Query 005110
Match_columns 714
No_of_seqs 100 out of 114
Neff 3.8
Searched_HMMs 46136
Date Thu Mar 28 18:12:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005110.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005110hhsearch_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 1.5E-52 3.1E-57 450.4 5.5 153 111-271 90-256 (446)
2 PF00041 fn3: Fibronectin type 98.6 2.9E-07 6.3E-12 75.5 8.7 82 323-406 2-83 (85)
3 cd00063 FN3 Fibronectin type 3 98.0 7.3E-05 1.6E-09 59.4 9.9 72 327-402 7-81 (93)
4 smart00060 FN3 Fibronectin typ 97.1 0.0054 1.2E-07 47.1 9.1 74 327-402 7-81 (83)
5 KOG4221 Receptor mediating net 95.7 0.018 3.8E-07 70.8 6.5 76 325-403 620-699 (1381)
6 PF09294 Interfer-bind: Interf 95.6 0.029 6.4E-07 49.4 6.1 85 324-412 5-103 (106)
7 KOG3513 Neural cell adhesion m 94.1 0.22 4.8E-06 61.2 9.8 89 318-407 817-905 (1051)
8 KOG4221 Receptor mediating net 94.0 0.18 4E-06 62.4 8.8 88 327-418 527-615 (1381)
9 smart00249 PHD PHD zinc finger 94.0 0.059 1.3E-06 40.2 3.1 46 142-206 2-47 (47)
10 KOG0196 Tyrosine kinase, EPH ( 93.2 0.29 6.3E-06 58.8 8.5 88 325-414 447-537 (996)
11 KOG3513 Neural cell adhesion m 85.6 2.2 4.7E-05 52.9 7.8 76 326-404 620-700 (1051)
12 PF00628 PHD: PHD-finger; Int 84.9 0.17 3.7E-06 39.8 -1.2 48 142-207 2-49 (51)
13 PF07498 Rho_N: Rho terminatio 82.2 2.2 4.8E-05 33.6 4.0 39 22-62 2-40 (43)
14 PF11781 RRN7: RNA polymerase 69.5 2.1 4.6E-05 32.9 0.8 16 196-211 21-36 (36)
15 PF11793 FANCL_C: FANCL C-term 57.5 4.4 9.5E-05 34.9 0.6 62 141-210 4-65 (70)
16 PF01807 zf-CHC2: CHC2 zinc fi 51.9 11 0.00025 34.1 2.4 18 199-216 53-70 (97)
17 KOG4222 Axon guidance receptor 51.0 33 0.00071 43.6 6.7 71 331-403 759-832 (1281)
18 KOG4222 Axon guidance receptor 50.5 18 0.00039 45.7 4.4 69 331-400 652-723 (1281)
19 PLN02533 probable purple acid 42.2 59 0.0013 36.8 6.6 80 326-415 46-135 (427)
20 KOG4802 Adhesion-type protein 40.9 3.1E+02 0.0067 32.0 11.6 98 319-418 251-356 (516)
21 PHA02739 hypothetical protein; 40.1 30 0.00065 33.3 3.3 27 325-364 40-66 (116)
22 PF09423 PhoD: PhoD-like phosp 33.5 39 0.00085 37.9 3.5 19 379-397 65-83 (453)
23 KOG0955 PHD finger protein BR1 31.0 36 0.00078 43.0 2.9 52 130-207 215-267 (1051)
24 KOG0196 Tyrosine kinase, EPH ( 30.8 2.6E+02 0.0056 35.2 9.6 87 322-408 332-428 (996)
25 PF07353 Uroplakin_II: Uroplak 26.9 1.1E+02 0.0024 31.4 4.9 45 374-418 98-142 (184)
26 smart00109 C1 Protein kinase C 26.4 41 0.00089 25.4 1.5 31 142-182 14-44 (49)
27 cd00029 C1 Protein kinase C co 25.5 41 0.00089 25.8 1.4 33 142-183 14-46 (50)
28 PF01108 Tissue_fac: Tissue fa 25.2 4.1E+02 0.0089 23.9 8.0 81 318-401 19-102 (107)
29 KOG4258 Insulin/growth factor 25.0 4.2E+02 0.0091 33.5 10.0 110 292-401 451-589 (1025)
30 KOG1948 Metalloproteinase-rela 24.6 1.2E+02 0.0026 38.1 5.5 64 334-400 883-968 (1165)
31 PF13248 zf-ribbon_3: zinc-rib 23.2 38 0.00082 24.1 0.7 16 125-140 7-22 (26)
32 KOG4802 Adhesion-type protein 22.7 1.2E+02 0.0025 35.2 4.7 81 319-408 144-239 (516)
33 PF07649 C1_3: C1-like domain; 22.6 46 0.001 24.1 1.1 18 155-180 13-30 (30)
34 PF04775 Bile_Hydr_Trans: Acyl 20.1 1.5E+02 0.0031 28.3 4.1 36 379-414 6-41 (126)
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=1.5e-52 Score=450.38 Aligned_cols=153 Identities=39% Similarity=0.770 Sum_probs=143.7
Q ss_pred CCCCCCcccccccccccccccCCc----------CCcCCceeeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhh
Q 005110 111 SGSDLVNAIYCKNSACRATLRKED----------VFCKRCSCCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECA 180 (714)
Q Consensus 111 ~~~~~~~~~~C~N~aCra~L~~ed----------~FCr~CsC~IC~kfD~nkd~~~Wl~C~s~~~~~~~~Cgh~cHleCA 180 (714)
.=.++|.+.+|||+||||+||++| |||++||||||+|||+|+|||+||+|| +||||||+|||
T Consensus 90 ~LveiFl~~rCrN~aC~s~LP~ddc~C~iC~~~~gFC~~C~C~iC~kfD~~~n~~~Wi~Cd--------~CgH~cH~dCA 161 (446)
T PF07227_consen 90 ELVEIFLYKRCRNLACRSQLPVDDCDCKICCSEPGFCRRCMCCICSKFDDNKNTCSWIGCD--------VCGHWCHLDCA 161 (446)
T ss_pred HHHHHHHHHhcCCHHhhccCCccccCcchhcCCCCccccCCccccCCcccCCCCeeEEecc--------CCCceehhhhh
Confidence 345689999999999999999976 999999999999999999999999998 99999999999
Q ss_pred hhcccccccc--CCCccCcceeEEeccCCCccchhHHHHHHHHHhhccccchhhhhhhhchhhhccccH--HHHHHHHHH
Q 005110 181 LKNERSGIGK--DRCYSGLDGSFYCISCRKVNDLLGCWKKQLVVAKNTRRVDILCYRLSLGQKLVNATE--KYKNLSKIV 256 (714)
Q Consensus 181 Lr~~~~G~~~--~g~~~~lD~~f~C~~Cgk~sdLlg~w~Kql~~ake~rrvD~Lc~rL~l~~kll~GS~--~~k~L~~~v 256 (714)
||+++||+|. .|+.+++||+|||++|||+|||||||+++|.+|+++||+|+||+||++++|||+||+ +||+||+++
T Consensus 162 Lr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~seLlG~vk~vf~~ca~~~~~d~L~~eL~l~~rIf~GSed~rgk~L~~~~ 241 (446)
T PF07227_consen 162 LRHELIGTGPSVKGSIGTLDMQFHCRACGKTSELLGFVKKVFQTCAKAWRVDVLCKELDLVRRIFRGSEDYRGKELHEKV 241 (446)
T ss_pred cccccccCCccCCCCCccCceEEEccCCCChhhHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhCccchhHHHHHHHH
Confidence 9999997765 466688999999999999999999999999999999999999999999999999999 479999999
Q ss_pred HHHHHHhhhccCCCC
Q 005110 257 DDAVKMLEDEVGPLT 271 (714)
Q Consensus 257 e~A~~KLe~evgpl~ 271 (714)
++|++|||++++++.
T Consensus 242 e~al~KL~~~~~~~~ 256 (446)
T PF07227_consen 242 EEALAKLENGVIDSS 256 (446)
T ss_pred HHHHHHHhCCCCCHH
Confidence 999999999997653
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=98.58 E-value=2.9e-07 Score=75.49 Aligned_cols=82 Identities=26% Similarity=0.403 Sum_probs=67.9
Q ss_pred cCceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecCCceeEeecCCcceeeeEEEEeccCCc
Q 005110 323 VPNMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNGTT 402 (714)
Q Consensus 323 ~~~~~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~~~ 402 (714)
++..+++.+++++||+|-+.........+.||.|.++..... .......+....+.++|.||.|.|.|.|||.+++..|
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 005110 403 ELGR 406 (714)
Q Consensus 403 elg~ 406 (714)
.|.
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=97.98 E-value=7.3e-05 Score=59.43 Aligned_cols=72 Identities=31% Similarity=0.465 Sum_probs=56.9
Q ss_pred EEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeee---cCCceeEeecCCcceeeeEEEEeccCCc
Q 005110 327 VKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLF---APNTRFVVTGLCPATEYQFKVVSSNGTT 402 (714)
Q Consensus 327 ~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~~---~p~~r~~vs~L~P~TEY~fkvvsF~~~~ 402 (714)
|++....+.++.|.+.........+.+|.|++++..+. ....+. ....++.|.+|.|.|.|.|+|.++...+
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 3678999999999999999999998744
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=97.08 E-value=0.0054 Score=47.07 Aligned_cols=74 Identities=28% Similarity=0.385 Sum_probs=52.3
Q ss_pred EEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecC-CceeEeecCCcceeeeEEEEeccCCc
Q 005110 327 VKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAP-NTRFVVTGLCPATEYQFKVVSSNGTT 402 (714)
Q Consensus 327 ~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~~~p-~~r~~vs~L~P~TEY~fkvvsF~~~~ 402 (714)
+....+.+.++.|-.+..... .. .+|.+++.........+-..+...+ +.++.|.+|.|.|-|.|+|.+++..|
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=95.69 E-value=0.018 Score=70.77 Aligned_cols=76 Identities=21% Similarity=0.305 Sum_probs=60.8
Q ss_pred ceEEEEEeeceeEEEEeCcCCC--CCCCcceEEEEeeecCCC-CCCCCceeeec-CCceeEeecCCcceeeeEEEEeccC
Q 005110 325 NMVKFEDVRATSLTVVLGSEDP--SPGNIISYTLWHRRAHEG-FPARPTCTLFA-PNTRFVVTGLCPATEYQFKVVSSNG 400 (714)
Q Consensus 325 ~~~rFE~vt~tSv~vvL~~~~~--s~~~i~Gy~LWhrks~~~-y~~ept~~~~~-p~~r~~vs~L~P~TEY~fkvvsF~~ 400 (714)
.-++.|-+.++||.|-+....+ .-..|+||++=||+...+ +-. -++.. -.++.++.+|.|.|+|.|||-++|-
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 3499999999999999998875 357899999999966554 221 24444 6788899999999999999999987
Q ss_pred Ccc
Q 005110 401 TTE 403 (714)
Q Consensus 401 ~~e 403 (714)
-|.
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=95.60 E-value=0.029 Score=49.42 Aligned_cols=85 Identities=18% Similarity=0.164 Sum_probs=56.8
Q ss_pred CceEEEEEeeceeEEEEeCcCC---------CCCCCcce---EEEEeeecCCCCCCCCceeeecCCceeEeecCCcceee
Q 005110 324 PNMVKFEDVRATSLTVVLGSED---------PSPGNIIS---YTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEY 391 (714)
Q Consensus 324 ~~~~rFE~vt~tSv~vvL~~~~---------~s~~~i~G---y~LWhrks~~~y~~ept~~~~~p~~r~~vs~L~P~TEY 391 (714)
+..|.+ .+...+|.|.+.... .+..++-+ |+|-||+.... .-+-.+...++.++|.+|.|.|+|
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 344777 788888888766654 12344544 99999998764 234466778889999999999999
Q ss_pred eEEEEeccCCc-cCc-ceeeEEe
Q 005110 392 QFKVVSSNGTT-ELG-RCEIWFS 412 (714)
Q Consensus 392 ~fkvvsF~~~~-elg-~~E~k~~ 412 (714)
+|+|-+|.... .-| .++.+|.
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 3445554
No 7
>KOG3513 consensus Neural cell adhesion molecule L1 [Signal transduction mechanisms]
Probab=94.09 E-value=0.22 Score=61.17 Aligned_cols=89 Identities=16% Similarity=0.224 Sum_probs=74.3
Q ss_pred CCCcccCceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecCCceeEeecCCcceeeeEEEEe
Q 005110 318 GSNVIVPNMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEYQFKVVS 397 (714)
Q Consensus 318 ~~~l~~~~~~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~~~p~~r~~vs~L~P~TEY~fkvvs 397 (714)
+-...++..+....++++.++|..+-..---+-++||.|=||+..+.|-..+.-.+....++..|+||.|-|-|.|.|-+
T Consensus 817 d~P~~ap~~~~~~~~s~s~~~v~W~~~~~~nG~l~gY~v~Y~~~~~~~~~~~~~~i~~~~~~~~ltgL~~~T~Y~~~vrA 896 (1051)
T KOG3513|consen 817 DEPPVAPTKLSAKPLSSSEVNLSWKPPLWDNGKLTGYEVKYWKINEKEGSLSRVQIAGNRTSWRLTGLEPNTKYRFYVRA 896 (1051)
T ss_pred CCCCCCCccceeecccCceEEEEecCcCccCCccceeEEEEEEcCCCcccccceeecCCcceEeeeCCCCCceEEEEEEE
Confidence 33455667788889999999999865532227899999999999998877777778888899999999999999999999
Q ss_pred ccCCccCcce
Q 005110 398 SNGTTELGRC 407 (714)
Q Consensus 398 F~~~~elg~~ 407 (714)
+|..| .|..
T Consensus 897 ~nsaG-~Gp~ 905 (1051)
T KOG3513|consen 897 YTSAG-GGPA 905 (1051)
T ss_pred ecCCC-CCCC
Confidence 99999 7744
No 8
>KOG4221 consensus Receptor mediating netrin-dependent axon guidance [Signal transduction mechanisms]
Probab=93.97 E-value=0.18 Score=62.39 Aligned_cols=88 Identities=22% Similarity=0.272 Sum_probs=65.1
Q ss_pred EEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecCCceeEeecCCcceeeeEEEEeccCCc-cCc
Q 005110 327 VKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNGTT-ELG 405 (714)
Q Consensus 327 ~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~~~-elg 405 (714)
+.--...++++.|......--.+.|+||+|.|-..... .+ .-+-...+-..|.||.|-|||.|+||+|+..| -..
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 LQAYATSPTTILVTWEPPPFGNGPITGYKLFYSEDDTG--KE--LRVENNATEYTINGLEKYTEYSIRVVAYNSAGSGVS 602 (1381)
T ss_pred ccccccCcceEEEEecCCCCCCCCceEEEEEEEcCCCC--ce--EEEecCccEEEeecCCCccceEEEEEEecCCCCCCC
Confidence 44445667777777766654567899999999888322 11 11233467889999999999999999999988 567
Q ss_pred ceeeEEecCcccc
Q 005110 406 RCEIWFSTGSSRD 418 (714)
Q Consensus 406 ~~E~k~~T~s~e~ 418 (714)
..++++.|-+..-
T Consensus 603 S~~i~V~Tlsd~P 615 (1381)
T KOG4221|consen 603 SADITVRTLSDVP 615 (1381)
T ss_pred CCceEEEeccCCC
Confidence 8899999976433
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=93.21 E-value=0.29 Score=58.80 Aligned_cols=88 Identities=23% Similarity=0.295 Sum_probs=70.5
Q ss_pred ceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceeeecCCceeEeecCCcceeeeEEEEeccCCc--
Q 005110 325 NMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNGTT-- 402 (714)
Q Consensus 325 ~~~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~~~-- 402 (714)
.-+|.+.++++||++-+...+.....|.-|-|=|+...+. +.--.++..+.++..|.+|.|.|.|.|+|=+.|..|
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 4699999999999999999997767799999988887643 112236778889999999999999999999999865
Q ss_pred cCc-ceeeEEecC
Q 005110 403 ELG-RCEIWFSTG 414 (714)
Q Consensus 403 elg-~~E~k~~T~ 414 (714)
-|+ ..|++..+.
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=85.63 E-value=2.2 Score=52.94 Aligned_cols=76 Identities=28% Similarity=0.335 Sum_probs=54.0
Q ss_pred eEEEEEeeceeEEEEeCcCC-CCCCCcceEEEEeeecCCC-CCCCCceeeecCCc---eeEeecCCcceeeeEEEEeccC
Q 005110 326 MVKFEDVRATSLTVVLGSED-PSPGNIISYTLWHRRAHEG-FPARPTCTLFAPNT---RFVVTGLCPATEYQFKVVSSNG 400 (714)
Q Consensus 326 ~~rFE~vt~tSv~vvL~~~~-~s~~~i~Gy~LWhrks~~~-y~~ept~~~~~p~~---r~~vs~L~P~TEY~fkvvsF~~ 400 (714)
.+..++|+++++.|-..-.. .-+. |.+|.+=.|-..-. .-. -+ +++--.+ ...|-||.|=+||.|||++++.
T Consensus 620 ~v~~~~i~~t~~~lsW~~g~dn~Sp-I~~Y~iq~rt~~~~~W~~-v~-~vp~~~~~~~sa~vv~L~Pwv~YeFRV~AvN~ 696 (1051)
T KOG3513|consen 620 DVHVDDISDTTARLSWSPGSDNNSP-IEKYTIQFRTPFPGKWKA-VT-TVPGNITGDESATVVNLSPWVEYEFRVVAVNS 696 (1051)
T ss_pred ceeEeeeccceEEEEeecCCCCCCC-ceEEeEEecCCCCCcceE-ee-ECCCcccCccceeEEccCCCcceEEEEEEEcc
Confidence 79999999999999888775 4344 99999866654332 111 11 2222222 4778999999999999999998
Q ss_pred CccC
Q 005110 401 TTEL 404 (714)
Q Consensus 401 ~~el 404 (714)
.|.=
T Consensus 697 iG~g 700 (1051)
T KOG3513|consen 697 IGIG 700 (1051)
T ss_pred cccC
Confidence 7643
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=84.92 E-value=0.17 Score=39.81 Aligned_cols=48 Identities=31% Similarity=0.719 Sum_probs=34.5
Q ss_pred eeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhhhccccccccCCCccCcceeEEeccCC
Q 005110 142 CCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECALKNERSGIGKDRCYSGLDGSFYCISCR 207 (714)
Q Consensus 142 C~IC~kfD~nkd~~~Wl~C~s~~~~~~~~Cgh~cHleCALr~~~~G~~~~g~~~~lD~~f~C~~Cg 207 (714)
|.||.+ ..+...||.|+ .|+.|-|+.|.--....-.. .+..|+|..|-
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=82.16 E-value=2.2 Score=33.57 Aligned_cols=39 Identities=36% Similarity=0.514 Sum_probs=32.1
Q ss_pred hchhcHHHHHHHHHHHhCCcccccCcchHHHHHHHHhhhcc
Q 005110 22 LRSWTRQEILQILCAELGKERKYTGLTKLKIIENLLKLVSE 62 (714)
Q Consensus 22 LqswsR~Eil~ilcAe~gkERKytgltK~k~ie~Llk~vs~ 62 (714)
|+++|..||.+ |+.++|-+ -|+++.|..+|..|++.-++
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=69.54 E-value=2.1 Score=32.92 Aligned_cols=16 Identities=31% Similarity=0.802 Sum_probs=13.9
Q ss_pred CcceeEEeccCCCccc
Q 005110 196 GLDGSFYCISCRKVND 211 (714)
Q Consensus 196 ~lD~~f~C~~Cgk~sd 211 (714)
.-||.|||.+||++.+
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=57.45 E-value=4.4 Score=34.91 Aligned_cols=62 Identities=23% Similarity=0.332 Sum_probs=23.4
Q ss_pred eeeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhhhccccccccCCCccCcceeEEeccCCCcc
Q 005110 141 SCCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECALKNERSGIGKDRCYSGLDGSFYCISCRKVN 210 (714)
Q Consensus 141 sC~IC~kfD~nkd~~~Wl~C~s~~~~~~~~Cgh~cHleCALr~~~~G~~~~g~~~~lD~~f~C~~Cgk~s 210 (714)
.|.||+.+....+.-..+.|+ ...|++..|+.|-.+-.+.-......-+.. .=.|..|.++-
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 238999999999776654322111001122 22488888753
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=51.94 E-value=11 Score=34.07 Aligned_cols=18 Identities=28% Similarity=0.645 Sum_probs=12.7
Q ss_pred eeEEeccCCCccchhHHH
Q 005110 199 GSFYCISCRKVNDLLGCW 216 (714)
Q Consensus 199 ~~f~C~~Cgk~sdLlg~w 216 (714)
+.|+|-+||+.-|.+.++
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 479999999999999944
No 17
>KOG4222 consensus Axon guidance receptor Dscam [Signal transduction mechanisms]
Probab=51.01 E-value=33 Score=43.55 Aligned_cols=71 Identities=14% Similarity=0.179 Sum_probs=51.6
Q ss_pred EeeceeEEEEeCcCCC--CCCCcceEEEEeeecCCC-CCCCCceeeecCCceeEeecCCcceeeeEEEEeccCCcc
Q 005110 331 DVRATSLTVVLGSEDP--SPGNIISYTLWHRRAHEG-FPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNGTTE 403 (714)
Q Consensus 331 ~vt~tSv~vvL~~~~~--s~~~i~Gy~LWhrks~~~-y~~ept~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~~~e 403 (714)
.-.-|+.-|+..-+.. .-+.+.||++|.=--.+. +-.+-|.. .+-...+|.+|.|.+-|.|++.++|+.|+
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 3345555666555532 457899999998655434 44444433 77788999999999999999999999774
No 18
>KOG4222 consensus Axon guidance receptor Dscam [Signal transduction mechanisms]
Probab=50.49 E-value=18 Score=45.74 Aligned_cols=69 Identities=23% Similarity=0.223 Sum_probs=50.9
Q ss_pred EeeceeEEEEeCcCCC-CCCCcceEEEEeeecCCC--CCCCCceeeecCCceeEeecCCcceeeeEEEEeccC
Q 005110 331 DVRATSLTVVLGSEDP-SPGNIISYTLWHRRAHEG--FPARPTCTLFAPNTRFVVTGLCPATEYQFKVVSSNG 400 (714)
Q Consensus 331 ~vt~tSv~vvL~~~~~-s~~~i~Gy~LWhrks~~~--y~~ept~~~~~p~~r~~vs~L~P~TEY~fkvvsF~~ 400 (714)
.++|++|-+-..-.-. .++-|.||++=||-..-. -...-..+.+.|+ -+||.||.|.|.|.|++.+|..
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
>PLN02533 probable purple acid phosphatase
Probab=42.23 E-value=59 Score=36.83 Aligned_cols=80 Identities=18% Similarity=0.203 Sum_probs=42.9
Q ss_pred eEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCCCCCCCceee--------ecC--CceeEeecCCcceeeeEEE
Q 005110 326 MVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEGFPARPTCTL--------FAP--NTRFVVTGLCPATEYQFKV 395 (714)
Q Consensus 326 ~~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~y~~ept~~~--------~~p--~~r~~vs~L~P~TEY~fkv 395 (714)
+|++-=..+++++|..-..++.. -.+.|..+...+....+.+. ..+ --+.+|++|+|.|+|.|||
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 55544445788888776665311 12344433322222222221 011 1257999999999999999
Q ss_pred EeccCCccCcceeeEEecCc
Q 005110 396 VSSNGTTELGRCEIWFSTGS 415 (714)
Q Consensus 396 vsF~~~~elg~~E~k~~T~s 415 (714)
-.-+ ...+..|.|..
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 20
>KOG4802 consensus Adhesion-type protein [Extracellular structures]
Probab=40.92 E-value=3.1e+02 Score=32.03 Aligned_cols=98 Identities=15% Similarity=0.152 Sum_probs=59.9
Q ss_pred CCcccCceEEEEEeeceeE--EEEeCcCCCCCCCcceEEE---EeeecCCC-CCCCCceeeecCCceeEeecCCcceeee
Q 005110 319 SNVIVPNMVKFEDVRATSL--TVVLGSEDPSPGNIISYTL---WHRRAHEG-FPARPTCTLFAPNTRFVVTGLCPATEYQ 392 (714)
Q Consensus 319 ~~l~~~~~~rFE~vt~tSv--~vvL~~~~~s~~~i~Gy~L---Whrks~~~-y~~ept~~~~~p~~r~~vs~L~P~TEY~ 392 (714)
..-|+++-.++-.|.+.-. ++|..-..++-=-|..|++ ||=++-+. -+..-+...-..+ |.|.+|.|-..|.
T Consensus 251 kaPp~P~dl~l~~v~~dG~~~~~v~w~P~~sdlPv~~Yki~Ws~~v~s~k~~m~tks~~~k~thq--~si~~L~Pns~Y~ 328 (516)
T KOG4802|consen 251 KAPPSPNDLKLIGVQFDGRYMLKVVWCPSKSDLPVEKYKITWSLYVNSAKASMITKSSYVKDTHQ--FSIKELLPNSSYY 328 (516)
T ss_pred CCCcCcccceeeeeeecceEEEEEEeCCCCCCCcceeeEEEeehhhhhhhhhcccccceeeccch--hhhhhcCCCCeEE
Confidence 3444555566666655433 2344444445556888987 44444444 4445554444444 4499999999998
Q ss_pred EEE--EeccCCccCcceeeEEecCcccc
Q 005110 393 FKV--VSSNGTTELGRCEIWFSTGSSRD 418 (714)
Q Consensus 393 fkv--vsF~~~~elg~~E~k~~T~s~e~ 418 (714)
.-| |+|.++++|-.--.-.||....-
T Consensus 329 VevqAi~y~g~~rLksek~~~F~~T~~~ 356 (516)
T KOG4802|consen 329 VEVQAISYLGSRRLKSEKWMLFNTTLQP 356 (516)
T ss_pred EEEEEEEeccCcccccceEEEEeeccCc
Confidence 765 77888888875555677766544
No 21
>PHA02739 hypothetical protein; Provisional
Probab=40.06 E-value=30 Score=33.29 Aligned_cols=27 Identities=26% Similarity=0.406 Sum_probs=22.4
Q ss_pred ceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCC
Q 005110 325 NMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEG 364 (714)
Q Consensus 325 ~~~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~ 364 (714)
..++|++|||-|.. -+|.||.||..+.
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 22
>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=33.47 E-value=39 Score=37.87 Aligned_cols=19 Identities=42% Similarity=0.726 Sum_probs=14.0
Q ss_pred eeEeecCCcceeeeEEEEe
Q 005110 379 RFVVTGLCPATEYQFKVVS 397 (714)
Q Consensus 379 r~~vs~L~P~TEY~fkvvs 397 (714)
++.|+||+|.|.|.||+..
T Consensus 65 ~v~v~gL~p~t~Y~Y~~~~ 83 (453)
T PF09423_consen 65 KVDVTGLQPGTRYYYRFVV 83 (453)
T ss_dssp EEEE-S--TT-EEEEEEEE
T ss_pred ecccCCCCCCceEEEEEEE
Confidence 5889999999999999999
No 23
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=30.96 E-value=36 Score=42.97 Aligned_cols=52 Identities=33% Similarity=0.738 Sum_probs=35.9
Q ss_pred ccCCcCCcCCceeeeecccc-CCCCCccEEecCCCCCCCCCcccchhhhhhhhhccccccccCCCccCcceeEEeccCC
Q 005110 130 LRKEDVFCKRCSCCICRKYD-DNKDPSLWLTCSSEPPFGGDSCGMSCHLECALKNERSGIGKDRCYSGLDGSFYCISCR 207 (714)
Q Consensus 130 L~~ed~FCr~CsC~IC~kfD-~nkd~~~Wl~C~s~~~~~~~~Cgh~cHleCALr~~~~G~~~~g~~~~lD~~f~C~~Cg 207 (714)
+-.+|++| +||.+-+ +|.|.. |.|| -|+...|.+|-= +- .-.||+.-|++|.
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 44567875 7777776 555554 6899 999999999953 21 2356777777774
No 24
>KOG0196 consensus Tyrosine kinase, EPH (ephrin) receptor family [Signal transduction mechanisms]
Probab=30.85 E-value=2.6e+02 Score=35.18 Aligned_cols=87 Identities=21% Similarity=0.268 Sum_probs=57.8
Q ss_pred ccCceEEEEEeeceeEEEEeCcCCCC-CCCcceEEEEeeecCCC----CCCCCceee-----ecCCceeEeecCCcceee
Q 005110 322 IVPNMVKFEDVRATSLTVVLGSEDPS-PGNIISYTLWHRRAHEG----FPARPTCTL-----FAPNTRFVVTGLCPATEY 391 (714)
Q Consensus 322 ~~~~~~rFE~vt~tSv~vvL~~~~~s-~~~i~Gy~LWhrks~~~----y~~ept~~~-----~~p~~r~~vs~L~P~TEY 391 (714)
|++.+=.+-+|+.|||.+-+.....+ .-.=.-|.+=+++-.-. -+=.+...+ -..++++.|+||-|-|.|
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 44455555569999999988877543 32333466655544311 112223222 123678999999999999
Q ss_pred eEEEEeccCCccCccee
Q 005110 392 QFKVVSSNGTTELGRCE 408 (714)
Q Consensus 392 ~fkvvsF~~~~elg~~E 408 (714)
+|-|-+-++..+++..=
T Consensus 412 TFeV~AvNgVS~lsp~~ 428 (996)
T KOG0196|consen 412 TFEVEAVNGVSDLSPFP 428 (996)
T ss_pred EEEEEEeecccccCCCC
Confidence 99999999999888664
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=26.89 E-value=1.1e+02 Score=31.37 Aligned_cols=45 Identities=27% Similarity=0.345 Sum_probs=34.5
Q ss_pred ecCCceeEeecCCcceeeeEEEEeccCCccCcceeeEEecCcccc
Q 005110 374 FAPNTRFVVTGLCPATEYQFKVVSSNGTTELGRCEIWFSTGSSRD 418 (714)
Q Consensus 374 ~~p~~r~~vs~L~P~TEY~fkvvsF~~~~elg~~E~k~~T~s~e~ 418 (714)
..+..-+.|+||+|.|-|.|+-.-=++..-...+|.-..|....+
T Consensus 98 ~trlsaYqVtNL~pGTkY~isY~VtkgtstESS~~i~msT~n~~~ 142 (184)
T PF07353_consen 98 VTRLSAYQVTNLQPGTKYYISYLVTKGTSTESSNEIPMSTLNRKN 142 (184)
T ss_pred eccceeEEeeccCCCcEEEEEEEEecCccceecceeccccccccc
Confidence 345567889999999999999887677776777777777765444
No 26
>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=26.36 E-value=41 Score=25.44 Aligned_cols=31 Identities=45% Similarity=0.883 Sum_probs=22.8
Q ss_pred eeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhhh
Q 005110 142 CCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECALK 182 (714)
Q Consensus 142 C~IC~kfD~nkd~~~Wl~C~s~~~~~~~~Cgh~cHleCALr 182 (714)
|.+|.++.-... -++.|. .|+..+|-.|+-+
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 27
>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=25.49 E-value=41 Score=25.77 Aligned_cols=33 Identities=39% Similarity=0.634 Sum_probs=23.7
Q ss_pred eeeeccccCCCCCccEEecCCCCCCCCCcccchhhhhhhhhc
Q 005110 142 CCICRKYDDNKDPSLWLTCSSEPPFGGDSCGMSCHLECALKN 183 (714)
Q Consensus 142 C~IC~kfD~nkd~~~Wl~C~s~~~~~~~~Cgh~cHleCALr~ 183 (714)
|.+|.++.-.. +--++.|+ .|+..+|-.|+-+-
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 28
>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=25.21 E-value=4.1e+02 Score=23.92 Aligned_cols=81 Identities=16% Similarity=0.249 Sum_probs=56.3
Q ss_pred CCCcccCceEEEEEeeceeEEEEeCcCCCCCCCcceEEEEeeecCCC-CCCCCceeeecCCceeEeecCC--cceeeeEE
Q 005110 318 GSNVIVPNMVKFEDVRATSLTVVLGSEDPSPGNIISYTLWHRRAHEG-FPARPTCTLFAPNTRFVVTGLC--PATEYQFK 394 (714)
Q Consensus 318 ~~~l~~~~~~rFE~vt~tSv~vvL~~~~~s~~~i~Gy~LWhrks~~~-y~~ept~~~~~p~~r~~vs~L~--P~TEY~fk 394 (714)
...++++.-++|.-+.-. .++-.+.... ...-.-|.+.|+..... ...-|.|.=.. ++..-+++.. +.-.|.+|
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-HILRWDPGPG-SPPNVTYTVQYKKYGSSSWKDVPGCQNIT-ETSCDLTDETSDPSESYYAR 95 (107)
T ss_dssp -SSGSSCEEEEEEEETTE-EEEEEEESTT-SSSTEEEEEEEEESSTSCEEEECCEEEES-SSEEECTTCCTTTTSEEEEE
T ss_pred cccCCCCCeeEEEEECCc-eEEEeCCCCC-CCCCeEEEEEEEecCCcceeeccceeccc-ccceeCcchhhcCcCCEEEE
Confidence 457788888888877555 4455666332 33567899999955555 66667786443 4777887755 78889999
Q ss_pred EEeccCC
Q 005110 395 VVSSNGT 401 (714)
Q Consensus 395 vvsF~~~ 401 (714)
|.++.+.
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 29
>KOG4258 consensus Insulin/growth factor receptor (contains protein kinase domain) [Signal transduction mechanisms]
Probab=25.01 E-value=4.2e+02 Score=33.55 Aligned_cols=110 Identities=19% Similarity=0.254 Sum_probs=69.7
Q ss_pred HHHHHHHHHhhhhhhcCCC-C--CCCCCCCCCcccCc-----eEEEEEeeceeEEEEe-CcCCCCCCCcceEEEEeeecC
Q 005110 292 QKLCACAVESLDKMISNTI-L--PNPSVQGSNVIVPN-----MVKFEDVRATSLTVVL-GSEDPSPGNIISYTLWHRRAH 362 (714)
Q Consensus 292 QKLCs~Aie~~Ds~ls~~~-~--~~~~~q~~~l~~~~-----~~rFE~vt~tSv~vvL-~~~~~s~~~i~Gy~LWhrks~ 362 (714)
-|||-.-|-.|.+.+...- + .+-..+-..-.++| +|-.--.++.||.+.+ .+..+-..+..||.|.|.-+.
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 00011111111222 3444455667788874 444346789999999987765
Q ss_pred CC----CCCCCcee--------eecC-------C-ceeEeecCCcceeeeEEEEeccCC
Q 005110 363 EG----FPARPTCT--------LFAP-------N-TRFVVTGLCPATEYQFKVVSSNGT 401 (714)
Q Consensus 363 ~~----y~~ept~~--------~~~p-------~-~r~~vs~L~P~TEY~fkvvsF~~~ 401 (714)
.+ |-..+.|. +.-| + -++++.+|+|-|.|.+=|-.|+-+
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 44555543 1222 2 389999999999999988877544
No 30
>KOG1948 consensus Metalloproteinase-related collagenase pM5 [Posttranslational modification, protein turnover, chaperones]
Probab=24.63 E-value=1.2e+02 Score=38.06 Aligned_cols=64 Identities=14% Similarity=0.147 Sum_probs=48.3
Q ss_pred ceeEEEEeCcCCCCCCCcceEEEEeeec---------------------CCC-CCCCCceeeecCCceeEeecCCcceee
Q 005110 334 ATSLTVVLGSEDPSPGNIISYTLWHRRA---------------------HEG-FPARPTCTLFAPNTRFVVTGLCPATEY 391 (714)
Q Consensus 334 ~tSv~vvL~~~~~s~~~i~Gy~LWhrks---------------------~~~-y~~ept~~~~~p~~r~~vs~L~P~TEY 391 (714)
|+|.+|.+++...+.-.++||+.=|--- ... |++|- ...-+-.+-|-||.|.++|
T Consensus 883 Pst~mIevkeGq~~~vvl~gkRvAySayGtvssLsGdp~~gVaieA~sdn~~~y~eea---ttdenG~yRiRGL~Pdc~Y 959 (1165)
T KOG1948|consen 883 PSTSMIEVKEGQHENVVLKGKRVAYSAYGTVSSLSGDPMKGVAIEALSDNCDLYQEEA---TTDENGTYRIRGLLPDCEY 959 (1165)
T ss_pred CCceeEEeccCceEEEEEEEEEEEEEeeeehhhccCCcccCeEEEEecCCCCcccccc---ccccCCcEEEeccCCCceE
Confidence 7888999998887777788888766321 112 44443 3455778999999999999
Q ss_pred eEEEEeccC
Q 005110 392 QFKVVSSNG 400 (714)
Q Consensus 392 ~fkvvsF~~ 400 (714)
..|+.++-+
T Consensus 960 ~V~vk~~~~ 968 (1165)
T KOG1948|consen 960 QVHVKSYAD 968 (1165)
T ss_pred EEEEeeccC
Confidence 999999854
No 31
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=23.22 E-value=38 Score=24.06 Aligned_cols=16 Identities=31% Similarity=0.933 Sum_probs=14.1
Q ss_pred cccccccCCcCCcCCc
Q 005110 125 ACRATLRKEDVFCKRC 140 (714)
Q Consensus 125 aCra~L~~ed~FCr~C 140 (714)
.|.+.+..++.||..|
T Consensus 7 ~Cg~~~~~~~~fC~~C 22 (26)
T PF13248_consen 7 NCGAEIDPDAKFCPNC 22 (26)
T ss_pred ccCCcCCcccccChhh
Confidence 5888899999999887
No 32
>KOG4802 consensus Adhesion-type protein [Extracellular structures]
Probab=22.74 E-value=1.2e+02 Score=35.23 Aligned_cols=81 Identities=16% Similarity=0.082 Sum_probs=58.1
Q ss_pred CCcccCceEEEEEeeceeEEEEeCcCCCCC--CCc-------------ceEEEEeeecCCCCCCCCceeeecCCceeEee
Q 005110 319 SNVIVPNMVKFEDVRATSLTVVLGSEDPSP--GNI-------------ISYTLWHRRAHEGFPARPTCTLFAPNTRFVVT 383 (714)
Q Consensus 319 ~~l~~~~~~rFE~vt~tSv~vvL~~~~~s~--~~i-------------~Gy~LWhrks~~~y~~ept~~~~~p~~r~~vs 383 (714)
--|++-..++|+.-..+|+.|-+...-.+. ..+ .+--.|||+..+ ...+.-++..+
T Consensus 144 ~~l~Pr~k~~y~r~~~g~~av~w~~~~~~~v~~~~~~vr~~w~~g~hase~~~thwQtv~---------~t~~e~~~~~t 214 (516)
T KOG4802|consen 144 TQLPPRPKILYFRRSRGSHAVDWKIESSLLVYYVHVEVRSHWGRGFHASELGPTHWQTVE---------KTMEENTYIFT 214 (516)
T ss_pred CCCCCcchhhhhhhccCceeeeeeeccccceeeeehhhhhhhcccccccccccccceeee---------ecCCCceeeee
Confidence 356777899999999999999888776431 111 112235555544 23333388999
Q ss_pred cCCcceeeeEEEEeccCCccCccee
Q 005110 384 GLCPATEYQFKVVSSNGTTELGRCE 408 (714)
Q Consensus 384 ~L~P~TEY~fkvvsF~~~~elg~~E 408 (714)
++.|+-=|.|||-+-+-.|-+|-+|
T Consensus 215 ~~rPgRwyefrvaavn~~G~rGFs~ 239 (516)
T KOG4802|consen 215 DMRPGRWYEFRVAAVNAYGFRGFSE 239 (516)
T ss_pred ecCcceeEEEEEeeeecccccccCC
Confidence 9999999999999999999888665
No 33
>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=22.58 E-value=46 Score=24.07 Aligned_cols=18 Identities=39% Similarity=0.923 Sum_probs=9.0
Q ss_pred ccEEecCCCCCCCCCcccchhhhhhh
Q 005110 155 SLWLTCSSEPPFGGDSCGMSCHLECA 180 (714)
Q Consensus 155 ~~Wl~C~s~~~~~~~~Cgh~cHleCA 180 (714)
..+-.|. .|...-|++||
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 34
>PF04775 Bile_Hydr_Trans: Acyl-CoA thioester hydrolase/BAAT N-terminal region; InterPro: IPR006862 This entry presents the N-termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT) []. This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism []. For example, in peroxisomes, the hydrolase acts on bile-CoA esters [].; GO: 0016290 palmitoyl-CoA hydrolase activity, 0006629 lipid metabolic process; PDB: 3HLK_B 3K2I_B.
Probab=20.10 E-value=1.5e+02 Score=28.29 Aligned_cols=36 Identities=17% Similarity=0.189 Sum_probs=24.8
Q ss_pred eeEeecCCcceeeeEEEEeccCCccCcceeeEEecC
Q 005110 379 RFVVTGLCPATEYQFKVVSSNGTTELGRCEIWFSTG 414 (714)
Q Consensus 379 r~~vs~L~P~TEY~fkvvsF~~~~elg~~E~k~~T~ 414 (714)
+|.|+||.|.++|.++.....+.|..=+++|.+...
T Consensus 6 ~I~v~GL~p~~~vtl~a~~~~~~g~~w~S~A~f~Ad 41 (126)
T PF04775_consen 6 DIRVSGLPPGQEVTLRARLTDDNGVQWQSYATFRAD 41 (126)
T ss_dssp EEEEES--TT-EEEEEEEEE-TTS-EEEEEEEEE--
T ss_pred EEEEeCCCCCCEEEEEEEEEeCCCCEEEEEEEEEcC
Confidence 789999999999999999987767666777777654
Done!