Query 042013
Match_columns 321
No_of_seqs 120 out of 165
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 13:05:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042013.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042013hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04078 Rcd1: Cell differenti 100.0 7E-125 2E-129 879.0 21.5 261 42-302 1-261 (262)
2 KOG3036 Protein involved in ce 100.0 1E-123 3E-128 866.3 25.0 271 34-304 22-292 (293)
3 COG5209 RCD1 Uncharacterized p 100.0 2E-105 3E-110 741.4 19.9 265 39-303 48-312 (315)
4 cd00020 ARM Armadillo/beta-cat 95.1 0.088 1.9E-06 40.9 6.6 96 106-207 22-118 (120)
5 PF10508 Proteasom_PSMB: Prote 92.8 9.1 0.0002 39.5 17.8 195 50-264 174-394 (503)
6 KOG2160 Armadillo/beta-catenin 91.6 0.85 1.8E-05 45.6 8.3 145 49-212 96-243 (342)
7 cd00020 ARM Armadillo/beta-cat 91.1 1.8 3.9E-05 33.4 8.2 117 128-258 3-119 (120)
8 PF10508 Proteasom_PSMB: Prote 90.6 8 0.00017 39.9 14.6 225 38-303 3-231 (503)
9 PF05804 KAP: Kinesin-associat 82.9 20 0.00044 39.2 12.9 147 106-269 305-451 (708)
10 PF04826 Arm_2: Armadillo-like 81.4 18 0.0004 34.4 10.7 231 34-298 11-242 (254)
11 PLN03200 cellulose synthase-in 81.3 33 0.00071 41.9 14.7 237 34-302 9-260 (2102)
12 PF03224 V-ATPase_H_N: V-ATPas 78.3 5.3 0.00012 38.2 6.1 148 112-269 31-189 (312)
13 PF03224 V-ATPase_H_N: V-ATPas 77.2 9.9 0.00021 36.4 7.6 216 33-300 70-311 (312)
14 PF01602 Adaptin_N: Adaptin N 71.9 1.1E+02 0.0024 30.5 13.7 126 39-172 80-227 (526)
15 PLN03200 cellulose synthase-in 65.9 70 0.0015 39.3 12.4 106 105-216 418-524 (2102)
16 PF05804 KAP: Kinesin-associat 65.7 67 0.0014 35.3 11.4 106 157-273 269-376 (708)
17 PF13251 DUF4042: Domain of un 58.0 43 0.00094 30.6 7.2 106 153-260 2-132 (182)
18 PF12231 Rif1_N: Rap1-interact 53.9 78 0.0017 31.4 8.8 131 116-261 31-165 (372)
19 cd00256 VATPase_H VATPase_H, r 52.7 1.9E+02 0.0042 30.0 11.6 137 123-269 41-183 (429)
20 PF12348 CLASP_N: CLASP N term 48.0 2E+02 0.0043 25.5 11.1 184 48-260 19-207 (228)
21 cd00256 VATPase_H VATPase_H, r 44.9 3.8E+02 0.0082 27.9 12.7 131 159-302 166-307 (429)
22 cd07920 Pumilio Pumilio-family 44.8 2.5E+02 0.0054 26.3 10.3 38 37-80 57-94 (322)
23 KOG1991 Nuclear transport rece 41.6 6.2E+02 0.013 29.4 14.0 192 43-260 381-600 (1010)
24 PF14911 MMS22L_C: S-phase gen 40.4 1.6E+02 0.0035 30.1 8.7 180 114-301 148-372 (373)
25 PF14225 MOR2-PAG1_C: Cell mor 39.8 98 0.0021 29.8 6.8 117 157-273 82-218 (262)
26 cd07920 Pumilio Pumilio-family 33.7 85 0.0018 29.4 5.3 28 244-271 146-173 (322)
27 cd06224 REM Guanine nucleotide 33.1 1.4E+02 0.0029 23.9 5.7 72 41-123 3-83 (122)
28 KOG0301 Phospholipase A2-activ 32.7 3.4E+02 0.0073 30.2 10.0 133 155-302 523-659 (745)
29 PLN00211 predicted protein; Pr 30.7 35 0.00075 26.3 1.7 20 80-99 31-50 (61)
30 PF00618 RasGEF_N: RasGEF N-te 29.2 74 0.0016 25.1 3.5 72 39-122 6-88 (104)
31 PF14664 RICTOR_N: Rapamycin-i 29.0 5.3E+02 0.011 26.0 10.2 174 53-269 3-186 (371)
32 PF10167 NEP: Uncharacterised 29.0 88 0.0019 27.0 4.1 40 220-259 6-48 (118)
33 PF10521 DUF2454: Protein of u 27.8 1.8E+02 0.0039 27.7 6.5 77 181-257 120-201 (282)
34 TIGR01204 bioW 6-carboxyhexano 24.7 52 0.0011 31.6 2.2 72 104-179 147-227 (232)
35 PF13513 HEAT_EZ: HEAT-like re 24.6 1.4E+02 0.003 20.8 3.9 51 153-205 3-53 (55)
36 PF03378 CAS_CSE1: CAS/CSE pro 23.3 2.9E+02 0.0063 28.5 7.4 48 70-123 165-215 (435)
37 PF00514 Arm: Armadillo/beta-c 23.2 2E+02 0.0042 19.1 4.3 38 169-206 1-38 (41)
38 PF05536 Neurochondrin: Neuroc 22.9 3.6E+02 0.0077 28.6 8.1 107 110-219 24-138 (543)
39 PRK01322 6-carboxyhexanoate--C 22.6 58 0.0013 31.4 2.1 73 104-180 154-235 (242)
40 PF05536 Neurochondrin: Neuroc 22.2 3.1E+02 0.0067 29.1 7.4 143 63-211 69-215 (543)
41 PF04802 SMK-1: Component of I 21.6 98 0.0021 28.6 3.3 61 141-202 14-74 (193)
42 PF12452 DUF3685: Protein of u 21.4 52 0.0011 30.7 1.4 37 107-154 49-87 (193)
43 KOG4523 Uncharacterized conser 21.1 1.3E+02 0.0029 26.8 3.8 35 219-253 5-42 (157)
44 PF06371 Drf_GBD: Diaphanous G 20.2 5.5E+02 0.012 21.9 8.2 80 210-301 105-185 (187)
No 1
>PF04078 Rcd1: Cell differentiation family, Rcd1-like ; InterPro: IPR007216 Rcd1 (Required cell differentiation 1) -like proteins are found among a wide range of organisms []. Rcd1 was initially identified as an essential factor in nitrogen starvation-invoked differentiation in fission yeast. This results largely from a defect in nitrogen starvation-invoked induction of ste11+, a key transcriptional factor gene required for the onset of sexual development. It is one of the most conserved proteins in eukaryotes, and its mammalian homologue is expressed in a variety of differentiating tissues [, ]. The mammalian Rcd1 is a novel transcriptional cofactor and is critical for retinoic acid-induced differentiation of F9 mouse teratocarcinoma cells, at least in part, via forming complexes with retinoic acid receptor and activation transcription factor-2 (ATF-2) []. Two of the members in this family have been characterised as being involved in regulation of Ste11 regulated sex genes [, ].; PDB: 2FV2_B.
Probab=100.00 E-value=7.4e-125 Score=878.96 Aligned_cols=261 Identities=80% Similarity=1.261 Sum_probs=244.3
Q ss_pred HHHHhcCCcchHHHHHHHHhhhhhcccchhhHHhhhhchHHHHHHHHHhhcCCCCCCCCChhhhhHHHHHHHHHHHHhcC
Q 042013 42 HLVLDLSNPDLRENALLELSKNKELFQDLAPFVWNSFGTIAALIQEIVSIYPVLSPPNLTPAQSNRVCNALALLQCVASH 121 (321)
Q Consensus 42 q~I~~L~~p~~Re~AL~eLsk~re~~~~La~~LW~S~Gtia~LLQEIisiYp~Lspp~Lt~~~SnRVCnaLaLLQ~vAsh 121 (321)
|||.||++|++||+||+||||+||++|||||+||||||||++|||||+++||+++||+||+++|||||||||||||||||
T Consensus 1 q~i~~L~~~~~Re~Al~eLsk~r~~~~~La~~LW~s~G~i~~LLqEIisiYp~l~~~~Lt~~~snRVcnaLaLlQ~vAsh 80 (262)
T PF04078_consen 1 QLILDLCNPETRENALLELSKKRESFPDLAPLLWHSFGTIAALLQEIISIYPALSPPNLTARQSNRVCNALALLQCVASH 80 (262)
T ss_dssp HHHHHTSSHHHHHHHHHHHHHTCCC-TTHHHHHHTSTTHHHHHHHHHHGGGGGTTTT---HHHHHHHHHHHHHHHHHHH-
T ss_pred ChhHHhcCcchHHHHHHHHHHhhhcccchhHHHHcCCChHHHHHHHHHHHcccCCCcccCHHHHHHHHHHHHHHHHHHcC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhchhhhhhhhccccchhhHHHHH
Q 042013 122 PDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEIIPLCLRTMEMGSELSKTVAT 201 (321)
Q Consensus 122 petR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEiiPLCLriME~GselSKtvAt 201 (321)
||||.+||+||||+||||||||++|+|||||||||||||||||||+||+|||+||++|||||+|||+||+|||+||||||
T Consensus 81 petr~~Fl~a~iplyLyPfL~tt~k~r~~E~LRLtsLGVIgaLvK~d~~evi~fLl~tEiiplcLr~me~GselSKtvAt 160 (262)
T PF04078_consen 81 PETRMPFLKAHIPLYLYPFLNTTSKTRPFEYLRLTSLGVIGALVKTDDPEVISFLLQTEIIPLCLRIMEFGSELSKTVAT 160 (262)
T ss_dssp TTTHHHHHHTTGGGGGHHHHH----SHHHHHHHHHHHHHHHHHHTT--HHHHHHHHCTTHHHHHHHHHHHS-HHHHHHHH
T ss_pred hHHHHHHHHcCchhhehhhhhccccccccchhhHhHHHHHHHHHcCCcHHHHHHHHhhchHHHHHHHHHhccHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhccccchhhhhhhhhHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHhhCChhhHHHHHhcCCcccchhhhh
Q 042013 202 FIVQKILLDDVGLDYICTTAERFFAVGRVLGNMVAALAEQPSSRLLKHIIRCYLRLSDNPRACDALRSCLPDMLRDATFS 281 (321)
Q Consensus 202 fIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~~ps~RLLKhiirCYlRLs~n~rar~aL~~~LP~~Lrd~~f~ 281 (321)
||+||||+||+||+|+|||+|||+||++||++||.+++++||+||||||||||+|||||||||++|++|||++|||++|+
T Consensus 161 fIlqKIL~dd~GL~yiC~t~eRf~av~~vL~~mV~~l~~~pS~RLLKhIIrCYlRLsdnprar~aL~~~LP~~Lrd~~f~ 240 (262)
T PF04078_consen 161 FILQKILLDDVGLNYICQTAERFFAVAMVLNKMVEQLVKQPSPRLLKHIIRCYLRLSDNPRAREALRQCLPDQLRDGTFS 240 (262)
T ss_dssp HHHHHHHHSHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHS--HHHHHHHHHHHHHHTTSTTHHHHHHHHS-GGGTSSTTT
T ss_pred HHHHHHHcchhHHHHHhcCHHHHHHHHHHHHHHHHHHccCCChhHHHHHHHHHHHHccCHHHHHHHHHhCcHHHhcHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCHHHHHHHHHHHHHhC
Q 042013 282 SCLREDPTTRRWLQQLLHNVG 302 (321)
Q Consensus 282 ~~l~~D~~~k~~l~qLl~nl~ 302 (321)
+++++|+++|+|++||+.|++
T Consensus 241 ~~l~~D~~~k~~l~qLl~nl~ 261 (262)
T PF04078_consen 241 NILKDDPSTKRWLQQLLSNLN 261 (262)
T ss_dssp TGGCS-HHHHHHHHHHHHHTT
T ss_pred HHHhcCHHHHHHHHHHHHHhc
Confidence 999999999999999999997
No 2
>KOG3036 consensus Protein involved in cell differentiation/sexual development [General function prediction only]
Probab=100.00 E-value=1.4e-123 Score=866.34 Aligned_cols=271 Identities=75% Similarity=1.145 Sum_probs=266.9
Q ss_pred chhhhHHHHHHHhcCCcchHHHHHHHHhhhhhcccchhhHHhhhhchHHHHHHHHHhhcCCCCCCCCChhhhhHHHHHHH
Q 042013 34 DRKMASAEHLVLDLSNPDLRENALLELSKNKELFQDLAPFVWNSFGTIAALIQEIVSIYPVLSPPNLTPAQSNRVCNALA 113 (321)
Q Consensus 34 ~~~~~~v~q~I~~L~~p~~Re~AL~eLsk~re~~~~La~~LW~S~Gtia~LLQEIisiYp~Lspp~Lt~~~SnRVCnaLa 113 (321)
+.+.|+++|||.++.+|++||+||+|||||||.+||||++||||||++++|||||+++||.|+||+||+++||||||||+
T Consensus 22 ~~~~dk~~~~i~~l~~~p~rE~aL~ELskkre~~~dlA~~lW~s~g~~~~LLqEivaiYp~l~p~~l~~~qsnRVcnaL~ 101 (293)
T KOG3036|consen 22 ASNNDKAYQLILSLVSPPTREMALLELSKKREPFPDLAPMLWHSFGTMVALLQEIVAIYPSLSPPTLTPAQSNRVCNALA 101 (293)
T ss_pred cccccchhhHHHHhhCCchHHHHHHHHHHhccCCccccHHHHHhcchHHHHHHHHHhcccccCCCCCCccccchHHHHHH
Confidence 34455699999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcCchhhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhchhhhhhhhccccc
Q 042013 114 LLQCVASHPDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEIIPLCLRTMEMGS 193 (321)
Q Consensus 114 LLQ~vAshpetR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEiiPLCLriME~Gs 193 (321)
||||||||||||+.||+||||+||||||+|++|+|||||||||||||||||||+||+|||+||++|||||+||||||.||
T Consensus 102 LlQcvASHpdTr~~FL~A~iPlylYpfL~Tt~~~r~fEyLRLtsLGVIgaLvk~dd~eVi~fLl~TeIVPlCLrime~GS 181 (293)
T KOG3036|consen 102 LLQCVASHPDTRRAFLRAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKNDDQEVIRFLLTTEIVPLCLRIMESGS 181 (293)
T ss_pred HHHHHhcCcchHHHHHHccChhhhHHhhhccccCCchHHHhHHHHHHHHHHHhcCcHHHHHHHHHhhhHHHHHHHHhccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHHHHHHHHHHhccccchhhhhhhhhHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHhhCChhhHHHHHhcCCc
Q 042013 194 ELSKTVATFIVQKILLDDVGLDYICTTAERFFAVGRVLGNMVAALAEQPSSRLLKHIIRCYLRLSDNPRACDALRSCLPD 273 (321)
Q Consensus 194 elSKtvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~~ps~RLLKhiirCYlRLs~n~rar~aL~~~LP~ 273 (321)
|+|||||+||+||||+||+||+|+|||+|||+||+.+||+||.++++.||+||||||||||+|||||||||++|++|+||
T Consensus 182 elSKtvA~fIlqKIlldD~GL~YiCqt~eRF~av~~~L~kmv~~l~~~ps~RllKhviRcYlrLsdnprar~aL~~clPd 261 (293)
T KOG3036|consen 182 ELSKTVATFILQKILLDDVGLYYICQTAERFSAVALVLGKMVFQLVSMPSPRLLKHVIRCYLRLSDNPRARAALRSCLPD 261 (293)
T ss_pred HHHHHHHHHHHHHHhhccccHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCCHHHHHHHHhhCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhhhhhhhcCCHHHHHHHHHHHHHhCCC
Q 042013 274 MLRDATFSSCLREDPTTRRWLQQLLHNVGVN 304 (321)
Q Consensus 274 ~Lrd~~f~~~l~~D~~~k~~l~qLl~nl~~~ 304 (321)
+|||+||+.++++|+++|+||+||+.|++.+
T Consensus 262 ~Lrd~tfs~~l~~D~~~k~~l~~ll~~l~~~ 292 (293)
T KOG3036|consen 262 QLRDGTFSLLLKDDPETKQWLQQLLKNLCTG 292 (293)
T ss_pred hhccchHHHHHhcChhHHHHHHHHHHHhccC
Confidence 9999999999999999999999999999864
No 3
>COG5209 RCD1 Uncharacterized protein involved in cell differentiation/sexual development [General function prediction only]
Probab=100.00 E-value=1.5e-105 Score=741.36 Aligned_cols=265 Identities=59% Similarity=0.897 Sum_probs=262.1
Q ss_pred HHHHHHHhcCCcchHHHHHHHHhhhhhcccchhhHHhhhhchHHHHHHHHHhhcCCCCCCCCChhhhhHHHHHHHHHHHH
Q 042013 39 SAEHLVLDLSNPDLRENALLELSKNKELFQDLAPFVWNSFGTIAALIQEIVSIYPVLSPPNLTPAQSNRVCNALALLQCV 118 (321)
Q Consensus 39 ~v~q~I~~L~~p~~Re~AL~eLsk~re~~~~La~~LW~S~Gtia~LLQEIisiYp~Lspp~Lt~~~SnRVCnaLaLLQ~v 118 (321)
-++.||+++.....||.||.||++|||++||||..||+|+|+|++||||||++||.|+|++|+.+.||||||||+||||+
T Consensus 48 lvy~wicqlv~g~~kEqaL~EL~rkreq~~dlAl~lW~s~gvmt~LLqEiisvYpiL~p~~l~~~~snRvcnaL~lLQcl 127 (315)
T COG5209 48 LVYSWICQLVVGNPKEQALDELFRKREQSPDLALELWRSDGVMTFLLQEIISVYPILSPSKLDERESNRVCNALNLLQCL 127 (315)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHhcCCCeeeeehhccchHHHHHHHHHhhhhccCccccCchhhhHHHHHHHHHHHH
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCchhhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhchhhhhhhhccccchhhHH
Q 042013 119 ASHPDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEIIPLCLRTMEMGSELSKT 198 (321)
Q Consensus 119 AshpetR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEiiPLCLriME~GselSKt 198 (321)
|||||||+.|++||||+||||||||++++++|||||||||||||||||+|+++||+||++|||||+||||||.|||+|||
T Consensus 128 aShPetk~~Fl~AhiplflypfLntss~~~~fEyLRltsLGVIgaLvkNdsq~vi~fLltTeivPLcLrIme~gSElSkt 207 (315)
T COG5209 128 ASHPETKKVFLDAHIPLFLYPFLNTSSSNSKFEYLRLTSLGVIGALVKNDSQYVIKFLLTTEIVPLCLRIMELGSELSKT 207 (315)
T ss_pred hcCcchheeeeecccceeeHhhhhccccCCccceeeehHHHHHHHHHhCCCHHHHHHHHhhhHHHHHHHHHHhhhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhccccchhhhhhhhhHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHhhCChhhHHHHHhcCCcccchh
Q 042013 199 VATFIVQKILLDDVGLDYICTTAERFFAVGRVLGNMVAALAEQPSSRLLKHIIRCYLRLSDNPRACDALRSCLPDMLRDA 278 (321)
Q Consensus 199 vAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~~ps~RLLKhiirCYlRLs~n~rar~aL~~~LP~~Lrd~ 278 (321)
||.||+||||.||+||+|+|||+|||+||+.||++||.|++..++.|||||+||||+||||+|+||++|+.|+|+.|||+
T Consensus 208 vaifI~qkil~dDvGLqYiCqT~eRFyAv~~vln~mv~qlVs~~~~RLlKh~iRcYlRLsd~p~aR~lL~~~lP~~Lrd~ 287 (315)
T COG5209 208 VAIFIFQKILGDDVGLQYICQTFERFYAVNLVLNSMVSQLVSLGSTRLLKHAIRCYLRLSDKPHARALLSSKLPDGLRDD 287 (315)
T ss_pred HHHHHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHHhhccchhHHHHHHHHheeecCCHhHHHHHhccCCcccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhcCCHHHHHHHHHHHHHhCC
Q 042013 279 TFSSCLREDPTTRRWLQQLLHNVGV 303 (321)
Q Consensus 279 ~f~~~l~~D~~~k~~l~qLl~nl~~ 303 (321)
||+..+++|...|+++.||+.+++.
T Consensus 288 tfs~vl~dD~~sk~ClAqll~~ln~ 312 (315)
T COG5209 288 TFSLVLADDGGSKECLAQLLTFLNL 312 (315)
T ss_pred HHHHHHHhcCChHHHHHHHHHHHHh
Confidence 9999999999999999999998863
No 4
>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=95.08 E-value=0.088 Score=40.86 Aligned_cols=96 Identities=16% Similarity=0.050 Sum_probs=78.8
Q ss_pred hHHHHHHHHHHHHhcC-chhhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhchhhh
Q 042013 106 NRVCNALALLQCVASH-PDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEIIPL 184 (321)
Q Consensus 106 nRVCnaLaLLQ~vAsh-petR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEiiPL 184 (321)
.-..+++..|..++++ |+.+..|++.++.-.|.++|+. +...+|-.+++.++-+... .++....+....++|.
T Consensus 22 ~~~~~a~~~l~~l~~~~~~~~~~~~~~~~i~~l~~~l~~-----~~~~v~~~a~~~L~~l~~~-~~~~~~~~~~~g~l~~ 95 (120)
T cd00020 22 NVQREAAWALSNLSAGNNDNIQAVVEAGGLPALVQLLKS-----EDEEVVKAALWALRNLAAG-PEDNKLIVLEAGGVPK 95 (120)
T ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHCCChHHHHHHHhC-----CCHHHHHHHHHHHHHHccC-cHHHHHHHHHCCChHH
Confidence 3445778888889988 8999999998888888888875 3568899999999999985 4567777888899999
Q ss_pred hhhhccccchhhHHHHHHHHHHH
Q 042013 185 CLRTMEMGSELSKTVATFIVQKI 207 (321)
Q Consensus 185 CLriME~GselSKtvAtfIlqKI 207 (321)
.++.+..++.-.+..|.+++..+
T Consensus 96 l~~~l~~~~~~~~~~a~~~l~~l 118 (120)
T cd00020 96 LVNLLDSSNEDIQKNATGALSNL 118 (120)
T ss_pred HHHHHhcCCHHHHHHHHHHHHHh
Confidence 99999998877777777776544
No 5
>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=92.84 E-value=9.1 Score=39.48 Aligned_cols=195 Identities=22% Similarity=0.206 Sum_probs=133.2
Q ss_pred cchHHHHHHHHhhhhhcccchhhHHhhhhchHHHHHHHHHhhcCCCCCCCCChhhhhHHHHHHHHHHHHhcCchhhhhhh
Q 042013 50 PDLRENALLELSKNKELFQDLAPFVWNSFGTIAALIQEIVSIYPVLSPPNLTPAQSNRVCNALALLQCVASHPDTRMLFL 129 (321)
Q Consensus 50 p~~Re~AL~eLsk~re~~~~La~~LW~S~Gtia~LLQEIisiYp~Lspp~Lt~~~SnRVCnaLaLLQ~vAshpetR~~FL 129 (321)
..-|-.++.-+.+-=...++.+...|.+ |.+..++.|+-+ ...-=--||+.+|.-+|.++.......
T Consensus 174 ~~vR~Rv~el~v~i~~~S~~~~~~~~~s-gll~~ll~eL~~------------dDiLvqlnalell~~La~~~~g~~yL~ 240 (503)
T PF10508_consen 174 DIVRCRVYELLVEIASHSPEAAEAVVNS-GLLDLLLKELDS------------DDILVQLNALELLSELAETPHGLQYLE 240 (503)
T ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHhc-cHHHHHHHHhcC------------ccHHHHHHHHHHHHHHHcChhHHHHHH
Confidence 3456666555555555678999999988 888888887643 111122399999999999999999989
Q ss_pred hhccccccccccccccCCCCcchhhhhhhhhhhh------hcccCchHHHHHHhhhchhhhhhhhccccchhhHHHHHHH
Q 042013 130 NAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGA------LVKVDDTEVISFLLSTEIIPLCLRTMEMGSELSKTVATFI 203 (321)
Q Consensus 130 ~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIga------LvK~dd~evI~fLL~tEiiPLCLriME~GselSKtvAtfI 203 (321)
+..+.--|+..+... ++.| |+.++-+.|. +...+.+++..-. ..++....+.++.+..-.+-+|.-.
T Consensus 241 ~~gi~~~L~~~l~~~-~~dp----~~~~~~l~g~~~f~g~la~~~~~~v~~~~--p~~~~~l~~~~~s~d~~~~~~A~dt 313 (503)
T PF10508_consen 241 QQGIFDKLSNLLQDS-EEDP----RLSSLLLPGRMKFFGNLARVSPQEVLELY--PAFLERLFSMLESQDPTIREVAFDT 313 (503)
T ss_pred hCCHHHHHHHHHhcc-ccCC----cccchhhhhHHHHHHHHHhcChHHHHHHH--HHHHHHHHHHhCCCChhHHHHHHHH
Confidence 998988888888755 3334 4444444443 4445555554311 2344455567788888888999889
Q ss_pred HHHHhccccchhhh-hhhhhHHHHHHHHHH-------------------HHHHHHhhCCChhhHHHHHHHHHHhhCChhh
Q 042013 204 VQKILLDDVGLDYI-CTTAERFFAVGRVLG-------------------NMVAALAEQPSSRLLKHIIRCYLRLSDNPRA 263 (321)
Q Consensus 204 lqKIL~dd~GL~Yi-C~t~eRF~av~~vL~-------------------~mV~~l~~~ps~RLLKhiirCYlRLs~n~ra 263 (321)
+.-|=+..+|...+ .++.+++.++..-.+ ++...-...++.+++.-.-..|..++++|.-
T Consensus 314 lg~igst~~G~~~L~~~~~~~~~~~l~~~~~~~~~~~~~lk~r~l~al~~il~~~~~~~~~~i~~~~~~w~~~~~~~~~~ 393 (503)
T PF10508_consen 314 LGQIGSTVEGKQLLLQKQGPAMKHVLKAIGDAIKSGSTELKLRALHALASILTSGTDRQDNDILSITESWYESLSGSPLS 393 (503)
T ss_pred HHHHhCCHHHHHHHHhhcchHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHHHHHhcCCchH
Confidence 99999999998888 666555555444333 3322223456778888888888888888765
Q ss_pred H
Q 042013 264 C 264 (321)
Q Consensus 264 r 264 (321)
.
T Consensus 394 ~ 394 (503)
T PF10508_consen 394 N 394 (503)
T ss_pred H
Confidence 4
No 6
>KOG2160 consensus Armadillo/beta-catenin-like repeat-containing protein [Posttranslational modification, protein turnover, chaperones]
Probab=91.56 E-value=0.85 Score=45.63 Aligned_cols=145 Identities=21% Similarity=0.160 Sum_probs=109.0
Q ss_pred CcchHHHHHHHHhhhhhcccchhhHHhhhhchHHHHHHHHHhhcCCCCCCCCChhhhhHHHHHHHHHHHHhcCchhhhhh
Q 042013 49 NPDLRENALLELSKNKELFQDLAPFVWNSFGTIAALIQEIVSIYPVLSPPNLTPAQSNRVCNALALLQCVASHPDTRMLF 128 (321)
Q Consensus 49 ~p~~Re~AL~eLsk~re~~~~La~~LW~S~Gtia~LLQEIisiYp~Lspp~Lt~~~SnRVCnaLaLLQ~vAshpetR~~F 128 (321)
++++||.|+.+|-..-|++. .|..|=..=|....+. . +.. .+..-|...|=.+=-|+-.+|.....+
T Consensus 96 ~le~ke~ald~Le~lve~iD-nAndl~~~ggl~~ll~-~-------l~~----~~~~lR~~Aa~Vigt~~qNNP~~Qe~v 162 (342)
T KOG2160|consen 96 DLEDKEDALDNLEELVEDID-NANDLISLGGLVPLLG-Y-------LEN----SDAELRELAARVIGTAVQNNPKSQEQV 162 (342)
T ss_pred CHHHHHHHHHHHHHHHHhhh-hHHhHhhccCHHHHHH-H-------hcC----CcHHHHHHHHHHHHHHHhcCHHHHHHH
Confidence 67889999999999888874 4555544435444443 2 222 234457777766777999999999999
Q ss_pred hhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhchhhhhhh-hccc--cchhhHHHHHHHHH
Q 042013 129 LNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEIIPLCLR-TMEM--GSELSKTVATFIVQ 205 (321)
Q Consensus 129 L~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEiiPLCLr-iME~--GselSKtvAtfIlq 205 (321)
+..+ +|-..+..-+ +..-.+.|--.|+-|++|+++..+-+-.|+.-.- --||+ +|+. -+-..|.+|.|.++
T Consensus 163 ~E~~---~L~~Ll~~ls-~~~~~~~r~kaL~AissLIRn~~~g~~~fl~~~G--~~~L~~vl~~~~~~~~lkrK~~~Ll~ 236 (342)
T KOG2160|consen 163 IELG---ALSKLLKILS-SDDPNTVRTKALFAISSLIRNNKPGQDEFLKLNG--YQVLRDVLQSNNTSVKLKRKALFLLS 236 (342)
T ss_pred HHcc---cHHHHHHHHc-cCCCchHHHHHHHHHHHHHhcCcHHHHHHHhcCC--HHHHHHHHHcCCcchHHHHHHHHHHH
Confidence 9999 6777776666 3445778889999999999998888878887766 23555 8898 67789999999999
Q ss_pred HHhcccc
Q 042013 206 KILLDDV 212 (321)
Q Consensus 206 KIL~dd~ 212 (321)
+++..+.
T Consensus 237 ~Ll~~~~ 243 (342)
T KOG2160|consen 237 LLLQEDK 243 (342)
T ss_pred HHHHhhh
Confidence 9998753
No 7
>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=91.11 E-value=1.8 Score=33.41 Aligned_cols=117 Identities=11% Similarity=0.114 Sum_probs=75.1
Q ss_pred hhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhchhhhhhhhccccchhhHHHHHHHHHHH
Q 042013 128 FLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEIIPLCLRTMEMGSELSKTVATFIVQKI 207 (321)
Q Consensus 128 FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEiiPLCLriME~GselSKtvAtfIlqKI 207 (321)
|++.++--+|-.+|...+ .++|..++..++.+.+.+ ++...++.+.+++|.++..|..+..--+-.|...+..|
T Consensus 3 ~~~~~~i~~l~~~l~~~~-----~~~~~~a~~~l~~l~~~~-~~~~~~~~~~~~i~~l~~~l~~~~~~v~~~a~~~L~~l 76 (120)
T cd00020 3 VIQAGGLPALVSLLSSSD-----ENVQREAAWALSNLSAGN-NDNIQAVVEAGGLPALVQLLKSEDEEVVKAALWALRNL 76 (120)
T ss_pred HHHcCChHHHHHHHHcCC-----HHHHHHHHHHHHHHhcCC-HHHHHHHHHCCChHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 344444444555554332 578999999999988774 66667778889999999999988777777788888887
Q ss_pred hccccchhhhhhhhhHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHhh
Q 042013 208 LLDDVGLDYICTTAERFFAVGRVLGNMVAALAEQPSSRLLKHIIRCYLRLS 258 (321)
Q Consensus 208 L~dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~~ps~RLLKhiirCYlRLs 258 (321)
..+...-. .+..-..++..++..+ ..++.+.-+++..+-..|+
T Consensus 77 ~~~~~~~~-------~~~~~~g~l~~l~~~l-~~~~~~~~~~a~~~l~~l~ 119 (120)
T cd00020 77 AAGPEDNK-------LIVLEAGGVPKLVNLL-DSSNEDIQKNATGALSNLA 119 (120)
T ss_pred ccCcHHHH-------HHHHHCCChHHHHHHH-hcCCHHHHHHHHHHHHHhh
Confidence 65543111 1111112334444433 3457777777777766554
No 8
>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=90.56 E-value=8 Score=39.88 Aligned_cols=225 Identities=20% Similarity=0.251 Sum_probs=136.5
Q ss_pred hHHHHHHHhcCCcchHHHHHHHHhhhhhccc---chhhHHhhhhchHHHHHHHHHhhcCCCCCCCCChhhhhHHHHHHHH
Q 042013 38 ASAEHLVLDLSNPDLRENALLELSKNKELFQ---DLAPFVWNSFGTIAALIQEIVSIYPVLSPPNLTPAQSNRVCNALAL 114 (321)
Q Consensus 38 ~~v~q~I~~L~~p~~Re~AL~eLsk~re~~~---~La~~LW~S~Gtia~LLQEIisiYp~Lspp~Lt~~~SnRVCnaLaL 114 (321)
+.+..++.+|...+.|-.+|.+|--.-...+ ++...+ +|-.+++. +.++.+=+|.+|..
T Consensus 3 ~~~~~~l~~l~~~~~~~~~L~~l~~~~~~~~~l~~~~~~~----------------lf~~L~~~--~~e~v~~~~~iL~~ 64 (503)
T PF10508_consen 3 EWINELLEELSSKAERLEALPELKTELSSSPFLERLPEPV----------------LFDCLNTS--NREQVELICDILKR 64 (503)
T ss_pred hHHHHHHHHHhcccchHHHHHHHHHHHhhhhHHHhchHHH----------------HHHHHhhc--ChHHHHHHHHHHHH
Confidence 3456678888888888888887765444433 221111 44444433 45566666766543
Q ss_pred HHHHhcCchhhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhchhhhhhhhccccch
Q 042013 115 LQCVASHPDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEIIPLCLRTMEMGSE 194 (321)
Q Consensus 115 LQ~vAshpetR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEiiPLCLriME~Gse 194 (321)
+=. +..|+. +..++.-||--.|. .|...+|--.+..||-++..+ ...+..+.+.+++|+.+..+..+.+
T Consensus 65 ~l~-~~~~~~----l~~~~~~~L~~gL~-----h~~~~Vr~l~l~~l~~~~~~~-~~~~~~~~~~~l~~~i~~~L~~~d~ 133 (503)
T PF10508_consen 65 LLS-ALSPDS----LLPQYQPFLQRGLT-----HPSPKVRRLALKQLGRIARHS-EGAAQLLVDNELLPLIIQCLRDPDL 133 (503)
T ss_pred HHh-ccCHHH----HHHHHHHHHHHHhc-----CCCHHHHHHHHHHHHHHhcCC-HHHHHHhcCccHHHHHHHHHcCCcH
Confidence 221 112211 12333333333332 367789999888898888654 5578899999999999999998888
Q ss_pred hhHHHHHHHHHHHhccccchhhhhhhhhHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHhh-CChhhHHHHHhcCCc
Q 042013 195 LSKTVATFIVQKILLDDVGLDYICTTAERFFAVGRVLGNMVAALAEQPSSRLLKHIIRCYLRLS-DNPRACDALRSCLPD 273 (321)
Q Consensus 195 lSKtvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~~ps~RLLKhiirCYlRLs-~n~rar~aL~~~LP~ 273 (321)
-....|.-++.+|.....|++-+-...- +..+.. +..+++.-+--.|..+...++ .++.+.+... ..
T Consensus 134 ~Va~~A~~~L~~l~~~~~~~~~l~~~~~--------~~~L~~-l~~~~~~~vR~Rv~el~v~i~~~S~~~~~~~~---~s 201 (503)
T PF10508_consen 134 SVAKAAIKALKKLASHPEGLEQLFDSNL--------LSKLKS-LMSQSSDIVRCRVYELLVEIASHSPEAAEAVV---NS 201 (503)
T ss_pred HHHHHHHHHHHHHhCCchhHHHHhCcch--------HHHHHH-HHhccCHHHHHHHHHHHHHHHhcCHHHHHHHH---hc
Confidence 8888899999999999888763311111 222222 223334333334555555664 3454444443 34
Q ss_pred ccchhhhhhhhcCCHHHHHHHHHHHHHhCC
Q 042013 274 MLRDATFSSCLREDPTTRRWLQQLLHNVGV 303 (321)
Q Consensus 274 ~Lrd~~f~~~l~~D~~~k~~l~qLl~nl~~ 303 (321)
.+.+..+..+-.+|.-++.-..+++..+..
T Consensus 202 gll~~ll~eL~~dDiLvqlnalell~~La~ 231 (503)
T PF10508_consen 202 GLLDLLLKELDSDDILVQLNALELLSELAE 231 (503)
T ss_pred cHHHHHHHHhcCccHHHHHHHHHHHHHHHc
Confidence 566666665556777778777777777764
No 9
>PF05804 KAP: Kinesin-associated protein (KAP)
Probab=82.95 E-value=20 Score=39.20 Aligned_cols=147 Identities=18% Similarity=0.193 Sum_probs=115.3
Q ss_pred hHHHHHHHHHHHHhcCchhhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhchhhhh
Q 042013 106 NRVCNALALLQCVASHPDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEIIPLC 185 (321)
Q Consensus 106 nRVCnaLaLLQ~vAshpetR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEiiPLC 185 (321)
.=+++++++|+-+.-++|-|......++.--|-.++... .+.++-.+|+.+.-|. -|+++-..+.+..+||-.
T Consensus 305 ellil~v~fLkkLSi~~ENK~~m~~~giV~kL~kLl~s~-----~~~l~~~aLrlL~NLS--fd~~~R~~mV~~GlIPkL 377 (708)
T PF05804_consen 305 ELLILAVTFLKKLSIFKENKDEMAESGIVEKLLKLLPSE-----NEDLVNVALRLLFNLS--FDPELRSQMVSLGLIPKL 377 (708)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHcCCHHHHHHHhcCC-----CHHHHHHHHHHHHHhC--cCHHHHHHHHHCCCcHHH
Confidence 345668889999999999999999999887788888642 3567778888888776 678888899999999999
Q ss_pred hhhccccchhhHHHHHHHHHHHhccccchhhhhhhhhHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHhhCChhhHH
Q 042013 186 LRTMEMGSELSKTVATFIVQKILLDDVGLDYICTTAERFFAVGRVLGNMVAALAEQPSSRLLKHIIRCYLRLSDNPRACD 265 (321)
Q Consensus 186 LriME~GselSKtvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~~ps~RLLKhiirCYlRLs~n~rar~ 265 (321)
...++.+. .+-+|..|++-|=.||.+-.-+..|- ++..++..+...|.+++=...+.--.-||-|+|.-+
T Consensus 378 v~LL~d~~--~~~val~iLy~LS~dd~~r~~f~~Td--------cIp~L~~~Ll~~~~~~v~~eliaL~iNLa~~~rnaq 447 (708)
T PF05804_consen 378 VELLKDPN--FREVALKILYNLSMDDEARSMFAYTD--------CIPQLMQMLLENSEEEVQLELIALLINLALNKRNAQ 447 (708)
T ss_pred HHHhCCCc--hHHHHHHHHHHhccCHhhHHHHhhcc--------hHHHHHHHHHhCCCccccHHHHHHHHHHhcCHHHHH
Confidence 98887654 55789999999999999877666652 345566666677888876667777778899998877
Q ss_pred HHHh
Q 042013 266 ALRS 269 (321)
Q Consensus 266 aL~~ 269 (321)
.+.+
T Consensus 448 lm~~ 451 (708)
T PF05804_consen 448 LMCE 451 (708)
T ss_pred HHHh
Confidence 7764
No 10
>PF04826 Arm_2: Armadillo-like; InterPro: IPR006911 This entry consists of mammalian proteins of unknown function.
Probab=81.35 E-value=18 Score=34.41 Aligned_cols=231 Identities=18% Similarity=0.231 Sum_probs=139.8
Q ss_pred chhhhHHHHHHHhcCCcchHHHHHHHHhhhhhcccchhhHHhhhhchHHHHHHHHHhhcCCCCCCCCChhhhhHHHHHHH
Q 042013 34 DRKMASAEHLVLDLSNPDLRENALLELSKNKELFQDLAPFVWNSFGTIAALIQEIVSIYPVLSPPNLTPAQSNRVCNALA 113 (321)
Q Consensus 34 ~~~~~~v~q~I~~L~~p~~Re~AL~eLsk~re~~~~La~~LW~S~Gtia~LLQEIisiYp~Lspp~Lt~~~SnRVCnaLa 113 (321)
..+-+++..++..-.+|.-+|.|+.-|+.. ..| ...-.+|.-+|.+..+..=+ +.|. ..-| -.||.
T Consensus 11 ~~~l~~Ll~lL~~t~dp~i~e~al~al~n~-aaf-~~nq~~Ir~~Ggi~lI~~lL-------~~p~----~~vr-~~AL~ 76 (254)
T PF04826_consen 11 AQELQKLLCLLESTEDPFIQEKALIALGNS-AAF-PFNQDIIRDLGGISLIGSLL-------NDPN----PSVR-EKALN 76 (254)
T ss_pred HHHHHHHHHHHhcCCChHHHHHHHHHHHhh-ccC-hhHHHHHHHcCCHHHHHHHc-------CCCC----hHHH-HHHHH
Confidence 344455555555455899999999999985 334 47888999999988775433 2221 1222 34555
Q ss_pred HHHHHhcCchhhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhh-cccCchHHHHHHhhhchhhhhhhhcccc
Q 042013 114 LLQCVASHPDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGAL-VKVDDTEVISFLLSTEIIPLCLRTMEMG 192 (321)
Q Consensus 114 LLQ~vAshpetR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaL-vK~dd~evI~fLL~tEiiPLCLriME~G 192 (321)
.+--++.+.|-+.. ++. |+---+..+.-..--..+.++.|+.++-| +..+..+++ ...||-+++....|
T Consensus 77 aL~Nls~~~en~~~-Ik~----~i~~Vc~~~~s~~lns~~Q~agLrlL~nLtv~~~~~~~l-----~~~i~~ll~LL~~G 146 (254)
T PF04826_consen 77 ALNNLSVNDENQEQ-IKM----YIPQVCEETVSSPLNSEVQLAGLRLLTNLTVTNDYHHML-----ANYIPDLLSLLSSG 146 (254)
T ss_pred HHHhcCCChhhHHH-HHH----HHHHHHHHHhcCCCCCHHHHHHHHHHHccCCCcchhhhH-----HhhHHHHHHHHHcC
Confidence 55556666665554 444 33333332222222345567889999888 444444443 23688899999999
Q ss_pred chhhHHHHHHHHHHHhccccchhhhhhhhhHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHhhCChhhHHHHHhcCC
Q 042013 193 SELSKTVATFIVQKILLDDVGLDYICTTAERFFAVGRVLGNMVAALAEQPSSRLLKHIIRCYLRLSDNPRACDALRSCLP 272 (321)
Q Consensus 193 selSKtvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~~ps~RLLKhiirCYlRLs~n~rar~aL~~~LP 272 (321)
++-.|.-+.-++--+=.+.+=..+.. -+.++.+.+.-+...-+.-+|-+++..+.+++++-+-...+.-.
T Consensus 147 ~~~~k~~vLk~L~nLS~np~~~~~Ll--------~~q~~~~~~~Lf~~~~~~~~l~~~l~~~~ni~~~~~~~~~~~~~-- 216 (254)
T PF04826_consen 147 SEKTKVQVLKVLVNLSENPDMTRELL--------SAQVLSSFLSLFNSSESKENLLRVLTFFENINENIKKEAYVFVQ-- 216 (254)
T ss_pred ChHHHHHHHHHHHHhccCHHHHHHHH--------hccchhHHHHHHccCCccHHHHHHHHHHHHHHHhhCcccceecc--
Confidence 99998877766544332222212211 12456666655556667888999999999999887666544411
Q ss_pred cccchhhhhhhhcCCHHHHHHHHHHH
Q 042013 273 DMLRDATFSSCLREDPTTRRWLQQLL 298 (321)
Q Consensus 273 ~~Lrd~~f~~~l~~D~~~k~~l~qLl 298 (321)
+.+..+....++.+...+.+.|..|.
T Consensus 217 ~~~~~~~L~~~~~e~~~~~~~l~~l~ 242 (254)
T PF04826_consen 217 DDFSEDSLFSLFGESSQLAKKLQALA 242 (254)
T ss_pred ccCCchhHHHHHccHHHHHHHHHHHH
Confidence 22333333366777776666666664
No 11
>PLN03200 cellulose synthase-interactive protein; Provisional
Probab=81.32 E-value=33 Score=41.95 Aligned_cols=237 Identities=15% Similarity=0.105 Sum_probs=137.2
Q ss_pred chhhhHHHHHHHhcCCc----chHHHHHHH---HhhhhhcccchhhHHhhhhchHHHHHHHHHhhcCCCCCCCCChhhhh
Q 042013 34 DRKMASAEHLVLDLSNP----DLRENALLE---LSKNKELFQDLAPFVWNSFGTIAALIQEIVSIYPVLSPPNLTPAQSN 106 (321)
Q Consensus 34 ~~~~~~v~q~I~~L~~p----~~Re~AL~e---Lsk~re~~~~La~~LW~S~Gtia~LLQEIisiYp~Lspp~Lt~~~Sn 106 (321)
......+..||.+|... +.|+.|+.+ |+|..+ +---.+=..-|.+..|+.=+.+ ++ ..-
T Consensus 9 ~~~~~~v~~Lve~L~s~~ss~~~~~~Al~~Lr~Lak~~~---enR~~Ia~~aGaIP~LV~lL~s-------g~----~~v 74 (2102)
T PLN03200 9 DGTLASVAQCIEQLRAKSSSPQEKELTTARLLELAKTRE---EARKAIGSHSQAMPLLVSLLRS-------GT----LGA 74 (2102)
T ss_pred cchHHHHHHHHHHHHcccCCHHHHHHHHHHHHHHHhcCh---HHHHHHHHccCcHHHHHHHHcC-------CC----HHH
Confidence 44577899999999966 888866554 555543 2223333335888877665532 11 111
Q ss_pred HHHHHHHHHHHHhcCchhhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccC--chHHHHHHhhhchhhh
Q 042013 107 RVCNALALLQCVASHPDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVD--DTEVISFLLSTEIIPL 184 (321)
Q Consensus 107 RVCnaLaLLQ~vAshpetR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~d--d~evI~fLL~tEiiPL 184 (321)
| -|+.+.|-.++.|++-|...+.+..--.|-=.|+..+ ...|-.+.+++..|...+ |..=..-......||.
T Consensus 75 k-~nAaaaL~nLS~~e~nk~~Iv~~GaIppLV~LL~sGs-----~eaKe~AA~AL~sLS~~~~~D~~~~~I~v~~GaVp~ 148 (2102)
T PLN03200 75 K-VNAAAVLGVLCKEEDLRVKVLLGGCIPPLLSLLKSGS-----AEAQKAAAEAIYAVSSGGLSDHVGSKIFSTEGVVPS 148 (2102)
T ss_pred H-HHHHHHHHHHhcCHHHHHHHHHcCChHHHHHHHHCCC-----HHHHHHHHHHHHHHHcCcchhhhhhhhhhhcCChHH
Confidence 1 1777899999999999988887543322333443332 347888999999998764 2211122335889999
Q ss_pred hhhhccccchhhHH---HHHHHHHHHhccccchhhhhhhhhHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHhhCC-
Q 042013 185 CLRTMEMGSELSKT---VATFIVQKILLDDVGLDYICTTAERFFAVGRVLGNMVAALAEQPSSRLLKHIIRCYLRLSDN- 260 (321)
Q Consensus 185 CLriME~GselSKt---vAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~~ps~RLLKhiirCYlRLs~n- 260 (321)
.++.++.|+.-.|. .|+-.+..+-.++++..-.. .=+.+...+|.-+ +.+++.+-.+...+..+++.+
T Consensus 149 Lv~lL~~gsk~d~~L~~~Av~AL~nLs~~~en~~~~I-------IeaGaVp~LV~LL-sS~d~~lQ~eAa~aLa~Lass~ 220 (2102)
T PLN03200 149 LWDQLQPGNKQDKVVEGLLTGALRNLCGSTDGFWSAT-------LEAGGVDILVKLL-SSGNSDAQANAASLLARLMMAF 220 (2102)
T ss_pred HHHHHhCCchhhHHHHHHHHHHHHHHhcCccchHHHH-------HHcCCHHHHHHHH-cCCCHHHHHHHHHHHHHHHcCC
Confidence 99999999754553 34455555544444321111 0012334444433 357788888888876666644
Q ss_pred hhhHHHHHhcCCcccchhhhhhhhcC--CHHHHHHHHHHHHHhC
Q 042013 261 PRACDALRSCLPDMLRDATFSSCLRE--DPTTRRWLQQLLHNVG 302 (321)
Q Consensus 261 ~rar~aL~~~LP~~Lrd~~f~~~l~~--D~~~k~~l~qLl~nl~ 302 (321)
++.++++.+. .. =+.|-.++++ |+.+|..=.-.|.||.
T Consensus 221 ee~~~aVIea---Ga-VP~LV~LL~sg~~~~VRE~AA~AL~nLA 260 (2102)
T PLN03200 221 ESSISKVLDA---GA-VKQLLKLLGQGNEVSVRAEAAGALEALS 260 (2102)
T ss_pred hHHHHHHHHC---CC-HHHHHHHHccCCChHHHHHHHHHHHHHh
Confidence 6666666531 11 1233344532 3455555555555654
No 12
>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=78.34 E-value=5.3 Score=38.18 Aligned_cols=148 Identities=18% Similarity=0.219 Sum_probs=77.2
Q ss_pred HHHHHHHhcCc-hhhhhhhhhccccccccccccccCC-CCcchhhhhhhhhhhhhcccCchHHHHHHhh------hchhh
Q 042013 112 LALLQCVASHP-DTRMLFLNAHIPLYLYPFLNTTSKS-RPFEYLRLTSLGVIGALVKVDDTEVISFLLS------TEIIP 183 (321)
Q Consensus 112 LaLLQ~vAshp-etR~~FL~a~iplyLyPfL~ttsk~-r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~------tEiiP 183 (321)
+.+++.+.+-+ +.|..+++++-+.|---|++.-++. ..-+.+ --.|-.|+-++..+. +....+.. .+.+.
T Consensus 31 ~~~ik~~~~~~~~~~~~~~~~~~~~~~~~~l~lL~~~~~~~d~v-~yvL~li~dll~~~~-~~~~~~~~~~~~~~~~~~~ 108 (312)
T PF03224_consen 31 LSLIKKLDKQSKEERRELLEEDGDQYASLFLNLLNKLSSNDDTV-QYVLTLIDDLLSDDP-SRVELFLELAKQDDSDPYS 108 (312)
T ss_dssp HHHHHHHHHHHH-------------------HHHHHH---HHHH-HHHHHHHHHHHH-SS-SSHHHHHHHHH-TTH--HH
T ss_pred HHHHHHHHCCCHHHHHHHHHhchhhHHHHHHHHHHHccCcHHHH-HHHHHHHHHHHhcCH-HHHHHHHHhcccccchhHH
Confidence 44556655433 5577788888888877777655554 323333 345666777665433 54444444 23788
Q ss_pred hhhhhccccchhhHHHHHHHHHHHhccccchhhhhhhhhHHHHHHHHHHHHHHHHhh---CCChhhHHHHHHHHHHhhCC
Q 042013 184 LCLRTMEMGSELSKTVATFIVQKILLDDVGLDYICTTAERFFAVGRVLGNMVAALAE---QPSSRLLKHIIRCYLRLSDN 260 (321)
Q Consensus 184 LCLriME~GselSKtvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~---~ps~RLLKhiirCYlRLs~n 260 (321)
..++.++.+....+..|.+|+.+++..+..-...= +..++...+..+.+ ..+..+....++|+..|..+
T Consensus 109 ~fl~ll~~~D~~i~~~a~~iLt~Ll~~~~~~~~~~--------~~~~l~~ll~~L~~~l~~~~~~~~~~av~~L~~LL~~ 180 (312)
T PF03224_consen 109 PFLKLLDRNDSFIQLKAAFILTSLLSQGPKRSEKL--------VKEALPKLLQWLSSQLSSSDSELQYIAVQCLQNLLRS 180 (312)
T ss_dssp HHHHH-S-SSHHHHHHHHHHHHHHHTSTTT--HHH--------HHHHHHHHHHHHH-TT-HHHH---HHHHHHHHHHHTS
T ss_pred HHHHHhcCCCHHHHHHHHHHHHHHHHcCCccccch--------HHHHHHHHHHHHHHhhcCCCcchHHHHHHHHHHHhCc
Confidence 89999999999999999999999987765443321 13334444444332 34456679999999999999
Q ss_pred hhhHHHHHh
Q 042013 261 PRACDALRS 269 (321)
Q Consensus 261 ~rar~aL~~ 269 (321)
++.|..+-+
T Consensus 181 ~~~R~~f~~ 189 (312)
T PF03224_consen 181 KEYRQVFWK 189 (312)
T ss_dssp HHHHHHHHT
T ss_pred chhHHHHHh
Confidence 999998865
No 13
>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=77.20 E-value=9.9 Score=36.36 Aligned_cols=216 Identities=16% Similarity=0.160 Sum_probs=102.8
Q ss_pred cchhhhHHHHHHHhcC-CcchHHHHHHHHhhhhhc--ccchhhHHhhhh-------------------chHHHHHHHHHh
Q 042013 33 KDRKMASAEHLVLDLS-NPDLRENALLELSKNKEL--FQDLAPFVWNSF-------------------GTIAALIQEIVS 90 (321)
Q Consensus 33 ~~~~~~~v~q~I~~L~-~p~~Re~AL~eLsk~re~--~~~La~~LW~S~-------------------Gtia~LLQEIis 90 (321)
.....+.+..+|.|++ +-..|.++++++++.-+. |.-+-..+.++= ......-+|++.
T Consensus 70 ~~d~v~yvL~li~dll~~~~~~~~~~~~~~~~~~~~~~~~fl~ll~~~D~~i~~~a~~iLt~Ll~~~~~~~~~~~~~~l~ 149 (312)
T PF03224_consen 70 NDDTVQYVLTLIDDLLSDDPSRVELFLELAKQDDSDPYSPFLKLLDRNDSFIQLKAAFILTSLLSQGPKRSEKLVKEALP 149 (312)
T ss_dssp -HHHHHHHHHHHHHHHH-SSSSHHHHHHHHH-TTH--HHHHHHH-S-SSHHHHHHHHHHHHHHHTSTTT--HHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHhcCHHHHHHHHHhcccccchhHHHHHHHhcCCCHHHHHHHHHHHHHHHHcCCccccchHHHHHH
Confidence 4455567777788877 333688889888885442 222222333321 111111122222
Q ss_pred hc-CCCCCCCCChhhhhHHHHHHHHHHHHhcCchhhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCc
Q 042013 91 IY-PVLSPPNLTPAQSNRVCNALALLQCVASHPDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDD 169 (321)
Q Consensus 91 iY-p~Lspp~Lt~~~SnRVCnaLaLLQ~vAshpetR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd 169 (321)
.| ..+.. .++...++=+--++.+||-+..+++.|..|.+++.--.|.+.|. ..++.+.
T Consensus 150 ~ll~~L~~-~l~~~~~~~~~~av~~L~~LL~~~~~R~~f~~~~~v~~l~~iL~--------------------~~~~~~~ 208 (312)
T PF03224_consen 150 KLLQWLSS-QLSSSDSELQYIAVQCLQNLLRSKEYRQVFWKSNGVSPLFDILR--------------------KQATNSN 208 (312)
T ss_dssp HHHHHHH--TT-HHHH---HHHHHHHHHHHTSHHHHHHHHTHHHHHHHHHHHH---------------------------
T ss_pred HHHHHHHH-hhcCCCcchHHHHHHHHHHHhCcchhHHHHHhcCcHHHHHHHHH--------------------hhcccCC
Confidence 22 11111 23333333335677888888888888888888777666666553 0011111
Q ss_pred hHHHHHHhhhchhhhhhhhccccchhhHHHHHHHHHHHhccccchhhhhhhhhHHHHHHHHHHHHHHHHhhCCChhhHHH
Q 042013 170 TEVISFLLSTEIIPLCLRTMEMGSELSKTVATFIVQKILLDDVGLDYICTTAERFFAVGRVLGNMVAALAEQPSSRLLKH 249 (321)
Q Consensus 170 ~evI~fLL~tEiiPLCLriME~GselSKtvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~~ps~RLLKh 249 (321)
.-.++- .. =+-+|+-.+-+..+..+.+. +=. +...++.-+...+...+.+-
T Consensus 209 ~~~~Ql--~Y-~~ll~lWlLSF~~~~~~~~~-------------------------~~~-~i~~L~~i~~~~~KEKvvRv 259 (312)
T PF03224_consen 209 SSGIQL--QY-QALLCLWLLSFEPEIAEELN-------------------------KKY-LIPLLADILKDSIKEKVVRV 259 (312)
T ss_dssp --HHHH--HH-HHHHHHHHHTTSHHHHHHHH-------------------------TTS-HHHHHHHHHHH--SHHHHHH
T ss_pred CCchhH--HH-HHHHHHHHHhcCHHHHHHHh-------------------------ccc-hHHHHHHHHHhcccchHHHH
Confidence 111111 11 11234444444333322221 111 33444444445566688888
Q ss_pred HHHHHHHhhCChh---hHHHHHhcCCcccchhhhhhhhcCCHHHHHHHHHHHHH
Q 042013 250 IIRCYLRLSDNPR---ACDALRSCLPDMLRDATFSSCLREDPTTRRWLQQLLHN 300 (321)
Q Consensus 250 iirCYlRLs~n~r---ar~aL~~~LP~~Lrd~~f~~~l~~D~~~k~~l~qLl~n 300 (321)
++.+..-|.+.+. +..++-..+|..+..=.-.. -+|++...-+++|-..
T Consensus 260 ~la~l~Nl~~~~~~~~~~~mv~~~~l~~l~~L~~rk--~~Dedl~edl~~L~e~ 311 (312)
T PF03224_consen 260 SLAILRNLLSKAPKSNIELMVLCGLLKTLQNLSERK--WSDEDLTEDLEFLKEI 311 (312)
T ss_dssp HHHHHHHTTSSSSTTHHHHHHHH-HHHHHHHHHSS----SSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhccHHHHHHHHHHccHHHHHHHHhcCC--CCCHHHHHHHHHHHhh
Confidence 8888888888766 34444455555544322221 2688888888877654
No 14
>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=71.93 E-value=1.1e+02 Score=30.46 Aligned_cols=126 Identities=21% Similarity=0.236 Sum_probs=62.2
Q ss_pred HHHHHHHhcCCcc--hHHHHHHHHhhhhhcccchhhHHhhhhc--------h----HHHHHHHHHhhcCCCCCCC-----
Q 042013 39 SAEHLVLDLSNPD--LRENALLELSKNKELFQDLAPFVWNSFG--------T----IAALIQEIVSIYPVLSPPN----- 99 (321)
Q Consensus 39 ~v~q~I~~L~~p~--~Re~AL~eLsk~re~~~~La~~LW~S~G--------t----ia~LLQEIisiYp~Lspp~----- 99 (321)
.+..+..||.++. -|..||.-|+.-+. |++++.+-.... . -+.-+-.|...+|.+.+..
T Consensus 80 ~~n~l~kdl~~~n~~~~~lAL~~l~~i~~--~~~~~~l~~~v~~ll~~~~~~VRk~A~~~l~~i~~~~p~~~~~~~~~~l 157 (526)
T PF01602_consen 80 IINSLQKDLNSPNPYIRGLALRTLSNIRT--PEMAEPLIPDVIKLLSDPSPYVRKKAALALLKIYRKDPDLVEDELIPKL 157 (526)
T ss_dssp HHHHHHHHHCSSSHHHHHHHHHHHHHH-S--HHHHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHCHCCHHGGHHHHH
T ss_pred HHHHHHHhhcCCCHHHHHHHHhhhhhhcc--cchhhHHHHHHHHHhcCCchHHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence 4556777887544 68999999998652 444443322111 1 1123344555555553321
Q ss_pred ---CChhhhhHHHHHHHHHHHHhcCchhhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHH
Q 042013 100 ---LTPAQSNRVCNALALLQCVASHPDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEV 172 (321)
Q Consensus 100 ---Lt~~~SnRVCnaLaLLQ~vAshpetR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~ev 172 (321)
|......-+.+|+.++..+...|+-...++... +..|..-- ..+-+.++...+.+++.+.+.+..+.
T Consensus 158 ~~lL~d~~~~V~~~a~~~l~~i~~~~~~~~~~~~~~-----~~~L~~~l-~~~~~~~q~~il~~l~~~~~~~~~~~ 227 (526)
T PF01602_consen 158 KQLLSDKDPSVVSAALSLLSEIKCNDDSYKSLIPKL-----IRILCQLL-SDPDPWLQIKILRLLRRYAPMEPEDA 227 (526)
T ss_dssp HHHTTHSSHHHHHHHHHHHHHHHCTHHHHTTHHHHH-----HHHHHHHH-TCCSHHHHHHHHHHHTTSTSSSHHHH
T ss_pred hhhccCCcchhHHHHHHHHHHHccCcchhhhhHHHH-----HHHhhhcc-cccchHHHHHHHHHHHhcccCChhhh
Confidence 222223344466777766622222212222222 22221110 34556677777777777777655544
No 15
>PLN03200 cellulose synthase-interactive protein; Provisional
Probab=65.94 E-value=70 Score=39.33 Aligned_cols=106 Identities=13% Similarity=0.086 Sum_probs=78.9
Q ss_pred hhHHHHHHHHHHHHhcC-chhhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhchhh
Q 042013 105 SNRVCNALALLQCVASH-PDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEIIP 183 (321)
Q Consensus 105 SnRVCnaLaLLQ~vAsh-petR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEiiP 183 (321)
...-+++..-|-.++.| ++-+..+.+....-+|-.||...+ +..|-..+.++|.+.+.++ +......+...||
T Consensus 418 ~evQ~~Av~aL~~L~~~~~e~~~aIi~~ggIp~LV~LL~s~s-----~~iQ~~A~~~L~nLa~~nd-enr~aIieaGaIP 491 (2102)
T PLN03200 418 ADVQEELIRALSSLCCGKGGLWEALGGREGVQLLISLLGLSS-----EQQQEYAVALLAILTDEVD-ESKWAITAAGGIP 491 (2102)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHcCcHHHHHHHHcCCC-----HHHHHHHHHHHHHHHcCCH-HHHHHHHHCCCHH
Confidence 34555555555556644 688888888888888888887542 5667777888999988644 4445677899999
Q ss_pred hhhhhccccchhhHHHHHHHHHHHhccccchhh
Q 042013 184 LCLRTMEMGSELSKTVATFIVQKILLDDVGLDY 216 (321)
Q Consensus 184 LCLriME~GselSKtvAtfIlqKIL~dd~GL~Y 216 (321)
.+.+.++.|+.-.|.-|..++..|-.++....+
T Consensus 492 ~LV~LL~s~~~~iqeeAawAL~NLa~~~~qir~ 524 (2102)
T PLN03200 492 PLVQLLETGSQKAKEDSATVLWNLCCHSEDIRA 524 (2102)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHhCCcHHHHH
Confidence 999999999999999999888877655444443
No 16
>PF05804 KAP: Kinesin-associated protein (KAP)
Probab=65.66 E-value=67 Score=35.32 Aligned_cols=106 Identities=16% Similarity=0.253 Sum_probs=76.6
Q ss_pred hhhhhhhhcccCchHHHHHHhhhchhhhhhhhccccchhhHHHHHHHHHHHhccccchhhhhhhhhHHHHHHHHHHHHHH
Q 042013 157 SLGVIGALVKVDDTEVISFLLSTEIIPLCLRTMEMGSELSKTVATFIVQKILLDDVGLDYICTTAERFFAVGRVLGNMVA 236 (321)
Q Consensus 157 SLGVIgaLvK~dd~evI~fLL~tEiiPLCLriME~GselSKtvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~ 236 (321)
++.+...|. +|..+-.=..+..+|++..+.++.+++-..+.++-.++|+=..++.-+-+-+ ..++.+.+
T Consensus 269 ~~~lLlNLA--ed~~ve~kM~~~~iV~~Lv~~Ldr~n~ellil~v~fLkkLSi~~ENK~~m~~--------~giV~kL~- 337 (708)
T PF05804_consen 269 AFYLLLNLA--EDPRVELKMVNKGIVSLLVKCLDRENEELLILAVTFLKKLSIFKENKDEMAE--------SGIVEKLL- 337 (708)
T ss_pred HHHHHHHHh--cChHHHHHHHhcCCHHHHHHHHcCCCHHHHHHHHHHHHHHcCCHHHHHHHHH--------cCCHHHHH-
Confidence 444454444 5566666677889999999999999999999999999998665544332211 11233322
Q ss_pred HHhhCCChhhHHHHHHHHHHhhCChhhHHHHHh--cCCc
Q 042013 237 ALAEQPSSRLLKHIIRCYLRLSDNPRACDALRS--CLPD 273 (321)
Q Consensus 237 ~l~~~ps~RLLKhiirCYlRLs~n~rar~aL~~--~LP~ 273 (321)
.+...++..+++..+|.-..||-|+..|..+.+ ++|.
T Consensus 338 kLl~s~~~~l~~~aLrlL~NLSfd~~~R~~mV~~GlIPk 376 (708)
T PF05804_consen 338 KLLPSENEDLVNVALRLLFNLSFDPELRSQMVSLGLIPK 376 (708)
T ss_pred HHhcCCCHHHHHHHHHHHHHhCcCHHHHHHHHHCCCcHH
Confidence 223457789999999999999999999999885 6673
No 17
>PF13251 DUF4042: Domain of unknown function (DUF4042)
Probab=58.00 E-value=43 Score=30.61 Aligned_cols=106 Identities=18% Similarity=0.284 Sum_probs=74.9
Q ss_pred hhhhhhhhhhhhccc-CchHHHHHHhhhchhhhh------------hhhccccchhhHHHHHHHHHHHhcc-ccchhhhh
Q 042013 153 LRLTSLGVIGALVKV-DDTEVISFLLSTEIIPLC------------LRTMEMGSELSKTVATFIVQKILLD-DVGLDYIC 218 (321)
Q Consensus 153 LRLtSLGVIgaLvK~-dd~evI~fLL~tEiiPLC------------LriME~GselSKtvAtfIlqKIL~d-d~GL~YiC 218 (321)
+|.+.|.-+++++|. |-.....|. ..++|-. --+.--.+.-.+..|...+.-+|.. ..=|.+.+
T Consensus 2 vR~~Al~~L~al~k~~~~r~l~~yW--~~llP~~~~~~~~~~~sLlt~il~Dp~~kvR~aA~~~l~~lL~gsk~~L~~Ae 79 (182)
T PF13251_consen 2 VRQAALQCLQALAKSTDKRSLFGYW--PALLPDSVLQGRPATPSLLTCILKDPSPKVRAAAASALAALLEGSKPFLAQAE 79 (182)
T ss_pred hhHHHHHHHHHHHHhcCCceeHhhH--HHHCCCCCCcCCCCCcchhHHHHcCCchhHHHHHHHHHHHHHHccHHHHHHHH
Confidence 699999999999998 666665552 3344433 3344455667788888888888766 23344444
Q ss_pred hhhh---HHHHHHHHHHHHHHHH--------hhCCChhhHHHHHHHHHHhhCC
Q 042013 219 TTAE---RFFAVGRVLGNMVAAL--------AEQPSSRLLKHIIRCYLRLSDN 260 (321)
Q Consensus 219 ~t~e---RF~av~~vL~~mV~~l--------~~~ps~RLLKhiirCYlRLs~n 260 (321)
.+-. -|...+..|+.|+.++ ..+.++.++-++++|-.-|.++
T Consensus 80 ~~~~~~~sFtslS~tLa~~i~~lH~~Ll~~L~~E~~~~~l~q~lK~la~Lv~~ 132 (182)
T PF13251_consen 80 ESKGPSGSFTSLSSTLASMIMELHRGLLLALQAEKSPPVLTQLLKCLAVLVQA 132 (182)
T ss_pred hcCCCCCCcccHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHcc
Confidence 3331 2888899999999873 4778899999999997776665
No 18
>PF12231 Rif1_N: Rap1-interacting factor 1 N terminal; InterPro: IPR022031 This domain family is found in eukaryotes, and is typically between 135 and 146 amino acids in length. Rif1 is a protein which interacts with Rap1 to regulate telomere length. Interaction with telomeres limits their length. The N-terminal region contains many HEAT- and ARMADILLO- type repeats. These are helical folds which form extended curved proteins or RNA interface surfaces.
Probab=53.95 E-value=78 Score=31.43 Aligned_cols=131 Identities=19% Similarity=0.261 Sum_probs=81.8
Q ss_pred HHHhcCchhhhhhhhhccccccccccccccCCCC-cchhhhhhhhhhhhhcccCchHHHHHHhhh---chhhhhhhhccc
Q 042013 116 QCVASHPDTRMLFLNAHIPLYLYPFLNTTSKSRP-FEYLRLTSLGVIGALVKVDDTEVISFLLST---EIIPLCLRTMEM 191 (321)
Q Consensus 116 Q~vAshpetR~~FL~a~iplyLyPfL~ttsk~r~-~E~LRLtSLGVIgaLvK~dd~evI~fLL~t---EiiPLCLriME~ 191 (321)
|.++.|-+.-..|++.+|- ...++..| -..|-..+|-..|.++ -++++++.|-.. .++=.|++.++.
T Consensus 31 ~~l~~k~~~l~~~i~rDi~-------~~~~~~~p~~~~L~~qALkll~~~l--~~~~i~~~l~~d~~~~~i~~~i~~l~~ 101 (372)
T PF12231_consen 31 QALQDKMSLLLQFIQRDIS-------SSSSKGDPFDSRLVIQALKLLGFFL--YHPEIVSTLSDDFASFIIDHSIESLQN 101 (372)
T ss_pred HHHHHHHHHHHHHHHHHHh-------cccCCCCCcchHHHHHHHHHHHHHH--ccHHHHhhCChHHHHHHHHHHHHHHcC
Confidence 4556666677777777776 45556666 5667777888888887 456666665553 366777777666
Q ss_pred cchhhHHHHHHHHHHHhccccchhhhhhhhhHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHhhCCh
Q 042013 192 GSELSKTVATFIVQKILLDDVGLDYICTTAERFFAVGRVLGNMVAALAEQPSSRLLKHIIRCYLRLSDNP 261 (321)
Q Consensus 192 GselSKtvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~~ps~RLLKhiirCYlRLs~n~ 261 (321)
++ .+|++++.-+.=+=.-.-+-.+. |.+|-..+..++.+|-.. -+|.-+.-..+.||.||-.+.
T Consensus 102 ~~-~~K~i~~~~l~~ls~Q~f~~~~~--~~~~~~~l~~~l~~i~~~---~~s~si~~erL~i~~~ll~q~ 165 (372)
T PF12231_consen 102 PN-SPKSICTHYLWCLSDQKFSPKIM--TSDRVERLLAALHNIKNR---FPSKSIISERLNIYKRLLSQF 165 (372)
T ss_pred CC-CCHHHHHHHHHHHHcCCCCCccc--chhhHHHHHHHHHHhhcc---CCchhHHHHHHHHHHHHHHHH
Confidence 55 58999888776554444444433 444444444444443322 466666666777777666543
No 19
>cd00256 VATPase_H VATPase_H, regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is that of a superhelical spiral, in part the geometry is similar to superhelices composed of armadillo repeat motifs, as found in importins for example.
Probab=52.68 E-value=1.9e+02 Score=29.96 Aligned_cols=137 Identities=12% Similarity=0.070 Sum_probs=93.3
Q ss_pred hhhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhh-----chhhhhhhhccccchhhH
Q 042013 123 DTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLST-----EIIPLCLRTMEMGSELSK 197 (321)
Q Consensus 123 etR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~t-----EiiPLCLriME~GselSK 197 (321)
+.|...++..-|.|...|+|..+++..-+.++ -.|-.|.-|+.. ++.-+.++... +..-..++.+..+.....
T Consensus 41 ~~~~~~~~~~~~~y~~~~l~ll~~~~~~d~vq-yvL~Li~dll~~-~~~~~~~f~~~~~~~~~~~~~fl~lL~~~d~~i~ 118 (429)
T cd00256 41 RVKEEILDVLSGQYVKTFVNLLSQIDKDDTVR-YVLTLIDDMLQE-DDTRVKLFHDDALLKKKTWEPFFNLLNRQDQFIV 118 (429)
T ss_pred HHHHHHhcccHHHHHHHHHHHHhccCcHHHHH-HHHHHHHHHHHh-chHHHHHHHHHhhccccchHHHHHHHcCCchhHH
Confidence 46777888888999999999877777655554 456777777766 55555555553 555556667778888899
Q ss_pred HHHHHHHHHHhccccchhhhhhhhhHHHHHHH-HHHHHHHHHhhCCChhhHHHHHHHHHHhhCChhhHHHHHh
Q 042013 198 TVATFIVQKILLDDVGLDYICTTAERFFAVGR-VLGNMVAALAEQPSSRLLKHIIRCYLRLSDNPRACDALRS 269 (321)
Q Consensus 198 tvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~-vL~~mV~~l~~~ps~RLLKhiirCYlRLs~n~rar~aL~~ 269 (321)
-.|.+|+.+++...... .+..... .++....++...-+.+...-.++|+..|-..++.|...-+
T Consensus 119 ~~a~~iLt~l~~~~~~~--------~~~~~l~~~~~~l~~~l~~~~~~~~~~~~v~~L~~LL~~~~~R~~f~~ 183 (429)
T cd00256 119 HMSFSILAKLACFGLAK--------MEGSDLDYYFNWLKEQLNNITNNDYVQTAARCLQMLLRVDEYRFAFVL 183 (429)
T ss_pred HHHHHHHHHHHhcCccc--------cchhHHHHHHHHHHHHhhccCCcchHHHHHHHHHHHhCCchHHHHHHH
Confidence 99999999987643221 1111111 2223333444334588888899999999999999987753
No 20
>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=48.03 E-value=2e+02 Score=25.52 Aligned_cols=184 Identities=15% Similarity=0.171 Sum_probs=93.8
Q ss_pred CCcchHHHHHHHHhhhhhcc--cchhhHHhhhhchHHHHHHHHHhhcCCCCCCCCChhhhhHHHHHHHHHHHHhcCchhh
Q 042013 48 SNPDLRENALLELSKNKELF--QDLAPFVWNSFGTIAALIQEIVSIYPVLSPPNLTPAQSNRVCNALALLQCVASHPDTR 125 (321)
Q Consensus 48 ~~p~~Re~AL~eLsk~re~~--~~La~~LW~S~Gtia~LLQEIisiYp~Lspp~Lt~~~SnRVCnaLaLLQ~vAshpetR 125 (321)
.|=+.|.+||..|-.--... .+..+.++..+. +++ +.+. ..++..-|.=+-+|+.+++-++.+-...
T Consensus 19 ~~W~~r~~al~~L~~l~~~~~~~~~~~~~~~~l~-------~~~---~~i~-~~l~d~Rs~v~~~A~~~l~~l~~~l~~~ 87 (228)
T PF12348_consen 19 SDWEERVEALQKLRSLIKGNAPEDFPPDFVECLR-------QLL---DAII-KQLSDLRSKVSKTACQLLSDLARQLGSH 87 (228)
T ss_dssp SSHHHHHHHHHHHHHHHHH-B-----HHHHHHHH-------------HHHH-H-S-HH---HHHHHHHHHHHHHHHHGGG
T ss_pred cCHHHHHHHHHHHHHHHHcCCccccHHHHHHHHH-------HhH---HHHH-HHHhhhHHHHHHHHHHHHHHHHHHHhHh
Confidence 46678999999887754432 233333333322 111 1111 1233334555558888888888765443
Q ss_pred hhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhch-hhhhhhhccccchhhHHHHHHHH
Q 042013 126 MLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEI-IPLCLRTMEMGSELSKTVATFIV 204 (321)
Q Consensus 126 ~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEi-iPLCLriME~GselSKtvAtfIl 204 (321)
++..+..++-+.|.....++. .+|=+.--++-++++.-. ..+.+ ++.+...+...+-..|..+.-.+
T Consensus 88 ---~~~~~~~~l~~Ll~~~~~~~~--~i~~~a~~~L~~i~~~~~-------~~~~~~~~~l~~~~~~Kn~~vR~~~~~~l 155 (228)
T PF12348_consen 88 ---FEPYADILLPPLLKKLGDSKK--FIREAANNALDAIIESCS-------YSPKILLEILSQGLKSKNPQVREECAEWL 155 (228)
T ss_dssp ---GHHHHHHHHHHHHHGGG---H--HHHHHHHHHHHHHHTTS--------H--HHHHHHHHHHTT-S-HHHHHHHHHHH
T ss_pred ---HHHHHHHHHHHHHHHHccccH--HHHHHHHHHHHHHHHHCC-------cHHHHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 455567777777776665543 466666666666665433 01233 45555566777777776666666
Q ss_pred HHHhccccchhhhhhhhhHHHHHH--HHHHHHHHHHhhCCChhhHHHHHHHHHHhhCC
Q 042013 205 QKILLDDVGLDYICTTAERFFAVG--RVLGNMVAALAEQPSSRLLKHIIRCYLRLSDN 260 (321)
Q Consensus 205 qKIL~dd~GL~YiC~t~eRF~av~--~vL~~mV~~l~~~ps~RLLKhiirCYlRLs~n 260 (321)
..++..-. .+.+.+..-. .-+-+++.....++++.+=+..-+||..+..+
T Consensus 156 ~~~l~~~~------~~~~~l~~~~~~~~l~~~l~~~l~D~~~~VR~~Ar~~~~~l~~~ 207 (228)
T PF12348_consen 156 AIILEKWG------SDSSVLQKSAFLKQLVKALVKLLSDADPEVREAARECLWALYSH 207 (228)
T ss_dssp HHHHTT-----------GGG--HHHHHHHHHHHHHHHTSS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHcc------chHhhhcccchHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Confidence 65554432 1111121111 33555666677788888888888888777554
No 21
>cd00256 VATPase_H VATPase_H, regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is that of a superhelical spiral, in part the geometry is similar to superhelices composed of armadillo repeat motifs, as found in importins for example.
Probab=44.87 E-value=3.8e+02 Score=27.85 Aligned_cols=131 Identities=11% Similarity=0.180 Sum_probs=62.1
Q ss_pred hhhhhhcccCchHHHHHHhhhchhhhhhhhccccchhhHHHHHHHHHHHhccccchhhhhhhhhHHHHHHHHHHHHHHHH
Q 042013 159 GVIGALVKVDDTEVISFLLSTEIIPLCLRTMEMGSELSKTVATFIVQKILLDDVGLDYICTTAERFFAVGRVLGNMVAAL 238 (321)
Q Consensus 159 GVIgaLvK~dd~evI~fLL~tEiiPLCLriME~GselSKtvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL~~mV~~l 238 (321)
...++|++.+.--. .+...+.++....++...+ ...-+.+.++.-==-|.|-+...+.+.. ..++..++.-+
T Consensus 166 ~~L~~LL~~~~~R~--~f~~~~~v~~L~~~L~~~~-----~~~Ql~Y~~ll~lWlLSF~~~~~~~~~~-~~~i~~l~~i~ 237 (429)
T cd00256 166 RCLQMLLRVDEYRF--AFVLADGVPTLVKLLSNAT-----LGFQLQYQSIFCIWLLTFNPHAAEVLKR-LSLIQDLSDIL 237 (429)
T ss_pred HHHHHHhCCchHHH--HHHHccCHHHHHHHHhhcc-----ccHHHHHHHHHHHHHHhccHHHHHhhcc-ccHHHHHHHHH
Confidence 44455565544331 2223445555555554322 2233444444433334444443332211 22333344444
Q ss_pred hhCCChhhHHHHHHHHHHhhCCh--------hhHHHHHhcCCcccc---hhhhhhhhcCCHHHHHHHHHHHHHhC
Q 042013 239 AEQPSSRLLKHIIRCYLRLSDNP--------RACDALRSCLPDMLR---DATFSSCLREDPTTRRWLQQLLHNVG 302 (321)
Q Consensus 239 ~~~ps~RLLKhiirCYlRLs~n~--------rar~aL~~~LP~~Lr---d~~f~~~l~~D~~~k~~l~qLl~nl~ 302 (321)
...+-.++.+-++-+..-|.+.+ .+-.++-..+|..+. ...| .|++...-+.+|-..|.
T Consensus 238 k~s~KEKvvRv~l~~l~Nll~~~~~~~~~~~~~~~mv~~~l~~~l~~L~~rk~-----~DedL~edl~~L~e~L~ 307 (429)
T cd00256 238 KESTKEKVIRIVLAIFRNLISKRVDREVKKTAALQMVQCKVLKTLQSLEQRKY-----DDEDLTDDLKFLTEELK 307 (429)
T ss_pred HhhhhHHHHHHHHHHHHHHhhcccccchhhhHHHHHHHcChHHHHHHHhcCCC-----CcHHHHHHHHHHHHHHH
Confidence 44455566666666666666643 122333445555433 3333 57777777777766654
No 22
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=44.84 E-value=2.5e+02 Score=26.25 Aligned_cols=38 Identities=8% Similarity=0.126 Sum_probs=22.6
Q ss_pred hhHHHHHHHhcCCcchHHHHHHHHhhhhhcccchhhHHhhhhch
Q 042013 37 MASAEHLVLDLSNPDLRENALLELSKNKELFQDLAPFVWNSFGT 80 (321)
Q Consensus 37 ~~~v~q~I~~L~~p~~Re~AL~eLsk~re~~~~La~~LW~S~Gt 80 (321)
.-.+.|.+.+.++++.|..-+.++. +++..+.=|.+|+
T Consensus 57 g~~vvq~~l~~~~~~~~~~i~~~~~------~~~~~l~~~~~g~ 94 (322)
T cd07920 57 GNYVIQKLFEHGTEEQRLQLLEKIL------GHVVRLSLDMYGC 94 (322)
T ss_pred ccHHHHHHHHhCCHHHHHHHHHHHH------HHHHHHcccchhH
Confidence 3466677777788888866555543 3344444455554
No 23
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=41.58 E-value=6.2e+02 Score=29.36 Aligned_cols=192 Identities=20% Similarity=0.351 Sum_probs=118.3
Q ss_pred HHHhcCCcchHHHH-HHHHhhhh--hcccchhhHHhhhhchHHHHHHHHHhhcCCCCCCCCChhh---hhHHHHHHHHHH
Q 042013 43 LVLDLSNPDLRENA-LLELSKNK--ELFQDLAPFVWNSFGTIAALIQEIVSIYPVLSPPNLTPAQ---SNRVCNALALLQ 116 (321)
Q Consensus 43 ~I~~L~~p~~Re~A-L~eLsk~r--e~~~~La~~LW~S~Gtia~LLQEIisiYp~Lspp~Lt~~~---SnRVCnaLaLLQ 116 (321)
-..|...|++-... +.++.+|| |.+| |+|+ ++-+|..-|-.=++++-.+++ +-|+-..|+
T Consensus 381 i~ed~~sp~~Aa~~~l~~~~~KR~ke~l~----------k~l~-F~~~Il~~~~~~~~~~~~~rqkdGAL~~vgsl~--- 446 (1010)
T KOG1991|consen 381 IFEDGYSPDTAALDFLTTLVSKRGKETLP----------KILS-FIVDILTRYKEASPPNKNPRQKDGALRMVGSLA--- 446 (1010)
T ss_pred hhcccCCCcHHHHHHHHHHHHhcchhhhh----------hHHH-HHHHHHHhhcccCCCccChhhhhhHHHHHHHHH---
Confidence 34566677775444 45666677 4555 3443 344566666555555444333 333333332
Q ss_pred HHhcCch----hhhhhhhhccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhchhhhhhhhcccc
Q 042013 117 CVASHPD----TRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEIIPLCLRTMEMG 192 (321)
Q Consensus 117 ~vAshpe----tR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEiiPLCLriME~G 192 (321)
.+-.-++ .=..||.. |++|+++ .|.-|||=-+.-|++.....|=++=..+ .+++-+..+.|-..
T Consensus 447 ~~L~K~s~~~~~mE~flv~----hVfP~f~-----s~~g~Lrarac~vl~~~~~~df~d~~~l---~~ale~t~~~l~~d 514 (1010)
T KOG1991|consen 447 SILLKKSPYKSQMEYFLVN----HVFPEFQ-----SPYGYLRARACWVLSQFSSIDFKDPNNL---SEALELTHNCLLND 514 (1010)
T ss_pred HHHccCCchHHHHHHHHHH----HhhHhhc-----CchhHHHHHHHHHHHHHHhccCCChHHH---HHHHHHHHHHhccC
Confidence 3322222 22334443 4567775 4678999888888888754333333333 44555556666656
Q ss_pred chh-hHHHHHHHHHHHhccccch-hh----hhhhhhHHHHHH---------HHHHHHHHHHhhCCC---hhhHHHHHHHH
Q 042013 193 SEL-SKTVATFIVQKILLDDVGL-DY----ICTTAERFFAVG---------RVLGNMVAALAEQPS---SRLLKHIIRCY 254 (321)
Q Consensus 193 sel-SKtvAtfIlqKIL~dd~GL-~Y----iC~t~eRF~av~---------~vL~~mV~~l~~~ps---~RLLKhiirCY 254 (321)
+|+ -|.-|++=+|-.++++.-. .| +=.+.+.|.++. +|+.+||.+..++-+ +-|-+|..+.+
T Consensus 515 ~~lPV~VeAalALq~fI~~~~~~~e~~~~hvp~~mq~lL~L~ne~End~Lt~vme~iV~~fseElsPfA~eL~q~La~~F 594 (1010)
T KOG1991|consen 515 NELPVRVEAALALQSFISNQEQADEKVSAHVPPIMQELLKLSNEVENDDLTNVMEKIVCKFSEELSPFAVELCQNLAETF 594 (1010)
T ss_pred CcCchhhHHHHHHHHHHhcchhhhhhHhhhhhHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHhhchhHHHHHHHHHHHH
Confidence 666 7889999999999998866 44 445666776654 477788887776544 67889999999
Q ss_pred HHhhCC
Q 042013 255 LRLSDN 260 (321)
Q Consensus 255 lRLs~n 260 (321)
+|+.++
T Consensus 595 ~k~l~~ 600 (1010)
T KOG1991|consen 595 LKVLQT 600 (1010)
T ss_pred HHHHhc
Confidence 999885
No 24
>PF14911 MMS22L_C: S-phase genomic integrity recombination mediator, C-terminal
Probab=40.43 E-value=1.6e+02 Score=30.08 Aligned_cols=180 Identities=21% Similarity=0.229 Sum_probs=99.8
Q ss_pred HHHHHhcCchhhhhhhhhc----cccccccccc---cccCCC----------Ccchhhhhhhhhhhhh--------cccC
Q 042013 114 LLQCVASHPDTRMLFLNAH----IPLYLYPFLN---TTSKSR----------PFEYLRLTSLGVIGAL--------VKVD 168 (321)
Q Consensus 114 LLQ~vAshpetR~~FL~a~----iplyLyPfL~---ttsk~r----------~~E~LRLtSLGVIgaL--------vK~d 168 (321)
+||.+.+.+-.+-.+|+.. |.-|+--|+- .....+ .-|.+|-+.|.||..= .+..
T Consensus 148 ~lqGl~~~~~~~dayL~~~l~~ii~~y~~~Fl~~~~~~~~~~l~~~~~~~~~~~~~l~~~il~~i~~~fl~~~~~~p~p~ 227 (373)
T PF14911_consen 148 FLQGLGRLSQRQDAYLNQQLRNIIQQYLPRFLPASPSKLVARLSTLLSAFTPRNEELRKFILQVIRSNFLEFKGSAPPPR 227 (373)
T ss_pred HHHHHHhcccccChHHHHHHHHHHHHHHhHhccCCCccccccccccccchhhhhhHHHHHHHHHHHHHHhcCCCCCCCCc
Confidence 5677777777777776664 2334333332 222223 3566777777777542 1122
Q ss_pred chHHHHHHhh---h--------------chhhhhhh-hcccc-chhhHHHHHHHHHHHhccccchhhhhhhhhHHHHHHH
Q 042013 169 DTEVISFLLS---T--------------EIIPLCLR-TMEMG-SELSKTVATFIVQKILLDDVGLDYICTTAERFFAVGR 229 (321)
Q Consensus 169 d~evI~fLL~---t--------------EiiPLCLr-iME~G-selSKtvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~ 229 (321)
-.-|+.|+.+ . -+.|-.|+ .|-.+ .+-+|..|+-+++.|+..-. +++=..+..
T Consensus 228 l~~vL~fl~~Ll~~~~~~~~~~~~~~~~~~lp~lL~c~~~v~e~~~~k~~a~e~l~~mv~~~~--------~~~~~~~~~ 299 (373)
T PF14911_consen 228 LASVLAFLQQLLKRLQRQNENQILTLLRLVLPSLLECLMLVNEEPQVKKLATELLQYMVESCQ--------VGSSGEPRE 299 (373)
T ss_pred HHHHHHHHHHHHHhcCcccchhHHHHHHHhhHHHHHHHhhcCCCcchhHHHHHHHHHHHHccc--------ccCcchHHH
Confidence 2334444332 1 14455555 45566 77899999999999998643 222233444
Q ss_pred HHHHHHHHHhhCCChhhHHHHHHHHHHhhC-ChhhHHHHHhcCCcccchhhhhhhhcCCHHHHHHHHHHHHHh
Q 042013 230 VLGNMVAALAEQPSSRLLKHIIRCYLRLSD-NPRACDALRSCLPDMLRDATFSSCLREDPTTRRWLQQLLHNV 301 (321)
Q Consensus 230 vL~~mV~~l~~~ps~RLLKhiirCYlRLs~-n~rar~aL~~~LP~~Lrd~~f~~~l~~D~~~k~~l~qLl~nl 301 (321)
.+.+.+.+.+++--..==.++.+.--.+++ ||..-..|-..+-..++|.+-..=+..|...|+.+.+|+.-+
T Consensus 300 ~l~s~lrsfvqk~l~~~t~~~f~~l~~vA~l~p~lV~~Lip~i~q~l~~~E~kRG~G~d~~lR~~~~rL~~~l 372 (373)
T PF14911_consen 300 QLTSVLRSFVQKYLAHYTYQYFQFLEKVAELDPQLVISLIPTIRQSLKDSERKRGLGRDVALRKALSRLLSHL 372 (373)
T ss_pred HHHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHhcCCcCHHHHHHHHHHHHhc
Confidence 444444444432221111222222223333 555555555555566777777666788999999999998654
No 25
>PF14225 MOR2-PAG1_C: Cell morphogenesis C-terminal
Probab=39.84 E-value=98 Score=29.76 Aligned_cols=117 Identities=20% Similarity=0.239 Sum_probs=80.7
Q ss_pred hhhhhhhhcccCchHHHH-----HHh-hhchhhhhhhhccccc-----hhhHHHHHHHHHHHhc-cccchhhhhhhhhH-
Q 042013 157 SLGVIGALVKVDDTEVIS-----FLL-STEIIPLCLRTMEMGS-----ELSKTVATFIVQKILL-DDVGLDYICTTAER- 223 (321)
Q Consensus 157 SLGVIgaLvK~dd~evI~-----fLL-~tEiiPLCLriME~Gs-----elSKtvAtfIlqKIL~-dd~GL~YiC~t~eR- 223 (321)
++.+..-|++..+.++|. +++ =...+|-||..+|.++ +..+.+|.-|-+--=. ...+|.-+=..|.+
T Consensus 82 tl~lL~~L~~~~~~~lig~~~~rll~~~la~LP~ll~~~d~~~~i~~~~~~~~~A~~La~~a~~~~~~~La~il~~ya~~ 161 (262)
T PF14225_consen 82 TLRLLSRLTPLPDDPLIGDSQSRLLFLLLALLPRLLHAFDDPNPIQPDQECIEIAEALAQVAEAQGLPNLARILSSYAKG 161 (262)
T ss_pred HHHHHHHHhcCCCccccCCCCccHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHhCCCccHHHHHHHHHhc
Confidence 566777777755544443 333 3678999999999999 7788888887776521 24555555555543
Q ss_pred -HHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHhhCCh------hhHHHHHhcCCc
Q 042013 224 -FFAVGRVLGNMVAALAEQPSSRLLKHIIRCYLRLSDNP------RACDALRSCLPD 273 (321)
Q Consensus 224 -F~av~~vL~~mV~~l~~~ps~RLLKhiirCYlRLs~n~------rar~aL~~~LP~ 273 (321)
|.....-+..++..+.+..-|+.--+++-.+..|-+|. ..-..|+..+|.
T Consensus 162 ~fr~~~dfl~~v~~~l~~~f~P~~~~~~l~~Ll~lL~n~~~w~~~~~L~iL~~ll~~ 218 (262)
T PF14225_consen 162 RFRDKDDFLSQVVSYLREAFFPDHEFQILTFLLGLLENGPPWLRRKTLQILKVLLPH 218 (262)
T ss_pred CCCCHHHHHHHHHHHHHHHhCchhHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHhcc
Confidence 66777788888888888887888888888888888875 233444444554
No 26
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=33.65 E-value=85 Score=29.40 Aligned_cols=28 Identities=21% Similarity=0.521 Sum_probs=15.2
Q ss_pred hhhHHHHHHHHHHhhCChhhHHHHHhcC
Q 042013 244 SRLLKHIIRCYLRLSDNPRACDALRSCL 271 (321)
Q Consensus 244 ~RLLKhiirCYlRLs~n~rar~aL~~~L 271 (321)
..+++.+.+=+..|+.|+.+...+.+++
T Consensus 146 ~~i~~~l~~~~~~l~~~~~G~~vvq~~l 173 (322)
T cd07920 146 QFIIDAFKGNCVALSTHPYGCRVIQRCL 173 (322)
T ss_pred HHHHHHHHHHHHHHHcCccccHHHHHHH
Confidence 3445555555566666665555555444
No 27
>cd06224 REM Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few.
Probab=33.12 E-value=1.4e+02 Score=23.90 Aligned_cols=72 Identities=25% Similarity=0.318 Sum_probs=49.4
Q ss_pred HHHHHhcCCcchHHHHHHHHhhhhhcccchhhHHhhhhchHHHHHHHHHhhcCCCCCCCC---------ChhhhhHHHHH
Q 042013 41 EHLVLDLSNPDLRENALLELSKNKELFQDLAPFVWNSFGTIAALIQEIVSIYPVLSPPNL---------TPAQSNRVCNA 111 (321)
Q Consensus 41 ~q~I~~L~~p~~Re~AL~eLsk~re~~~~La~~LW~S~Gtia~LLQEIisiYp~Lspp~L---------t~~~SnRVCna 111 (321)
.++|.-|+++.. ..-+.|-+--.+-..+|.+-..||..+++.|....+... ....-.|||++
T Consensus 3 ~~Li~~L~~~~~---------~~d~~f~~~FllTyrsF~s~~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~~~~~v~~~ 73 (122)
T cd06224 3 EALIEHLTSTFD---------MPDPSFVSTFLLTYRSFTTPTELLEKLIERYEIAPPENLEYNDWDKKKSKPIRLRVLNV 73 (122)
T ss_pred HHHHHHHcCCCc---------cccHHHHHHHHHHhhhhCCHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHH
Confidence 456666766654 123345566677889999999999999999998766542 22334577777
Q ss_pred HHHHHHHhcCch
Q 042013 112 LALLQCVASHPD 123 (321)
Q Consensus 112 LaLLQ~vAshpe 123 (321)
+ -+.|..||+
T Consensus 74 l--~~Wv~~~~~ 83 (122)
T cd06224 74 L--RTWVENYPY 83 (122)
T ss_pred H--HHHHHhCCC
Confidence 6 366777774
No 28
>KOG0301 consensus Phospholipase A2-activating protein (contains WD40 repeats) [Lipid transport and metabolism]
Probab=32.74 E-value=3.4e+02 Score=30.23 Aligned_cols=133 Identities=18% Similarity=0.141 Sum_probs=99.3
Q ss_pred hhhhhhhhhhcccCc---hHHHHHHhhhchhhhhhhhccccchhhHHHHHHHHHHHhccccchhhhhhhhhHHHHHHHHH
Q 042013 155 LTSLGVIGALVKVDD---TEVISFLLSTEIIPLCLRTMEMGSELSKTVATFIVQKILLDDVGLDYICTTAERFFAVGRVL 231 (321)
Q Consensus 155 LtSLGVIgaLvK~dd---~evI~fLL~tEiiPLCLriME~GselSKtvAtfIlqKIL~dd~GL~YiC~t~eRF~av~~vL 231 (321)
+..++.|-++.|..+ .|+..-| +||.+...-..--++-|.=|+.-+..+.-+-.|.|-. |++.. .+
T Consensus 523 ~~~~eeil~li~~s~~~~~e~~~~l-------~~l~~l~~wp~~~~fPalDilRl~v~h~~~~s~~~~~-~~~~~---~~ 591 (745)
T KOG0301|consen 523 INGLEEILSLIKNSSHYSSEVLQSL-------LALAILLQWPVEMMFPALDILRLAVKHHSSNSLFCDR-EEGQN---LV 591 (745)
T ss_pred hhhHHHHHHhhcCCCCccchhHHHH-------HHHHHHhcCCHHHhhhHHHHHHHHHhccchhhhhhhh-hhhhH---HH
Confidence 557888888888655 4444333 7888888888889999999999999999999999974 33332 23
Q ss_pred HHHHHHHhhCCChhhHHHHHHHHHHhhCChhhHHHHHhcCCcccchhhhhhh-hcCCHHHHHHHHHHHHHhC
Q 042013 232 GNMVAALAEQPSSRLLKHIIRCYLRLSDNPRACDALRSCLPDMLRDATFSSC-LREDPTTRRWLQQLLHNVG 302 (321)
Q Consensus 232 ~~mV~~l~~~ps~RLLKhiirCYlRLs~n~rar~aL~~~LP~~Lrd~~f~~~-l~~D~~~k~~l~qLl~nl~ 302 (321)
+..+-.+. -++-..=.++||..-+-.||-.|+.+.+. ....+..|.++ ...+..++.-+..|..|..
T Consensus 592 ~~li~~~~--~~~an~ll~vR~L~N~f~~~~g~~~~~s~--~~~i~~~~~~~~s~~~knl~ia~atlaln~s 659 (745)
T KOG0301|consen 592 GTLIPILN--ADPANQLLVVRCLANLFSNPAGRELFMSR--LESILDPVIEASSLSNKNLQIALATLALNYS 659 (745)
T ss_pred Hhhhcccc--cchhHHHHHHHHHHHhccCHHHHHHHHHH--HHHHhhhhhhhhcccchhHHHHHHHHHHHHH
Confidence 33333333 44666667999999999999999999877 55556667666 4566888888888888865
No 29
>PLN00211 predicted protein; Provisional
Probab=30.69 E-value=35 Score=26.30 Aligned_cols=20 Identities=30% Similarity=0.491 Sum_probs=17.2
Q ss_pred hHHHHHHHHHhhcCCCCCCC
Q 042013 80 TIAALIQEIVSIYPVLSPPN 99 (321)
Q Consensus 80 tia~LLQEIisiYp~Lspp~ 99 (321)
-|+.+|-||.|||..|+.++
T Consensus 31 hMtsfLAeIwSVyr~LSqES 50 (61)
T PLN00211 31 HMTSFLAEIWSVYRPLSHES 50 (61)
T ss_pred HHHHHHHHHHHHhchhhhhh
Confidence 47899999999999998653
No 30
>PF00618 RasGEF_N: RasGEF N-terminal motif; InterPro: IPR000651 The crystal structure of the guanine nucleotide exchange factor (GEF) region of human Sos1 complexes with Ras has been solved []. The structure consists of two distinct alpha helical structural domains: the N-terminal domain which seems to have a purely structural role and the C-terminal domain which is sufficient for catalytic activity and contains all residues that interact with Ras. A main feature of the catalytic domain is the protrusion of a helical hairpin important for the nucleotide-exchange mechanism. The N-terminal domain is likely to be important for the stability and correct placement of the hairpin structure. This entry represents a domain found in several GEF for Ras-like small GTPases which lies N-terminal to the RasGef (Cdc25-like) domain. ; GO: 0005085 guanyl-nucleotide exchange factor activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3CF6_E 2BYV_E 1NVW_S 1BKD_S 1XDV_A 2II0_A 1NVU_S 1NVX_S 1NVV_S 1XD4_B ....
Probab=29.25 E-value=74 Score=25.11 Aligned_cols=72 Identities=25% Similarity=0.388 Sum_probs=44.7
Q ss_pred HHHHHHHhcCCc-chHHHHHHHHhhhhhcccchhhHHhhhhchHHHHHHHHHhhcCCCCCCCCChh----------hhhH
Q 042013 39 SAEHLVLDLSNP-DLRENALLELSKNKELFQDLAPFVWNSFGTIAALIQEIVSIYPVLSPPNLTPA----------QSNR 107 (321)
Q Consensus 39 ~v~q~I~~L~~p-~~Re~AL~eLsk~re~~~~La~~LW~S~Gtia~LLQEIisiYp~Lspp~Lt~~----------~SnR 107 (321)
.+.++|.-|+++ +.. -+.|-+--.+-+.+|-+-.-||+-++..|..-.|+..... .-.|
T Consensus 6 tl~~Li~~L~~~~~~~----------d~~f~~~FllTyr~F~tp~~Ll~~L~~ry~~~~~~~~~~~~~~~~~~~~~i~~r 75 (104)
T PF00618_consen 6 TLEKLIERLTSSFNSD----------DEEFVDTFLLTYRSFTTPEELLDKLIQRYNIPPPNGLSQDESWDQDSQEPIRLR 75 (104)
T ss_dssp -HHHHHHHHCHC-SS-----------HHHHHHHHHHHHHHCS-HHHHHHHHHHHHT---SSS-HHHHT-HHHHHHHHHHH
T ss_pred CHHHHHHHHhcccccC----------CHHHHHHHHHHhHhhCCHHHHHHHHHHHhcccCCccccccchhhhhhhHHHHHH
Confidence 345667777655 333 2245566678889999999999999999986666655443 2347
Q ss_pred HHHHHHHHHHHhcCc
Q 042013 108 VCNALALLQCVASHP 122 (321)
Q Consensus 108 VCnaLaLLQ~vAshp 122 (321)
||++|- +-|-.|+
T Consensus 76 v~~~l~--~Wi~~~~ 88 (104)
T PF00618_consen 76 VLNVLK--YWIENYP 88 (104)
T ss_dssp HHHHHH--HHHHHHC
T ss_pred HHHHHH--HHHHHCh
Confidence 888774 4555555
No 31
>PF14664 RICTOR_N: Rapamycin-insensitive companion of mTOR, N-term
Probab=29.05 E-value=5.3e+02 Score=26.00 Aligned_cols=174 Identities=22% Similarity=0.306 Sum_probs=100.9
Q ss_pred HHHHHHHHhhhhhcccchhh-HHhhhhchHHHHHHHHHhhcCCCCCCCCChhhhhHHHHHHHHHHHHhcCchhhhhhhhh
Q 042013 53 RENALLELSKNKELFQDLAP-FVWNSFGTIAALIQEIVSIYPVLSPPNLTPAQSNRVCNALALLQCVASHPDTRMLFLNA 131 (321)
Q Consensus 53 Re~AL~eLsk~re~~~~La~-~LW~S~Gtia~LLQEIisiYp~Lspp~Lt~~~SnRVCnaLaLLQ~vAshpetR~~FL~a 131 (321)
+.|.|..|.|+ .|.+-. ..|.. +.++|.. ..++ .. +.-++.++-++=.+..+++.-..|++-
T Consensus 3 ~~N~Lv~l~~~---~p~l~~~~~~~~------~~~~i~~--~lL~-----~~-~~vraa~yRilRy~i~d~~~l~~~~~l 65 (371)
T PF14664_consen 3 KANDLVDLLKR---HPTLKYDLVLSF------FGERIQC--MLLS-----DS-KEVRAAGYRILRYLISDEESLQILLKL 65 (371)
T ss_pred hHHHHHHHHHh---CchhhhhhhHHH------HHHHHHH--HHCC-----Cc-HHHHHHHHHHHHHHHcCHHHHHHHHHc
Confidence 45666666654 343322 33444 3344443 2333 22 445566777788888999999999999
Q ss_pred ccccccccccccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhchhhhhhhhccccchhhHHHHHHHHHHHhccc
Q 042013 132 HIPLYLYPFLNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEIIPLCLRTMEMGSELSKTVATFIVQKILLDD 211 (321)
Q Consensus 132 ~iplyLyPfL~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEiiPLCLriME~GselSKtvAtfIlqKIL~dd 211 (321)
|++.|+--=|...++. |.=|...|-.|-+++..+ +.-+|+++.++.-|+.=.-..|
T Consensus 66 ~id~~ii~SL~~~~~~---~~ER~QALkliR~~l~~~---------------------~~~~~~~~~vvralvaiae~~~ 121 (371)
T PF14664_consen 66 HIDIFIIRSLDRDNKN---DVEREQALKLIRAFLEIK---------------------KGPKEIPRGVVRALVAIAEHED 121 (371)
T ss_pred CCchhhHhhhcccCCC---hHHHHHHHHHHHHHHHhc---------------------CCcccCCHHHHHHHHHHHhCCc
Confidence 9999987666654433 334555555555443221 1123455555555555555555
Q ss_pred cchhhhhh---------hhhHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHhhCChhhHHHHHh
Q 042013 212 VGLDYICT---------TAERFFAVGRVLGNMVAALAEQPSSRLLKHIIRCYLRLSDNPRACDALRS 269 (321)
Q Consensus 212 ~GL~YiC~---------t~eRF~av~~vL~~mV~~l~~~ps~RLLKhiirCYlRLs~n~rar~aL~~ 269 (321)
+.+..+|- .++-+.+- ..++-++..+.+ ++..+-.-++...+.+-|+|+.|.-++.
T Consensus 122 D~lr~~cletL~El~l~~P~lv~~~-gG~~~L~~~l~d-~~~~~~~~l~~~lL~lLd~p~tR~yl~~ 186 (371)
T PF14664_consen 122 DRLRRICLETLCELALLNPELVAEC-GGIRVLLRALID-GSFSISESLLDTLLYLLDSPRTRKYLRP 186 (371)
T ss_pred hHHHHHHHHHHHHHHhhCHHHHHHc-CCHHHHHHHHHh-ccHhHHHHHHHHHHHHhCCcchhhhhcC
Confidence 55544442 11111111 223555555665 4444888889999999999988887664
No 32
>PF10167 NEP: Uncharacterised conserved protein; InterPro: IPR019320 This entry represents the uncharacterised protein family UPF0402. It contains a characteristic NEP sequence motif. Their function is not known.
Probab=29.04 E-value=88 Score=26.97 Aligned_cols=40 Identities=20% Similarity=0.360 Sum_probs=31.0
Q ss_pred hhhHHHHHHHHHHHHHHHHhhCCCh---hhHHHHHHHHHHhhC
Q 042013 220 TAERFFAVGRVLGNMVAALAEQPSS---RLLKHIIRCYLRLSD 259 (321)
Q Consensus 220 t~eRF~av~~vL~~mV~~l~~~ps~---RLLKhiirCYlRLs~ 259 (321)
+.+||..+..-++.|+..++++||- ||=.||-|.-=++-+
T Consensus 6 ~~~~~~~~~~~~se~i~~~ANEPSlgLYrlQeHvrkslP~lv~ 48 (118)
T PF10167_consen 6 LEDKVKKVTERISENIHIVANEPSLGLYRLQEHVRKSLPKLVE 48 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhHHHHH
Confidence 5679999999999999999999994 555666665544443
No 33
>PF10521 DUF2454: Protein of unknown function (DUF2454); InterPro: IPR018870 Putative protein of unknown function; subunit of the ASTRA complex which is part of the chromatin remodeling machinery; similar to Schizosaccharomyces pombe (Fission yeast) Tti2p; may interact with Rsm23p [].
Probab=27.85 E-value=1.8e+02 Score=27.68 Aligned_cols=77 Identities=22% Similarity=0.156 Sum_probs=55.6
Q ss_pred hhhhhhhhccccchhhHHHHHHHHHHHhccccchh-hhhhhhhHHHHHHHHHHHHHHHHh----hCCChhhHHHHHHHHH
Q 042013 181 IIPLCLRTMEMGSELSKTVATFIVQKILLDDVGLD-YICTTAERFFAVGRVLGNMVAALA----EQPSSRLLKHIIRCYL 255 (321)
Q Consensus 181 iiPLCLriME~GselSKtvAtfIlqKIL~dd~GL~-YiC~t~eRF~av~~vL~~mV~~l~----~~ps~RLLKhiirCYl 255 (321)
++|..|.++|..+.--|.-+--+++.++..-..-. -.=+...++.-+-..|.++...+- ++.|..|+..+..|..
T Consensus 120 iiP~iL~llDD~~~~~K~~G~~lL~~ll~~~~~~~~~~L~~tGl~~v~~~al~~~L~~LP~~tp~~~s~~Ll~~ay~~L~ 199 (282)
T PF10521_consen 120 IIPPILNLLDDYSPEIKIQGCQLLHHLLEKVPAAEWDILRRTGLFSVFEDALFPCLYYLPPITPEDESLELLQAAYPALL 199 (282)
T ss_pred HHhhHHHHhcCCCHHHHHHHHHHHHHHHHhCChhhhHHHHHcChHHHHHHHHHHHhhcCCCCCCchhhHHHHHHHHHHHH
Confidence 89999999999999999999999999997422211 222233334444445555555442 4778999999999999
Q ss_pred Hh
Q 042013 256 RL 257 (321)
Q Consensus 256 RL 257 (321)
+|
T Consensus 200 ~L 201 (282)
T PF10521_consen 200 SL 201 (282)
T ss_pred HH
Confidence 99
No 34
>TIGR01204 bioW 6-carboxyhexanoate--CoA ligase. Alternate name: pimeloyl-CoA synthase.
Probab=24.73 E-value=52 Score=31.55 Aligned_cols=72 Identities=25% Similarity=0.296 Sum_probs=58.8
Q ss_pred hhhHHHHHHHHHHHHhcCchhhhhhhhhccccccccccccccCCCCcchhhhhhhh----hhhh---hccc--CchHHHH
Q 042013 104 QSNRVCNALALLQCVASHPDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLG----VIGA---LVKV--DDTEVIS 174 (321)
Q Consensus 104 ~SnRVCnaLaLLQ~vAshpetR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLG----VIga---LvK~--dd~evI~ 174 (321)
-..|+.-||+|--+|++||.+--.+--++=|-|-.=|..+ +.+-|.|++-|- -.|+ +|+. |-.++|+
T Consensus 147 ~~~r~~eAlaLAsKV~~~pgvvAElC~SDDP~YtTGYVA~----~~~gY~RI~~lK~~G~~~GGRvffv~~~~~l~~~i~ 222 (232)
T TIGR01204 147 YTLRTVEALALAFKVLFCPAVVAELCWSDDPDYVTGYVSG----KEIGYVRITPLKEKGDELGGRVFFVSRKNELSEYIH 222 (232)
T ss_pred chhHHHHHHHHHHHHhcCCCeEEEEEecCCCCCeeEEEEe----CCCCeEeCccccccCCCCCCEEEEEeCCCCHHHHHH
Confidence 3459999999999999999999999999999998877764 446799999764 4556 7887 5689999
Q ss_pred HHhhh
Q 042013 175 FLLST 179 (321)
Q Consensus 175 fLL~t 179 (321)
||=++
T Consensus 223 yLE~~ 227 (232)
T TIGR01204 223 CLEQK 227 (232)
T ss_pred HHhcC
Confidence 98654
No 35
>PF13513 HEAT_EZ: HEAT-like repeat; PDB: 2Z5J_A 2OT8_B 2Z5O_A 2H4M_A 2QMR_A 1QBK_B 2Z5M_A 2Z5K_A 2Z5N_A 1GCJ_B ....
Probab=24.57 E-value=1.4e+02 Score=20.80 Aligned_cols=51 Identities=12% Similarity=0.195 Sum_probs=34.6
Q ss_pred hhhhhhhhhhhhcccCchHHHHHHhhhchhhhhhhhccccchhhHHHHHHHHH
Q 042013 153 LRLTSLGVIGALVKVDDTEVISFLLSTEIIPLCLRTMEMGSELSKTVATFIVQ 205 (321)
Q Consensus 153 LRLtSLGVIgaLvK~dd~evI~fLL~tEiiPLCLriME~GselSKtvAtfIlq 205 (321)
+|-.++-.||.+......+.-. ...+++|.+...++..++--+.-|.+-+.
T Consensus 3 vR~~A~~aLg~l~~~~~~~~~~--~~~~~~~~L~~~L~d~~~~VR~~A~~aLg 53 (55)
T PF13513_consen 3 VRRAAAWALGRLAEGCPELLQP--YLPELLPALIPLLQDDDDSVRAAAAWALG 53 (55)
T ss_dssp HHHHHHHHHHCTTTTTHHHHHH--HHHHHHHHHHHHTTSSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHhhHhcccHHHHHH--HHHHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 5677777888877665555444 45789999988887766655655555443
No 36
>PF03378 CAS_CSE1: CAS/CSE protein, C-terminus; InterPro: IPR005043 Mammalian cellular apoptosis susceptibility (CAS) proteins and the yeast chromosome-segregation protein, CSE1 are homologous []. CAS is involved in both cellular apoptosis and proliferation [, ]. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation. Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle [], as is the protein MEK, which is thought to regulate the intracellular localization (predominantly nuclear vs. predominantly cytosolic) of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway []. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins []. Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins []. This entry represents the C-terminal portion of these proteins. Structural studies of the yeast CSE1 protein indicate that this domain binds to both the transport-orchestrating protein RanGTP and the cargo molecule that is being exported [].; GO: 0005515 protein binding; PDB: 1Z3H_B 1WA5_C.
Probab=23.33 E-value=2.9e+02 Score=28.45 Aligned_cols=48 Identities=25% Similarity=0.445 Sum_probs=34.4
Q ss_pred hhhHHhhhhchHHH---HHHHHHhhcCCCCCCCCChhhhhHHHHHHHHHHHHhcCch
Q 042013 70 LAPFVWNSFGTIAA---LIQEIVSIYPVLSPPNLTPAQSNRVCNALALLQCVASHPD 123 (321)
Q Consensus 70 La~~LW~S~Gtia~---LLQEIisiYp~Lspp~Lt~~~SnRVCnaLaLLQ~vAshpe 123 (321)
|+|.+|++.|-|.+ ||+-++...|..- .+.+++-.+|+.||-+.++..
T Consensus 165 l~p~lWe~~gniPalvrLL~a~i~k~~~~i------~~~~~l~~iLgvFQkLi~sk~ 215 (435)
T PF03378_consen 165 LSPALWERRGNIPALVRLLQAYIKKDPSFI------VANNQLEPILGVFQKLIASKA 215 (435)
T ss_dssp TSGGGGGSTTTHHHHHHHHHHHHHHHGGG----------S-CHHHHHHHHHHHT-TT
T ss_pred cCcchhccCCCcCcHHHHHHHHHHhCchhh------cchhhHHHHHHHHHHHHCCCC
Confidence 58899999999985 6788888887643 234677789999999977653
No 37
>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=23.18 E-value=2e+02 Score=19.06 Aligned_cols=38 Identities=11% Similarity=0.106 Sum_probs=29.8
Q ss_pred chHHHHHHhhhchhhhhhhhccccchhhHHHHHHHHHH
Q 042013 169 DTEVISFLLSTEIIPLCLRTMEMGSELSKTVATFIVQK 206 (321)
Q Consensus 169 d~evI~fLL~tEiiPLCLriME~GselSKtvAtfIlqK 206 (321)
++|-+..+.+...||..++.|+.+++--+.-|.--+..
T Consensus 1 ~~~~~~~i~~~g~i~~Lv~ll~~~~~~v~~~a~~al~n 38 (41)
T PF00514_consen 1 SPENKQAIVEAGGIPPLVQLLKSPDPEVQEEAAWALGN 38 (41)
T ss_dssp SHHHHHHHHHTTHHHHHHHHTTSSSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHcccHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 35667778889999999999998888888777665543
No 38
>PF05536 Neurochondrin: Neurochondrin
Probab=22.92 E-value=3.6e+02 Score=28.60 Aligned_cols=107 Identities=26% Similarity=0.252 Sum_probs=73.8
Q ss_pred HHHHHHHHHhcCch----hhhhhhhhccccccccccccccCC---CCcchhhhhhhhhhhhhcccCchHHHHHHhhhchh
Q 042013 110 NALALLQCVASHPD----TRMLFLNAHIPLYLYPFLNTTSKS---RPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEII 182 (321)
Q Consensus 110 naLaLLQ~vAshpe----tR~~FL~a~iplyLyPfL~ttsk~---r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEii 182 (321)
-+|.++-.+..+.+ +|+...+|==|-||...|+|.+.. .+.+|+.| .+.|+.|..- ++|+..==--.+-|
T Consensus 24 agL~lvtk~~~~~~~~~~~~~~v~~aig~~Fl~RLL~t~~~~~~~~~~~~~~L-avsvL~~f~~--~~~~a~~~~~~~~I 100 (543)
T PF05536_consen 24 AGLLLVTKLLDADDEDSQTRRRVFEAIGFKFLDRLLRTGSVPSDCPPEEYLSL-AVSVLAAFCR--DPELASSPQMVSRI 100 (543)
T ss_pred HHHHHHHHcCCCchhhHHHHHHHHHhcChhHHHHHhcCCCCCCCCCHHHHHHH-HHHHHHHHcC--ChhhhcCHHHHHHH
Confidence 35566666665444 343344666678999999987653 34556554 3455665554 55554322225789
Q ss_pred hhhhhhccccch-hhHHHHHHHHHHHhccccchhhhhh
Q 042013 183 PLCLRTMEMGSE-LSKTVATFIVQKILLDDVGLDYICT 219 (321)
Q Consensus 183 PLCLriME~Gse-lSKtvAtfIlqKIL~dd~GL~YiC~ 219 (321)
|+.+.+|..+++ -.-.-|-.++.-|-....|-+++++
T Consensus 101 P~Lle~l~~~s~~~~v~dalqcL~~Ias~~~G~~aLl~ 138 (543)
T PF05536_consen 101 PLLLEILSSSSDLETVDDALQCLLAIASSPEGAKALLE 138 (543)
T ss_pred HHHHHHHHcCCchhHHHHHHHHHHHHHcCcHhHHHHHh
Confidence 999999999988 6777788999999999999998887
No 39
>PRK01322 6-carboxyhexanoate--CoA ligase; Provisional
Probab=22.60 E-value=58 Score=31.42 Aligned_cols=73 Identities=30% Similarity=0.403 Sum_probs=59.1
Q ss_pred hhhHHHHHHHHHHHHhcCchhhhhhhhhccccccccccccccCCCCcchhhhhhhh----hhhh---hccc--CchHHHH
Q 042013 104 QSNRVCNALALLQCVASHPDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLRLTSLG----VIGA---LVKV--DDTEVIS 174 (321)
Q Consensus 104 ~SnRVCnaLaLLQ~vAshpetR~~FL~a~iplyLyPfL~ttsk~r~~E~LRLtSLG----VIga---LvK~--dd~evI~ 174 (321)
..+|+.-||+|--+|++||.+--.+--++=|-|-.=|..+ +.+-|.|++-+- -.|+ +|+. |-.++|+
T Consensus 154 ~~~r~~eAlaLAsKV~~~pgivAElC~SDDP~YtTGYVA~----~~~gY~RI~~mK~~G~~~GGRvffv~~~~~~~~~i~ 229 (242)
T PRK01322 154 LTERTVDALALASKVIAHPGVIAELCWSDDPDYTTGYVAT----KKLGYHRITNLKEEGTPYGGRIFFVDDSIDLEELIS 229 (242)
T ss_pred cchHHHHHHHHHHHHhcCCCeEEEEEecCCCCCeeEEEEe----CCCCeEeCccccccCCCCCCEEEEEeCccCHHHHHH
Confidence 4579999999999999999999999999999998877764 346789999764 3466 7776 5688999
Q ss_pred HHhhhc
Q 042013 175 FLLSTE 180 (321)
Q Consensus 175 fLL~tE 180 (321)
||=++=
T Consensus 230 yLE~~p 235 (242)
T PRK01322 230 YLENKP 235 (242)
T ss_pred HHhcCc
Confidence 986653
No 40
>PF05536 Neurochondrin: Neurochondrin
Probab=22.18 E-value=3.1e+02 Score=29.06 Aligned_cols=143 Identities=20% Similarity=0.156 Sum_probs=81.5
Q ss_pred hhhcccchhhHHhhhhchHHHHH--HHHHhhcCCCCCCCCChhhhhHHHHHHHHHHHHhcCchhhhhhhhhccccccccc
Q 042013 63 NKELFQDLAPFVWNSFGTIAALI--QEIVSIYPVLSPPNLTPAQSNRVCNALALLQCVASHPDTRMLFLNAHIPLYLYPF 140 (321)
Q Consensus 63 ~re~~~~La~~LW~S~Gtia~LL--QEIisiYp~Lspp~Lt~~~SnRVCnaLaLLQ~vAshpetR~~FL~a~iplyLyPf 140 (321)
.++.+.+||.-+-+.|.+..-+- .++++.-|.|..--.+.....=+..++.+|+.|++||+-+..|++.+-..-|...
T Consensus 69 ~~~~~~~LavsvL~~f~~~~~~a~~~~~~~~IP~Lle~l~~~s~~~~v~dalqcL~~Ias~~~G~~aLl~~g~v~~L~ei 148 (543)
T PF05536_consen 69 PPEEYLSLAVSVLAAFCRDPELASSPQMVSRIPLLLEILSSSSDLETVDDALQCLLAIASSPEGAKALLESGAVPALCEI 148 (543)
T ss_pred CHHHHHHHHHHHHHHHcCChhhhcCHHHHHHHHHHHHHHHcCCchhHHHHHHHHHHHHHcCcHhHHHHHhcCCHHHHHHH
Confidence 35678888888888888866443 5555555554421111111356789999999999999999999998876666666
Q ss_pred cccccCCCCcchhhhhhhhhhhhhcccCchHHHH--HHhhhchhhhhhhhccccchhhHHHHHHHHHHHhccc
Q 042013 141 LNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVIS--FLLSTEIIPLCLRTMEMGSELSKTVATFIVQKILLDD 211 (321)
Q Consensus 141 L~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~--fLL~tEiiPLCLriME~GselSKtvAtfIlqKIL~dd 211 (321)
+.. +.+..|. .+.+...++-..+.+.+. .-.-+.+++-.=+.+....+..|--+..++..+|...
T Consensus 149 ~~~--~~~~~E~----Al~lL~~Lls~~~~~~~~~~~~~l~~il~~La~~fs~~~~~~kfell~~L~~~L~~~ 215 (543)
T PF05536_consen 149 IPN--QSFQMEI----ALNLLLNLLSRLGQKSWAEDSQLLHSILPSLARDFSSFHGEDKFELLEFLSAFLPRS 215 (543)
T ss_pred HHh--CcchHHH----HHHHHHHHHHhcchhhhhhhHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHhcCcC
Confidence 544 3333332 233333333222222221 0000123333444445555555555556666665554
No 41
>PF04802 SMK-1: Component of IIS longevity pathway SMK-1; InterPro: IPR006887 This is a conserved region which characterises a number of eukaryotic proteins of unknown function.
Probab=21.60 E-value=98 Score=28.58 Aligned_cols=61 Identities=23% Similarity=0.328 Sum_probs=41.9
Q ss_pred cccccCCCCcchhhhhhhhhhhhhcccCchHHHHHHhhhchhhhhhhhccccchhhHHHHHH
Q 042013 141 LNTTSKSRPFEYLRLTSLGVIGALVKVDDTEVISFLLSTEIIPLCLRTMEMGSELSKTVATF 202 (321)
Q Consensus 141 L~ttsk~r~~E~LRLtSLGVIgaLvK~dd~evI~fLL~tEiiPLCLriME~GselSKtvAtf 202 (321)
+++.......|.|...+ .++-+|+--+|+++++.+++-|.+.-+..++|...|+...-|.+
T Consensus 14 F~~~E~~~~~~~L~~l~-~Ivk~li~ln~~~i~e~llsde~i~~vvG~LEYDp~~~~~ka~h 74 (193)
T PF04802_consen 14 FHQCEDLEDLEGLHLLF-DIVKTLILLNDPEIFEILLSDENIMDVVGILEYDPEFPQPKANH 74 (193)
T ss_pred HHHHHcCCCHHHHHHHH-HHHHHHHHcCCchHHHHHhchHHHHHHhhhhccCCcccccccch
Confidence 34444444444443221 23334444689999999999999999999999999998755543
No 42
>PF12452 DUF3685: Protein of unknown function (DUF3685) ; InterPro: IPR022552 This entry represents proteins annotated as Ycf55. It is found encoded in the chloroplast genomes of algae, it is also found in plants and in the cyanobacteria. The function is unknown, though there are two completely conserved residues (L and D) that may be functionally important. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis. Some members of this family are predicted to be response regulators because they contain an N-terminal CheY-like receiver domain.
Probab=21.44 E-value=52 Score=30.70 Aligned_cols=37 Identities=24% Similarity=0.438 Sum_probs=0.0
Q ss_pred HHHHHHH--HHHHHhcCchhhhhhhhhccccccccccccccCCCCcchhh
Q 042013 107 RVCNALA--LLQCVASHPDTRMLFLNAHIPLYLYPFLNTTSKSRPFEYLR 154 (321)
Q Consensus 107 RVCnaLa--LLQ~vAshpetR~~FL~a~iplyLyPfL~ttsk~r~~E~LR 154 (321)
|+||..+ +|.+.+.+|++|..|.+.++- .||+.|-+|
T Consensus 49 ~~An~V~~~lLn~~s~~~~ik~~l~~~~ll-----------STReLeRfR 87 (193)
T PF12452_consen 49 QVANGVAQPLLNNFSDWEEIKQYLYNSSLL-----------STRELERFR 87 (193)
T ss_pred HHHHHHHHHHHHHCCCcHHHHHHhcchhhh-----------chHHHHHHH
No 43
>KOG4523 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.13 E-value=1.3e+02 Score=26.84 Aligned_cols=35 Identities=23% Similarity=0.466 Sum_probs=29.0
Q ss_pred hhhhHHHHHHHHHHHHHHHHhhCCC---hhhHHHHHHH
Q 042013 219 TTAERFFAVGRVLGNMVAALAEQPS---SRLLKHIIRC 253 (321)
Q Consensus 219 ~t~eRF~av~~vL~~mV~~l~~~ps---~RLLKhiirC 253 (321)
.+.+||.-|..-+.-||..++.+|| .||=.||.+.
T Consensus 5 e~~dgfaeInE~iaEmik~iaNEPSl~LY~iQeHirna 42 (157)
T KOG4523|consen 5 EIEDGFAEINERIAEMIKLIANEPSLALYRIQEHIRNA 42 (157)
T ss_pred ehhhhhHHHHHHHHHHHHHHcCCchHHHHHHHHHHHhh
Confidence 3568999999999999999999999 4566676664
No 44
>PF06371 Drf_GBD: Diaphanous GTPase-binding Domain; InterPro: IPR010473 Diaphanous-related formins (Drfs) are a family of formin homology (FH) proteins that act as effectors of Rho small GTPases during growth factor-induced cytoskeletal remodelling, stress fibre formation, and cell division []. Drf proteins are characterised by a variety of shared domains: an N-terminal GTPase-binding domain (GBD), formin-homology domains FH1, FH2 (IPR003104 from INTERPRO) and FH3 (IPR010472 from INTERPRO), and a C-terminal conserved Dia-autoregulatory domain (DAD) that binds the GBD. This entry represents the GBD, which is a bifunctional autoinhibitory domain that interacts with and is regulated by activated Rho family members. Mammalian Drf3 contains a CRIB-like motif within its GBD for binding to Cdc42, which is required for Cdc42 to activate and guide Drf3 towards the cell cortex where it remodels the actin skeleton [].; GO: 0003779 actin binding, 0017048 Rho GTPase binding, 0030036 actin cytoskeleton organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=20.24 E-value=5.5e+02 Score=21.92 Aligned_cols=80 Identities=19% Similarity=0.237 Sum_probs=53.5
Q ss_pred cccchhhhhhhhhHHHHHHHHHHHHHHHHhh-CCChhhHHHHHHHHHHhhCChhhHHHHHhcCCcccchhhhhhhhcCCH
Q 042013 210 DDVGLDYICTTAERFFAVGRVLGNMVAALAE-QPSSRLLKHIIRCYLRLSDNPRACDALRSCLPDMLRDATFSSCLREDP 288 (321)
Q Consensus 210 dd~GL~YiC~t~eRF~av~~vL~~mV~~l~~-~ps~RLLKhiirCYlRLs~n~rar~aL~~~LP~~Lrd~~f~~~l~~D~ 288 (321)
+..|+...+ .+|..+...-.. +....+...++||.--+.++..+++++-+ -|+.+. .-...+.-.++
T Consensus 105 ~~~G~~~L~----------~~L~~~~~~~~~~~~~~~~~~~~l~Clkal~n~~~G~~~v~~-~~~~v~-~i~~~L~s~~~ 172 (187)
T PF06371_consen 105 ELGGLEALL----------NVLSKLNKKKEKSEEDIDIEHECLRCLKALMNTKYGLEAVLS-HPDSVN-LIALSLDSPNI 172 (187)
T ss_dssp HHHHHHHHH----------HHHHHHHTHHCTCTTCHHHHHHHHHHHHHHTSSHHHHHHHHC-SSSHHH-HHHHT--TTSH
T ss_pred cCCCHHHHH----------HHHHHhhhhhhhcchhHHHHHHHHHHHHHHHccHHHHHHHHc-CcHHHH-HHHHHHCCCCH
Confidence 346775544 344444443333 36678889999999999999998888877 555552 22333346789
Q ss_pred HHHHHHHHHHHHh
Q 042013 289 TTRRWLQQLLHNV 301 (321)
Q Consensus 289 ~~k~~l~qLl~nl 301 (321)
.++.+..++|.-+
T Consensus 173 ~~r~~~leiL~~l 185 (187)
T PF06371_consen 173 KTRKLALEILAAL 185 (187)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988654
Done!