02 Score=70.62 Aligned_cols=76 Identities=21% Similarity=0.305 Sum_probs=60.9
Q ss_pred ceEEEEEeeceeEEEEeCcCCC--CCCCcceEEEEeeecCCC-CCCCCceeeec-CCceeEeecCCcceeeeEEEEeccC
Q 004540 357 NMVKFEDVRATSLTVVLGSEDP--SPGNIISYTLWHRRAHEG-FPARPTCTLFA-PNTRFVVTGLCPATEYQFKVVSSNG 432 (746)
Q Consensus 357 ~~~rFEevt~tSv~vvL~~~~~--s~~~i~Gy~LWhrks~~~-y~~ePt~~~~~-p~~r~~vs~L~P~TEY~fkvvsF~~ 432 (746)
.-++.|-+.++||.|-+....+ .-..|+||++=||+...+ +-. -++.. -.++.++.+|.|.|+|.|||-++|-
T Consensus 620 ~Nl~lev~sStsVrVsW~pP~~~t~ng~itgYkIRy~~~~~~~~~~---~t~v~~n~~~~l~~~Lep~T~Y~vrIsa~t~ 696 (1381)
T KOG4221|consen 620 QNLSLEVVSSTSVRVSWLPPPSETQNGQITGYKIRYRKLSREDEVN---ETVVKGNTTQYLFNGLEPNTQYRVRISAMTV 696 (1381)
T ss_pred cceEEEecCCCeEEEEccCCCcccccceEEEEEEEecccCcccccc---eeecccchhhhHhhcCCCCceEEEEEEEecc
Confidence 3489999999999999998875 467899999999966554 221 24444 6788899999999999999999987
Q ss_pred Ccc
Q 004540 433 TTE 435 (746)
Q Consensus 433 ~~e 435 (746)
-|.
T Consensus 697 nGt 699 (1381)
T KOG4221|consen 697 NGT 699 (1381)
T ss_pred CCC
Confidence 553
No 6
>PF09294 Interfer-bind: Interferon-alpha/beta receptor, fibronectin type III; InterPro: IPR015373 Members of this family adopt a secondary structure consisting of seven beta-strands arranged in an immunoglobulin-like beta-sandwich, in a Greek-key topology. They are required for binding to interferon-alpha []. ; PDB: 1A21_A 3LQM_B 3ELA_T 1AHW_C 2A2Q_T 1TFH_B 1FAK_T 1WSS_T 1W2K_T 2FIR_T ....
Probab=95.49 E-value=0.034 Score=49.26 Aligned_cols=85 Identities=18% Similarity=0.164 Sum_probs=56.9
Q ss_pred CceEEEEEeeceeEEEEeCcCC---------CCCCCcce---EEEEeeecCCCCCCCCceeeecCCceeEeecCCcceee
Q 004540 356 PNMVKFEDVRATSLTVVLGSED---------PSPGNIIS---YTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEY 423 (746)
Q Consensus 356 ~~~~rFEevt~tSv~vvL~~~~---------~s~~~i~G---y~LWhrks~~~y~~ePt~~~~~p~~r~~vs~L~P~TEY 423 (746)
+..|.+ .+...+|.|.+.... .+..++-+ |+|-||+.... .-+-.+...++.++|.+|.|.|+|
T Consensus 5 PP~v~v-~~~~~~l~V~i~~P~~~~~~~~~~~~l~~~~~~~~Y~v~~~~~~~~---~~~~~~~~~~~~~~l~~L~p~t~Y 80 (106)
T PF09294_consen 5 PPSVNV-SSCGGSLHVTIKPPMTPLRAGGKNSSLRDIYPSLSYNVSYWKNGSN---EKKKEIETKNSSVTLSDLKPGTNY 80 (106)
T ss_dssp SSEEEE-EEETTEEEEEEEESEEEEECSSSEEEHHHHHGG-EEEEEEEETTTS---CEEEEEESSSEEEEEES--TTSEE
T ss_pred CCEEEE-EECCCEEEEEEECCCcccccCCCCCcHHHhCCCeEEEEEEEeCCCc---cceEEEeecCCEEEEeCCCCCCCE
Confidence 345777 788888888776654 12344544 99999998764 234466778889999999999999
Q ss_pred eEEEEeccCCc-cCc-ceeeEEe
Q 004540 424 QFKVVSSNGTT-ELG-RCEIWFS 444 (746)
Q Consensus 424 ~fkvvsF~~~~-elg-~~E~k~~ 444 (746)
+|+|-+|.... .-| .++.+|.
T Consensus 81 Cv~V~~~~~~~~~~s~~S~~~C~ 103 (106)
T PF09294_consen 81 CVSVQAFSPSQNKNSQPSEPQCI 103 (106)
T ss_dssp EEEEEEEECSSTEEEEEBSEEEE
T ss_pred EEEEEEEeccCCCcCCCCCCEeE
Confidence 99999844322 222 3345554
No 7
>KOG4221 consensus Receptor mediating netrin-dependent axon guidance [Signal transduction mechanisms]
Probab=94.17 E-value=0.18 Score=62.60 Aligned_cols=88 Identities=22% Similarity=0.261 Sum_probs=65.3
Q ss_pred EEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecCCceeEeecCCcceeeeEEEEeccCCc-cCc
Q 004540 359 VKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNGTT-ELG 437 (746)
Q Consensus 359 ~rFEevt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ePt~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~~~-elg 437 (746)
+.--...++++.|+.....--.+.|+||+|.|-..+..+ + .-+-...+-..|.||.|-|||.|+||+|+..| -..
T Consensus 527 ~~a~ats~~ti~v~WepP~~~n~~I~~yk~~ys~~~~~~--~--~~~~~n~~e~ti~gL~k~TeY~~~vvA~N~~G~g~s 602 (1381)
T KOG4221|consen 527 LQAYATSPTTILVTWEPPPFGNGPITGYKLFYSEDDTGK--E--LRVENNATEYTINGLEKYTEYSIRVVAYNSAGSGVS 602 (1381)
T ss_pred ccccccCcceEEEEecCCCCCCCCceEEEEEEEcCCCCc--e--EEEecCccEEEeecCCCccceEEEEEEecCCCCCCC
Confidence 444446677777777766545678999999998883321 1 11233466889999999999999999999988 567
Q ss_pred ceeeEEecCcccc
Q 004540 438 RCEIWFSTGSSRD 450 (746)
Q Consensus 438 ~~E~k~~T~s~e~ 450 (746)
..++++.|.+..-
T Consensus 603 S~~i~V~Tlsd~P 615 (1381)
T KOG4221|consen 603 SADITVRTLSDVP 615 (1381)
T ss_pred CCceEEEeccCCC
Confidence 8899999986543
No 8
>KOG3513 consensus Neural cell adhesion molecule L1 [Signal transduction mechanisms]
Probab=94.10 E-value=0.21 Score=61.67 Aligned_cols=88 Identities=16% Similarity=0.226 Sum_probs=74.1
Q ss_pred CCcccCceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecCCceeEeecCCcceeeeEEEEec
Q 004540 351 SNVIVPNMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSS 430 (746)
Q Consensus 351 ~~l~~~~~~rFEevt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ePt~~~~~p~~r~~vs~L~P~TEY~fkvvsF 430 (746)
-...++..+....++++.++|..+-..---+-++||.|=||+..+.|-..+...+....++..|+||.|-|-|.|.|-++
T Consensus 818 ~P~~ap~~~~~~~~s~s~~~v~W~~~~~~nG~l~gY~v~Y~~~~~~~~~~~~~~i~~~~~~~~ltgL~~~T~Y~~~vrA~ 897 (1051)
T KOG3513|consen 818 EPPVAPTKLSAKPLSSSEVNLSWKPPLWDNGKLTGYEVKYWKINEKEGSLSRVQIAGNRTSWRLTGLEPNTKYRFYVRAY 897 (1051)
T ss_pred CCCCCCccceeecccCceEEEEecCcCccCCccceeEEEEEEcCCCcccccceeecCCcceEeeeCCCCCceEEEEEEEe
Confidence 34556677888899999999998655322378999999999999988778887788888999999999999999999999
Q ss_pred cCCccCcce
Q 004540 431 NGTTELGRC 439 (746)
Q Consensus 431 ~~~~elg~~ 439 (746)
|..| .|..
T Consensus 898 nsaG-~Gp~ 905 (1051)
T KOG3513|consen 898 TSAG-GGPA 905 (1051)
T ss_pred cCCC-CCCC
Confidence 9999 7744
No 9
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG0196 consensus Tyrosine kinase, EPH (ephrin) receptor family [Signal transduction mechanisms]
Probab=93.11 E-value=0.31 Score=58.86 Aligned_cols=88 Identities=23% Similarity=0.295 Sum_probs=70.5
Q ss_pred ceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecCCceeEeecCCcceeeeEEEEeccCCc--
Q 004540 357 NMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNGTT-- 434 (746)
Q Consensus 357 ~~~rFEevt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ePt~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~~~-- 434 (746)
.-+|.+.++++||++-+...+.....|.-|-|=|+...+. +.--.++..+.++..|.+|.|.|.|.|+|=+.|..|
T Consensus 447 ~~~r~~~~~~~sitlsW~~p~~png~ildYEvky~ek~~~--e~~~~~~~t~~~~~ti~gL~p~t~YvfqVRarT~aG~G 524 (996)
T KOG0196|consen 447 SVLRQVSRTSDSITLSWSEPDQPNGVILDYEVKYYEKDED--ERSYSTLKTKTTTATITGLKPGTVYVFQVRARTAAGYG 524 (996)
T ss_pred ceEEEeeeccCceEEecCCCCCCCCcceeEEEEEeecccc--ccceeEEecccceEEeeccCCCcEEEEEEEEecccCCC
Confidence 4699999999999999999997777799999988887643 112236778889999999999999999999999865
Q ss_pred cCc-ceeeEEecC
Q 004540 435 ELG-RCEIWFSTG 446 (746)
Q Consensus 435 elg-~~E~k~~T~ 446 (746)
.|+ ..|++..+.
T Consensus 525 ~~S~~~~fqT~~~ 537 (996)
T KOG0196|consen 525 PYSGKHEFQTLPS 537 (996)
T ss_pred CCCCceeeeecCc
Confidence 333 556666554
No 11
>KOG3513 consensus Neural cell adhesion molecule L1 [Signal transduction mechanisms]
Probab=84.90 E-value=2.5 Score=52.68 Aligned_cols=85 Identities=28% Similarity=0.342 Sum_probs=57.3
Q ss_pred CCCCCcccCceEEEEEeeceeEEEEeCcCC-CCCCCcceEEEEeeecCCC-CCCCCceeeecCCc---eeEeecCCccee
Q 004540 348 VQGSNVIVPNMVKFEDVRATSLTVVLGSED-PSPGNIISYTLWHRRAHEG-FPARPTCTLFAPNT---RFVVTGLCPATE 422 (746)
Q Consensus 348 ~q~~~l~~~~~~rFEevt~tSv~vvL~~~~-~s~~~i~Gy~LWhrks~~~-y~~ePt~~~~~p~~---r~~vs~L~P~TE 422 (746)
+++...|+. .+..++|+++++.|-..-.. .-+. |.+|.+=.|-..-. .-. -+ +++--.+ ...|-||.|=.|
T Consensus 611 V~gpPgpP~-~v~~~~i~~t~~~lsW~~g~dn~Sp-I~~Y~iq~rt~~~~~W~~-v~-~vp~~~~~~~sa~vv~L~Pwv~ 686 (1051)
T KOG3513|consen 611 VRGPPGPPP-DVHVDDISDTTARLSWSPGSDNNSP-IEKYTIQFRTPFPGKWKA-VT-TVPGNITGDESATVVNLSPWVE 686 (1051)
T ss_pred EecCCCCCC-ceeEeeeccceEEEEeecCCCCCCC-ceEEeEEecCCCCCcceE-ee-ECCCcccCccceeEEccCCCcc
Confidence 344333333 79999999999999888775 3234 99999866654332 111 11 2222222 477899999999
Q ss_pred eeEEEEeccCCccC
Q 004540 423 YQFKVVSSNGTTEL 436 (746)
Q Consensus 423 Y~fkvvsF~~~~el 436 (746)
|.|||++++..|.=
T Consensus 687 YeFRV~AvN~iG~g 700 (1051)
T KOG3513|consen 687 YEFRVVAVNSIGIG 700 (1051)
T ss_pred eEEEEEEEcccccC
Confidence 99999999987643
No 12
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=84.22 E-value=0.19 Score=39.75 Aligned_cols=48 Identities=31% Similarity=0.719 Sum_probs=34.6
Q ss_pred eeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhhhccccccccCCCccccceeEEeccCC
Q 004540 174 CCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECALKNERSGIGKDRCYSGLDGSFYCISCR 239 (746)
Q Consensus 174 C~IC~kfD~nkdp~~Wl~C~s~~~~~~~~CghscHleCALr~~~~G~~~~g~~~~lD~~f~C~~Cg 239 (746)
|.||.+ ..+...||.|+ .|+.|-|+.|.--....-.. .+..|+|..|-
T Consensus 2 C~vC~~---~~~~~~~i~C~--------~C~~~~H~~C~~~~~~~~~~-------~~~~w~C~~C~ 49 (51)
T PF00628_consen 2 CPVCGQ---SDDDGDMIQCD--------SCNRWYHQECVGPPEKAEEI-------PSGDWYCPNCR 49 (51)
T ss_dssp BTTTTS---SCTTSSEEEBS--------TTSCEEETTTSTSSHSHHSH-------HSSSBSSHHHH
T ss_pred CcCCCC---cCCCCCeEEcC--------CCChhhCcccCCCChhhccC-------CCCcEECcCCc
Confidence 678888 45588999999 99999999997554442222 22278887763
No 13
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=82.53 E-value=2.1 Score=33.87 Aligned_cols=39 Identities=36% Similarity=0.514 Sum_probs=32.1
Q ss_pred hchhcHHHHHHHHHHHhCCcccccCcchHHHHHHHHhhhcc
Q 004540 54 LRSWTRQEILQILCAELGKERKYTGLTKLKIIENLLKLVSE 94 (746)
Q Consensus 54 LqswsR~Eil~ilCAe~gkERKYtgltK~k~ie~Llk~vs~ 94 (746)
|+++|..||.+ |+.++|-+ .|+++.|..+|..|++.-++
T Consensus 2 L~~~~~~eL~~-iAk~lgI~-~~~~~~K~eLI~~Il~~q~~ 40 (43)
T PF07498_consen 2 LKSMTLSELRE-IAKELGIE-GYSKMRKQELIFAILKAQAE 40 (43)
T ss_dssp HHCS-HHHHHH-HHHCTT-T-TGCCS-HHHHHHHHHHHHCT
T ss_pred cccCCHHHHHH-HHHHcCCC-CCCcCCHHHHHHHHHHHHHH
Confidence 78889999988 89999998 58999999999999998875
No 14
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=67.72 E-value=2.4 Score=32.80 Aligned_cols=16 Identities=31% Similarity=0.802 Sum_probs=13.9
Q ss_pred ccceeEEeccCCCccc
Q 004540 228 GLDGSFYCISCRKVND 243 (746)
Q Consensus 228 ~lD~~f~C~~Cgk~sd 243 (746)
.-||.|||.+||++.+
T Consensus 21 ~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 21 SDDGFYYCDRCGHQSE 36 (36)
T ss_pred ccCCEEEhhhCceEcC
Confidence 4699999999999865
No 15
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=56.30 E-value=4.8 Score=34.84 Aligned_cols=62 Identities=23% Similarity=0.323 Sum_probs=23.3
Q ss_pred eeeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhhhccccccccCCCccccceeEEeccCCCcc
Q 004540 173 SCCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECALKNERSGIGKDRCYSGLDGSFYCISCRKVN 242 (746)
Q Consensus 173 sC~IC~kfD~nkdp~~Wl~C~s~~~~~~~~CghscHleCALr~~~~G~~~~g~~~~lD~~f~C~~Cgk~s 242 (746)
.|.||+.+....+.-..+.|+ ...|++..|+.|-.+-.+.-......-+... =.|..|.++-
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~------n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~--G~CP~C~~~i 65 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCP------NPSCGKKFHLLCLSEWFLSLEKSRQSFIPIF--GECPYCSSPI 65 (70)
T ss_dssp S-SSS--SS-TT-----B--S-------TT----B-SGGGHHHHHHHHSSS-TTT--E--EE-TTT-SEE
T ss_pred CCCcCCcEecCCCCcCceEcC------CcccCCHHHHHHHHHHHHHcccCCeeecccc--cCCcCCCCee
Confidence 589999886655556678997 2389999999997766543221110001222 2488887753
No 16
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=50.26 E-value=13 Score=33.97 Aligned_cols=18 Identities=28% Similarity=0.645 Sum_probs=12.6
Q ss_pred eeEEeccCCCccchhHHH
Q 004540 231 GSFYCISCRKVNDLLGCW 248 (746)
Q Consensus 231 ~~f~C~~Cgk~sdLlg~w 248 (746)
+.|+|-+||+.-|.+.++
T Consensus 53 ~~~~Cf~Cg~~Gd~i~~v 70 (97)
T PF01807_consen 53 NRFKCFGCGKGGDVIDFV 70 (97)
T ss_dssp TEEEETTT--EE-HHHHH
T ss_pred CeEEECCCCCCCcHHhHH
Confidence 479999999999999843
No 17
>KOG4222 consensus Axon guidance receptor Dscam [Signal transduction mechanisms]
Probab=50.22 E-value=34 Score=43.59 Aligned_cols=71 Identities=14% Similarity=0.179 Sum_probs=51.7
Q ss_pred EeeceeEEEEeCcCCC--CCCCcceEEEEeeecCCC-CCCCCceeeecCCceeEeecCCcceeeeEEEEeccCCcc
Q 004540 363 DVRATSLTVVLGSEDP--SPGNIISYTLWHRRAHEG-FPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNGTTE 435 (746)
Q Consensus 363 evt~tSv~vvL~~~~~--s~~~i~Gy~LWhrks~~~-y~~ePt~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~~~e 435 (746)
.-.-|+.-|+..-..+ .-+.+.||++|.=--.+. +-.+-|.. .+-...+|.+|.|.+-|.|++.++|+.|+
T Consensus 759 ~~n~Ta~~Vsw~~pp~d~~ng~~qg~ki~~~~~e~tr~h~n~t~~--a~~~sv~i~~l~~g~ay~vtv~a~T~aGv 832 (1281)
T KOG4222|consen 759 SYNGTAGSVSWAPPPADVQNGILQGYKIECSGGEKTRIHINKTTN--ARTGSVTIGNLVTGIAYSVTVAARTGAGV 832 (1281)
T ss_pred cCCCceeeEEecCCcccccCCcccceeEEeecCcccccccccccc--CCCCceEeccccccceEEEEEeeecCCcc
Confidence 3344555666555532 468899999998655434 44444433 77788999999999999999999999774
No 18
>KOG4222 consensus Axon guidance receptor Dscam [Signal transduction mechanisms]
Probab=47.59 E-value=21 Score=45.34 Aligned_cols=69 Identities=23% Similarity=0.223 Sum_probs=50.7
Q ss_pred EeeceeEEEEeCcCCC-CCCCcceEEEEeeecCCC--CCCCCceeeecCCceeEeecCCcceeeeEEEEeccC
Q 004540 363 DVRATSLTVVLGSEDP-SPGNIISYTLWHRRAHEG--FPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNG 432 (746)
Q Consensus 363 evt~tSv~vvL~~~~~-s~~~i~Gy~LWhrks~~~--y~~ePt~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~ 432 (746)
.++|++|-+-..-.-. .++-|.||++=||-..-. --..-..+.+.|+ -+||.||.|.|.|.|++.+|..
T Consensus 652 ~L~asslr~~w~~~kq~~~~~i~g~~I~~r~~~~~~a~~s~~~v~~~t~~-s~v~~nl~p~t~ye~f~~Pf~~ 723 (1281)
T KOG4222|consen 652 VLNASSLRLGWTKDKQHGSQYIQGYRISYRSLGSQLAQWSNAGVTVPTPE-SVVVPNLKPGTNYEFFVRPFFP 723 (1281)
T ss_pred ccchhheeeeeeeecccCcccccceEEEeccCccccccccccceeccCCc-ceeccccCCCccceeeccCccC
Confidence 3556666665444433 478899999999988764 3334444555554 7899999999999999999998
No 19
>PHA02739 hypothetical protein; Provisional
Probab=39.90 E-value=30 Score=33.47 Aligned_cols=27 Identities=26% Similarity=0.406 Sum_probs=22.4
Q ss_pred ceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCC
Q 004540 357 NMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEG 396 (746)
Q Consensus 357 ~~~rFEevt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~ 396 (746)
..++|++|||.|.. -+|.||.||..+.
T Consensus 40 v~~~~ngVtA~l~~-------------~~~~lWFRK~~D~ 66 (116)
T PHA02739 40 VKGAYNGVTAESIE-------------FSGYLWFRKLDDT 66 (116)
T ss_pred EEEEEccEEEEEee-------------cCCeEeEEEcCCC
Confidence 47899999998864 3688999999886
No 20
>PF09423 PhoD: PhoD-like phosphatase; InterPro: IPR018946 This entry contains a number of putative proteins as well as Alkaline phosphatase D which catalyses the reaction: A phosphate monoester + H(2)O = an alcohol + phosphate ; PDB: 2YEQ_B.
Probab=34.80 E-value=36 Score=38.31 Aligned_cols=34 Identities=29% Similarity=0.342 Sum_probs=17.4
Q ss_pred eeEeecCCcceeeeEEEEeccCCccCcceeeEEecC
Q 004540 411 RFVVTGLCPATEYQFKVVSSNGTTELGRCEIWFSTG 446 (746)
Q Consensus 411 r~~vs~L~P~TEY~fkvvsF~~~~elg~~E~k~~T~ 446 (746)
++.|+||+|.|.|.||+..- .+..-.-.-++.|.
T Consensus 65 ~v~v~gL~p~t~Y~Y~~~~~--~~~~~s~~g~~rT~ 98 (453)
T PF09423_consen 65 KVDVTGLQPGTRYYYRFVVD--GGGQTSPVGRFRTA 98 (453)
T ss_dssp EEEE-S--TT-EEEEEEEE----TTEE---EEEE--
T ss_pred ecccCCCCCCceEEEEEEEe--cCCCCCCceEEEcC
Confidence 58899999999999999992 11222233466666
No 21
>KOG4802 consensus Adhesion-type protein [Extracellular structures]
Probab=33.89 E-value=4.6e+02 Score=30.84 Aligned_cols=95 Identities=15% Similarity=0.132 Sum_probs=58.3
Q ss_pred ccCceEEEEEeeceeE--EEEeCcCCCCCCCcceEEE---EeeecCCC-CCCCCceeeecCCceeEeecCCcceeeeEEE
Q 004540 354 IVPNMVKFEDVRATSL--TVVLGSEDPSPGNIISYTL---WHRRAHEG-FPARPTCTLFAPNTRFVVTGLCPATEYQFKV 427 (746)
Q Consensus 354 ~~~~~~rFEevt~tSv--~vvL~~~~~s~~~i~Gy~L---Whrks~~~-y~~ePt~~~~~p~~r~~vs~L~P~TEY~fkv 427 (746)
|+++-.++-.|.+.-. ++|..-..++-=-|..|++ ||=++-+. -+..-+...-..+. .|.+|.|-..|..-|
T Consensus 254 p~P~dl~l~~v~~dG~~~~~v~w~P~~sdlPv~~Yki~Ws~~v~s~k~~m~tks~~~k~thq~--si~~L~Pns~Y~Vev 331 (516)
T KOG4802|consen 254 PSPNDLKLIGVQFDGRYMLKVVWCPSKSDLPVEKYKITWSLYVNSAKASMITKSSYVKDTHQF--SIKELLPNSSYYVEV 331 (516)
T ss_pred cCcccceeeeeeecceEEEEEEeCCCCCCCcceeeEEEeehhhhhhhhhcccccceeeccchh--hhhhcCCCCeEEEEE
Confidence 4444555555554432 2344444445455888987 44444444 45555555544444 499999999998765
Q ss_pred --EeccCCccCcceeeEEecCcccc
Q 004540 428 --VSSNGTTELGRCEIWFSTGSSRD 450 (746)
Q Consensus 428 --vsF~~~~elg~~E~k~~T~s~e~ 450 (746)
|+|.++++|-.--.-.||...+-
T Consensus 332 qAi~y~g~~rLksek~~~F~~T~~~ 356 (516)
T KOG4802|consen 332 QAISYLGSRRLKSEKWMLFNTTLQP 356 (516)
T ss_pred EEEEeccCcccccceEEEEeeccCc
Confidence 77888888875555677765544
No 22
>PLN02533 probable purple acid phosphatase
Probab=32.68 E-value=29 Score=39.34 Aligned_cols=80 Identities=18% Similarity=0.203 Sum_probs=43.1
Q ss_pred eEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceee--e------cC--CceeEeecCCcceeeeEEE
Q 004540 358 MVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTL--F------AP--NTRFVVTGLCPATEYQFKV 427 (746)
Q Consensus 358 ~~rFEevt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ePt~~~--~------~p--~~r~~vs~L~P~TEY~fkv 427 (746)
+|++-=..+++++|..-..+... -.+.|..+...+....+.+. . .+ --+.+|++|+|.|+|.|||
T Consensus 46 qvhls~~~~~~m~V~W~T~~~~~-----~~V~yG~~~~~l~~~a~g~~~~~~~~~~~~~g~iH~v~l~~L~p~T~Y~Yrv 120 (427)
T PLN02533 46 QVHISLVGPDKMRISWITQDSIP-----PSVVYGTVSGKYEGSANGTSSSYHYLLIYRSGQINDVVIGPLKPNTVYYYKC 120 (427)
T ss_pred eEEEEEcCCCeEEEEEECCCCCC-----CEEEEecCCCCCcceEEEEEEEEeccccccCCeEEEEEeCCCCCCCEEEEEE
Confidence 55554445788888776665311 12444433322222222221 0 11 1257999999999999999
Q ss_pred EeccCCccCcceeeEEecCc
Q 004540 428 VSSNGTTELGRCEIWFSTGS 447 (746)
Q Consensus 428 vsF~~~~elg~~E~k~~T~s 447 (746)
-.-+ ...+..|.|..
T Consensus 121 g~~~-----~s~~~~F~T~p 135 (427)
T PLN02533 121 GGPS-----STQEFSFRTPP 135 (427)
T ss_pred CCCC-----CccceEEECCC
Confidence 5311 13345677754
No 23
>KOG0196 consensus Tyrosine kinase, EPH (ephrin) receptor family [Signal transduction mechanisms]
Probab=29.50 E-value=2.8e+02 Score=35.04 Aligned_cols=87 Identities=21% Similarity=0.268 Sum_probs=57.7
Q ss_pred ccCceEEEEEeeceeEEEEeCcCCCC-CCCcceEEEEeeecCCC----CCCCCceee-----ecCCceeEeecCCcceee
Q 004540 354 IVPNMVKFEDVRATSLTVVLGSEDPS-PGNIISYTLWHRRAHEG----FPARPTCTL-----FAPNTRFVVTGLCPATEY 423 (746)
Q Consensus 354 ~~~~~~rFEevt~tSv~vvL~~~~~s-~~~i~Gy~LWhrks~~~----y~~ePt~~~-----~~p~~r~~vs~L~P~TEY 423 (746)
|++.+=.+-+|+.|||.+-+.....+ .-+=.-|.+=+++-.-. -+=.+...+ -..++++.|+||-|-|.|
T Consensus 332 PSaP~nlis~vn~Ts~~L~W~~P~d~GGR~Di~y~v~Ck~c~~~~~~C~~Cg~~V~f~P~q~gLt~~~V~v~~L~ah~~Y 411 (996)
T KOG0196|consen 332 PSAPRNLISNVNGTSLILEWSPPADTGGREDITYNVICKKCGGGRGACEPCGDNVRFTPRQRGLTETSVTVSDLLAHTNY 411 (996)
T ss_pred CCccceeeeecccceEEEEecCCcccCCCcceEEEEEeeccCCCCCccccCCCCceECCCCCCcccceEEEecccccccc
Confidence 34445455569999999988877642 33333466655544311 122223222 123678999999999999
Q ss_pred eEEEEeccCCccCccee
Q 004540 424 QFKVVSSNGTTELGRCE 440 (746)
Q Consensus 424 ~fkvvsF~~~~elg~~E 440 (746)
+|-|-+-|+..+++..=
T Consensus 412 TFeV~AvNgVS~lsp~~ 428 (996)
T KOG0196|consen 412 TFEVEAVNGVSDLSPFP 428 (996)
T ss_pred EEEEEEeecccccCCCC
Confidence 99999999999888664
No 24
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=27.88 E-value=43 Score=42.50 Aligned_cols=53 Identities=32% Similarity=0.728 Sum_probs=36.6
Q ss_pred cccCCcCCcCCceeeeecccc-CCCCCccEEecCCCCCCCCCcccchhhhhhhhhccccccccCCCccccceeEEeccCC
Q 004540 161 TLRKEDVFCKRCSCCICRKYD-DNKDPSLWLTCSSEPPFGGDSCGMSCHLECALKNERSGIGKDRCYSGLDGSFYCISCR 239 (746)
Q Consensus 161 ~L~~ed~FCr~CsC~IC~kfD-~nkdp~~Wl~C~s~~~~~~~~CghscHleCALr~~~~G~~~~g~~~~lD~~f~C~~Cg 239 (746)
.+-.+|++| +||.+-+ +|.|.. |.|| -|+...|.+|-= +- .-.||+.-|++|.
T Consensus 214 ~~~~~D~~C-----~iC~~~~~~n~n~i--vfCD--------~Cnl~VHq~Cyg------i~-----~ipeg~WlCr~Cl 267 (1051)
T KOG0955|consen 214 ALLEEDAVC-----CICLDGECQNSNVI--VFCD--------GCNLAVHQECYG------IP-----FIPEGQWLCRRCL 267 (1051)
T ss_pred cccCCCccc-----eeecccccCCCceE--EEcC--------CCcchhhhhccC------CC-----CCCCCcEeehhhc
Confidence 344677875 7777776 555554 6899 999999999953 21 2256777777774
No 25
>PF07353 Uroplakin_II: Uroplakin II; InterPro: IPR009952 This family contains uroplakin II, which is approximately 180 residues long and seems to be restricted to mammals. Uroplakin II is an integral membrane protein, and is one of the components of the apical plaques of mammalian urothelium formed by the asymmetric unit membrane - this is believed to play a role in strengthening the urothelial apical surface to prevent the cells from rupturing during bladder distension [].; GO: 0016044 cellular membrane organization, 0030176 integral to endoplasmic reticulum membrane
Probab=25.57 E-value=1.2e+02 Score=31.28 Aligned_cols=45 Identities=27% Similarity=0.345 Sum_probs=34.6
Q ss_pred ecCCceeEeecCCcceeeeEEEEeccCCccCcceeeEEecCcccc
Q 004540 406 FAPNTRFVVTGLCPATEYQFKVVSSNGTTELGRCEIWFSTGSSRD 450 (746)
Q Consensus 406 ~~p~~r~~vs~L~P~TEY~fkvvsF~~~~elg~~E~k~~T~s~e~ 450 (746)
..+..-+.|+||+|.|-|.|+-.-=++..-...+|.-..|....+
T Consensus 98 ~trlsaYqVtNL~pGTkY~isY~VtkgtstESS~~i~msT~n~~~ 142 (184)
T PF07353_consen 98 VTRLSAYQVTNLQPGTKYYISYLVTKGTSTESSNEIPMSTLNRKN 142 (184)
T ss_pred eccceeEEeeccCCCcEEEEEEEEecCccceecceeccccccccc
Confidence 345567789999999999999887677776777777777765444
No 26
>KOG4258 consensus Insulin/growth factor receptor (contains protein kinase domain) [Signal transduction mechanisms]
Probab=25.44 E-value=4.1e+02 Score=33.83 Aligned_cols=110 Identities=19% Similarity=0.254 Sum_probs=70.2
Q ss_pred HHHHHHHHHhhhhhhcCCC-C--CCCCCCCCCcccCc-----eEEEEEeeceeEEEEe-CcCCCCCCCcceEEEEeeecC
Q 004540 324 QKLCACAVESLDKMISNTI-L--PNPSVQGSNVIVPN-----MVKFEDVRATSLTVVL-GSEDPSPGNIISYTLWHRRAH 394 (746)
Q Consensus 324 QKLCs~Aie~~Ds~ls~~~-~--~~~~~q~~~l~~~~-----~~rFEevt~tSv~vvL-~~~~~s~~~i~Gy~LWhrks~ 394 (746)
-|||-.-|-.|.+.+...- + .+-..+-..--++| +|-.--.++.||.+.+ .+..+-..+..||.|.|.-+.
T Consensus 451 pkLC~~~I~qle~~~~t~~~~~~~dis~~TNGera~Ce~~~l~~~~~~~~~dsi~lrW~~~~~~d~r~llg~~~~yKEaP 530 (1025)
T KOG4258|consen 451 PKLCLEEIHQLEEVLGTKGRQSKADISLRTNGERAICEDLVLQFSSTVTSADSILLRWERYQPPDMRDLLGFLLHYKEAP 530 (1025)
T ss_pred hHHHHHHHHHHHHhhCCCCCccccccCccCCCceeecccceeeeeeEEeecceeEEEecccCCcchhhhheeeEeeccCC
Confidence 5899999999999987543 1 00011111112222 3444455677888874 444346889999999987765
Q ss_pred CC----CCCCCcee--------eecC-------C-ceeEeecCCcceeeeEEEEeccCC
Q 004540 395 EG----FPARPTCT--------LFAP-------N-TRFVVTGLCPATEYQFKVVSSNGT 433 (746)
Q Consensus 395 ~~----y~~ePt~~--------~~~p-------~-~r~~vs~L~P~TEY~fkvvsF~~~ 433 (746)
.+ |-..+.|. +.-| + -++++.+|+|-|.|.+=|-.|+-+
T Consensus 531 ~qNvT~~dg~~aCg~~~W~~~~v~~~~~~p~~~~~~~~~l~~LkP~TqYAvfVkT~t~t 589 (1025)
T KOG4258|consen 531 FQNVTEEDGRDACGSNSWNVVDVDPPDLIPNDGTHPGFLLDGLKPWTQYAVFVKTLTVT 589 (1025)
T ss_pred ccccceecCccccccCcceEEeccCCcCCCccccccceehhcCCccceeEEEEeeeehh
Confidence 43 44445542 1222 2 389999999999999988887554
No 27
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=25.31 E-value=43 Score=25.45 Aligned_cols=31 Identities=45% Similarity=0.883 Sum_probs=22.9
Q ss_pred eeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhhh
Q 004540 174 CCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECALK 214 (746)
Q Consensus 174 C~IC~kfD~nkdp~~Wl~C~s~~~~~~~~CghscHleCALr 214 (746)
|.+|.++.-... -++.|. .|+..+|-.|+-+
T Consensus 14 C~~C~~~i~~~~--~~~~C~--------~C~~~~H~~C~~~ 44 (49)
T smart00109 14 CCVCRKSIWGSF--QGLRCS--------WCKVKCHKKCAEK 44 (49)
T ss_pred ccccccccCcCC--CCcCCC--------CCCchHHHHHHhh
Confidence 556666654432 378898 9999999999865
No 28
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=24.39 E-value=44 Score=25.75 Aligned_cols=33 Identities=39% Similarity=0.634 Sum_probs=23.7
Q ss_pred eeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhhhc
Q 004540 174 CCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECALKN 215 (746)
Q Consensus 174 C~IC~kfD~nkdp~~Wl~C~s~~~~~~~~CghscHleCALr~ 215 (746)
|.+|.++.-.. +--++.|+ .|+..+|-.|+-+-
T Consensus 14 C~~C~~~i~~~-~~~~~~C~--------~C~~~~H~~C~~~v 46 (50)
T cd00029 14 CDVCRKSIWGL-FKQGLRCS--------WCKVKCHKKCADKV 46 (50)
T ss_pred hhhcchhhhcc-ccceeEcC--------CCCCchhhhhhccC
Confidence 55666665432 45677898 99999999998553
No 29
>PF01108 Tissue_fac: Tissue factor; PDB: 3OG4_B 3OG6_B 1FYH_E 1FG9_D 1JRH_I 3DGC_R 3DLQ_R 1LQS_R 1Y6M_R 1J7V_R ....
Probab=23.21 E-value=4.8e+02 Score=23.65 Aligned_cols=81 Identities=16% Similarity=0.256 Sum_probs=56.3
Q ss_pred CCCcccCceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCC-CCCCCceeeecCCceeEeecCC--cceeeeEE
Q 004540 350 GSNVIVPNMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEG-FPARPTCTLFAPNTRFVVTGLC--PATEYQFK 426 (746)
Q Consensus 350 ~~~l~~~~~~rFEevt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~-y~~ePt~~~~~p~~r~~vs~L~--P~TEY~fk 426 (746)
...++++.-++|.-+.-. .++-.+... ....-.-|.+.|+..... ...-|.|.=. .++..-+++.. +.-.|.+|
T Consensus 19 ~~~lp~P~nv~~~s~nf~-~iL~W~~~~-~~~~~~~ytVq~~~~~~~~W~~v~~C~~i-~~~~Cdlt~~~~~~~~~Y~~r 95 (107)
T PF01108_consen 19 SASLPAPQNVTVDSVNFK-HILRWDPGP-GSPPNVTYTVQYKKYGSSSWKDVPGCQNI-TETSCDLTDETSDPSESYYAR 95 (107)
T ss_dssp -SSGSSCEEEEEEEETTE-EEEEEEEST-TSSSTEEEEEEEEESSTSCEEEECCEEEE-SSSEEECTTCCTTTTSEEEEE
T ss_pred cccCCCCCeeEEEEECCc-eEEEeCCCC-CCCCCeEEEEEEEecCCcceeeccceecc-cccceeCcchhhcCcCCEEEE
Confidence 457788888888877555 455566633 233567899999955555 6666777544 34777787755 78889999
Q ss_pred EEeccCC
Q 004540 427 VVSSNGT 433 (746)
Q Consensus 427 vvsF~~~ 433 (746)
|.++.+.
T Consensus 96 V~A~~~~ 102 (107)
T PF01108_consen 96 VRAEVGN 102 (107)
T ss_dssp EEEEETT
T ss_pred EEEEeCC
Confidence 9997654
No 30
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.27 E-value=40 Score=24.09 Aligned_cols=16 Identities=31% Similarity=0.933 Sum_probs=14.1
Q ss_pred cccccccCCcCCcCCc
Q 004540 157 ACRATLRKEDVFCKRC 172 (746)
Q Consensus 157 aCra~L~~ed~FCr~C 172 (746)
.|.+.+..++.||..|
T Consensus 7 ~Cg~~~~~~~~fC~~C 22 (26)
T PF13248_consen 7 NCGAEIDPDAKFCPNC 22 (26)
T ss_pred ccCCcCCcccccChhh
Confidence 5888899999999887
No 31
>KOG1948 consensus Metalloproteinase-related collagenase pM5 [Posttranslational modification, protein turnover, chaperones]
Probab=22.12 E-value=1.4e+02 Score=37.59 Aligned_cols=68 Identities=19% Similarity=0.226 Sum_probs=50.3
Q ss_pred EEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecC--------------------C-C-CCCCCceeeecCCceeEeec
Q 004540 359 VKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAH--------------------E-G-FPARPTCTLFAPNTRFVVTG 416 (746)
Q Consensus 359 ~rFEevt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~--------------------~-~-y~~ePt~~~~~p~~r~~vs~ 416 (746)
++|| |+|.+|.+++.+...-.++||+.=|---. . . |++|-| ..-+-.+-|-|
T Consensus 879 ykFe---Pst~mIevkeGq~~~vvl~gkRvAySayGtvssLsGdp~~gVaieA~sdn~~~y~eeat---tdenG~yRiRG 952 (1165)
T KOG1948|consen 879 YKFE---PSTSMIEVKEGQHENVVLKGKRVAYSAYGTVSSLSGDPMKGVAIEALSDNCDLYQEEAT---TDENGTYRIRG 952 (1165)
T ss_pred cCcC---CCceeEEeccCceEEEEEEEEEEEEEeeeehhhccCCcccCeEEEEecCCCCccccccc---cccCCcEEEec
Confidence 4554 78889999988877777888887663211 1 2 554433 45677899999
Q ss_pred CCcceeeeEEEEeccC
Q 004540 417 LCPATEYQFKVVSSNG 432 (746)
Q Consensus 417 L~P~TEY~fkvvsF~~ 432 (746)
|.|.++|..|+.++-+
T Consensus 953 L~Pdc~Y~V~vk~~~~ 968 (1165)
T KOG1948|consen 953 LLPDCEYQVHVKSYAD 968 (1165)
T ss_pred cCCCceEEEEEeeccC
Confidence 9999999999999854
No 32
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=21.93 E-value=48 Score=24.12 Aligned_cols=18 Identities=39% Similarity=0.923 Sum_probs=9.0
Q ss_pred ccEEecCCCCCCCCCcccchhhhhhh
Q 004540 187 SLWLTCSSEPPFGGDSCGMSCHLECA 212 (746)
Q Consensus 187 ~~Wl~C~s~~~~~~~~CghscHleCA 212 (746)
..+-.|. .|...-|++||
T Consensus 13 ~~~Y~C~--------~Cdf~lH~~Ca 30 (30)
T PF07649_consen 13 GWFYRCS--------ECDFDLHEECA 30 (30)
T ss_dssp --EEE-T--------TT-----HHHH
T ss_pred CceEECc--------cCCCccChhcC
Confidence 5778898 99999999998
No 33
>KOG4802 consensus Adhesion-type protein [Extracellular structures]
Probab=20.48 E-value=1.4e+02 Score=34.82 Aligned_cols=80 Identities=16% Similarity=0.077 Sum_probs=57.4
Q ss_pred CcccCceEEEEEeeceeEEEEeCcCCCCC--CCc-------------ceEEEEeeecCCCCCCCCceeeecCCceeEeec
Q 004540 352 NVIVPNMVKFEDVRATSLTVVLGSEDPSP--GNI-------------ISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTG 416 (746)
Q Consensus 352 ~l~~~~~~rFEevt~tSv~vvL~~~~~s~--~~i-------------~Gy~LWhrks~~~y~~ePt~~~~~p~~r~~vs~ 416 (746)
-+++-..++|+.-..+|+.|-+...-.+. ..+ .+--.|||+..+ ...+.-++..++
T Consensus 145 ~l~Pr~k~~y~r~~~g~~av~w~~~~~~~v~~~~~~vr~~w~~g~hase~~~thwQtv~---------~t~~e~~~~~t~ 215 (516)
T KOG4802|consen 145 QLPPRPKILYFRRSRGSHAVDWKIESSLLVYYVHVEVRSHWGRGFHASELGPTHWQTVE---------KTMEENTYIFTD 215 (516)
T ss_pred CCCCcchhhhhhhccCceeeeeeeccccceeeeehhhhhhhcccccccccccccceeee---------ecCCCceeeeee
Confidence 46677889999999999999888776431 111 112235555544 233334888999
Q ss_pred CCcceeeeEEEEeccCCccCccee
Q 004540 417 LCPATEYQFKVVSSNGTTELGRCE 440 (746)
Q Consensus 417 L~P~TEY~fkvvsF~~~~elg~~E 440 (746)
+.|+-=|.|||-+-+-.|-+|-.|
T Consensus 216 ~rPgRwyefrvaavn~~G~rGFs~ 239 (516)
T KOG4802|consen 216 MRPGRWYEFRVAAVNAYGFRGFSE 239 (516)
T ss_pred cCcceeEEEEEeeeecccccccCC
Confidence 999999999999999999888655
Done!