Query 004714
Match_columns 734
No_of_seqs 101 out of 114
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 11:40:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004714.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004714hhsearch_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 2.2E-52 4.8E-57 450.1 6.4 152 132-291 91-256 (446)
2 PF00041 fn3: Fibronectin type 98.6 3.2E-07 6.9E-12 75.5 8.6 82 343-426 2-83 (85)
3 cd00063 FN3 Fibronectin type 3 98.0 7.8E-05 1.7E-09 59.4 9.9 72 347-422 7-81 (93)
4 smart00060 FN3 Fibronectin typ 97.1 0.0058 1.2E-07 47.1 9.1 74 347-422 7-81 (83)
5 KOG4221 Receptor mediating net 95.7 0.018 3.9E-07 70.9 6.5 76 345-423 620-699 (1381)
6 PF09294 Interfer-bind: Interf 95.6 0.031 6.7E-07 49.5 6.0 85 344-432 5-103 (106)
7 KOG4221 Receptor mediating net 94.3 0.16 3.5E-06 63.0 9.4 88 347-438 527-615 (1381)
8 KOG3513 Neural cell adhesion m 94.2 0.19 4E-06 61.9 9.6 88 339-427 818-905 (1051)
9 smart00249 PHD PHD zinc finger 93.8 0.062 1.3E-06 40.2 3.1 46 162-226 2-47 (47)
10 KOG0196 Tyrosine kinase, EPH ( 93.2 0.28 6.1E-06 59.1 8.5 88 345-434 447-537 (996)
11 KOG3513 Neural cell adhesion m 85.2 2.3 5.1E-05 52.8 7.8 85 336-424 611-700 (1051)
12 PF00628 PHD: PHD-finger; Int 84.7 0.18 3.9E-06 39.8 -1.2 48 162-227 2-49 (51)
13 PF07498 Rho_N: Rho terminatio 82.7 2.1 4.5E-05 33.9 4.0 39 42-82 2-40 (43)
14 PF11781 RRN7: RNA polymerase 68.3 2.3 5E-05 32.8 0.8 16 216-231 21-36 (36)
15 PF11793 FANCL_C: FANCL C-term 56.7 4.8 0.0001 34.8 0.7 62 161-230 4-65 (70)
16 KOG4222 Axon guidance receptor 51.6 32 0.00068 43.8 6.7 71 351-423 759-832 (1281)
17 PF01807 zf-CHC2: CHC2 zinc fi 49.9 13 0.00027 33.9 2.3 18 219-236 53-70 (97)
18 KOG4222 Axon guidance receptor 49.5 19 0.00041 45.7 4.4 69 351-420 652-723 (1281)
19 PHA02739 hypothetical protein; 41.2 28 0.00061 33.6 3.3 27 345-384 40-66 (116)
20 PF09423 PhoD: PhoD-like phosp 35.7 34 0.00074 38.5 3.5 34 399-434 65-98 (453)
21 PLN02533 probable purple acid 33.5 28 0.00061 39.5 2.3 80 346-435 46-135 (427)
22 KOG0196 Tyrosine kinase, EPH ( 31.1 2.1E+02 0.0045 36.0 8.9 88 342-429 332-429 (996)
23 KOG0955 PHD finger protein BR1 28.1 43 0.00092 42.5 2.8 52 150-227 215-267 (1051)
24 KOG4802 Adhesion-type protein 26.7 7.2E+02 0.016 29.3 11.6 95 342-438 254-356 (516)
25 PF07353 Uroplakin_II: Uroplak 26.5 1.1E+02 0.0024 31.4 4.9 45 394-438 98-142 (184)
26 KOG4258 Insulin/growth factor 26.4 3.8E+02 0.0082 34.0 10.0 110 312-421 451-589 (1025)
27 smart00109 C1 Protein kinase C 26.0 41 0.0009 25.5 1.5 31 162-202 14-44 (49)
28 cd00029 C1 Protein kinase C co 25.1 42 0.00091 25.8 1.4 33 162-203 14-46 (50)
29 PF01108 Tissue_fac: Tissue fa 23.9 4.5E+02 0.0097 23.8 8.0 81 338-421 19-102 (107)
30 KOG1948 Metalloproteinase-rela 22.8 1.4E+02 0.0029 37.7 5.5 68 347-420 879-968 (1165)
31 PF07649 C1_3: C1-like domain; 22.5 46 0.001 24.2 1.1 18 175-200 13-30 (30)
32 PF13248 zf-ribbon_3: zinc-rib 22.4 39 0.00085 24.1 0.7 16 145-160 7-22 (26)
33 KOG4802 Adhesion-type protein 21.5 1.3E+02 0.0028 35.0 4.7 80 340-428 145-239 (516)
34 TIGR03853 matur_matur probable 20.1 1.6E+02 0.0035 26.8 4.1 36 43-78 16-56 (77)
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=2.2e-52 Score=450.10 Aligned_cols=152 Identities=39% Similarity=0.770 Sum_probs=143.2
Q ss_pred CCCCCccccccCccccccccCCc----------CCcCCceeeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhh
Q 004714 132 GSDLVNAIYCKNSACRATLRKED----------VFCKRCSCCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECAL 201 (734)
Q Consensus 132 ~~~~~~~~~C~N~aCra~L~~ed----------~FCr~CsC~IC~kfD~nkd~~~Wl~C~s~~~~~~~~Cgh~cHleCAL 201 (734)
=.++|.+.+|||+||||+||++| |||++||||||+|||+|+|||+||+|| +||||||+||||
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 hcccccccc--CCCccccceeEEeccCCCccchhHHHHHHHHHhhccccchhhhhhhhchhhhccccHH--HHHHHHHHH
Q 004714 202 KNERSGIGK--DRCYSGLDGSFYCISCRKVNDLLGCWKKQLVVAKNTRRVDILCYRLSLGQKLVNATEK--YKNLSKIVD 277 (734)
Q Consensus 202 r~~~~G~~~--~g~~~~lD~~f~C~~Cgk~sdLlg~w~Kql~~ake~rrvD~Lc~rL~l~~kll~GS~~--~k~L~~~ve 277 (734)
|+++||+|. .|+.+++||+|||++|||+|||||||+++|.+|+++||+|+||+||++++|||+||++ ||+||++++
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 999997765 4666889999999999999999999999999999999999999999999999999994 799999999
Q ss_pred HHHHHhhhccCCCC
Q 004714 278 DAVKMLEDEVGPLT 291 (734)
Q Consensus 278 ~A~~KLe~evgpl~ 291 (734)
+|++|||++++++.
T Consensus 243 ~al~KL~~~~~~~~ 256 (446)
T PF07227_consen 243 EALAKLENGVIDSS 256 (446)
T ss_pred HHHHHHhCCCCCHH
Confidence 99999999997653
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=98.57 E-value=3.2e-07 Score=75.51 Aligned_cols=82 Identities=26% Similarity=0.403 Sum_probs=67.8
Q ss_pred cCceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecCCceeEeecCCcceeeeEEEEeccCCc
Q 004714 343 VPNMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNGTT 422 (734)
Q Consensus 343 ~~~~~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~~~ 422 (734)
++..+++.+++++||+|-+.........+.||.|.++..... .......+....+.++|.||.|.|.|.|||.+++..|
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 004714 423 ELGR 426 (734)
Q Consensus 423 elg~ 426 (734)
.|.
T Consensus 81 -~g~ 83 (85)
T PF00041_consen 81 -EGP 83 (85)
T ss_dssp -EEE
T ss_pred -CcC
Confidence 544
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=97.97 E-value=7.8e-05 Score=59.44 Aligned_cols=72 Identities=31% Similarity=0.465 Sum_probs=56.9
Q ss_pred EEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeee---cCCceeEeecCCcceeeeEEEEeccCCc
Q 004714 347 VKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLF---APNTRFVVTGLCPATEYQFKVVSSNGTT 422 (734)
Q Consensus 347 ~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~~---~p~~r~~vs~L~P~TEY~fkvvsF~~~~ 422 (734)
|++....+.++.|.+.........+.+|.|++++..+. ....+. ....++.|.+|.|.|.|.|+|.++...+
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 111222 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=97.06 E-value=0.0058 Score=47.08 Aligned_cols=74 Identities=28% Similarity=0.385 Sum_probs=52.3
Q ss_pred EEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecC-CceeEeecCCcceeeeEEEEeccCCc
Q 004714 347 VKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAP-NTRFVVTGLCPATEYQFKVVSSNGTT 422 (734)
Q Consensus 347 ~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~~~p-~~r~~vs~L~P~TEY~fkvvsF~~~~ 422 (734)
+..+.+.+.++.|-.+..... .. .+|.+++.........+-..+...+ +.++.|.+|.|.|-|.|+|.+++..|
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 778888888899888733222 22 8999998877554211222222223 58999999999999999999988643
No 5
>KOG4221 consensus Receptor mediating netrin-dependent axon guidance [Signal transduction mechanisms]
Probab=95.67 E-value=0.018 Score=70.85 Aligned_cols=76 Identities=21% Similarity=0.305 Sum_probs=60.9
Q ss_pred ceEEEEEeeceeEEEEeCcCCC--CCCCcceEEEEeeecCCC-CCCCCceeeec-CCceeEeecCCcceeeeEEEEeccC
Q 004714 345 NMVKFEDVRATSLTVVLGSEDP--SPGNIISYTLWHRRAHEG-FPARPTCTLFA-PNTRFVVTGLCPATEYQFKVVSSNG 420 (734)
Q Consensus 345 ~~~rFE~vt~tSv~vvL~~~~~--s~~~i~Gy~LWhrks~~~-y~~ept~~~~~-p~~r~~vs~L~P~TEY~fkvvsF~~ 420 (734)
.-++.|-+.++||.|-+....+ .-..|+||++=||+...+ +-. -++.. -.++.++.+|.|.|+|.|||-++|-
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 004714 421 TTE 423 (734)
Q Consensus 421 ~~e 423 (734)
-|.
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=95.55 E-value=0.031 Score=49.45 Aligned_cols=85 Identities=18% Similarity=0.164 Sum_probs=56.9
Q ss_pred CceEEEEEeeceeEEEEeCcCC---------CCCCCcce---EEEEeeecCCCCCCCCceeeecCCceeEeecCCcceee
Q 004714 344 PNMVKFEDVRATSLTVVLGSED---------PSPGNIIS---YTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEY 411 (734)
Q Consensus 344 ~~~~rFE~vt~tSv~vvL~~~~---------~s~~~i~G---y~LWhrks~~~y~~ept~~~~~p~~r~~vs~L~P~TEY 411 (734)
+..|.+ .+...+|.|.+.... .+..++-+ |+|-||+.... .-+-.+...++.++|.+|.|.|+|
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 004714 412 QFKVVSSNGTT-ELG-RCEIWFS 432 (734)
Q Consensus 412 ~fkvvsF~~~~-elg-~~E~k~~ 432 (734)
+|+|-+|.... .-| .++.+|.
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 3344554
No 7
>KOG4221 consensus Receptor mediating netrin-dependent axon guidance [Signal transduction mechanisms]
Probab=94.33 E-value=0.16 Score=62.99 Aligned_cols=88 Identities=22% Similarity=0.261 Sum_probs=65.3
Q ss_pred EEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecCCceeEeecCCcceeeeEEEEeccCCc-cCc
Q 004714 347 VKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNGTT-ELG 425 (734)
Q Consensus 347 ~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~~~-elg 425 (734)
+.--...++++.|+.....--.+.|+||+|.|-..+..+ + .-+-...+-..|.||.|-|||.|+||+|+..| -..
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 0 11233466889999999999999999999988 567
Q ss_pred ceeeEEecCcccc
Q 004714 426 RCEIWFSTGSSRD 438 (734)
Q Consensus 426 ~~E~k~~T~s~e~ 438 (734)
..++++.|.+..-
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=94.23 E-value=0.19 Score=61.95 Aligned_cols=88 Identities=16% Similarity=0.226 Sum_probs=74.1
Q ss_pred CCcccCceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecCCceeEeecCCcceeeeEEEEec
Q 004714 339 SNVIVPNMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSS 418 (734)
Q Consensus 339 ~~l~~~~~~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~~~p~~r~~vs~L~P~TEY~fkvvsF 418 (734)
-...++..+....++++.++|..+-..---+-++||.|=||+..+.|-..+...+....++..|+||.|-|-|.|.|-++
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 33556677888899999999998655322378999999999999988777887788888999999999999999999999
Q ss_pred cCCccCcce
Q 004714 419 NGTTELGRC 427 (734)
Q Consensus 419 ~~~~elg~~ 427 (734)
|..| .|..
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=93.24 E-value=0.28 Score=59.06 Aligned_cols=88 Identities=23% Similarity=0.295 Sum_probs=70.6
Q ss_pred ceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecCCceeEeecCCcceeeeEEEEeccCCc--
Q 004714 345 NMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNGTT-- 422 (734)
Q Consensus 345 ~~~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~~~-- 422 (734)
.-+|.+.++++||++-+...+.....|.-|-|=|+...+. +.--.++..+.++..|.+|.|.|.|.|+|=+.|..|
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 112236777889999999999999999999999865
Q ss_pred cCc-ceeeEEecC
Q 004714 423 ELG-RCEIWFSTG 434 (734)
Q Consensus 423 elg-~~E~k~~T~ 434 (734)
-|+ ..|++..+.
T Consensus 525 ~~S~~~~fqT~~~ 537 (996)
T KOG0196|consen 525 PYSGKHEFQTLPS 537 (996)
T ss_pred CCCCceeeeecCc
Confidence 333 556666654
No 11
>KOG3513 consensus Neural cell adhesion molecule L1 [Signal transduction mechanisms]
Probab=85.22 E-value=2.3 Score=52.84 Aligned_cols=85 Identities=28% Similarity=0.342 Sum_probs=57.4
Q ss_pred CCCCCcccCceEEEEEeeceeEEEEeCcCC-CCCCCcceEEEEeeecCCC-CCCCCceeeecCCc---eeEeecCCccee
Q 004714 336 VQGSNVIVPNMVKFEDVRATSLTVVLGSED-PSPGNIISYTLWHRRAHEG-FPARPTCTLFAPNT---RFVVTGLCPATE 410 (734)
Q Consensus 336 ~q~~~l~~~~~~rFE~vt~tSv~vvL~~~~-~s~~~i~Gy~LWhrks~~~-y~~ept~~~~~p~~---r~~vs~L~P~TE 410 (734)
+++...|+. .+..++|+++++.|-..-.. .-+. |.+|.+=.|-..-. .-. -+ +++--.+ ...|-||.|=+|
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 004714 411 YQFKVVSSNGTTEL 424 (734)
Q Consensus 411 Y~fkvvsF~~~~el 424 (734)
|.|||++++..|.=
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=84.69 E-value=0.18 Score=39.80 Aligned_cols=48 Identities=31% Similarity=0.719 Sum_probs=34.6
Q ss_pred eeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhhhccccccccCCCccccceeEEeccCC
Q 004714 162 CCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECALKNERSGIGKDRCYSGLDGSFYCISCR 227 (734)
Q Consensus 162 C~IC~kfD~nkd~~~Wl~C~s~~~~~~~~Cgh~cHleCALr~~~~G~~~~g~~~~lD~~f~C~~Cg 227 (734)
|.||.+ ..+...||.|+ .|+.|-|+.|.--....-.. .+..|+|..|-
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=82.73 E-value=2.1 Score=33.87 Aligned_cols=39 Identities=36% Similarity=0.514 Sum_probs=32.1
Q ss_pred hchhcHHHHHHHHHHHhCCcccccCcchHHHHHHHHHhhcc
Q 004714 42 LRSWTRQEILQILCAELGKERKYTGLTKLKIIENLLKLVSE 82 (734)
Q Consensus 42 LqswsR~Eil~ilCAe~gkERKytgltK~k~ie~Llk~vs~ 82 (734)
|+++|..||.+ |+.++|-+ .|+++.|..+|..|++.-++
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 58999999999999998874
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=68.34 E-value=2.3 Score=32.83 Aligned_cols=16 Identities=31% Similarity=0.802 Sum_probs=13.9
Q ss_pred ccceeEEeccCCCccc
Q 004714 216 GLDGSFYCISCRKVND 231 (734)
Q Consensus 216 ~lD~~f~C~~Cgk~sd 231 (734)
.-||.|||.+||++.+
T Consensus 21 ~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 21 SDDGFYYCDRCGHQSE 36 (36)
T ss_pred ccCCEEEhhhCceEcC
Confidence 4699999999999864
No 15
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=56.65 E-value=4.8 Score=34.79 Aligned_cols=62 Identities=23% Similarity=0.332 Sum_probs=23.4
Q ss_pred eeeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhhhccccccccCCCccccceeEEeccCCCcc
Q 004714 161 SCCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECALKNERSGIGKDRCYSGLDGSFYCISCRKVN 230 (734)
Q Consensus 161 sC~IC~kfD~nkd~~~Wl~C~s~~~~~~~~Cgh~cHleCALr~~~~G~~~~g~~~~lD~~f~C~~Cgk~s 230 (734)
.|.||+.+....+.-..+.|+ ...|++..|+.|-.+-.+.-......-+.. .=.|..|.++-
T Consensus 4 ~C~IC~~~~~~~~~~p~~~C~------n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~--~G~CP~C~~~i 65 (70)
T PF11793_consen 4 ECGICYSYRLDDGEIPDVVCP------NPSCGKKFHLLCLSEWFLSLEKSRQSFIPI--FGECPYCSSPI 65 (70)
T ss_dssp S-SSS--SS-TT-----B--S-------TT----B-SGGGHHHHHHHHSSS-TTT----EEE-TTT-SEE
T ss_pred CCCcCCcEecCCCCcCceEcC------CcccCCHHHHHHHHHHHHHcccCCeeeccc--ccCCcCCCCee
Confidence 589999886655556678997 238999999999776654322111000112 22488887753
No 16
>KOG4222 consensus Axon guidance receptor Dscam [Signal transduction mechanisms]
Probab=51.62 E-value=32 Score=43.82 Aligned_cols=71 Identities=14% Similarity=0.179 Sum_probs=51.7
Q ss_pred EeeceeEEEEeCcCCC--CCCCcceEEEEeeecCCC-CCCCCceeeecCCceeEeecCCcceeeeEEEEeccCCcc
Q 004714 351 DVRATSLTVVLGSEDP--SPGNIISYTLWHRRAHEG-FPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNGTTE 423 (734)
Q Consensus 351 ~vt~tSv~vvL~~~~~--s~~~i~Gy~LWhrks~~~-y~~ept~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~~~e 423 (734)
.-.-|+.-|+..-..+ .-+.+.||++|.=--.+. +-.+-|.. .+-...+|.+|.|.+-|.|++.++|+.|+
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 3344555566555532 468899999998655434 44444433 77788999999999999999999999774
No 17
>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=49.92 E-value=13 Score=33.92 Aligned_cols=18 Identities=28% Similarity=0.645 Sum_probs=12.6
Q ss_pred eeEEeccCCCccchhHHH
Q 004714 219 GSFYCISCRKVNDLLGCW 236 (734)
Q Consensus 219 ~~f~C~~Cgk~sdLlg~w 236 (734)
+.|||-+||+.-|.+.++
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 479999999999999844
No 18
>KOG4222 consensus Axon guidance receptor Dscam [Signal transduction mechanisms]
Probab=49.49 E-value=19 Score=45.66 Aligned_cols=69 Identities=23% Similarity=0.223 Sum_probs=50.7
Q ss_pred EeeceeEEEEeCcCCC-CCCCcceEEEEeeecCCC--CCCCCceeeecCCceeEeecCCcceeeeEEEEeccC
Q 004714 351 DVRATSLTVVLGSEDP-SPGNIISYTLWHRRAHEG--FPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNG 420 (734)
Q Consensus 351 ~vt~tSv~vvL~~~~~-s~~~i~Gy~LWhrks~~~--y~~ept~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~ 420 (734)
.++|++|-+-..-.-. .++-|.||++=||-..-. --..-..+.+.|+ -+||.||.|.|.|.|++.+|..
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 3566666665444433 478899999999988764 3334444555554 7899999999999999999998
No 19
>PHA02739 hypothetical protein; Provisional
Probab=41.17 E-value=28 Score=33.59 Aligned_cols=27 Identities=26% Similarity=0.406 Sum_probs=22.4
Q ss_pred ceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCC
Q 004714 345 NMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEG 384 (734)
Q Consensus 345 ~~~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~ 384 (734)
..++|++|||.|.. -+|.||.||..+.
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=35.75 E-value=34 Score=38.46 Aligned_cols=34 Identities=29% Similarity=0.342 Sum_probs=17.4
Q ss_pred eeEeecCCcceeeeEEEEeccCCccCcceeeEEecC
Q 004714 399 RFVVTGLCPATEYQFKVVSSNGTTELGRCEIWFSTG 434 (734)
Q Consensus 399 r~~vs~L~P~TEY~fkvvsF~~~~elg~~E~k~~T~ 434 (734)
++.|+||+|.|.|.||+..- .+..-.-.-++.|.
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
>PLN02533 probable purple acid phosphatase
Probab=33.50 E-value=28 Score=39.46 Aligned_cols=80 Identities=18% Similarity=0.203 Sum_probs=43.0
Q ss_pred eEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceee--------ecC--CceeEeecCCcceeeeEEE
Q 004714 346 MVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTL--------FAP--NTRFVVTGLCPATEYQFKV 415 (734)
Q Consensus 346 ~~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~--------~~p--~~r~~vs~L~P~TEY~fkv 415 (734)
+|++-=..+++++|..-..+... -.+.|..+...+....+.+. ..+ --+.+|++|+|.|+|.|||
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 12344433322222222221 011 1257999999999999999
Q ss_pred EeccCCccCcceeeEEecCc
Q 004714 416 VSSNGTTELGRCEIWFSTGS 435 (734)
Q Consensus 416 vsF~~~~elg~~E~k~~T~s 435 (734)
-.-+ ...+..|.|..
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 22
>KOG0196 consensus Tyrosine kinase, EPH (ephrin) receptor family [Signal transduction mechanisms]
Probab=31.07 E-value=2.1e+02 Score=36.02 Aligned_cols=88 Identities=20% Similarity=0.255 Sum_probs=58.1
Q ss_pred ccCceEEEEEeeceeEEEEeCcCCCC-CCCcceEEEEeeecCCC----CCCCCceee-----ecCCceeEeecCCcceee
Q 004714 342 IVPNMVKFEDVRATSLTVVLGSEDPS-PGNIISYTLWHRRAHEG----FPARPTCTL-----FAPNTRFVVTGLCPATEY 411 (734)
Q Consensus 342 ~~~~~~rFE~vt~tSv~vvL~~~~~s-~~~i~Gy~LWhrks~~~----y~~ept~~~-----~~p~~r~~vs~L~P~TEY 411 (734)
|++.+=.+-+|+.|||.+-+.....+ .-.=.-|.+=+++-.-. -+=.+...+ -..++++.|+||-|-|.|
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 112223222 123678999999999999
Q ss_pred eEEEEeccCCccCcceee
Q 004714 412 QFKVVSSNGTTELGRCEI 429 (734)
Q Consensus 412 ~fkvvsF~~~~elg~~E~ 429 (734)
+|-|-+-++..+++..=-
T Consensus 412 TFeV~AvNgVS~lsp~~~ 429 (996)
T KOG0196|consen 412 TFEVEAVNGVSDLSPFPR 429 (996)
T ss_pred EEEEEEeecccccCCCCC
Confidence 999999999998886643
No 23
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=28.08 E-value=43 Score=42.48 Aligned_cols=52 Identities=33% Similarity=0.738 Sum_probs=36.0
Q ss_pred ccCCcCCcCCceeeeecccc-CCCCCccEEecCCCCCCCCCcccchhhhhhhhhccccccccCCCccccceeEEeccCC
Q 004714 150 LRKEDVFCKRCSCCICRKYD-DNKDPSLWLTCSSEPPFGGDSCGMSCHLECALKNERSGIGKDRCYSGLDGSFYCISCR 227 (734)
Q Consensus 150 L~~ed~FCr~CsC~IC~kfD-~nkd~~~Wl~C~s~~~~~~~~Cgh~cHleCALr~~~~G~~~~g~~~~lD~~f~C~~Cg 227 (734)
+-.+|++| +||.+-+ +|.|.. |.|| -|+...|.+|-= +- .-.||+.-|++|.
T Consensus 215 ~~~~D~~C-----~iC~~~~~~n~n~i--vfCD--------~Cnl~VHq~Cyg------i~-----~ipeg~WlCr~Cl 267 (1051)
T KOG0955|consen 215 LLEEDAVC-----CICLDGECQNSNVI--VFCD--------GCNLAVHQECYG------IP-----FIPEGQWLCRRCL 267 (1051)
T ss_pred ccCCCccc-----eeecccccCCCceE--EEcC--------CCcchhhhhccC------CC-----CCCCCcEeehhhc
Confidence 44577875 7777776 555554 6899 999999999953 21 2256777777774
No 24
>KOG4802 consensus Adhesion-type protein [Extracellular structures]
Probab=26.65 E-value=7.2e+02 Score=29.31 Aligned_cols=95 Identities=16% Similarity=0.164 Sum_probs=58.3
Q ss_pred ccCceEEEEEeeceeE--EEEeCcCCCCCCCcceEEE---EeeecCCC-CCCCCceeeecCCceeEeecCCcceeeeEEE
Q 004714 342 IVPNMVKFEDVRATSL--TVVLGSEDPSPGNIISYTL---WHRRAHEG-FPARPTCTLFAPNTRFVVTGLCPATEYQFKV 415 (734)
Q Consensus 342 ~~~~~~rFE~vt~tSv--~vvL~~~~~s~~~i~Gy~L---Whrks~~~-y~~ept~~~~~p~~r~~vs~L~P~TEY~fkv 415 (734)
|+++-.++-.|.+.-. ++|..-..++-=-|..|++ ||=++-+. -+..-+...-..+ |.|.+|.|-..|..-|
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 PSPNDLKLIGVQFDGRYMLKVVWCPSKSDLPVEKYKITWSLYVNSAKASMITKSSYVKDTHQ--FSIKELLPNSSYYVEV 331 (516)
T ss_pred cCcccceeeeeeecceEEEEEEeCCCCCCCcceeeEEEeehhhhhhhhhcccccceeeccch--hhhhhcCCCCeEEEEE
Confidence 4444555555554432 2344444445455888987 44444444 5555555554444 4499999999998765
Q ss_pred --EeccCCccCcceeeEEecCcccc
Q 004714 416 --VSSNGTTELGRCEIWFSTGSSRD 438 (734)
Q Consensus 416 --vsF~~~~elg~~E~k~~T~s~e~ 438 (734)
|+|.++++|-.--.-.||...+-
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 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=26.49 E-value=1.1e+02 Score=31.43 Aligned_cols=45 Identities=27% Similarity=0.345 Sum_probs=34.6
Q ss_pred ecCCceeEeecCCcceeeeEEEEeccCCccCcceeeEEecCcccc
Q 004714 394 FAPNTRFVVTGLCPATEYQFKVVSSNGTTELGRCEIWFSTGSSRD 438 (734)
Q Consensus 394 ~~p~~r~~vs~L~P~TEY~fkvvsF~~~~elg~~E~k~~T~s~e~ 438 (734)
..+..-+.|+||+|.|-|.|+-.-=++..-...+|.-..|....+
T Consensus 98 ~trlsaYqVtNL~pGTkY~isY~VtkgtstESS~~i~msT~n~~~ 142 (184)
T PF07353_consen 98 VTRLSAYQVTNLQPGTKYYISYLVTKGTSTESSNEIPMSTLNRKN 142 (184)
T ss_pred eccceeEEeeccCCCcEEEEEEEEecCccceecceeccccccccc
Confidence 345567789999999999999887677777777777777765444
No 26
>KOG4258 consensus Insulin/growth factor receptor (contains protein kinase domain) [Signal transduction mechanisms]
Probab=26.43 E-value=3.8e+02 Score=34.01 Aligned_cols=110 Identities=19% Similarity=0.254 Sum_probs=70.2
Q ss_pred HHHHHHHHHhhhhhhcCCC-C--CCCCCCCCCcccCc-----eEEEEEeeceeEEEEe-CcCCCCCCCcceEEEEeeecC
Q 004714 312 QKLCACAVESLDKMISNTI-L--PNPSVQGSNVIVPN-----MVKFEDVRATSLTVVL-GSEDPSPGNIISYTLWHRRAH 382 (734)
Q Consensus 312 QKLCs~Aie~~Ds~ls~~~-~--~~~~~q~~~l~~~~-----~~rFE~vt~tSv~vvL-~~~~~s~~~i~Gy~LWhrks~ 382 (734)
-|||-.-|-.|.+.+...- + .+-..+-..--++| +|-.--.++.||.+.+ .+.-+-..+..||.|.|.-+.
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 3444556677888874 444346889999999987765
Q ss_pred CC----CCCCCcee--------eecC-------C-ceeEeecCCcceeeeEEEEeccCC
Q 004714 383 EG----FPARPTCT--------LFAP-------N-TRFVVTGLCPATEYQFKVVSSNGT 421 (734)
Q Consensus 383 ~~----y~~ept~~--------~~~p-------~-~r~~vs~L~P~TEY~fkvvsF~~~ 421 (734)
.+ |-..+.|. +.-| + -++++.+|+|-|.|.+=|-.|+-+
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 44455542 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=25.96 E-value=41 Score=25.50 Aligned_cols=31 Identities=45% Similarity=0.883 Sum_probs=22.9
Q ss_pred eeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhhh
Q 004714 162 CCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECALK 202 (734)
Q Consensus 162 C~IC~kfD~nkd~~~Wl~C~s~~~~~~~~Cgh~cHleCALr 202 (734)
|.+|.++.-... -++.|. .|+..+|-.|+-+
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 566666654432 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=25.06 E-value=42 Score=25.81 Aligned_cols=33 Identities=39% Similarity=0.634 Sum_probs=23.7
Q ss_pred eeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhhhc
Q 004714 162 CCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECALKN 203 (734)
Q Consensus 162 C~IC~kfD~nkd~~~Wl~C~s~~~~~~~~Cgh~cHleCALr~ 203 (734)
|.+|.++.-.. +--++.|+ .|+..+|-.|+-+-
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=23.85 E-value=4.5e+02 Score=23.78 Aligned_cols=81 Identities=16% Similarity=0.256 Sum_probs=56.3
Q ss_pred CCCcccCceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCC-CCCCCceeeecCCceeEeecCC--cceeeeEE
Q 004714 338 GSNVIVPNMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEG-FPARPTCTLFAPNTRFVVTGLC--PATEYQFK 414 (734)
Q Consensus 338 ~~~l~~~~~~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~-y~~ept~~~~~p~~r~~vs~L~--P~TEY~fk 414 (734)
...++++.-++|.-+.-. .++-.+... ....-.-|.+.|+..... ...-|.|.=. .++..-+++.. +.-.|.+|
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 456788888888877555 455566633 233567899999955555 6666777544 34777787755 78889999
Q ss_pred EEeccCC
Q 004714 415 VVSSNGT 421 (734)
Q Consensus 415 vvsF~~~ 421 (734)
|.++.+.
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
>KOG1948 consensus Metalloproteinase-related collagenase pM5 [Posttranslational modification, protein turnover, chaperones]
Probab=22.79 E-value=1.4e+02 Score=37.72 Aligned_cols=68 Identities=19% Similarity=0.226 Sum_probs=50.3
Q ss_pred EEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecC--------------------C-C-CCCCCceeeecCCceeEeec
Q 004714 347 VKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAH--------------------E-G-FPARPTCTLFAPNTRFVVTG 404 (734)
Q Consensus 347 ~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~--------------------~-~-y~~ept~~~~~p~~r~~vs~ 404 (734)
++|| |+|.+|.+++.....-.++||++=|---. . . |++|-| ..-+-.+-|-|
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 444433 45677899999
Q ss_pred CCcceeeeEEEEeccC
Q 004714 405 LCPATEYQFKVVSSNG 420 (734)
Q Consensus 405 L~P~TEY~fkvvsF~~ 420 (734)
|.|.++|..|+.++-+
T Consensus 953 L~Pdc~Y~V~vk~~~~ 968 (1165)
T KOG1948|consen 953 LLPDCEYQVHVKSYAD 968 (1165)
T ss_pred cCCCceEEEEEeeccC
Confidence 9999999999999854
No 31
>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=22.53 E-value=46 Score=24.16 Aligned_cols=18 Identities=39% Similarity=0.923 Sum_probs=9.0
Q ss_pred ccEEecCCCCCCCCCcccchhhhhhh
Q 004714 175 SLWLTCSSEPPFGGDSCGMSCHLECA 200 (734)
Q Consensus 175 ~~Wl~C~s~~~~~~~~Cgh~cHleCA 200 (734)
..+-.|. .|...-|++||
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 32
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.41 E-value=39 Score=24.06 Aligned_cols=16 Identities=31% Similarity=0.933 Sum_probs=14.1
Q ss_pred cccccccCCcCCcCCc
Q 004714 145 ACRATLRKEDVFCKRC 160 (734)
Q Consensus 145 aCra~L~~ed~FCr~C 160 (734)
.|.+.+..++.||..|
T Consensus 7 ~Cg~~~~~~~~fC~~C 22 (26)
T PF13248_consen 7 NCGAEIDPDAKFCPNC 22 (26)
T ss_pred ccCCcCCcccccChhh
Confidence 5888899999999887
No 33
>KOG4802 consensus Adhesion-type protein [Extracellular structures]
Probab=21.50 E-value=1.3e+02 Score=35.03 Aligned_cols=80 Identities=16% Similarity=0.077 Sum_probs=57.4
Q ss_pred CcccCceEEEEEeeceeEEEEeCcCCCCC--CCc-------------ceEEEEeeecCCCCCCCCceeeecCCceeEeec
Q 004714 340 NVIVPNMVKFEDVRATSLTVVLGSEDPSP--GNI-------------ISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTG 404 (734)
Q Consensus 340 ~l~~~~~~rFE~vt~tSv~vvL~~~~~s~--~~i-------------~Gy~LWhrks~~~y~~ept~~~~~p~~r~~vs~ 404 (734)
-|++-..++|+.-.-+|+.|-+...-.+. ..+ .+--.|||+..+ ...+.-++..++
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 004714 405 LCPATEYQFKVVSSNGTTELGRCE 428 (734)
Q Consensus 405 L~P~TEY~fkvvsF~~~~elg~~E 428 (734)
+.|+-=|.|||-+-+-.|-+|-.|
T Consensus 216 ~rPgRwyefrvaavn~~G~rGFs~ 239 (516)
T KOG4802|consen 216 MRPGRWYEFRVAAVNAYGFRGFSE 239 (516)
T ss_pred cCcceeEEEEEeeeecccccccCC
Confidence 999999999999999999888655
No 34
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=20.08 E-value=1.6e+02 Score=26.78 Aligned_cols=36 Identities=22% Similarity=0.540 Sum_probs=29.7
Q ss_pred chhcHHHHHHHHHHHhCCcccc-----cCcchHHHHHHHHH
Q 004714 43 RSWTRQEILQILCAELGKERKY-----TGLTKLKIIENLLK 78 (734)
Q Consensus 43 qswsR~Eil~ilCAe~gkERKy-----tgltK~k~ie~Llk 78 (734)
+++||++|.+.|.+.+|.+-.| .|+|-..+|+.|.+
T Consensus 16 ~~~t~~~L~~~i~~~FG~~arFhTCSa~~m~a~~Li~FL~~ 56 (77)
T TIGR03853 16 EPYTRESLKAAIEQKFGEDARFHTCSAEGMTADELLQFLLK 56 (77)
T ss_pred CCcCHHHHHHHHHHHhCCCceEeecccccCCHHHHHHHHHH
Confidence 6899999999999999998766 47777777776654
Done!