Query 006008
Match_columns 665
No_of_seqs 209 out of 370
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 17:01:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006008.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006008hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1060 Vesicle coat complex A 100.0 1E-113 3E-118 953.9 37.4 521 1-658 426-968 (968)
2 PF14796 AP3B1_C: Clathrin-ada 100.0 6.4E-38 1.4E-42 296.8 10.9 132 340-493 2-145 (145)
3 PTZ00429 beta-adaptin; Provisi 100.0 7.8E-31 1.7E-35 301.8 12.3 143 1-165 402-547 (746)
4 KOG1061 Vesicle coat complex A 100.0 1.5E-30 3.3E-35 292.8 11.1 180 3-220 385-572 (734)
5 PF01602 Adaptin_N: Adaptin N 99.8 2E-20 4.3E-25 204.5 8.6 147 2-164 375-524 (526)
6 COG5096 Vesicle coat complex, 99.6 3.8E-16 8.2E-21 179.4 3.4 153 2-165 392-563 (757)
7 KOG1060 Vesicle coat complex A 98.4 1.1E-06 2.5E-11 101.3 11.7 128 459-596 767-915 (968)
8 KOG1062 Vesicle coat complex A 97.2 0.068 1.5E-06 63.2 23.6 160 39-227 446-622 (866)
9 PF14807 AP4E_app_platf: Adapt 95.4 0.15 3.3E-06 47.0 10.1 104 519-659 1-104 (104)
10 smart00809 Alpha_adaptinC2 Ada 95.0 0.28 6.1E-06 43.4 10.4 84 392-501 3-87 (104)
11 KOG1058 Vesicle coat complex C 93.0 0.053 1.1E-06 63.8 2.3 71 1-82 393-463 (948)
12 PF12717 Cnd1: non-SMC mitotic 91.7 0.15 3.4E-06 49.9 3.3 91 67-164 2-92 (178)
13 PF13646 HEAT_2: HEAT repeats; 91.4 0.4 8.6E-06 40.4 5.1 82 54-154 1-82 (88)
14 COG5240 SEC21 Vesicle coat com 90.1 0.89 1.9E-05 52.8 7.8 123 35-164 433-555 (898)
15 PF14764 SPG48: AP-5 complex s 89.4 1.2 2.7E-05 50.5 8.2 31 67-98 320-354 (459)
16 KOG1078 Vesicle coat complex C 88.9 0.8 1.7E-05 54.6 6.5 121 38-164 377-532 (865)
17 PF14797 SEEEED: Serine-rich r 88.0 0.59 1.3E-05 44.2 3.8 14 254-267 3-16 (130)
18 PF02883 Alpha_adaptinC2: Adap 88.0 1.8 4E-05 39.1 7.0 72 393-488 8-79 (115)
19 PF10633 NPCBM_assoc: NPCBM-as 86.1 1.1 2.3E-05 38.2 4.1 61 413-494 6-66 (78)
20 KOG0413 Uncharacterized conser 84.3 1.6 3.6E-05 53.2 5.8 122 31-160 947-1069(1529)
21 PRK09687 putative lyase; Provi 82.9 4.1 8.9E-05 43.2 7.7 92 53-158 91-182 (280)
22 PF02296 Alpha_adaptin_C: Alph 81.7 13 0.00029 34.6 9.6 105 517-650 1-110 (113)
23 KOG1077 Vesicle coat complex A 79.5 3.8 8.2E-05 48.8 6.4 113 46-164 472-587 (938)
24 COG1470 Predicted membrane pro 79.3 5.3 0.00011 45.7 7.2 76 415-511 400-483 (513)
25 PF01602 Adaptin_N: Adaptin N 75.1 2.5 5.3E-05 47.1 3.3 102 5-121 153-259 (526)
26 PF09066 B2-adapt-app_C: Beta2 74.5 29 0.00064 31.5 9.6 111 518-659 2-114 (114)
27 KOG1059 Vesicle coat complex A 70.8 6.2 0.00013 47.2 5.2 122 39-164 437-580 (877)
28 PF12717 Cnd1: non-SMC mitotic 70.4 17 0.00037 35.7 7.5 124 35-164 8-137 (178)
29 PF12755 Vac14_Fab1_bd: Vacuol 69.7 9 0.00019 34.7 5.0 73 89-162 23-95 (97)
30 cd00020 ARM Armadillo/beta-cat 64.7 5.9 0.00013 34.2 2.8 66 5-82 8-78 (120)
31 KOG1824 TATA-binding protein-i 63.5 10 0.00023 46.6 5.3 116 35-151 194-317 (1233)
32 PF04931 DNA_pol_phi: DNA poly 63.3 6.3 0.00014 47.5 3.5 13 36-48 325-337 (784)
33 PF12348 CLASP_N: CLASP N term 62.0 8 0.00017 38.6 3.5 126 29-163 67-205 (228)
34 PF10508 Proteasom_PSMB: Prote 55.0 14 0.00029 42.4 4.2 108 4-124 119-233 (503)
35 PF05110 AF-4: AF-4 proto-onco 52.2 16 0.00035 46.3 4.5 15 54-68 51-65 (1191)
36 PF06483 ChiC: Chitinase C; I 51.4 45 0.00098 33.9 6.6 111 395-511 35-164 (180)
37 PRK09687 putative lyase; Provi 49.7 52 0.0011 35.0 7.3 73 66-156 141-213 (280)
38 PF11611 DUF4352: Domain of un 48.6 67 0.0015 28.7 6.9 75 410-499 34-112 (123)
39 PF14874 PapD-like: Flagellar- 47.5 1.6E+02 0.0035 25.7 9.0 74 414-512 22-99 (102)
40 KOG1189 Global transcriptional 44.8 19 0.0004 43.6 3.2 14 33-46 565-578 (960)
41 TIGR01451 B_ant_repeat conserv 43.3 31 0.00067 27.8 3.4 31 412-446 12-42 (53)
42 PRK15098 beta-D-glucoside gluc 41.3 51 0.0011 40.0 6.3 60 411-489 666-728 (765)
43 PF00927 Transglut_C: Transglu 38.6 39 0.00085 30.2 3.7 62 413-491 16-79 (107)
44 KOG1832 HIV-1 Vpr-binding prot 36.0 34 0.00073 42.3 3.6 10 221-230 1346-1355(1516)
45 PF01345 DUF11: Domain of unkn 35.5 44 0.00095 28.1 3.4 30 412-445 41-70 (76)
46 KOG1824 TATA-binding protein-i 32.2 55 0.0012 40.8 4.5 195 4-226 47-252 (1233)
47 PF07705 CARDB: CARDB; InterP 31.7 1.7E+02 0.0036 24.8 6.4 55 411-489 18-72 (101)
48 PF13513 HEAT_EZ: HEAT-like re 29.7 22 0.00048 27.8 0.6 51 67-117 1-52 (55)
49 PF13646 HEAT_2: HEAT repeats; 29.5 94 0.002 25.8 4.4 84 6-115 1-85 (88)
50 KOG1058 Vesicle coat complex C 29.2 1.8E+02 0.004 35.7 8.0 152 414-617 736-896 (948)
51 KOG1832 HIV-1 Vpr-binding prot 28.8 42 0.0009 41.6 2.8 17 221-237 1355-1371(1516)
52 cd05700 S1_Rrp5_repeat_hs9 S1_ 28.7 47 0.001 28.4 2.3 17 473-489 40-57 (65)
53 COG2847 Copper(I)-binding prot 28.5 1.9E+02 0.0041 28.7 6.8 104 395-515 25-131 (151)
54 PF05753 TRAP_beta: Translocon 28.3 1.1E+02 0.0023 31.0 5.2 58 412-487 38-96 (181)
55 cd00020 ARM Armadillo/beta-cat 25.3 37 0.00079 29.3 1.2 101 54-156 9-112 (120)
56 PF09478 CBM49: Carbohydrate b 25.0 1.1E+02 0.0024 26.4 4.1 24 413-436 18-41 (80)
57 PF11614 FixG_C: IG-like fold 24.9 1.8E+02 0.0038 26.5 5.7 72 414-509 33-110 (118)
58 PHA02664 hypothetical protein; 24.2 86 0.0019 34.7 3.9 11 72-82 158-168 (534)
59 PF10725 DUF2517: Protein of u 24.1 40 0.00086 28.7 1.1 12 152-163 32-43 (63)
60 PF12348 CLASP_N: CLASP N term 23.8 90 0.002 31.1 3.8 125 32-162 24-158 (228)
61 COG2912 Uncharacterized conser 23.6 63 0.0014 34.8 2.8 111 47-164 99-231 (269)
62 PLN02171 endoglucanase 23.6 2.2E+02 0.0047 34.2 7.4 71 411-499 552-623 (629)
63 KOG2236 Uncharacterized conser 23.4 88 0.0019 36.1 3.9 19 213-231 72-91 (483)
64 PF09624 DUF2393: Protein of u 23.2 3.1E+02 0.0067 26.1 7.2 76 411-499 61-144 (149)
65 KOG3116 Predicted C3H1-type Zn 22.8 1.3E+02 0.0029 30.0 4.5 6 137-142 31-36 (177)
66 COG5406 Nucleosome binding fac 22.8 72 0.0016 38.2 3.2 11 69-79 536-546 (1001)
67 KOG2081 Nuclear transport regu 22.3 48 0.001 38.9 1.7 137 3-157 386-526 (559)
68 PRK10941 hypothetical protein; 22.1 75 0.0016 33.9 3.0 35 129-164 197-231 (269)
69 PTZ00429 beta-adaptin; Provisi 21.9 1.5E+02 0.0033 36.2 5.8 89 26-117 190-280 (746)
70 PF04314 DUF461: Protein of un 21.7 2.1E+02 0.0045 26.2 5.4 72 399-482 2-73 (110)
71 PRK13800 putative oxidoreducta 21.6 1.9E+02 0.0041 35.8 6.6 15 67-81 789-803 (897)
72 KOG1078 Vesicle coat complex C 21.4 1.3E+03 0.028 28.9 13.0 198 397-646 635-856 (865)
73 PF07718 Coatamer_beta_C: Coat 21.0 2E+02 0.0044 28.2 5.4 55 414-490 71-125 (140)
74 smart00185 ARM Armadillo/beta- 20.3 56 0.0012 23.3 1.1 28 5-43 13-40 (41)
75 PF12719 Cnd3: Nuclear condens 20.2 3.3E+02 0.0072 28.9 7.4 38 91-128 112-149 (298)
76 KOG1086 Cytosolic sorting prot 20.2 1.6E+02 0.0034 34.1 5.0 56 392-451 474-529 (594)
No 1
>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.2e-113 Score=953.94 Aligned_cols=521 Identities=30% Similarity=0.423 Sum_probs=412.9
Q ss_pred ChhHHHHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCchHHHHHHHHhhcCCCCcccchhheeeeeccc
Q 006008 1 MANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEY 80 (665)
Q Consensus 1 va~~Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~~P~ARAsIIWLIGEY 80 (665)
|+++|++||++||+ +.++.||+|+|+|||.|||++|.+|.+||.+|++++|+|.+|.|||+||||||||
T Consensus 426 v~~tCL~gLv~Lls-----------shde~Vv~eaV~vIk~Llq~~p~~h~~ii~~La~lldti~vp~ARA~IiWLige~ 494 (968)
T KOG1060|consen 426 VTDTCLNGLVQLLS-----------SHDELVVAEAVVVIKRLLQKDPAEHLEILFQLARLLDTILVPAARAGIIWLIGEY 494 (968)
T ss_pred hhhHHHHHHHHHHh-----------cccchhHHHHHHHHHHHHhhChHHHHHHHHHHHHHhhhhhhhhhhceeeeeehhh
Confidence 68999999999999 4678999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCcccchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhccCCCccchhhHHHHHH
Q 006008 81 SSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKK 160 (665)
Q Consensus 81 ~~~~e~ip~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD~nyDVRDRARfy~r 160 (665)
| +.+|+|||||||+|||+|++|.++||||||+++||||++++. ++++++|||++||+||+|||||||||||+.
T Consensus 495 ~---e~vpri~PDVLR~laksFs~E~~evKlQILnL~aKLyl~~~~----~~kll~~Yv~~L~~yD~sYDiRDRaRF~r~ 567 (968)
T KOG1060|consen 495 C---EIVPRIAPDVLRKLAKSFSDEGDEVKLQILNLSAKLYLTNID----QTKLLVQYVFELARYDLSYDIRDRARFLRQ 567 (968)
T ss_pred h---hhcchhchHHHHHHHHhhccccchhhHHHHHhhhhheEechh----hHHHHHHHHHHHhccCCCcchhHHHHHHHH
Confidence 9 479999999999999999999999999999999999999986 689999999999999999999999999999
Q ss_pred hhcCCCCCCCCcccchhcccCcchHHHHHhhhccCCCCCC-CCCCcccccccccHHHHhhccCCCCccCCCCCCccCccc
Q 006008 161 LFSHNLCSQVPEETNALQENKDLPLVLVECIFRKQENLAA-SEPINDRFYLPGSLSQIVLHAAPGYEPLPKPCSSLCDDL 239 (665)
Q Consensus 161 LLs~~~~~~~~~~~~~~s~~~~~~~~~a~~if~~k~p~~~-~~~~~~r~~~lGSLSh~l~~~~~GY~~LP~p~~~~~~~~ 239 (665)
|+++.. ..++|++.+|.++||++. ++.|++++|++||+||+++++++||+|||+|+...++.
T Consensus 568 l~~~~~----------------~Ls~h~~ei~l~~Kpa~~~es~f~~~~~~~gslS~lLn~~a~GY~~lp~~~~~~~d~- 630 (968)
T KOG1060|consen 568 LISPLE----------------ALSKHAREIFLASKPAPVLESSFKDRHYQLGSLSLLLNAPAPGYEPLPNWPAVAPDP- 630 (968)
T ss_pred HhccHH----------------HHHHHHHHHhhccCCCccCcccccCCCcccchHHHHhcCcCcCCccCCCccccCCCC-
Confidence 999741 347899999999998888 66899899999999999999999999999999998861
Q ss_pred CccccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc-ccccccccc
Q 006008 240 GQFSNSIDRTTALGEEWTGSSSNGTDDPDTSGSLDEESGSNYDSQQSIPGLSDNSGTGDSASEGDRNCDP-LIQISDAGI 318 (665)
Q Consensus 240 ~~~~~~~~~~~k~~~~~f~S~se~~d~~~~s~ss~~es~s~~~se~~~~~~s~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 318 (665)
.+.. .+++.|++++|++++..+++.++++++++++++.+.++++ +..++++.++++. .-+.+.++.
T Consensus 631 ----~~~~----~~a~~~~~~~e~~e~~~~~~~s~~~ses~~~~~~~~e~ge-----~~dsn~~~~~~~d~sdqss~~~s 697 (968)
T KOG1060|consen 631 ----FPDS----ERAKLLDSDSEEEETGDDESWSDPESESGESSNFSREGGE-----ENDSNEEKDSEDDFSDQSSYEES 697 (968)
T ss_pred ----Ccch----hhcccccCCccccccccccCCCCCccccccCCcccccccc-----cccccccccccccccccchhccc
Confidence 1111 2355688888877554444434444333322222211111 0111111111000 000000100
Q ss_pred ccCCCCCCCCCCCCCcccc--------cchhcccccccCCCCCCC-C------Cchhhh-----hhhcccceeeecccCc
Q 006008 319 ACSNENGASHSGFPDLEGM--------MSKRALESWLDEQPGSSS-P------SASEQI-----QVRQSSARISIGNIGR 378 (665)
Q Consensus 319 ~~~~~~~~~~s~s~~~~e~--------~s~~~l~~~LD~~p~~~~-~------~~s~~~-----~~~~s~~~~s~~~~~~ 378 (665)
+.++ ..++|+++.+. .+.++..+.+++..+.+. | .+.++. ++..+..+..+.. |.
T Consensus 698 s~~d----~~s~se~e~e~~~e~~k~~pet~~~sl~l~d~~~~n~~P~~~~~~~~~l~~d~~~~~~~~s~~~~~~~~-p~ 772 (968)
T KOG1060|consen 698 SAED----SESSSEAESEPTPEKLKEKPETKDVSLDLNDFTPQNGKPVLPERNDPDLAADDEFFSLTGSRNSKPLKI-PT 772 (968)
T ss_pred cccc----cccccccccccCCCccCCCcccccccccccccCCCCCCCCCCCCCChhhhccccccccccccccccccC-Cc
Confidence 0000 01111111111 011122246666544332 1 122221 3334444455554 55
Q ss_pred cccCceeecccccCCCCeeEEEEecCCCCCCCCCeEEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhccccccc
Q 006008 379 QVKAKSYTLLDPANGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTS 458 (665)
Q Consensus 379 ~v~~k~~eLL~~~~G~GL~v~Y~F~r~p~~~s~~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~ 458 (665)
.++.|++||||++.|+||.++|+|+|+| + |+|+++|+|.++.++.+||+ |+|.||+
T Consensus 773 ~i~~~~~ell~~~~g~gl~~~y~f~r~~----~--~~i~~~~~n~~~~~~~~~~l------~~p~gm~------------ 828 (968)
T KOG1060|consen 773 HIEEKSIELLNEVEGSGLDLEYSFSRLP----D--VSISLHFTNKSDLELLGIHL------KLPAGMS------------ 828 (968)
T ss_pred cCcchhHhhhhhcccCCcceeeeccCCC----C--eeEEEecccCCCccccccee------ecccccc------------
Confidence 6899999999999999999999999999 2 99999999999999999999 6799995
Q ss_pred CCCCCCcccCCCccccCCCCeeEEEEEEecCCCCccceEEEEEcCceeeeEEecCcccccccccCCHHHHHHHhccCCCC
Q 006008 459 QSDLPTLVPMEEITSLEPGQTMKRILEVRFHHHLLPLKLALHCNGKKLPVKLRPDIGYFIKPVPMDMETFIEMESRLPGM 538 (665)
Q Consensus 459 ~~~~~~i~~f~eI~sL~Pg~s~t~~lgIdF~dstq~~~f~l~~~~~~f~V~i~PpvGElv~Pv~mse~~F~~eq~kL~GM 538 (665)
|++|.+|++|+||+++++.|||||||+||++.|+||+.+| +|+++|||||+++||.|++++|+||||+|+||
T Consensus 829 ------i~ef~~i~s~~pg~~~~~~~~i~F~dst~~~~~~l~~~~g--~~~~~~pvge~~~~v~~~~~~~~~E~~~L~gl 900 (968)
T KOG1060|consen 829 ------IKEFSPIESLPPGASASVVLGIDFCDSTQAAEWQLLTDDG--RVRFQPPVGELVQPVRMSEEDFKKERGKLGGL 900 (968)
T ss_pred ------ccccccccccCCCcceeeeeeeeccccccceeEEEEeccC--cEEecCchhhhhccccCCHHHHHhhhhhhccc
Confidence 9999999999999999999999999999999999999999 99999999999999999999999999999999
Q ss_pred cccceeeeeccCcCccCccccchhhccchhhhhhhHHHHHHhhccceeeeeccCccccccCCCCCceeeeeeccccCCce
Q 006008 539 FEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAAKFDDASGLSLRFSSEILGNSVP 618 (665)
Q Consensus 539 nE~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~kv~~~aN~~~V~~~~p~~~~~~d~~~~~~rFa~~tlss~s~ 618 (665)
||| .|.+.. ++..||++.|+++ ..+||||||+|+++|
T Consensus 901 n~~--~~~l~~-----------------------------~~~~an~~~~~~g------------~~~rFa~~tlss~~~ 937 (968)
T KOG1060|consen 901 NEH--VIQLEN-----------------------------PNPSANVLFVPSG------------SSHRFAGQTLSSKSL 937 (968)
T ss_pred chh--heeeec-----------------------------ccchhhhhcccCC------------cceeeeeeeccCCce
Confidence 999 444431 0568999999874 349999999999999
Q ss_pred EEEEEEeccccCCCcceEEEEcccchHHHHHHHHHHHHhh
Q 006008 619 CLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVNFL 658 (665)
Q Consensus 619 ~LiTi~~~~~~~~~~~~~l~vNcEk~ViGs~Ll~~~~~~l 658 (665)
|||||++ + ||+|||||||||+||||+|.++|
T Consensus 938 ~llT~~~--k-------~l~ince~~ViG~~ll~~~~~~~ 968 (968)
T KOG1060|consen 938 VLLTVDE--K-------TLEINCEKTVIGSMLLNEVSNAL 968 (968)
T ss_pred EEEEeeh--h-------eeEecchhhhHHHHHHHHHHhhC
Confidence 9999998 3 69999999999999999999986
No 2
>PF14796 AP3B1_C: Clathrin-adaptor complex-3 beta-1 subunit C-terminal
Probab=100.00 E-value=6.4e-38 Score=296.83 Aligned_cols=132 Identities=31% Similarity=0.408 Sum_probs=110.8
Q ss_pred hhcccccccCC----CCCCC---CCchhhh-----hhhcccceeeecccCccccCceeecccccCCCCeeEEEEecCCCC
Q 006008 340 KRALESWLDEQ----PGSSS---PSASEQI-----QVRQSSARISIGNIGRQVKAKSYTLLDPANGNGLKVYYSFSSEAS 407 (665)
Q Consensus 340 ~~~l~~~LD~~----p~~~~---~~~s~~~-----~~~~s~~~~s~~~~~~~v~~k~~eLL~~~~G~GL~v~Y~F~r~p~ 407 (665)
|++++++||.+ |+..+ ++|++.. ++..++...++.+ ++++++|+||||||++|+||+|+|||+||||
T Consensus 2 k~~~~~LLDLddf~~p~~~P~~~~spsl~~~L~~ls~s~~~~~~~~~~-ps~v~~k~~eLL~~v~G~GL~v~Y~F~RqP~ 80 (145)
T PF14796_consen 2 KSKEDSLLDLDDFAVPPVAPVSILSPSLGSDLEGLSLSDSSSVPSVVS-PSFVPPKKYELLNRVNGKGLSVEYRFSRQPS 80 (145)
T ss_pred CcccccccccccccCCCcCCccccCcchhhhccCCCcCcccccccccC-CcccCcceEEeeeccCCCceeEEEEEccCCc
Confidence 34556666643 33322 4666643 3334445555555 6679999999999999999999999999999
Q ss_pred CCCCCeEEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCccccCCCCeeEEEEEEe
Q 006008 408 TISPQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQTMKRILEVR 487 (665)
Q Consensus 408 ~~s~~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL~Pg~s~t~~lgId 487 (665)
+||++||||||+|+|+|+++|+||||++| ++++||+ |++|++|++|+||++++++||||
T Consensus 81 ~~s~~mvsIql~ftN~s~~~i~~I~i~~k---~l~~g~~------------------i~~F~~I~~L~pg~s~t~~lgID 139 (145)
T PF14796_consen 81 LYSPSMVSIQLTFTNNSDEPIKNIHIGEK---KLPAGMR------------------IHEFPEIESLEPGASVTVSLGID 139 (145)
T ss_pred CCCCCcEEEEEEEEecCCCeecceEECCC---CCCCCcE------------------eeccCcccccCCCCeEEEEEEEe
Confidence 99999999999999999999999999999 8899994 99999999999999999999999
Q ss_pred cCCCCc
Q 006008 488 FHHHLL 493 (665)
Q Consensus 488 F~dstq 493 (665)
|||+||
T Consensus 140 F~DStQ 145 (145)
T PF14796_consen 140 FNDSTQ 145 (145)
T ss_pred cccCCC
Confidence 999998
No 3
>PTZ00429 beta-adaptin; Provisional
Probab=99.97 E-value=7.8e-31 Score=301.84 Aligned_cols=143 Identities=25% Similarity=0.414 Sum_probs=126.6
Q ss_pred ChhHHHHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCchHHHHHHHHhhc--CCCCcccchhheeeeec
Q 006008 1 MANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSL--DSIKVPEARVMIIWMVG 78 (665)
Q Consensus 1 va~~Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~~~iI~~Lak~l--d~i~~P~ARAsIIWLIG 78 (665)
+++.|++.|++||+. +.+ +++|+|+|||+|+|+||+.| +|..|++.+ +.+++|+|||+||||+|
T Consensus 402 ~a~~cV~~Ll~ll~~-----------~~~-~v~e~i~vik~IlrkyP~~~--il~~L~~~~~~~~i~e~~AKaaiiWILG 467 (746)
T PTZ00429 402 VAPDCANLLLQIVDR-----------RPE-LLPQVVTAAKDIVRKYPELL--MLDTLVTDYGADEVVEEEAKVSLLWMLG 467 (746)
T ss_pred HHHHHHHHHHHHhcC-----------Cch-hHHHHHHHHHHHHHHCccHH--HHHHHHHhhcccccccHHHHHHHHHHHH
Confidence 368999999999983 334 57799999999999999976 788888876 89999999999999999
Q ss_pred cccCCCCCcccchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhh-ccCCCccchhhHHH
Q 006008 79 EYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELA-ECDLNYDVRDRARF 157 (665)
Q Consensus 79 EY~~~~e~ip~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LA-kyD~nyDVRDRARf 157 (665)
|||+ .|++ +|++||.++++|.+|+.+||+|+||+++|+|++.|.+ .+.++++||+.| ++|.||||||||||
T Consensus 468 Ey~~---~I~~-a~~~L~~~i~~f~~E~~~VqlqlLta~vKlfl~~p~~----~~~~l~~vL~~~t~~~~d~DVRDRA~~ 539 (746)
T PTZ00429 468 EYCD---FIEN-GKDIIQRFIDTIMEHEQRVQLAILSAAVKMFLRDPQG----MEPQLNRVLETVTTHSDDPDVRDRAFA 539 (746)
T ss_pred hhHh---hHhh-HHHHHHHHHhhhccCCHHHHHHHHHHHHHHHhcCcHH----HHHHHHHHHHHHHhcCCChhHHHHHHH
Confidence 9994 6777 8999999999999999999999999999999999863 467888888655 77889999999999
Q ss_pred HHHhhcCC
Q 006008 158 FKKLFSHN 165 (665)
Q Consensus 158 y~rLLs~~ 165 (665)
|||||+.+
T Consensus 540 Y~rLLs~~ 547 (746)
T PTZ00429 540 YWRLLSKG 547 (746)
T ss_pred HHHHHcCC
Confidence 99999864
No 4
>KOG1061 consensus Vesicle coat complex AP-1/AP-2/AP-4, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=1.5e-30 Score=292.78 Aligned_cols=180 Identities=29% Similarity=0.498 Sum_probs=153.8
Q ss_pred hHHHHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCchHHHHHHHHhhcCCCCcccchhheeeeeccccC
Q 006008 3 NTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSS 82 (665)
Q Consensus 3 ~~Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~~P~ARAsIIWLIGEY~~ 82 (665)
..|+..||+|+.. +..|||+|+++|||+|+|+||+.|+.++..|+.+++++++|+||+++|||+|||+
T Consensus 385 ~~cv~~lLell~~-----------~~~yvvqE~~vvi~dilRkyP~~~~~vv~~l~~~~~sl~epeak~amiWilg~y~- 452 (734)
T KOG1061|consen 385 NDCVSILLELLET-----------KVDYVVQEAIVVIRDILRKYPNKYESVVAILCENLDSLQEPEAKAALIWILGEYA- 452 (734)
T ss_pred hhhHHHHHHHHhh-----------cccceeeehhHHHHhhhhcCCCchhhhhhhhcccccccCChHHHHHHHHHHhhhh-
Confidence 4599999999996 4579999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcccchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhccCC-CccchhhHHHHHHh
Q 006008 83 VGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDL-NYDVRDRARFFKKL 161 (665)
Q Consensus 83 ~~e~ip~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD~-nyDVRDRARfy~rL 161 (665)
+.||+ ++.+||.|.++|.+|+.+||+++||+++|+|++.|.+ .+.|+|.||.+|+-|. |+|+||||+|||||
T Consensus 453 --~~i~~-a~elL~~f~en~~dE~~~Vql~LLta~ik~Fl~~p~~----tq~~l~~vL~~~~~d~~~~dlrDr~l~Y~Rl 525 (734)
T KOG1061|consen 453 --ERIEN-ALELLESFLENFKDETAEVQLELLTAAIKLFLKKPTE----TQELLQGVLPLATADTDNPDLRDRGLIYWRL 525 (734)
T ss_pred --hccCc-HHHHHHHHHhhcccchHHHHHHHHHHHHHHHhcCCcc----HHHHHHHHHhhhhccccChhhhhhHHHHHHH
Confidence 46888 9999999999999999999999999999999999983 5789999999999997 89999999999999
Q ss_pred hcCCCCCCCCcccchhcccCcchHHHHHhhhccCCCCCCCC--CCc----cc-ccccccHHHHhhc
Q 006008 162 FSHNLCSQVPEETNALQENKDLPLVLVECIFRKQENLAASE--PIN----DR-FYLPGSLSQIVLH 220 (665)
Q Consensus 162 Ls~~~~~~~~~~~~~~s~~~~~~~~~a~~if~~k~p~~~~~--~~~----~r-~~~lGSLSh~l~~ 220 (665)
|+.+ ...|+.+..+++|..... ... ++ .-.+||||.++.+
T Consensus 526 Ls~~-------------------~~~a~~v~~~~kP~is~~~~~~~p~~le~l~~~i~tlssVY~K 572 (734)
T KOG1061|consen 526 LSED-------------------PLIAKDVVLAEKPLISEETDSLDPTLLEELLCDIGTLSSVYHK 572 (734)
T ss_pred hhcC-------------------HHHHHHHHhcCCCccccCCCCCCchHHHHHHHhhccccceeec
Confidence 9953 235666555555444421 121 12 3347888888754
No 5
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=99.81 E-value=2e-20 Score=204.49 Aligned_cols=147 Identities=31% Similarity=0.470 Sum_probs=133.3
Q ss_pred hhHHHHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCchHHHHHHHHhhcCCCCcccchhheeeeecccc
Q 006008 2 ANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYS 81 (665)
Q Consensus 2 a~~Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~~P~ARAsIIWLIGEY~ 81 (665)
++.|++.|+.|+.. ...+++.|++.+|++|++++|+.+..++.+|++.++.+..|.++++++|++|||+
T Consensus 375 ~~~~v~~l~~ll~~-----------~~~~~~~~~~~~i~~ll~~~~~~~~~~l~~L~~~l~~~~~~~~~~~~~wilGEy~ 443 (526)
T PF01602_consen 375 AEWYVDTLLKLLEI-----------SGDYVSNEIINVIRDLLSNNPELREKILKKLIELLEDISSPEALAAAIWILGEYG 443 (526)
T ss_dssp HHHHHHHHHHHHHC-----------TGGGCHCHHHHHHHHHHHHSTTTHHHHHHHHHHHHTSSSSHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHhhhh-----------ccccccchHHHHHHHHhhcChhhhHHHHHHHHHHHHHhhHHHHHHHHHhhhcccC
Confidence 46899999999984 4467899999999999999999999999999999999999999999999999999
Q ss_pred CCCCCccc--chHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhccCC-CccchhhHHHH
Q 006008 82 SVGVKIPR--MLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDL-NYDVRDRARFF 158 (665)
Q Consensus 82 ~~~e~ip~--iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD~-nyDVRDRARfy 158 (665)
+ .+++ .+++++|.+++.|.+|+..||+++|++.+|+|.+.|... ....+++++++++++|. |+||||||++|
T Consensus 444 ~---~~~~~~~~~~~~~~l~~~~~~~~~~vk~~ilt~~~Kl~~~~~~~~--~~~~i~~~~~~~~~~~s~~~evr~Ra~~y 518 (526)
T PF01602_consen 444 E---LIENTESAPDILRSLIENFIEESPEVKLQILTALAKLFKRNPENE--VQNEILQFLLSLATEDSSDPEVRDRAREY 518 (526)
T ss_dssp H---HHTTTTHHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHSCSTT--HHHHHHHHHHCHHHHS-SSHHHHHHHHHH
T ss_pred C---cccccccHHHHHHHHHHhhccccHHHHHHHHHHHHHHHhhCCchh--hHHHHHHHHHHHhccCCCCHHHHHHHHHH
Confidence 5 4555 899999999999999999999999999999999998643 44689999999999876 99999999999
Q ss_pred HHhhcC
Q 006008 159 KKLFSH 164 (665)
Q Consensus 159 ~rLLs~ 164 (665)
|+||..
T Consensus 519 ~~ll~~ 524 (526)
T PF01602_consen 519 LRLLNS 524 (526)
T ss_dssp HHHHHH
T ss_pred HHHHcc
Confidence 999974
No 6
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=99.59 E-value=3.8e-16 Score=179.39 Aligned_cols=153 Identities=24% Similarity=0.386 Sum_probs=121.7
Q ss_pred hhHHHHHHHHHHhhccccccccCCCCCcceeeeh-----HHHHH---HHHhhCCCc-hHHHHHHHHhhcCCCC----ccc
Q 006008 2 ANTCVEGLLALIRQELLTSDIESGNGEADVLIQS-----IISIK---SIIKQDPSC-HEKVIIQLFRSLDSIK----VPE 68 (665)
Q Consensus 2 a~~Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~Es-----VvVIk---~LLqk~P~~-~~~iI~~Lak~ld~i~----~P~ 68 (665)
...|+..+++|++- . + -+..|++.|+ |.|+| .+||++|+. +......++++.+.++ .|.
T Consensus 392 ~~~~I~~~lel~~g--~-----~-~~~~Yi~~e~~~~~~i~v~r~~~~~lr~l~~~~~~~~~~~l~~~~e~l~~~~~~P~ 463 (757)
T COG5096 392 VNDCISELLELLEG--V-----W-IRGSYIVQEVRIVDCISVIRISVLVLRILPNEYPKILLRGLYALEETLELQSREPR 463 (757)
T ss_pred HHHHHHHHHHhccc--h-----h-hccchhhhhhcccceeeeeehhcchhhhcCCcchhhhHHHHHHHHHHhhccccCcH
Confidence 35799999999970 0 1 1235778777 77888 899999998 5666778888888777 899
Q ss_pred chhhe-----eeeeccccCCCCCcccchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhh
Q 006008 69 ARVMI-----IWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELA 143 (665)
Q Consensus 69 ARAsI-----IWLIGEY~~~~e~ip~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LA 143 (665)
||.+. +||+|||++ .+|+.+|++||.+.++|.+|+.+||+|||++++|++++.+....+--..+.+-++..|
T Consensus 464 ~k~~~~~~~~~wl~ge~~~---~i~r~~~~~l~~~~~~~~~E~levq~~Il~~svkl~~~~~~~~~~~~~~~d~~v~~~~ 540 (757)
T COG5096 464 AKSVTDKYLGAWLLGEFSD---IIPRLEPELLRIAISNFVDETLEVQYTILMSSVKLIANSIRKAKQCNSELDQDVLRRC 540 (757)
T ss_pred HHHHHhhhhHHHhHHHHHH---HHhhhhHHHHHHHHHHhcccchHHHHHHHHHHHHHHHhCcHhhhhccchhccHHHHHH
Confidence 99888 999999994 6899999999999999999999999999999999999998632110002445566666
Q ss_pred c-cCCCccchhhHHHHHHhhcCC
Q 006008 144 E-CDLNYDVRDRARFFKKLFSHN 165 (665)
Q Consensus 144 k-yD~nyDVRDRARfy~rLLs~~ 165 (665)
. |-.++|+||||+|||++++.+
T Consensus 541 ~~~v~~~DlRDra~my~~~lst~ 563 (757)
T COG5096 541 FDYVLVPDLRDRARMYSRLLSTP 563 (757)
T ss_pred HhccCChhHHHHHHHHHHHhcCC
Confidence 4 334899999999999999953
No 7
>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=98.44 E-value=1.1e-06 Score=101.27 Aligned_cols=128 Identities=21% Similarity=0.163 Sum_probs=108.4
Q ss_pred CCCCCCcccCCCccccCCCCeeEEEEEEecCCCCccceEEEEEcCceeeeEEecCcccccccccCCHHHHHHHhccCCCC
Q 006008 459 QSDLPTLVPMEEITSLEPGQTMKRILEVRFHHHLLPLKLALHCNGKKLPVKLRPDIGYFIKPVPMDMETFIEMESRLPGM 538 (665)
Q Consensus 459 ~~~~~~i~~f~eI~sL~Pg~s~t~~lgIdF~dstq~~~f~l~~~~~~f~V~i~PpvGElv~Pv~mse~~F~~eq~kL~GM 538 (665)
+-..|+.+++.+|+.|.+-+.....+.+.|+++. ++..++..+.++..+.+.|.+ ..|.-|+.++|..-+..+|||
T Consensus 767 ~~~~p~~i~~~~~ell~~~~g~gl~~~y~f~r~~-~~~i~~~~~n~~~~~~~~~~l---~~p~gm~i~ef~~i~s~~pg~ 842 (968)
T KOG1060|consen 767 PLKIPTHIEEKSIELLNEVEGSGLDLEYSFSRLP-DVSISLHFTNKSDLELLGIHL---KLPAGMSIKEFSPIESLPPGA 842 (968)
T ss_pred cccCCccCcchhHhhhhhcccCCcceeeeccCCC-CeeEEEecccCCCccccccee---eccccccccccccccccCCCc
Confidence 4567889999999999999999999999999998 699999999999999998887 999999999999999999999
Q ss_pred cccce---------------------eeeeccCcCccCccccchhhccchhhhhhhHHHHHHhhccceeeeeccCcccc
Q 006008 539 FEYAR---------------------SCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAA 596 (665)
Q Consensus 539 nE~~~---------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~kv~~~aN~~~V~~~~p~~~ 596 (665)
+++++ +|+|.+|..++- ..-..++++..++....+.++..|+.++.. .|+++
T Consensus 843 ~~~~~~~i~F~dst~~~~~~l~~~~g~~~~~~pvge~~-----~~v~~~~~~~~~E~~~L~gln~~~~~l~~~-~~~an 915 (968)
T KOG1060|consen 843 SASVVLGIDFCDSTQAAEWQLLTDDGRVRFQPPVGELV-----QPVRMSEEDFKKERGKLGGLNEHVIQLENP-NPSAN 915 (968)
T ss_pred ceeeeeeeeccccccceeEEEEeccCcEEecCchhhhh-----ccccCCHHHHHhhhhhhcccchhheeeecc-cchhh
Confidence 99864 455555554442 122567889999999999999999999976 46644
No 8
>KOG1062 consensus Vesicle coat complex AP-1, gamma subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.22 E-value=0.068 Score=63.22 Aligned_cols=160 Identities=19% Similarity=0.270 Sum_probs=102.1
Q ss_pred HHHHHhhC-CCchHHHHHHHHhhcCC-----CCcccchhheeeeeccccCCC-C--------C-cccchHHHHHHHHhhh
Q 006008 39 IKSIIKQD-PSCHEKVIIQLFRSLDS-----IKVPEARVMIIWMVGEYSSVG-V--------K-IPRMLTTVLKYLAWCF 102 (665)
Q Consensus 39 Ik~LLqk~-P~~~~~iI~~Lak~ld~-----i~~P~ARAsIIWLIGEY~~~~-e--------~-ip~iaPdvLR~laksF 102 (665)
+-.||-.- ++.|++.+.+|.+.+-. |..+.=--.++|-||||.+.- + . -+.-+-|+|.+++.+.
T Consensus 446 ll~LIa~~~~e~~~y~~~rLy~a~~~~~~~~is~e~l~qVa~W~IGEYGdlll~~~~~~~p~~vtesdivd~l~~v~~~~ 525 (866)
T KOG1062|consen 446 LLRLIANAFQELHEYAVLRLYLALSEDTLLDISQEPLLQVASWCIGEYGDLLLDGANEEEPIKVTESDIVDKLEKVLMSH 525 (866)
T ss_pred HHHHHhcCCcchhhHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHhhhhhHHhhcCccccCCCcCCHHHHHHHHHHHHHhc
Confidence 33344344 77899999888876643 444444778899999998410 0 0 0122446777777777
Q ss_pred cCChHHHHHHHHHhhhheeeeccCCChhHHHHHH-HHHHHhhccCCCccchhhHHHHHHhhcCCCCCCCCcccchhcccC
Q 006008 103 KSEAVETKLQILNTTIKVLLCAKGGDMWTITRLF-SYLLELAECDLNYDVRDRARFFKKLFSHNLCSQVPEETNALQENK 181 (665)
Q Consensus 103 ~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~-qyVL~LAkyD~nyDVRDRARfy~rLLs~~~~~~~~~~~~~~s~~~ 181 (665)
... ..+|-=+|++..||+.+.+.. .+++++|. .|- --.+-+++-||.=|..|+...
T Consensus 526 ~s~-~~tk~yal~Al~KLSsr~~s~-~~ri~~lI~~~~-----~s~~~elQQRa~E~~~l~~~~---------------- 582 (866)
T KOG1062|consen 526 SSD-STTKGYALTALLKLSSRFHSS-SERIKQLISSYK-----SSLDTELQQRAVEYNALFAKD---------------- 582 (866)
T ss_pred cch-HHHHHHHHHHHHHHHhhcccc-HHHHHHHHHHhc-----ccccHHHHHHHHHHHHHHHHH----------------
Confidence 666 889999999999999998763 33555443 332 223679999999999999642
Q ss_pred cchHHHHHhhhccCCCCCCCCCCcccccccccHHHHhhccCCCCcc
Q 006008 182 DLPLVLVECIFRKQENLAASEPINDRFYLPGSLSQIVLHAAPGYEP 227 (665)
Q Consensus 182 ~~~~~~a~~if~~k~p~~~~~~~~~r~~~lGSLSh~l~~~~~GY~~ 227 (665)
...++...++.|..-...+..+. -|..-+.+...+.+|-+
T Consensus 583 ----~~lr~siLe~mp~~e~~~~~~~~--~g~~~~~i~~~~~p~~~ 622 (866)
T KOG1062|consen 583 ----KHLRKSILERMPSCEDITVDARL--DGNGPAAIEQGAEPYKS 622 (866)
T ss_pred ----HHHHHHhcccCcccccccccccc--ccchHHHHHhccCCCcc
Confidence 12233334555444433332221 37777777777777765
No 9
>PF14807 AP4E_app_platf: Adaptin AP4 complex epsilon appendage platform
Probab=95.41 E-value=0.15 Score=47.01 Aligned_cols=104 Identities=16% Similarity=0.218 Sum_probs=79.6
Q ss_pred ccccCCHHHHHHHhccCCCCcccceeeeeccCcCccCccccchhhccchhhhhhhHHHHHHhhccceeeeeccCcccccc
Q 006008 519 KPVPMDMETFIEMESRLPGMFEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAAKF 598 (665)
Q Consensus 519 ~Pv~mse~~F~~eq~kL~GMnE~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~kv~~~aN~~~V~~~~p~~~~~ 598 (665)
||..|+-++|=+.=.++. ||. +.+++... -.....+.+++.+.+|++.|-+=
T Consensus 1 RPl~isTeeFG~~W~s~~--~e~--k~~l~~~~-----------------~~t~~~~l~~l~~~l~lh~VevI------- 52 (104)
T PF14807_consen 1 RPLQISTEEFGQLWLSFS--NER--KQNLPSSS-----------------QRTLPEFLQRLQQKLRLHVVEVI------- 52 (104)
T ss_pred CCccccHHHHHHHHHcCC--CeE--EEeccccC-----------------cCCHHHHHHHHHHhcCceEEEEe-------
Confidence 799999999977777765 565 55553110 11235677889999999999751
Q ss_pred CCCCCceeeeeeccccCCceEEEEEEeccccCCCcceEEEEcccchHHHHHHHHHHHHhhc
Q 006008 599 DDASGLSLRFSSEILGNSVPCLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVNFLV 659 (665)
Q Consensus 599 ~d~~~~~~rFa~~tlss~s~~LiTi~~~~~~~~~~~~~l~vNcEk~ViGs~Ll~~~~~~l~ 659 (665)
|.+.=|||+.+.++..||+-+.+.+. .+.|+|++-.+-++=-|++.++.+|.
T Consensus 53 ----g~E~I~A~~ll~~~~~~L~H~~~~~~-----~l~l~vrs~~~~l~d~ll~~~~~~~~ 104 (104)
T PF14807_consen 53 ----GNEGIFACQLLNSSPVCLLHCRVNAG-----TLDLWVRSSDSPLTDCLLYQCQKILQ 104 (104)
T ss_pred ----CccceeeeeccCCCCeEEEEEEecCC-----eEEEEEEcCCCCcHHHHHHHHHHHhC
Confidence 33556999999999999999988332 57899999999999999999998763
No 10
>smart00809 Alpha_adaptinC2 Adaptin C-terminal domain. Adaptins are components of the adaptor complexes which link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Gamma-adaptin is a subunit of the golgi adaptor. Alpha adaptin is a heterotetramer that regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This Ig-fold domain is found in alpha, beta and gamma adaptins and consists of a beta-sandwich containing 7 strands in 2 beta-sheets in a greek-key topology PUBMED:10430869, PUBMED:12176391. The adaptor appendage contains an additional N-terminal strand.
Probab=94.98 E-value=0.28 Score=43.40 Aligned_cols=84 Identities=24% Similarity=0.396 Sum_probs=55.6
Q ss_pred CCCCeeEEEEecCCCCCCCCCeEEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCc
Q 006008 392 NGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEI 471 (665)
Q Consensus 392 ~G~GL~v~Y~F~r~p~~~s~~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI 471 (665)
.++||.|.|++.|.+ ..+.|.++|.|.+..+|+++.+.=- -|.++... +.+...
T Consensus 3 ~~~~l~I~~~~~~~~-----~~~~i~~~~~N~s~~~it~f~~~~a----vpk~~~l~----------------l~~~s~- 56 (104)
T smart00809 3 EKNGLQIGFKFERRP-----GLIRITLTFTNKSPSPITNFSFQAA----VPKSLKLQ----------------LQPPSS- 56 (104)
T ss_pred cCCCEEEEEEEEcCC-----CeEEEEEEEEeCCCCeeeeEEEEEE----cccceEEE----------------EcCCCC-
Confidence 367999999999874 4689999999999999999998532 24444321 122211
Q ss_pred cccCCCCeeEEEEEEecCCC-CccceEEEEE
Q 006008 472 TSLEPGQTMKRILEVRFHHH-LLPLKLALHC 501 (665)
Q Consensus 472 ~sL~Pg~s~t~~lgIdF~ds-tq~~~f~l~~ 501 (665)
..|+||+.++-.|.|.=... ..++++.+..
T Consensus 57 ~~l~p~~~i~q~~~i~~~~~~~~~~~~~vsy 87 (104)
T smart00809 57 PTLPPGGQITQVLKVENPGKFPLRLRLRLSY 87 (104)
T ss_pred CccCCCCCEEEEEEEECCCCCCEEEEEEEEE
Confidence 36899998887777742221 2344555533
No 11
>KOG1058 consensus Vesicle coat complex COPI, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=93.04 E-value=0.053 Score=63.82 Aligned_cols=71 Identities=21% Similarity=0.422 Sum_probs=58.0
Q ss_pred ChhHHHHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCchHHHHHHHHhhcCCCCcccchhheeeeeccc
Q 006008 1 MANTCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEY 80 (665)
Q Consensus 1 va~~Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~~P~ARAsIIWLIGEY 80 (665)
||.+-+..||+-|+ |.++.--...+.-||..++++|+--..||.+|..-++.|..+.+--+.+||+|||
T Consensus 393 ~aatvV~~ll~fis-----------D~N~~aas~vl~FvrE~iek~p~Lr~~ii~~l~~~~~~irS~ki~rgalwi~GeY 461 (948)
T KOG1058|consen 393 VAATVVSLLLDFIS-----------DSNEAAASDVLMFVREAIEKFPNLRASIIEKLLETFPQIRSSKICRGALWILGEY 461 (948)
T ss_pred HHHHHHHHHHHHhc-----------cCCHHHHHHHHHHHHHHHHhCchHHHHHHHHHHHhhhhhcccccchhHHHHHHHH
Confidence 46777888999887 3333222234445999999999988999999999999999999999999999999
Q ss_pred cC
Q 006008 81 SS 82 (665)
Q Consensus 81 ~~ 82 (665)
|.
T Consensus 462 ce 463 (948)
T KOG1058|consen 462 CE 463 (948)
T ss_pred Hh
Confidence 95
No 12
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=91.66 E-value=0.15 Score=49.90 Aligned_cols=91 Identities=24% Similarity=0.290 Sum_probs=67.8
Q ss_pred ccchhheeeeeccccCCCCCcccchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhccC
Q 006008 67 PEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECD 146 (665)
Q Consensus 67 P~ARAsIIWLIGEY~~~~e~ip~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD 146 (665)
|..|+.++=.+|.-|- ..|+++...+..+.+.+.|+...||.+.|....+|.+...-+- -..++.+++.+. -|
T Consensus 2 ~~vR~n~i~~l~DL~~---r~~~~ve~~~~~l~~~L~D~~~~VR~~al~~Ls~Li~~d~ik~---k~~l~~~~l~~l-~D 74 (178)
T PF12717_consen 2 PSVRNNAIIALGDLCI---RYPNLVEPYLPNLYKCLRDEDPLVRKTALLVLSHLILEDMIKV---KGQLFSRILKLL-VD 74 (178)
T ss_pred HHHHHHHHHHHHHHHH---hCcHHHHhHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCceee---hhhhhHHHHHHH-cC
Confidence 5667777777887774 4678888888889999999999999999999999988663221 123334444333 78
Q ss_pred CCccchhhHHHHHHhhcC
Q 006008 147 LNYDVRDRARFFKKLFSH 164 (665)
Q Consensus 147 ~nyDVRDRARfy~rLLs~ 164 (665)
.|++||+-|+++..=+..
T Consensus 75 ~~~~Ir~~A~~~~~e~~~ 92 (178)
T PF12717_consen 75 ENPEIRSLARSFFSELLK 92 (178)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 899999999987765544
No 13
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=91.36 E-value=0.4 Score=40.35 Aligned_cols=82 Identities=18% Similarity=0.146 Sum_probs=56.8
Q ss_pred HHHHHhhcCCCCcccchhheeeeeccccCCCCCcccchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHH
Q 006008 54 IIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTIT 133 (665)
Q Consensus 54 I~~Lak~ld~i~~P~ARAsIIWLIGEY~~~~e~ip~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~ 133 (665)
|..|.+.+..=.+|.-|..++|.+|++.+ +.++..+.+-+.++...||.+.+.+..++- ..
T Consensus 1 i~~L~~~l~~~~~~~vr~~a~~~L~~~~~---------~~~~~~L~~~l~d~~~~vr~~a~~aL~~i~----------~~ 61 (88)
T PF13646_consen 1 IPALLQLLQNDPDPQVRAEAARALGELGD---------PEAIPALIELLKDEDPMVRRAAARALGRIG----------DP 61 (88)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHHCCTH---------HHHHHHHHHHHTSSSHHHHHHHHHHHHCCH----------HH
T ss_pred CHHHHHHHhcCCCHHHHHHHHHHHHHcCC---------HhHHHHHHHHHcCCCHHHHHHHHHHHHHhC----------CH
Confidence 34566777666678899999999998752 244455555668999999999999999871 13
Q ss_pred HHHHHHHHhhccCCCccchhh
Q 006008 134 RLFSYLLELAECDLNYDVRDR 154 (665)
Q Consensus 134 ~L~qyVL~LAkyD~nyDVRDR 154 (665)
..++.+.++...|.+..||.-
T Consensus 62 ~~~~~L~~~l~~~~~~~vr~~ 82 (88)
T PF13646_consen 62 EAIPALIKLLQDDDDEVVREA 82 (88)
T ss_dssp HTHHHHHHHHTC-SSHHHHHH
T ss_pred HHHHHHHHHHcCCCcHHHHHH
Confidence 455666666666655555643
No 14
>COG5240 SEC21 Vesicle coat complex COPI, gamma subunit [Intracellular trafficking and secretion]
Probab=90.08 E-value=0.89 Score=52.81 Aligned_cols=123 Identities=15% Similarity=0.158 Sum_probs=91.7
Q ss_pred hHHHHHHHHhhCCCchHHHHHHHHhhcCCCCcccchhheeeeeccccCCCCCcccchHHHHHHHHhhhcCChHHHHHHHH
Q 006008 35 SIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQIL 114 (665)
Q Consensus 35 sVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~~P~ARAsIIWLIGEY~~~~e~ip~iaPdvLR~laksF~~E~~eVKLQIL 114 (665)
.|-+|-+++.-.|+.-+.++..||..++.-.-|+--.-|+-|+|+-. ++.++ -.-..|++.....=|...||-..+
T Consensus 433 ~Vdaisd~~~~~p~skEraLe~LC~fIEDcey~~I~vrIL~iLG~Eg---P~a~~-P~~yvrhIyNR~iLEN~ivRsaAv 508 (898)
T COG5240 433 MVDAISDAMENDPDSKERALEVLCTFIEDCEYHQITVRILGILGREG---PRAKT-PGKYVRHIYNRLILENNIVRSAAV 508 (898)
T ss_pred HHHHHHHHHhhCchHHHHHHHHHHHHHhhcchhHHHHHHHHHhcccC---CCCCC-cchHHHHHHHHHHHhhhHHHHHHH
Confidence 55667777777788888888888888877777777777888888853 23332 123456666677779999999999
Q ss_pred HhhhheeeeccCCChhHHHHHHHHHHHhhccCCCccchhhHHHHHHhhcC
Q 006008 115 NTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSH 164 (665)
Q Consensus 115 tlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD~nyDVRDRARfy~rLLs~ 164 (665)
.+..|+-++.... ...+-+..+|.-|-.|++-.|||||-|.-+-+..
T Consensus 509 ~aLskf~ln~~d~---~~~~sv~~~lkRclnD~DdeVRdrAsf~l~~~~~ 555 (898)
T COG5240 509 QALSKFALNISDV---VSPQSVENALKRCLNDQDDEVRDRASFLLRNMRL 555 (898)
T ss_pred HHHHHhccCcccc---ccHHHHHHHHHHHhhcccHHHHHHHHHHHHhhhh
Confidence 9999998877543 2344556667777788889999999998877753
No 15
>PF14764 SPG48: AP-5 complex subunit, vesicle trafficking
Probab=89.35 E-value=1.2 Score=50.53 Aligned_cols=31 Identities=23% Similarity=0.429 Sum_probs=19.6
Q ss_pred ccchh----heeeeeccccCCCCCcccchHHHHHHH
Q 006008 67 PEARV----MIIWMVGEYSSVGVKIPRMLTTVLKYL 98 (665)
Q Consensus 67 P~ARA----sIIWLIGEY~~~~e~ip~iaPdvLR~l 98 (665)
-.+|+ .++|+||||.+.+ +-.++-+++.+++
T Consensus 320 ~~~k~~l~~hlvWaIGEy~s~~-~d~rct~~~i~~~ 354 (459)
T PF14764_consen 320 IHSKEELFTHLVWAIGEYLSVS-YDRRCTVEQINEF 354 (459)
T ss_pred ccchhHHHHHHHHHHhcccccc-cCCccCHHHHHHH
Confidence 35555 5799999998632 2344556666544
No 16
>KOG1078 consensus Vesicle coat complex COPI, gamma subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.86 E-value=0.8 Score=54.56 Aligned_cols=121 Identities=18% Similarity=0.141 Sum_probs=73.0
Q ss_pred HHHHHHhhCCCchHHHHHHHHhhcCC-----------------CC-cccchhheeeeeccccCCCCCcccchHH------
Q 006008 38 SIKSIIKQDPSCHEKVIIQLFRSLDS-----------------IK-VPEARVMIIWMVGEYSSVGVKIPRMLTT------ 93 (665)
Q Consensus 38 VIk~LLqk~P~~~~~iI~~Lak~ld~-----------------i~-~P~ARAsIIWLIGEY~~~~e~ip~iaPd------ 93 (665)
.|+.|..+||.+|..++.-|.+.|.. |. .|++|-..+--+-||....+ .+.++-.
T Consensus 377 ai~sLc~~fp~k~~~~m~FL~~~Lr~eGg~e~K~aivd~Ii~iie~~pdsKe~~L~~LCefIEDce-~~~i~~rILhlLG 455 (865)
T KOG1078|consen 377 AIRSLCLKFPRKHTVMMNFLSNMLREEGGFEFKRAIVDAIIDIIEENPDSKERGLEHLCEFIEDCE-FTQIAVRILHLLG 455 (865)
T ss_pred HHHHHHhhccHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHhCcchhhHHHHHHHHHHHhcc-chHHHHHHHHHHh
Confidence 46666666666666666666555521 11 45666555544444432111 1222222
Q ss_pred -----------HHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhccCCCccchhhHHHHHHhh
Q 006008 94 -----------VLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLF 162 (665)
Q Consensus 94 -----------vLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD~nyDVRDRARfy~rLL 162 (665)
..|+....-.=|...|+-.-+.+.+|+-...+.-- ..+. -+|.-|-+|.+-.|||||+||-+.+
T Consensus 456 ~EgP~a~~Pskyir~iyNRviLEn~ivRaaAv~alaKfg~~~~~l~-~sI~----vllkRc~~D~DdevRdrAtf~l~~l 530 (865)
T KOG1078|consen 456 KEGPKAPNPSKYIRFIYNRVILENAIVRAAAVSALAKFGAQDVVLL-PSIL----VLLKRCLNDSDDEVRDRATFYLKNL 530 (865)
T ss_pred ccCCCCCCcchhhHHHhhhhhhhhhhhHHHHHHHHHHHhcCCCCcc-ccHH----HHHHHHhcCchHHHHHHHHHHHHHh
Confidence 33555555566888999999999999986554321 1233 3344466888889999999999888
Q ss_pred cC
Q 006008 163 SH 164 (665)
Q Consensus 163 s~ 164 (665)
..
T Consensus 531 ~~ 532 (865)
T KOG1078|consen 531 EE 532 (865)
T ss_pred hh
Confidence 63
No 17
>PF14797 SEEEED: Serine-rich region of AP3B1, clathrin-adaptor complex
Probab=88.02 E-value=0.59 Score=44.18 Aligned_cols=14 Identities=21% Similarity=0.159 Sum_probs=10.3
Q ss_pred CCCCCCCCCCCCCC
Q 006008 254 EEWTGSSSNGTDDP 267 (665)
Q Consensus 254 ~~~f~S~se~~d~~ 267 (665)
.+.||+++|+++++
T Consensus 3 ~~kFYsEsEEeeds 16 (130)
T PF14797_consen 3 DKKFYSESEEEEDS 16 (130)
T ss_pred cccccccccccccc
Confidence 45799999877543
No 18
>PF02883 Alpha_adaptinC2: Adaptin C-terminal domain; InterPro: IPR008152 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. GGAs (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) are a family of monomeric clathrin adaptor proteins that are conserved from yeasts to humans. GGAs regulate clathrin-mediated the transport of proteins (such as mannose 6-phosphate receptors) from the TGN to endosomes and lysosomes through interactions with TGN-sorting receptors, sometimes in conjunction with AP-1 [, ]. GGAs bind cargo, membranes, clathrin and accessory factors. GGA1, GGA2 and GGA3 all contain a domain homologous to the ear domain of gamma-adaptin. GGAs are composed of a single polypeptide with four domains: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The VHS domain is responsible for endocytosis and signal transduction, recognising transmembrane cargo through the ACLL sequence in the cytoplasmic domains of sorting receptors []. The GAT domain (also found in Tom1 proteins) interacts with ARF (ADP-ribosylation factor) to regulate membrane trafficking [], and with ubiquitin for receptor sorting []. The hinge region contains a clathrin box for recognition and binding to clathrin, similar to that found in AP adaptins. The GAE domain is similar to the AP gamma-adaptin ear domain, and is responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. This entry represents a beta-sandwich structural motif found in the appendage (ear) domain of alpha-, beta- and gamma-adaptin from AP clathrin adaptor complexes, and the GAE (gamma-adaptin ear) domain of GGA adaptor proteins. These domains have an immunoglobulin-like beta-sandwich fold containing 7 or 8 strands in 2 beta-sheets in a Greek key topology [, ]. Although these domains share a similar fold, there is little sequence identity between the alpha/beta-adaptins and gamma-adaptin/GAE. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 3MNM_B 3ZY7_B 1GYU_A 1GYW_B 2A7B_A 1GYV_A 2E9G_A 1E42_B 2G30_A 2IV9_B ....
Probab=87.99 E-value=1.8 Score=39.09 Aligned_cols=72 Identities=21% Similarity=0.367 Sum_probs=48.1
Q ss_pred CCCeeEEEEecCCCCCCCCCeEEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCcc
Q 006008 393 GNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEIT 472 (665)
Q Consensus 393 G~GL~v~Y~F~r~p~~~s~~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~ 472 (665)
-+||.|.|++.+ .-.+....|.++|.|++..+|+++++-= ..|.++...|. +- .-.
T Consensus 8 ~~~l~I~~~~~~---~~~~~~~~i~~~f~N~s~~~it~f~~q~----avpk~~~l~l~----------------~~-s~~ 63 (115)
T PF02883_consen 8 DNGLQIGFKSEK---SPNPNQGRIKLTFGNKSSQPITNFSFQA----AVPKSFKLQLQ----------------PP-SSS 63 (115)
T ss_dssp ETTEEEEEEEEE---CCETTEEEEEEEEEE-SSS-BEEEEEEE----EEBTTSEEEEE----------------ES-S-S
T ss_pred CCCEEEEEEEEe---cCCCCEEEEEEEEEECCCCCcceEEEEE----EeccccEEEEe----------------CC-CCC
Confidence 368999999998 3347889999999999999999999863 12344432211 11 123
Q ss_pred ccCCCCeeEEEEEEec
Q 006008 473 SLEPGQTMKRILEVRF 488 (665)
Q Consensus 473 sL~Pg~s~t~~lgIdF 488 (665)
.|+||+.++-.|-|.=
T Consensus 64 ~i~p~~~i~Q~~~v~~ 79 (115)
T PF02883_consen 64 TIPPGQQITQVIKVEN 79 (115)
T ss_dssp SB-TTTEEEEEEEEEE
T ss_pred eeCCCCeEEEEEEEEE
Confidence 6888888888777754
No 19
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=86.10 E-value=1.1 Score=38.22 Aligned_cols=61 Identities=16% Similarity=0.228 Sum_probs=34.6
Q ss_pred eEEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCccccCCCCeeEEEEEEecCCCC
Q 006008 413 LVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQTMKRILEVRFHHHL 492 (665)
Q Consensus 413 mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL~Pg~s~t~~lgIdF~dst 492 (665)
=+.+.++++|.++.++.++.+.- .+|+|-... ..-..+..|+||++.+..+-|.=-...
T Consensus 6 ~~~~~~tv~N~g~~~~~~v~~~l----~~P~GW~~~-----------------~~~~~~~~l~pG~s~~~~~~V~vp~~a 64 (78)
T PF10633_consen 6 TVTVTLTVTNTGTAPLTNVSLSL----SLPEGWTVS-----------------ASPASVPSLPPGESVTVTFTVTVPADA 64 (78)
T ss_dssp EEEEEEEEE--SSS-BSS-EEEE----E--TTSE--------------------EEEEE--B-TTSEEEEEEEEEE-TT-
T ss_pred EEEEEEEEEECCCCceeeEEEEE----eCCCCcccc-----------------CCccccccCCCCCEEEEEEEEECCCCC
Confidence 36789999999999999999964 467876310 011255599999999988877655544
Q ss_pred cc
Q 006008 493 LP 494 (665)
Q Consensus 493 q~ 494 (665)
.+
T Consensus 65 ~~ 66 (78)
T PF10633_consen 65 AP 66 (78)
T ss_dssp -S
T ss_pred CC
Confidence 43
No 20
>KOG0413 consensus Uncharacterized conserved protein related to condensin complex subunit 1 [Function unknown]
Probab=84.30 E-value=1.6 Score=53.18 Aligned_cols=122 Identities=17% Similarity=0.266 Sum_probs=90.0
Q ss_pred eeeehHHHHHHHHhhCCCchHHHHHHHHhhcCCCCcccchhheeeeeccccCCC-CCcccchHHHHHHHHhhhcCChHHH
Q 006008 31 VLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVG-VKIPRMLTTVLKYLAWCFKSEAVET 109 (665)
Q Consensus 31 VV~EsVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~~P~ARAsIIWLIGEY~~~~-e~ip~iaPdvLR~laksF~~E~~eV 109 (665)
|=+.+|+.+-++.-.+-.--++.++-|+|-|+.-+.-.-|.-||--+|.+|... -.+.+++| .+++...|-...|
T Consensus 947 vra~~vvTlakmcLah~~LaKr~~P~lvkeLe~~~~~aiRnNiV~am~D~C~~YTam~d~YiP----~I~~~L~Dp~~iV 1022 (1529)
T KOG0413|consen 947 VRAVGVVTLAKMCLAHDRLAKRLMPMLVKELEYNTAHAIRNNIVLAMGDICSSYTAMTDRYIP----MIAASLCDPSVIV 1022 (1529)
T ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhhHHHHhcceeeeehhhHHHHHHHHHHhhH----HHHHHhcCchHHH
Confidence 345577777777766665566678889999988888888999999999999521 01233333 3557888999999
Q ss_pred HHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhccCCCccchhhHHHHHH
Q 006008 110 KLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKK 160 (665)
Q Consensus 110 KLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD~nyDVRDRARfy~r 160 (665)
+.|.+++.+.|+-..-- .+.-..++.+++.| -|.|+|||.=|-||-.
T Consensus 1023 Rrqt~ilL~rLLq~~~v--Kw~G~Lf~Rf~l~l--~D~~edIr~~a~f~~~ 1069 (1529)
T KOG0413|consen 1023 RRQTIILLARLLQFGIV--KWNGELFIRFMLAL--LDANEDIRNDAKFYIS 1069 (1529)
T ss_pred HHHHHHHHHHHHhhhhh--hcchhhHHHHHHHH--cccCHHHHHHHHHHHH
Confidence 99999999999654321 11224678888877 8999999999999754
No 21
>PRK09687 putative lyase; Provisional
Probab=82.88 E-value=4.1 Score=43.21 Aligned_cols=92 Identities=17% Similarity=0.097 Sum_probs=50.9
Q ss_pred HHHHHHhhcCCCCcccchhheeeeeccccCCCCCcccchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHH
Q 006008 53 VIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTI 132 (665)
Q Consensus 53 iI~~Lak~ld~i~~P~ARAsIIWLIGEY~~~~e~ip~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~ 132 (665)
++..|...+..-.+|.-|++.+..+|+.+.. .+...|.++..+.....++...||.....+..++- .
T Consensus 91 a~~~L~~l~~~D~d~~VR~~A~~aLG~~~~~---~~~~~~~a~~~l~~~~~D~~~~VR~~a~~aLg~~~--~-------- 157 (280)
T PRK09687 91 VFNILNNLALEDKSACVRASAINATGHRCKK---NPLYSPKIVEQSQITAFDKSTNVRFAVAFALSVIN--D-------- 157 (280)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHhccccc---ccccchHHHHHHHHHhhCCCHHHHHHHHHHHhccC--C--------
Confidence 3444444434444566677777777776531 12223445555555666667777777766665541 1
Q ss_pred HHHHHHHHHhhccCCCccchhhHHHH
Q 006008 133 TRLFSYLLELAECDLNYDVRDRARFF 158 (665)
Q Consensus 133 ~~L~qyVL~LAkyD~nyDVRDRARfy 158 (665)
...+..++.+.+ |.+||||..|-+-
T Consensus 158 ~~ai~~L~~~L~-d~~~~VR~~A~~a 182 (280)
T PRK09687 158 EAAIPLLINLLK-DPNGDVRNWAAFA 182 (280)
T ss_pred HHHHHHHHHHhc-CCCHHHHHHHHHH
Confidence 122334444443 7788999888653
No 22
>PF02296 Alpha_adaptin_C: Alpha adaptin AP2, C-terminal domain; InterPro: IPR003164 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. AP adaptor alpha-adaptin can be divided into a trunk domain and the C-terminal appendage domain (or ear domain), separated by a linker region. The C-terminal appendage domain regulates translocation of endocytic accessory proteins to the bud site []. This entry represents a subdomain of the appendage (ear) domain of alpha-adaptin from AP clathrin adaptor complexes. This domain has a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1KYF_A 1B9K_A 1QTS_A 1KYU_A 2VJ0_A 1KY6_A 1W80_A 3HS8_A 1KYD_A 1QTP_A ....
Probab=81.66 E-value=13 Score=34.63 Aligned_cols=105 Identities=15% Similarity=0.223 Sum_probs=61.8
Q ss_pred ccccccCCHHHHHHHhccCCCCc-ccceeeeeccCcCccCccccchhhccchhhhhhhHHHHHHhhccceeeeeccCccc
Q 006008 517 FIKPVPMDMETFIEMESRLPGMF-EYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVA 595 (665)
Q Consensus 517 lv~Pv~mse~~F~~eq~kL~GMn-E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~kv~~~aN~~~V~~~~p~~ 595 (665)
|+.|+.|+.++|.+.=..|.|=- |. +..|+-. ...+ - ......++++.--.+++++
T Consensus 1 F~~p~~l~~~~Ff~RWkql~~~~~E~--Q~vf~~~--~~~~------------~-~~~~~~~~~l~g~~~~vl~------ 57 (113)
T PF02296_consen 1 FMEPTTLSSEDFFQRWKQLGGPPQEA--QEVFKLK--DAKR------------P-MDLESIRRKLEGFGFAVLD------ 57 (113)
T ss_dssp GEEE----HHHHHHHHTTT-SGGGEE--EEEEE------SS----------------HHHHHHHHHHHTSEEET------
T ss_pred CCCCccCCHHHHHHHHHhccCCcccc--EEEEccc--ccCC------------c-ccHHHHHHHHhcCCeEecC------
Confidence 68899999999999999998754 44 6666511 0000 0 1133566788888888874
Q ss_pred cccCCCCCceeeeeeccccCC----ceEEEEEEeccccCCCcceEEEEcccchHHHHHH
Q 006008 596 AKFDDASGLSLRFSSEILGNS----VPCLITITVEGKCSEPLKVSAKVNCEETVFGLNL 650 (665)
Q Consensus 596 ~~~~d~~~~~~rFa~~tlss~----s~~LiTi~~~~~~~~~~~~~l~vNcEk~ViGs~L 650 (665)
+.|.-.+ .=++|-+++++ ..||+.|+.. .... ...|||-|-+-.+--.|
T Consensus 58 -~vDpnp~--n~v~Agi~~t~~~g~~gcLlRlE~n-~~~~--~~RlTvRst~~~vs~~l 110 (113)
T PF02296_consen 58 -GVDPNPN--NIVGAGIFHTKSSGNVGCLLRLEPN-QDAK--MFRLTVRSTDPSVSKAL 110 (113)
T ss_dssp -SSSSSTT--SEEEEEEEE-S-S-EEEEEEEEEEE-TTTT--EEEEEEEESSHHHHHHH
T ss_pred -CCCCCcc--cEEEEEEEEecCCCcEEEEEEEeEC-CcCC--eEEEEEEECChhHHHHH
Confidence 2333222 23666666655 5799999874 2222 57899999888774443
No 23
>KOG1077 consensus Vesicle coat complex AP-2, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=79.52 E-value=3.8 Score=48.83 Aligned_cols=113 Identities=17% Similarity=0.160 Sum_probs=77.0
Q ss_pred CCCchHHHHHHHHhhcCCCC--cccchhheeeeeccccCCCCCcccchHH-HHHHHHhhhcCChHHHHHHHHHhhhheee
Q 006008 46 DPSCHEKVIIQLFRSLDSIK--VPEARVMIIWMVGEYSSVGVKIPRMLTT-VLKYLAWCFKSEAVETKLQILNTTIKVLL 122 (665)
Q Consensus 46 ~P~~~~~iI~~Lak~ld~i~--~P~ARAsIIWLIGEY~~~~e~ip~iaPd-vLR~laksF~~E~~eVKLQILtlaaKl~l 122 (665)
+++-+.....++...|+... +-+-|++ -+|+|||.+..-.-|++.|- .+..+...|.--+..+|--+|+.-+|++-
T Consensus 472 nedlq~yaak~~fe~Lq~~a~hE~mVKvg-gyiLGEfg~LIa~~prss~~~qFsllh~K~~~~s~~tr~lLLtTyiKl~n 550 (938)
T KOG1077|consen 472 NEDLQGYAAKRLFEYLQKPACHENMVKVG-GYILGEFGNLIADDPRSSPAVQFSLLHEKLHLCSPVTRALLLTTYIKLIN 550 (938)
T ss_pred chhhhHHHHHHHHHHHhhhHHHHHHHHhh-hhhhhhhhhhhcCCCCCChHHHHHHHHHHhccCChhHHHHHHHHHHHHHh
Confidence 34444555555555544332 2233333 47999998743334555554 45688899999999999999999999998
Q ss_pred eccCCChhHHHHHHHHHHHhhccCCCccchhhHHHHHHhhcC
Q 006008 123 CAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSH 164 (665)
Q Consensus 123 ~~p~e~~~~~~~L~qyVL~LAkyD~nyDVRDRARfy~rLLs~ 164 (665)
..|. ++..++.|+++--.=.+..+.-||.=|-.|..-
T Consensus 551 l~PE-----i~~~v~~vFq~~~n~~D~ElQqRa~EYLql~k~ 587 (938)
T KOG1077|consen 551 LFPE-----IKSNVQKVFQLYSNLIDVELQQRAVEYLQLSKL 587 (938)
T ss_pred hChh-----hhHHHHHHHHhhcccCCHHHHHHHHHHHHHHHh
Confidence 8884 455566666663322478899999999999865
No 24
>COG1470 Predicted membrane protein [Function unknown]
Probab=79.34 E-value=5.3 Score=45.66 Aligned_cols=76 Identities=16% Similarity=0.204 Sum_probs=56.2
Q ss_pred EEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCccccCCCCeeEEEEEEecCCCCcc
Q 006008 415 CLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQTMKRILEVRFHHHLLP 494 (665)
Q Consensus 415 ~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL~Pg~s~t~~lgIdF~dstq~ 494 (665)
.|.+.++|.++.+++||.|.= +.|.|.+ + .+.++ .|++|+||++.++.+-|.-..-+-+
T Consensus 400 ~i~i~I~NsGna~LtdIkl~v----~~PqgWe---------------i-~Vd~~-~I~sL~pge~~tV~ltI~vP~~a~a 458 (513)
T COG1470 400 TIRISIENSGNAPLTDIKLTV----NGPQGWE---------------I-EVDES-TIPSLEPGESKTVSLTITVPEDAGA 458 (513)
T ss_pred eEEEEEEecCCCccceeeEEe----cCCccce---------------E-EECcc-cccccCCCCcceEEEEEEcCCCCCC
Confidence 478889999999999999975 4577753 1 24555 8999999999999999988877776
Q ss_pred ceEEE--------EEcCceeeeEEe
Q 006008 495 LKLAL--------HCNGKKLPVKLR 511 (665)
Q Consensus 495 ~~f~l--------~~~~~~f~V~i~ 511 (665)
=...+ .+.+++++|.++
T Consensus 459 GdY~i~i~~ksDq~s~e~tlrV~V~ 483 (513)
T COG1470 459 GDYRITITAKSDQASSEDTLRVVVG 483 (513)
T ss_pred CcEEEEEEEeeccccccceEEEEEe
Confidence 54433 234555555543
No 25
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=75.11 E-value=2.5 Score=47.11 Aligned_cols=102 Identities=18% Similarity=0.246 Sum_probs=64.2
Q ss_pred HHHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCchHHHHHHHHhhcC---CCCcccchhheeeeecccc
Q 006008 5 CVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLD---SIKVPEARVMIIWMVGEYS 81 (665)
Q Consensus 5 Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~~~iI~~Lak~ld---~i~~P~ARAsIIWLIGEY~ 81 (665)
++..|..||. +.+..|+.-|+.++..| +..|..+..++..+.+.|. ....|-.+..++.+++.|+
T Consensus 153 ~~~~l~~lL~-----------d~~~~V~~~a~~~l~~i-~~~~~~~~~~~~~~~~~L~~~l~~~~~~~q~~il~~l~~~~ 220 (526)
T PF01602_consen 153 LIPKLKQLLS-----------DKDPSVVSAALSLLSEI-KCNDDSYKSLIPKLIRILCQLLSDPDPWLQIKILRLLRRYA 220 (526)
T ss_dssp HHHHHHHHTT-----------HSSHHHHHHHHHHHHHH-HCTHHHHTTHHHHHHHHHHHHHTCCSHHHHHHHHHHHTTST
T ss_pred HHHHHhhhcc-----------CCcchhHHHHHHHHHHH-ccCcchhhhhHHHHHHHhhhcccccchHHHHHHHHHHHhcc
Confidence 4666677775 44556777777778777 4444443455555555555 4567888999999999988
Q ss_pred CCCCCcccch--HHHHHHHHhhhcCChHHHHHHHHHhhhhee
Q 006008 82 SVGVKIPRML--TTVLKYLAWCFKSEAVETKLQILNTTIKVL 121 (665)
Q Consensus 82 ~~~e~ip~ia--PdvLR~laksF~~E~~eVKLQILtlaaKl~ 121 (665)
.. -+... ..++..+..-+.+-...|.++..++..++.
T Consensus 221 ~~---~~~~~~~~~~i~~l~~~l~s~~~~V~~e~~~~i~~l~ 259 (526)
T PF01602_consen 221 PM---EPEDADKNRIIEPLLNLLQSSSPSVVYEAIRLIIKLS 259 (526)
T ss_dssp SS---SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred cC---ChhhhhHHHHHHHHHHHhhccccHHHHHHHHHHHHhh
Confidence 53 22222 245555555555667777777777766554
No 26
>PF09066 B2-adapt-app_C: Beta2-adaptin appendage, C-terminal sub-domain; InterPro: IPR015151 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. This entry represents a subdomain of the appendage (ear) domain of beta-adaptin from AP clathrin adaptor complexes. This domain has a three-layer arrangement, alpha-beta-alpha, with a bifurcated antiparallel beta-sheet []. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15) []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 1E42_B 2G30_A 2IV9_B 2IV8_A 3HS9_A 3H1Z_A.
Probab=74.51 E-value=29 Score=31.46 Aligned_cols=111 Identities=23% Similarity=0.249 Sum_probs=65.3
Q ss_pred cccccCCHHHHHHHhccCCCCcccceeeeeccCcCccCccccchhhccchhhhhhhHHHHHHhhccceeeeeccCccccc
Q 006008 518 IKPVPMDMETFIEMESRLPGMFEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAAK 597 (665)
Q Consensus 518 v~Pv~mse~~F~~eq~kL~GMnE~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~kv~~~aN~~~V~~~~p~~~~ 597 (665)
+-.-.|+.++|...=..|+--++......+... ..... -.++-|+..|+..|.++ +
T Consensus 2 ~~d~~~~~~~F~~~W~sl~~~~~~e~~~~~~~~------------------~~~~~-~i~~~L~~~nI~~iA~~-----~ 57 (114)
T PF09066_consen 2 VEDGSMDPEEFQEMWKSLPDSNQQELSIQLNAS------------------VPSPD-AIEEKLQANNIFTIASG-----K 57 (114)
T ss_dssp -TT----HHHHHHHHHHS-GGG--EEEEEETT----------------------HH-HHHHHHHCTT-EEEEEE-----E
T ss_pred CCCCccCHHHHHHHHHhCCcccceEEEEecccc------------------CCcHH-HHHHHHHHCCEEEEecC-----C
Confidence 344679999999999999988855334444410 11223 34555699999999875 2
Q ss_pred cCCCCCceee--eeeccccCCceEEEEEEeccccCCCcceEEEEcccchHHHHHHHHHHHHhhc
Q 006008 598 FDDASGLSLR--FSSEILGNSVPCLITITVEGKCSEPLKVSAKVNCEETVFGLNLLNRIVNFLV 659 (665)
Q Consensus 598 ~~d~~~~~~r--Fa~~tlss~s~~LiTi~~~~~~~~~~~~~l~vNcEk~ViGs~Ll~~~~~~l~ 659 (665)
.+ +..+. ||+++ .++..+|+-+.+..... .++++|-|+..-+...++.-+..+|+
T Consensus 58 -~~--~~~~~~y~s~~~-~~~~~fL~El~~~~~~~---~~~v~vK~~~~~~~~~f~~~~~~iL~ 114 (114)
T PF09066_consen 58 -VD--NGQKFFYFSAKT-TNGIWFLVELTIDPGSP---SVKVTVKSENPEMAPLFLQLFESILK 114 (114)
T ss_dssp -CT--T-EEEEEEEEEB-TTS-EEEEEEEE-TT-S---SEEEEEEESSCCCHHHHHHHHHHHCC
T ss_pred -CC--ccccEEEEEEEc-CCCcEEEEEEEEcCCCc---cEEEEEecCCHHHHHHHHHHHHHHhC
Confidence 22 22333 77776 47889999998744322 47899999998887777766666653
No 27
>KOG1059 consensus Vesicle coat complex AP-3, delta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.83 E-value=6.2 Score=47.19 Aligned_cols=122 Identities=17% Similarity=0.217 Sum_probs=73.6
Q ss_pred HHHHHhhCCCchHHHHHHHHhhcCCC----------CcccchhheeeeeccccCCCCCcccchHHHHHHHHhhhc-CChH
Q 006008 39 IKSIIKQDPSCHEKVIIQLFRSLDSI----------KVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFK-SEAV 107 (665)
Q Consensus 39 Ik~LLqk~P~~~~~iI~~Lak~ld~i----------~~P~ARAsIIWLIGEY~~~~e~ip~iaPdvLR~laksF~-~E~~ 107 (665)
|+++--+=|.--...|.+++.+++.- +-++---+.+|+.|||+. .+.+ .-++|..|.+.-. --+.
T Consensus 437 i~Dv~iRV~~iR~fsV~~m~~Ll~~~~~~~s~q~n~~l~eVL~AaaWi~GEyse---~ven-~~~~leamlrpr~~~lp~ 512 (877)
T KOG1059|consen 437 IIDVAIRVPSIRPFSVSQMSALLDDPLLAGSAQINSQLCEVLYAAAWILGEYSE---FVEN-PNDTLEAMLRPRSDLLPG 512 (877)
T ss_pred HHHHheechhhhHhHHHHHHHHHhchhhccchhhccchhHHHHHHHHHHHHHHH---HhhC-HHHHHHHHhcCccccCch
Confidence 33333334444445577777777621 124445578999999995 4444 5577887776554 5688
Q ss_pred HHHHHHHHhhhheeeec-----cCCChhHHHHHHHHHHHh-hccC--CCccchhh---HHHHHHhhcC
Q 006008 108 ETKLQILNTTIKVLLCA-----KGGDMWTITRLFSYLLEL-AECD--LNYDVRDR---ARFFKKLFSH 164 (665)
Q Consensus 108 eVKLQILtlaaKl~l~~-----p~e~~~~~~~L~qyVL~L-AkyD--~nyDVRDR---ARfy~rLLs~ 164 (665)
-+|-=.+-.++|+|..- +..+.+-+..|++.++.- -.|- .+..|-.| +..|-+++..
T Consensus 513 ~iq~vyvqni~Klfc~~~~~~ee~~~~e~~~sL~~~i~~~l~qf~~s~d~EvQERA~~~~~li~~i~~ 580 (877)
T KOG1059|consen 513 HIQAVYVQNIVKLFCSWCSQFEETKDFEGIVSLVNLILSFLEQFSGSSDLEVQERASEVLELIRLIRE 580 (877)
T ss_pred HHHHHHHHHHHHHHHHHHhhcCcccchhHHHHHHHHHHHHhhcccCccchhHHHHHHHHHHHHHHHHH
Confidence 88888888899998654 233333344455554432 2233 25678889 5555555543
No 28
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=70.37 E-value=17 Score=35.67 Aligned_cols=124 Identities=13% Similarity=0.140 Sum_probs=86.2
Q ss_pred hHHHHHHHHhhCCCchHHHHHHHHhhcCCCCcccchhheeeeeccccCCCCCcccchHHHHHHHHhhhcCChHHHHHHHH
Q 006008 35 SIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQIL 114 (665)
Q Consensus 35 sVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~~P~ARAsIIWLIGEY~~~~e~ip~iaPdvLR~laksF~~E~~eVKLQIL 114 (665)
+|+++-+|..+||+--+..+..|.+.|..- +|..|...+=++..-... +. -++-+.++..+++-..|+..+||-...
T Consensus 8 ~i~~l~DL~~r~~~~ve~~~~~l~~~L~D~-~~~VR~~al~~Ls~Li~~-d~-ik~k~~l~~~~l~~l~D~~~~Ir~~A~ 84 (178)
T PF12717_consen 8 AIIALGDLCIRYPNLVEPYLPNLYKCLRDE-DPLVRKTALLVLSHLILE-DM-IKVKGQLFSRILKLLVDENPEIRSLAR 84 (178)
T ss_pred HHHHHHHHHHhCcHHHHhHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHc-Cc-eeehhhhhHHHHHHHcCCCHHHHHHHH
Confidence 788899999999998888888888888644 455666555544443321 22 244566667777888999999998888
Q ss_pred Hhhhheeee-ccCCChhHHHHHHHHHHHhhccCCC-----ccchhhHHHHHHhhcC
Q 006008 115 NTTIKVLLC-AKGGDMWTITRLFSYLLELAECDLN-----YDVRDRARFFKKLFSH 164 (665)
Q Consensus 115 tlaaKl~l~-~p~e~~~~~~~L~qyVL~LAkyD~n-----yDVRDRARfy~rLLs~ 164 (665)
.+-..+... .|.. ....+...+..+..+... -+--+|.++|.-||..
T Consensus 85 ~~~~e~~~~~~~~~---i~~~~~e~i~~l~~~~~~~~~~~~~~~~~~~I~~fll~~ 137 (178)
T PF12717_consen 85 SFFSELLKKRNPNI---IYNNFPELISSLNNCYEHPVYGPLSREKRKKIYKFLLDF 137 (178)
T ss_pred HHHHHHHHhccchH---HHHHHHHHHHHHhCccccccccccCHHHHHHHHHHHHHH
Confidence 887777766 3321 344566667777777643 3455788889999875
No 29
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=69.69 E-value=9 Score=34.71 Aligned_cols=73 Identities=19% Similarity=0.346 Sum_probs=49.9
Q ss_pred cchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhccCCCccchhhHHHHHHhh
Q 006008 89 RMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLF 162 (665)
Q Consensus 89 ~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD~nyDVRDRARfy~rLL 162 (665)
...+.++.-+.+.|.|++..||+--..+...+.-....+-...+..+|..+.++. .|.+++||.=|.++-|||
T Consensus 23 ~~l~~Il~pVL~~~~D~d~rVRy~AcEaL~ni~k~~~~~~l~~f~~IF~~L~kl~-~D~d~~Vr~~a~~Ld~ll 95 (97)
T PF12755_consen 23 KYLDEILPPVLKCFDDQDSRVRYYACEALYNISKVARGEILPYFNEIFDALCKLS-ADPDENVRSAAELLDRLL 95 (97)
T ss_pred HHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCchhHHHHHHHHHHHh
Confidence 3444555555579999999999866555444322122222224567888887774 488999999999999987
No 30
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=64.66 E-value=5.9 Score=34.23 Aligned_cols=66 Identities=12% Similarity=0.228 Sum_probs=48.4
Q ss_pred HHHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCchH-----HHHHHHHhhcCCCCcccchhheeeeecc
Q 006008 5 CVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHE-----KVIIQLFRSLDSIKVPEARVMIIWMVGE 79 (665)
Q Consensus 5 Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~~-----~iI~~Lak~ld~i~~P~ARAsIIWLIGE 79 (665)
++..|++++.. .+..+...++..|.++-...|.... .++..|.+.+.. ..+..+...+|.++.
T Consensus 8 ~i~~l~~~l~~-----------~~~~~~~~a~~~l~~l~~~~~~~~~~~~~~~~i~~l~~~l~~-~~~~v~~~a~~~L~~ 75 (120)
T cd00020 8 GLPALVSLLSS-----------SDENVQREAAWALSNLSAGNNDNIQAVVEAGGLPALVQLLKS-EDEEVVKAALWALRN 75 (120)
T ss_pred ChHHHHHHHHc-----------CCHHHHHHHHHHHHHHhcCCHHHHHHHHHCCChHHHHHHHhC-CCHHHHHHHHHHHHH
Confidence 56778888873 3445677788889998876555432 446677777765 578889999999999
Q ss_pred ccC
Q 006008 80 YSS 82 (665)
Q Consensus 80 Y~~ 82 (665)
.+.
T Consensus 76 l~~ 78 (120)
T cd00020 76 LAA 78 (120)
T ss_pred Hcc
Confidence 985
No 31
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=63.54 E-value=10 Score=46.60 Aligned_cols=116 Identities=15% Similarity=0.158 Sum_probs=72.1
Q ss_pred hHHHHHHHHhhCCC-chHHHHHHHHhhcCCCCcccchhheeeeeccccC-----CCCCcccchHHHHHHHHhhhcCChHH
Q 006008 35 SIISIKSIIKQDPS-CHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSS-----VGVKIPRMLTTVLKYLAWCFKSEAVE 108 (665)
Q Consensus 35 sVvVIk~LLqk~P~-~~~~iI~~Lak~ld~i~~P~ARAsIIWLIGEY~~-----~~e~ip~iaPdvLR~laksF~~E~~e 108 (665)
+|+-|-++.-..|. -|.++|.+|.+.|..=+.+.+--..|-++|+-|. .+.+.+++.|-|..|.-+- ..+++|
T Consensus 194 ai~~l~~la~~~~~~ly~~li~~Ll~~L~~~~q~~~~rt~Iq~l~~i~r~ag~r~~~h~~~ivp~v~~y~~~~-e~~dDE 272 (1233)
T KOG1824|consen 194 AITALGHLASSCNRDLYVELIEHLLKGLSNRTQMSATRTYIQCLAAICRQAGHRFGSHLDKIVPLVADYCNKI-EEDDDE 272 (1233)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHHhccCCCCchHHHHHHHHHHHHHHHHhcchhhcccchhhHHHHHHhccc-ccCcHH
Confidence 55555555554454 4889999999999877777777777777777663 3356889999888877433 455666
Q ss_pred HHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhccCCC--ccc
Q 006008 109 TKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLN--YDV 151 (665)
Q Consensus 109 VKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD~n--yDV 151 (665)
.+---|-+.--+..+.|.+-..-+..+.+-.++...||.| ||-
T Consensus 273 LrE~~lQale~fl~rcp~ei~p~~pei~~l~l~yisYDPNy~yd~ 317 (1233)
T KOG1824|consen 273 LREYCLQALESFLRRCPKEILPHVPEIINLCLSYISYDPNYNYDT 317 (1233)
T ss_pred HHHHHHHHHHHHHHhChhhhcccchHHHHHHHHHhccCCCCCCCC
Confidence 6654444443344555653221223333444444589985 554
No 32
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=63.30 E-value=6.3 Score=47.55 Aligned_cols=13 Identities=0% Similarity=0.038 Sum_probs=6.5
Q ss_pred HHHHHHHHhhCCC
Q 006008 36 IISIKSIIKQDPS 48 (665)
Q Consensus 36 VvVIk~LLqk~P~ 48 (665)
+..+.++++....
T Consensus 325 ~~~~~~lm~~~g~ 337 (784)
T PF04931_consen 325 VPFLWNLMRSLGN 337 (784)
T ss_pred hhHHHHHhccccc
Confidence 3445555555443
No 33
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=62.02 E-value=8 Score=38.56 Aligned_cols=126 Identities=17% Similarity=0.102 Sum_probs=71.4
Q ss_pred cceeeehHHHHHHHHhhCCCchHH----HHHHHHhhcCCCC---cccchhheeeeeccccCCCCCcccchHHH-HHHHHh
Q 006008 29 ADVLIQSIISIKSIIKQDPSCHEK----VIIQLFRSLDSIK---VPEARVMIIWMVGEYSSVGVKIPRMLTTV-LKYLAW 100 (665)
Q Consensus 29 ~~VV~EsVvVIk~LLqk~P~~~~~----iI~~Lak~ld~i~---~P~ARAsIIWLIGEY~~~~e~ip~iaPdv-LR~lak 100 (665)
..|+.++..+|+.|.+.....+.. ++..|.+.+..-+ ...|..++.=|+ +++. +.+.+ +..+..
T Consensus 67 s~v~~~A~~~l~~l~~~l~~~~~~~~~~~l~~Ll~~~~~~~~~i~~~a~~~L~~i~-~~~~-------~~~~~~~~~l~~ 138 (228)
T PF12348_consen 67 SKVSKTACQLLSDLARQLGSHFEPYADILLPPLLKKLGDSKKFIREAANNALDAII-ESCS-------YSPKILLEILSQ 138 (228)
T ss_dssp --HHHHHHHHHHHHHHHHGGGGHHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHH-TTS--------H--HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHH-HHCC-------cHHHHHHHHHHH
Confidence 458888999999999987776543 3445555554322 234555554433 3331 12344 666677
Q ss_pred hhcCChHHHHHHHHHhhhheeeecc--CCChh---HHHHHHHHHHHhhccCCCccchhhHHHHHHhhc
Q 006008 101 CFKSEAVETKLQILNTTIKVLLCAK--GGDMW---TITRLFSYLLELAECDLNYDVRDRARFFKKLFS 163 (665)
Q Consensus 101 sF~~E~~eVKLQILtlaaKl~l~~p--~e~~~---~~~~L~qyVL~LAkyD~nyDVRDRARfy~rLLs 163 (665)
.+.+-...||...+.+...+.-..+ ..... .+..+...+ .-+-.|.+++||+-||-.+..|.
T Consensus 139 ~~~~Kn~~vR~~~~~~l~~~l~~~~~~~~~l~~~~~~~~l~~~l-~~~l~D~~~~VR~~Ar~~~~~l~ 205 (228)
T PF12348_consen 139 GLKSKNPQVREECAEWLAIILEKWGSDSSVLQKSAFLKQLVKAL-VKLLSDADPEVREAARECLWALY 205 (228)
T ss_dssp HTT-S-HHHHHHHHHHHHHHHTT-----GGG--HHHHHHHHHHH-HHHHTSS-HHHHHHHHHHHHHHH
T ss_pred HHhCCCHHHHHHHHHHHHHHHHHccchHhhhcccchHHHHHHHH-HHHCCCCCHHHHHHHHHHHHHHH
Confidence 8888999999999988877766655 11111 123344433 33357999999999998555443
No 34
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=54.96 E-value=14 Score=42.45 Aligned_cols=108 Identities=14% Similarity=0.176 Sum_probs=73.8
Q ss_pred HHHHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCchHHH-----HHHHHhhcCCCCcccchhheeeeec
Q 006008 4 TCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKV-----IIQLFRSLDSIKVPEARVMIIWMVG 78 (665)
Q Consensus 4 ~Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~~~i-----I~~Lak~ld~i~~P~ARAsIIWLIG 78 (665)
.++..++.+|. +.+..|-..|+.+|++|... +.....+ +.+|.+.+.. ..+..|.-+++++.
T Consensus 119 ~l~~~i~~~L~-----------~~d~~Va~~A~~~L~~l~~~-~~~~~~l~~~~~~~~L~~l~~~-~~~~vR~Rv~el~v 185 (503)
T PF10508_consen 119 ELLPLIIQCLR-----------DPDLSVAKAAIKALKKLASH-PEGLEQLFDSNLLSKLKSLMSQ-SSDIVRCRVYELLV 185 (503)
T ss_pred cHHHHHHHHHc-----------CCcHHHHHHHHHHHHHHhCC-chhHHHHhCcchHHHHHHHHhc-cCHHHHHHHHHHHH
Confidence 35556666665 45556666688889999864 4444444 5666666543 24567777888887
Q ss_pred cccCCCCCcccchHH--HHHHHHhhhcCChHHHHHHHHHhhhheeeec
Q 006008 79 EYSSVGVKIPRMLTT--VLKYLAWCFKSEAVETKLQILNTTIKVLLCA 124 (665)
Q Consensus 79 EY~~~~e~ip~iaPd--vLR~laksF~~E~~eVKLQILtlaaKl~l~~ 124 (665)
+.+...+....++-. +|..+.+...+++..||+..|.+...|-.+.
T Consensus 186 ~i~~~S~~~~~~~~~sgll~~ll~eL~~dDiLvqlnalell~~La~~~ 233 (503)
T PF10508_consen 186 EIASHSPEAAEAVVNSGLLDLLLKELDSDDILVQLNALELLSELAETP 233 (503)
T ss_pred HHHhcCHHHHHHHHhccHHHHHHHHhcCccHHHHHHHHHHHHHHHcCh
Confidence 776543333333333 7888888999999999999999988887643
No 35
>PF05110 AF-4: AF-4 proto-oncoprotein; InterPro: IPR007797 This family consist of family member 1 (proto-oncogene AF4), family member 2 or FMR2 (Fragile X E mental retardation syndrome), family member 3 or LAF4 (lymphoid nuclear protein related to AF4) and family member 4 (protein lilliputian). Lilliputian is a Drosophila AF4 protein homologue which contains an AT-hook domain. It represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila []. These proteins have been linked to Homo sapiens diseases such as acute lymphoblastic leukemia and mental retardation [].
Probab=52.19 E-value=16 Score=46.32 Aligned_cols=15 Identities=13% Similarity=0.204 Sum_probs=9.1
Q ss_pred HHHHHhhcCCCCccc
Q 006008 54 IIQLFRSLDSIKVPE 68 (665)
Q Consensus 54 I~~Lak~ld~i~~P~ 68 (665)
|..|..++|.++++-
T Consensus 51 iQ~mLGnYeemk~~~ 65 (1191)
T PF05110_consen 51 IQNMLGNYEEMKELL 65 (1191)
T ss_pred HHHHhcCHHHHhccc
Confidence 556666666666653
No 36
>PF06483 ChiC: Chitinase C; InterPro: IPR009470 This ~170 aa region is found at the C-terminal to the catalytic domain (IPR001223 from INTERPRO) found in members of glycoside hydrolase family 18.
Probab=51.40 E-value=45 Score=33.88 Aligned_cols=111 Identities=19% Similarity=0.280 Sum_probs=65.3
Q ss_pred CeeEEEEecC-----CCCCCCCCeEEEEEEEEecCCcce---eeeEeeccc----cccchhhhhhhhhhcccc-----cc
Q 006008 395 GLKVYYSFSS-----EASTISPQLVCLETFFENCSSETM---SEVTLVDEE----SHKALDLADLTLATTASS-----LT 457 (665)
Q Consensus 395 GL~v~Y~F~r-----~p~~~s~~mv~Vql~f~N~s~~~i---~~I~i~~~~----~~~~~~g~~~~l~~~~~~-----~~ 457 (665)
=|.|.+.|.- +-.++.|+ |.|+|+|..+| .+|+..=.. ..|-+.|+..+.....|+ --
T Consensus 35 ~ldv~v~~~gf~~GD~NYPI~Pk-----l~iTNns~~~iPGGt~~~FD~ptSa~~~~kdqSG~g~~vi~sght~~g~NiG 109 (180)
T PF06483_consen 35 ALDVSVSFTGFKLGDSNYPINPK-----LTITNNSGQTIPGGTEFEFDYPTSAPDNAKDQSGFGLKVISSGHTAAGNNIG 109 (180)
T ss_pred eEEEEEEeCCcccCCCCCCcCCc-----EEEEcCCCcccCCccEEEEccccCCccccccccCCcEEEEecCCcccCCccc
Confidence 3555555553 34555665 57999999999 334432111 113334443222221111 00
Q ss_pred c-CCCCCCcc-cCCCccccCCCCeeEEEEEEecCCCCccceEEEEEcCceeeeEEe
Q 006008 458 S-QSDLPTLV-PMEEITSLEPGQTMKRILEVRFHHHLLPLKLALHCNGKKLPVKLR 511 (665)
Q Consensus 458 ~-~~~~~~i~-~f~eI~sL~Pg~s~t~~lgIdF~dstq~~~f~l~~~~~~f~V~i~ 511 (665)
| ..+.+++. ..+.-++|+||+++++.|=.--+=+. |.+|.+..+++.|-++-.
T Consensus 110 GL~gdfHrvs~tlp~wqslapG~s~~~~~~YyLPiSg-PsN~tv~~~g~~Yal~~d 164 (180)
T PF06483_consen 110 GLKGDFHRVSFTLPAWQSLAPGASVELDMVYYLPISG-PSNFTVNIGGKTYALKFD 164 (180)
T ss_pred ccCCceEEEEEECCCccccCCCCEEEEeEEEEeccCC-CceEEEEECCEEEEEecc
Confidence 1 11111111 13566899999999999988888887 999999999999876543
No 37
>PRK09687 putative lyase; Provisional
Probab=49.74 E-value=52 Score=34.98 Aligned_cols=73 Identities=10% Similarity=0.019 Sum_probs=46.9
Q ss_pred cccchhheeeeeccccCCCCCcccchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhcc
Q 006008 66 VPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAEC 145 (665)
Q Consensus 66 ~P~ARAsIIWLIGEY~~~~e~ip~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAky 145 (665)
++.-|-+.+|-+|++.+ +...+.++ .-..++...|+.....+..++-...| ..+..|.+ .| .
T Consensus 141 ~~~VR~~a~~aLg~~~~-----~~ai~~L~----~~L~d~~~~VR~~A~~aLg~~~~~~~----~~~~~L~~-~L----~ 202 (280)
T PRK09687 141 STNVRFAVAFALSVIND-----EAAIPLLI----NLLKDPNGDVRNWAAFALNSNKYDNP----DIREAFVA-ML----Q 202 (280)
T ss_pred CHHHHHHHHHHHhccCC-----HHHHHHHH----HHhcCCCHHHHHHHHHHHhcCCCCCH----HHHHHHHH-Hh----c
Confidence 67889999999998753 23344444 34457888899999988888722121 12222222 22 6
Q ss_pred CCCccchhhHH
Q 006008 146 DLNYDVRDRAR 156 (665)
Q Consensus 146 D~nyDVRDRAR 156 (665)
|.|.+||-.|.
T Consensus 203 D~~~~VR~~A~ 213 (280)
T PRK09687 203 DKNEEIRIEAI 213 (280)
T ss_pred CCChHHHHHHH
Confidence 77999987775
No 38
>PF11611 DUF4352: Domain of unknown function (DUF4352); InterPro: IPR021652 This entry is represented by Bacteriophage A118, Gp32. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a group of putative lipoproteins of unknown function.; PDB: 3CFU_A.
Probab=48.61 E-value=67 Score=28.73 Aligned_cols=75 Identities=15% Similarity=0.184 Sum_probs=38.8
Q ss_pred CCCeEEEEEEEEecCCccee----eeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCccccCCCCeeEEEEE
Q 006008 410 SPQLVCLETFFENCSSETMS----EVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQTMKRILE 485 (665)
Q Consensus 410 s~~mv~Vql~f~N~s~~~i~----~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL~Pg~s~t~~lg 485 (665)
.-+.+.|+++++|.+++++. +..+.+. +|-....... .. . ...-.....|.||+++++.|.
T Consensus 34 g~~fv~v~v~v~N~~~~~~~~~~~~f~l~d~------~g~~~~~~~~-----~~-~---~~~~~~~~~i~pG~~~~g~l~ 98 (123)
T PF11611_consen 34 GNKFVVVDVTVKNNGDEPLDFSPSDFKLYDS------DGNKYDPDFS-----AS-S---NDNDLFSETIKPGESVTGKLV 98 (123)
T ss_dssp -SEEEEEEEEEEE-SSS-EEEEGGGEEEE-T------T--B--EEE------CC-C---TTTB--EEEE-TT-EEEEEEE
T ss_pred CCEEEEEEEEEEECCCCcEEecccceEEEeC------CCCEEccccc-----ch-h---ccccccccEECCCCEEEEEEE
Confidence 35789999999999999884 2344322 1111000000 00 0 000023458999999999999
Q ss_pred EecCCCCccceEEE
Q 006008 486 VRFHHHLLPLKLAL 499 (665)
Q Consensus 486 IdF~dstq~~~f~l 499 (665)
.+=-...++..|+.
T Consensus 99 F~vp~~~~~~~l~~ 112 (123)
T PF11611_consen 99 FEVPKDDKPYTLEY 112 (123)
T ss_dssp EEESTT-GG-EEEE
T ss_pred EEECCCCccEEEEE
Confidence 88888888866655
No 39
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=47.49 E-value=1.6e+02 Score=25.69 Aligned_cols=74 Identities=19% Similarity=0.238 Sum_probs=42.3
Q ss_pred EEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCccccCCCCeeEEEEEEecC--CC
Q 006008 414 VCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQTMKRILEVRFH--HH 491 (665)
Q Consensus 414 v~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL~Pg~s~t~~lgIdF~--ds 491 (665)
.+..|++.|.|..+. ..++...+. .... +.-.+.=..|+||++.+. -|.|+ +.
T Consensus 22 ~~~~v~l~N~s~~p~-~f~v~~~~~--~~~~--------------------~~v~~~~g~l~PG~~~~~--~V~~~~~~~ 76 (102)
T PF14874_consen 22 YSRTVTLTNTSSIPA-RFRVRQPES--LSSF--------------------FSVEPPSGFLAPGESVEL--EVTFSPTKP 76 (102)
T ss_pred EEEEEEEEECCCCCE-EEEEEeCCc--CCCC--------------------EEEECCCCEECCCCEEEE--EEEEEeCCC
Confidence 357789999998885 444433210 0000 111112236999997654 55555 22
Q ss_pred C--ccceEEEEEcCceeeeEEec
Q 006008 492 L--LPLKLALHCNGKKLPVKLRP 512 (665)
Q Consensus 492 t--q~~~f~l~~~~~~f~V~i~P 512 (665)
. .-.++.+.+.++.|.|.|+.
T Consensus 77 ~g~~~~~l~i~~e~~~~~i~v~a 99 (102)
T PF14874_consen 77 LGDYEGSLVITTEGGSFEIPVKA 99 (102)
T ss_pred CceEEEEEEEEECCeEEEEEEEE
Confidence 2 23456667788888888775
No 40
>KOG1189 consensus Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism]
Probab=44.81 E-value=19 Score=43.56 Aligned_cols=14 Identities=21% Similarity=0.199 Sum_probs=8.3
Q ss_pred eehHHHHHHHHhhC
Q 006008 33 IQSIISIKSIIKQD 46 (665)
Q Consensus 33 ~EsVvVIk~LLqk~ 46 (665)
.++.-.||.+.++.
T Consensus 565 s~~f~~ik~l~k~~ 578 (960)
T KOG1189|consen 565 SEAFRQIKELQKRF 578 (960)
T ss_pred HHHHHHHHHHHHHH
Confidence 44555577766654
No 41
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=43.32 E-value=31 Score=27.82 Aligned_cols=31 Identities=10% Similarity=0.040 Sum_probs=26.5
Q ss_pred CeEEEEEEEEecCCcceeeeEeeccccccchhhhh
Q 006008 412 QLVCLETFFENCSSETMSEVTLVDEESHKALDLAD 446 (665)
Q Consensus 412 ~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~ 446 (665)
.-|...|+++|.++.+..+|.|.+ .||+|+.
T Consensus 12 d~v~Yti~v~N~g~~~a~~v~v~D----~lP~g~~ 42 (53)
T TIGR01451 12 DTITYTITVTNNGNVPATNVVVTD----ILPSGTT 42 (53)
T ss_pred CEEEEEEEEEECCCCceEeEEEEE----cCCCCCE
Confidence 456788999999999999999998 5788873
No 42
>PRK15098 beta-D-glucoside glucohydrolase; Provisional
Probab=41.29 E-value=51 Score=40.05 Aligned_cols=60 Identities=18% Similarity=0.190 Sum_probs=39.7
Q ss_pred CCeEEEEEEEEecCCcceee---eEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCccccCCCCeeEEEEEEe
Q 006008 411 PQLVCLETFFENCSSETMSE---VTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQTMKRILEVR 487 (665)
Q Consensus 411 ~~mv~Vql~f~N~s~~~i~~---I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL~Pg~s~t~~lgId 487 (665)
...+.|.++++|+++-+=.+ +-+..... +..+ -.-++..|..| .|+||++.++.+-|+
T Consensus 666 ~~~i~v~v~V~NtG~~~G~EVvQlYv~~~~~-----~~~~-------------P~k~L~gF~Kv-~L~pGes~~V~~~l~ 726 (765)
T PRK15098 666 DGKVTASVTVTNTGKREGATVVQLYLQDVTA-----SMSR-------------PVKELKGFEKI-MLKPGETQTVSFPID 726 (765)
T ss_pred CCeEEEEEEEEECCCCCccEEEEEeccCCCC-----CCCC-------------HHHhccCceeE-eECCCCeEEEEEeec
Confidence 34688999999999754333 33433211 1100 01148889999 699999999999887
Q ss_pred cC
Q 006008 488 FH 489 (665)
Q Consensus 488 F~ 489 (665)
..
T Consensus 727 ~~ 728 (765)
T PRK15098 727 IE 728 (765)
T ss_pred HH
Confidence 54
No 43
>PF00927 Transglut_C: Transglutaminase family, C-terminal ig like domain; InterPro: IPR008958 Synonym(s): Protein-glutamine gamma-glutamyltransferase, Fibrinoligase, TGase Transglutaminases catalyse the post-translational modification of proteins at glutamine residues, with formation of isopeptide bonds. Members of the transglutaminase family usually have three domains: N-terminal (IPR001102 from INTERPRO), middle (IPR013808 from INTERPRO) and C-terminal. The middle domain is usually well conserved, but family members can display major differences in their N- and C-terminal domains, although their overall structure is conserved []. This entry represents the C-terminal domain found in transglutaminases, which consists of an immunoglobulin-like beta-sandwich consisting of seven strands in two sheets with a Greek key topology. The best known transglutaminase is blood coagulation factor XIII, a plasma tetrameric protein composed of two catalytic A subunits and two non-catalytic B subunits. Factor XIII is responsible for cross-linking fibrin chains, thus stabilising the fibrin clot. Protein-glutamine gamma-glutamyltransferases (2.3.2.13 from EC) are calcium-dependent enzymes that catalyse the cross-linking of proteins by promoting the formation of isopeptide bonds between the gamma-carboxyl group of a glutamine in one polypeptide chain and the epsilon-amino group of a lysine in a second polypeptide chain. TGases also catalyse the conjugation of polyamines to proteins [, ].; GO: 0003810 protein-glutamine gamma-glutamyltransferase activity, 0018149 peptide cross-linking; PDB: 2XZZ_A 1GGY_B 1FIE_B 1GGU_B 1GGT_B 1F13_A 1QRK_B 1EVU_A 1EX0_B 1L9N_B ....
Probab=38.56 E-value=39 Score=30.23 Aligned_cols=62 Identities=19% Similarity=0.140 Sum_probs=36.9
Q ss_pred eEEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCC--cccCCCccccCCCCeeEEEEEEecCC
Q 006008 413 LVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPT--LVPMEEITSLEPGQTMKRILEVRFHH 490 (665)
Q Consensus 413 mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~--i~~f~eI~sL~Pg~s~t~~lgIdF~d 490 (665)
=+.|.+.|+|.+++++.+|.+.=-... + .+.+++. +..-.....|.||++.+..+-|.+.+
T Consensus 16 d~~v~v~~~N~~~~~l~~v~~~l~~~~-----v------------~ytG~~~~~~~~~~~~~~l~p~~~~~~~~~i~p~~ 78 (107)
T PF00927_consen 16 DFTVSVSFTNPSSEPLRNVSLNLCAFT-----V------------EYTGLTRDQFKKEKFEVTLKPGETKSVEVTITPSQ 78 (107)
T ss_dssp EEEEEEEEEE-SSS-EECEEEEEEEEE-----E------------ECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE-HHS
T ss_pred CEEEEEEEEeCCcCccccceeEEEEEE-----E------------EECCcccccEeEEEcceeeCCCCEEEEEEEEEcee
Confidence 356899999999999999876421000 0 0122321 22223445899999999999997776
Q ss_pred C
Q 006008 491 H 491 (665)
Q Consensus 491 s 491 (665)
-
T Consensus 79 y 79 (107)
T PF00927_consen 79 Y 79 (107)
T ss_dssp H
T ss_pred E
Confidence 5
No 44
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=35.96 E-value=34 Score=42.31 Aligned_cols=10 Identities=20% Similarity=0.338 Sum_probs=5.2
Q ss_pred cCCCCccCCC
Q 006008 221 AAPGYEPLPK 230 (665)
Q Consensus 221 ~~~GY~~LP~ 230 (665)
.+..|.++..
T Consensus 1346 ~a~dYs~iaT 1355 (1516)
T KOG1832|consen 1346 DAIDYSDIAT 1355 (1516)
T ss_pred ccccccccee
Confidence 3455555554
No 45
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=35.53 E-value=44 Score=28.08 Aligned_cols=30 Identities=13% Similarity=0.070 Sum_probs=25.8
Q ss_pred CeEEEEEEEEecCCcceeeeEeeccccccchhhh
Q 006008 412 QLVCLETFFENCSSETMSEVTLVDEESHKALDLA 445 (665)
Q Consensus 412 ~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~ 445 (665)
.-+...|.++|.+..++.||.|.+ .+|+|+
T Consensus 41 d~v~ytitvtN~G~~~a~nv~v~D----~lp~g~ 70 (76)
T PF01345_consen 41 DTVTYTITVTNTGPAPATNVVVTD----TLPAGL 70 (76)
T ss_pred CEEEEEEEEEECCCCeeEeEEEEE----cCCCCC
Confidence 456678999999999999999998 468887
No 46
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=32.16 E-value=55 Score=40.83 Aligned_cols=195 Identities=15% Similarity=0.129 Sum_probs=100.0
Q ss_pred HHHHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCch-HHHHHHHHhhcCCCCc---ccchhheeeeecc
Q 006008 4 TCVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCH-EKVIIQLFRSLDSIKV---PEARVMIIWMVGE 79 (665)
Q Consensus 4 ~Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~-~~iI~~Lak~ld~i~~---P~ARAsIIWLIGE 79 (665)
.-+..|+.||+ |....|-..||.-+--|.-|-|+.+ +.++..||-++=+=++ .-+--+.--.+++
T Consensus 47 kvv~~lLklL~-----------D~ngEVQnlAVKClg~lvsKvke~~le~~ve~L~~~~~s~keq~rdissi~Lktvi~n 115 (1233)
T KOG1824|consen 47 KVVKMLLKLLE-----------DKNGEVQNLAVKCLGPLVSKVKEDQLETIVENLCSNMLSGKEQLRDISSIGLKTVIAN 115 (1233)
T ss_pred HHHHHHHHHHh-----------ccCcHHHHHHHHHHHHHHhhchHHHHHHHHHHHhhhhccchhhhccHHHHHHHHHHhc
Confidence 34678999998 3444466669999999998888754 6667777777421111 0011111112233
Q ss_pred cc-CC-CCCcccchHHHHHHHHhhhcC--ChHHHHHHHHHhhhheeeeccC--CChhHHHHHHHHHHHhhccCCCccchh
Q 006008 80 YS-SV-GVKIPRMLTTVLKYLAWCFKS--EAVETKLQILNTTIKVLLCAKG--GDMWTITRLFSYLLELAECDLNYDVRD 153 (665)
Q Consensus 80 Y~-~~-~e~ip~iaPdvLR~laksF~~--E~~eVKLQILtlaaKl~l~~p~--e~~~~~~~L~qyVL~LAkyD~nyDVRD 153 (665)
-. .. ...-+++++.++-+|...... +..-+|+..|-..+-+..+.-+ ..++. ..+.--+.++ +-.---||-
T Consensus 116 l~P~~~~~la~tV~~~~t~~l~~~i~~qe~~sai~~e~lDil~d~lsr~g~ll~~fh~-~il~~l~~ql--~s~R~aVrK 192 (1233)
T KOG1824|consen 116 LPPSSSSFLAATVCKRITPKLKQAISKQEDVSAIKCEVLDILADVLSRFGTLLPNFHL-SILKCLLPQL--QSPRLAVRK 192 (1233)
T ss_pred CCCccccccccHHHHHHHHHHHHHhhhcccchhhHHHHHHHHHHHHHhhcccCcchHH-HHHHHHhhcc--cChHHHHHH
Confidence 21 00 012344555555555444333 3444899888888877766522 01111 1111111122 111235888
Q ss_pred hHHHHH-HhhcCCCCCCCCcccchhcccCcchHHHHHhhhccCCCCCCCCCCcccccccccHHHHhhccCCCCc
Q 006008 154 RARFFK-KLFSHNLCSQVPEETNALQENKDLPLVLVECIFRKQENLAASEPINDRFYLPGSLSQIVLHAAPGYE 226 (665)
Q Consensus 154 RARfy~-rLLs~~~~~~~~~~~~~~s~~~~~~~~~a~~if~~k~p~~~~~~~~~r~~~lGSLSh~l~~~~~GY~ 226 (665)
||-..- .|.+.. +.+++..+.+.++.+-.+++..+..+.-...+|+...-.+|+..-|.
T Consensus 193 kai~~l~~la~~~--------------~~~ly~~li~~Ll~~L~~~~q~~~~rt~Iq~l~~i~r~ag~r~~~h~ 252 (1233)
T KOG1824|consen 193 KAITALGHLASSC--------------NRDLYVELIEHLLKGLSNRTQMSATRTYIQCLAAICRQAGHRFGSHL 252 (1233)
T ss_pred HHHHHHHHHHHhc--------------CHHHHHHHHHHHHhccCCCCchHHHHHHHHHHHHHHHHhcchhhccc
Confidence 886533 333321 13466777777775544333332233334456777776676665543
No 47
>PF07705 CARDB: CARDB; InterPro: IPR011635 The APHP (acidic peptide-dependent hydrolases/peptidase) domain is found in a variety of different proteins.; PDB: 2KUT_A 2L0D_A 3IDU_A 2KL6_A.
Probab=31.72 E-value=1.7e+02 Score=24.84 Aligned_cols=55 Identities=22% Similarity=0.161 Sum_probs=34.9
Q ss_pred CCeEEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCccccCCCCeeEEEEEEecC
Q 006008 411 PQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQTMKRILEVRFH 489 (665)
Q Consensus 411 ~~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL~Pg~s~t~~lgIdF~ 489 (665)
..=+.|.+.+.|.+.....++.+.=- .+|- ...-..|..|+||++.+..+-+.+.
T Consensus 18 g~~~~i~~~V~N~G~~~~~~~~v~~~-----~~~~-------------------~~~~~~i~~L~~g~~~~v~~~~~~~ 72 (101)
T PF07705_consen 18 GEPVTITVTVKNNGTADAENVTVRLY-----LDGN-------------------SVSTVTIPSLAPGESETVTFTWTPP 72 (101)
T ss_dssp TSEEEEEEEEEE-SSS-BEEEEEEEE-----ETTE-------------------EEEEEEESEB-TTEEEEEEEEEE-S
T ss_pred CCEEEEEEEEEECCCCCCCCEEEEEE-----ECCc-------------------eeccEEECCcCCCcEEEEEEEEEeC
Confidence 45567888999999998888777521 1111 0122356899999999988877776
No 48
>PF13513 HEAT_EZ: HEAT-like repeat; PDB: 2Z5J_A 2OT8_B 2Z5O_A 2H4M_A 2QMR_A 1QBK_B 2Z5M_A 2Z5K_A 2Z5N_A 1GCJ_B ....
Probab=29.69 E-value=22 Score=27.79 Aligned_cols=51 Identities=14% Similarity=0.179 Sum_probs=35.8
Q ss_pred ccchhheeeeeccccCC-CCCcccchHHHHHHHHhhhcCChHHHHHHHHHhh
Q 006008 67 PEARVMIIWMVGEYSSV-GVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTT 117 (665)
Q Consensus 67 P~ARAsIIWLIGEY~~~-~e~ip~iaPdvLR~laksF~~E~~eVKLQILtla 117 (665)
|.-|.+-+|.+|+.+.. .+.+....|+++..+.+-..|....||.+...+.
T Consensus 1 p~vR~~A~~aLg~l~~~~~~~~~~~~~~~~~~L~~~L~d~~~~VR~~A~~aL 52 (55)
T PF13513_consen 1 PRVRRAAAWALGRLAEGCPELLQPYLPELLPALIPLLQDDDDSVRAAAAWAL 52 (55)
T ss_dssp HHHHHHHHHHHHCTTTTTHHHHHHHHHHHHHHHHHHTTSSSHHHHHHHHHHH
T ss_pred CHHHHHHHHHHhhHhcccHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 44578889999975531 1233446778888888888888889988766543
No 49
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=29.46 E-value=94 Score=25.82 Aligned_cols=84 Identities=14% Similarity=0.220 Sum_probs=50.1
Q ss_pred HHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHHhhCCCchHHHHHHHHhhcCCCCcccchhheeeeeccccCCCC
Q 006008 6 VEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIKVPEARVMIIWMVGEYSSVGV 85 (665)
Q Consensus 6 l~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~~P~ARAsIIWLIGEY~~~~e 85 (665)
+..|+++|.+ +.+..|-..++-+|. +. ....++..|.+.+.. .+|.-|...+|-+|.+..
T Consensus 1 i~~L~~~l~~----------~~~~~vr~~a~~~L~----~~--~~~~~~~~L~~~l~d-~~~~vr~~a~~aL~~i~~--- 60 (88)
T PF13646_consen 1 IPALLQLLQN----------DPDPQVRAEAARALG----EL--GDPEAIPALIELLKD-EDPMVRRAAARALGRIGD--- 60 (88)
T ss_dssp HHHHHHHHHT----------SSSHHHHHHHHHHHH----CC--THHHHHHHHHHHHTS-SSHHHHHHHHHHHHCCHH---
T ss_pred CHHHHHHHhc----------CCCHHHHHHHHHHHH----Hc--CCHhHHHHHHHHHcC-CCHHHHHHHHHHHHHhCC---
Confidence 3567888843 344444444444444 22 245778888888854 778999999999998742
Q ss_pred CcccchHHHHHHHHhhhcC-ChHHHHHHHHH
Q 006008 86 KIPRMLTTVLKYLAWCFKS-EAVETKLQILN 115 (665)
Q Consensus 86 ~ip~iaPdvLR~laksF~~-E~~eVKLQILt 115 (665)
+...+. +.+-+.+ ....||...+.
T Consensus 61 --~~~~~~----L~~~l~~~~~~~vr~~a~~ 85 (88)
T PF13646_consen 61 --PEAIPA----LIKLLQDDDDEVVREAAAE 85 (88)
T ss_dssp --HHTHHH----HHHHHTC-SSHHHHHHHHH
T ss_pred --HHHHHH----HHHHHcCCCcHHHHHHHHh
Confidence 333333 3333333 35566765544
No 50
>KOG1058 consensus Vesicle coat complex COPI, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.21 E-value=1.8e+02 Score=35.70 Aligned_cols=152 Identities=19% Similarity=0.233 Sum_probs=94.5
Q ss_pred EEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCccccCCCCeeEEEEEEecCCCCc
Q 006008 414 VCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQTMKRILEVRFHHHLL 493 (665)
Q Consensus 414 v~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL~Pg~s~t~~lgIdF~dstq 493 (665)
+.+++.|-|.+.+.+.|+++.=- |+++ + .+++-|.=-+|.|.+..+...-|.-.++--
T Consensus 736 IVLDvL~VNqT~~tLQNl~lelA-----------Tlgd----------L-Klve~p~p~~Laph~f~~ikatvKVsSten 793 (948)
T KOG1058|consen 736 IVLDVLLVNQTKETLQNLSLELA-----------TLGD----------L-KLVERPTPFSLAPHDFVNIKATVKVSSTEN 793 (948)
T ss_pred EEEEEEEecCChHHHhhheeeee-----------eccC----------c-eeeecCCCcccCcccceeEEEEEEEeeccC
Confidence 67899999999999999999532 1111 1 234434444899998665554444444333
Q ss_pred cceEE-EE------EcCceeee--EEecCcccccccccCCHHHHHHHhccCCCCcccceeeeeccCcCccCccccchhhc
Q 006008 494 PLKLA-LH------CNGKKLPV--KLRPDIGYFIKPVPMDMETFIEMESRLPGMFEYARSCTFTDHLGEVDKDTDESSLL 564 (665)
Q Consensus 494 ~~~f~-l~------~~~~~f~V--~i~PpvGElv~Pv~mse~~F~~eq~kL~GMnE~~~~~~~~~~~~~~~~~~~~~~~~ 564 (665)
.+=|- |. .++++.-| .|+-+|=+.+.|-.|++.+|+..-..+ |..-++++...++
T Consensus 794 GvIfGnIvY~~~~~a~~~~~VvLndIhidImDYI~Pa~~~d~~FRtmW~ef----EWENKvtv~t~~~------------ 857 (948)
T KOG1058|consen 794 GVIFGNIVYDTSEAANDRNVVVLNDIHIDIMDYIKPAKCDDDEFRTMWAEF----EWENKVTVNTTIK------------ 857 (948)
T ss_pred cEEEEEEEecCccccccceEEEeccccccHHHhcCCCcCChHHHHHHHHHh----hhcceeeeccccc------------
Confidence 33331 11 22333211 467899999999999999998766553 5545666653222
Q ss_pred cchhhhhhhHHHHHHhhccceeeeeccCccccccCCCCCceeeeeeccccCCc
Q 006008 565 KDKYLVICESLASKMLSNANIFLVSVDMPVAAKFDDASGLSLRFSSEILGNSV 617 (665)
Q Consensus 565 ~~~~~~~~~~i~~kv~~~aN~~~V~~~~p~~~~~~d~~~~~~rFa~~tlss~s 617 (665)
+.+....+|+..-|....--+ .+ -++.++|.+-.+-.++
T Consensus 858 ------~L~e~l~~i~kstNmkcLtpe-------~a-l~g~CgFlaaNlya~S 896 (948)
T KOG1058|consen 858 ------TLREFLGHISKSTNMKCLTPE-------AA-LDGDCGFLAANLYAKS 896 (948)
T ss_pred ------cHHHHHHHHHhhcCCcccCch-------hh-ccCccchhhhhHHHHh
Confidence 225688899999998765321 11 2336778777766554
No 51
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=28.78 E-value=42 Score=41.57 Aligned_cols=17 Identities=24% Similarity=0.268 Sum_probs=8.6
Q ss_pred cCCCCccCCCCCCccCc
Q 006008 221 AAPGYEPLPKPCSSLCD 237 (665)
Q Consensus 221 ~~~GY~~LP~p~~~~~~ 237 (665)
..+|-++|=|-|....+
T Consensus 1355 Ti~v~R~~~Dlct~~~D 1371 (1516)
T KOG1832|consen 1355 TIPVDRCLLDLCTEPTD 1371 (1516)
T ss_pred eeecccchhhhhcCCcc
Confidence 34555555555544444
No 52
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=28.67 E-value=47 Score=28.40 Aligned_cols=17 Identities=41% Similarity=0.714 Sum_probs=15.0
Q ss_pred ccCCCCeeEE-EEEEecC
Q 006008 473 SLEPGQTMKR-ILEVRFH 489 (665)
Q Consensus 473 sL~Pg~s~t~-~lgIdF~ 489 (665)
.|.|||.+++ +|+|||-
T Consensus 40 nl~pGqK~kaviLhvD~l 57 (65)
T cd05700 40 NVTPGCKLKAVILHVDFV 57 (65)
T ss_pred ecCCCceeEEEEEEEeeE
Confidence 5889999998 9999994
No 53
>COG2847 Copper(I)-binding protein [Inorganic ion transport and metabolism]
Probab=28.48 E-value=1.9e+02 Score=28.74 Aligned_cols=104 Identities=18% Similarity=0.179 Sum_probs=66.5
Q ss_pred CeeEEEEecCCCCCCCCCeEEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCcccc
Q 006008 395 GLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSL 474 (665)
Q Consensus 395 GL~v~Y~F~r~p~~~s~~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL 474 (665)
.+-|.=.|-| ...-+..|...=+++.|++++++.=+-+...- .++. -|+.+-+ ..++-.|++.++| .|
T Consensus 25 ~i~v~~a~~r-a~~pg~~~~a~~~ti~N~~~~~~~Lv~v~s~~----a~~~--ElHe~i~----~~gvmkMr~v~~i-~I 92 (151)
T COG2847 25 AIHVEDAWAR-ATPPGAKMGAAFMTITNNGDKDDRLVGVSSPI----AARA--ELHETIH----DGGVMKMRKVPGI-VI 92 (151)
T ss_pred ceEEeccEEE-ecCCCCcceeEEEEEeCCCCCCceEEEEecCc----ccee--EEEEEEe----cCCeEEEEEcCcE-EE
Confidence 4666666777 56667889999999999999988888776541 1111 1222111 1244456677766 68
Q ss_pred CCCCeeEE---EEEEecCCCCccceEEEEEcCceeeeEEecCcc
Q 006008 475 EPGQTMKR---ILEVRFHHHLLPLKLALHCNGKKLPVKLRPDIG 515 (665)
Q Consensus 475 ~Pg~s~t~---~lgIdF~dstq~~~f~l~~~~~~f~V~i~PpvG 515 (665)
+||+++.- -.+|=|-+--+|++ .+++|+|.|+=..|
T Consensus 93 pa~~~v~lkpGgyHvMlm~lK~pl~-----eGd~v~vtL~f~~~ 131 (151)
T COG2847 93 PAGGTVELKPGGYHVMLMGLKKPLK-----EGDKVPVTLKFEKA 131 (151)
T ss_pred CCCceEEecCCCEEEEEeccCCCcc-----CCCEEEEEEEEecC
Confidence 88888765 67777777777754 35555555554333
No 54
>PF05753 TRAP_beta: Translocon-associated protein beta (TRAPB); InterPro: IPR008856 This family consists of several eukaryotic translocon-associated protein beta (TRAPB) or signal sequence receptor beta subunit (SSR-beta) proteins. The normal translocation of nascent polypeptides into the lumen of the endoplasmic reticulum (ER) is thought to be aided in part by a translocon-associated protein (TRAP) complex consisting of 4 protein subunits. The association of mature proteins with the ER and Golgi, or other intracellular locales, such as lysosomes, depends on the initial targeting of the nascent polypeptide to the ER membrane. A similar scenario must also exist for proteins destined for secretion [].; GO: 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=28.26 E-value=1.1e+02 Score=31.03 Aligned_cols=58 Identities=19% Similarity=0.193 Sum_probs=37.9
Q ss_pred CeEEEEEEEEecCCcceeeeEeeccccccch-hhhhhhhhhcccccccCCCCCCcccCCCccccCCCCeeEEEEEEe
Q 006008 412 QLVCLETFFENCSSETMSEVTLVDEESHKAL-DLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQTMKRILEVR 487 (665)
Q Consensus 412 ~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~-~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL~Pg~s~t~~lgId 487 (665)
.=+.|++++-|.++.+..||.|.|. ..| +++. +.+ ...--.+++|+||+.++-..-|.
T Consensus 38 ~~v~V~~~iyN~G~~~A~dV~l~D~---~fp~~~F~--lvs-------------G~~s~~~~~i~pg~~vsh~~vv~ 96 (181)
T PF05753_consen 38 EDVTVTYTIYNVGSSAAYDVKLTDD---SFPPEDFE--LVS-------------GSLSASWERIPPGENVSHSYVVR 96 (181)
T ss_pred cEEEEEEEEEECCCCeEEEEEEECC---CCCccccE--ecc-------------CceEEEEEEECCCCeEEEEEEEe
Confidence 3456888999999999999999984 222 2221 000 11112467999999887665544
No 55
>cd00020 ARM Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified; related to the HEAT domain; three consecutive copies of the repeat are represented by this alignment model.
Probab=25.31 E-value=37 Score=29.26 Aligned_cols=101 Identities=18% Similarity=0.170 Sum_probs=51.4
Q ss_pred HHHHHhhcCCCCcccchhheeeeeccccCCC-CCcccchH-HHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCChhH
Q 006008 54 IIQLFRSLDSIKVPEARVMIIWMVGEYSSVG-VKIPRMLT-TVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGDMWT 131 (665)
Q Consensus 54 I~~Lak~ld~i~~P~ARAsIIWLIGEY~~~~-e~ip~iaP-dvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~~~~ 131 (665)
|..|.+.+..-. +..|-..+|.++..+... +....+.. .+++.+++-+.+....|+...+.+..-+....+......
T Consensus 9 i~~l~~~l~~~~-~~~~~~a~~~l~~l~~~~~~~~~~~~~~~~i~~l~~~l~~~~~~v~~~a~~~L~~l~~~~~~~~~~~ 87 (120)
T cd00020 9 LPALVSLLSSSD-ENVQREAAWALSNLSAGNNDNIQAVVEAGGLPALVQLLKSEDEEVVKAALWALRNLAAGPEDNKLIV 87 (120)
T ss_pred hHHHHHHHHcCC-HHHHHHHHHHHHHHhcCCHHHHHHHHHCCChHHHHHHHhCCCHHHHHHHHHHHHHHccCcHHHHHHH
Confidence 445555554332 667777777777776420 11111111 444455555666778888888888777754332110001
Q ss_pred H-HHHHHHHHHhhccCCCccchhhHH
Q 006008 132 I-TRLFSYLLELAECDLNYDVRDRAR 156 (665)
Q Consensus 132 ~-~~L~qyVL~LAkyD~nyDVRDRAR 156 (665)
. ..++.+++++...+ +.++|..|-
T Consensus 88 ~~~g~l~~l~~~l~~~-~~~~~~~a~ 112 (120)
T cd00020 88 LEAGGVPKLVNLLDSS-NEDIQKNAT 112 (120)
T ss_pred HHCCChHHHHHHHhcC-CHHHHHHHH
Confidence 1 11345555554433 455555443
No 56
>PF09478 CBM49: Carbohydrate binding domain CBM49; InterPro: IPR019028 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This domain is found at the C-terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose []. ; GO: 0030246 carbohydrate binding, 0005576 extracellular region
Probab=25.00 E-value=1.1e+02 Score=26.42 Aligned_cols=24 Identities=8% Similarity=0.145 Sum_probs=20.9
Q ss_pred eEEEEEEEEecCCcceeeeEeecc
Q 006008 413 LVCLETFFENCSSETMSEVTLVDE 436 (665)
Q Consensus 413 mv~Vql~f~N~s~~~i~~I~i~~~ 436 (665)
..-+.++++|++..+|+++.|.-.
T Consensus 18 y~qy~v~I~N~~~~~I~~~~i~~~ 41 (80)
T PF09478_consen 18 YTQYDVTITNNGSKPIKSLKISID 41 (80)
T ss_pred EEEEEEEEEECCCCeEEEEEEEEC
Confidence 345789999999999999999876
No 57
>PF11614 FixG_C: IG-like fold at C-terminal of FixG, putative oxidoreductase; PDB: 2R39_A.
Probab=24.93 E-value=1.8e+02 Score=26.55 Aligned_cols=72 Identities=18% Similarity=0.153 Sum_probs=39.7
Q ss_pred EEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCc-ccCCCccccCCCCeeEEEEEEecCC--
Q 006008 414 VCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTL-VPMEEITSLEPGQTMKRILEVRFHH-- 490 (665)
Q Consensus 414 v~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i-~~f~eI~sL~Pg~s~t~~lgIdF~d-- 490 (665)
+.-+|.+.|.++++.. +.|.-. + ++|+. + ...++| .|+||++.+..+-|...-
T Consensus 33 N~Y~lkl~Nkt~~~~~-~~i~~~---g-~~~~~------------------l~~~~~~i-~v~~g~~~~~~v~v~~p~~~ 88 (118)
T PF11614_consen 33 NQYTLKLTNKTNQPRT-YTISVE---G-LPGAE------------------LQGPENTI-TVPPGETREVPVFVTAPPDA 88 (118)
T ss_dssp EEEEEEEEE-SSS-EE-EEEEEE---S--SS-E------------------E-ES--EE-EE-TT-EEEEEEEEEE-GGG
T ss_pred EEEEEEEEECCCCCEE-EEEEEe---c-CCCeE------------------EECCCcce-EECCCCEEEEEEEEEECHHH
Confidence 3457889999988775 555433 2 22442 3 233455 789999999988887643
Q ss_pred ---CCccceEEEEEcCceeeeE
Q 006008 491 ---HLLPLKLALHCNGKKLPVK 509 (665)
Q Consensus 491 ---stq~~~f~l~~~~~~f~V~ 509 (665)
..+++.|.+.-.++...+.
T Consensus 89 ~~~~~~~i~f~v~~~~~~~~~~ 110 (118)
T PF11614_consen 89 LKSGSTPITFTVTDDDGGEIIT 110 (118)
T ss_dssp -SSSEEEEEEEEEEGGGTEEEE
T ss_pred ccCCCeeEEEEEEECCCCEEEE
Confidence 3467777776444444443
No 58
>PHA02664 hypothetical protein; Provisional
Probab=24.24 E-value=86 Score=34.73 Aligned_cols=11 Identities=9% Similarity=0.682 Sum_probs=6.9
Q ss_pred heeeeeccccC
Q 006008 72 MIIWMVGEYSS 82 (665)
Q Consensus 72 sIIWLIGEY~~ 82 (665)
+=+||..-|+.
T Consensus 158 spvwlaavfat 168 (534)
T PHA02664 158 SPVWLAAVFAT 168 (534)
T ss_pred Ccceeeeeehh
Confidence 45677776654
No 59
>PF10725 DUF2517: Protein of unknown function (DUF2517); InterPro: IPR019663 This entry represents proteins conserved in Proteobacteria and includes the predicted protein YbfA. The function is not known.
Probab=24.07 E-value=40 Score=28.73 Aligned_cols=12 Identities=50% Similarity=0.836 Sum_probs=10.1
Q ss_pred hhhHHHHHHhhc
Q 006008 152 RDRARFFKKLFS 163 (665)
Q Consensus 152 RDRARfy~rLLs 163 (665)
+||||||.-|-.
T Consensus 32 ~dRArfYSyLhr 43 (63)
T PF10725_consen 32 SDRARFYSYLHR 43 (63)
T ss_pred cchhHHHHHHHH
Confidence 899999987754
No 60
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=23.81 E-value=90 Score=31.08 Aligned_cols=125 Identities=10% Similarity=0.154 Sum_probs=61.0
Q ss_pred eeehHHHHHHHHhhC-CCch-HHH---HH----HHHhhcCCCCcccchhheeeeecccc-CCCCCcccchHHHHHHHHhh
Q 006008 32 LIQSIISIKSIIKQD-PSCH-EKV---II----QLFRSLDSIKVPEARVMIIWMVGEYS-SVGVKIPRMLTTVLKYLAWC 101 (665)
Q Consensus 32 V~EsVvVIk~LLqk~-P~~~-~~i---I~----~Lak~ld~i~~P~ARAsIIWLIGEY~-~~~e~ip~iaPdvLR~laks 101 (665)
-.+++.-|+.|+..+ |..+ ..+ +. -+++.+.....--+|.++.= +++.+ ..+..+..+++.++..+++.
T Consensus 24 r~~al~~L~~l~~~~~~~~~~~~~~~~l~~~~~~i~~~l~d~Rs~v~~~A~~~-l~~l~~~l~~~~~~~~~~~l~~Ll~~ 102 (228)
T PF12348_consen 24 RVEALQKLRSLIKGNAPEDFPPDFVECLRQLLDAIIKQLSDLRSKVSKTACQL-LSDLARQLGSHFEPYADILLPPLLKK 102 (228)
T ss_dssp HHHHHHHHHHHHHH-B-----HHHHHHHH---HHHHH-S-HH---HHHHHHHH-HHHHHHHHGGGGHHHHHHHHHHHHHG
T ss_pred HHHHHHHHHHHHHcCCccccHHHHHHHHHHhHHHHHHHHhhhHHHHHHHHHHH-HHHHHHHHhHhHHHHHHHHHHHHHHH
Confidence 456888899999988 3322 222 22 33334443333344444331 11111 11123445677778888888
Q ss_pred hcCChHHHHHHHHHhhhheeeeccCCChhHHHHHHHHHHHhhccCCCccchhhHHHHHHhh
Q 006008 102 FKSEAVETKLQILNTTIKVLLCAKGGDMWTITRLFSYLLELAECDLNYDVRDRARFFKKLF 162 (665)
Q Consensus 102 F~~E~~eVKLQILtlaaKl~l~~p~e~~~~~~~L~qyVL~LAkyD~nyDVRDRARfy~rLL 162 (665)
+.+....++-....+...++-+.+ -...++..++..+..+-|+.+|-++--|-..+
T Consensus 103 ~~~~~~~i~~~a~~~L~~i~~~~~-----~~~~~~~~~l~~~~~~Kn~~vR~~~~~~l~~~ 158 (228)
T PF12348_consen 103 LGDSKKFIREAANNALDAIIESCS-----YSPKILLEILSQGLKSKNPQVREECAEWLAII 158 (228)
T ss_dssp GG---HHHHHHHHHHHHHHHTTS------H--HHHHHHHHHHTT-S-HHHHHHHHHHHHHH
T ss_pred HccccHHHHHHHHHHHHHHHHHCC-----cHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 888877777766666655554443 01244445555556667999998876544443
No 61
>COG2912 Uncharacterized conserved protein [Function unknown]
Probab=23.64 E-value=63 Score=34.79 Aligned_cols=111 Identities=13% Similarity=0.082 Sum_probs=59.1
Q ss_pred CCchHHHHHHHHhhcCCC------------CcccchhheeeeeccccCCCCCcccchHHHHHHHHhhhcCChHHHHHHHH
Q 006008 47 PSCHEKVIIQLFRSLDSI------------KVPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQIL 114 (665)
Q Consensus 47 P~~~~~iI~~Lak~ld~i------------~~P~ARAsIIWLIGEY~~~~e~ip~iaPdvLR~laksF~~E~~eVKLQIL 114 (665)
|-.-..+...+++.+|-= ..+..+ -+|.+--+.. . .+-+..|+..+++-.....+-+-+.|
T Consensus 99 pvsLa~vll~ia~~l~lpl~gV~FP~~flLR~~~~~--~~~~idP~ng--~---~l~~~~l~~~l~~~~~~~ael~~~~L 171 (269)
T COG2912 99 PVSLAVVLLEIARRLDLPLYGVNFPTQLLLRAEVED--EPLLIDPFNG--G---TLSQHELQEWLKGTIGPSAELLPEDL 171 (269)
T ss_pred cchHHHHHHHHHHHcCCCCCccCCccceeEeeccCC--CceeeCCCCC--C---cccHHHHHHHHHhccCcHhhhhhhhh
Confidence 666777778888888631 112222 5677655542 1 12234455555444444444443333
Q ss_pred Hhhhheeee-----ccC---CChhHHHHHHHHHHHhhccCC--CccchhhHHHHHHhhcC
Q 006008 115 NTTIKVLLC-----AKG---GDMWTITRLFSYLLELAECDL--NYDVRDRARFFKKLFSH 164 (665)
Q Consensus 115 tlaaKl~l~-----~p~---e~~~~~~~L~qyVL~LAkyD~--nyDVRDRARfy~rLLs~ 164 (665)
.=+..--+. +-+ -...+....++++-.+..++. -|+||||+-+|.+|=-.
T Consensus 172 ~~a~~~~il~rll~~lk~~~~~e~~~~~al~~~~r~l~l~P~dp~eirDrGliY~ql~c~ 231 (269)
T COG2912 172 KQASNREILSRLLRNLKAALLRELQWELALRVAERLLDLNPEDPYEIRDRGLIYAQLGCY 231 (269)
T ss_pred hhccHHHHHHHHHHHHHHHHHHhhchHHHHHHHHHHHhhCCCChhhccCcHHHHHhcCCc
Confidence 222111000 000 000144567788888888875 48999999999987543
No 62
>PLN02171 endoglucanase
Probab=23.59 E-value=2.2e+02 Score=34.24 Aligned_cols=71 Identities=18% Similarity=0.119 Sum_probs=46.1
Q ss_pred CCeEEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCcc-ccCCCCeeEEEEEEecC
Q 006008 411 PQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEIT-SLEPGQTMKRILEVRFH 489 (665)
Q Consensus 411 ~~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~-sL~Pg~s~t~~lgIdF~ 489 (665)
...+-+.++++|+|..+|++|+|...+. .. .|-+.. ..+..-.||.+. +|.||++.+- -+| +
T Consensus 552 ~~y~qy~v~I~N~s~~~ik~i~i~~~~~---~~----~iW~v~-------~~~ngytlPs~~~sL~aG~s~tF-gyI--~ 614 (629)
T PLN02171 552 RTYYRYSTTVTNRSAKTLKELHLGISKL---YG----PLWGLT-------KAGYGYVLPSWMPSLPAGKSLEF-VYV--H 614 (629)
T ss_pred ceEEEEEEEEEECCCCceeeeeeeeccc---cc----cchhee-------ecCCcccCchhhcccCCCCeeEE-Eee--c
Confidence 4566689999999999999999986533 21 111100 112234566654 9999999984 345 2
Q ss_pred CCCccceEEE
Q 006008 490 HHLLPLKLAL 499 (665)
Q Consensus 490 dstq~~~f~l 499 (665)
. .+|++|.+
T Consensus 615 ~-~~pA~~~v 623 (629)
T PLN02171 615 S-ASPADVWV 623 (629)
T ss_pred C-CCCceEEE
Confidence 2 67777765
No 63
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.36 E-value=88 Score=36.05 Aligned_cols=19 Identities=16% Similarity=0.092 Sum_probs=10.4
Q ss_pred cHHHHhhccCCCCc-cCCCC
Q 006008 213 SLSQIVLHAAPGYE-PLPKP 231 (665)
Q Consensus 213 SLSh~l~~~~~GY~-~LP~p 231 (665)
+|+--|+..+.+|. ++|+.
T Consensus 72 ~l~~~i~~~~e~~~~~~~~d 91 (483)
T KOG2236|consen 72 PLAAKIEMKAEDGSVDQPDD 91 (483)
T ss_pred cchhhhccccccCccccccc
Confidence 55666665555543 55553
No 64
>PF09624 DUF2393: Protein of unknown function (DUF2393); InterPro: IPR013417 The function of this protein is unknown. It is always found as part of a two-gene operon with IPR013416 from INTERPRO, a protein that appears to span the membrane seven times. It has so far been found in the bacteria Anabaena sp. (strain PCC 7120), Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus.
Probab=23.22 E-value=3.1e+02 Score=26.13 Aligned_cols=76 Identities=9% Similarity=0.091 Sum_probs=45.7
Q ss_pred CCeEEEEEEEEecCCcceeeeEeeccccc---cchhhhhhhhhhcccccccCCCCCCcccC----CCccc-cCCCCeeEE
Q 006008 411 PQLVCLETFFENCSSETMSEVTLVDEESH---KALDLADLTLATTASSLTSQSDLPTLVPM----EEITS-LEPGQTMKR 482 (665)
Q Consensus 411 ~~mv~Vql~f~N~s~~~i~~I~i~~~~~~---~~~~g~~~~l~~~~~~~~~~~~~~~i~~f----~eI~s-L~Pg~s~t~ 482 (665)
.....|..+++|.|+.++++..|.-+=.. ....+.... .+ +..+| .+|.. |+||++..-
T Consensus 61 ~~~~~v~g~V~N~g~~~i~~c~i~~~l~~~~~~~~n~~~~~---------~~----~~~~f~~~~~~i~~~L~~~e~~~f 127 (149)
T PF09624_consen 61 SESFYVDGTVTNTGKFTIKKCKITVKLYNDKQVSGNKFKEI---------FY----QQIPFVKKSIPIADNLKPGESKEF 127 (149)
T ss_pred ccEEEEEEEEEECCCCEeeEEEEEEEEEeCCCccCchhhhh---------hc----cccchhccceeHHhhcCcccceeE
Confidence 45667999999999999999998754210 000111100 01 12234 44554 999999988
Q ss_pred EEEEecCCCCccceEEE
Q 006008 483 ILEVRFHHHLLPLKLAL 499 (665)
Q Consensus 483 ~lgIdF~dstq~~~f~l 499 (665)
.+=|+....-+..++.+
T Consensus 128 ~~~~~~~p~~~~~~~~~ 144 (149)
T PF09624_consen 128 RFIFPYPPYFGNYNIRV 144 (149)
T ss_pred EEEecCCccCCCceEEE
Confidence 87777555544444443
No 65
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=22.80 E-value=1.3e+02 Score=29.98 Aligned_cols=6 Identities=17% Similarity=0.063 Sum_probs=2.2
Q ss_pred HHHHHh
Q 006008 137 SYLLEL 142 (665)
Q Consensus 137 qyVL~L 142 (665)
|.+|+.
T Consensus 31 QKClq~ 36 (177)
T KOG3116|consen 31 QKCLQA 36 (177)
T ss_pred HHHHhh
Confidence 333333
No 66
>COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=22.77 E-value=72 Score=38.22 Aligned_cols=11 Identities=45% Similarity=0.546 Sum_probs=4.3
Q ss_pred chhheeeeecc
Q 006008 69 ARVMIIWMVGE 79 (665)
Q Consensus 69 ARAsIIWLIGE 79 (665)
||-+||-=||-
T Consensus 536 ~~qsIilPI~g 546 (1001)
T COG5406 536 ARQSIILPIGG 546 (1001)
T ss_pred ccceEEEeecC
Confidence 33444443333
No 67
>KOG2081 consensus Nuclear transport regulator [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.30 E-value=48 Score=38.86 Aligned_cols=137 Identities=17% Similarity=0.298 Sum_probs=85.3
Q ss_pred hHHHHHHHHHHhhccccccccCCCCCcceeee-hHHHHHHHHhhCCCchHHHHHHHHhhcCCCC--cccchhheeeeecc
Q 006008 3 NTCVEGLLALIRQELLTSDIESGNGEADVLIQ-SIISIKSIIKQDPSCHEKVIIQLFRSLDSIK--VPEARVMIIWMVGE 79 (665)
Q Consensus 3 ~~Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~E-sVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~--~P~ARAsIIWLIGE 79 (665)
++|+.-+..-+.. |...+-..| ++-+++.+++.-+-.-..++..+.+.+=++. .| -|..-+-++|+
T Consensus 386 ~e~lk~~~~~l~e----------~~~~We~~EAaLF~l~~~~~~~~~~e~~i~pevl~~i~nlp~Q~~-~~~ts~ll~g~ 454 (559)
T KOG2081|consen 386 DECLKQMYIRLKE----------NNASWEEVEAALFILRAVAKNVSPEENTIMPEVLKLICNLPEQAP-LRYTSILLLGE 454 (559)
T ss_pred HHHHHHHHHHHcc----------CCCchHHHHHHHHHHHHHhccCCccccchHHHHHHHHhCCccchh-HHHHHHHHHHH
Confidence 5677766655542 233444566 5556888888766666667777777765553 34 67777779999
Q ss_pred ccCCCCCcccchHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccC-CChhHHHHHHHHHHHhhccCCCccchhhHHH
Q 006008 80 YSSVGVKIPRMLTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKG-GDMWTITRLFSYLLELAECDLNYDVRDRARF 157 (665)
Q Consensus 80 Y~~~~e~ip~iaPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~-e~~~~~~~L~qyVL~LAkyD~nyDVRDRARf 157 (665)
|+...+..|....-|++++...+..-. |..++-++.++.. ........++-+.+.+++.=.+.-+|.-+-+
T Consensus 455 ~~ew~~~~p~~le~v~~~~~~~~~~~~-------~as~~a~~~~~i~~~c~~~~~~l~~~~~~l~~~l~~~~~~~e~a~ 526 (559)
T KOG2081|consen 455 YSEWVEQHPELLEPVLRYIRQGLQLKR-------LASAAALAFHRICSACRVQMTCLIPSLLELIRSLDSTQINEEAAC 526 (559)
T ss_pred HHHHHHhCcHHHHHHHHHHHHHhhhcc-------hhHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccHHHHH
Confidence 997666778888889998876665544 5566655655531 1111334566777777654334444444443
No 68
>PRK10941 hypothetical protein; Provisional
Probab=22.14 E-value=75 Score=33.94 Aligned_cols=35 Identities=29% Similarity=0.384 Sum_probs=24.3
Q ss_pred hhHHHHHHHHHHHhhccCCCccchhhHHHHHHhhcC
Q 006008 129 MWTITRLFSYLLELAECDLNYDVRDRARFFKKLFSH 164 (665)
Q Consensus 129 ~~~~~~L~qyVL~LAkyD~nyDVRDRARfy~rLLs~ 164 (665)
.+..-.....+|.+.--| -|++|||+.+|.+|=-.
T Consensus 197 ~~~AL~~~e~ll~l~P~d-p~e~RDRGll~~qL~c~ 231 (269)
T PRK10941 197 MELALRASEALLQFDPED-PYEIRDRGLIYAQLDCE 231 (269)
T ss_pred HHHHHHHHHHHHHhCCCC-HHHHHHHHHHHHHcCCc
Confidence 334455666666665444 58999999999988644
No 69
>PTZ00429 beta-adaptin; Provisional
Probab=21.86 E-value=1.5e+02 Score=36.15 Aligned_cols=89 Identities=7% Similarity=-0.032 Sum_probs=53.0
Q ss_pred CCCcceeeehHHHHHHHHhhCCCchHHHHHHHHhhcCCCC--cccchhheeeeeccccCCCCCcccchHHHHHHHHhhhc
Q 006008 26 NGEADVLIQSIISIKSIIKQDPSCHEKVIIQLFRSLDSIK--VPEARVMIIWMVGEYSSVGVKIPRMLTTVLKYLAWCFK 103 (665)
Q Consensus 26 ~~~~~VV~EsVvVIk~LLqk~P~~~~~iI~~Lak~ld~i~--~P~ARAsIIWLIGEY~~~~e~ip~iaPdvLR~laksF~ 103 (665)
|.+..||.-|+.++..|-+..|..+......+-+++..+. .+=++..|+=++..|.-. -..-+-+++..+...+.
T Consensus 190 D~dp~Vv~nAl~aL~eI~~~~~~~l~l~~~~~~~Ll~~L~e~~EW~Qi~IL~lL~~y~P~---~~~e~~~il~~l~~~Lq 266 (746)
T PTZ00429 190 DNNPVVASNAAAIVCEVNDYGSEKIESSNEWVNRLVYHLPECNEWGQLYILELLAAQRPS---DKESAETLLTRVLPRMS 266 (746)
T ss_pred CCCccHHHHHHHHHHHHHHhCchhhHHHHHHHHHHHHHhhcCChHHHHHHHHHHHhcCCC---CcHHHHHHHHHHHHHhc
Confidence 6677788889999999988888765444444444444443 355666777777776421 11123455665555555
Q ss_pred CChHHHHHHHHHhh
Q 006008 104 SEAVETKLQILNTT 117 (665)
Q Consensus 104 ~E~~eVKLQILtla 117 (665)
.-...|-|....+.
T Consensus 267 ~~N~AVVl~Aik~i 280 (746)
T PTZ00429 267 HQNPAVVMGAIKVV 280 (746)
T ss_pred CCCHHHHHHHHHHH
Confidence 55555555544443
No 70
>PF04314 DUF461: Protein of unknown function (DUF461); InterPro: IPR007410 This entry represents a domain found in of proteins of unknown function, including DR1885 from Deinococcus radiodurans and CC3502 from Caulobacter crescentus (Caulobacter vibrioides), which share a potential metal binding motif H(M)X10MX21HXM. DR1885 was found to bind copper(I) through a histidine and three Mets in a cupredoxin-like fold []. The surface location of the copper-binding site as well as the type of coordination are well poised for metal transfer chemistry, suggesting that DR1885 might transfer copper, taking the role of Cox17 in bacteria (Cox17 being an accessory protein required for correct assembly of eukaryotic cyochrome c oxidase). ; PDB: 2K6W_A 2K6Z_A 2K6Y_A 2K70_A 1X9L_A 2JQA_A.
Probab=21.74 E-value=2.1e+02 Score=26.23 Aligned_cols=72 Identities=13% Similarity=0.172 Sum_probs=35.2
Q ss_pred EEEecCCCCCCCCCeEEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCccccCCCC
Q 006008 399 YYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQ 478 (665)
Q Consensus 399 ~Y~F~r~p~~~s~~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL~Pg~ 478 (665)
+-+|.|.+-. ...+..+-++++|++++++.=+.+..... + .-.|+.+ ....+..+|...+.| .|+||+
T Consensus 2 ~~a~v~~~~~-~~~~~a~y~ti~N~g~~~~~L~~v~s~~a-----~-~v~lh~~----~~~~g~~~m~~v~~i-~ipa~~ 69 (110)
T PF04314_consen 2 SDAWVRAAPP-GANVTAAYFTITNNGDQDDRLVGVSSPAA-----A-RVELHET----VMEDGVMKMRPVDSI-PIPAGS 69 (110)
T ss_dssp --EEEESBST-T-SEEEEEEEEE-CSSSEEEEEEEE-TTC-----C-EEEEEEE----CCCCCEEEECCSS-E-EEETT-
T ss_pred cccEEEccCC-CCccEEEEEEEEeCCCCCeEEEEEEcCCC-----c-eEEEEEE----EccCCeEEEEECCCE-EECCCC
Confidence 3455555543 45688889999999998865554443211 0 1112221 112233345555655 567777
Q ss_pred eeEE
Q 006008 479 TMKR 482 (665)
Q Consensus 479 s~t~ 482 (665)
++..
T Consensus 70 ~v~l 73 (110)
T PF04314_consen 70 TVEL 73 (110)
T ss_dssp EEEE
T ss_pred eEEe
Confidence 6655
No 71
>PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional
Probab=21.64 E-value=1.9e+02 Score=35.79 Aligned_cols=15 Identities=20% Similarity=0.290 Sum_probs=8.2
Q ss_pred ccchhheeeeecccc
Q 006008 67 PEARVMIIWMVGEYS 81 (665)
Q Consensus 67 P~ARAsIIWLIGEY~ 81 (665)
|..|++.+.-+|++.
T Consensus 789 ~~VR~aA~~aLg~~g 803 (897)
T PRK13800 789 PLVRAAALAALAELG 803 (897)
T ss_pred HHHHHHHHHHHHhcC
Confidence 555555555555553
No 72
>KOG1078 consensus Vesicle coat complex COPI, gamma subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.39 E-value=1.3e+03 Score=28.89 Aligned_cols=198 Identities=14% Similarity=0.163 Sum_probs=105.4
Q ss_pred eEEEEecCCCCCCCCCeEEEEEEEEe-cCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCccccC
Q 006008 397 KVYYSFSSEASTISPQLVCLETFFEN-CSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLE 475 (665)
Q Consensus 397 ~v~Y~F~r~p~~~s~~mv~Vql~f~N-~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL~ 475 (665)
..+|.|-+=-|.|-.+||- |...+| .++..+.|+.++.... .| .-. + .-++-+-|+..+
T Consensus 635 e~e~~v~~vKh~f~~~~V~-qf~~~Ntl~d~~L~~v~vv~~~~----~~-~ev-------------l-~~i~~~slpy~q 694 (865)
T KOG1078|consen 635 EAEYVVKVVKHVFKDHVVL-QFDCTNTLNDQLLENVSVVLTPT----GG-EEV-------------L-EKVPTMSLPYDQ 694 (865)
T ss_pred cceEEeeeeehhhccceEE-EEeccCcchHHHHhhheeeecCC----CC-cee-------------e-eeccccCCCCCC
Confidence 4688888889999999984 555555 5588889988886532 22 100 0 111223455556
Q ss_pred CCCeeEEEEEEecCCCCccceEEEEEcCceeeeE-EecCccc----------ccccccCCHHHHHHHhcc---------C
Q 006008 476 PGQTMKRILEVRFHHHLLPLKLALHCNGKKLPVK-LRPDIGY----------FIKPVPMDMETFIEMESR---------L 535 (665)
Q Consensus 476 Pg~s~t~~lgIdF~dstq~~~f~l~~~~~~f~V~-i~PpvGE----------lv~Pv~mse~~F~~eq~k---------L 535 (665)
||...+ -+.|.|..-.+-=.=++...+|.|+ +-|.-|| -+-++..+-.||..+=.+ +
T Consensus 695 p~~~~t---l~~~p~~~p~~v~~sf~~tlkFtvkdcdp~TgepdedGyeDEY~LEdlevtv~D~iqkv~k~NF~aawde~ 771 (865)
T KOG1078|consen 695 PGSAFT---LVEFPKDDPWAIAEGFGNTLKFTVKDCDPNTGEPDDEGYEDEYVLEDLEVTVGDFVQKVRKSNFPAAWDEL 771 (865)
T ss_pred CcceEE---EEEcCCCCchhhhccceeeEEEEEEecCCCCCCCCccCcccceeeeceeeehhhhhhHhhcccchhhHHhc
Confidence 665444 3456644333222222334455433 3343333 455666666666544322 2
Q ss_pred CCCcccceeeeeccCcCccCccccchhhccchhhhhhhHHHHHHhhccceeeeeccCccccccCCCC-Ccee--eeeecc
Q 006008 536 PGMFEYARSCTFTDHLGEVDKDTDESSLLKDKYLVICESLASKMLSNANIFLVSVDMPVAAKFDDAS-GLSL--RFSSEI 612 (665)
Q Consensus 536 ~GMnE~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~kv~~~aN~~~V~~~~p~~~~~~d~~-~~~~--rFa~~t 612 (665)
+ +|-.....+.. . -+-+..+.||+..-++. || ..+.--.. .+.| -.+| +
T Consensus 772 ~--~e~eetF~Ls~----------------~---~tl~eAv~~Ii~~LgMq--pc----E~sd~vPenknsHtl~LsG-~ 823 (865)
T KOG1078|consen 772 G--FEAEETFNLST----------------V---KSIQEAVKKIIDLLGMQ--PC----ERTEKVPENKNSHTLLLSG-V 823 (865)
T ss_pred C--cchheeeeccc----------------c---chHHHHHHHHHHHhCCc--cc----cccccCCCCCCceEEEEee-e
Confidence 2 44422222221 0 12355677888766665 33 22210001 2222 3555 8
Q ss_pred ccCCceEEEEEEeccccCCCcceEEEEcccchHH
Q 006008 613 LGNSVPCLITITVEGKCSEPLKVSAKVNCEETVF 646 (665)
Q Consensus 613 lss~s~~LiTi~~~~~~~~~~~~~l~vNcEk~Vi 646 (665)
.-.|..+||.+.+--..++ .+.+|+|-||+--.
T Consensus 824 frgG~~vlvr~~ma~s~~~-vtm~Vtvrs~e~~~ 856 (865)
T KOG1078|consen 824 FRGGYKVLVRAKMALSSGG-ITMKVTVRSEDELV 856 (865)
T ss_pred eeCCceEEEeeeeeecCCC-cEEEEEEecCCccH
Confidence 8889999999985222222 57899999987543
No 73
>PF07718 Coatamer_beta_C: Coatomer beta C-terminal region; InterPro: IPR011710 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C-terminal domain of the beta subunit from coatomer proteins (Beta-coat proteins). The C-terminal domain probably adapts the function of the N-terminal IPR002553 from INTERPRO domain. Coatomer protein complex I (COPI)-coated vesicles are involved in transport between the endoplasmic reticulum and the Golgi but also participate in transport from early to late endosomes within the endocytic pathway []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat
Probab=21.04 E-value=2e+02 Score=28.21 Aligned_cols=55 Identities=20% Similarity=0.282 Sum_probs=38.3
Q ss_pred EEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhhcccccccCCCCCCcccCCCccccCCCCeeEEEEEEecCC
Q 006008 414 VCLETFFENCSSETMSEVTLVDEESHKALDLADLTLATTASSLTSQSDLPTLVPMEEITSLEPGQTMKRILEVRFHH 490 (665)
Q Consensus 414 v~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~~~~~~~~~~~~~~i~~f~eI~sL~Pg~s~t~~lgIdF~d 490 (665)
+.+++.+-|.+++.+.||+|.=-.. .++ .+++=+..-.|.|++..+...-|-...
T Consensus 71 IvLDvllvNqT~~tLqNl~vElat~---------------------gdL-klve~p~~~tL~P~~~~~i~~~iKVsS 125 (140)
T PF07718_consen 71 IVLDVLLVNQTNETLQNLTVELATL---------------------GDL-KLVERPQPITLAPHGFARIKATIKVSS 125 (140)
T ss_pred EEEEEEEEeCChhhhhcEEEEEEec---------------------CCc-EEccCCCceeeCCCcEEEEEEEEEEEe
Confidence 4689999999999999999962100 012 255545555799999887766555443
No 74
>smart00185 ARM Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin.
Probab=20.26 E-value=56 Score=23.31 Aligned_cols=28 Identities=11% Similarity=0.348 Sum_probs=20.2
Q ss_pred HHHHHHHHHhhccccccccCCCCCcceeeehHHHHHHHH
Q 006008 5 CVEGLLALIRQELLTSDIESGNGEADVLIQSIISIKSII 43 (665)
Q Consensus 5 Cl~~Ll~Ll~~~~~~~~~~~~~~~~~VV~EsVvVIk~LL 43 (665)
|+..|+.||.+ .+..++.+++-+|++|.
T Consensus 13 ~i~~L~~ll~~-----------~~~~i~~~a~~aL~nl~ 40 (41)
T smart00185 13 GLPALVELLKS-----------EDEEVVKEAAWALSNLS 40 (41)
T ss_pred CHHHHHHHHcC-----------CCHHHHHHHHHHHHHHc
Confidence 67888888873 34557777888888774
No 75
>PF12719 Cnd3: Nuclear condensing complex subunits, C-term domain
Probab=20.21 E-value=3.3e+02 Score=28.87 Aligned_cols=38 Identities=26% Similarity=0.267 Sum_probs=32.2
Q ss_pred hHHHHHHHHhhhcCChHHHHHHHHHhhhheeeeccCCC
Q 006008 91 LTTVLKYLAWCFKSEAVETKLQILNTTIKVLLCAKGGD 128 (665)
Q Consensus 91 aPdvLR~laksF~~E~~eVKLQILtlaaKl~l~~p~e~ 128 (665)
...+++.+.+-+.++..++|.....-.+||++...-.+
T Consensus 112 ~~~l~~~l~~~l~~~~~~~~~~a~EGl~KLlL~~~i~~ 149 (298)
T PF12719_consen 112 SKSLLKILTKFLDSENPELQAIAVEGLCKLLLSGRISD 149 (298)
T ss_pred HhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhcCCCCc
Confidence 45678888888888899999999999999999886544
No 76
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.16 E-value=1.6e+02 Score=34.05 Aligned_cols=56 Identities=11% Similarity=0.223 Sum_probs=44.3
Q ss_pred CCCCeeEEEEecCCCCCCCCCeEEEEEEEEecCCcceeeeEeeccccccchhhhhhhhhh
Q 006008 392 NGNGLKVYYSFSSEASTISPQLVCLETFFENCSSETMSEVTLVDEESHKALDLADLTLAT 451 (665)
Q Consensus 392 ~G~GL~v~Y~F~r~p~~~s~~mv~Vql~f~N~s~~~i~~I~i~~~~~~~~~~g~~~~l~~ 451 (665)
-.+|+.+.++|.+.+-..-+..-.|-|..-|+-..+|.+|.+-- +.|..|.-.|+.
T Consensus 474 d~~GfRILlhfaq~~~pg~sdV~v~vlsmlntap~pikdI~lq~----avpk~mkvkLQp 529 (594)
T KOG1086|consen 474 DSNGFRILLHFAQSDMPGRSDVLVVVLSMLNTAPQPIKDIVLQL----AVPKSMKVKLQP 529 (594)
T ss_pred ccCCcEEEeeeccCCCCCCCceEEEEEEeecCCCcchhhheeee----ccccceeeeccC
Confidence 47899999999999988666677788999999999999999865 345556544443
Done!