Query psy1379
Match_columns 446
No_of_seqs 231 out of 304
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 20:34:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1379.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1379hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2999|consensus 100.0 1.9E-57 4E-62 468.7 20.6 306 1-333 144-455 (713)
2 PF11841 DUF3361: Domain of un 100.0 2.2E-46 4.8E-51 340.3 13.3 151 287-439 3-160 (160)
3 KOG2998|consensus 100.0 3.3E-39 7.2E-44 314.8 12.7 195 139-389 95-291 (302)
4 PF11841 DUF3361: Domain of un 100.0 6.9E-39 1.5E-43 291.3 11.2 128 1-133 33-160 (160)
5 KOG2999|consensus 100.0 5.8E-34 1.3E-38 295.0 12.2 191 242-442 79-274 (713)
6 PF04727 ELMO_CED12: ELMO/CED- 100.0 1.2E-30 2.6E-35 241.0 10.4 153 154-334 2-156 (170)
7 PLN03200 cellulose synthase-in 92.4 6.5 0.00014 49.4 18.7 357 4-433 423-798 (2102)
8 cd00020 ARM Armadillo/beta-cat 90.5 1.7 3.7E-05 35.9 8.2 94 312-409 25-119 (120)
9 PF06367 Drf_FH3: Diaphanous F 89.9 1.9 4.2E-05 40.3 9.0 76 75-155 21-100 (197)
10 cd00020 ARM Armadillo/beta-cat 89.0 0.85 1.8E-05 37.7 5.2 93 4-103 26-119 (120)
11 PLN03200 cellulose synthase-in 84.6 7.2 0.00016 49.0 11.6 162 23-252 691-853 (2102)
12 cd03567 VHS_GGA VHS domain fam 82.3 16 0.00034 33.1 10.2 95 76-182 39-133 (139)
13 smart00288 VHS Domain present 80.5 23 0.00049 31.5 10.5 90 77-180 39-129 (133)
14 PF00790 VHS: VHS domain; Int 80.4 11 0.00025 33.6 8.6 78 76-165 43-120 (140)
15 cd03568 VHS_STAM VHS domain fa 75.9 38 0.00083 30.7 10.7 73 76-163 38-110 (144)
16 cd03569 VHS_Hrs_Vps27p VHS dom 75.2 36 0.00078 30.7 10.3 73 76-163 42-114 (142)
17 cd03565 VHS_Tom1 VHS domain fa 74.8 42 0.0009 30.3 10.6 75 77-163 40-115 (141)
18 KOG2160|consensus 65.9 23 0.00049 36.9 7.6 96 6-109 101-201 (342)
19 PF11864 DUF3384: Domain of un 65.5 14 0.0003 39.8 6.3 105 14-120 230-351 (464)
20 PF04826 Arm_2: Armadillo-like 63.3 1.6E+02 0.0035 29.2 13.2 113 23-160 9-121 (254)
21 cd03561 VHS VHS domain family; 58.1 1.3E+02 0.0028 26.6 10.2 75 76-163 38-112 (133)
22 KOG3036|consensus 58.1 41 0.00089 33.8 7.5 119 7-133 43-178 (293)
23 PF11698 V-ATPase_H_C: V-ATPas 57.9 17 0.00038 32.1 4.5 74 26-105 43-116 (119)
24 PF05804 KAP: Kinesin-associat 56.5 70 0.0015 36.6 10.0 130 9-155 474-607 (708)
25 PF04826 Arm_2: Armadillo-like 54.5 71 0.0015 31.7 8.7 73 332-408 9-81 (254)
26 PF01602 Adaptin_N: Adaptin N 54.0 29 0.00062 37.0 6.3 83 3-102 97-179 (526)
27 PF12717 Cnd1: non-SMC mitotic 53.0 89 0.0019 28.8 8.7 86 9-106 9-94 (178)
28 PF08045 CDC14: Cell division 51.7 91 0.002 31.2 8.9 68 351-418 103-171 (257)
29 PF08045 CDC14: Cell division 51.1 1.1E+02 0.0025 30.5 9.5 63 46-111 107-170 (257)
30 PF08167 RIX1: rRNA processing 51.1 45 0.00098 30.6 6.3 87 12-109 52-148 (165)
31 PF11588 DUF3243: Protein of u 49.6 8.4 0.00018 31.8 1.1 24 164-188 44-67 (81)
32 PF12348 CLASP_N: CLASP N term 49.5 2E+02 0.0043 27.0 10.7 112 5-122 27-144 (228)
33 PF03224 V-ATPase_H_N: V-ATPas 48.0 63 0.0014 32.6 7.4 67 352-418 70-142 (312)
34 PF06367 Drf_FH3: Diaphanous F 47.7 40 0.00087 31.4 5.5 62 373-434 12-78 (197)
35 PF03224 V-ATPase_H_N: V-ATPas 45.2 63 0.0014 32.6 6.9 71 42-112 69-142 (312)
36 PF00790 VHS: VHS domain; Int 43.0 1.7E+02 0.0036 26.0 8.5 37 383-419 44-80 (140)
37 cd03568 VHS_STAM VHS domain fa 41.5 97 0.0021 28.1 6.8 58 352-409 50-109 (144)
38 KOG1293|consensus 40.6 51 0.0011 37.0 5.6 99 3-107 437-536 (678)
39 KOG0166|consensus 39.7 4E+02 0.0086 29.5 12.1 120 2-129 254-414 (514)
40 PF05918 API5: Apoptosis inhib 38.6 3.3E+02 0.0072 30.3 11.5 39 147-186 214-254 (556)
41 PF10508 Proteasom_PSMB: Prote 38.5 5.5E+02 0.012 27.9 24.0 113 4-129 96-209 (503)
42 PF11698 V-ATPase_H_C: V-ATPas 38.0 1.4E+02 0.003 26.5 7.0 84 323-409 31-114 (119)
43 cd03561 VHS VHS domain family; 34.9 1.6E+02 0.0036 25.9 7.1 60 352-411 50-113 (133)
44 PF12830 Nipped-B_C: Sister ch 31.2 3.1E+02 0.0067 25.6 8.7 87 24-127 6-92 (187)
45 KOG1077|consensus 31.1 1.4E+02 0.003 34.3 7.0 86 8-102 171-268 (938)
46 cd03567 VHS_GGA VHS domain fam 30.2 60 0.0013 29.3 3.5 39 383-421 40-78 (139)
47 PF02899 Phage_int_SAM_1: Phag 30.1 1.6E+02 0.0035 22.7 5.7 52 4-57 24-76 (84)
48 cd00197 VHS_ENTH_ANTH VHS, ENT 29.6 2.9E+02 0.0063 23.3 7.6 33 77-109 39-71 (115)
49 cd03569 VHS_Hrs_Vps27p VHS dom 29.2 1.8E+02 0.0038 26.2 6.4 59 352-410 54-114 (142)
50 smart00288 VHS Domain present 28.9 67 0.0014 28.5 3.6 38 384-421 40-77 (133)
51 PF14500 MMS19_N: Dos2-interac 27.0 4.3E+02 0.0093 26.3 9.3 53 6-61 103-155 (262)
52 PF00514 Arm: Armadillo/beta-c 26.9 94 0.002 21.3 3.4 27 76-102 13-39 (41)
53 PTZ00429 beta-adaptin; Provisi 26.5 4.2E+02 0.0092 30.6 10.2 51 6-63 161-212 (746)
54 KOG1059|consensus 25.8 1.2E+02 0.0026 34.8 5.4 73 24-108 142-214 (877)
55 KOG2137|consensus 25.1 2.5E+02 0.0054 32.1 7.8 74 24-104 383-458 (700)
56 KOG2160|consensus 24.3 3.5E+02 0.0077 28.3 8.2 100 315-418 101-204 (342)
57 PHA00680 hypothetical protein 24.1 3.6E+02 0.0079 23.3 6.9 115 289-434 9-124 (143)
58 PTZ00429 beta-adaptin; Provisi 24.1 5.1E+02 0.011 29.9 10.3 121 308-438 193-322 (746)
59 PF12717 Cnd1: non-SMC mitotic 22.3 5.5E+02 0.012 23.5 8.6 89 327-423 17-106 (178)
60 smart00185 ARM Armadillo/beta- 22.3 1.2E+02 0.0026 20.0 3.1 27 76-102 13-39 (41)
61 cd03565 VHS_Tom1 VHS domain fa 21.5 4.2E+02 0.0092 23.7 7.4 61 42-103 51-114 (141)
62 KOG2759|consensus 21.1 1.8E+02 0.004 31.2 5.5 73 27-105 367-439 (442)
63 KOG2199|consensus 20.1 2.4E+02 0.0051 30.2 6.0 37 23-63 42-78 (462)
No 1
>KOG2999|consensus
Probab=100.00 E-value=1.9e-57 Score=468.74 Aligned_cols=306 Identities=39% Similarity=0.513 Sum_probs=273.8
Q ss_pred ChhhHHHHHHHHHhcCCcccccCchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHH
Q psy1379 1 MLAHCLLSFVELMDHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNL 80 (446)
Q Consensus 1 ~Lay~L~a~~~Lme~~~~~W~~l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~l 80 (446)
+|+|+|+||++|||||.|+|+.++.+||.++++||+.+ ..++||+++||+|||++|.+|+..| ++|.++|++++|
T Consensus 144 ~L~~~L~af~elmehgvvsW~~~~~~fV~~~a~~V~~~--~~~a~~~~~AL~~LE~~vl~s~~~~---~~v~eev~i~~l 218 (713)
T KOG2999|consen 144 LLSTSLRAFSELMEHGVVSWESVSNDFVVSMASYVNAK--REDANTLLAALQMLESLVLGSDTLR---QLVAEEVPIETL 218 (713)
T ss_pred HHHHHHHHHHHHHhhceeeeeecccHHHHHHHHHHhhh--hhcccchHHHHHHHHHHHhCChHHH---HHHHhcCcHHHH
Confidence 48999999999999999999999999999999999665 7999999999999999999999999 999999999999
Q ss_pred hhhccCCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhcchHHHHHHHHHHHH
Q psy1379 81 VMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQLYVLQTLTLGLLEQ 160 (446)
Q Consensus 81 v~~L~~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~L~~~Q~l~l~~Le~ 160 (446)
++||+.+|+.+|++|+||||||+++|++++|++++++|+++++|.+|++|+++ + ++.+|||++|.+++++++.
T Consensus 219 i~hlq~~n~~i~~~aial~nal~~~a~~~~R~~~~~~l~~~~~R~ai~~~~~~-~------~~~~~lyvlq~L~~glle~ 291 (713)
T KOG2999|consen 219 IRHLQVSNQRIQTCAIALLNALFRKAPDDKRFEMAKSLEQKQFRNAIHSNVIR-T------ERPIQLYVLQVLTLGLLEV 291 (713)
T ss_pred HHHHHhcchHHHHHHHHHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHhhhc-c------cchHHHHHHHHHHHhhhHH
Confidence 99999999999999999999999999999999999999999999999999986 3 5677999999999999999
Q ss_pred HhcccCCCCCHHHHHHHHHHHHHhccccccC--CCCCccccccCCCchhhhhhccccCCCcccccccCCchHhhHhHHHH
Q psy1379 161 RMNTKMDPQDQDAHDKIKELRRVAFEIDVIG--GVDASSKRQMGGYAKDYKKLGFKYDINPAQDFTETPPGMLALDCMIY 238 (446)
Q Consensus 161 r~~~~~d~~~~~h~~~L~~Lw~~a~p~~~~~--~~~~~~~R~~~~~s~~Wk~LGFq~~~dP~~DFr~~~~G~LgL~nL~y 238 (446)
||++++||.++++++.+++|+.++|+++..| .+.+.+.|+ .+++++||++||.++.||++||.|||||+|||+||+|
T Consensus 292 Rm~~~md~~~q~qr~~i~~lr~iaf~~~~~~~~~g~~~e~rk-~l~~~~ykklgf~n~~npa~df~etppG~LAldnMvy 370 (713)
T KOG2999|consen 292 RMRTKMDPQDQVQRELISELRRIAFDDESEPSRRGGGAEVRK-ILDIESYKKLGFENRINPAQDFGETPPGRLALDNMVY 370 (713)
T ss_pred hhhcccchhhHHHHHHHHHHHhcCcccccccccCCcchhhhh-hhhHHHHHhhcccccCChHHhcccCCchHHHHHHHHH
Confidence 9999999999999999999999999987554 133677777 8999999999999999999999999999999999999
Q ss_pred HHHhChHHHHHHHHhhhcchhhhhhhhhcCCCCccccchhhhccchHHHHHHHHHhhhhhhhcccccchhhhhhHHHHHH
Q psy1379 239 FARNHPEAYTKQKATKKTLEGTAEKVRLSGLPDTDTLSSDVSGQVRLYFSIQFLLDCFAVLVNHSQAGLCVMLAHCLLSF 318 (446)
Q Consensus 239 Fa~~~~d~fskllleQ~~~~~~q~~~k~~aL~~l~~yS~aVtgin~t~fa~efl~dgl~~l~~~~e~g~~~~La~~L~aF 318 (446)
||+|||+.|++++.|+++|++.|+| +|.-+.|-+|.++.|+++=|- .++....++.++++..-++|
T Consensus 371 FA~~~~~~y~riVlENSsRedkhec------------pfgr~sieltk~lcEilrVge--~p~E~~~df~pmfFthd~~F 436 (713)
T KOG2999|consen 371 FARNSPQDYRRIVLENSSREDKHEC------------PFGRMSIELTKILCELLRVGE--PPDELDRDFIPMFFTHDTPF 436 (713)
T ss_pred HHHhCHHHHHHHHHhcccccccCcC------------CcCccHHHHHHHHHHHHhcCC--CchhhcCccceeeecCCCcH
Confidence 9999999999999999999998765 566677888888888662221 12222222448999999999
Q ss_pred HHHHhhhcc----ccccch
Q psy1379 319 VELMDHGIV----SWNILE 333 (446)
Q Consensus 319 ~eLm~~~i~----swd~l~ 333 (446)
.|++|-.+. .|..++
T Consensus 437 ee~FciciqLlnkTWKEMr 455 (713)
T KOG2999|consen 437 EELFCICVQLLNRTWKEMR 455 (713)
T ss_pred HHHHHHHHHHHHhHHHHHH
Confidence 999997664 565443
No 2
>PF11841 DUF3361: Domain of unknown function (DUF3361)
Probab=100.00 E-value=2.2e-46 Score=340.26 Aligned_cols=151 Identities=47% Similarity=0.694 Sum_probs=147.4
Q ss_pred HHHHHH-Hhhhhhhhcccccchh------hhhhHHHHHHHHHHhhhccccccchHHHHHHHHHhhcCCCCCCchHHHHHH
Q psy1379 287 FSIQFL-LDCFAVLVNHSQAGLC------VMLAHCLLSFVELMDHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQAS 359 (446)
Q Consensus 287 fa~efl-~dgl~~l~~~~e~g~~------~~La~~L~aF~eLm~~~i~swd~l~~~Fikki~~~vn~~~~~~d~~il~~~ 359 (446)
||.||+ ++|+..+..++|+|.+ ++|+|+|++|+||||||+++||.++..||+||++|||.+ .+|++|+|+|
T Consensus 3 FA~EFI~~~Gl~~L~~~iE~g~~~~~~~~~~La~~L~af~eLMeHg~vsWd~l~~~FI~Kia~~Vn~~--~~d~~i~q~s 80 (160)
T PF11841_consen 3 FAQEFISRDGLTLLIKMIEEGTEIQPCKGEILAYALTAFVELMEHGIVSWDTLSDSFIKKIASYVNSS--AMDASILQRS 80 (160)
T ss_pred hHHHHHhccCHHHHHHHHHcCCccCcchHHHHHHHHHHHHHHHhcCcCchhhccHHHHHHHHHHHccc--cccchHHHHH
Confidence 999999 9999999999999873 899999999999999999999999999999999999987 5799999999
Q ss_pred HHHHhhhhhcCchhhhHHhhhcchhhhhhhcccCChHHHHhHHHHHHHHhccCCchhHHHhhHhhhhhhhHHHHHhcccc
Q psy1379 360 LSILESIALNSVGKFSQVENHLTLTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQ 439 (446)
Q Consensus 360 l~iLE~~vl~s~~~~~~v~~Ev~l~~l~~~lq~~~~~~~~~a~al~nal~~~a~~~~r~~~~~~l~~~~~r~~i~~~ii~ 439 (446)
|+|||++|+||+++|++|++|||+++|++|||++|++||+||||||||||+||++++|++|+++|++||+|++|++||||
T Consensus 81 LaILEs~Vl~S~~ly~~V~~evt~~~Li~hLq~~~~~iq~naiaLinAL~~kA~~~~r~~i~~~l~~k~~R~~I~~~ii~ 160 (160)
T PF11841_consen 81 LAILESIVLNSPKLYQLVEQEVTLESLIRHLQVSNQEIQTNAIALINALFLKADDSKRKEIAETLSQKQIRQVILKNIIR 160 (160)
T ss_pred HHHHHHHHhCCHHHHHHHhccCCHHHHHHHHHcCCHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHcccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999997
No 3
>KOG2998|consensus
Probab=100.00 E-value=3.3e-39 Score=314.78 Aligned_cols=195 Identities=21% Similarity=0.267 Sum_probs=160.6
Q ss_pred CchhhhhcchHHHHHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHhccccccCCCCCccccccCCCchhhhhhccccCCC
Q psy1379 139 VGAEMAHQLYVLQTLTLGLLEQRMNTKMDPQDQDAHDKIKELRRVAFEIDVIGGVDASSKRQMGGYAKDYKKLGFKYDIN 218 (446)
Q Consensus 139 ~~~e~ah~L~~~Q~l~l~~Le~r~~~~~d~~~~~h~~~L~~Lw~~a~p~~~~~~~~~~~~R~~~~~s~~Wk~LGFq~~~d 218 (446)
++.-+...+...|...+..+++++.+|||.+||+|+++|++||+.++|++.++ ++++++||++|||| +|
T Consensus 95 ~~~~~~~~~~~~~~~l~~~~e~~~~~~yDs~n~~H~e~L~~lwk~~~p~~~l~----------~lvs~qW~emGfQG-~d 163 (302)
T KOG2998|consen 95 IDLAACRHLIPGYRELLQRLEELRQEPYDSDNPDHEELLLDLWKLLYPDKELP----------GLVSKQWKEMGFQG-AD 163 (302)
T ss_pred hhhhhccccccCcHHHHHHHHHHHhccCCCCChhHHHHHHHHHHHhCCCCccc----------hhHHHHHHHhccCC-CC
Confidence 44444555677778889999999999999999999999999999999998765 67899999999999 99
Q ss_pred cccccccCCchHhhHhHHHHHHHhChHHHHHHHHhhhcchhhhhhhhhcCCCCccccchhhhccchHHHHHHHHHhhhhh
Q psy1379 219 PAQDFTETPPGMLALDCMIYFARNHPEAYTKQKATKKTLEGTAEKVRLSGLPDTDTLSSDVSGQVRLYFSIQFLLDCFAV 298 (446)
Q Consensus 219 P~~DFr~~~~G~LgL~nL~yFa~~~~d~fskllleQ~~~~~~q~~~k~~aL~~l~~yS~aVtgin~t~fa~efl~dgl~~ 298 (446)
|+|||| |||+|||+||+|||++||+.|++++.++. +++ |+|||||+|||||+||++++..|...
T Consensus 164 PsTDFR--G~GfL~LeNLlyFa~~~~~~aq~lL~~s~-------~~r-------~eYpfAVvgINIT~m~~qmL~~eal~ 227 (302)
T KOG2998|consen 164 PSTDFR--GMGFLGLENLLYFARTYPTSAQRLLLKSR-------HPR-------WEYPFAVVGINITFMAIQMLDLEALK 227 (302)
T ss_pred CCcccc--cchHHHHHHHHHHHHhhhHHHHHHHHhcC-------CCc-------cCCceEEEeecHHHHHHHHHHhhhcc
Confidence 999999 99999999999999999999999998654 233 99999999999999999988555553
Q ss_pred -hhcccccchhhhhhHHHHHHHHHHhhhccccccchHHHHHHHHHhhcCCCCCCchHHHHHHHHHHh-hhhhcCchhhhH
Q psy1379 299 -LVNHSQAGLCVMLAHCLLSFVELMDHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILE-SIALNSVGKFSQ 376 (446)
Q Consensus 299 -l~~~~e~g~~~~La~~L~aF~eLm~~~i~swd~l~~~Fikki~~~vn~~~~~~d~~il~~~l~iLE-~~vl~s~~~~~~ 376 (446)
-.+.+..+ +.+..+|..|||+- |. .||+.|+....+||| |.|+.++ +.+
T Consensus 228 ~~~~~~~~~-----~~~~~~F~~lYc~a-----------------f~-----~~d~~Wl~~~~simefn~Vlk~~--~~q 278 (302)
T KOG2998|consen 228 KHFNNIVKV-----FETEPAFDLLYCYA-----------------FL-----EFDKQWLEQRATIMEFNTVLKSF--RRQ 278 (302)
T ss_pred ccccccccc-----cccHHHHHHHHHHH-----------------HH-----HHHHHHHHhhccHHHHHHHHHHH--HHH
Confidence 22333222 13445555555533 33 578889999999999 9999996 999
Q ss_pred Hhhhcchhhhhhh
Q psy1379 377 VENHLTLTNLVMH 389 (446)
Q Consensus 377 v~~Ev~l~~l~~~ 389 (446)
+++|+.++++...
T Consensus 279 ler~L~~~d~~~~ 291 (302)
T KOG2998|consen 279 LERELSLDDVLLI 291 (302)
T ss_pred HHHhhhhhhhccc
Confidence 9999999988543
No 4
>PF11841 DUF3361: Domain of unknown function (DUF3361)
Probab=100.00 E-value=6.9e-39 Score=291.30 Aligned_cols=128 Identities=52% Similarity=0.742 Sum_probs=124.7
Q ss_pred ChhhHHHHHHHHHhcCCcccccCchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHH
Q psy1379 1 MLAHCLLSFVELMDHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNL 80 (446)
Q Consensus 1 ~Lay~L~a~~~Lme~~~~~W~~l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~l 80 (446)
+|||+|+||++|||||++|||++++.||+|||+|||++ +.|++|+|+||+|||++|++|+.+| +.|++|||+++|
T Consensus 33 ~La~~L~af~eLMeHg~vsWd~l~~~FI~Kia~~Vn~~--~~d~~i~q~sLaILEs~Vl~S~~ly---~~V~~evt~~~L 107 (160)
T PF11841_consen 33 ILAYALTAFVELMEHGIVSWDTLSDSFIKKIASYVNSS--AMDASILQRSLAILESIVLNSPKLY---QLVEQEVTLESL 107 (160)
T ss_pred HHHHHHHHHHHHHhcCcCchhhccHHHHHHHHHHHccc--cccchHHHHHHHHHHHHHhCCHHHH---HHHhccCCHHHH
Confidence 58999999999999999999999999999999999987 4699999999999999999999989 999999999999
Q ss_pred hhhccCCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHHhhhc
Q psy1379 81 VMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQ 133 (446)
Q Consensus 81 v~~L~~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~ 133 (446)
++||+++|+++|+||+|||||||.||++++|+++.++|.++++|++|++||||
T Consensus 108 i~hLq~~~~~iq~naiaLinAL~~kA~~~~r~~i~~~l~~k~~R~~I~~~ii~ 160 (160)
T PF11841_consen 108 IRHLQVSNQEIQTNAIALINALFLKADDSKRKEIAETLSQKQIRQVILKNIIR 160 (160)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHcccC
Confidence 99999999999999999999999999999999999999999999999999986
No 5
>KOG2999|consensus
Probab=100.00 E-value=5.8e-34 Score=294.99 Aligned_cols=191 Identities=32% Similarity=0.469 Sum_probs=174.8
Q ss_pred hChHHHHHHHHhhhcchhhhhhhhhcCCCCccccchhhhccchHHHHHHHH-Hhhhhhhhcccccchh----hhhhHHHH
Q psy1379 242 NHPEAYTKQKATKKTLEGTAEKVRLSGLPDTDTLSSDVSGQVRLYFSIQFL-LDCFAVLVNHSQAGLC----VMLAHCLL 316 (446)
Q Consensus 242 ~~~d~fskllleQ~~~~~~q~~~k~~aL~~l~~yS~aVtgin~t~fa~efl-~dgl~~l~~~~e~g~~----~~La~~L~ 316 (446)
..|+.|.+-+++-..- + +...+..+++++.++|.|+| ||.+|+ ++|+..+..++++|.. .+|+++|+
T Consensus 79 ~sp~~~a~~i~e~l~~-~-~~~~~~~a~k~l~sls~d~~------fa~efi~~~gl~~L~~liedg~~~~~~~~L~~~L~ 150 (713)
T KOG2999|consen 79 ASPSHYAKRIMEILTE-G-NNISKMEALKELDSLSLDPT------FAEEFIRCSGLELLFSLIEDGRVCMSSELLSTSLR 150 (713)
T ss_pred cCchHHHHHHHHHHhC-C-CcHHHHHHHHHHhhccccHH------HHHHHHhcchHHHHHHHHHcCccchHHHHHHHHHH
Confidence 5688888777653322 2 23556668889999999999 999999 9999999999998863 89999999
Q ss_pred HHHHHHhhhccccccchHHHHHHHHHhhcCCCCCCchHHHHHHHHHHhhhhhcCchhhhHHhhhcchhhhhhhcccCChH
Q psy1379 317 SFVELMDHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQVENHLTLTNLVMHLQNQSPI 396 (446)
Q Consensus 317 aF~eLm~~~i~swd~l~~~Fikki~~~vn~~~~~~d~~il~~~l~iLE~~vl~s~~~~~~v~~Ev~l~~l~~~lq~~~~~ 396 (446)
+|+++|+||+++|+.++..||+++++|||.+ .+|++++++||++||++|++|+.+|++|..|||+++|++|||++|++
T Consensus 151 af~elmehgvvsW~~~~~~fV~~~a~~V~~~--~~~a~~~~~AL~~LE~~vl~s~~~~~~v~eev~i~~li~hlq~~n~~ 228 (713)
T KOG2999|consen 151 AFSELMEHGVVSWESVSNDFVVSMASYVNAK--REDANTLLAALQMLESLVLGSDTLRQLVAEEVPIETLIRHLQVSNQR 228 (713)
T ss_pred HHHHHHhhceeeeeecccHHHHHHHHHHhhh--hhcccchHHHHHHHHHHHhCChHHHHHHHhcCcHHHHHHHHHhcchH
Confidence 9999999999999999999999999999776 79999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHHHHHHhccCCchhHHHhhHhhhhhhhHHHHHhccccCCC
Q psy1379 397 IQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQPSG 442 (446)
Q Consensus 397 ~~~~a~al~nal~~~a~~~~r~~~~~~l~~~~~r~~i~~~ii~~~~ 442 (446)
+|++|+|||||||+||++++|++|+++++++|+|++|++|+|++..
T Consensus 229 i~~~aial~nal~~~a~~~~R~~~~~~l~~~~~R~ai~~~~~~~~~ 274 (713)
T KOG2999|consen 229 IQTCAIALLNALFRKAPDDKRFEMAKSLEQKQFRNAIHSNVIRTER 274 (713)
T ss_pred HHHHHHHHHHHHHhhCChHHHHHHHHHHHHHHHHHHHHHhhhcccc
Confidence 9999999999999999999999999999999999999999998754
No 6
>PF04727 ELMO_CED12: ELMO/CED-12 family; InterPro: IPR006816 This entry represents the ELMO (EnguLfment and Cell MOtility) domain, which is found in a number of eukaryotic proteins involved in the cytoskeletal rearrangements required for phagocytosis of apoptotic cells and cell motility, including CED-12, ELMO-1 and ELMO-2. ELMO-1 and ELMO-2 are components of signalling pathways that regulate phagocytosis and cell migration and are mammalian orthologues of the Caenorhabditis elegans gene, ced-12 that is required for the engulfment of dying cells and cell migration. ELMO-1/2 act in association with DOCK1 and CRK. ELMO-1/2 interact with the SH3-domain of DOCK1 via an SH3-binding site to enhance the guanine nucleotide exchange factor (GEF) activity of DOCK1. ELMO-1/2 could be part of a complex with DOCK1 and Rac1 that could be required to activate Rac Rho small GTPases. Regulatory GTPases in the Ras superfamily employ a cycle of alternating GTP binding and hydrolysis, controlled by guanine nucleotide exchange factors and GTPase-activating proteins (GAPs), as essential features of their actions in cells. Within the Ras superfamily, the Arf family is composed of 30 members, including 22 Arf-like (Arl) proteins. The ELMO domain has been proposed to be a GAP domain for ARL2 and other members of the Arf family [].; GO: 0006909 phagocytosis, 0005856 cytoskeleton
Probab=99.97 E-value=1.2e-30 Score=240.96 Aligned_cols=153 Identities=22% Similarity=0.313 Sum_probs=124.4
Q ss_pred HHHHHHHHhcccCCCCCHHHHHHHHHHHHHhccccccCCCCCccccccCCCchhhhhhccccCCCcccccccCCchHhhH
Q psy1379 154 TLGLLEQRMNTKMDPQDQDAHDKIKELRRVAFEIDVIGGVDASSKRQMGGYAKDYKKLGFKYDINPAQDFTETPPGMLAL 233 (446)
Q Consensus 154 ~l~~Le~r~~~~~d~~~~~h~~~L~~Lw~~a~p~~~~~~~~~~~~R~~~~~s~~Wk~LGFq~~~dP~~DFr~~~~G~LgL 233 (446)
+++.|++++++|||++|++|+++|++||.+++|+++. . ++.+++|++||||| +||+|||| |+|+|||
T Consensus 2 ~l~~l~~~~~~~~d~~~~~h~~~L~~Lw~~~~~~~~~------~----~~~~~~W~~lGFQ~-~dP~tDFR--~~G~LgL 68 (170)
T PF04727_consen 2 TLNLLRALAKTPFDPENPEHEELLQELWNALFPDEPP------F----SRISEHWKELGFQG-EDPATDFR--GMGLLGL 68 (170)
T ss_pred hHHHHHHHHcCCCCCCCHHHHHHHHHHHHHhCCCCcc------C----CcCccHHHHhCCCC-CCcHHHHh--hhhHHHH
Confidence 5889999999999999999999999999999997532 2 34678999999999 99999999 9999999
Q ss_pred hHHHHHHHhChHHHHHHHHhhhcchhhhhhhhhcCCCCccccchhhhccchHHHHHHHHHhhhhh--hhcccccchhhhh
Q psy1379 234 DCMIYFARNHPEAYTKQKATKKTLEGTAEKVRLSGLPDTDTLSSDVSGQVRLYFSIQFLLDCFAV--LVNHSQAGLCVML 311 (446)
Q Consensus 234 ~nL~yFa~~~~d~fskllleQ~~~~~~q~~~k~~aL~~l~~yS~aVtgin~t~fa~efl~dgl~~--l~~~~e~g~~~~L 311 (446)
+||+||+++||+.|++++.++..++.. .+||+|++|||+|.++.+++..|... .++.. .. ..+
T Consensus 69 ~~L~yf~~~~~~~~~~~l~~~~~~~~~------------~~~Pfa~~~invt~~l~~~l~~~~~~~~~~~~~-~~--~~~ 133 (170)
T PF04727_consen 69 DCLLYFAENYPDEFRRILREQSSRSDE------------NWYPFAVASINVTSLLCELLKLGALDSEFYKRI-NF--LSF 133 (170)
T ss_pred HHHHHHHHHChHHHHHHHHHccCcccc------------cccHHHHHHHHHHHHHHHHHhhcccCHHHhhcc-cc--ccc
Confidence 999999999999999999987765332 47999999999999999988333321 11110 00 014
Q ss_pred hHHHHHHHHHHhhhccccccchH
Q psy1379 312 AHCLLSFVELMDHGIVSWNILET 334 (446)
Q Consensus 312 a~~L~aF~eLm~~~i~swd~l~~ 334 (446)
...+.+|.+|+|..+..|+..+.
T Consensus 134 ~~~~~~f~elf~~~f~~f~~~W~ 156 (170)
T PF04727_consen 134 FSSLEAFEELFCACFQLFDRTWK 156 (170)
T ss_pred CccHHHHHHHHHHHHHHHHHHHc
Confidence 67778899999988877776654
No 7
>PLN03200 cellulose synthase-interactive protein; Provisional
Probab=92.40 E-value=6.5 Score=49.42 Aligned_cols=357 Identities=13% Similarity=0.106 Sum_probs=186.5
Q ss_pred hHHHHHHHHHhcCCcccccC-chHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhh
Q psy1379 4 HCLLSFVELMDHGIVSWNIL-ETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVM 82 (446)
Q Consensus 4 y~L~a~~~Lme~~~~~W~~l-~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~ 82 (446)
.+-.++..|.+++.-.|+.+ +...|..+++++.+. +.++.+.|...|..+...+...- ..|-+.=.++.|++
T Consensus 423 ~Av~aL~~L~~~~~e~~~aIi~~ggIp~LV~LL~s~----s~~iQ~~A~~~L~nLa~~ndenr---~aIieaGaIP~LV~ 495 (2102)
T PLN03200 423 ELIRALSSLCCGKGGLWEALGGREGVQLLISLLGLS----SEQQQEYAVALLAILTDEVDESK---WAITAAGGIPPLVQ 495 (2102)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHcCcHHHHHHHHcCC----CHHHHHHHHHHHHHHHcCCHHHH---HHHHHCCCHHHHHH
Confidence 45566677777765557653 566889999999984 57888999999998876554332 44555556899999
Q ss_pred hccCCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhcchHHHHHHHHHHHHHh
Q psy1379 83 HLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQLYVLQTLTLGLLEQRM 162 (446)
Q Consensus 83 ~L~~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~L~~~Q~l~l~~Le~r~ 162 (446)
.|.+.+..+|.+|..-|=.|-.+ +.. .-..+.+.|....++. +++ +.. ...|......|.+-.
T Consensus 496 LL~s~~~~iqeeAawAL~NLa~~--~~q---ir~iV~~aGAIppLV~-LL~-sgd----------~~~q~~Aa~AL~nLi 558 (2102)
T PLN03200 496 LLETGSQKAKEDSATVLWNLCCH--SED---IRACVESAGAVPALLW-LLK-NGG----------PKGQEIAAKTLTKLV 558 (2102)
T ss_pred HHcCCCHHHHHHHHHHHHHHhCC--cHH---HHHHHHHCCCHHHHHH-HHh-CCC----------HHHHHHHHHHHHHHH
Confidence 99999999999987766555442 222 2333445566666666 554 221 122333333333322
Q ss_pred cccCCCCCHHHHHHHHHHHHHhccccccCCCCCccccccCCCchhhhhhccccCCCcccccc----cCCchHhhHhHHHH
Q psy1379 163 NTKMDPQDQDAHDKIKELRRVAFEIDVIGGVDASSKRQMGGYAKDYKKLGFKYDINPAQDFT----ETPPGMLALDCMIY 238 (446)
Q Consensus 163 ~~~~d~~~~~h~~~L~~Lw~~a~p~~~~~~~~~~~~R~~~~~s~~Wk~LGFq~~~dP~~DFr----~~~~G~LgL~nL~y 238 (446)
. + .+++ .+..||.+...++.. . . ..-=+-+|---..-...|+. ++.. |++.|.-
T Consensus 559 ~---~-~d~~---~I~~Lv~LLlsdd~~------~-~-----~~aL~vLgnIlsl~~~~d~~~~g~~~~g---gL~~Lv~ 616 (2102)
T PLN03200 559 R---T-ADAA---TISQLTALLLGDLPE------S-K-----VHVLDVLGHVLSVASLEDLVREGSAAND---ALRTLIQ 616 (2102)
T ss_pred h---c-cchh---HHHHHHHHhcCCChh------H-H-----HHHHHHHHHHHhhcchhHHHHHhhhccc---cHHHHHH
Confidence 2 1 1222 334455443222100 0 0 00000111100000011111 1122 5555555
Q ss_pred HHHhChHHHHHHHHhhhcchhhhhhhhhcCCCCccccchhhhccchHHHHHHHH-HhhhhhhhcccccchhhhhhHHHHH
Q psy1379 239 FARNHPEAYTKQKATKKTLEGTAEKVRLSGLPDTDTLSSDVSGQVRLYFSIQFL-LDCFAVLVNHSQAGLCVMLAHCLLS 317 (446)
Q Consensus 239 Fa~~~~d~fskllleQ~~~~~~q~~~k~~aL~~l~~yS~aVtgin~t~fa~efl-~dgl~~l~~~~e~g~~~~La~~L~a 317 (446)
.-++..+.-++.-. ... ........++. .+++ .+|..-+......|..+.-.-+-.+
T Consensus 617 LL~sgs~~ikk~Aa--~iL------------snL~a~~~d~~--------~avv~agaIpPLV~LLss~~~~v~keAA~A 674 (2102)
T PLN03200 617 LLSSSKEETQEKAA--SVL------------ADIFSSRQDLC--------ESLATDEIINPCIKLLTNNTEAVATQSARA 674 (2102)
T ss_pred HHcCCCHHHHHHHH--HHH------------HHHhcCChHHH--------HHHHHcCCHHHHHHHHhcCChHHHHHHHHH
Confidence 55444332221111 000 00011111111 1111 1122112222222222222222222
Q ss_pred HHHHHhhhcccc--ccchHHHHHHHHHhhcCCCCCCchHHHHHHHHHHhhhhhcCchhhhHHhhhcchhhhhhhcccCCh
Q psy1379 318 FVELMDHGIVSW--NILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQVENHLTLTNLVMHLQNQSP 395 (446)
Q Consensus 318 F~eLm~~~i~sw--d~l~~~Fikki~~~vn~~~~~~d~~il~~~l~iLE~~vl~s~~~~~~v~~Ev~l~~l~~~lq~~~~ 395 (446)
-..+...+.-.. ..+...-++-....++.+ |..+.+.++..|++++......-+.+..+. ++.|++.|+..++
T Consensus 675 L~nL~~~~~~~q~~~~v~~GaV~pL~~LL~~~----d~~v~e~Al~ALanLl~~~e~~~ei~~~~~-I~~Lv~lLr~G~~ 749 (2102)
T PLN03200 675 LAALSRSIKENRKVSYAAEDAIKPLIKLAKSS----SIEVAEQAVCALANLLSDPEVAAEALAEDI-ILPLTRVLREGTL 749 (2102)
T ss_pred HHHHHhCCCHHHHHHHHHcCCHHHHHHHHhCC----ChHHHHHHHHHHHHHHcCchHHHHHHhcCc-HHHHHHHHHhCCh
Confidence 333332111000 112333455566677553 678999999999999988874333343434 8999999999999
Q ss_pred HHHHhHHHHHHHHhccCCchh-H------H----HhhHhhhhhhhHHHH
Q psy1379 396 IIQQNAIALINALFIKAEPSK-R------K----VISATMCSKQVRNAI 433 (446)
Q Consensus 396 ~~~~~a~al~nal~~~a~~~~-r------~----~~~~~l~~~~~r~~i 433 (446)
.-..||.+.+..|+.+.+.+. = . .+.+.|..-+.+++.
T Consensus 750 ~~k~~Aa~AL~~L~~~~~~~~~~~~~~~~~g~v~~l~~~L~~~~~~~~~ 798 (2102)
T PLN03200 750 EGKRNAARALAQLLKHFPVDDVLKDSVQCRGTVLALVDLLNSTDLDSSA 798 (2102)
T ss_pred HHHHHHHHHHHHHHhCCChhHHHHHHHHHhCcHHHHHHHHhcCCcchhh
Confidence 999999999999999998543 1 1 556667777777655
No 8
>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=90.51 E-value=1.7 Score=35.88 Aligned_cols=94 Identities=18% Similarity=0.154 Sum_probs=65.4
Q ss_pred hHHHHHHHHHHhhhcccccc-chHHHHHHHHHhhcCCCCCCchHHHHHHHHHHhhhhhcCchhhhHHhhhcchhhhhhhc
Q psy1379 312 AHCLLSFVELMDHGIVSWNI-LETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQVENHLTLTNLVMHL 390 (446)
Q Consensus 312 a~~L~aF~eLm~~~i~swd~-l~~~Fikki~~~vn~~~~~~d~~il~~~l~iLE~~vl~s~~~~~~v~~Ev~l~~l~~~l 390 (446)
..++.++..+.....-.++. +...++..++.+++.+ |..+...++..|-+++.+.+.....+.+.=.++.++..+
T Consensus 25 ~~a~~~l~~l~~~~~~~~~~~~~~~~i~~l~~~l~~~----~~~v~~~a~~~L~~l~~~~~~~~~~~~~~g~l~~l~~~l 100 (120)
T cd00020 25 REAAWALSNLSAGNNDNIQAVVEAGGLPALVQLLKSE----DEEVVKAALWALRNLAAGPEDNKLIVLEAGGVPKLVNLL 100 (120)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHCCChHHHHHHHhCC----CHHHHHHHHHHHHHHccCcHHHHHHHHHCCChHHHHHHH
Confidence 34444444544432222222 3336677788888764 678999999999999988765455555544688899999
Q ss_pred ccCChHHHHhHHHHHHHHh
Q psy1379 391 QNQSPIIQQNAIALINALF 409 (446)
Q Consensus 391 q~~~~~~~~~a~al~nal~ 409 (446)
+..+..++.++..++..|.
T Consensus 101 ~~~~~~~~~~a~~~l~~l~ 119 (120)
T cd00020 101 DSSNEDIQKNATGALSNLA 119 (120)
T ss_pred hcCCHHHHHHHHHHHHHhh
Confidence 9889999999998887764
No 9
>PF06367 Drf_FH3: Diaphanous FH3 Domain; InterPro: IPR010472 Formin homology (FH) proteins play a crucial role in the reorganisation of the actin cytoskeleton, which mediates various functions of the cell cortex including motility, adhesion, and cytokinesis []. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains []. The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain (IPR003104 from INTERPRO) is required to inhibit actin polymerisation. The FH3 domain is less well conserved and is required for directing formins to the correct intracellular location, such the mitotic spindle [], or the projection tip during conjugation []. In addition, some formins can contain a GTPase-binding domain (GBD) (IPR010473 from INTERPRO) required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD). This entry represents the FH3 domain.; GO: 0003779 actin binding, 0016043 cellular component organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=89.92 E-value=1.9 Score=40.33 Aligned_cols=76 Identities=12% Similarity=0.107 Sum_probs=57.3
Q ss_pred cchhHHhhhcc---CCChHHHHhHHHHHHHHhhccCC-hhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhcchHH
Q psy1379 75 LTLTNLVMHLQ---NQSPIIQQNAIALINALFIKAEP-SKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQLYVL 150 (446)
Q Consensus 75 v~~~~lv~~L~---~~d~~iq~nalaLiNaL~~~a~~-~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~L~~~ 150 (446)
..|..+|..+. ..+.+.++.+|+|||+|+..+.+ ..|-.+-..+...|+...+-+ +- .. -.+++-.|+-.|
T Consensus 21 ~RF~~lv~~l~~~~~~~~e~~~~~l~~IN~li~~~~d~~~R~~lr~e~~~~GL~~il~~-l~--~~--~~~~L~~Qi~~f 95 (197)
T PF06367_consen 21 GRFQSLVGALESVDSSDIEYKTACLQFINSLINSPEDLNFRVHLRNEFERLGLLDILEK-LR--NL--EDDDLQEQIDIF 95 (197)
T ss_dssp -TTHHHHHHCS--TTS-HHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTTHHHHHHH-HT--TS----HHHHHHHHHH
T ss_pred ccHHHHHHHHHccccCcHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCcHHHHHH-HH--hc--chHHHHHHHHHH
Confidence 34788888887 48999999999999999999876 457799999999999988876 32 22 246777788777
Q ss_pred HHHHH
Q psy1379 151 QTLTL 155 (446)
Q Consensus 151 Q~l~l 155 (446)
.....
T Consensus 96 ~~~~~ 100 (197)
T PF06367_consen 96 EENEE 100 (197)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 77754
No 10
>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=89.02 E-value=0.85 Score=37.73 Aligned_cols=93 Identities=18% Similarity=0.158 Sum_probs=65.5
Q ss_pred hHHHHHHHHHhcCCccccc-CchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhh
Q psy1379 4 HCLLSFVELMDHGIVSWNI-LETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVM 82 (446)
Q Consensus 4 y~L~a~~~Lme~~~~~W~~-l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~ 82 (446)
.++.++..+.....-.++. +...++..++.+++.+ +..+.+.|+..|.+++.+.+..- ..+.+.=.++.|++
T Consensus 26 ~a~~~l~~l~~~~~~~~~~~~~~~~i~~l~~~l~~~----~~~v~~~a~~~L~~l~~~~~~~~---~~~~~~g~l~~l~~ 98 (120)
T cd00020 26 EAAWALSNLSAGNNDNIQAVVEAGGLPALVQLLKSE----DEEVVKAALWALRNLAAGPEDNK---LIVLEAGGVPKLVN 98 (120)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHCCChHHHHHHHhCC----CHHHHHHHHHHHHHHccCcHHHH---HHHHHCCChHHHHH
Confidence 4555566665552223333 3447788888888874 78999999999999988765322 33333335788999
Q ss_pred hccCCChHHHHhHHHHHHHHh
Q psy1379 83 HLQNQSPIIQQNAIALINALF 103 (446)
Q Consensus 83 ~L~~~d~~iq~nalaLiNaL~ 103 (446)
.++..|..++.+++.++..|.
T Consensus 99 ~l~~~~~~~~~~a~~~l~~l~ 119 (120)
T cd00020 99 LLDSSNEDIQKNATGALSNLA 119 (120)
T ss_pred HHhcCCHHHHHHHHHHHHHhh
Confidence 999989999999998887764
No 11
>PLN03200 cellulose synthase-interactive protein; Provisional
Probab=84.58 E-value=7.2 Score=49.04 Aligned_cols=162 Identities=15% Similarity=0.213 Sum_probs=114.5
Q ss_pred CchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhhhccCCChHHHHhHHHHHHHH
Q psy1379 23 LETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVMHLQNQSPIIQQNAIALINAL 102 (446)
Q Consensus 23 l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~~L~~~d~~iq~nalaLiNaL 102 (446)
+....|.-.+.++.. .+..+...|+..|.+++..+...- +++... .++.|++.|++.++.-..||-+.+..|
T Consensus 691 v~~GaV~pL~~LL~~----~d~~v~e~Al~ALanLl~~~e~~~---ei~~~~-~I~~Lv~lLr~G~~~~k~~Aa~AL~~L 762 (2102)
T PLN03200 691 AAEDAIKPLIKLAKS----SSIEVAEQAVCALANLLSDPEVAA---EALAED-IILPLTRVLREGTLEGKRNAARALAQL 762 (2102)
T ss_pred HHcCCHHHHHHHHhC----CChHHHHHHHHHHHHHHcCchHHH---HHHhcC-cHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence 445566677777766 478999999999999998886432 233333 389999999999999999999999999
Q ss_pred hhccCChhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhcchHHHHHHHHHHHHHhcccCCCCCHHHHHHHHHHHH
Q psy1379 103 FIKAEPSKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQLYVLQTLTLGLLEQRMNTKMDPQDQDAHDKIKELRR 182 (446)
Q Consensus 103 ~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~L~~~Q~l~l~~Le~r~~~~~d~~~~~h~~~L~~Lw~ 182 (446)
.++.+.++ .+.+..+..|+.-++.. ++ ...|.++.+--++|..|=.
T Consensus 763 ~~~~~~~~--~~~~~~~~~g~v~~l~~-~L-------------------------------~~~~~~~~~~~~al~~l~~ 808 (2102)
T PLN03200 763 LKHFPVDD--VLKDSVQCRGTVLALVD-LL-------------------------------NSTDLDSSATSEALEALAL 808 (2102)
T ss_pred HhCCChhH--HHHHHHHHhCcHHHHHH-HH-------------------------------hcCCcchhhHHHHHHHHHH
Confidence 98766332 34455555554444433 22 2347777777788888877
Q ss_pred HhccccccCCCCCccccccCCCchhhhhhccccCCCcccccccCCchHhhH-hHHHHHHHhChHHHHHHHH
Q psy1379 183 VAFEIDVIGGVDASSKRQMGGYAKDYKKLGFKYDINPAQDFTETPPGMLAL-DCMIYFARNHPEAYTKQKA 252 (446)
Q Consensus 183 ~a~p~~~~~~~~~~~~R~~~~~s~~Wk~LGFq~~~dP~~DFr~~~~G~LgL-~nL~yFa~~~~d~fsklll 252 (446)
.+...+ |++...+|-..|-|.|.|+--| .|+ +..+|+.+.|.+.
T Consensus 809 l~~~~~-----------------------~~~~~~~~~~~~~e~p~~l~~l~~~l---~~~~p~~~~kai~ 853 (2102)
T PLN03200 809 LARTKG-----------------------GANFSHPPWAVLAEVPSSLEPLVRCL---AEGHPLVQDKAIE 853 (2102)
T ss_pred HHhhcc-----------------------cCCCCCCchhhHHhccCchHHHHHHH---HcCChHHHHHHHH
Confidence 775432 1222246888999988888888 777 7788888887654
No 12
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=82.34 E-value=16 Score=33.09 Aligned_cols=95 Identities=11% Similarity=0.160 Sum_probs=58.9
Q ss_pred chhHHhhhccCCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhcchHHHHHHH
Q psy1379 76 TLTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQLYVLQTLTL 155 (446)
Q Consensus 76 ~~~~lv~~L~~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~L~~~Q~l~l 155 (446)
....|.++|++.++..|..||.|+.+++.+|++.=. ..+.++.+-..+.+ ++. . ...+. ..=-.+|...+
T Consensus 39 a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh----~evas~~Fl~el~k-l~~-~-k~~~~---~~~~~Vk~kil 108 (139)
T cd03567 39 AVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFH----SEVGKFRFLNELIK-LVS-P-KYLGS---RTSEKVKTKII 108 (139)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHH----HHHHhHHHHHHHHH-Hhc-c-ccCCC---CCCHHHHHHHH
Confidence 345577888899999999999999999999995333 33334444445445 442 1 00000 00146777778
Q ss_pred HHHHHHhcccCCCCCHHHHHHHHHHHH
Q psy1379 156 GLLEQRMNTKMDPQDQDAHDKIKELRR 182 (446)
Q Consensus 156 ~~Le~r~~~~~d~~~~~h~~~L~~Lw~ 182 (446)
.+++.|.. .|. .+|.-.+....|..
T Consensus 109 ~li~~W~~-~f~-~~p~~~~~Y~~Lk~ 133 (139)
T cd03567 109 ELLYSWTL-ELP-HEPKIKEAYDMLKK 133 (139)
T ss_pred HHHHHHHH-Hhc-ccchHHHHHHHHHH
Confidence 88888886 443 45555555555543
No 13
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=80.48 E-value=23 Score=31.48 Aligned_cols=90 Identities=18% Similarity=0.239 Sum_probs=54.6
Q ss_pred hhHHhhhccCCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhcchHHHHHHHH
Q psy1379 77 LTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQLYVLQTLTLG 156 (446)
Q Consensus 77 ~~~lv~~L~~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~L~~~Q~l~l~ 156 (446)
..-|-++|++.++..|..||.|+.+++.++++. |-..+.+..+-..+.+ ++. . .... + ..+...+.
T Consensus 39 ~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~----f~~ev~s~~fl~~L~~-l~~-~-~~~~-----~--~Vk~kil~ 104 (133)
T smart00288 39 VRLLKKRLNNKNPHVALLALTLLDACVKNCGSK----FHLEVASKEFLNELVK-LIK-P-KYPL-----P--LVKKRILE 104 (133)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHH----HHHHHHhHHHHHHHHH-HHc-C-CCCc-----H--HHHHHHHH
Confidence 445778889999999999999999999999853 3333334444444443 442 2 2111 1 16666677
Q ss_pred HHHHHhccc-CCCCCHHHHHHHHHH
Q psy1379 157 LLEQRMNTK-MDPQDQDAHDKIKEL 180 (446)
Q Consensus 157 ~Le~r~~~~-~d~~~~~h~~~L~~L 180 (446)
.+..|...- -||+-+.-.+....|
T Consensus 105 li~~W~~~f~~~~~~~~i~~~y~~L 129 (133)
T smart00288 105 LIQEWADAFKNDPDLSQIVDVYDLL 129 (133)
T ss_pred HHHHHHHHHcCCCCchHHHHHHHHH
Confidence 777776622 245544444444443
No 14
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=80.39 E-value=11 Score=33.56 Aligned_cols=78 Identities=19% Similarity=0.301 Sum_probs=49.3
Q ss_pred chhHHhhhccCCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhcchHHHHHHH
Q psy1379 76 TLTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQLYVLQTLTL 155 (446)
Q Consensus 76 ~~~~lv~~L~~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~L~~~Q~l~l 155 (446)
....|-++|++.++..|.+||.|+.+|+.++++. |-..+.+..+-..+.+ ++. + +..+ ... .++...+
T Consensus 43 a~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~----f~~ev~~~~fl~~l~~-l~~-~-~~~~-~~~----~Vk~k~l 110 (140)
T PF00790_consen 43 AARALRKRLKHGNPNVQLLALTLLDALVKNCGPR----FHREVASKEFLDELVK-LIK-S-KKTD-PET----PVKEKIL 110 (140)
T ss_dssp HHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHH----HHHHHTSHHHHHHHHH-HHH-H-TTTH-HHS----HHHHHHH
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHH----HHHHHhHHHHHHHHHH-HHc-c-CCCC-chh----HHHHHHH
Confidence 3455788999999999999999999999998743 3333333344444444 332 1 1111 111 1666667
Q ss_pred HHHHHHhccc
Q psy1379 156 GLLEQRMNTK 165 (446)
Q Consensus 156 ~~Le~r~~~~ 165 (446)
.++..|...-
T Consensus 111 ~ll~~W~~~f 120 (140)
T PF00790_consen 111 ELLQEWAEAF 120 (140)
T ss_dssp HHHHHHHHHT
T ss_pred HHHHHHHHHH
Confidence 7787777644
No 15
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=75.86 E-value=38 Score=30.70 Aligned_cols=73 Identities=14% Similarity=0.240 Sum_probs=49.7
Q ss_pred chhHHhhhccCCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhcchHHHHHHH
Q psy1379 76 TLTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQLYVLQTLTL 155 (446)
Q Consensus 76 ~~~~lv~~L~~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~L~~~Q~l~l 155 (446)
....|.++|++.|+..|..||.|+.+++.+|++. |-..+.++.+-..+.+ ++. .. .. ...+..++
T Consensus 38 a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~----fh~evask~Fl~eL~k-l~~-~~--~~-------~~Vk~kil 102 (144)
T cd03568 38 CLKAIMKRLNHKDPNVQLRALTLLDACAENCGKR----FHQEVASRDFTQELKK-LIN-DR--VH-------PTVKEKLR 102 (144)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHH----HHHHHhhHHHHHHHHH-Hhc-cc--CC-------HHHHHHHH
Confidence 3455778888899999999999999999999953 3333344555555555 553 21 11 35666667
Q ss_pred HHHHHHhc
Q psy1379 156 GLLEQRMN 163 (446)
Q Consensus 156 ~~Le~r~~ 163 (446)
.+++.|..
T Consensus 103 ~li~~W~~ 110 (144)
T cd03568 103 EVVKQWAD 110 (144)
T ss_pred HHHHHHHH
Confidence 77777664
No 16
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=75.20 E-value=36 Score=30.74 Aligned_cols=73 Identities=12% Similarity=0.203 Sum_probs=51.9
Q ss_pred chhHHhhhccCCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhcchHHHHHHH
Q psy1379 76 TLTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQLYVLQTLTL 155 (446)
Q Consensus 76 ~~~~lv~~L~~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~L~~~Q~l~l 155 (446)
...-|.++|++.|+..|..||.|+.+++.+|+. .|-..+.++.+-..+.+ ++. . ..-..++...+
T Consensus 42 a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~----~fh~evas~~fl~~l~~-l~~-~---------~~~~~Vk~kil 106 (142)
T cd03569 42 AMRALKKRLLSKNPNVQLYALLLLESCVKNCGT----HFHDEVASREFMDELKD-LIK-T---------TKNEEVRQKIL 106 (142)
T ss_pred HHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCH----HHHHHHhhHHHHHHHHH-HHc-c---------cCCHHHHHHHH
Confidence 455677888999999999999999999999984 34444445555555555 543 2 12256677778
Q ss_pred HHHHHHhc
Q psy1379 156 GLLEQRMN 163 (446)
Q Consensus 156 ~~Le~r~~ 163 (446)
.+++.|..
T Consensus 107 ~li~~W~~ 114 (142)
T cd03569 107 ELIQAWAL 114 (142)
T ss_pred HHHHHHHH
Confidence 88888875
No 17
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=74.82 E-value=42 Score=30.29 Aligned_cols=75 Identities=11% Similarity=0.170 Sum_probs=47.4
Q ss_pred hhHHhhhcc-CCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhcchHHHHHHH
Q psy1379 77 LTNLVMHLQ-NQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQLYVLQTLTL 155 (446)
Q Consensus 77 ~~~lv~~L~-~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~L~~~Q~l~l 155 (446)
...|-++|+ +.|+..|..||.|+.+++.+|+.. |-.++.++.+-..++..++. ...... ..++...+
T Consensus 40 ~ralkkRl~~~~n~~v~l~aL~LLe~~vkNCG~~----fh~eiask~Fl~e~L~~~i~-~~~~~~-------~~Vk~kil 107 (141)
T cd03565 40 VRALKKRLNGNKNHKEVMLTLTVLETCVKNCGHR----FHVLVAKKDFIKDVLVKLIN-PKNNPP-------TIVQEKVL 107 (141)
T ss_pred HHHHHHHHccCCCHHHHHHHHHHHHHHHHHccHH----HHHHHHHHHhhhHHHHHHHc-ccCCCc-------HHHHHHHH
Confidence 344556676 368999999999999999999953 33444445555552223553 211111 35677778
Q ss_pred HHHHHHhc
Q psy1379 156 GLLEQRMN 163 (446)
Q Consensus 156 ~~Le~r~~ 163 (446)
.+++.|..
T Consensus 108 ~li~~W~~ 115 (141)
T cd03565 108 ALIQAWAD 115 (141)
T ss_pred HHHHHHHH
Confidence 88888775
No 18
>KOG2160|consensus
Probab=65.88 E-value=23 Score=36.87 Aligned_cols=96 Identities=14% Similarity=0.160 Sum_probs=71.4
Q ss_pred HHHHHHHHhc----CCcccccCchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHh
Q psy1379 6 LLSFVELMDH----GIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLV 81 (446)
Q Consensus 6 L~a~~~Lme~----~~~~W~~l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv 81 (446)
.-||-+|++| | ..-+..+-.+..-++.++++. ++++=..|+.++...|+|-|..- +.|-+-=.++.|+
T Consensus 101 e~ald~Le~lve~iD-nAndl~~~ggl~~ll~~l~~~----~~~lR~~Aa~Vigt~~qNNP~~Q---e~v~E~~~L~~Ll 172 (342)
T KOG2160|consen 101 EDALDNLEELVEDID-NANDLISLGGLVPLLGYLENS----DAELRELAARVIGTAVQNNPKSQ---EQVIELGALSKLL 172 (342)
T ss_pred HHHHHHHHHHHHhhh-hHHhHhhccCHHHHHHHhcCC----cHHHHHHHHHHHHHHHhcCHHHH---HHHHHcccHHHHH
Confidence 3467777764 2 234556777778888988874 78998899999999999998654 4444444789999
Q ss_pred hhccCCC-hHHHHhHHHHHHHHhhccCCh
Q psy1379 82 MHLQNQS-PIIQQNAIALINALFIKAEPS 109 (446)
Q Consensus 82 ~~L~~~d-~~iq~nalaLiNaL~~~a~~~ 109 (446)
..|.+.+ .....+||--|-+|+|+-.+.
T Consensus 173 ~~ls~~~~~~~r~kaL~AissLIRn~~~g 201 (342)
T KOG2160|consen 173 KILSSDDPNTVRTKALFAISSLIRNNKPG 201 (342)
T ss_pred HHHccCCCchHHHHHHHHHHHHHhcCcHH
Confidence 9998744 444588999999999986653
No 19
>PF11864 DUF3384: Domain of unknown function (DUF3384); InterPro: IPR024584 This entry represents the N-terminal domain of tuberin which is functionally uncharacterised.
Probab=65.55 E-value=14 Score=39.77 Aligned_cols=105 Identities=18% Similarity=0.275 Sum_probs=72.4
Q ss_pred hcCCcccccC--------chHHHHHHHHhh--cCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhccc--chhHHh
Q psy1379 14 DHGIVSWNIL--------ETVFIKTVADHV--NNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHL--TLTNLV 81 (446)
Q Consensus 14 e~~~~~W~~l--------~~~fI~ki~~~v--~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v--~~~~lv 81 (446)
+.....|+++ ....|.-..+++ .......+++++|+|+.+|+.++-++... |...|.-.. -++.+.
T Consensus 230 ~l~~~~w~~m~nL~~S~~g~~~i~~L~~iL~~~~~~~~~~~~~lRGAv~~l~~ll~~~~~~--~~~~l~~~~~~vl~sl~ 307 (464)
T PF11864_consen 230 SLCKPSWRTMRNLLKSHLGHSAIRTLCDILRSPDPQNKRDINVLRGAVFFLRMLLWGSGEQ--GYPSLPFSPSSVLPSLL 307 (464)
T ss_pred ccchhHHHHHHHHHcCccHHHHHHHHHHHHcccCccccccHHHHhhHHHHHHHHHhccccC--CcceecccHHHHHHHHH
Confidence 4444467754 356677788888 44333468999999999999998887321 224443333 356677
Q ss_pred hhccCCChHHHHhHHHHHHHHh-hcc----CChhhHHHHHHhhh
Q psy1379 82 MHLQNQSPIIQQNAIALINALF-IKA----EPSKRKVISATMCS 120 (446)
Q Consensus 82 ~~L~~~d~~iq~nalaLiNaL~-~~a----~~~~~~~~~~~L~~ 120 (446)
.-++..+..+-...+.++++|+ .+- .+..|..+.+.+..
T Consensus 308 ~al~~~~~~v~~eIl~~i~~ll~~~~~~~l~~~~W~~~~~i~~~ 351 (464)
T PF11864_consen 308 NALKSNSPRVDYEILLLINRLLDGKYGRELSEEDWDIILDIIEE 351 (464)
T ss_pred HHHhCCCCeehHHHHHHHHHHHhHhhhhhhcccCchHHHHHHHH
Confidence 7777888888889999999999 332 24578877776665
No 20
>PF04826 Arm_2: Armadillo-like; InterPro: IPR006911 This entry consists of mammalian proteins of unknown function.
Probab=63.29 E-value=1.6e+02 Score=29.18 Aligned_cols=113 Identities=13% Similarity=0.132 Sum_probs=71.7
Q ss_pred CchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhhhccCCChHHHHhHHHHHHHH
Q psy1379 23 LETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVMHLQNQSPIIQQNAIALINAL 102 (446)
Q Consensus 23 l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~~L~~~d~~iq~nalaLiNaL 102 (446)
+++.-+++.+.++... .|+.|.+.++..+......+. .. ..+.+-=.++.+...|...++.++.+|+..+|.|
T Consensus 9 l~~~~l~~Ll~lL~~t---~dp~i~e~al~al~n~aaf~~-nq---~~Ir~~Ggi~lI~~lL~~p~~~vr~~AL~aL~Nl 81 (254)
T PF04826_consen 9 LEAQELQKLLCLLEST---EDPFIQEKALIALGNSAAFPF-NQ---DIIRDLGGISLIGSLLNDPNPSVREKALNALNNL 81 (254)
T ss_pred cCHHHHHHHHHHHhcC---CChHHHHHHHHHHHhhccChh-HH---HHHHHcCCHHHHHHHcCCCChHHHHHHHHHHHhc
Confidence 4467779999999986 699999999999987643332 21 2333322477888999999999999998777765
Q ss_pred hhccCChhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhcchHHHHHHHHHHHH
Q psy1379 103 FIKAEPSKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQLYVLQTLTLGLLEQ 160 (446)
Q Consensus 103 ~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~L~~~Q~l~l~~Le~ 160 (446)
+.+.+-+..++. ....|.+.+. +.+++ .+.|...++.|..
T Consensus 82 ---s~~~en~~~Ik~-----~i~~Vc~~~~---s~~ln-------s~~Q~agLrlL~n 121 (254)
T PF04826_consen 82 ---SVNDENQEQIKM-----YIPQVCEETV---SSPLN-------SEVQLAGLRLLTN 121 (254)
T ss_pred ---CCChhhHHHHHH-----HHHHHHHHHh---cCCCC-------CHHHHHHHHHHHc
Confidence 333333333332 2233434232 12333 5666666777755
No 21
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=58.09 E-value=1.3e+02 Score=26.55 Aligned_cols=75 Identities=11% Similarity=0.119 Sum_probs=46.1
Q ss_pred chhHHhhhccCCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhcchHHHHHHH
Q psy1379 76 TLTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQLYVLQTLTL 155 (446)
Q Consensus 76 ~~~~lv~~L~~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~L~~~Q~l~l 155 (446)
....|-++|++.++..|..||.|+.+|+.++++.=..++.+ +.+=..+.+ ++. ..... =...+...+
T Consensus 38 a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s----~~fl~~l~~-l~~-~~~~~-------~~~Vk~kil 104 (133)
T cd03561 38 AARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVAD----KEFLLELVK-IAK-NSPKY-------DPKVREKAL 104 (133)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhh----HHHHHHHHH-HhC-CCCCC-------CHHHHHHHH
Confidence 34567788889999999999999999999998633333222 222223333 442 21011 134566667
Q ss_pred HHHHHHhc
Q psy1379 156 GLLEQRMN 163 (446)
Q Consensus 156 ~~Le~r~~ 163 (446)
..+..|..
T Consensus 105 ~ll~~W~~ 112 (133)
T cd03561 105 ELILAWSE 112 (133)
T ss_pred HHHHHHHH
Confidence 77777665
No 22
>KOG3036|consensus
Probab=58.08 E-value=41 Score=33.75 Aligned_cols=119 Identities=13% Similarity=0.276 Sum_probs=77.5
Q ss_pred HHHHHHHhc-C------CcccccCc--hHHHHHHHHh---hcCCC-CCCCchhhhHHHHHHHHHhhCCCCCccchhhhhc
Q psy1379 7 LSFVELMDH-G------IVSWNILE--TVFIKTVADH---VNNPN-PVPEKEIVQASLSILESIALNSVGKFSQFSQVEN 73 (446)
Q Consensus 7 ~a~~~Lme~-~------~~~W~~l~--~~fI~ki~~~---v~~~~-~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~ 73 (446)
+|++||-+- . .+=|..+. .....+|+.. ++..+ .+...|=+=.||++|-.+++++.++. ..+..
T Consensus 43 ~aL~ELskkre~~~dlA~~lW~s~g~~~~LLqEivaiYp~l~p~~l~~~qsnRVcnaL~LlQcvASHpdTr~---~FL~A 119 (293)
T KOG3036|consen 43 MALLELSKKREPFPDLAPMLWHSFGTMVALLQEIVAIYPSLSPPTLTPAQSNRVCNALALLQCVASHPDTRR---AFLRA 119 (293)
T ss_pred HHHHHHHHhccCCccccHHHHHhcchHHHHHHHHHhcccccCCCCCCccccchHHHHHHHHHHHhcCcchHH---HHHHc
Confidence 466666652 1 12387764 4445555543 22221 11223444569999999999999887 77889
Q ss_pred ccch---hHHhhhcc-CCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHHhhhc
Q psy1379 74 HLTL---TNLVMHLQ-NQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQ 133 (446)
Q Consensus 74 ~v~~---~~lv~~L~-~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~ 133 (446)
.|++ +=|..-.. .+.+-+..-||+.|+||..... ++.+..|-..+|.---++ +|.
T Consensus 120 ~iPlylYpfL~Tt~~~r~fEyLRLtsLGVIgaLvk~dd----~eVi~fLl~TeIVPlCLr-ime 178 (293)
T KOG3036|consen 120 HIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKNDD----QEVIRFLLTTEIVPLCLR-IME 178 (293)
T ss_pred cChhhhHHhhhccccCCchHHHhHHHHHHHHHHHhcCc----HHHHHHHHHhhhHHHHHH-HHh
Confidence 9983 44444444 4888899999999999996533 346777777777766666 665
No 23
>PF11698 V-ATPase_H_C: V-ATPase subunit H; InterPro: IPR011987 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents the C-terminal domain of subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=57.92 E-value=17 Score=32.12 Aligned_cols=74 Identities=7% Similarity=0.152 Sum_probs=50.8
Q ss_pred HHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhhhccCCChHHHHhHHHHHHHHhhc
Q psy1379 26 VFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVMHLQNQSPIIQQNAIALINALFIK 105 (446)
Q Consensus 26 ~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~~L~~~d~~iq~nalaLiNaL~~~ 105 (446)
..+++.+.++.++ .|+.++..|..=|..+|-+-|.+. .+|.+-=.-+.+.+.+...|++++-+||--+-.||.+
T Consensus 43 ~llk~L~~lL~~s---~d~~~laVac~Dig~~vr~~p~gr---~ii~~lg~K~~vM~Lm~h~d~eVr~eAL~avQklm~~ 116 (119)
T PF11698_consen 43 ELLKKLIKLLDKS---DDPTTLAVACHDIGEFVRHYPNGR---NIIEKLGAKERVMELMNHEDPEVRYEALLAVQKLMVN 116 (119)
T ss_dssp HHHHHHHHHH-SH---HHHHHHHHHHHHHHHHHHH-GGGH---HHHHHHSHHHHHHHHTS-SSHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHccC---CCcceeehhhcchHHHHHHChhHH---HHHHhcChHHHHHHHhcCCCHHHHHHHHHHHHHHHHh
Confidence 4577788888664 477777788888888888877543 5553333345556677778999999998888887764
No 24
>PF05804 KAP: Kinesin-associated protein (KAP)
Probab=56.53 E-value=70 Score=36.57 Aligned_cols=130 Identities=19% Similarity=0.255 Sum_probs=86.5
Q ss_pred HHHHHhcCCcccccCchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccc-hhHHhhhccC-
Q psy1379 9 FVELMDHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLT-LTNLVMHLQN- 86 (446)
Q Consensus 9 ~~~Lme~~~~~W~~l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~-~~~lv~~L~~- 86 (446)
+.++=.|+. .=...-.+||..++..+... .+-...=-+|+||.++...+. .| ..+-++-. ++-|...|+.
T Consensus 474 IRNiS~h~~-~~k~~f~~~i~~L~~~v~~~---~~ee~~vE~LGiLaNL~~~~l-d~---~~ll~~~~llp~L~~~L~~g 545 (708)
T PF05804_consen 474 IRNISQHDG-PLKELFVDFIGDLAKIVSSG---DSEEFVVECLGILANLTIPDL-DW---AQLLQEYNLLPWLKDLLKPG 545 (708)
T ss_pred HHHHHhcCc-hHHHHHHHHHHHHHHHhhcC---CcHHHHHHHHHHHHhcccCCc-CH---HHHHHhCCHHHHHHHHhCCC
Confidence 344445542 22233467888888888664 356677779999999976543 33 55554544 4556666654
Q ss_pred -CChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHHhhhcCCCCCCchhhhhc-chHHHHHHH
Q psy1379 87 -QSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILTSVLQPSGGQVGAEMAHQ-LYVLQTLTL 155 (446)
Q Consensus 87 -~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~~ii~~~~~~~~~e~ah~-L~~~Q~l~l 155 (446)
++.++++.++.++=++-.+ ++-+..|.+.|+..+++. +++ + .+=++|+.-| +|+|+.+..
T Consensus 546 ~~~dDl~LE~Vi~~gtla~d------~~~A~lL~~sgli~~Li~-LL~-~-kqeDdE~VlQil~~f~~ll~ 607 (708)
T PF05804_consen 546 ASEDDLLLEVVILLGTLASD------PECAPLLAKSGLIPTLIE-LLN-A-KQEDDEIVLQILYVFYQLLF 607 (708)
T ss_pred CCChHHHHHHHHHHHHHHCC------HHHHHHHHhCChHHHHHH-HHH-h-hCchHHHHHHHHHHHHHHHc
Confidence 6778999998888776653 455777888899988888 664 3 3347888765 477777743
No 25
>PF04826 Arm_2: Armadillo-like; InterPro: IPR006911 This entry consists of mammalian proteins of unknown function.
Probab=54.50 E-value=71 Score=31.72 Aligned_cols=73 Identities=15% Similarity=0.177 Sum_probs=55.3
Q ss_pred chHHHHHHHHHhhcCCCCCCchHHHHHHHHHHhhhhhcCchhhhHHhhhcchhhhhhhcccCChHHHHhHHHHHHHH
Q psy1379 332 LETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQVENHLTLTNLVMHLQNQSPIIQQNAIALINAL 408 (446)
Q Consensus 332 l~~~Fikki~~~vn~~~~~~d~~il~~~l~iLE~~vl~s~~~~~~v~~Ev~l~~l~~~lq~~~~~~~~~a~al~nal 408 (446)
++...+++++.++... -|+.|.+.++..|-+..-.+. .+..+.+-=.++-+...|...++.++.+|+-.++.|
T Consensus 9 l~~~~l~~Ll~lL~~t---~dp~i~e~al~al~n~aaf~~-nq~~Ir~~Ggi~lI~~lL~~p~~~vr~~AL~aL~Nl 81 (254)
T PF04826_consen 9 LEAQELQKLLCLLEST---EDPFIQEKALIALGNSAAFPF-NQDIIRDLGGISLIGSLLNDPNPSVREKALNALNNL 81 (254)
T ss_pred cCHHHHHHHHHHHhcC---CChHHHHHHHHHHHhhccChh-HHHHHHHcCCHHHHHHHcCCCChHHHHHHHHHHHhc
Confidence 5566779999999875 488999999999998765553 344444433477778888889999999997777765
No 26
>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=54.01 E-value=29 Score=36.97 Aligned_cols=83 Identities=16% Similarity=0.250 Sum_probs=61.7
Q ss_pred hhHHHHHHHHHhcCCcccccCchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhh
Q psy1379 3 AHCLLSFVELMDHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVM 82 (446)
Q Consensus 3 ay~L~a~~~Lme~~~~~W~~l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~ 82 (446)
+.||+++..+.... +-+.++.-|..+++.. ++.|-+.|.--+.++...+|+. +..+ -++.+.+
T Consensus 97 ~lAL~~l~~i~~~~------~~~~l~~~v~~ll~~~----~~~VRk~A~~~l~~i~~~~p~~------~~~~-~~~~l~~ 159 (526)
T PF01602_consen 97 GLALRTLSNIRTPE------MAEPLIPDVIKLLSDP----SPYVRKKAALALLKIYRKDPDL------VEDE-LIPKLKQ 159 (526)
T ss_dssp HHHHHHHHHH-SHH------HHHHHHHHHHHHHHSS----SHHHHHHHHHHHHHHHHHCHCC------HHGG-HHHHHHH
T ss_pred HHHHhhhhhhcccc------hhhHHHHHHHHHhcCC----chHHHHHHHHHHHHHhccCHHH------HHHH-HHHHHhh
Confidence 56777777776443 2466778888888874 5788887777777787776643 3443 3677888
Q ss_pred hccCCChHHHHhHHHHHHHH
Q psy1379 83 HLQNQSPIIQQNAIALINAL 102 (446)
Q Consensus 83 ~L~~~d~~iq~nalaLiNaL 102 (446)
.|.+.|+.++.+|+.++..+
T Consensus 160 lL~d~~~~V~~~a~~~l~~i 179 (526)
T PF01602_consen 160 LLSDKDPSVVSAALSLLSEI 179 (526)
T ss_dssp HTTHSSHHHHHHHHHHHHHH
T ss_pred hccCCcchhHHHHHHHHHHH
Confidence 88999999999999999999
No 27
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=52.98 E-value=89 Score=28.82 Aligned_cols=86 Identities=17% Similarity=0.317 Sum_probs=64.7
Q ss_pred HHHHHhcCCcccccCchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhhhccCCC
Q psy1379 9 FVELMDHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVMHLQNQS 88 (446)
Q Consensus 9 ~~~Lme~~~~~W~~l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~~L~~~d 88 (446)
+..+-|.. +-+..+=+.++..+...+.. +++.|=+.|+-+|..++++..-+ ++..+ +..++..|...|
T Consensus 9 i~~l~DL~-~r~~~~ve~~~~~l~~~L~D----~~~~VR~~al~~Ls~Li~~d~ik------~k~~l-~~~~l~~l~D~~ 76 (178)
T PF12717_consen 9 IIALGDLC-IRYPNLVEPYLPNLYKCLRD----EDPLVRKTALLVLSHLILEDMIK------VKGQL-FSRILKLLVDEN 76 (178)
T ss_pred HHHHHHHH-HhCcHHHHhHHHHHHHHHCC----CCHHHHHHHHHHHHHHHHcCcee------ehhhh-hHHHHHHHcCCC
Confidence 33444543 35566667788888888887 47899999999999999875422 33332 366777889999
Q ss_pred hHHHHhHHHHHHHHhhcc
Q psy1379 89 PIIQQNAIALINALFIKA 106 (446)
Q Consensus 89 ~~iq~nalaLiNaL~~~a 106 (446)
++|+..|..++..+..+-
T Consensus 77 ~~Ir~~A~~~~~e~~~~~ 94 (178)
T PF12717_consen 77 PEIRSLARSFFSELLKKR 94 (178)
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 999999999999999983
No 28
>PF08045 CDC14: Cell division control protein 14, SIN component; InterPro: IPR012535 Cdc14 is a component of the septation initiation network (SIN) and is required for the localisation and activity of Sid1. Sid1 is a protein kinase that localises asymmetrically to one spindle pole body (SPB) in anaphase disappears prior to cell separation [], [].
Probab=51.70 E-value=91 Score=31.21 Aligned_cols=68 Identities=13% Similarity=0.274 Sum_probs=57.6
Q ss_pred CchHHHHHHHHHHhhhhhcCchhhhHHhhhcchhhhhhhcc-cCChHHHHhHHHHHHHHhccCCchhHH
Q psy1379 351 PEKEIVQASLSILESIALNSVGKFSQVENHLTLTNLVMHLQ-NQSPIIQQNAIALINALFIKAEPSKRK 418 (446)
Q Consensus 351 ~d~~il~~~l~iLE~~vl~s~~~~~~v~~Ev~l~~l~~~lq-~~~~~~~~~a~al~nal~~~a~~~~r~ 418 (446)
.+...+..||.+||.+++-.|.-+....++-.++-++..|. ...+.+|..++-.+-+.+.+.++..|.
T Consensus 103 ~~~~li~~aL~vLQGl~LLHp~Sr~lF~r~~~m~lll~LL~~~~~~~i~~a~L~tLv~iLld~p~N~r~ 171 (257)
T PF08045_consen 103 SNDSLIALALRVLQGLCLLHPPSRKLFHREQNMELLLDLLSPSNPPAIQSACLDTLVCILLDSPENQRD 171 (257)
T ss_pred chhHHHHHHHHHHHHHHHcCchHHHHHhhhhhHHHHHHHhccCCCchHHHHHHHHHHHHHHcChHHHHH
Confidence 34455677999999999988877888899999999999994 467899999999999999999887775
No 29
>PF08045 CDC14: Cell division control protein 14, SIN component; InterPro: IPR012535 Cdc14 is a component of the septation initiation network (SIN) and is required for the localisation and activity of Sid1. Sid1 is a protein kinase that localises asymmetrically to one spindle pole body (SPB) in anaphase disappears prior to cell separation [], [].
Probab=51.10 E-value=1.1e+02 Score=30.51 Aligned_cols=63 Identities=14% Similarity=0.282 Sum_probs=49.3
Q ss_pred hhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhhhcc-CCChHHHHhHHHHHHHHhhccCChhh
Q psy1379 46 IVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVMHLQ-NQSPIIQQNAIALINALFIKAEPSKR 111 (446)
Q Consensus 46 i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~~L~-~~d~~iq~nalaLiNaL~~~a~~~~~ 111 (446)
.+-.||.+|+.+++--|..- ....++...+.++..|+ ..++.+|..+|-.+-+++.+.+..-|
T Consensus 107 li~~aL~vLQGl~LLHp~Sr---~lF~r~~~m~lll~LL~~~~~~~i~~a~L~tLv~iLld~p~N~r 170 (257)
T PF08045_consen 107 LIALALRVLQGLCLLHPPSR---KLFHREQNMELLLDLLSPSNPPAIQSACLDTLVCILLDSPENQR 170 (257)
T ss_pred HHHHHHHHHHHHHHcCchHH---HHHhhhhhHHHHHHHhccCCCchHHHHHHHHHHHHHHcChHHHH
Confidence 34558899999888666554 55667778899999994 57899999999988888888776544
No 30
>PF08167 RIX1: rRNA processing/ribosome biogenesis
Probab=51.05 E-value=45 Score=30.64 Aligned_cols=87 Identities=14% Similarity=0.295 Sum_probs=62.5
Q ss_pred HHhcCCcccccC---chHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccc-------hhHHh
Q psy1379 12 LMDHGIVSWNIL---ETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLT-------LTNLV 81 (446)
Q Consensus 12 Lme~~~~~W~~l---~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~-------~~~lv 81 (446)
+++.+ +||.+ ...|+..+...+..+ ..+.+...|...|..+..... ||+.+.+|+. ++.++
T Consensus 52 ~~~~~--~~e~l~~~~~~W~~~Ll~~L~~~---~~~~~~~~ai~~L~~l~~~~~----~~p~l~Rei~tp~l~~~i~~ll 122 (165)
T PF08167_consen 52 TVEQC--SWEILLSHGSQWLRALLSILEKP---DPPSVLEAAIITLTRLFDLIR----GKPTLTREIATPNLPKFIQSLL 122 (165)
T ss_pred HHHHh--hHHHHHHHHHHHHHHHHHHHcCC---CCHHHHHHHHHHHHHHHHHhc----CCCchHHHHhhccHHHHHHHHH
Confidence 44554 69988 488999999999985 678888999999988876553 5577777764 34455
Q ss_pred hhccCCChHHHHhHHHHHHHHhhccCCh
Q psy1379 82 MHLQNQSPIIQQNAIALINALFIKAEPS 109 (446)
Q Consensus 82 ~~L~~~d~~iq~nalaLiNaL~~~a~~~ 109 (446)
..+++ .....-++..+.+|+.+-+..
T Consensus 123 ~l~~~--~~~~~~~l~~L~~ll~~~ptt 148 (165)
T PF08167_consen 123 QLLQD--SSCPETALDALATLLPHHPTT 148 (165)
T ss_pred HHHhc--cccHHHHHHHHHHHHHHCCcc
Confidence 55543 455556888888888866643
No 31
>PF11588 DUF3243: Protein of unknown function (DUF3243); InterPro: IPR021637 This family of proteins with unknown function includes uncharacterised proteins ymfJ and yflH. The family appears to be restricted to Firmicutes.; PDB: 3D0W_B.
Probab=49.63 E-value=8.4 Score=31.85 Aligned_cols=24 Identities=33% Similarity=0.458 Sum_probs=13.7
Q ss_pred ccCCCCCHHHHHHHHHHHHHhcccc
Q psy1379 164 TKMDPQDQDAHDKIKELRRVAFEID 188 (446)
Q Consensus 164 ~~~d~~~~~h~~~L~~Lw~~a~p~~ 188 (446)
..+||.|+ +++.|++||..+-+++
T Consensus 44 ~~vdP~N~-EerlLkELW~va~e~E 67 (81)
T PF11588_consen 44 KNVDPKNP-EERLLKELWDVADEEE 67 (81)
T ss_dssp T-----SH-HHHHHHHHHHC--HHH
T ss_pred hcCCCCCH-HHHHHHHHHHhCCHHH
Confidence 47799998 4789999999986654
No 32
>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=49.49 E-value=2e+02 Score=27.03 Aligned_cols=112 Identities=15% Similarity=0.236 Sum_probs=59.2
Q ss_pred HHHHHHHHHhcCCcccccCchHHHHHHH---HhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHh
Q psy1379 5 CLLSFVELMDHGIVSWNILETVFIKTVA---DHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLV 81 (446)
Q Consensus 5 ~L~a~~~Lme~~~~~W~~l~~~fI~ki~---~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv 81 (446)
+|+-+..+...+ +. ....+.|+..+- ..+....+.....|.+.|+..+..++..-... |... -+.-++.|+
T Consensus 27 al~~L~~l~~~~-~~-~~~~~~~~~~l~~~~~~i~~~l~d~Rs~v~~~A~~~l~~l~~~l~~~---~~~~-~~~~l~~Ll 100 (228)
T PF12348_consen 27 ALQKLRSLIKGN-AP-EDFPPDFVECLRQLLDAIIKQLSDLRSKVSKTACQLLSDLARQLGSH---FEPY-ADILLPPLL 100 (228)
T ss_dssp HHHHHHHHHHH--B------HHHHHHHH---HHHHH-S-HH---HHHHHHHHHHHHHHHHGGG---GHHH-HHHHHHHHH
T ss_pred HHHHHHHHHHcC-Cc-cccHHHHHHHHHHhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhHh---HHHH-HHHHHHHHH
Confidence 455555555554 11 122344444333 33333322345778888999998887665422 2322 222368999
Q ss_pred hhccCCChHHHHhHHHHHHHHhhccC-Chh--hHHHHHHhhhhh
Q psy1379 82 MHLQNQSPIIQQNAIALINALFIKAE-PSK--RKVISATMCSKQ 122 (446)
Q Consensus 82 ~~L~~~d~~iq~nalaLiNaL~~~a~-~~~--~~~~~~~L~~~~ 122 (446)
.++.++...+...|...+.+++..++ ..+ ...+......++
T Consensus 101 ~~~~~~~~~i~~~a~~~L~~i~~~~~~~~~~~~~~l~~~~~~Kn 144 (228)
T PF12348_consen 101 KKLGDSKKFIREAANNALDAIIESCSYSPKILLEILSQGLKSKN 144 (228)
T ss_dssp HGGG---HHHHHHHHHHHHHHHTTS-H--HHHHHHHHHHTT-S-
T ss_pred HHHccccHHHHHHHHHHHHHHHHHCCcHHHHHHHHHHHHHhCCC
Confidence 99999999999999999999999988 433 234444455553
No 33
>PF03224 V-ATPase_H_N: V-ATPase subunit H; InterPro: IPR004908 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=47.99 E-value=63 Score=32.60 Aligned_cols=67 Identities=13% Similarity=0.235 Sum_probs=50.4
Q ss_pred chHHHHHHHHHHhhhhhcCchhhhHHhh------hcchhhhhhhcccCChHHHHhHHHHHHHHhccCCchhHH
Q psy1379 352 EKEIVQASLSILESIALNSVGKFSQVEN------HLTLTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRK 418 (446)
Q Consensus 352 d~~il~~~l~iLE~~vl~s~~~~~~v~~------Ev~l~~l~~~lq~~~~~~~~~a~al~nal~~~a~~~~r~ 418 (446)
+..+++-.|..+..++..++...+.+.. +.++..++.++...|+.++..|.-++..|+..++.....
T Consensus 70 ~~d~v~yvL~li~dll~~~~~~~~~~~~~~~~~~~~~~~~fl~ll~~~D~~i~~~a~~iLt~Ll~~~~~~~~~ 142 (312)
T PF03224_consen 70 NDDTVQYVLTLIDDLLSDDPSRVELFLELAKQDDSDPYSPFLKLLDRNDSFIQLKAAFILTSLLSQGPKRSEK 142 (312)
T ss_dssp -HHHHHHHHHHHHHHHH-SSSSHHHHHHHHH-TTH--HHHHHHH-S-SSHHHHHHHHHHHHHHHTSTTT--HH
T ss_pred cHHHHHHHHHHHHHHHhcCHHHHHHHHHhcccccchhHHHHHHHhcCCCHHHHHHHHHHHHHHHHcCCccccc
Confidence 5679999999999988888765555543 347899999999999999999999999999999886555
No 34
>PF06367 Drf_FH3: Diaphanous FH3 Domain; InterPro: IPR010472 Formin homology (FH) proteins play a crucial role in the reorganisation of the actin cytoskeleton, which mediates various functions of the cell cortex including motility, adhesion, and cytokinesis []. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains []. The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain (IPR003104 from INTERPRO) is required to inhibit actin polymerisation. The FH3 domain is less well conserved and is required for directing formins to the correct intracellular location, such the mitotic spindle [], or the projection tip during conjugation []. In addition, some formins can contain a GTPase-binding domain (GBD) (IPR010473 from INTERPRO) required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD). This entry represents the FH3 domain.; GO: 0003779 actin binding, 0016043 cellular component organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=47.71 E-value=40 Score=31.40 Aligned_cols=62 Identities=16% Similarity=0.193 Sum_probs=42.2
Q ss_pred hhhHHhhh-cchhhhhhhcc---cCChHHHHhHHHHHHHHhccCCc-hhHHHhhHhhhhhhhHHHHH
Q psy1379 373 KFSQVENH-LTLTNLVMHLQ---NQSPIIQQNAIALINALFIKAEP-SKRKVISATMCSKQVRNAIL 434 (446)
Q Consensus 373 ~~~~v~~E-v~l~~l~~~lq---~~~~~~~~~a~al~nal~~~a~~-~~r~~~~~~l~~~~~r~~i~ 434 (446)
.|..+.+| ..++.++..+. ..+....+.+|.+||+|...+++ ..|-.+-..+...++..++-
T Consensus 12 ~~~~~~~e~~RF~~lv~~l~~~~~~~~e~~~~~l~~IN~li~~~~d~~~R~~lr~e~~~~GL~~il~ 78 (197)
T PF06367_consen 12 NFKEVKGERGRFQSLVGALESVDSSDIEYKTACLQFINSLINSPEDLNFRVHLRNEFERLGLLDILE 78 (197)
T ss_dssp HHHHHHT-S-TTHHHHHHCS--TTS-HHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTTHHHHHH
T ss_pred HHHHHhCCcccHHHHHHHHHccccCcHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHCCcHHHHH
Confidence 35555554 44788888887 37789999999999999999977 55656666666666555443
No 35
>PF03224 V-ATPase_H_N: V-ATPase subunit H; InterPro: IPR004908 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=45.22 E-value=63 Score=32.57 Aligned_cols=71 Identities=14% Similarity=0.282 Sum_probs=50.3
Q ss_pred CCchhhhHHHHHHHHHhhCCCCCccchhhhh---cccchhHHhhhccCCChHHHHhHHHHHHHHhhccCChhhH
Q psy1379 42 PEKEIVQASLSILESIALNSVGKFSQFSQVE---NHLTLTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRK 112 (446)
Q Consensus 42 ~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~---~~v~~~~lv~~L~~~d~~iq~nalaLiNaL~~~a~~~~~~ 112 (446)
.+..+++-.|..+..++...+..+.-|.... +.-++..++++++..|.-++.-|..++-.|+..++.....
T Consensus 69 ~~~d~v~yvL~li~dll~~~~~~~~~~~~~~~~~~~~~~~~fl~ll~~~D~~i~~~a~~iLt~Ll~~~~~~~~~ 142 (312)
T PF03224_consen 69 SNDDTVQYVLTLIDDLLSDDPSRVELFLELAKQDDSDPYSPFLKLLDRNDSFIQLKAAFILTSLLSQGPKRSEK 142 (312)
T ss_dssp --HHHHHHHHHHHHHHHH-SSSSHHHHHHHHH-TTH--HHHHHHH-S-SSHHHHHHHHHHHHHHHTSTTT--HH
T ss_pred CcHHHHHHHHHHHHHHHhcCHHHHHHHHHhcccccchhHHHHHHHhcCCCHHHHHHHHHHHHHHHHcCCccccc
Confidence 4688899999999999999987652222222 2347899999999999999999999999999987764433
No 36
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=43.02 E-value=1.7e+02 Score=26.02 Aligned_cols=37 Identities=24% Similarity=0.337 Sum_probs=30.9
Q ss_pred hhhhhhhcccCChHHHHhHHHHHHHHhccCCchhHHH
Q psy1379 383 LTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKV 419 (446)
Q Consensus 383 l~~l~~~lq~~~~~~~~~a~al~nal~~~a~~~~r~~ 419 (446)
+.-|-.+|+..||..|.+|+.|+.++..+|.+.=+.+
T Consensus 44 ~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~e 80 (140)
T PF00790_consen 44 ARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHRE 80 (140)
T ss_dssp HHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHH
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence 3347788888999999999999999999998765554
No 37
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=41.49 E-value=97 Score=28.07 Aligned_cols=58 Identities=12% Similarity=0.211 Sum_probs=43.9
Q ss_pred chHHHHHHHHHHhhhhhcCchh-hhHHhhhcchhhhhhhccc-CChHHHHhHHHHHHHHh
Q psy1379 352 EKEIVQASLSILESIALNSVGK-FSQVENHLTLTNLVMHLQN-QSPIIQQNAIALINALF 409 (446)
Q Consensus 352 d~~il~~~l~iLE~~vl~s~~~-~~~v~~Ev~l~~l~~~lq~-~~~~~~~~a~al~nal~ 409 (446)
|+.+.-+||.+||..|-|--.. +..|...==+++|...+.. .++.++.+.+.||.+.-
T Consensus 50 n~~v~l~AL~LLe~~vkNCG~~fh~evask~Fl~eL~kl~~~~~~~~Vk~kil~li~~W~ 109 (144)
T cd03568 50 DPNVQLRALTLLDACAENCGKRFHQEVASRDFTQELKKLINDRVHPTVKEKLREVVKQWA 109 (144)
T ss_pred CHHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHhcccCCHHHHHHHHHHHHHHH
Confidence 6789999999999999986433 3344333236667777777 89999999999999863
No 38
>KOG1293|consensus
Probab=40.58 E-value=51 Score=37.00 Aligned_cols=99 Identities=14% Similarity=0.202 Sum_probs=76.3
Q ss_pred hhHHHHHHHH-HhcCCcccccCchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHh
Q psy1379 3 AHCLLSFVEL-MDHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLV 81 (446)
Q Consensus 3 ay~L~a~~~L-me~~~~~W~~l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv 81 (446)
+-+|.|+.+| ||++..-=..+...+|+++.+++.+ ++.|+.+.++-.|..++-++.... +|+..+ .|+-.-++
T Consensus 437 ~~~lgai~NlVmefs~~kskfl~~ngId~l~s~~~~----~~~n~r~~~~~~Lr~l~f~~de~~-k~~~~~-ki~a~~i~ 510 (678)
T KOG1293|consen 437 GITLGAICNLVMEFSNLKSKFLRNNGIDILESMLTD----PDFNSRANSLWVLRHLMFNCDEEE-KFQLLA-KIPANLIL 510 (678)
T ss_pred HHHHHHHHHHHhhcccHHHHHHHcCcHHHHHHHhcC----CCchHHHHHHHHHHHHHhcchHHH-HHHHHH-HhhHHHHH
Confidence 4578888884 6887655556788899999999987 589999999999999999997654 333332 24444455
Q ss_pred hhccCCChHHHHhHHHHHHHHhhccC
Q psy1379 82 MHLQNQSPIIQQNAIALINALFIKAE 107 (446)
Q Consensus 82 ~~L~~~d~~iq~nalaLiNaL~~~a~ 107 (446)
......|.++|..+++|+-.|.-.+.
T Consensus 511 ~l~nd~d~~Vqeq~fqllRNl~c~~~ 536 (678)
T KOG1293|consen 511 DLINDPDWAVQEQCFQLLRNLTCNSR 536 (678)
T ss_pred HHHhCCCHHHHHHHHHHHHHhhcCcH
Confidence 66677999999999999988887644
No 39
>KOG0166|consensus
Probab=39.70 E-value=4e+02 Score=29.47 Aligned_cols=120 Identities=14% Similarity=0.149 Sum_probs=72.7
Q ss_pred hhhHHHHHHHHHhcCCccccc-CchHHHHHHHHhhcCCCCCCCchhh-----------------------hHHHHHHHHH
Q psy1379 2 LAHCLLSFVELMDHGIVSWNI-LETVFIKTVADHVNNPNPVPEKEIV-----------------------QASLSILESI 57 (446)
Q Consensus 2 Lay~L~a~~~Lme~~~~~W~~-l~~~fI~ki~~~v~~~~~~~~~~i~-----------------------~~alsIL~~~ 57 (446)
|+.|..|+..|-|++.-.-.. ++...+.|++.++.+. .++|. .++|..|..+
T Consensus 254 l~Da~WAlsyLsdg~ne~iq~vi~~gvv~~LV~lL~~~----~~~v~~PaLRaiGNIvtG~d~QTq~vi~~~~L~~l~~l 329 (514)
T KOG0166|consen 254 LTDACWALSYLTDGSNEKIQMVIDAGVVPRLVDLLGHS----SPKVVTPALRAIGNIVTGSDEQTQVVINSGALPVLSNL 329 (514)
T ss_pred HHHHHHHHHHHhcCChHHHHHHHHccchHHHHHHHcCC----CcccccHHHhhccceeeccHHHHHHHHhcChHHHHHHH
Confidence 456677777777765411111 3566778888988885 34444 4455555555
Q ss_pred hhCCCCCc-----------------cchhhhhcccchhHHhhhccCCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhh
Q psy1379 58 ALNSVGKF-----------------SQFSQVENHLTLTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCS 120 (446)
Q Consensus 58 V~~s~~~y-----------------~gf~~v~~~v~~~~lv~~L~~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~ 120 (446)
..+++... +.-+.|-..=-++.|++.|+++|..+|.-|.=-|-.+...+. ++-+.+|-+
T Consensus 330 l~~s~~~~ikkEAcW~iSNItAG~~~qiqaVida~l~p~Li~~l~~~ef~~rKEAawaIsN~ts~g~----~~qi~yLv~ 405 (514)
T KOG0166|consen 330 LSSSPKESIKKEACWTISNITAGNQEQIQAVIDANLIPVLINLLQTAEFDIRKEAAWAISNLTSSGT----PEQIKYLVE 405 (514)
T ss_pred hccCcchhHHHHHHHHHHHhhcCCHHHHHHHHHcccHHHHHHHHhccchHHHHHHHHHHHhhcccCC----HHHHHHHHH
Confidence 55444321 011112222236899999999999999885544444444443 556888888
Q ss_pred hhhHHHHHH
Q psy1379 121 KQVRNAILT 129 (446)
Q Consensus 121 ~~~r~~v~~ 129 (446)
.|+.+.+..
T Consensus 406 ~giI~plcd 414 (514)
T KOG0166|consen 406 QGIIKPLCD 414 (514)
T ss_pred cCCchhhhh
Confidence 888887765
No 40
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=38.64 E-value=3.3e+02 Score=30.34 Aligned_cols=39 Identities=23% Similarity=0.414 Sum_probs=23.4
Q ss_pred chHHHHHHHHHHHHHh--cccCCCCCHHHHHHHHHHHHHhcc
Q psy1379 147 LYVLQTLTLGLLEQRM--NTKMDPQDQDAHDKIKELRRVAFE 186 (446)
Q Consensus 147 L~~~Q~l~l~~Le~r~--~~~~d~~~~~h~~~L~~Lw~~a~p 186 (446)
.--.|.| +..+.+.. ..++|++|+++-+.+-.-=..|.|
T Consensus 214 ~~g~qeL-v~ii~eQa~Ld~~f~~sD~e~Idrli~C~~~Alp 254 (556)
T PF05918_consen 214 IEGRQEL-VDIIEEQADLDQPFDPSDPESIDRLISCLRQALP 254 (556)
T ss_dssp HHHHHHH-HHHHHHHHTTTS---SSSHHHHHHHHHHHHHHGG
T ss_pred hHHHHHH-HHHHHHHhccCCCCCCcCHHHHHHHHHHHHHhhH
Confidence 3445554 77777666 778999999999876554333334
No 41
>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=38.46 E-value=5.5e+02 Score=27.89 Aligned_cols=113 Identities=12% Similarity=0.210 Sum_probs=79.2
Q ss_pred hHHHHHHHHHhcCCccccc-CchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhh
Q psy1379 4 HCLLSFVELMDHGIVSWNI-LETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVM 82 (446)
Q Consensus 4 y~L~a~~~Lme~~~~~W~~-l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~ 82 (446)
.+|..+.++.+|..-.=+. .+.+++.-|+..+.. ++.+|...|..+|..+..++. |.+.+.+.-....|..
T Consensus 96 l~l~~l~~~~~~~~~~~~~~~~~~l~~~i~~~L~~----~d~~Va~~A~~~L~~l~~~~~----~~~~l~~~~~~~~L~~ 167 (503)
T PF10508_consen 96 LALKQLGRIARHSEGAAQLLVDNELLPLIIQCLRD----PDLSVAKAAIKALKKLASHPE----GLEQLFDSNLLSKLKS 167 (503)
T ss_pred HHHHHHHHHhcCCHHHHHHhcCccHHHHHHHHHcC----CcHHHHHHHHHHHHHHhCCch----hHHHHhCcchHHHHHH
Confidence 4566666776664211222 467788888888876 589999999999999987664 3466655444777777
Q ss_pred hccCCChHHHHhHHHHHHHHhhccCChhhHHHHHHhhhhhhHHHHHH
Q psy1379 83 HLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAILT 129 (446)
Q Consensus 83 ~L~~~d~~iq~nalaLiNaL~~~a~~~~~~~~~~~L~~~~~r~~v~~ 129 (446)
.+...+..+....+.++-.+...+. +..+.....|+-..+++
T Consensus 168 l~~~~~~~vR~Rv~el~v~i~~~S~-----~~~~~~~~sgll~~ll~ 209 (503)
T PF10508_consen 168 LMSQSSDIVRCRVYELLVEIASHSP-----EAAEAVVNSGLLDLLLK 209 (503)
T ss_pred HHhccCHHHHHHHHHHHHHHHhcCH-----HHHHHHHhccHHHHHHH
Confidence 7777777888888888888876543 34555556676666666
No 42
>PF11698 V-ATPase_H_C: V-ATPase subunit H; InterPro: IPR011987 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents the C-terminal domain of subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=38.01 E-value=1.4e+02 Score=26.49 Aligned_cols=84 Identities=6% Similarity=0.097 Sum_probs=54.1
Q ss_pred hhhccccccchHHHHHHHHHhhcCCCCCCchHHHHHHHHHHhhhhhcCchhhhHHhhhcchhhhhhhcccCChHHHHhHH
Q psy1379 323 DHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQVENHLTLTNLVMHLQNQSPIIQQNAI 402 (446)
Q Consensus 323 ~~~i~swd~l~~~Fikki~~~vn~~~~~~d~~il~~~l~iLE~~vl~s~~~~~~v~~Ev~l~~l~~~lq~~~~~~~~~a~ 402 (446)
-++..-|+.=...-+++++.++..+ -|+.++..|..=+...|-.-|..+..|++-=-=+.+...+...|+.++-+|+
T Consensus 31 ~ENa~kf~~~~~~llk~L~~lL~~s---~d~~~laVac~Dig~~vr~~p~gr~ii~~lg~K~~vM~Lm~h~d~eVr~eAL 107 (119)
T PF11698_consen 31 RENADKFEENNFELLKKLIKLLDKS---DDPTTLAVACHDIGEFVRHYPNGRNIIEKLGAKERVMELMNHEDPEVRYEAL 107 (119)
T ss_dssp HHHSGGGSSGGGHHHHHHHHHH-SH---HHHHHHHHHHHHHHHHHHH-GGGHHHHHHHSHHHHHHHHTS-SSHHHHHHHH
T ss_pred HHHHHHHHHcccHHHHHHHHHHccC---CCcceeehhhcchHHHHHHChhHHHHHHhcChHHHHHHHhcCCCHHHHHHHH
Confidence 3455555544455678888888554 3888888888888888877776666664443345555566667777777777
Q ss_pred HHHHHHh
Q psy1379 403 ALINALF 409 (446)
Q Consensus 403 al~nal~ 409 (446)
--+..|.
T Consensus 108 ~avQklm 114 (119)
T PF11698_consen 108 LAVQKLM 114 (119)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 6666554
No 43
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=34.94 E-value=1.6e+02 Score=25.85 Aligned_cols=60 Identities=25% Similarity=0.238 Sum_probs=43.9
Q ss_pred chHHHHHHHHHHhhhhhcCch-hhhHHhhhcchhhhhhhccc---CChHHHHhHHHHHHHHhcc
Q psy1379 352 EKEIVQASLSILESIALNSVG-KFSQVENHLTLTNLVMHLQN---QSPIIQQNAIALINALFIK 411 (446)
Q Consensus 352 d~~il~~~l~iLE~~vl~s~~-~~~~v~~Ev~l~~l~~~lq~---~~~~~~~~a~al~nal~~~ 411 (446)
++.+.-+||.+||.+|.|... .+..|...=-+++++..+.. .++.++.+++.++...-..
T Consensus 50 n~~vql~AL~lLd~~vkNcg~~f~~~i~s~~fl~~l~~l~~~~~~~~~~Vk~kil~ll~~W~~~ 113 (133)
T cd03561 50 NPHVQLLALTLLELLVKNCGKPFHLQVADKEFLLELVKIAKNSPKYDPKVREKALELILAWSES 113 (133)
T ss_pred CHHHHHHHHHHHHHHHHhCChHHHHHHhhHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 678999999999999999755 34555542234447666653 6889999999998876543
No 44
>PF12830 Nipped-B_C: Sister chromatid cohesion C-terminus
Probab=31.22 E-value=3.1e+02 Score=25.59 Aligned_cols=87 Identities=20% Similarity=0.283 Sum_probs=65.8
Q ss_pred chHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhhhccCCChHHHHhHHHHHHHHh
Q psy1379 24 ETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVMHLQNQSPIIQQNAIALINALF 103 (446)
Q Consensus 24 ~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~~L~~~d~~iq~nalaLiNaL~ 103 (446)
-..|+++|.++--. ++..+-..|+.+++.++.. ..|-|--.++.||....+.++.+...|..+...|.
T Consensus 6 ~Qryl~~Il~~~~~----~~~~vr~~Al~~l~~il~q--------GLvnP~~cvp~lIAL~ts~~~~ir~~A~~~l~~l~ 73 (187)
T PF12830_consen 6 VQRYLKNILELCLS----SDDSVRLAALQVLELILRQ--------GLVNPKQCVPTLIALETSPNPSIRSRAYQLLKELH 73 (187)
T ss_pred HHHHHHHHHHHHhC----CCHHHHHHHHHHHHHHHhc--------CCCChHHHHhHhhhhhCCCChHHHHHHHHHHHHHH
Confidence 35688888886665 4788989999999977543 23666667899999999999999999999999987
Q ss_pred hccCChhhHHHHHHhhhhhhHHHH
Q psy1379 104 IKAEPSKRKVISATMCSKQVRNAI 127 (446)
Q Consensus 104 ~~a~~~~~~~~~~~L~~~~~r~~v 127 (446)
. +.+.|++.--..|++.+.
T Consensus 74 e-----K~~s~v~~~~~~gi~~af 92 (187)
T PF12830_consen 74 E-----KHESLVESRYSEGIRLAF 92 (187)
T ss_pred H-----HhHHHHHHHHHHHHHHHH
Confidence 6 455666655555666544
No 45
>KOG1077|consensus
Probab=31.08 E-value=1.4e+02 Score=34.31 Aligned_cols=86 Identities=13% Similarity=0.294 Sum_probs=55.6
Q ss_pred HHHHHHhcCCcccccCc-hHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccc-hhHHhhhcc
Q psy1379 8 SFVELMDHGIVSWNILE-TVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLT-LTNLVMHLQ 85 (446)
Q Consensus 8 a~~~Lme~~~~~W~~l~-~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~-~~~lv~~L~ 85 (446)
||.+|..- +=|.+. .+++.||+.+++.+ +-.|+-.+.+.++.+|..-|..| .+ .+-.+|+ +.+++.--.
T Consensus 171 clL~L~r~---spDl~~~~~W~~riv~LL~D~----~~gv~ta~~sLi~~lvk~~p~~y-k~-~~~~avs~L~riv~~~~ 241 (938)
T KOG1077|consen 171 CLLRLFRK---SPDLVNPGEWAQRIVHLLDDQ----HMGVVTAATSLIEALVKKNPESY-KT-CLPLAVSRLSRIVVVVG 241 (938)
T ss_pred HHHHHHhc---CccccChhhHHHHHHHHhCcc----ccceeeehHHHHHHHHHcCCHHH-hh-hHHHHHHHHHHHHhhcc
Confidence 45566554 225554 48999999999996 68889999999999999999887 22 2333443 333332211
Q ss_pred ----------CCChHHHHhHHHHHHHH
Q psy1379 86 ----------NQSPIIQQNAIALINAL 102 (446)
Q Consensus 86 ----------~~d~~iq~nalaLiNaL 102 (446)
...+=+|.+.+-|+-.+
T Consensus 242 t~~qdYTyy~vP~PWL~vKl~rlLq~~ 268 (938)
T KOG1077|consen 242 TSLQDYTYYFVPAPWLQVKLLRLLQIY 268 (938)
T ss_pred cchhhceeecCCChHHHHHHHHHHHhC
Confidence 13455666666665554
No 46
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=30.19 E-value=60 Score=29.33 Aligned_cols=39 Identities=10% Similarity=0.109 Sum_probs=33.3
Q ss_pred hhhhhhhcccCChHHHHhHHHHHHHHhccCCchhHHHhh
Q psy1379 383 LTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVIS 421 (446)
Q Consensus 383 l~~l~~~lq~~~~~~~~~a~al~nal~~~a~~~~r~~~~ 421 (446)
+.-|...|+..||..|..|+.|+.++...|.+.=+.+++
T Consensus 40 ~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~eva 78 (139)
T cd03567 40 VRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSEVG 78 (139)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHH
Confidence 344778899999999999999999999999987666555
No 47
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=30.13 E-value=1.6e+02 Score=22.75 Aligned_cols=52 Identities=15% Similarity=0.334 Sum_probs=35.1
Q ss_pred hHHHHHHHHHhc-CCcccccCchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHH
Q psy1379 4 HCLLSFVELMDH-GIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESI 57 (446)
Q Consensus 4 y~L~a~~~Lme~-~~~~W~~l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~ 57 (446)
..|..|.+-++. |...|+.++..-|...+...... ...++.....++.|.++
T Consensus 24 ~~l~~f~~~~~~~~~~~~~~i~~~~v~~f~~~~~~~--~~s~~T~~~~~~alr~f 76 (84)
T PF02899_consen 24 RDLRRFIRWLEEHGIIDWEDITEEDVRDFLEYLAKE--GLSPSTINRRLSALRAF 76 (84)
T ss_dssp HHHHHHHHHHHHTTS-CGGG--HHHHHHHHHHHHCT--T--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHcc--CCCHHHHHHHHHHHHHH
Confidence 457778887765 88899999998888888888774 23456666677777654
No 48
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=29.58 E-value=2.9e+02 Score=23.32 Aligned_cols=33 Identities=12% Similarity=0.257 Sum_probs=28.0
Q ss_pred hhHHhhhccCCChHHHHhHHHHHHHHhhccCCh
Q psy1379 77 LTNLVMHLQNQSPIIQQNAIALINALFIKAEPS 109 (446)
Q Consensus 77 ~~~lv~~L~~~d~~iq~nalaLiNaL~~~a~~~ 109 (446)
...|-++|++.++..+..||.|+-+|+.++++.
T Consensus 39 ~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g~~ 71 (115)
T cd00197 39 VDAIKKRINNKNPHVVLKALTLLEYCVKNCGER 71 (115)
T ss_pred HHHHHHHhcCCcHHHHHHHHHHHHHHHHHccHH
Confidence 345667788889999999999999999999853
No 49
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=29.20 E-value=1.8e+02 Score=26.23 Aligned_cols=59 Identities=19% Similarity=0.221 Sum_probs=42.8
Q ss_pred chHHHHHHHHHHhhhhhcC-chhhhHHhhhcchhhhhhhcc-cCChHHHHhHHHHHHHHhc
Q psy1379 352 EKEIVQASLSILESIALNS-VGKFSQVENHLTLTNLVMHLQ-NQSPIIQQNAIALINALFI 410 (446)
Q Consensus 352 d~~il~~~l~iLE~~vl~s-~~~~~~v~~Ev~l~~l~~~lq-~~~~~~~~~a~al~nal~~ 410 (446)
++.+.-+||.+||..|-|- ...+..|...==+++|...+. ..++.++.+.+.+|.+.-.
T Consensus 54 n~~vql~AL~LLe~~vkNCG~~fh~evas~~fl~~l~~l~~~~~~~~Vk~kil~li~~W~~ 114 (142)
T cd03569 54 NPNVQLYALLLLESCVKNCGTHFHDEVASREFMDELKDLIKTTKNEEVRQKILELIQAWAL 114 (142)
T ss_pred ChHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHHcccCCHHHHHHHHHHHHHHHH
Confidence 5679999999999999995 333444443323566766665 4788999999999987643
No 50
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=28.88 E-value=67 Score=28.49 Aligned_cols=38 Identities=18% Similarity=0.222 Sum_probs=32.1
Q ss_pred hhhhhhcccCChHHHHhHHHHHHHHhccCCchhHHHhh
Q psy1379 384 TNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVIS 421 (446)
Q Consensus 384 ~~l~~~lq~~~~~~~~~a~al~nal~~~a~~~~r~~~~ 421 (446)
.-|-..|+..||..|..|+.|+.++...|.+.-..+++
T Consensus 40 r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev~ 77 (133)
T smart00288 40 RLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVA 77 (133)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHH
Confidence 34778888999999999999999999999886666554
No 51
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=26.96 E-value=4.3e+02 Score=26.28 Aligned_cols=53 Identities=9% Similarity=0.116 Sum_probs=37.5
Q ss_pred HHHHHHHHhcCCcccccCchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCC
Q psy1379 6 LLSFVELMDHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNS 61 (446)
Q Consensus 6 L~a~~~Lme~~~~~W~~l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s 61 (446)
+.=+..||++-...-....++||..+++.+.+- -|+.-+--+..|+..+..+-
T Consensus 103 ~~ll~~l~~~~~~~l~~~~~~fv~~~i~~~~gE---kDPRnLl~~F~l~~~i~~~~ 155 (262)
T PF14500_consen 103 YQLLDSLLENHREALQSMGDDFVYGFIQLIDGE---KDPRNLLLSFKLLKVILQEF 155 (262)
T ss_pred HHHHHHHHHHhHHHHHhchhHHHHHHHHHhccC---CCHHHHHHHHHHHHHHHHhc
Confidence 334556676521122445789999999999995 58888888999988776653
No 52
>PF00514 Arm: Armadillo/beta-catenin-like repeat; InterPro: IPR000225 The armadillo (Arm) repeat is an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila melanogaster segment polarity gene armadillo involved in signal transduction through wingless. Animal Arm-repeat proteins function in various processes, including intracellular signalling and cytoskeletal regulation, and include such proteins as beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumour suppressor protein, and the nuclear transport factor importin-alpha, amongst others []. A subset of these proteins is conserved across eukaryotic kingdoms. In higher plants, some Arm-repeat proteins function in intracellular signalling like their mammalian counterparts, while others have novel functions []. The 3-dimensional fold of an armadillo repeat is known from the crystal structure of beta-catenin, where the 12 repeats form a superhelix of alpha helices with three helices per unit []. The cylindrical structure features a positively charged grove, which presumably interacts with the acidic surfaces of the known interaction partners of beta-catenin.; GO: 0005515 protein binding; PDB: 2Z6G_A 1IQ1_C 3RZX_A 2C1M_A 3BTR_C 3OQS_A 3TPO_A 1IAL_A 1Q1S_C 1PJM_B ....
Probab=26.94 E-value=94 Score=21.28 Aligned_cols=27 Identities=26% Similarity=0.361 Sum_probs=22.5
Q ss_pred chhHHhhhccCCChHHHHhHHHHHHHH
Q psy1379 76 TLTNLVMHLQNQSPIIQQNAIALINAL 102 (446)
Q Consensus 76 ~~~~lv~~L~~~d~~iq~nalaLiNaL 102 (446)
.++.|++.|.+.|..++.+|...+-.|
T Consensus 13 ~i~~Lv~ll~~~~~~v~~~a~~al~nl 39 (41)
T PF00514_consen 13 GIPPLVQLLKSPDPEVQEEAAWALGNL 39 (41)
T ss_dssp HHHHHHHHTTSSSHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 478899999999999999988766544
No 53
>PTZ00429 beta-adaptin; Provisional
Probab=26.55 E-value=4.2e+02 Score=30.61 Aligned_cols=51 Identities=10% Similarity=0.227 Sum_probs=36.1
Q ss_pred HHHHHHHHhcCCcccccC-chHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCC
Q psy1379 6 LLSFVELMDHGIVSWNIL-ETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVG 63 (446)
Q Consensus 6 L~a~~~Lme~~~~~W~~l-~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~ 63 (446)
.-|...+..++- +.+ ...|+.++.++++. .++.|+..|++.|..+...++.
T Consensus 161 alai~Kly~~~p---elv~~~~~~~~L~~LL~D----~dp~Vv~nAl~aL~eI~~~~~~ 212 (746)
T PTZ00429 161 AMGLGKLFHDDM---QLFYQQDFKKDLVELLND----NNPVVASNAAAIVCEVNDYGSE 212 (746)
T ss_pred HHHHHHHHhhCc---ccccccchHHHHHHHhcC----CCccHHHHHHHHHHHHHHhCch
Confidence 344555555432 333 35688899998876 4899999999999999877654
No 54
>KOG1059|consensus
Probab=25.79 E-value=1.2e+02 Score=34.82 Aligned_cols=73 Identities=16% Similarity=0.228 Sum_probs=55.9
Q ss_pred chHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhhhccCCChHHHHhHHHHHHHHh
Q psy1379 24 ETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVMHLQNQSPIIQQNAIALINALF 103 (446)
Q Consensus 24 ~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~~L~~~d~~iq~nalaLiNaL~ 103 (446)
..++-..|..++++. -+-|-..|.-+|=++.+..| +++++ .|+.|+..|+..|+.+|..|+..|=-|=
T Consensus 142 ARDLa~Dv~tLL~ss----kpYvRKkAIl~lykvFLkYP------eAlr~--~FprL~EkLeDpDp~V~SAAV~VICELA 209 (877)
T KOG1059|consen 142 ARDLADDVFTLLNSS----KPYVRKKAILLLYKVFLKYP------EALRP--CFPRLVEKLEDPDPSVVSAAVSVICELA 209 (877)
T ss_pred hHHHHHHHHHHHhcC----chHHHHHHHHHHHHHHHhhh------HhHhh--hHHHHHHhccCCCchHHHHHHHHHHHHH
Confidence 455556677777764 35566667777777777666 33443 6899999999999999999999999999
Q ss_pred hccCC
Q psy1379 104 IKAEP 108 (446)
Q Consensus 104 ~~a~~ 108 (446)
+|.+.
T Consensus 210 rKnPk 214 (877)
T KOG1059|consen 210 RKNPQ 214 (877)
T ss_pred hhCCc
Confidence 99873
No 55
>KOG2137|consensus
Probab=25.13 E-value=2.5e+02 Score=32.07 Aligned_cols=74 Identities=15% Similarity=0.231 Sum_probs=57.8
Q ss_pred chHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccc--hhHHhhhccCCChHHHHhHHHHHHH
Q psy1379 24 ETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLT--LTNLVMHLQNQSPIIQQNAIALINA 101 (446)
Q Consensus 24 ~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~--~~~lv~~L~~~d~~iq~nalaLiNa 101 (446)
+++|.++|..++-.+-+..++.|...+|.|+-.+ ..+=+ | ..|++.|= +..| .++.++..++.|+|.-++.
T Consensus 383 ~e~~~~~IlplL~~S~~~~~~~iQ~~~L~~lptv-~e~iD-~---~~vk~~ilP~l~~l--~~~tt~~~vkvn~L~c~~~ 455 (700)
T KOG2137|consen 383 PEEVKEKILPLLYRSLEDSDVQIQELALQILPTV-AESID-V---PFVKQAILPRLKNL--AFKTTNLYVKVNVLPCLAG 455 (700)
T ss_pred hHHHHHHHHHHHHHHhcCcchhhHHHHHHhhhHH-HHhcc-H---HHHHHHHHHHhhcc--hhcccchHHHHHHHHHHHH
Confidence 5788899999998876678899999999999855 44433 5 66777662 3333 5567999999999999999
Q ss_pred Hhh
Q psy1379 102 LFI 104 (446)
Q Consensus 102 L~~ 104 (446)
|+.
T Consensus 456 l~q 458 (700)
T KOG2137|consen 456 LIQ 458 (700)
T ss_pred HHH
Confidence 994
No 56
>KOG2160|consensus
Probab=24.30 E-value=3.5e+02 Score=28.28 Aligned_cols=100 Identities=14% Similarity=0.177 Sum_probs=71.2
Q ss_pred HHHHHHHHhh--h-ccccccchHHHHHHHHHhhcCCCCCCchHHHHHHHHHHhhhhhcCchhhhHHhhhcchhhhhhhcc
Q psy1379 315 LLSFVELMDH--G-IVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQVENHLTLTNLVMHLQ 391 (446)
Q Consensus 315 L~aF~eLm~~--~-i~swd~l~~~Fikki~~~vn~~~~~~d~~il~~~l~iLE~~vl~s~~~~~~v~~Ev~l~~l~~~lq 391 (446)
..+|-+|++| + .++=|...-.+..-++.|+++. |+++=..|+..+-..|.|.|.--++|-+-=-+..|+.-|-
T Consensus 101 e~ald~Le~lve~iDnAndl~~~ggl~~ll~~l~~~----~~~lR~~Aa~Vigt~~qNNP~~Qe~v~E~~~L~~Ll~~ls 176 (342)
T KOG2160|consen 101 EDALDNLEELVEDIDNANDLISLGGLVPLLGYLENS----DAELRELAARVIGTAVQNNPKSQEQVIELGALSKLLKILS 176 (342)
T ss_pred HHHHHHHHHHHHhhhhHHhHhhccCHHHHHHHhcCC----cHHHHHHHHHHHHHHHhcCHHHHHHHHHcccHHHHHHHHc
Confidence 3456665543 2 2355556666777788899886 7889999999999999999854444533335788888777
Q ss_pred cCCh-HHHHhHHHHHHHHhccCCchhHH
Q psy1379 392 NQSP-IIQQNAIALINALFIKAEPSKRK 418 (446)
Q Consensus 392 ~~~~-~~~~~a~al~nal~~~a~~~~r~ 418 (446)
..++ ...++|+--|-+|+++-++.-.+
T Consensus 177 ~~~~~~~r~kaL~AissLIRn~~~g~~~ 204 (342)
T KOG2160|consen 177 SDDPNTVRTKALFAISSLIRNNKPGQDE 204 (342)
T ss_pred cCCCchHHHHHHHHHHHHHhcCcHHHHH
Confidence 6333 55578888899999888886655
No 57
>PHA00680 hypothetical protein
Probab=24.14 E-value=3.6e+02 Score=23.34 Aligned_cols=115 Identities=21% Similarity=0.298 Sum_probs=58.0
Q ss_pred HHHHHhhhhhhhcccccchhhhhhHHHHHHHHHHh-hhccccccchHHHHHHHHHhhcCCCCCCchHHHHHHHHHHhhhh
Q psy1379 289 IQFLLDCFAVLVNHSQAGLCVMLAHCLLSFVELMD-HGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIA 367 (446)
Q Consensus 289 ~efl~dgl~~l~~~~e~g~~~~La~~L~aF~eLm~-~~i~swd~l~~~Fikki~~~vn~~~~~~d~~il~~~l~iLE~~v 367 (446)
-||+++.++..-....+ .+=+-+++.|..|++ |+--.++.+. .. -.|++++---|.-|+..-
T Consensus 9 eeflrhalavqdpltss---aieaeclrrfealldthdseayelvt------------er--eldasvlcetldtldahd 71 (143)
T PHA00680 9 EEFLRHALAVQDPLTSS---AIEAECLRRFEALLDTHDSEAYELVT------------ER--ELDASVLCETLDTLDAHD 71 (143)
T ss_pred HHHHHHHHHhcCcchHH---HHHHHHHHHHHHHHhccchHHHHHHH------------HH--hhhHHHHHHhhccchhhc
Confidence 46666666542111111 234678999999988 5533333222 22 357887776666665322
Q ss_pred hcCchhhhHHhhhcchhhhhhhcccCChHHHHhHHHHHHHHhccCCchhHHHhhHhhhhhhhHHHHH
Q psy1379 368 LNSVGKFSQVENHLTLTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMCSKQVRNAIL 434 (446)
Q Consensus 368 l~s~~~~~~v~~Ev~l~~l~~~lq~~~~~~~~~a~al~nal~~~a~~~~r~~~~~~l~~~~~r~~i~ 434 (446)
..--. ..|+-.- +.+. .-|+-||+|||-..--|++-.--++---.||+|..+-
T Consensus 72 iepga-laqlcda-------mlig------pantaallnalaaadldapeslkaeldlakqfralve 124 (143)
T PHA00680 72 IEPGA-LAQLCDA-------MLIG------PANTAALLNALAAADLDAPESLKAELDLAKQFRALVE 124 (143)
T ss_pred CCchH-HHHHhHH-------HhcC------cccHHHHHHHHHhhccCChHHHHHHHhHHHHHHHHHH
Confidence 22211 1111111 1122 1267788898864333343333334445678887653
No 58
>PTZ00429 beta-adaptin; Provisional
Probab=24.09 E-value=5.1e+02 Score=29.95 Aligned_cols=121 Identities=16% Similarity=0.176 Sum_probs=72.7
Q ss_pred hhhhhHHHHHHHHHHhhhccccccchHHHHHHHHHhhcCCCCCCchHHHHHHHHHHhhhhhcCchhhhHHhhhcchhhhh
Q psy1379 308 CVMLAHCLLSFVELMDHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQVENHLTLTNLV 387 (446)
Q Consensus 308 ~~~La~~L~aF~eLm~~~i~swd~l~~~Fikki~~~vn~~~~~~d~~il~~~l~iLE~~vl~s~~~~~~v~~Ev~l~~l~ 387 (446)
..+.+.++.++.++-+++-..|+. ....+.++...++. ++ +|.|. .|||-+..-.|.-- -+-+--++.+.
T Consensus 193 p~Vv~nAl~aL~eI~~~~~~~l~l-~~~~~~~Ll~~L~e----~~-EW~Qi--~IL~lL~~y~P~~~--~e~~~il~~l~ 262 (746)
T PTZ00429 193 PVVASNAAAIVCEVNDYGSEKIES-SNEWVNRLVYHLPE----CN-EWGQL--YILELLAAQRPSDK--ESAETLLTRVL 262 (746)
T ss_pred ccHHHHHHHHHHHHHHhCchhhHH-HHHHHHHHHHHhhc----CC-hHHHH--HHHHHHHhcCCCCc--HHHHHHHHHHH
Confidence 356788888888887765434543 34444555555532 22 68876 67776644322111 12234578889
Q ss_pred hhcccCChHHHHhHHHHHHHHhccCCchhHHHhhH-------hhh--hhhhHHHHHhccc
Q psy1379 388 MHLQNQSPIIQQNAIALINALFIKAEPSKRKVISA-------TMC--SKQVRNAILTSVL 438 (446)
Q Consensus 388 ~~lq~~~~~~~~~a~al~nal~~~a~~~~r~~~~~-------~l~--~~~~r~~i~~~ii 438 (446)
.+||..|+.+-..|+-++-.+....++.-.+.... +|. ..++|.++++||.
T Consensus 263 ~~Lq~~N~AVVl~Aik~il~l~~~~~~~~~~~~~~rl~~pLv~L~ss~~eiqyvaLr~I~ 322 (746)
T PTZ00429 263 PRMSHQNPAVVMGAIKVVANLASRCSQELIERCTVRVNTALLTLSRRDAETQYIVCKNIH 322 (746)
T ss_pred HHhcCCCHHHHHHHHHHHHHhcCcCCHHHHHHHHHHHHHHHHHhhCCCccHHHHHHHHHH
Confidence 99999999988888877777765444333333221 222 2468888888764
No 59
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=22.33 E-value=5.5e+02 Score=23.51 Aligned_cols=89 Identities=13% Similarity=0.259 Sum_probs=64.1
Q ss_pred cccccchHHHHHHHHHhhcCCCCCCchHHHHHHHHHHhhhhhcCchhhhHHhhhcchhhhhhhcccCChHHHHhHHHHHH
Q psy1379 327 VSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQVENHLTLTNLVMHLQNQSPIIQQNAIALIN 406 (446)
Q Consensus 327 ~swd~l~~~Fikki~~~vn~~~~~~d~~il~~~l~iLE~~vl~s~~~~~~v~~Ev~l~~l~~~lq~~~~~~~~~a~al~n 406 (446)
+.|..+=+.++..+..-++.+ |+.+=..|+-.|-.++++. +-+++.++ +.+++..+...|+.|+..|..++.
T Consensus 17 ~r~~~~ve~~~~~l~~~L~D~----~~~VR~~al~~Ls~Li~~d---~ik~k~~l-~~~~l~~l~D~~~~Ir~~A~~~~~ 88 (178)
T PF12717_consen 17 IRYPNLVEPYLPNLYKCLRDE----DPLVRKTALLVLSHLILED---MIKVKGQL-FSRILKLLVDENPEIRSLARSFFS 88 (178)
T ss_pred HhCcHHHHhHHHHHHHHHCCC----CHHHHHHHHHHHHHHHHcC---ceeehhhh-hHHHHHHHcCCCHHHHHHHHHHHH
Confidence 456666677788888888765 5667777888888888886 44444433 477788889999999999999999
Q ss_pred HHhcc-CCchhHHHhhHh
Q psy1379 407 ALFIK-AEPSKRKVISAT 423 (446)
Q Consensus 407 al~~~-a~~~~r~~~~~~ 423 (446)
-+..+ .+..=..-+.+.
T Consensus 89 e~~~~~~~~~i~~~~~e~ 106 (178)
T PF12717_consen 89 ELLKKRNPNIIYNNFPEL 106 (178)
T ss_pred HHHHhccchHHHHHHHHH
Confidence 99888 343344433333
No 60
>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=22.29 E-value=1.2e+02 Score=20.00 Aligned_cols=27 Identities=22% Similarity=0.246 Sum_probs=21.3
Q ss_pred chhHHhhhccCCChHHHHhHHHHHHHH
Q psy1379 76 TLTNLVMHLQNQSPIIQQNAIALINAL 102 (446)
Q Consensus 76 ~~~~lv~~L~~~d~~iq~nalaLiNaL 102 (446)
.++.|+..|++.|+.++.+++..|-.|
T Consensus 13 ~i~~L~~ll~~~~~~i~~~a~~aL~nl 39 (41)
T smart00185 13 GLPALVELLKSEDEEVVKEAAWALSNL 39 (41)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 467788888888999999988776544
No 61
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=21.49 E-value=4.2e+02 Score=23.74 Aligned_cols=61 Identities=23% Similarity=0.305 Sum_probs=39.1
Q ss_pred CCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhhhccC---CChHHHHhHHHHHHHHh
Q psy1379 42 PEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVMHLQN---QSPIIQQNAIALINALF 103 (446)
Q Consensus 42 ~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~~L~~---~d~~iq~nalaLiNaL~ 103 (446)
.++++...||.+|+.+|.|--..+ .-++.+.+..-+.|++.+.. .+..++...+.||.+.=
T Consensus 51 ~n~~v~l~aL~LLe~~vkNCG~~f-h~eiask~Fl~e~L~~~i~~~~~~~~~Vk~kil~li~~W~ 114 (141)
T cd03565 51 KNHKEVMLTLTVLETCVKNCGHRF-HVLVAKKDFIKDVLVKLINPKNNPPTIVQEKVLALIQAWA 114 (141)
T ss_pred CCHHHHHHHHHHHHHHHHHccHHH-HHHHHHHHhhhHHHHHHHcccCCCcHHHHHHHHHHHHHHH
Confidence 478898999999999999985433 11122222222337777752 34577777888777643
No 62
>KOG2759|consensus
Probab=21.07 E-value=1.8e+02 Score=31.18 Aligned_cols=73 Identities=11% Similarity=0.137 Sum_probs=54.3
Q ss_pred HHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCCCccchhhhhcccchhHHhhhccCCChHHHHhHHHHHHHHhhc
Q psy1379 27 FIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVGKFSQFSQVENHLTLTNLVMHLQNQSPIIQQNAIALINALFIK 105 (446)
Q Consensus 27 fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~~y~gf~~v~~~v~~~~lv~~L~~~d~~iq~nalaLiNaL~~~ 105 (446)
.++..+.++.++ .|+.|+..|..=+..+|-+.|.+- .+|.+-=.-+.+-++|...|+++.-+||.-+-.||.+
T Consensus 367 llkiL~~lLe~s---~Dp~iL~VAc~DIge~Vr~yP~gk---~vv~k~ggKe~vM~Llnh~d~~Vry~ALlavQ~lm~~ 439 (442)
T KOG2759|consen 367 LLKILIKLLETS---NDPIILCVACHDIGEYVRHYPEGK---AVVEKYGGKERVMNLLNHEDPEVRYHALLAVQKLMVH 439 (442)
T ss_pred HHHHHHHHHhcC---CCCceeehhhhhHHHHHHhCchHh---HHHHHhchHHHHHHHhcCCCchHHHHHHHHHHHHHhh
Confidence 344556666665 477777887777777888888543 6665544567778888889999999999988888865
No 63
>KOG2199|consensus
Probab=20.13 E-value=2.4e+02 Score=30.21 Aligned_cols=37 Identities=16% Similarity=0.265 Sum_probs=28.5
Q ss_pred CchHHHHHHHHhhcCCCCCCCchhhhHHHHHHHHHhhCCCC
Q psy1379 23 LETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALNSVG 63 (446)
Q Consensus 23 l~~~fI~ki~~~v~~~~~~~~~~i~~~alsIL~~~V~~s~~ 63 (446)
..-+.|+-|-.=+++. |++|.-.||+.|.++|.|=-.
T Consensus 42 ~~kd~lk~i~KRln~~----dphV~L~AlTLlda~~~NCg~ 78 (462)
T KOG2199|consen 42 GGKDCLKAIMKRLNHK----DPHVVLQALTLLDACVANCGK 78 (462)
T ss_pred ccHHHHHHHHHHhcCC----CcchHHHHHHHHHHHHHhcch
Confidence 4556666666667764 899999999999999998643
Done!