Query 004857
Match_columns 727
No_of_seqs 296 out of 1658
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 14:05:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004857.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004857hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1488 Translational represso 100.0 9.7E-72 2.1E-76 616.9 35.5 345 381-726 153-502 (503)
2 cd07920 Pumilio Pumilio-family 100.0 6.4E-57 1.4E-61 482.2 32.9 319 400-719 3-322 (322)
3 PF07990 NABP: Nucleic acid bi 100.0 5.8E-51 1.3E-55 436.5 15.0 234 145-402 135-385 (385)
4 COG5099 RNA-binding protein of 100.0 2.7E-48 5.8E-53 452.1 26.5 312 412-724 447-762 (777)
5 KOG2049 Translational represso 100.0 5.5E-45 1.2E-49 407.3 21.2 313 401-719 212-532 (536)
6 cd07920 Pumilio Pumilio-family 100.0 1.4E-40 3.1E-45 356.0 29.6 298 379-683 16-322 (322)
7 KOG1488 Translational represso 100.0 9.6E-42 2.1E-46 378.4 19.0 245 399-644 245-498 (503)
8 KOG2050 Puf family RNA-binding 100.0 1E-39 2.3E-44 359.2 25.6 305 364-721 135-442 (652)
9 KOG2049 Translational represso 100.0 6.1E-30 1.3E-34 286.7 13.9 263 376-640 256-531 (536)
10 COG5099 RNA-binding protein of 100.0 7.1E-29 1.5E-33 290.0 20.8 236 484-725 447-683 (777)
11 KOG2188 Predicted RNA-binding 99.9 2.7E-25 5.8E-30 248.0 23.4 314 400-719 93-605 (650)
12 KOG2188 Predicted RNA-binding 99.9 9E-21 2E-25 212.0 23.6 289 435-724 92-574 (650)
13 KOG2050 Puf family RNA-binding 99.8 1.2E-19 2.6E-24 201.4 24.3 264 454-725 135-408 (652)
14 KOG4574 RNA-binding protein (c 99.6 1.1E-15 2.4E-20 174.6 11.1 289 430-721 534-851 (1007)
15 KOG4574 RNA-binding protein (c 99.3 1.3E-11 2.8E-16 141.9 11.3 309 379-697 515-863 (1007)
16 PF00806 PUF: Pumilio-family R 98.1 8.5E-07 1.8E-11 65.1 1.4 35 439-473 1-35 (35)
17 smart00025 Pumilio Pumilio-lik 97.7 1.2E-05 2.7E-10 58.0 0.8 32 441-472 3-34 (36)
18 PF00806 PUF: Pumilio-family R 97.6 5.1E-05 1.1E-09 55.6 3.0 35 403-437 1-35 (35)
19 smart00025 Pumilio Pumilio-lik 97.4 9.7E-05 2.1E-09 53.3 2.7 34 404-437 2-35 (36)
20 PRK05686 fliG flagellar motor 95.3 3.5 7.6E-05 45.6 22.5 81 596-699 201-286 (339)
21 TIGR00207 fliG flagellar motor 94.0 12 0.00026 41.5 23.7 82 597-701 199-285 (338)
22 PRK05686 fliG flagellar motor 91.3 21 0.00046 39.5 20.0 85 416-509 80-165 (339)
23 PF08144 CPL: CPL (NUC119) dom 88.5 0.83 1.8E-05 44.7 5.4 71 617-687 58-133 (148)
24 PF04286 DUF445: Protein of un 88.2 43 0.00093 36.5 20.8 49 611-659 289-339 (367)
25 COG2733 Predicted membrane pro 85.1 63 0.0014 36.5 18.0 192 523-721 162-371 (415)
26 PF12231 Rif1_N: Rap1-interact 80.7 1E+02 0.0022 34.5 18.3 165 526-709 178-357 (372)
27 PF04286 DUF445: Protein of un 78.1 1.1E+02 0.0024 33.3 19.0 21 689-709 289-309 (367)
28 PF08144 CPL: CPL (NUC119) dom 77.2 15 0.00031 36.1 8.9 65 581-645 58-133 (148)
29 KOG2213 Apoptosis inhibitor 5/ 75.4 59 0.0013 36.9 13.7 112 609-721 120-243 (460)
30 PF09770 PAT1: Topoisomerase I 70.4 6.1 0.00013 48.7 5.5 93 407-499 576-694 (808)
31 COG1747 Uncharacterized N-term 69.4 2.4E+02 0.0053 33.4 18.0 38 481-518 57-94 (711)
32 COG1536 FliG Flagellar motor s 68.1 2.1E+02 0.0045 32.1 22.1 90 598-705 203-292 (339)
33 cd03567 VHS_GGA VHS domain fam 67.8 93 0.002 30.2 11.9 74 636-726 60-135 (139)
34 cd03569 VHS_Hrs_Vps27p VHS dom 62.1 1.6E+02 0.0034 28.6 13.6 74 635-726 62-136 (142)
35 KOG1086 Cytosolic sorting prot 60.0 2.9E+02 0.0063 31.9 15.2 30 631-660 171-203 (594)
36 PF05918 API5: Apoptosis inhib 58.2 1.8E+02 0.0039 34.7 14.0 111 608-721 144-271 (556)
37 cd03568 VHS_STAM VHS domain fa 57.3 1.9E+02 0.0042 28.1 12.6 74 635-726 58-132 (144)
38 PF11573 Med23: Mediator compl 56.3 1.4E+02 0.0029 39.2 13.5 44 615-658 272-315 (1341)
39 COG5593 Nucleic-acid-binding p 56.0 3.1E+02 0.0068 32.5 14.9 17 418-434 119-135 (821)
40 cd03565 VHS_Tom1 VHS domain fa 53.9 2.2E+02 0.0047 27.6 13.1 78 634-726 59-137 (141)
41 TIGR00207 fliG flagellar motor 52.9 3.6E+02 0.0079 29.9 18.3 53 426-478 50-104 (338)
42 PLN03218 maturation of RBCL 1; 52.9 6.3E+02 0.014 32.7 18.6 57 420-477 443-499 (1060)
43 KOG1992 Nuclear export recepto 51.0 4.7E+02 0.01 32.7 15.9 53 562-614 701-757 (960)
44 PLN03083 E3 UFM1-protein ligas 50.6 6E+02 0.013 31.8 18.5 46 456-505 532-577 (803)
45 COG1747 Uncharacterized N-term 48.9 3.9E+02 0.0085 31.7 14.2 25 601-625 227-253 (711)
46 KOG2160 Armadillo/beta-catenin 45.3 4.9E+02 0.011 29.2 21.8 122 428-573 95-222 (342)
47 KOG2199 Signal transducing ada 44.1 4.4E+02 0.0096 30.2 13.4 41 686-726 100-140 (462)
48 KOG1991 Nuclear transport rece 43.8 6.7E+02 0.015 31.9 16.0 180 446-630 397-599 (1010)
49 COG5240 SEC21 Vesicle coat com 43.3 4.4E+02 0.0096 31.7 13.7 110 588-706 344-462 (898)
50 smart00288 VHS Domain present 42.6 3.1E+02 0.0067 26.1 12.4 75 635-726 58-133 (133)
51 PF05918 API5: Apoptosis inhib 41.7 5.7E+02 0.012 30.6 14.7 21 464-484 145-165 (556)
52 PF02854 MIF4G: MIF4G domain; 38.5 2.9E+02 0.0062 26.9 10.3 32 693-724 169-204 (209)
53 PF01602 Adaptin_N: Adaptin N 38.0 6.2E+02 0.013 28.9 14.4 9 691-699 356-364 (526)
54 PF10508 Proteasom_PSMB: Prote 36.2 7.6E+02 0.017 28.9 21.8 303 381-703 2-346 (503)
55 PF11510 FA_FANCE: Fanconi Ana 36.1 3E+02 0.0066 29.7 10.5 22 420-441 39-60 (263)
56 KOG4368 Predicted RNA binding 35.9 6.4E+02 0.014 30.3 13.5 11 669-679 242-252 (757)
57 PF14666 RICTOR_M: Rapamycin-i 35.8 1.6E+02 0.0035 30.9 8.3 39 614-653 178-216 (226)
58 PF12231 Rif1_N: Rap1-interact 35.1 3.6E+02 0.0079 30.2 11.5 48 598-646 177-224 (372)
59 PF08625 Utp13: Utp13 specific 35.1 4.3E+02 0.0094 25.7 11.3 108 602-724 17-128 (141)
60 PF09770 PAT1: Topoisomerase I 34.8 30 0.00066 42.7 3.2 41 443-483 576-616 (808)
61 KOG4368 Predicted RNA binding 34.3 9E+02 0.019 29.1 16.5 81 568-659 129-214 (757)
62 KOG2236 Uncharacterized conser 34.2 1.3E+02 0.0029 34.7 7.7 39 56-94 298-338 (483)
63 PRK07194 fliG flagellar motor 32.9 7.2E+02 0.016 27.6 21.2 53 425-477 47-101 (334)
64 COG2733 Predicted membrane pro 32.5 8.1E+02 0.018 28.1 13.3 45 404-451 155-199 (415)
65 TIGR00400 mgtE Mg2+ transporte 30.5 2E+02 0.0044 33.0 8.8 14 493-506 107-120 (449)
66 PF14666 RICTOR_M: Rapamycin-i 30.5 2.3E+02 0.0051 29.7 8.5 75 622-703 144-224 (226)
67 COG4399 Uncharacterized protei 29.1 8.8E+02 0.019 27.4 13.1 9 419-427 94-102 (376)
68 PRK07003 DNA polymerase III su 28.7 2.6E+02 0.0056 34.9 9.3 28 687-714 319-346 (830)
69 KOG1059 Vesicle coat complex A 28.0 1.3E+03 0.027 28.8 17.2 25 439-463 218-242 (877)
70 PF03224 V-ATPase_H_N: V-ATPas 27.8 8E+02 0.017 26.5 12.6 24 366-393 16-39 (312)
71 PLN03218 maturation of RBCL 1; 27.8 1.4E+03 0.031 29.5 19.4 22 420-441 376-397 (1060)
72 COG1536 FliG Flagellar motor s 26.8 9.4E+02 0.02 27.0 19.8 61 634-702 263-323 (339)
73 KOG4347 GTPase-activating prot 26.2 9.7E+02 0.021 29.2 13.1 166 454-622 291-481 (671)
74 PF00790 VHS: VHS domain; Int 25.9 3.8E+02 0.0081 25.6 8.4 36 691-726 105-140 (140)
75 KOG1992 Nuclear export recepto 25.9 1.7E+02 0.0037 36.2 7.1 61 418-478 701-766 (960)
76 cd03569 VHS_Hrs_Vps27p VHS dom 25.6 1.9E+02 0.0041 28.1 6.3 33 563-595 63-95 (142)
77 PF14500 MMS19_N: Dos2-interac 25.2 8.6E+02 0.019 26.0 15.4 29 614-644 188-216 (262)
78 PF11510 FA_FANCE: Fanconi Ana 24.6 9.1E+02 0.02 26.1 12.0 114 511-630 95-213 (263)
79 PTZ00429 beta-adaptin; Provisi 23.7 1.5E+03 0.032 28.2 20.6 259 420-694 239-536 (746)
80 PF12069 DUF3549: Protein of u 23.7 1.1E+03 0.023 26.6 13.9 29 430-458 125-153 (340)
81 KOG1070 rRNA processing protei 23.4 1.4E+03 0.031 30.5 14.5 39 406-444 1446-1488(1710)
82 PF01602 Adaptin_N: Adaptin N 23.4 1.1E+03 0.025 26.8 17.2 37 688-724 467-503 (526)
83 KOG1820 Microtubule-associated 23.3 3.7E+02 0.008 33.7 9.5 113 578-701 349-471 (815)
84 PRK07764 DNA polymerase III su 23.0 1.3E+03 0.028 29.0 14.3 29 685-713 324-352 (824)
85 TIGR00400 mgtE Mg2+ transporte 22.5 2.1E+02 0.0046 32.9 7.0 60 419-478 21-80 (449)
86 PF10521 DUF2454: Protein of u 22.4 8.1E+02 0.018 26.2 11.1 84 427-523 107-205 (282)
87 PLN03081 pentatricopeptide (PP 22.1 1.4E+03 0.031 27.4 19.3 58 419-477 128-185 (697)
88 PF10521 DUF2454: Protein of u 21.8 1E+03 0.022 25.5 12.8 53 488-540 95-154 (282)
89 PF05794 Tcp11: T-complex prot 21.2 3.5E+02 0.0076 30.7 8.4 29 597-626 100-128 (441)
90 KOG0166 Karyopherin (importin) 21.2 1.4E+03 0.031 27.1 17.0 82 483-564 209-296 (514)
91 KOG1060 Vesicle coat complex A 21.0 1.7E+03 0.037 28.0 14.4 86 610-707 386-479 (968)
92 PF02854 MIF4G: MIF4G domain; 20.4 3.6E+02 0.0078 26.2 7.4 14 487-500 70-83 (209)
93 KOG1924 RhoA GTPase effector D 20.2 7.8E+02 0.017 30.7 10.9 47 438-484 716-762 (1102)
94 KOG2072 Translation initiation 20.1 1.1E+03 0.023 29.7 12.0 48 445-492 172-219 (988)
No 1
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.7e-72 Score=616.94 Aligned_cols=345 Identities=55% Similarity=0.914 Sum_probs=328.9
Q ss_pred ChhhhHHHHHhhcc-ccccchHHhHHHHHHHHhcCCCccHHHHHhhhcCCH-HHHHHHHHHHhhchhhhccCccccchhh
Q 004857 381 DSKKHSFLEELKSS-NAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSA-EEKVSVFKEVLPHASKLMTDVFGNYVIQ 458 (727)
Q Consensus 381 d~~r~~LLeeL~~~-~~~~~~L~~I~GkIveLa~dq~gSRvLQ~lLk~~t~-Eqr~~If~EI~~~~~eL~tD~fGn~VVQ 458 (727)
-..+..+++++.+. ..+.+.+.++.|++++++.||+||||||+.|+.++. +++..||+||.+.+.+||+|.|||||||
T Consensus 153 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~v~f~~Dq~GsrfiQqkl~~~~~~~ek~~if~ei~~~~~~L~~dvFGNyvIQ 232 (503)
T KOG1488|consen 153 STGPSFLLDPFRSNSLSKTLELVDIPGHLVEFAKDQHGSRFIQQKLETASDNEEKQAVFDEILPPALELMTDVFGNYVIQ 232 (503)
T ss_pred CCCCCccccccccccccccccccccCCCceeecCCcccchHHHHhccccccHHHHHHHHHHHHHHHHHHHHHHhcCchhh
Confidence 34556677777766 567778889999999999999999999999999988 9999999999999999999999999999
Q ss_pred hhhccCCHHHHHHHHHHHhcChhhhccCcchhHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhhcccCchhhhHhhhcCCh
Q 004857 459 KFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPA 538 (727)
Q Consensus 459 KLLe~gs~eqr~~Ii~~L~G~v~~La~h~yGSrVIQklIe~as~eqr~~Lv~EL~g~i~~L~~D~~GNhVIQklLe~~~~ 538 (727)
|+||+++++++..+...++|++..|+.|+|||||||++|+..+.+++.+|++||.+++..|++|++||||||||||+.+.
T Consensus 233 kffE~gt~~q~~~l~~~~~g~v~~Lsld~ygCRVIQkale~id~~~~~~Li~ELd~~vl~~v~DQngnHViQK~ie~~p~ 312 (503)
T KOG1488|consen 233 KFFEHGTEDQRNLLHSQIKGHVLELSLDMYGCRVIQKALEKVDVSLQIQLIDELDGHLLKCVKDQNGNHVIQKCIETLPP 312 (503)
T ss_pred hhhccCCHHHHHHHHHHHHhhhhhhhcccccchhHHHHHHhcCHHHHHHHHHHHHhhHHHHHhhcccceehhhhhhccCh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHhhh--hHhhhccCCCCchHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhCcCccHHHHHHHHcCCchhHHH
Q 004857 539 EKIEFIISAFRG--QVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQ 616 (727)
Q Consensus 539 e~~~~Ii~~L~~--~l~~Ls~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~GNyVVQ~lLe~~~~k~r~~ 616 (727)
+.+.+|++.|.+ ++..+|+|+|||+|||++||+|..+ ++..++++|..++..|++|+||||||||+|+++++.++..
T Consensus 313 ~~~~Fiv~~f~~~~~~~~ls~~~YGCRVIQr~lE~c~~~-~~~~i~~ei~~~~~~L~~dQygNYVIQHVie~g~~~~~~~ 391 (503)
T KOG1488|consen 313 DAWQFIVDFFSGDDNLLELSTHKYGCRVIQRILEHCSED-QKQPLMEEIIRNCDQLAQDQYGNYVIQHVIEHGSPYRDTI 391 (503)
T ss_pred HHHHHHHHHhcCCCceeEeeccCcccHHHHHHhhcCChH-hhhHHHHHHHHHHHHHHhhhhhhHHHHHHHhcCChhhhhh
Confidence 999999999999 9999999999999999999999976 5566999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcCchHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCh-hHHHhhhcCCChHHHHHHHHhcCCHHHHHHH
Q 004857 617 ILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEEN-DNLLVMMKDQYANYVVQKILEKCNEKLRETL 695 (727)
Q Consensus 617 II~~L~g~lveLs~~K~GS~VVEk~L~~as~k~Rk~IIkeLl~~~~~~-e~L~~La~DqyGnyVVQklL~~~d~~~Rk~L 695 (727)
|++.|.+++++|++|||+|+|||+||.++++.+|..|++|++....+. +.|..||+|+|||||||++|++|++++|+.|
T Consensus 392 I~~~l~~~ll~~Sq~KfASnVVEk~~~~a~~~~r~~i~~Ei~~~~~~~~~~L~~mmkdQYgNYVVQkmi~~~~~~q~~~i 471 (503)
T KOG1488|consen 392 IIKCLLGNLLSMSQHKFASNVVEKAFLFAPPLLRALIMNEIFPGYVEHPDALDIMMKDQYGNYVVQKMIDICGPEQRELI 471 (503)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcCCccCCccHHHHHHHHhhhhhHHHHHHHhcCHHHHHHH
Confidence 999999999999999999999999999999999999999999876554 7899999999999999999999999999999
Q ss_pred HHHHHHhHHHHhcCCChHHHHHHHHHHHhcC
Q 004857 696 ISRIRVHCDALKKYTYGKHIVARFEQLYGEG 726 (727)
Q Consensus 696 l~~Lk~~l~~L~~~~yGk~Vv~~Lekli~~g 726 (727)
..+|++|+..|++++|||||+++|||+...+
T Consensus 472 ~~rI~~h~~~Lrk~syGKhIia~lek~~~~~ 502 (503)
T KOG1488|consen 472 KSRVKPHASRLRKFSYGKHIIAKLEKLRSKG 502 (503)
T ss_pred HHHHHHHHHHHccCccHHHHHHHHHHhcccC
Confidence 9999999999999999999999999998654
No 2
>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=100.00 E-value=6.4e-57 Score=482.21 Aligned_cols=319 Identities=59% Similarity=0.948 Sum_probs=306.5
Q ss_pred hHHhHH-HHHHHHhcCCCccHHHHHhhhcCCHHHHHHHHHHHhhchhhhccCccccchhhhhhccCCHHHHHHHHHHHhc
Q 004857 400 ELSDIA-GRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVG 478 (727)
Q Consensus 400 ~L~~I~-GkIveLa~dq~gSRvLQ~lLk~~t~Eqr~~If~EI~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G 478 (727)
.++++. |++++++.|++|||+||++|+.++++++.+||+++.+++.+||+|+|||||||++|++++++++..|++.+.+
T Consensus 3 ~~~~~~~~~~~~l~~~~~gsr~lQ~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~g~~vvq~~l~~~~~~~~~~i~~~~~~ 82 (322)
T cd07920 3 TLQDIKAGHIVEFAKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKILG 82 (322)
T ss_pred CHHhccCcchhhccCCchhhHHHHHHhccCCHHHHHHHHHHHHHhHHHHhcCccccHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 355666 9999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhhhccCcchhHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhhcccCchhhhHhhhcCChhHHHHHHHHhhhhHhhhccC
Q 004857 479 QVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTH 558 (727)
Q Consensus 479 ~v~~La~h~yGSrVIQklIe~as~eqr~~Lv~EL~g~i~~L~~D~~GNhVIQklLe~~~~e~~~~Ii~~L~~~l~~Ls~h 558 (727)
++..|+.|+|||||||++|+.++.+++..|++||.+++..|+.|++||||+|+++++.+++.++.|++.+.+++.+++.|
T Consensus 83 ~~~~l~~~~~g~~vlqkll~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~ 162 (322)
T cd07920 83 HVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTH 162 (322)
T ss_pred HHHHHcccchhHHHHHHHHHhcCHHHHHHHHHHHHHCHHHHhhcccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCchHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhCcCccHHHHHHHHcCCchhHHHHHHHHHHHHHHHhcCchHHHHH
Q 004857 559 PYGCRVIQRVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVV 638 (727)
Q Consensus 559 k~GS~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~GNyVVQ~lLe~~~~k~r~~II~~L~g~lveLs~~K~GS~VV 638 (727)
++||+|+|++|+.+. ++.++.+++++.+++..|+.|+|||||||++|+++.++.++.|++.+.+++.+|+++||||+|+
T Consensus 163 ~~G~~vvq~~l~~~~-~~~~~~l~~~l~~~~~~L~~d~~Gn~vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~k~Gs~Vv 241 (322)
T cd07920 163 PYGCRVIQRCLEHCS-EEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVV 241 (322)
T ss_pred ccccHHHHHHHHhCC-HHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHhcCCHHHHHHHHHHHHHHHHHHHcCcchHHHH
Confidence 999999999999987 4578889999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhCCHHHHHHHHHHHhcCCCChhHHHhhhcCCChHHHHHHHHhcCCHHHHHHHHHHHHHhHHHHhcCCChHHHHHH
Q 004857 639 EKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGKHIVAR 718 (727)
Q Consensus 639 Ek~L~~as~k~Rk~IIkeLl~~~~~~e~L~~La~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~ 718 (727)
|+||+.++++.|+.++++|+....+.+++.+|++|+|||||||++|+.+++..++.|++.|++++.+|+.++||++|+++
T Consensus 242 e~~l~~~~~~~~~~ii~~l~~~~~~~~~l~~l~~d~~Gn~Viq~~l~~~~~~~~~~i~~~l~~~~~~L~~~~~G~~v~~~ 321 (322)
T cd07920 242 EKCLKHASKEERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIRPHLPSLRKSPYGKHILAK 321 (322)
T ss_pred HHHHHHCCHHHHHHHHHHHhcCCCchhHHHHHhCCCcccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCCcHHHHHHh
Confidence 99999999999999999999754223689999999999999999999999999999999999999999999999999986
Q ss_pred H
Q 004857 719 F 719 (727)
Q Consensus 719 L 719 (727)
|
T Consensus 322 ~ 322 (322)
T cd07920 322 L 322 (322)
T ss_pred C
Confidence 4
No 3
>PF07990 NABP: Nucleic acid binding protein NABP; InterPro: IPR012940 This domain occurs in some putative nucleic acid binding proteins. One of these proteins has been partially characterised [] and contains two putative phosphorylation sites and a possible dimerisation / leucine zipper domain.
Probab=100.00 E-value=5.8e-51 Score=436.51 Aligned_cols=234 Identities=36% Similarity=0.571 Sum_probs=213.7
Q ss_pred CCCCCCCCCCCCCCCCCCCCcccCCCCCCCCcccCCCCCCCCCCCCCC-CCCCC---CCCcccccCCCCCCCCC-----C
Q 004857 145 FYPSFQPSGAGVYPSQYNVGGYALNSALFPPFVAGYPSQGPVPMPFDA-TSGSS---FNIRTTSVSTGEGIPHI-----G 215 (727)
Q Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~---~~~~~~~~~~~~~~~~~-----~ 215 (727)
.|||++. ++|..+||++||+. |+||.+++++|++|++||+ +++++ +++++ |++|+++.++ +
T Consensus 135 ~~q~~~~-------~n~~~~gy~~n~~~-~s~~~~~~~~gn~p~~fd~~~~~s~~~~~~~~s--~~~g~~~~s~~~~~~~ 204 (385)
T PF07990_consen 135 PYQNSDN-------PNSSFGGYALNPAL-PSMMASQLNNGNIPPLFDNSAAASALASPGMDS--RSLGGGLDSGGNQGAS 204 (385)
T ss_pred cccCCCc-------ccccccccccCccc-hhhhhccccCCCCCccccccccchhhccCCCcc--cccCCccccccccccc
Confidence 3677666 44455999999998 9999999999999999999 55555 77777 9999999986 6
Q ss_pred Ccccc-cccCCC-CCCCCCCCCCchhhhhccCCcccccccc-ccCcCCCCCCC-CCCCCCCCCchhhHHhhhhhcccccc
Q 004857 216 STQHQ-KFYGHQ-GLMLQSPFVDPLHMQYFQHPFGDAYNAS-VQHRLASSGVN-GALADPSSKKEPIVAAYMGDQNLQSS 291 (727)
Q Consensus 216 ~~~~~-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 (727)
|++|+ |+|||+ |.++|+||+||+|+||||++++++++++ +.||+++|+++ ++++|+++.||+||++||++||+||+
T Consensus 205 d~~~l~r~gnq~~g~~lq~~~~DP~Y~Qylq~~~~aa~~~a~~~dP~~~R~~~G~s~~dl~~~qKayl~~lL~~QK~Qy~ 284 (385)
T PF07990_consen 205 DGQNLNRFGNQVAGSALQSPFVDPLYLQYLQAPEYAAQQAAAQNDPSVDRNYMGSSYMDLLGLQKAYLEALLAQQKSQYG 284 (385)
T ss_pred chhhhhhhcccccCcccCCCCCCchHHHHhccccchhhhhhccCCcccccCCcCccccchHHHHHHHHHHHHHHHHHhhC
Confidence 99999 999998 7999999999999999999999998888 99999999999 99999999999999999999999999
Q ss_pred CCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccc---cCCCCCCCCCCCC-CCCCC
Q 004857 292 LNGGPSISNPRKVGMPVGGYYGGLPGMGVMGQFPTSPIASPVLPSSPVGSTSQLGLRH---EMRLPQGLNRNTG-IYSGW 367 (727)
Q Consensus 292 ~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~g-~~~~W 367 (727)
+ |+ .|+|..+++||| +|.||++|+|||+|+++|+||++|+|+++ |+|| ++||++++|+.+| ++|.|
T Consensus 285 ~---P~----~~~~~~n~~y~g-np~~G~gm~Y~gsplaspvlPsspvG~gs--p~r~~er~~R~~s~mRn~~GG~~GsW 354 (385)
T PF07990_consen 285 V---PL----KKSGSMNHGYYG-NPSYGLGMPYPGSPLASPVLPSSPVGPGS--PLRHNERNMRFPSGMRNSSGGSMGSW 354 (385)
T ss_pred C---cc----ccCCCCCCCCCC-CCCccccCCCCCCCCcCCCCCCCCCCCCC--CCcCCccccccCcccccccccccccc
Confidence 8 65 899999999999 88899999999999999999999999997 4555 6999999999945 99999
Q ss_pred ccccccCCCcccCChhhhHHHHHhhccccccchHH
Q 004857 368 QGQRTFEGQRTFEDSKKHSFLEELKSSNAQKFELS 402 (727)
Q Consensus 368 ~~~r~~~~~~~~~d~~r~~LLeeL~~~~~~~~~L~ 402 (727)
+.++..+ +++.+.+.||||||++|+|+|||+
T Consensus 355 ~~d~g~~----~d~~~~sSlLEEFKsNKtr~FELS 385 (385)
T PF07990_consen 355 HSDAGGN----MDENFASSLLEEFKSNKTRSFELS 385 (385)
T ss_pred ccccccc----ccccchhHHHHHHhcCCccceecC
Confidence 9999777 899999999999999999999984
No 4
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.7e-48 Score=452.13 Aligned_cols=312 Identities=42% Similarity=0.684 Sum_probs=296.1
Q ss_pred hcCCCccHHHHHhhhcCCHHHHHHHHHHHhhchhhhccCccccchhhhhhccCCHHHHHHHHHHHhcChhhhccCcchhH
Q 004857 412 SVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCR 491 (727)
Q Consensus 412 a~dq~gSRvLQ~lLk~~t~Eqr~~If~EI~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G~v~~La~h~yGSr 491 (727)
++||+|||+||++|+.-+.++.+.||.|+.+...+||.|.|||||||||||+++++|+..++..+.++++.|+.|+||||
T Consensus 447 ~~Dq~g~r~LQk~Lds~s~~~~~~~~~e~~d~~~eLs~d~fGNyliQK~fe~~s~~q~~~ml~~~~~~~~~ls~~~~Gtr 526 (777)
T COG5099 447 CKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTR 526 (777)
T ss_pred cCCcHHHHHHHHHhcccchHHHHHHHHHHhhhhHHHHHhhhcchhhHHHHHhccHHHHHHHHHHhhhhHHHhhccccccH
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhCHHHHH-HHHHHHHHHHHHHhhcccCchhhhHhhhcCChhHHHHHHHHhhhhHhhhccCCCCchHHHHHHh
Q 004857 492 VIQKALEVIELHQKS-QLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLE 570 (727)
Q Consensus 492 VIQklIe~as~eqr~-~Lv~EL~g~i~~L~~D~~GNhVIQklLe~~~~e~~~~Ii~~L~~~l~~Ls~hk~GS~VLQk~Le 570 (727)
|+||+|+++..+.+. .|++||.+.+..|++|++||||||||++....+...+|++.+.+++.++++|+|||+|||+|||
T Consensus 527 v~QK~id~~~t~~qi~~lv~~l~~~~~~li~dqngNHviqKci~~~~~~~~~fif~~~~~~~~~is~~r~Gs~vvq~~le 606 (777)
T COG5099 527 VLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLE 606 (777)
T ss_pred HHHHHHhccCchhhHHHHHHHhhhhhHHHHHhccCCHHHHHHHHhcCccccchHHHHHHhhhHhhhccccccHHHHHHHH
Confidence 999999999888877 8899999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCcHHHHHHHHHHHHHHHHHHhhCcCccHHHHHHHHcCCchhHHHHHHHHHH-HHHHHhcCchHHHHHHHHHHhCCHHH
Q 004857 571 HCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAG-KIVQMSQHKYASNVVEKCLEYGDTAE 649 (727)
Q Consensus 571 ~~~~~~~r~~Ll~eI~~~l~~La~Dq~GNyVVQ~lLe~~~~k~r~~II~~L~g-~lveLs~~K~GS~VVEk~L~~as~k~ 649 (727)
+|..+. .+.++++|+.+...|++|+||||||||+|+.+.+..++.|+..+.. ++++|+.|||||+||||||.++...+
T Consensus 607 ~~~~~~-~~~~~~~Ii~~~~~L~~dq~GNyvvq~il~~g~~~~k~~i~~~~l~~~v~elS~~kfaSnvVeK~i~~~~~~~ 685 (777)
T COG5099 607 NCNSED-KENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIKYASDSF 685 (777)
T ss_pred hccHhH-HHHHHHHHHHHHHhhccCCcchhhhhHHhhcCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcch
Confidence 998764 4789999999999999999999999999999999999999998888 99999999999999999999988887
Q ss_pred -HHHHHHHHhcCCCChh-HHHhhhcCCChHHHHHHHHhcCCHHHHHHHHHHHHHhHHHHhcCCChHHHHHHHHHHHh
Q 004857 650 -RELLIEEILGQSEEND-NLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGKHIVARFEQLYG 724 (727)
Q Consensus 650 -Rk~IIkeLl~~~~~~e-~L~~La~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~Lekli~ 724 (727)
|++|+.++..-.-+.+ .|..|+.|+|||||+|++++......|..+.+.|+.++..|++.+||+||.++||+...
T Consensus 686 ~~~ril~~~~~~~~~~~~~l~~i~~d~y~Nyv~q~~~~~s~~~~~~l~~~~i~~~~~~l~~s~~g~~i~~~le~~~~ 762 (777)
T COG5099 686 KRSRILNELTNRGIEKPGFLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILALLEKVGS 762 (777)
T ss_pred HHHHHHHHHhcccccCChHHHHHHHhhhcchHHHHHHhhCchhhHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHhc
Confidence 5999999987222223 48999999999999999999999999999999999999999999999999999998753
No 5
>KOG2049 consensus Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.5e-45 Score=407.29 Aligned_cols=313 Identities=31% Similarity=0.500 Sum_probs=292.2
Q ss_pred HHhHHHHHHHHhcCCCccHHHHHhhhcCCHHHHHHHHHHHhhchhhhccCccccchhhhhhccCCHHHHHHHHHHHhc--
Q 004857 401 LSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVG-- 478 (727)
Q Consensus 401 L~~I~GkIveLa~dq~gSRvLQ~lLk~~t~Eqr~~If~EI~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G-- 478 (727)
+.++.|.+..+|+|++|||++|+.+..++......||.|+..++.+||.|+|||+++||++++|+++|+..|+..+..
T Consensus 212 ~~~~~~~~~~~akd~~gc~~lq~~~~~~~~~~~~~if~~~~~~~~~Lm~d~fGny~vqkl~~~~~~eq~~~i~~~lts~p 291 (536)
T KOG2049|consen 212 MVEIQGSINLIAKDQHGCRLLQKLLSEGTKVSILKIFLETIQDVPELMEDPFGNYLVQKLLEVCDEEQLTKIVSLLTSDP 291 (536)
T ss_pred hhccchhhhhhcccccCCcccccCcccCccccHHHHHHHHHHHHHHHHhccchhHHHHHHHHhhCHHHHHHHHHHHhcCc
Confidence 446779999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred -ChhhhccCcchhHHHHHHHHhhCHHH-HHHHHHHHHHHHHHHhhcccCchhhhHhhhcCChhHHHHHHHHhhhhHhhhc
Q 004857 479 -QVLPLSLQMYGCRVIQKALEVIELHQ-KSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLS 556 (727)
Q Consensus 479 -~v~~La~h~yGSrVIQklIe~as~eq-r~~Lv~EL~g~i~~L~~D~~GNhVIQklLe~~~~e~~~~Ii~~L~~~l~~Ls 556 (727)
.++.++.++||+++||++++.....+ ...++..|...+..|++|.||+||||+||+..+++..+++++.+..++..+|
T Consensus 292 ~~fv~i~~N~~GTr~iQkl~~~~~~~dqI~~~~~ai~~~fl~L~~D~~g~~Viq~cl~~f~~~~~~~l~e~i~~~c~~iA 371 (536)
T KOG2049|consen 292 RLFVEICTNMYGTRAVQKLLGKSDSVDQISLFLDAIKPNFLHLIKDKNGNHVIQRCLRVFSKEKNEFLYEAILRYCLDLA 371 (536)
T ss_pred cceeEeeecCchhHHHHHHHhccccHHHHHHHHHHHHhhhHHhhhhcchhHHHHHHHHhcCchhhhHHHHHHHHHHHHHH
Confidence 69999999999999999998776544 4555688999999999999999999999999999999999999999999999
Q ss_pred cCCCCchHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhCcCccHHHHHHHHcCCchhHHHHHHHHHHHHHHHhcCchHHH
Q 004857 557 THPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASN 636 (727)
Q Consensus 557 ~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~GNyVVQ~lLe~~~~k~r~~II~~L~g~lveLs~~K~GS~ 636 (727)
+|++||+|||+||..... ++|+.++++|..+...|+.|+|||||||++|+...+.....|++.|.+++++|+.+||||+
T Consensus 372 ~~~hGCcvLq~cl~~~~~-~~rd~Lv~~i~~naL~Ls~d~~GNyvVQyvl~L~~~~~t~~i~~~L~g~~veLS~qKfgS~ 450 (536)
T KOG2049|consen 372 TDQHGCCVLQKCLDYSRG-EQRDRLVEEISRNALLLSNDPYGNYVVQYVLELNDPSCTVNIAEKLRGHYVELSFQKFGSH 450 (536)
T ss_pred HhccccchhHHHhcchhH-HHHHHHHHHHHHHhHhhhcCccccchhhhhhhhcCcchHHHHHHhhhhHHHHHHHHhhccH
Confidence 999999999999999875 5899999999999999999999999999999999999899999999999999999999999
Q ss_pred HHHHHHHhCCHHHHHHHHHHHhcCCCChhHHHhhhcCCChHHHHHHHHhcCCH----HHHHHHHHHHHHhHHHHhcCCCh
Q 004857 637 VVEKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQKILEKCNE----KLRETLISRIRVHCDALKKYTYG 712 (727)
Q Consensus 637 VVEk~L~~as~k~Rk~IIkeLl~~~~~~e~L~~La~DqyGnyVVQklL~~~d~----~~Rk~Ll~~Lk~~l~~L~~~~yG 712 (727)
||||||+..... +..|+.||++. +.+..|+.|+|||||||++|...+. ..+..++..+++.+..|+.+++|
T Consensus 451 vVEk~L~~~~~~-~~~iV~ell~~----~~~~~Ll~D~ygNyViq~AL~vtk~~~~~~~~~~lv~~~~~~~~~lr~~p~~ 525 (536)
T KOG2049|consen 451 VVEKLLKVRESS-RAQIVLELLSC----DELDRLLRDPYGNYVIQTALRVTKVKLREDLFGLLVQKLMPRIRLLRNNPGG 525 (536)
T ss_pred HHHHHHhcCcch-hhHHHHHHHcc----ccHHHHhhCccchHHHHHHHHHhhhcccchhhHHHHHHHhhhhHHhhcCccc
Confidence 999999986644 37888999986 4699999999999999999999886 78999999999999999999999
Q ss_pred HHHHHHH
Q 004857 713 KHIVARF 719 (727)
Q Consensus 713 k~Vv~~L 719 (727)
++|..+.
T Consensus 526 ~~~~~~~ 532 (536)
T KOG2049|consen 526 NIALIKD 532 (536)
T ss_pred ceeeehh
Confidence 9987654
No 6
>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=100.00 E-value=1.4e-40 Score=356.01 Aligned_cols=298 Identities=25% Similarity=0.422 Sum_probs=281.8
Q ss_pred cCChhhhHHHHHhhc---cccccchHHhHHHHHHHHhcCCCccHHHHHhhhcCCHHHHHHHHHHHhhchhhhccCccccc
Q 004857 379 FEDSKKHSFLEELKS---SNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNY 455 (727)
Q Consensus 379 ~~d~~r~~LLeeL~~---~~~~~~~L~~I~GkIveLa~dq~gSRvLQ~lLk~~t~Eqr~~If~EI~~~~~eL~tD~fGn~ 455 (727)
+.|...+.+++++-. .+.+...++++.+++.+++.|++|++++|++|+.++++++..|++++.+++.+|++|+||++
T Consensus 16 ~~~~~gsr~lQ~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~g~~vvq~~l~~~~~~~~~~i~~~~~~~~~~l~~~~~g~~ 95 (322)
T cd07920 16 AKDQHGSRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKILGHVVRLSLDMYGCR 95 (322)
T ss_pred cCCchhhHHHHHHhccCCHHHHHHHHHHHHHhHHHHhcCccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcccchhHH
Confidence 567788888887543 45567778889999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhccCCHHHHHHHHHHHhcChhhhccCcchhHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhhcccCchhhhHhhhc
Q 004857 456 VIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIEC 535 (727)
Q Consensus 456 VVQKLLe~gs~eqr~~Ii~~L~G~v~~La~h~yGSrVIQklIe~as~eqr~~Lv~EL~g~i~~L~~D~~GNhVIQklLe~ 535 (727)
||||+|++++++++..|++++.+++.+|+.|.+|++|+|++++.++++++..|+++|.+++..++.|++|++|+|++|+.
T Consensus 96 vlqkll~~~~~~~~~~i~~~l~~~~~~L~~d~~gn~Vvq~~l~~~~~~~~~~i~~~l~~~~~~l~~~~~G~~vvq~~l~~ 175 (322)
T cd07920 96 VIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCLEH 175 (322)
T ss_pred HHHHHHHhcCHHHHHHHHHHHHHCHHHHhhcccccHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHcCccccHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChhHHHHHHHHhhhhHhhhccCCCCchHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhCcCccHHHHHHHHcCCchhHH
Q 004857 536 VPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERT 615 (727)
Q Consensus 536 ~~~e~~~~Ii~~L~~~l~~Ls~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~GNyVVQ~lLe~~~~k~r~ 615 (727)
.+++.++.+++.+.+++..|+.++||++|||++++... ++.+..+++.+.+++..|+.++||++|++++|+++.++.++
T Consensus 176 ~~~~~~~~l~~~l~~~~~~L~~d~~Gn~vvq~~l~~~~-~~~~~~i~~~l~~~~~~l~~~k~Gs~Vve~~l~~~~~~~~~ 254 (322)
T cd07920 176 CSEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGD-PDDTSRIIEKLLGNIVQLSCHKFASNVVEKCLKHASKEERE 254 (322)
T ss_pred CCHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHhcCC-HHHHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHCCHHHHH
Confidence 99999999999999999999999999999999999976 45788999999999999999999999999999999999999
Q ss_pred HHHHHHH------HHHHHHhcCchHHHHHHHHHHhCCHHHHHHHHHHHhcCCCChhHHHhhhcCCChHHHHHHH
Q 004857 616 QILSKLA------GKIVQMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQKI 683 (727)
Q Consensus 616 ~II~~L~------g~lveLs~~K~GS~VVEk~L~~as~k~Rk~IIkeLl~~~~~~e~L~~La~DqyGnyVVQkl 683 (727)
.|++.|. +++.+|+.++||+.||+++|+.+++..++.|+..|. +++..|+.++||+.|+.++
T Consensus 255 ~ii~~l~~~~~~~~~l~~l~~d~~Gn~Viq~~l~~~~~~~~~~i~~~l~------~~~~~L~~~~~G~~v~~~~ 322 (322)
T cd07920 255 LIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAKEEQRELLVEAIR------PHLPSLRKSPYGKHILAKL 322 (322)
T ss_pred HHHHHHhcCCCchhHHHHHhCCCcccHHHHHHHHhCCHHHHHHHHHHHH------HHHHHHcCCCcHHHHHHhC
Confidence 9999995 589999999999999999999999999999999998 5799999999999999874
No 7
>KOG1488 consensus Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.6e-42 Score=378.35 Aligned_cols=245 Identities=30% Similarity=0.437 Sum_probs=234.2
Q ss_pred chHHhHHHHHHHHhcCCCccHHHHHhhhcCCHHHHHHHHHHHhhchhhhccCccccchhhhhhccCCHHHHHHHHHHHhc
Q 004857 399 FELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVG 478 (727)
Q Consensus 399 ~~L~~I~GkIveLa~dq~gSRvLQ~lLk~~t~Eqr~~If~EI~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G 478 (727)
.....+.|++++||.|.+||||||+.|+.-+.++..++++||..+++.+++|++|||||||+||..+++...+|++.|.+
T Consensus 245 ~l~~~~~g~v~~Lsld~ygCRVIQkale~id~~~~~~Li~ELd~~vl~~v~DQngnHViQK~ie~~p~~~~~Fiv~~f~~ 324 (503)
T KOG1488|consen 245 LLHSQIKGHVLELSLDMYGCRVIQKALEKVDVSLQIQLIDELDGHLLKCVKDQNGNHVIQKCIETLPPDAWQFIVDFFSG 324 (503)
T ss_pred HHHHHHHhhhhhhhcccccchhHHHHHHhcCHHHHHHHHHHHHhhHHHHHhhcccceehhhhhhccChHHHHHHHHHhcC
Confidence 33446889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred --ChhhhccCcchhHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhhcccCchhhhHhhhcCChhHHHHHHHHhhhhHhhhc
Q 004857 479 --QVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLS 556 (727)
Q Consensus 479 --~v~~La~h~yGSrVIQklIe~as~eqr~~Lv~EL~g~i~~L~~D~~GNhVIQklLe~~~~e~~~~Ii~~L~~~l~~Ls 556 (727)
++..|+.|+|||||||+++|+|+++++..+++||..++..|+.|+|||||||++|+++.++++..|++.+.+++++++
T Consensus 325 ~~~~~~ls~~~YGCRVIQr~lE~c~~~~~~~i~~ei~~~~~~L~~dQygNYVIQHVie~g~~~~~~~I~~~l~~~ll~~S 404 (503)
T KOG1488|consen 325 DDNLLELSTHKYGCRVIQRILEHCSEDQKQPLMEEIIRNCDQLAQDQYGNYVIQHVIEHGSPYRDTIIIKCLLGNLLSMS 404 (503)
T ss_pred CCceeEeeccCcccHHHHHHhhcCChHhhhHHHHHHHHHHHHHHhhhhhhHHHHHHHhcCChhhhhhHHHHHHhhHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCchHHHHHHhhCCcHHHHHHHHHHHHH-------HHHHHhhCcCccHHHHHHHHcCCchhHHHHHHHHHHHHHHHh
Q 004857 557 THPYGCRVIQRVLEHCSDEQQGQCIVDEILE-------SAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIVQMS 629 (727)
Q Consensus 557 ~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~-------~l~~La~Dq~GNyVVQ~lLe~~~~k~r~~II~~L~g~lveLs 629 (727)
+|||+|+|||+||.++... .+..|++||.. -+..|+.|+|||||||++|+.+.+++|+.|+.+++.|+..|-
T Consensus 405 q~KfASnVVEk~~~~a~~~-~r~~i~~Ei~~~~~~~~~~L~~mmkdQYgNYVVQkmi~~~~~~q~~~i~~rI~~h~~~Lr 483 (503)
T KOG1488|consen 405 QHKFASNVVEKAFLFAPPL-LRALIMNEIFPGYVEHPDALDIMMKDQYGNYVVQKMIDICGPEQRELIKSRVKPHASRLR 483 (503)
T ss_pred HHHHHHHHHHHHHhhCCHH-HHHHHHHHhcCCccCCccHHHHHHHHhhhhhHHHHHHHhcCHHHHHHHHHHHHHHHHHHc
Confidence 9999999999999998754 78999999985 488999999999999999999999999999999999999999
Q ss_pred cCchHHHHHHHHHHh
Q 004857 630 QHKYASNVVEKCLEY 644 (727)
Q Consensus 630 ~~K~GS~VVEk~L~~ 644 (727)
+.+||.|+++++-+.
T Consensus 484 k~syGKhIia~lek~ 498 (503)
T KOG1488|consen 484 KFSYGKHIIAKLEKL 498 (503)
T ss_pred cCccHHHHHHHHHHh
Confidence 999999999986543
No 8
>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1e-39 Score=359.17 Aligned_cols=305 Identities=21% Similarity=0.353 Sum_probs=265.0
Q ss_pred CCCCccccccCCCcccCChhhhHHHHHhhccccccchHHhHHHHHHHHhcCCCccHHHHHhhhcCCHHHHHHHHHHHhhc
Q 004857 364 YSGWQGQRTFEGQRTFEDSKKHSFLEELKSSNAQKFELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPH 443 (727)
Q Consensus 364 ~~~W~~~r~~~~~~~~~d~~r~~LLeeL~~~~~~~~~L~~I~GkIveLa~dq~gSRvLQ~lLk~~t~Eqr~~If~EI~~~ 443 (727)
-+.|+.+|+++ +++++|.+|++|+.. .++|+|.+++..|++|||||++++++++++|+.||+||.|.
T Consensus 135 kslWEkLR~k~----~~ke~R~klv~el~~---------likg~i~~lv~aHDtSRViQt~Vky~s~~~r~~if~eL~p~ 201 (652)
T KOG2050|consen 135 KSLWEKLRRKT----TPKEERDKLVSELYK---------LIKGKISKLVFAHDTSRVIQTCVKYGSEAQREQIFEELLPF 201 (652)
T ss_pred HHHHHHHhccC----CcHHHHHHHHHHHHH---------HHhhhHHHHHHHhhhHHHHHHHHHhcCHHHHHHHHHHHhHH
Confidence 35799999998 799999999999775 89999999999999999999999999999999999999999
Q ss_pred hhhhccCccccchhhhhhccCCHHHHHHHHHHHhcChhhhccCcchhHHHHHHH-HhhCHHHHHHHHHHHHHHHHHHhhc
Q 004857 444 ASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKAL-EVIELHQKSQLVLELDGHVMRCVRD 522 (727)
Q Consensus 444 ~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G~v~~La~h~yGSrVIQklI-e~as~eqr~~Lv~EL~g~i~~L~~D 522 (727)
+++||+++||.|+|||+|.||+++++..|+++|+||++.|++|+.|+.|++.+| ++++.+||..|+.||||..+.++++
T Consensus 202 ~v~l~kskY~k~~v~KmLkyGsk~q~a~iI~sl~Ghv~kLlRH~eaa~Vve~ay~~~A~l~Qr~~li~EfYG~efqlfK~ 281 (652)
T KOG2050|consen 202 FVELAKSKYAKFFVQKMLKYGSKAQKAKIINSLRGHVVKLLRHREAAYVVEYAYNDFATLEQRQYLIQEFYGDEFQLFKD 281 (652)
T ss_pred HHHHHHhHHHHHHHHHHHhcCCHHHHHHHHHHHhhhHHHHHhhhHHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHhc
Confidence 999999999999999999999999999999999999999999999999999999 6799999999999999999999999
Q ss_pred ccCchhhhHhhhcCChhHHHHHHHHhhhhHhhhccCCCCchHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhCcCccHHH
Q 004857 523 QNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVT 602 (727)
Q Consensus 523 ~~GNhVIQklLe~~~~e~~~~Ii~~L~~~l~~Ls~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~GNyVV 602 (727)
.+--+ |.++++. .++.+..|+..++..+..+ ++... ..-.|+ ..++
T Consensus 282 sn~~T-l~kil~~-~pekk~~I~~~l~~~I~~v-------------~eKg~---v~~tiv----------------Hk~m 327 (652)
T KOG2050|consen 282 SNDKT-LDKILAE-APEKKASILRHLKAIITPV-------------AEKGS---VDHTIV----------------HKLM 327 (652)
T ss_pred cCccc-HHHHHHh-ChHhHHHHHHHHHHHhHHH-------------hhcch---hHHHHH----------------HHHH
Confidence 54443 4444443 2455566665554443222 22111 011122 1234
Q ss_pred HHHHHcCCchhHHHHHHHHHHHHHHHhcCchHHHHHHHHHHhCCHHHHHHHHHHHhcCCCChhHHHhhhcCCChHHHHHH
Q 004857 603 QHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQK 682 (727)
Q Consensus 603 Q~lLe~~~~k~r~~II~~L~g~lveLs~~K~GS~VVEk~L~~as~k~Rk~IIkeLl~~~~~~e~L~~La~DqyGnyVVQk 682 (727)
--+|.+++++++.++++.+.+.+.+|++++.||+|..+|++++++++|+.|++.|. +++.++|.|+|||.|+..
T Consensus 328 lEy~~~ade~e~~e~l~ll~elv~e~vHT~dGS~vAm~li~~a~aKeRK~IiK~~K------~h~~K~A~~~yGh~vlia 401 (652)
T KOG2050|consen 328 LEYLTIADEEEKSELLELLKELVPEMVHTRDGSRVAMKLIWHATAKERKLIIKNMK------EHVEKIANDEYGHLVLIA 401 (652)
T ss_pred HHHHHhCCHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHhhCCHHHHHHHHHHHH------HHHHHHHhhccCceehhh
Confidence 44567889999999999999999999999999999999999999999999999999 789999999999999999
Q ss_pred HHhcCCHH--HHHHHHHHHHHhHHHHhcCCChHHHHHHHHH
Q 004857 683 ILEKCNEK--LRETLISRIRVHCDALKKYTYGKHIVARFEQ 721 (727)
Q Consensus 683 lL~~~d~~--~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~Lek 721 (727)
+|++.||+ .++.|.++++.++.+|..++||++|+.++-.
T Consensus 402 ~ldc~DDT~l~kk~i~~e~~~el~~li~Dk~Grrv~lyll~ 442 (652)
T KOG2050|consen 402 LLDCTDDTKLLKKLIYDELKSELKSLISDKYGRRVILYLLA 442 (652)
T ss_pred hhcccchHHHHHHHHHHHHHHHHHHHhccchhhhhhhhhcc
Confidence 99999999 7899999999999999999999999987643
No 9
>KOG2049 consensus Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=6.1e-30 Score=286.72 Aligned_cols=263 Identities=25% Similarity=0.314 Sum_probs=229.7
Q ss_pred CcccCChhhhHHHHHhhc--cccccchH-HhHH---HHHHHHhcCCCccHHHHHhhhcC-CHHHHHHHHHHHhhchhhhc
Q 004857 376 QRTFEDSKKHSFLEELKS--SNAQKFEL-SDIA---GRIVEFSVDQHGSRFIQQKLEHC-SAEEKVSVFKEVLPHASKLM 448 (727)
Q Consensus 376 ~~~~~d~~r~~LLeeL~~--~~~~~~~L-~~I~---GkIveLa~dq~gSRvLQ~lLk~~-t~Eqr~~If~EI~~~~~eL~ 448 (727)
++.|.|++...++..|.+ +++++..+ +.+. +.+++++.+.+|+|.||++++.. +.+|...|++.|.+.++.|+
T Consensus 256 ~~Lm~d~fGny~vqkl~~~~~~eq~~~i~~~lts~p~~fv~i~~N~~GTr~iQkl~~~~~~~dqI~~~~~ai~~~fl~L~ 335 (536)
T KOG2049|consen 256 PELMEDPFGNYLVQKLLEVCDEEQLTKIVSLLTSDPRLFVEICTNMYGTRAVQKLLGKSDSVDQISLFLDAIKPNFLHLI 335 (536)
T ss_pred HHHHhccchhHHHHHHHHhhCHHHHHHHHHHHhcCccceeEeeecCchhHHHHHHHhccccHHHHHHHHHHHHhhhHHhh
Confidence 344677777777776654 33333222 2233 46889999999999999999875 56788899999999999999
Q ss_pred cCccccchhhhhhccCCHHHHHHHHHHHhcChhhhccCcchhHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhhcccCchh
Q 004857 449 TDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHV 528 (727)
Q Consensus 449 tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G~v~~La~h~yGSrVIQklIe~as~eqr~~Lv~EL~g~i~~L~~D~~GNhV 528 (727)
+|.||+||||+||...++++.+.+++.+..++.++|+|.+||.|||++|.....++|..|++|+..+...|+.|+|||||
T Consensus 336 ~D~~g~~Viq~cl~~f~~~~~~~l~e~i~~~c~~iA~~~hGCcvLq~cl~~~~~~~rd~Lv~~i~~naL~Ls~d~~GNyv 415 (536)
T KOG2049|consen 336 KDKNGNHVIQRCLRVFSKEKNEFLYEAILRYCLDLATDQHGCCVLQKCLDYSRGEQRDRLVEEISRNALLLSNDPYGNYV 415 (536)
T ss_pred hhcchhHHHHHHHHhcCchhhhHHHHHHHHHHHHHHHhccccchhHHHhcchhHHHHHHHHHHHHHHhHhhhcCccccch
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHhhhcCChhHHHHHHHHhhhhHhhhccCCCCchHHHHHHhhCCcHHHHHHHHHHHHH--HHHHHhhCcCccHHHHHHH
Q 004857 529 IQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILE--SAFALAQDQYGNYVTQHVL 606 (727)
Q Consensus 529 IQklLe~~~~e~~~~Ii~~L~~~l~~Ls~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~--~l~~La~Dq~GNyVVQ~lL 606 (727)
+|.+|+.-.......|++.|.+++++|+.+||||+|||+||+.+... +..++.|+++ ++..|+.|+|||||||+.|
T Consensus 416 VQyvl~L~~~~~t~~i~~~L~g~~veLS~qKfgS~vVEk~L~~~~~~--~~~iV~ell~~~~~~~Ll~D~ygNyViq~AL 493 (536)
T KOG2049|consen 416 VQYVLELNDPSCTVNIAEKLRGHYVELSFQKFGSHVVEKLLKVRESS--RAQIVLELLSCDELDRLLRDPYGNYVIQTAL 493 (536)
T ss_pred hhhhhhhcCcchHHHHHHhhhhHHHHHHHHhhccHHHHHHHhcCcch--hhHHHHHHHccccHHHHhhCccchHHHHHHH
Confidence 99999998888889999999999999999999999999999997643 3678889998 9999999999999999999
Q ss_pred HcCCc----hhHHHHHHHHHHHHHHHhcCchHHHHHHH
Q 004857 607 ERGKS----YERTQILSKLAGKIVQMSQHKYASNVVEK 640 (727)
Q Consensus 607 e~~~~----k~r~~II~~L~g~lveLs~~K~GS~VVEk 640 (727)
...+. ..+..++..++..+..|...++|-.+.++
T Consensus 494 ~vtk~~~~~~~~~~lv~~~~~~~~~lr~~p~~~~~~~~ 531 (536)
T KOG2049|consen 494 RVTKVKLREDLFGLLVQKLMPRIRLLRNNPGGNIALIK 531 (536)
T ss_pred HHhhhcccchhhHHHHHHHhhhhHHhhcCcccceeeeh
Confidence 98775 55667778888888888888887766544
No 10
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=7.1e-29 Score=289.95 Aligned_cols=236 Identities=28% Similarity=0.421 Sum_probs=196.5
Q ss_pred ccCcchhHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhhcccCchhhhHhhhcCChhHHHHHHHHhhhhHhhhccCCCCch
Q 004857 484 SLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCR 563 (727)
Q Consensus 484 a~h~yGSrVIQklIe~as~eqr~~Lv~EL~g~i~~L~~D~~GNhVIQklLe~~~~e~~~~Ii~~L~~~l~~Ls~hk~GS~ 563 (727)
+.+.+|||-||+.++....++...++.|+.+...+|+.|.+||||+|||+|++..+.+..++..+.+++..++.|+||||
T Consensus 447 ~~Dq~g~r~LQk~Lds~s~~~~~~~~~e~~d~~~eLs~d~fGNyliQK~fe~~s~~q~~~ml~~~~~~~~~ls~~~~Gtr 526 (777)
T COG5099 447 CKDQHGSRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTR 526 (777)
T ss_pred cCCcHHHHHHHHHhcccchHHHHHHHHHHhhhhHHHHHhhhcchhhHHHHHhccHHHHHHHHHHhhhhHHHhhccccccH
Confidence 67888888888888887777777788888888888888888888888888888888888888888888888888888888
Q ss_pred HHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhCcCccHHHHHHHHcCCchhHHHHHHHHHHHHHHHhcCchHHHHHHHHHH
Q 004857 564 VIQRVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLE 643 (727)
Q Consensus 564 VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~GNyVVQ~lLe~~~~k~r~~II~~L~g~lveLs~~K~GS~VVEk~L~ 643 (727)
|+|++++...++.+...+++++..++..|++|++||+|+|++++..+.+....|++.+.+++.++++++|||+||++||+
T Consensus 527 v~QK~id~~~t~~qi~~lv~~l~~~~~~li~dqngNHviqKci~~~~~~~~~fif~~~~~~~~~is~~r~Gs~vvq~~le 606 (777)
T COG5099 527 VLQKAIDIVSTDIQISLLVEELRPYCLQLIKDQNGNHVIQKCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLE 606 (777)
T ss_pred HHHHHHhccCchhhHHHHHHHhhhhhHHHHHhccCCHHHHHHHHhcCccccchHHHHHHhhhHhhhccccccHHHHHHHH
Confidence 88888888887777777888888888888888888888888888888888888888888888888888888888888888
Q ss_pred hCCHHHHHHHHHHHhcCCCChhHHHhhhcCCChHHHHHHHHhcCCHHHHHHHHHHHHH-hHHHHhcCCChHHHHHHHHHH
Q 004857 644 YGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRV-HCDALKKYTYGKHIVARFEQL 722 (727)
Q Consensus 644 ~as~k~Rk~IIkeLl~~~~~~e~L~~La~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~-~l~~L~~~~yGk~Vv~~Lekl 722 (727)
++..++.+.++++|+ .....|+.|+|||||||++|+......+++|+..+.. ++.+|..++||+.|++++-++
T Consensus 607 ~~~~~~~~~~~~~Ii------~~~~~L~~dq~GNyvvq~il~~g~~~~k~~i~~~~l~~~v~elS~~kfaSnvVeK~i~~ 680 (777)
T COG5099 607 NCNSEDKENLVEEII------SNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIKY 680 (777)
T ss_pred hccHhHHHHHHHHHH------HHHHhhccCCcchhhhhHHhhcCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 888888888888888 4577888888888888888888888888888877777 888888888888887777666
Q ss_pred Hhc
Q 004857 723 YGE 725 (727)
Q Consensus 723 i~~ 725 (727)
+.+
T Consensus 681 ~~~ 683 (777)
T COG5099 681 ASD 683 (777)
T ss_pred CCc
Confidence 543
No 11
>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=2.7e-25 Score=248.02 Aligned_cols=314 Identities=18% Similarity=0.299 Sum_probs=252.8
Q ss_pred hHHhHHHHHHHHhcCCCccHHHHHhhhcCCHHHHHHHHHHHhhchhhhccCccccchhhhhhccCC--------------
Q 004857 400 ELSDIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGS-------------- 465 (727)
Q Consensus 400 ~L~~I~GkIveLa~dq~gSRvLQ~lLk~~t~Eqr~~If~EI~~~~~eL~tD~fGn~VVQKLLe~gs-------------- 465 (727)
++++..|++++++++|.+|.++|.++..++..|...+|.++.+++..+++|+||+||+|++|+...
T Consensus 93 i~ee~~grel~l~tnqi~Sk~le~l~~f~d~~ql~~ff~~~~g~lr~i~~~r~gshVle~~L~~~a~~vg~e~~~~s~de 172 (650)
T KOG2188|consen 93 IFEEVYGRELDLATNQIGSKVLEDLLGFSDSRQLCDFFSALNGVLRSIAQHRFGSHVLESALEKLAALVGQEAALLSEDE 172 (650)
T ss_pred HHHHhccceeehhccchhHHHHHHHhccCCchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHhCccccccchhh
Confidence 578899999999999999999999999999999999999999999999999999999999997522
Q ss_pred ------------HHHHHHHHHHHhcChh-hhccCcchhHHHHHHHHhhCH-----HHHHH--------------------
Q 004857 466 ------------PDQRKELAEKLVGQVL-PLSLQMYGCRVIQKALEVIEL-----HQKSQ-------------------- 507 (727)
Q Consensus 466 ------------~eqr~~Ii~~L~G~v~-~La~h~yGSrVIQklIe~as~-----eqr~~-------------------- 507 (727)
++....+++++..++. .|+.|.+|+||+.+++..+.. +....
T Consensus 173 a~~~ke~p~~t~e~~~~~m~nei~~~~~~~l~~~~~gshv~rt~~l~l~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 252 (650)
T KOG2188|consen 173 AAVEKEGPFVTCENLLLLMLNEISPHVLKTLMELIFGSHVLRTILLLLFSMCPIAESEHKLALRKAAHRGMDDWDAVTTP 252 (650)
T ss_pred hcccccCcccccchHHHHHHHHhhHHHHHHHHHHHHhHHHHHHHHHHHccCcchhhhHHHHHHHHHhhccccchhhhhcC
Confidence 3345677888999998 999999999999998854221 00000
Q ss_pred ---------------------------------HHH-------------HHH----------------------------
Q 004857 508 ---------------------------------LVL-------------ELD---------------------------- 513 (727)
Q Consensus 508 ---------------------------------Lv~-------------EL~---------------------------- 513 (727)
.++ ++.
T Consensus 253 pqsFp~~l~~~i~~~l~~~~~~s~~~~~~~k~~~vDk~~s~v~q~~i~l~~~~~~~~~~~~~~~lv~~~~~~~e~d~~~~ 332 (650)
T KOG2188|consen 253 PQSFPQRLIVWICTGLSALQDVSESKKRDLKGYEVDKSSSNVLQKAIRLAFDENKNDQFMESPRLVTKFQLFNEKDGLWG 332 (650)
T ss_pred hhhccHHHHHHHhhhccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhcchhhhhhhhHHHhhhhccccCcccc
Confidence 000 000
Q ss_pred ---HHHHHHhhcccCchhhhHhhhcCChhHHHHHHHHhhhhHhhhccCCCCchHHHHHHhhCCcHHHHHHHHHHHHHHHH
Q 004857 514 ---GHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAF 590 (727)
Q Consensus 514 ---g~i~~L~~D~~GNhVIQklLe~~~~e~~~~Ii~~L~~~l~~Ls~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~~l~ 590 (727)
+-...+..|+.|+|+|..+++..+++....+...|.+++.+|+.|+.+..+||++|++..+.+....|++|+..++.
T Consensus 333 kE~~~~k~~l~d~tgSrllE~Imeva~~~~~~lf~~~f~~rl~~La~~p~aNF~lQrli~h~~~~e~v~~v~eeL~P~~~ 412 (650)
T KOG2188|consen 333 KERSFLKELLSDQTGSRLLEVIMEVASESLLSLFYIVFCGRLDELAVHPIANFPLQRLINHLTSLEDVGSVIEELAPKLS 412 (650)
T ss_pred cccHHHHHHHhcCcccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhCccccchHHHHHHhccCHHHHHHHHHHHhHHHH
Confidence 00344557899999999999999999997777888999999999999999999999999988888889998887655
Q ss_pred HHhhCc-----------------------------------------------------------------CccHHHHHH
Q 004857 591 ALAQDQ-----------------------------------------------------------------YGNYVTQHV 605 (727)
Q Consensus 591 ~La~Dq-----------------------------------------------------------------~GNyVVQ~l 605 (727)
.|.... .|+.++|++
T Consensus 413 ~LL~~g~~gVv~sLia~~~rl~s~q~~~l~~Li~a~~~~~~~~k~il~~lL~~~~~~g~~~~~~~t~~~h~~ga~lle~l 492 (650)
T KOG2188|consen 413 SLLEQGNSGVVASLIAASARLGSYQDKMLQQLIQAFHAASESKKNILPCLLFSLTLFGCVGEWFLTEKFHQKGAVLLEEL 492 (650)
T ss_pred HHHHcCCchHhHHHHHHHHhhchhHHHHHHHHHHHHhcCChhhcchHHHHHHHhhhcccccccccHHHHhhchhHHHHHH
Confidence 543322 233444444
Q ss_pred HHcCCch---hHHHHHHHHHHHHHHHhcCchHHHHHHHHHHh--CCHHHHHHHHHHHhcCCCChhHHHhhhcCCChHHHH
Q 004857 606 LERGKSY---ERTQILSKLAGKIVQMSQHKYASNVVEKCLEY--GDTAERELLIEEILGQSEENDNLLVMMKDQYANYVV 680 (727)
Q Consensus 606 Le~~~~k---~r~~II~~L~g~lveLs~~K~GS~VVEk~L~~--as~k~Rk~IIkeLl~~~~~~e~L~~La~DqyGnyVV 680 (727)
+...++. ..+.+.+...++|.+++++.+||||||.+|.. .+++.|+.+|..+-+ ...+|+.+.+|++|+
T Consensus 493 v~f~k~~i~~litsll~L~~eqi~e~~~~~~~ShlIeavL~S~~l~~~~~~kLi~~l~g------~~~~La~~~~GSrv~ 566 (650)
T KOG2188|consen 493 VNFSKTHIQTLITSLLSLSEEQILEMSCNGVGSHLIEAVLASKDLGEKIKEKLINILDG------SFVTLALSTFGSRVF 566 (650)
T ss_pred HhhchhhhHHHHHHHHhhhHHHHHHHhcCCchHHHHHHHHHhccccHHHHHHHHHHhhc------cchheeecCcccHHH
Confidence 4443331 12233344478899999999999999999998 778889999988875 378999999999999
Q ss_pred HHHHhcCCHHHHHHHHHHHHHhHHHHhcCCChHHHHHHH
Q 004857 681 QKILEKCNEKLRETLISRIRVHCDALKKYTYGKHIVARF 719 (727)
Q Consensus 681 QklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~L 719 (727)
.++|+.+++..|++|+.+|-..-+.+++++||+.|+.++
T Consensus 567 eK~wea~~~~~k~rIakeL~~~~~~vk~s~~gk~v~~~~ 605 (650)
T KOG2188|consen 567 EKCWEATDVLYKERIAKELVGIHNDVKSSKYGKFVMLNW 605 (650)
T ss_pred HHHHHHhhHHHHHHHHHHHHhhccccccCcchHHHHHhc
Confidence 999999999999999999999999999999999998764
No 12
>KOG2188 consensus Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=9e-21 Score=212.04 Aligned_cols=289 Identities=17% Similarity=0.269 Sum_probs=218.3
Q ss_pred HHHHHHhhchhhhccCccccchhhhhhccCCHHHHHHHHHHHhcChhhhccCcchhHHHHHHHHhhC-------------
Q 004857 435 SVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIE------------- 501 (727)
Q Consensus 435 ~If~EI~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G~v~~La~h~yGSrVIQklIe~as------------- 501 (727)
.||+|..+..+.|++++.|++++|+++..++..|...++.++.|+++.|+.|++|+||+|++++.+.
T Consensus 92 ~i~ee~~grel~l~tnqi~Sk~le~l~~f~d~~ql~~ff~~~~g~lr~i~~~r~gshVle~~L~~~a~~vg~e~~~~s~d 171 (650)
T KOG2188|consen 92 SIFEEVYGRELDLATNQIGSKVLEDLLGFSDSRQLCDFFSALNGVLRSIAQHRFGSHVLESALEKLAALVGQEAALLSED 171 (650)
T ss_pred hHHHHhccceeehhccchhHHHHHHHhccCCchhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHhCccccccchh
Confidence 4899999999999999999999999999999999999999999999999999999999999997531
Q ss_pred -------------HHHHHHHHHHHHHHHH-HHhhcccCchhhhHhhhcCCh-----------------------------
Q 004857 502 -------------LHQKSQLVLELDGHVM-RCVRDQNGNHVIQKCIECVPA----------------------------- 538 (727)
Q Consensus 502 -------------~eqr~~Lv~EL~g~i~-~L~~D~~GNhVIQklLe~~~~----------------------------- 538 (727)
++....|..|+.+++. .++.+.+|.||+..+|-+...
T Consensus 172 ea~~~ke~p~~t~e~~~~~m~nei~~~~~~~l~~~~~gshv~rt~~l~l~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 251 (650)
T KOG2188|consen 172 EAAVEKEGPFVTCENLLLLMLNEISPHVLKTLMELIFGSHVLRTILLLLFSMCPIAESEHKLALRKAAHRGMDDWDAVTT 251 (650)
T ss_pred hhcccccCcccccchHHHHHHHHhhHHHHHHHHHHHHhHHHHHHHHHHHccCcchhhhHHHHHHHHHhhccccchhhhhc
Confidence 1112335678888888 899999999999877654211
Q ss_pred -----------------------------hHHHHHHHHhhh---------------------------------------
Q 004857 539 -----------------------------EKIEFIISAFRG--------------------------------------- 550 (727)
Q Consensus 539 -----------------------------e~~~~Ii~~L~~--------------------------------------- 550 (727)
+.+..++++...
T Consensus 252 ~pqsFp~~l~~~i~~~l~~~~~~s~~~~~~~k~~~vDk~~s~v~q~~i~l~~~~~~~~~~~~~~~lv~~~~~~~e~d~~~ 331 (650)
T KOG2188|consen 252 PPQSFPQRLIVWICTGLSALQDVSESKKRDLKGYEVDKSSSNVLQKAIRLAFDENKNDQFMESPRLVTKFQLFNEKDGLW 331 (650)
T ss_pred ChhhccHHHHHHHhhhccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhcchhhhhhhhHHHhhhhccccCccc
Confidence 000000000000
Q ss_pred -----hHhhhccCCCCchHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhCcCccHHHHHHHHcCC-chhHHHHHHHHHHH
Q 004857 551 -----QVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGK-SYERTQILSKLAGK 624 (727)
Q Consensus 551 -----~l~~Ls~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~GNyVVQ~lLe~~~-~k~r~~II~~L~g~ 624 (727)
-+.++..|+.||++++.+++.+... ....+-..+...+..|+.++.+||+||.+|+|.. .++...|++.|.++
T Consensus 332 ~kE~~~~k~~l~d~tgSrllE~Imeva~~~-~~~lf~~~f~~rl~~La~~p~aNF~lQrli~h~~~~e~v~~v~eeL~P~ 410 (650)
T KOG2188|consen 332 GKERSFLKELLSDQTGSRLLEVIMEVASES-LLSLFYIVFCGRLDELAVHPIANFPLQRLINHLTSLEDVGSVIEELAPK 410 (650)
T ss_pred ccccHHHHHHHhcCcccHHHHHHHHhcCHH-HHHHHHHHHHHHHHHHHhCccccchHHHHHHhccCHHHHHHHHHHHhHH
Confidence 1122234678999999999998865 4477777888899999999999999999999987 88889999999877
Q ss_pred HHHHhcCchH-----------------HHHHHHHHHh---CCHHHH-----------------------------HHHHH
Q 004857 625 IVQMSQHKYA-----------------SNVVEKCLEY---GDTAER-----------------------------ELLIE 655 (727)
Q Consensus 625 lveLs~~K~G-----------------S~VVEk~L~~---as~k~R-----------------------------k~IIk 655 (727)
+..|..+.+. ..+++.++.. ++++.+ ..++.
T Consensus 411 ~~~LL~~g~~gVv~sLia~~~rl~s~q~~~l~~Li~a~~~~~~~~k~il~~lL~~~~~~g~~~~~~~t~~~h~~ga~lle 490 (650)
T KOG2188|consen 411 LSSLLEQGNSGVVASLIAASARLGSYQDKMLQQLIQAFHAASESKKNILPCLLFSLTLFGCVGEWFLTEKFHQKGAVLLE 490 (650)
T ss_pred HHHHHHcCCchHhHHHHHHHHhhchhHHHHHHHHHHHHhcCChhhcchHHHHHHHhhhcccccccccHHHHhhchhHHHH
Confidence 7766633321 1222222221 111111 12233
Q ss_pred HHhcCCC-------------ChhHHHhhhcCCChHHHHHHHHhc--CCHHHHHHHHHHHHHhHHHHhcCCChHHHHHHHH
Q 004857 656 EILGQSE-------------ENDNLLVMMKDQYANYVVQKILEK--CNEKLRETLISRIRVHCDALKKYTYGKHIVARFE 720 (727)
Q Consensus 656 eLl~~~~-------------~~e~L~~La~DqyGnyVVQklL~~--~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~Le 720 (727)
+|+.... ..++|.+++++.+|++||+.+|++ .++..|++|+..+..+..+|+.+++|+||+++|+
T Consensus 491 ~lv~f~k~~i~~litsll~L~~eqi~e~~~~~~~ShlIeavL~S~~l~~~~~~kLi~~l~g~~~~La~~~~GSrv~eK~w 570 (650)
T KOG2188|consen 491 ELVNFSKTHIQTLITSLLSLSEEQILEMSCNGVGSHLIEAVLASKDLGEKIKEKLINILDGSFVTLALSTFGSRVFEKCW 570 (650)
T ss_pred HHHhhchhhhHHHHHHHHhhhHHHHHHHhcCCchHHHHHHHHHhccccHHHHHHHHHHhhccchheeecCcccHHHHHHH
Confidence 3332211 147899999999999999999998 6788999999999999999999999999999999
Q ss_pred HHHh
Q 004857 721 QLYG 724 (727)
Q Consensus 721 kli~ 724 (727)
+.++
T Consensus 571 ea~~ 574 (650)
T KOG2188|consen 571 EATD 574 (650)
T ss_pred HHhh
Confidence 8765
No 13
>KOG2050 consensus Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=1.2e-19 Score=201.37 Aligned_cols=264 Identities=18% Similarity=0.280 Sum_probs=219.4
Q ss_pred cchhhhhhccC-CHHHHHHH----HHHHhcChhhhccCcchhHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhhcccCchh
Q 004857 454 NYVIQKFFEHG-SPDQRKEL----AEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHV 528 (727)
Q Consensus 454 n~VVQKLLe~g-s~eqr~~I----i~~L~G~v~~La~h~yGSrVIQklIe~as~eqr~~Lv~EL~g~i~~L~~D~~GNhV 528 (727)
+-+++||=..- +.|.|..+ ++.++|++.+|+.-+..+||||.++.+++..+|.+|++||.+.+.+|+++.||-|.
T Consensus 135 kslWEkLR~k~~~ke~R~klv~el~~likg~i~~lv~aHDtSRViQt~Vky~s~~~r~~if~eL~p~~v~l~kskY~k~~ 214 (652)
T KOG2050|consen 135 KSLWEKLRRKTTPKEERDKLVSELYKLIKGKISKLVFAHDTSRVIQTCVKYGSEAQREQIFEELLPFFVELAKSKYAKFF 214 (652)
T ss_pred HHHHHHHhccCCcHHHHHHHHHHHHHHHhhhHHHHHHHhhhHHHHHHHHHhcCHHHHHHHHHHHhHHHHHHHHhHHHHHH
Confidence 34445544332 34555444 45568899999999999999999999999999999999999999999999999999
Q ss_pred hhHhhhcCChhHHHHHHHHhhhhHhhhccCCCCchHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhCcCccHHHHHHHHc
Q 004857 529 IQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLER 608 (727)
Q Consensus 529 IQklLe~~~~e~~~~Ii~~L~~~l~~Ls~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~GNyVVQ~lLe~ 608 (727)
+|++|.++.+..++.|+..|+|+++.|..|+.|+.|++-++....+..||+.|+.|+.+....+..+.. -.-|..+|+.
T Consensus 215 v~KmLkyGsk~q~a~iI~sl~Ghv~kLlRH~eaa~Vve~ay~~~A~l~Qr~~li~EfYG~efqlfK~sn-~~Tl~kil~~ 293 (652)
T KOG2050|consen 215 VQKMLKYGSKAQKAKIINSLRGHVVKLLRHREAAYVVEYAYNDFATLEQRQYLIQEFYGDEFQLFKDSN-DKTLDKILAE 293 (652)
T ss_pred HHHHHhcCCHHHHHHHHHHHhhhHHHHHhhhHHHHHHHHHHHhhccHHHHHHHHHHHhhHHHHHHhccC-cccHHHHHHh
Confidence 999999999999999999999999999999999999998888777778999999999999999998833 2344555554
Q ss_pred CCchhHHHHHHHHHHHHHHHhcC-chH----HHHHHHHHHhCCHHHHHHHHHHHhcCCCChhHHHhhhcCCChHHHHHHH
Q 004857 609 GKSYERTQILSKLAGKIVQMSQH-KYA----SNVVEKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQKI 683 (727)
Q Consensus 609 ~~~k~r~~II~~L~g~lveLs~~-K~G----S~VVEk~L~~as~k~Rk~IIkeLl~~~~~~e~L~~La~DqyGnyVVQkl 683 (727)
.++.+..|++.|.+.+-.++.. -.+ ..++...|..++++++..++..+. +.+..|+..+-|+.|..++
T Consensus 294 -~pekk~~I~~~l~~~I~~v~eKg~v~~tivHk~mlEy~~~ade~e~~e~l~ll~------elv~e~vHT~dGS~vAm~l 366 (652)
T KOG2050|consen 294 -APEKKASILRHLKAIITPVAEKGSVDHTIVHKLMLEYLTIADEEEKSELLELLK------ELVPEMVHTRDGSRVAMKL 366 (652)
T ss_pred -ChHhHHHHHHHHHHHhHHHhhcchhHHHHHHHHHHHHHHhCCHHHHHHHHHHHH------HHHHHHhcCCchHHHHHHH
Confidence 4667778888887777665532 223 344555667799999999888887 6799999999999999999
Q ss_pred HhcCCHHHHHHHHHHHHHhHHHHhcCCChHHHHHHHHHHHhc
Q 004857 684 LEKCNEKLRETLISRIRVHCDALKKYTYGKHIVARFEQLYGE 725 (727)
Q Consensus 684 L~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~Lekli~~ 725 (727)
+-.++++.|+.|+..++.|+..++++.||+.|+-.+..+++|
T Consensus 367 i~~a~aKeRK~IiK~~K~h~~K~A~~~yGh~vlia~ldc~DD 408 (652)
T KOG2050|consen 367 IWHATAKERKLIIKNMKEHVEKIANDEYGHLVLIALLDCTDD 408 (652)
T ss_pred HhhCCHHHHHHHHHHHHHHHHHHHhhccCceehhhhhcccch
Confidence 999999999999999999999999999999999888888765
No 14
>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]
Probab=99.62 E-value=1.1e-15 Score=174.62 Aligned_cols=289 Identities=20% Similarity=0.255 Sum_probs=228.1
Q ss_pred HHHHHHHHHHHhhchhhhccCccccchhhhhhccCCHHHHHHHHHHHhcChhhhccCcchhHHHHHHHHhhCHHHH-HHH
Q 004857 430 AEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQK-SQL 508 (727)
Q Consensus 430 ~Eqr~~If~EI~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G~v~~La~h~yGSrVIQklIe~as~eqr-~~L 508 (727)
..|.+.+.-++.+...+|..|-.||-|+||+|++++...++.+......++..+..|++|.++.|++|+.+..+.. ..+
T Consensus 534 ~pEied~ai~mLDe~~elsSdylGNtVvqkfFe~sS~~ik~aml~r~s~ylts~gvHknGtw~~qk~ik~a~te~qik~i 613 (1007)
T KOG4574|consen 534 APEIEDLAILMLDELPELSSDYLGNTVVQKFFELSSDIIKDAMLRRGSKYLTSMGVHKNGTWACQKIIKMAFTERQIKLI 613 (1007)
T ss_pred chhHHHHHHHHhccCCcchhhhhcchhhHHHHhhccHHHHHHHHhhhhhhhhhccccccchHHHHHHHHHhhchhhhhee
Confidence 3455667777888999999999999999999999999999999999999999999999999999999998866554 445
Q ss_pred HHHHHHHHHHHhhcccCchhhhHhhhcCChhHHHHHHHHhhhhHhhhccCCCCchHHHHHHhhCCcHHHHHHHHHHHH--
Q 004857 509 VLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEIL-- 586 (727)
Q Consensus 509 v~EL~g~i~~L~~D~~GNhVIQklLe~~~~e~~~~Ii~~L~~~l~~Ls~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~-- 586 (727)
+.-..+....++.|++||||+|.+|...-+ ...+|++.+..+++++....||++.+.+|++......+.+.+..+.+
T Consensus 614 v~g~dpyc~~l~~dqfgnyvaqd~LkF~fp-~nsFVfE~v~s~~~~ivQsrfGsravrAcle~lNa~~e~qsl~~~s~iI 692 (1007)
T KOG4574|consen 614 VRGVDPYCTPLLNDQFGNYVAQDSLKFGFP-WNSFVFESVFSHFWDIVQSRFGSRAVRACLEALNANTEDQSLVRESCII 692 (1007)
T ss_pred eeccCcchhhHHHHhhcceeeeeehhccCc-cchHHHHHHHHHHHHHHHHhhhhHHHHHHHHHhccCchhhhhhhhhhhh
Confidence 677788888999999999999999997543 35788999999999999999999999999996443323333333332
Q ss_pred HHHHHHhhCcCccHHHHHHHHcCCchhH-HHHHHHHHHHHHHHhcCchHHHHHHHHHHhCC-HHHHHHHHHHHhcCC---
Q 004857 587 ESAFALAQDQYGNYVTQHVLERGKSYER-TQILSKLAGKIVQMSQHKYASNVVEKCLEYGD-TAERELLIEEILGQS--- 661 (727)
Q Consensus 587 ~~l~~La~Dq~GNyVVQ~lLe~~~~k~r-~~II~~L~g~lveLs~~K~GS~VVEk~L~~as-~k~Rk~IIkeLl~~~--- 661 (727)
.....++.+.-|-..|.++|+.+..-.| ..++..+.++++.+|.||.|+-+|.|+++... +..|++|++.|+...
T Consensus 693 s~ss~latnsng~llvtw~lDns~~~nrh~~l~~~lt~el~~lC~h~Lgsttv~Kl~n~~qepvs~ekii~hlf~~~n~k 772 (1007)
T KOG4574|consen 693 SKSSYLATNSNGLLLVTWLLDNSSLPNRHTILAHGLTKELVMLCFHKLGSTTVLKLLNLRQEPVSREKIIEHLFHLRNFK 772 (1007)
T ss_pred hchhhhhhcCccceeeeeecccccccchhhHHhhhhhhccchhhhhhccchhhhhhhhcCCChHHHHHHHHHHhhccccc
Confidence 3356788999999999999998764444 45667788999999999999999999999955 555999999998421
Q ss_pred CC---------------------hhHHHhhhcCCChHHHHHHHHhcCCHHHHHHHHHHHHHhHHHHhcCCChHHHHHHHH
Q 004857 662 EE---------------------NDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGKHIVARFE 720 (727)
Q Consensus 662 ~~---------------------~e~L~~La~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~Le 720 (727)
++ .+.+.....|+++++|.|.++...-..... ++.|...+.-++.++||+.-+..+-
T Consensus 773 d~~lt~Vl~~~~~gpmfiikvi~~p~iel~f~dQf~kvvrq~il~~~a~~nar--v~~LleevgliSasksgs~s~q~~~ 850 (1007)
T KOG4574|consen 773 DSALTEVLTEANYGPMFIIKVITKPTIELAFRDQFIKVVRQVILNSPAVSNAR--VQRLLEEVGLISASKSGSQSIQMHI 850 (1007)
T ss_pred cchhhhhhhhhccccceeeeeeccccchHHHHHHHHHHHHHHHHhcCCccHHH--HHHHHHHHhhhccccchhHHHHhhh
Confidence 10 245666778999999999999874333211 1455556666777888888665554
Q ss_pred H
Q 004857 721 Q 721 (727)
Q Consensus 721 k 721 (727)
+
T Consensus 851 s 851 (1007)
T KOG4574|consen 851 S 851 (1007)
T ss_pred c
Confidence 4
No 15
>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]
Probab=99.28 E-value=1.3e-11 Score=141.90 Aligned_cols=309 Identities=17% Similarity=0.212 Sum_probs=208.5
Q ss_pred cCChhhhHHHHHhhccccccchHHhHHHHH----HHHhcCCCccHHHHHhhhcCCHHHHHHHHHHHhhchhhhccCcccc
Q 004857 379 FEDSKKHSFLEELKSSNAQKFELSDIAGRI----VEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGN 454 (727)
Q Consensus 379 ~~d~~r~~LLeeL~~~~~~~~~L~~I~GkI----veLa~dq~gSRvLQ~lLk~~t~Eqr~~If~EI~~~~~eL~tD~fGn 454 (727)
.+-+++.++.....++.--..+++++.+-. -++..|-.|.-|+|++.+.+..--++...+.....+..+..|+||.
T Consensus 515 fe~~klRe~rksedsn~~S~pEied~ai~mLDe~~elsSdylGNtVvqkfFe~sS~~ik~aml~r~s~ylts~gvHknGt 594 (1007)
T KOG4574|consen 515 FEAPKLRELRKSEDSNRLSAPEIEDLAILMLDELPELSSDYLGNTVVQKFFELSSDIIKDAMLRRGSKYLTSMGVHKNGT 594 (1007)
T ss_pred CccchhhHHhhhcccCcccchhHHHHHHHHhccCCcchhhhhcchhhHHHHhhccHHHHHHHHhhhhhhhhhccccccch
Confidence 333444444444444433344455544432 3566677788899999999999999999999999999999999999
Q ss_pred chhhhhhccC-CHHHHHHHHHHHhcChhhhccCcchhHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhhcccCchhhhHhh
Q 004857 455 YVIQKFFEHG-SPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKCI 533 (727)
Q Consensus 455 ~VVQKLLe~g-s~eqr~~Ii~~L~G~v~~La~h~yGSrVIQklIe~as~eqr~~Lv~EL~g~i~~L~~D~~GNhVIQklL 533 (727)
+.+||+|+.+ ++.+.+.|+.-....+..|..+.||++|+|.+|.+.-.-. .-++++++.++..+....+|..-+.+||
T Consensus 595 w~~qk~ik~a~te~qik~iv~g~dpyc~~l~~dqfgnyvaqd~LkF~fp~n-sFVfE~v~s~~~~ivQsrfGsravrAcl 673 (1007)
T KOG4574|consen 595 WACQKIIKMAFTERQIKLIVRGVDPYCTPLLNDQFGNYVAQDSLKFGFPWN-SFVFESVFSHFWDIVQSRFGSRAVRACL 673 (1007)
T ss_pred HHHHHHHHHhhchhhhheeeeccCcchhhHHHHhhcceeeeeehhccCccc-hHHHHHHHHHHHHHHHHhhhhHHHHHHH
Confidence 9999999987 5667888888888899999999999999999997654311 1236888899999999999999999999
Q ss_pred hcC--ChhHHHHHHHHh-hhhHhhhccCCCCchHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhCcCccHHHHHHHHcCC
Q 004857 534 ECV--PAEKIEFIISAF-RGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVLERGK 610 (727)
Q Consensus 534 e~~--~~e~~~~Ii~~L-~~~l~~Ls~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~GNyVVQ~lLe~~~ 610 (727)
|.. ..+...+.++.. ......++++-.|-+.|..+++.+.-......++..+.+++..++.|.-|+-+|+++++.+.
T Consensus 674 e~lNa~~e~qsl~~~s~iIs~ss~latnsng~llvtw~lDns~~~nrh~~l~~~lt~el~~lC~h~Lgsttv~Kl~n~~q 753 (1007)
T KOG4574|consen 674 EALNANTEDQSLVRESCIISKSSYLATNSNGLLLVTWLLDNSSLPNRHTILAHGLTKELVMLCFHKLGSTTVLKLLNLRQ 753 (1007)
T ss_pred HHhccCchhhhhhhhhhhhhchhhhhhcCccceeeeeecccccccchhhHHhhhhhhccchhhhhhccchhhhhhhhcCC
Confidence 853 233333333332 22255667777777777777777665544444555555777888888888888888888776
Q ss_pred chh-HHHHHHHHHH------------------------------HHHHHhcCchHHHHHHHHHHhCCH-HHHHHHHHHHh
Q 004857 611 SYE-RTQILSKLAG------------------------------KIVQMSQHKYASNVVEKCLEYGDT-AERELLIEEIL 658 (727)
Q Consensus 611 ~k~-r~~II~~L~g------------------------------~lveLs~~K~GS~VVEk~L~~as~-k~Rk~IIkeLl 658 (727)
+.. |+.|++.|.. .+.....++++-.|.+.|+..... ..| +..|+
T Consensus 754 epvs~ekii~hlf~~~n~kd~~lt~Vl~~~~~gpmfiikvi~~p~iel~f~dQf~kvvrq~il~~~a~~nar---v~~Ll 830 (1007)
T KOG4574|consen 754 EPVSREKIIEHLFHLRNFKDSALTEVLTEANYGPMFIIKVITKPTIELAFRDQFIKVVRQVILNSPAVSNAR---VQRLL 830 (1007)
T ss_pred ChHHHHHHHHHHhhccccccchhhhhhhhhccccceeeeeeccccchHHHHHHHHHHHHHHHHhcCCccHHH---HHHHH
Confidence 554 6666655521 011111334444455555554221 111 12333
Q ss_pred cCCCChhHHHhhhcCCChHHHHHHHHhcCCHHHHHHHHH
Q 004857 659 GQSEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLIS 697 (727)
Q Consensus 659 ~~~~~~e~L~~La~DqyGnyVVQklL~~~d~~~Rk~Ll~ 697 (727)
+.+.-++...+|.+-+|.+++..+......++.
T Consensus 831 ------eevgliSasksgs~s~q~~~sss~~~~~qrlls 863 (1007)
T KOG4574|consen 831 ------EEVGLISASKSGSQSIQMHISSSKTPFAQRLLS 863 (1007)
T ss_pred ------HHHhhhccccchhHHHHhhhccCCcccccchhh
Confidence 234567888999999999998877665555544
No 16
>PF00806 PUF: Pumilio-family RNA binding repeat; InterPro: IPR001313 The drosophila pumilio gene codes for an unusual protein that binds through the Puf domain that usually occurs as a tandem repeat of eight domains. The FBF-2 protein of Caenorhabditis elegans also has a Puf domain. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs [, ]. The same type of repetitive domain has been found in in a number of other proteins from all eukaryotic kingdoms. The Puf proteins characterised to date have been reported to bind to 3'-untranslated region (UTR) sequences encompassing a so-called UGUR tetranucleotide motif and thereby to repress gene expression by affecting mRNA translation or stability. In Saccharomyces cerevisiae (Baker's yeast), five proteins, termed Puf1p to Puf5p, bear six to eight Puf repeats []. Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. This suggests the existence of an extensive network of RNA-protein interactions that coordinate the post-transcriptional fate of large sets of cytotopically and functionally related RNAs through each stage of its lifecycle.; GO: 0003723 RNA binding; PDB: 3BX2_A 4DZS_B 3BX3_B 3BWT_A 3GVT_B 3GVO_A 1IB2_A 3Q0N_A 2YJY_A 1M8Z_A ....
Probab=98.14 E-value=8.5e-07 Score=65.06 Aligned_cols=35 Identities=43% Similarity=0.727 Sum_probs=23.9
Q ss_pred HHhhchhhhccCccccchhhhhhccCCHHHHHHHH
Q 004857 439 EVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELA 473 (727)
Q Consensus 439 EI~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii 473 (727)
||.+++.+|++|+||||||||+|++++++++..|+
T Consensus 1 ~i~~~~~~l~~d~~Gn~VvQk~le~~~~~~~~~il 35 (35)
T PF00806_consen 1 EIKGNLVELSKDQYGNYVVQKCLEHASPEQRQLIL 35 (35)
T ss_dssp CHTTTHHHHHTSTTHHHHHHHHHHHSSHHHHHHHH
T ss_pred ChHHHHHHHHhccccCHHHHHHHHHCCHHHHHhhC
Confidence 35667777777777777777777777776666553
No 17
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=97.68 E-value=1.2e-05 Score=58.04 Aligned_cols=32 Identities=41% Similarity=0.642 Sum_probs=15.5
Q ss_pred hhchhhhccCccccchhhhhhccCCHHHHHHH
Q 004857 441 LPHASKLMTDVFGNYVIQKFFEHGSPDQRKEL 472 (727)
Q Consensus 441 ~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~I 472 (727)
.+++.+|++|+|||+||||+|++++++++..|
T Consensus 3 ~~~~~~l~~~~~g~~viqk~l~~~~~~~~~~i 34 (36)
T smart00025 3 KGHLLELSKDQYGNRVVQKLLEHASESQREQI 34 (36)
T ss_pred hHHHHHHHhcchhhHHHHHHHHHCCHHHHHHh
Confidence 34444555555555555555555554444443
No 18
>PF00806 PUF: Pumilio-family RNA binding repeat; InterPro: IPR001313 The drosophila pumilio gene codes for an unusual protein that binds through the Puf domain that usually occurs as a tandem repeat of eight domains. The FBF-2 protein of Caenorhabditis elegans also has a Puf domain. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs [, ]. The same type of repetitive domain has been found in in a number of other proteins from all eukaryotic kingdoms. The Puf proteins characterised to date have been reported to bind to 3'-untranslated region (UTR) sequences encompassing a so-called UGUR tetranucleotide motif and thereby to repress gene expression by affecting mRNA translation or stability. In Saccharomyces cerevisiae (Baker's yeast), five proteins, termed Puf1p to Puf5p, bear six to eight Puf repeats []. Puf3p binds nearly exclusively to cytoplasmic mRNAs that encode mitochondrial proteins; Puf1p and Puf2p interact preferentially with mRNAs encoding membrane-associated proteins; Puf4p preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors; and Puf5p is associated with mRNAs encoding chromatin modifiers and components of the spindle pole body. This suggests the existence of an extensive network of RNA-protein interactions that coordinate the post-transcriptional fate of large sets of cytotopically and functionally related RNAs through each stage of its lifecycle.; GO: 0003723 RNA binding; PDB: 3BX2_A 4DZS_B 3BX3_B 3BWT_A 3GVT_B 3GVO_A 1IB2_A 3Q0N_A 2YJY_A 1M8Z_A ....
Probab=97.60 E-value=5.1e-05 Score=55.62 Aligned_cols=35 Identities=40% Similarity=0.639 Sum_probs=32.1
Q ss_pred hHHHHHHHHhcCCCccHHHHHhhhcCCHHHHHHHH
Q 004857 403 DIAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVF 437 (727)
Q Consensus 403 ~I~GkIveLa~dq~gSRvLQ~lLk~~t~Eqr~~If 437 (727)
++.+++.+++.|++||+|||++|+.+++++++.|+
T Consensus 1 ~i~~~~~~l~~d~~Gn~VvQk~le~~~~~~~~~il 35 (35)
T PF00806_consen 1 EIKGNLVELSKDQYGNYVVQKCLEHASPEQRQLIL 35 (35)
T ss_dssp CHTTTHHHHHTSTTHHHHHHHHHHHSSHHHHHHHH
T ss_pred ChHHHHHHHHhccccCHHHHHHHHHCCHHHHHhhC
Confidence 36789999999999999999999999999998875
No 19
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=97.44 E-value=9.7e-05 Score=53.28 Aligned_cols=34 Identities=38% Similarity=0.662 Sum_probs=31.7
Q ss_pred HHHHHHHHhcCCCccHHHHHhhhcCCHHHHHHHH
Q 004857 404 IAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVF 437 (727)
Q Consensus 404 I~GkIveLa~dq~gSRvLQ~lLk~~t~Eqr~~If 437 (727)
+.+++.+++.|++||||||++|+.++.+++..|+
T Consensus 2 ~~~~~~~l~~~~~g~~viqk~l~~~~~~~~~~i~ 35 (36)
T smart00025 2 IKGHLLELSKDQYGNRVVQKLLEHASESQREQII 35 (36)
T ss_pred chHHHHHHHhcchhhHHHHHHHHHCCHHHHHHhh
Confidence 5789999999999999999999999999998876
No 20
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=95.31 E-value=3.5 Score=45.57 Aligned_cols=81 Identities=21% Similarity=0.270 Sum_probs=46.7
Q ss_pred cCccHHHHHHHHcCCchhHHHHHHHHHHHHHHHhcCchHHHHHHHHHHh-----CCHHHHHHHHHHHhcCCCChhHHHhh
Q 004857 596 QYGNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEY-----GDTAERELLIEEILGQSEENDNLLVM 670 (727)
Q Consensus 596 q~GNyVVQ~lLe~~~~k~r~~II~~L~g~lveLs~~K~GS~VVEk~L~~-----as~k~Rk~IIkeLl~~~~~~e~L~~L 670 (727)
.-|...+-.||...+....+.|++.|...=.+ .+-.|-+++|.+ -++.....|++++
T Consensus 201 ~~g~~~~a~Iln~~~~~~~~~il~~L~~~d~~-----~a~~Ir~~mF~Fedl~~l~~~~l~~ll~~v------------- 262 (339)
T PRK05686 201 MGGVKTVAEILNNLDRQTEKTILESLEEEDPE-----LAEKIKDLMFVFEDLVDLDDRSIQRLLREV------------- 262 (339)
T ss_pred cCcHHHHHHHHhcCCchHHHHHHHHHHhhCHH-----HHHHHHHHhcCHHHHhcCCHHHHHHHHHhC-------------
Confidence 34677788999988888888888888754333 233555555544 2233333333333
Q ss_pred hcCCChHHHHHHHHhcCCHHHHHHHHHHH
Q 004857 671 MKDQYANYVVQKILEKCNEKLRETLISRI 699 (727)
Q Consensus 671 a~DqyGnyVVQklL~~~d~~~Rk~Ll~~L 699 (727)
.+-++-.+|..++++.|+.|++-+
T Consensus 263 -----~~~~L~~ALkga~~~~~~~il~nm 286 (339)
T PRK05686 263 -----DNDVLALALKGASEELREKFLSNM 286 (339)
T ss_pred -----CHHHHHHHHCCCCHHHHHHHHHhc
Confidence 344555555555555555555443
No 21
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=94.02 E-value=12 Score=41.48 Aligned_cols=82 Identities=12% Similarity=0.182 Sum_probs=46.0
Q ss_pred CccHHHHHHHHcCCchhHHHHHHHHHHHHHHHhcCchHHHHHHHHHHh-----CCHHHHHHHHHHHhcCCCChhHHHhhh
Q 004857 597 YGNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEY-----GDTAERELLIEEILGQSEENDNLLVMM 671 (727)
Q Consensus 597 ~GNyVVQ~lLe~~~~k~r~~II~~L~g~lveLs~~K~GS~VVEk~L~~-----as~k~Rk~IIkeLl~~~~~~e~L~~La 671 (727)
-|.-.+..||...+....+.|++.|...=.++ +-.|-+++|.+ -++.....|++++
T Consensus 199 gG~~~~a~ILN~~~~~~~~~il~~L~~~dp~l-----a~~Ir~~mF~Fedl~~ld~~~l~~llrev-------------- 259 (338)
T TIGR00207 199 GGVRAVAEIINLMDRKTEKTIITSLEEFDPEL-----AEEIKKEMFVFEDIVDLDDRSIQRVLREV-------------- 259 (338)
T ss_pred ChHHHHHHHHHhCCchHHHHHHHHHHHhCHHH-----HHHHHHHccCHHHHhcCCHHHHHHHHHhC--------------
Confidence 36677888999888888888888886533332 23444444443 2333333443333
Q ss_pred cCCChHHHHHHHHhcCCHHHHHHHHHHHHH
Q 004857 672 KDQYANYVVQKILEKCNEKLRETLISRIRV 701 (727)
Q Consensus 672 ~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~ 701 (727)
-+-++-.+|..++++.|+.|++-+..
T Consensus 260 ----~~~~L~~ALkga~~e~~~~il~nmS~ 285 (338)
T TIGR00207 260 ----DSEDLLLALKGAEQPLREKFLNNMSQ 285 (338)
T ss_pred ----CHHHHHHHHCcCCHHHHHHHHHHhhH
Confidence 24455555555555555555554443
No 22
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=91.32 E-value=21 Score=39.47 Aligned_cols=85 Identities=14% Similarity=0.187 Sum_probs=43.7
Q ss_pred CccHHHHHhhhc-CCHHHHHHHHHHHhhchhhhccCccccchhhhhhccCCHHHHHHHHHHHhcChhhhccCcchhHHHH
Q 004857 416 HGSRFIQQKLEH-CSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQ 494 (727)
Q Consensus 416 ~gSRvLQ~lLk~-~t~Eqr~~If~EI~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G~v~~La~h~yGSrVIQ 494 (727)
.|-..+..+|.. ...++-+.|++++.+.-. .++++.| ...+++.+..++.....+...++...--..+-.
T Consensus 80 gg~~~~~~iL~~~l~~~~a~~il~~i~~~~~--------~~~fe~L-~~ld~~~l~~lL~~EhpqtiA~iLs~l~~~~aa 150 (339)
T PRK05686 80 GGIDYARSLLEKALGEEKADSILERILESLG--------TSGFDFL-RKMDPQQLANFIRNEHPQTIALILSYLKPDQAA 150 (339)
T ss_pred ChHHHHHHHHHHHcCHHHHHHHHHHHhcccc--------CchHHHH-hcCCHHHHHHHHHhcCHHHHHHHHhCCCHHHHH
Confidence 334456666654 555666666666654311 1344433 344666666666665555555544444444444
Q ss_pred HHHHhhCHHHHHHHH
Q 004857 495 KALEVIELHQKSQLV 509 (727)
Q Consensus 495 klIe~as~eqr~~Lv 509 (727)
+++...+.+.+..++
T Consensus 151 ~vL~~l~~~~~~~v~ 165 (339)
T PRK05686 151 EILSLLPEELRADVM 165 (339)
T ss_pred HHHHhCCHHHHHHHH
Confidence 444444444444443
No 23
>PF08144 CPL: CPL (NUC119) domain; InterPro: IPR012959 This C-terminal domain is found in Penguin-like proteins (CPL) and is associated with Pumilio like repeats [].; GO: 0003723 RNA binding
Probab=88.52 E-value=0.83 Score=44.72 Aligned_cols=71 Identities=8% Similarity=0.186 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHhcCchHHHHHHHHHHhCCHH---HHHHHHHHHhcC--CCChhHHHhhhcCCChHHHHHHHHhcC
Q 004857 617 ILSKLAGKIVQMSQHKYASNVVEKCLEYGDTA---ERELLIEEILGQ--SEENDNLLVMMKDQYANYVVQKILEKC 687 (727)
Q Consensus 617 II~~L~g~lveLs~~K~GS~VVEk~L~~as~k---~Rk~IIkeLl~~--~~~~e~L~~La~DqyGnyVVQklL~~~ 687 (727)
|++.+..+..+|..+++|+.+|..+|..++.+ ..+.|++.+... ..+.+.=..++.+++|++++.++++..
T Consensus 58 Ll~~i~~~~~~ll~~~~g~~~i~eiL~~~~gdk~~a~~Aia~~~~~~~~~~~~~~e~H~i~~p~~~r~lK~Liq~~ 133 (148)
T PF08144_consen 58 LLEAIAENAEELLSSSFGCQFITEILLSATGDKSAALEAIASLAAEPLFPGDIDEEYHLIEHPFGHRMLKKLIQGD 133 (148)
T ss_pred HHHHHHHhHHHHHhcCcccHHHHHHHhccCccHHHHHHHHHHHHhhccCCCCCcCccchhcCchHHHHHHHHHHCC
Confidence 34455677788999999999999999886432 223344444332 011111135779999999999999753
No 24
>PF04286 DUF445: Protein of unknown function (DUF445); InterPro: IPR007383 This entry contains proteins of unknown function. They are predicted to be transmembrane proteins with 2 or 3 TM domains.
Probab=88.25 E-value=43 Score=36.47 Aligned_cols=49 Identities=24% Similarity=0.224 Sum_probs=28.8
Q ss_pred chhHHHHHHHHHHHHHHHhcC--chHHHHHHHHHHhCCHHHHHHHHHHHhc
Q 004857 611 SYERTQILSKLAGKIVQMSQH--KYASNVVEKCLEYGDTAERELLIEEILG 659 (727)
Q Consensus 611 ~k~r~~II~~L~g~lveLs~~--K~GS~VVEk~L~~as~k~Rk~IIkeLl~ 659 (727)
++.++.|.+.+...+..+... -.=..+|+.-+..-+.++...++....+
T Consensus 289 ~~l~~~i~~~i~~~l~~~v~~~~~~i~~~V~~~l~~~~~~~l~~~i~~~v~ 339 (367)
T PF04286_consen 289 PELREKINRFIENLLERIVESNHIDIGEIVEEKLNSLDDEELEELIESKVG 339 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 455666666666666666655 3334555555565566666666666554
No 25
>COG2733 Predicted membrane protein [Function unknown]
Probab=85.08 E-value=63 Score=36.55 Aligned_cols=192 Identities=14% Similarity=0.081 Sum_probs=80.6
Q ss_pred ccCchhhhHhhhcCChhHH-HHHHHHhhhhHhhhccCCCC----chHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhCcC
Q 004857 523 QNGNHVIQKCIECVPAEKI-EFIISAFRGQVATLSTHPYG----CRVIQRVLEHCSDEQQGQCIVDEILESAFALAQDQY 597 (727)
Q Consensus 523 ~~GNhVIQklLe~~~~e~~-~~Ii~~L~~~l~~Ls~hk~G----S~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~ 597 (727)
.+-....-++|++...+.+ +.|++.+.+.+.....+..- +.+|.++++......-.....+.+.+.... .-
T Consensus 162 ~~~~~~~~~vL~~l~~d~r~q~l~D~~~~~L~r~~~~~~v~~~i~~~i~r~~~ee~p~f~~~~~~~~v~~~~I~----~a 237 (415)
T COG2733 162 VYLGPTAGRVLESLTADDRHQALLDKLIDRLIRWLLNDKVREFIAAVIVRYLEEEHPLFAPIIIVSLVGKRDIS----DA 237 (415)
T ss_pred ccccchHHHHHHHHHhcccHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcCccchhhhhHHHHhhchHH----HH
Confidence 3444444455555444444 55666655555554444332 356666666544322222222222222110 11
Q ss_pred ccHHHHHHHHcCCchhHHHHHHHHHHHHHHHhcCchHHHHHHHHHHh-CCHHHHHHHHHHHhcCCCChhHHHhhhcCCCh
Q 004857 598 GNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEY-GDTAERELLIEEILGQSEENDNLLVMMKDQYA 676 (727)
Q Consensus 598 GNyVVQ~lLe~~~~k~r~~II~~L~g~lveLs~~K~GS~VVEk~L~~-as~k~Rk~IIkeLl~~~~~~e~L~~La~DqyG 676 (727)
++-.++.++...+-+.|+..-..+.+-+..|-+++-=..=+|++... -..+.....+..|.++. ..++..--+.-+
T Consensus 238 ~~~~~D~v~~~p~h~~rk~~~R~~~~~i~~L~~Dp~~~~r~e~iK~~~~~~~~i~~~~~~~w~~~---~~~l~~D~e~~~ 314 (415)
T COG2733 238 VNSFLDEVRRDPDHKMRKDFDRFLFDLIDDLYHDPGMAARAEAIKSYLKEDEAIATAAGDMWTSL---SEWLKEDYESED 314 (415)
T ss_pred HHHHHHHHHhCcCccchHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhcChHHHHHHHHHHHHH---HHHHHhcccCch
Confidence 22344555553333344444445555555555553333333333332 12223333344444321 001111111111
Q ss_pred HH-------HHHHHHhc--CCHHHHHHHHHHHHHhHHHHhcC---CChHHHHHHHHH
Q 004857 677 NY-------VVQKILEK--CNEKLRETLISRIRVHCDALKKY---TYGKHIVARFEQ 721 (727)
Q Consensus 677 ny-------VVQklL~~--~d~~~Rk~Ll~~Lk~~l~~L~~~---~yGk~Vv~~Lek 721 (727)
+. +++.+-+. .|++.|..+-+.+..-...|... .-|++|.+.+++
T Consensus 315 s~l~~~l~~~~~~~Ge~l~~D~~lr~kln~~~~~aa~~l~e~~~~~it~~I~dTv~~ 371 (415)
T COG2733 315 SMLRKRLARAVQSVGEELIADDALRAKLNEHLVQAAERLAEEKHAEITKHISDTVKR 371 (415)
T ss_pred hHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhh
Confidence 21 12222222 46666766666666555555533 337777766654
No 26
>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=80.72 E-value=1e+02 Score=34.53 Aligned_cols=165 Identities=13% Similarity=0.066 Sum_probs=81.4
Q ss_pred chhhhHhhhcCChhHHHHHHHHhhhhHhhhccCCCCchHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhC-cCccHHHH-
Q 004857 526 NHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFALAQD-QYGNYVTQ- 603 (727)
Q Consensus 526 NhVIQklLe~~~~e~~~~Ii~~L~~~l~~Ls~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~D-q~GNyVVQ- 603 (727)
.+++..++.... +.+..++.....-...+..++.-++.+..+++....+. .+++++.+.+..|+.+ ..+.+|.|
T Consensus 178 ~~l~~~l~~~~k-~ir~~a~~l~~~~~~~l~~~~~~s~~~~~~~~~~~~~~---~~~~~~~~~L~~mi~~~~~~~~a~~i 253 (372)
T PF12231_consen 178 PILFPDLLSSAK-DIRTKAISLLLEAKKCLGPNKELSKSVLEDLQRSLENG---KLIQLYCERLKEMIKSKDEYKLAMQI 253 (372)
T ss_pred HHHHHHHhhcch-HHHHHHHHHHHHHHHHhChhHHHHHHHHHHhccccccc---cHHHHHHHHHHHHHhCcCCcchHHHH
Confidence 355666655432 33333333333333344445556666666666544331 5778888888888877 44444433
Q ss_pred -----HHHHcCCc-hhHHHHHHHHHHHHHHHhcCchHHHHHHHHHHhCCHHHHHH-------HHHHHhcCCCChhHHHhh
Q 004857 604 -----HVLERGKS-YERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAEREL-------LIEEILGQSEENDNLLVM 670 (727)
Q Consensus 604 -----~lLe~~~~-k~r~~II~~L~g~lveLs~~K~GS~VVEk~L~~as~k~Rk~-------IIkeLl~~~~~~e~L~~L 670 (727)
.+| +.+ .+.-..++.. =.|.|+||+..++..|.. ++..+...........+|
T Consensus 254 W~~~i~LL--~~~~~~~w~~~n~w-------------L~v~e~cFn~~d~~~k~~A~~aW~~liy~~~~~~~~~~k~l~l 318 (372)
T PF12231_consen 254 WSVVILLL--GSSRLDSWEHLNEW-------------LKVPEKCFNSSDPQVKIQAFKAWRRLIYASNPNELTSPKRLKL 318 (372)
T ss_pred HHHHHHHh--CCchhhccHhHhHH-------------HHHHHHHhcCCCHHHHHHHHHHHHHHHHHhcCCccccHHHHHH
Confidence 111 111 1111111111 178999999988877653 233221111122344455
Q ss_pred hcCCChHHHHHHHHhcCCHHHHHHHHHHHHHhHHHHhcC
Q 004857 671 MKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKY 709 (727)
Q Consensus 671 a~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~ 709 (727)
...|....+=.+......++.+..++..+...+......
T Consensus 319 L~~Pl~~~l~~~~~~~~~~~~~~~ll~~l~~lly~~f~p 357 (372)
T PF12231_consen 319 LCQPLSSQLRREKSSKTKEEVWWYLLYSLCNLLYYAFRP 357 (372)
T ss_pred HHHHHHHHhCccccccccHHHHHHHHHHHhchHHHHhCC
Confidence 555553332222222233356667777766666554443
No 27
>PF04286 DUF445: Protein of unknown function (DUF445); InterPro: IPR007383 This entry contains proteins of unknown function. They are predicted to be transmembrane proteins with 2 or 3 TM domains.
Probab=78.10 E-value=1.1e+02 Score=33.31 Aligned_cols=21 Identities=19% Similarity=0.176 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHhHHHHhcC
Q 004857 689 EKLRETLISRIRVHCDALKKY 709 (727)
Q Consensus 689 ~~~Rk~Ll~~Lk~~l~~L~~~ 709 (727)
++.++.|-+.+..++..+...
T Consensus 289 ~~l~~~i~~~i~~~l~~~v~~ 309 (367)
T PF04286_consen 289 PELREKINRFIENLLERIVES 309 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 455666666666666555544
No 28
>PF08144 CPL: CPL (NUC119) domain; InterPro: IPR012959 This C-terminal domain is found in Penguin-like proteins (CPL) and is associated with Pumilio like repeats [].; GO: 0003723 RNA binding
Probab=77.16 E-value=15 Score=36.09 Aligned_cols=65 Identities=17% Similarity=0.251 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHhhCcCccHHHHHHHHcCCchhH---HHHHHHHHHH--------HHHHhcCchHHHHHHHHHHhC
Q 004857 581 IVDEILESAFALAQDQYGNYVTQHVLERGKSYER---TQILSKLAGK--------IVQMSQHKYASNVVEKCLEYG 645 (727)
Q Consensus 581 Ll~eI~~~l~~La~Dq~GNyVVQ~lLe~~~~k~r---~~II~~L~g~--------lveLs~~K~GS~VVEk~L~~a 645 (727)
|++.+.++...|+.+.+|+.||..+|..+..+.. +.|++.+.+. =..+..+.+|++++.+++..+
T Consensus 58 Ll~~i~~~~~~ll~~~~g~~~i~eiL~~~~gdk~~a~~Aia~~~~~~~~~~~~~~e~H~i~~p~~~r~lK~Liq~~ 133 (148)
T PF08144_consen 58 LLEAIAENAEELLSSSFGCQFITEILLSATGDKSAALEAIASLAAEPLFPGDIDEEYHLIEHPFGHRMLKKLIQGD 133 (148)
T ss_pred HHHHHHHhHHHHHhcCcccHHHHHHHhccCccHHHHHHHHHHHHhhccCCCCCcCccchhcCchHHHHHHHHHHCC
Confidence 4455555666777777777777777776543321 2233333222 124667888888888888654
No 29
>KOG2213 consensus Apoptosis inhibitor 5/fibroblast growth factor 2-interacting factor 2, and related proteins [Signal transduction mechanisms]
Probab=75.40 E-value=59 Score=36.87 Aligned_cols=112 Identities=13% Similarity=0.170 Sum_probs=72.1
Q ss_pred CCchhHHHHHHHHHHHH----HHHhcCchHHHHHHHH---HHhCCHHHHHHHHHHHhc-----CCCChhHHHhhhcCCCh
Q 004857 609 GKSYERTQILSKLAGKI----VQMSQHKYASNVVEKC---LEYGDTAERELLIEEILG-----QSEENDNLLVMMKDQYA 676 (727)
Q Consensus 609 ~~~k~r~~II~~L~g~l----veLs~~K~GS~VVEk~---L~~as~k~Rk~IIkeLl~-----~~~~~e~L~~La~DqyG 676 (727)
+++..|++.+..|+.++ .++.....-.++++.+ |...+.++...+++-|.. ...+...|.+|+.-+-|
T Consensus 120 ~D~~irek~l~fi~tKl~~l~~e~L~kevE~~iv~eikkal~dVtgeef~lfm~~L~~lk~~~~k~~~a~lqeLa~~~e~ 199 (460)
T KOG2213|consen 120 GDEQIREKVLKFIRTKLITLKGEVLTKEVERHIVDEIKKALEDVTGEEFTLFMDILASLKSLQTKAGEARLQELAEEQEG 199 (460)
T ss_pred hhHHHHHHHHHHHHHHhhcccHHHhhhHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhhhcccCCCCHHHHHHHHHHHhh
Confidence 34555655555554443 3444555555665544 444566666665554433 12345778888877776
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHhHHHHhcCCChHHHHHHHHH
Q 004857 677 NYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGKHIVARFEQ 721 (727)
Q Consensus 677 nyVVQklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~Lek 721 (727)
--=+.. ++.+|++.-.++++.+.-.++-.++.-.+++.+..+-+
T Consensus 200 ~a~lda-f~~sD~d~VdRfisCl~~AvPfFargapSskf~~y~n~ 243 (460)
T KOG2213|consen 200 LADLDA-FNVSDADYVDRFISCLLMAVPFFARGAPSSKFVEYLNK 243 (460)
T ss_pred hhccCc-ccCCChHHHHHHHHHHHHhhhhhhcCCchhHHHHHHHh
Confidence 655555 77788888899999998888888888777777666544
No 30
>PF09770 PAT1: Topoisomerase II-associated protein PAT1; InterPro: IPR019167 Proteins in this entry are necessary for accurate chromosome transmission during cell division []. ; PDB: 2XER_C 2XES_B 2XEQ_D.
Probab=70.40 E-value=6.1 Score=48.71 Aligned_cols=93 Identities=13% Similarity=0.245 Sum_probs=59.6
Q ss_pred HHHHHhcCCCccHHHHHhhhcCCHHHHHHHHHHHhhch-----------------hhhc----cCccccchhhhhhccCC
Q 004857 407 RIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHA-----------------SKLM----TDVFGNYVIQKFFEHGS 465 (727)
Q Consensus 407 kIveLa~dq~gSRvLQ~lLk~~t~Eqr~~If~EI~~~~-----------------~eL~----tD~fGn~VVQKLLe~gs 465 (727)
.++.+.+=.-|=++|-.+|...+.+++..|+.-|.-++ ..+. .|.|-..|+.-|+.+..
T Consensus 576 ~fi~~ls~~KGkkll~R~~~~l~~~q~~~il~~i~~~l~~l~vv~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~l~~~i~ 655 (808)
T PF09770_consen 576 PFISILSVRKGKKLLPRIFPFLSQEQRLTILTMIFRHLDQLDVVRRASYTDGEDQPLLIKRDDIELFLQAVMPPLMNVIN 655 (808)
T ss_dssp HHHHHTTSHHHHHHHHHHGGGS-HHHHHHHHHHHHHTH-----------------HHHHHTTTTT--GGGGHHHS-HHHH
T ss_pred cceEEEeeCChheeHHhhhhhCChhHHHHHHHHHHHHhhhhcccccccccccccCccccchHhHHHHHHHHHHHHHHHHH
Confidence 34455555556778888889999999999988888777 2333 35566667666666655
Q ss_pred HHHHHHHHHHH-----hcChhhhccCcchhHHHHHHHHh
Q 004857 466 PDQRKELAEKL-----VGQVLPLSLQMYGCRVIQKALEV 499 (727)
Q Consensus 466 ~eqr~~Ii~~L-----~G~v~~La~h~yGSrVIQklIe~ 499 (727)
.-....|+..+ ..++..++++++|.-+|-.+|..
T Consensus 656 ~~~~~~i~gll~~~~~~~~~~~i~~tk~Gls~lt~llsR 694 (808)
T PF09770_consen 656 EAPFNEIIGLLGLLINNNNVSFIAQTKFGLSLLTMLLSR 694 (808)
T ss_dssp HHHHHHHTTSTTT-S--HHHHHHHTSHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHHHhCCCceEEEEChHHHHHHHHHHHH
Confidence 54444443322 23566788889999888888743
No 31
>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]
Probab=69.37 E-value=2.4e+02 Score=33.36 Aligned_cols=38 Identities=24% Similarity=0.289 Sum_probs=17.9
Q ss_pred hhhccCcchhHHHHHHHHhhCHHHHHHHHHHHHHHHHH
Q 004857 481 LPLSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMR 518 (727)
Q Consensus 481 ~~La~h~yGSrVIQklIe~as~eqr~~Lv~EL~g~i~~ 518 (727)
..++++.---..+-.++.......+.+|++.|...+..
T Consensus 57 ~~~s~~~l~d~~l~~~~~~f~~n~k~~~veh~c~~~l~ 94 (711)
T COG1747 57 ISLSKQLLDDSCLVTLLTIFGDNHKNQIVEHLCTRVLE 94 (711)
T ss_pred HHhhhccccchHHHHHHHHhccchHHHHHHHHHHHHHH
Confidence 33444443333444555555555555555555444333
No 32
>COG1536 FliG Flagellar motor switch protein [Cell motility and secretion]
Probab=68.11 E-value=2.1e+02 Score=32.06 Aligned_cols=90 Identities=19% Similarity=0.244 Sum_probs=42.0
Q ss_pred ccHHHHHHHHcCCchhHHHHHHHHHHHHHHHhcCchHHHHHHHHHHhCCHHHHHHHHHHHhcCCCChhHHHhhhcCCChH
Q 004857 598 GNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQYAN 677 (727)
Q Consensus 598 GNyVVQ~lLe~~~~k~r~~II~~L~g~lveLs~~K~GS~VVEk~L~~as~k~Rk~IIkeLl~~~~~~e~L~~La~DqyGn 677 (727)
|.-.+-.+|.+.+....+.+++.+.. ....++..|-+++|.+ +.|...+ +.-.........+
T Consensus 203 g~~~~aeIlN~~d~~~e~~il~~l~~-----~~~~la~~I~~kmF~F----------ediv~ld---d~~iq~lL~~v~~ 264 (339)
T COG1536 203 GIKAAAEILNLLDRGTEKTILESLEE-----EDPELAEEIKEKMFVF----------EDIVLLD---DRSIQRLLREVDK 264 (339)
T ss_pred cHhHHHHHHHhcchhHHHHHHHHHhh-----cCHHHHHHHHHHHhhH----------HHHHhcc---HHHHHHHHHHcCH
Confidence 45556666666665555555555543 2233444555555543 1112111 1111111222245
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHHHhHHH
Q 004857 678 YVVQKILEKCNEKLRETLISRIRVHCDA 705 (727)
Q Consensus 678 yVVQklL~~~d~~~Rk~Ll~~Lk~~l~~ 705 (727)
.++..+|.-++++.|++|++-+.+...+
T Consensus 265 ~~La~aLkg~~~~lrekilsnmskR~~e 292 (339)
T COG1536 265 EDLAIALKGASEELREKILSNMSKRAAE 292 (339)
T ss_pred HHHHHHHcCCCHHHHHHHHHhccHHHHH
Confidence 5555666666666666666554444333
No 33
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=67.78 E-value=93 Score=30.19 Aligned_cols=74 Identities=18% Similarity=0.291 Sum_probs=40.2
Q ss_pred HHHHHHHHhCCHHHHHHHH-HHHhcCCCChhHHHhhhcCCC-hHHHHHHHHhcCCHHHHHHHHHHHHHhHHHHhcCCChH
Q 004857 636 NVVEKCLEYGDTAERELLI-EEILGQSEENDNLLVMMKDQY-ANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGK 713 (727)
Q Consensus 636 ~VVEk~L~~as~k~Rk~II-keLl~~~~~~e~L~~La~Dqy-GnyVVQklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk 713 (727)
.+++.|.+.|.......|. ++++. .|.+++...| | ...+..++++|++-|..=-..+...+.
T Consensus 60 ~LLe~~vkNCG~~fh~evas~~Fl~------el~kl~~~k~~~--------~~~~~~Vk~kil~li~~W~~~f~~~p~-- 123 (139)
T cd03567 60 TVLEACMKNCGERFHSEVGKFRFLN------ELIKLVSPKYLG--------SRTSEKVKTKIIELLYSWTLELPHEPK-- 123 (139)
T ss_pred HHHHHHHHHcCHHHHHHHHhHHHHH------HHHHHhccccCC--------CCCCHHHHHHHHHHHHHHHHHhcccch--
Confidence 5778888887776655554 44442 2555554332 1 112455666666666655555554333
Q ss_pred HHHHHHHHHHhcC
Q 004857 714 HIVARFEQLYGEG 726 (727)
Q Consensus 714 ~Vv~~Lekli~~g 726 (727)
+.+.-+.|...|
T Consensus 124 -~~~~Y~~Lk~~G 135 (139)
T cd03567 124 -IKEAYDMLKKQG 135 (139)
T ss_pred -HHHHHHHHHHCC
Confidence 445555555544
No 34
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=62.12 E-value=1.6e+02 Score=28.60 Aligned_cols=74 Identities=23% Similarity=0.348 Sum_probs=46.6
Q ss_pred HHHHHHHHHhCCHHHHHHHH-HHHhcCCCChhHHHhhhcCCChHHHHHHHHhcCCHHHHHHHHHHHHHhHHHHhcCCChH
Q 004857 635 SNVVEKCLEYGDTAERELLI-EEILGQSEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGK 713 (727)
Q Consensus 635 S~VVEk~L~~as~k~Rk~II-keLl~~~~~~e~L~~La~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk 713 (727)
=.+++.|++.|.......+. ++++ +.|..|+.+ ..+..+++++++-|..-...++..+.=.
T Consensus 62 L~LLe~~vkNCG~~fh~evas~~fl------~~l~~l~~~------------~~~~~Vk~kil~li~~W~~~f~~~~~l~ 123 (142)
T cd03569 62 LLLLESCVKNCGTHFHDEVASREFM------DELKDLIKT------------TKNEEVRQKILELIQAWALAFRNKPQLK 123 (142)
T ss_pred HHHHHHHHHHCCHHHHHHHhhHHHH------HHHHHHHcc------------cCCHHHHHHHHHHHHHHHHHhCCCcccH
Confidence 35778888877665544332 2333 335555554 3456677788877777777777665556
Q ss_pred HHHHHHHHHHhcC
Q 004857 714 HIVARFEQLYGEG 726 (727)
Q Consensus 714 ~Vv~~Lekli~~g 726 (727)
.|.+.-+.+...|
T Consensus 124 ~i~~~y~~L~~~G 136 (142)
T cd03569 124 YVVDTYQILKAEG 136 (142)
T ss_pred HHHHHHHHHHHcC
Confidence 6777777776665
No 35
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.02 E-value=2.9e+02 Score=31.90 Aligned_cols=30 Identities=13% Similarity=0.269 Sum_probs=16.9
Q ss_pred CchHHHHHHHHHHhCCHHHH---HHHHHHHhcC
Q 004857 631 HKYASNVVEKCLEYGDTAER---ELLIEEILGQ 660 (727)
Q Consensus 631 ~K~GS~VVEk~L~~as~k~R---k~IIkeLl~~ 660 (727)
+..-|.++.++|+...+++. ..+|++|.+.
T Consensus 171 dEEksklL~rLLkSn~PeDLqaANkLIK~lVke 203 (594)
T KOG1086|consen 171 DEEKSKLLARLLKSNHPEDLQAANKLIKTLVKE 203 (594)
T ss_pred cHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHH
Confidence 33456666667766555543 3456666653
No 36
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=58.15 E-value=1.8e+02 Score=34.68 Aligned_cols=111 Identities=15% Similarity=0.171 Sum_probs=53.5
Q ss_pred cCCchhHHHHHHHHHHHHHHHhcCchH------HH---HHHHHHHhCCHHHHHHHHHHHhcCCC--------ChhHHHhh
Q 004857 608 RGKSYERTQILSKLAGKIVQMSQHKYA------SN---VVEKCLEYGDTAERELLIEEILGQSE--------ENDNLLVM 670 (727)
Q Consensus 608 ~~~~k~r~~II~~L~g~lveLs~~K~G------S~---VVEk~L~~as~k~Rk~IIkeLl~~~~--------~~e~L~~L 670 (727)
.+++..|+++++.|..++..|.....- .. .+.++|.-.+.++.+.++.-|....- +...|+.|
T Consensus 144 ~~de~~Re~~lkFl~~kl~~l~~~~~~p~~E~e~~i~~~ikkvL~DVTaeEF~l~m~lL~~lk~~~~~~t~~g~qeLv~i 223 (556)
T PF05918_consen 144 SGDEQVRERALKFLREKLKPLKPELLTPQKEMEEFIVDEIKKVLQDVTAEEFELFMSLLKSLKIYGGKQTIEGRQELVDI 223 (556)
T ss_dssp HS-HHHHHHHHHHHHHHGGGS-TTTS---HHHHHHHHHHHHHHCTT--HHHHHHHHHHHHTSGG---GSSHHHHHHHHHH
T ss_pred cCchHHHHHHHHHHHHHHhhCcHHHhhchHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHhCccccccCChHHHHHHHHH
Confidence 345556888888888777766544433 22 23334444567777776654433110 00112221
Q ss_pred hcCCChHHHHHHHHhcCCHHHHHHHHHHHHHhHHHHhcCCChHHHHHHHHH
Q 004857 671 MKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGKHIVARFEQ 721 (727)
Q Consensus 671 a~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~Lek 721 (727)
+.++ -.+..-++..|++.-.+++..++-.++-......+..++..+.+
T Consensus 224 i~eQ---a~Ld~~f~~sD~e~Idrli~C~~~Alp~fs~~v~Sskfv~y~~~ 271 (556)
T PF05918_consen 224 IEEQ---ADLDQPFDPSDPESIDRLISCLRQALPFFSRGVSSSKFVNYMCE 271 (556)
T ss_dssp HHHH---HTTTS---SSSHHHHHHHHHHHHHHGGG-BTTB--HHHHHHHHH
T ss_pred HHHH---hccCCCCCCcCHHHHHHHHHHHHHhhHHhcCCCChHHHHHHHHH
Confidence 1110 00111144566677777888888777777777777776665543
No 37
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=57.33 E-value=1.9e+02 Score=28.10 Aligned_cols=74 Identities=15% Similarity=0.271 Sum_probs=47.5
Q ss_pred HHHHHHHHHhCCHHHHHHHHH-HHhcCCCChhHHHhhhcCCChHHHHHHHHhcCCHHHHHHHHHHHHHhHHHHhcCCChH
Q 004857 635 SNVVEKCLEYGDTAERELLIE-EILGQSEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGK 713 (727)
Q Consensus 635 S~VVEk~L~~as~k~Rk~IIk-eLl~~~~~~e~L~~La~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk 713 (727)
=.+++.|.+.|.......|.. +++ +.|..|+.++ .+.+++++|++-|..=...+...+.=+
T Consensus 58 L~LLe~~vkNCG~~fh~evask~Fl------~eL~kl~~~~------------~~~~Vk~kil~li~~W~~~f~~~~~l~ 119 (144)
T cd03568 58 LTLLDACAENCGKRFHQEVASRDFT------QELKKLINDR------------VHPTVKEKLREVVKQWADEFKNDPSLS 119 (144)
T ss_pred HHHHHHHHHHCCHHHHHHHhhHHHH------HHHHHHhccc------------CCHHHHHHHHHHHHHHHHHhCCCcccH
Confidence 357777888777665544432 233 2355555554 456778888887877777777666666
Q ss_pred HHHHHHHHHHhcC
Q 004857 714 HIVARFEQLYGEG 726 (727)
Q Consensus 714 ~Vv~~Lekli~~g 726 (727)
.|.+.-.++...|
T Consensus 120 ~i~~~y~~L~~~G 132 (144)
T cd03568 120 LMSDLYKKLKNEG 132 (144)
T ss_pred HHHHHHHHHHHcC
Confidence 6777777766665
No 38
>PF11573 Med23: Mediator complex subunit 23; InterPro: IPR021629 Med23 is one of the subunits of the Tail portion of the Mediator complex that regulates RNA polymerase II activity. Med23 is required for heat-shock-specific gene expression, and has been shown to mediate transcriptional activation of E1A in mice.
Probab=56.26 E-value=1.4e+02 Score=39.20 Aligned_cols=44 Identities=18% Similarity=0.283 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHhcCchHHHHHHHHHHhCCHHHHHHHHHHHh
Q 004857 615 TQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELLIEEIL 658 (727)
Q Consensus 615 ~~II~~L~g~lveLs~~K~GS~VVEk~L~~as~k~Rk~IIkeLl 658 (727)
.++.+.-..-+..+..+.+|--.|..+|.....+.|....++++
T Consensus 272 ~el~~~q~~lL~~vL~Qp~srd~v~~~l~~~~~k~~~~~~ee~l 315 (1341)
T PF11573_consen 272 PELLEPQTRLLYYVLRQPYSRDMVCSMLGLQQQKQRCPALEELL 315 (1341)
T ss_pred hHHcchHHHHHHHHHcCcchHHHHHHHhcccccCccchHHHHHH
Confidence 33444444556667788899999988887765555544444433
No 39
>COG5593 Nucleic-acid-binding protein possibly involved in ribosomal biogenesis [Translation, ribosomal structure and biogenesis]
Probab=56.03 E-value=3.1e+02 Score=32.48 Aligned_cols=17 Identities=12% Similarity=0.401 Sum_probs=10.0
Q ss_pred cHHHHHhhhcCCHHHHH
Q 004857 418 SRFIQQKLEHCSAEEKV 434 (727)
Q Consensus 418 SRvLQ~lLk~~t~Eqr~ 434 (727)
..-++++|.+|....|+
T Consensus 119 ~k~letLls~C~kksrn 135 (821)
T COG5593 119 AKNLETLLSFCEKKSRN 135 (821)
T ss_pred HHHHHHHHHHHhccccc
Confidence 45666777666554443
No 40
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=53.89 E-value=2.2e+02 Score=27.61 Aligned_cols=78 Identities=18% Similarity=0.305 Sum_probs=46.0
Q ss_pred HHHHHHHHHHhCCHHHHHHHH-HHHhcCCCChhHHHhhhcCCChHHHHHHHHhcCCHHHHHHHHHHHHHhHHHHhcCCCh
Q 004857 634 ASNVVEKCLEYGDTAERELLI-EEILGQSEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYG 712 (727)
Q Consensus 634 GS~VVEk~L~~as~k~Rk~II-keLl~~~~~~e~L~~La~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yG 712 (727)
+=.+++.|++.|.......|. ++++. +.|..++.+++ ....+++++|++-|..=-..++..+.=
T Consensus 59 aL~LLe~~vkNCG~~fh~eiask~Fl~-----e~L~~~i~~~~----------~~~~~Vk~kil~li~~W~~~f~~~~~l 123 (141)
T cd03565 59 TLTVLETCVKNCGHRFHVLVAKKDFIK-----DVLVKLINPKN----------NPPTIVQEKVLALIQAWADAFRGSPDL 123 (141)
T ss_pred HHHHHHHHHHHccHHHHHHHHHHHhhh-----HHHHHHHcccC----------CCcHHHHHHHHHHHHHHHHHhCCCccc
Confidence 345677777777765543332 22221 11333333222 123467888888888777777766655
Q ss_pred HHHHHHHHHHHhcC
Q 004857 713 KHIVARFEQLYGEG 726 (727)
Q Consensus 713 k~Vv~~Lekli~~g 726 (727)
+.|.+..+.+...|
T Consensus 124 ~~i~~~y~~L~~~G 137 (141)
T cd03565 124 TGVVEVYEELKKKG 137 (141)
T ss_pred hHHHHHHHHHHHcC
Confidence 67777777777766
No 41
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=52.92 E-value=3.6e+02 Score=29.94 Aligned_cols=53 Identities=13% Similarity=0.138 Sum_probs=27.2
Q ss_pred hcCCHHHHHHHHHHHhhchhhhccCccc-cchhhhhhccC-CHHHHHHHHHHHhc
Q 004857 426 EHCSAEEKVSVFKEVLPHASKLMTDVFG-NYVIQKFFEHG-SPDQRKELAEKLVG 478 (727)
Q Consensus 426 k~~t~Eqr~~If~EI~~~~~eL~tD~fG-n~VVQKLLe~g-s~eqr~~Ii~~L~G 478 (727)
..-++++.+.|++|+...+..-..-..| .-.++++|+.. .++.-..|++.+.+
T Consensus 50 ~~v~~~~~~~vl~eF~~~~~~~~~~~~g~~~~~~~~L~~alg~~~a~~il~~i~~ 104 (338)
T TIGR00207 50 TQIDNQQKDDVLEEFEQIAEAQAYINIGGLDYAREVLEKALGEEKAASILNDLTS 104 (338)
T ss_pred CCCCHHHHHHHHHHHHHHHHhcCCccCChHHHHHHHHHHhcCHHHHHHHHHHHhc
Confidence 4556777777777766555443322222 33445555443 44455556555543
No 42
>PLN03218 maturation of RBCL 1; Provisional
Probab=52.87 E-value=6.3e+02 Score=32.69 Aligned_cols=57 Identities=14% Similarity=0.099 Sum_probs=24.9
Q ss_pred HHHHhhhcCCHHHHHHHHHHHhhchhhhccCccccchhhhhhccCCHHHHHHHHHHHh
Q 004857 420 FIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLV 477 (727)
Q Consensus 420 vLQ~lLk~~t~Eqr~~If~EI~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~ 477 (727)
+|..+.+.+..++-..+|+++...-+..-. .--+.+|.-+.+.+..+.-..+++.+.
T Consensus 443 LL~a~~k~g~~e~A~~lf~~M~~~Gl~pD~-~tynsLI~~y~k~G~vd~A~~vf~eM~ 499 (1060)
T PLN03218 443 LMSVCASSQDIDGALRVLRLVQEAGLKADC-KLYTTLISTCAKSGKVDAMFEVFHEMV 499 (1060)
T ss_pred HHHHHHhCcCHHHHHHHHHHHHHcCCCCCH-HHHHHHHHHHHhCcCHHHHHHHHHHHH
Confidence 344444455555555555555432111100 111344444445555555555555543
No 43
>KOG1992 consensus Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=50.96 E-value=4.7e+02 Score=32.68 Aligned_cols=53 Identities=25% Similarity=0.248 Sum_probs=35.8
Q ss_pred chHHHHHHhhCCcHHHHHHHHHHHHHHHHHH----hhCcCccHHHHHHHHcCCchhH
Q 004857 562 CRVIQRVLEHCSDEQQGQCIVDEILESAFAL----AQDQYGNYVTQHVLERGKSYER 614 (727)
Q Consensus 562 S~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~L----a~Dq~GNyVVQ~lLe~~~~k~r 614 (727)
-++++.+|+..........-+.-+++.+..| +.|++|-|++++++++-++...
T Consensus 701 vrLl~aflk~g~~~~~~~~~l~~iLGifqkLiaSka~Dh~GF~LLn~i~~~~~~~~~ 757 (960)
T KOG1992|consen 701 VRLLQAFLKTGSQIVEAADKLSGILGIFQKLIASKANDHHGFYLLNTIIESIPPNEL 757 (960)
T ss_pred HHHHHHHHhcCchhhcccccchhHHHHHHHHhcCcccchhHHHHHHHHHhcCCHhhh
Confidence 4778888887664433222344555555554 5689999999999998876643
No 44
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=50.59 E-value=6e+02 Score=31.76 Aligned_cols=46 Identities=24% Similarity=0.379 Sum_probs=23.9
Q ss_pred hhhhhhccCCHHHHHHHHHHHhcChhhhccCcchhHHHHHHHHhhCHHHH
Q 004857 456 VIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIELHQK 505 (727)
Q Consensus 456 VVQKLLe~gs~eqr~~Ii~~L~G~v~~La~h~yGSrVIQklIe~as~eqr 505 (727)
+++.+++ .+.+.|+.....+...+..|..+. +..+|.++.++.+..
T Consensus 532 ~~~~~~~-~~~~~rr~~~~~lq~k~~~l~~n~---~LfeKgl~lF~dd~~ 577 (803)
T PLN03083 532 RRKALFT-ENAERRRRLLDNLQKKIDESFLNM---QLYEKALDLFEDDQS 577 (803)
T ss_pred HHHHHHh-cchHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhhCCcccc
Confidence 4566666 555556666666655555554443 244444544444433
No 45
>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]
Probab=48.88 E-value=3.9e+02 Score=31.73 Aligned_cols=25 Identities=28% Similarity=0.604 Sum_probs=18.1
Q ss_pred HHHHHHHcCC--chhHHHHHHHHHHHH
Q 004857 601 VTQHVLERGK--SYERTQILSKLAGKI 625 (727)
Q Consensus 601 VVQ~lLe~~~--~k~r~~II~~L~g~l 625 (727)
++.++|++.. -..|+.|++.|+..+
T Consensus 227 Ilk~il~~d~k~~~ar~~~i~~lRd~y 253 (711)
T COG1747 227 ILKHILEHDEKDVWARKEIIENLRDKY 253 (711)
T ss_pred HHHHHhhhcchhhhHHHHHHHHHHHHh
Confidence 6777888754 346888998887754
No 46
>KOG2160 consensus Armadillo/beta-catenin-like repeat-containing protein [Posttranslational modification, protein turnover, chaperones]
Probab=45.27 E-value=4.9e+02 Score=29.22 Aligned_cols=122 Identities=16% Similarity=0.192 Sum_probs=60.8
Q ss_pred CCHHHHHHHHHHHhh------chhhhccCccccchhhhhhccCCHHHHHHHHHHHhcChhhhccCcchhHHHHHHHHhhC
Q 004857 428 CSAEEKVSVFKEVLP------HASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRVIQKALEVIE 501 (727)
Q Consensus 428 ~t~Eqr~~If~EI~~------~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G~v~~La~h~yGSrVIQklIe~as 501 (727)
.+.+++..-|++|.. ++..|.+...---|+- .++..+.+.|.. +.+||-++...-.
T Consensus 95 ~~le~ke~ald~Le~lve~iDnAndl~~~ggl~~ll~-~l~~~~~~lR~~-----------------Aa~Vigt~~qNNP 156 (342)
T KOG2160|consen 95 VDLEDKEDALDNLEELVEDIDNANDLISLGGLVPLLG-YLENSDAELREL-----------------AARVIGTAVQNNP 156 (342)
T ss_pred CCHHHHHHHHHHHHHHHHhhhhHHhHhhccCHHHHHH-HhcCCcHHHHHH-----------------HHHHHHHHHhcCH
Confidence 467778777777654 5566666655555554 777777776653 4566666665533
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccCchhhhHhhhcCChhHHHHHHHHhhhhHhhhccCCCCchHHHHHHhhCC
Q 004857 502 LHQKSQLVLELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPYGCRVIQRVLEHCS 573 (727)
Q Consensus 502 ~eqr~~Lv~EL~g~i~~L~~D~~GNhVIQklLe~~~~e~~~~Ii~~L~~~l~~Ls~hk~GS~VLQk~Le~~~ 573 (727)
..|...|=.-...++..++....-+++.-+.|=.... ++..+.. ......--+|-.++..+++...
T Consensus 157 ~~Qe~v~E~~~L~~Ll~~ls~~~~~~~r~kaL~Aiss-----LIRn~~~-g~~~fl~~~G~~~L~~vl~~~~ 222 (342)
T KOG2160|consen 157 KSQEQVIELGALSKLLKILSSDDPNTVRTKALFAISS-----LIRNNKP-GQDEFLKLNGYQVLRDVLQSNN 222 (342)
T ss_pred HHHHHHHHcccHHHHHHHHccCCCchHHHHHHHHHHH-----HHhcCcH-HHHHHHhcCCHHHHHHHHHcCC
Confidence 3332222112334444444444444553332221111 1111000 0111122357778888888743
No 47
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=44.15 E-value=4.4e+02 Score=30.15 Aligned_cols=41 Identities=24% Similarity=0.289 Sum_probs=32.6
Q ss_pred cCCHHHHHHHHHHHHHhHHHHhcCCChHHHHHHHHHHHhcC
Q 004857 686 KCNEKLRETLISRIRVHCDALKKYTYGKHIVARFEQLYGEG 726 (727)
Q Consensus 686 ~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~Lekli~~g 726 (727)
.+-.++++++...++.-..+.++.+.=+.|.+.++|+..+|
T Consensus 100 ~~h~kV~~k~~~lv~eWsee~K~Dp~lsLi~~l~~klk~~g 140 (462)
T KOG2199|consen 100 KAHPKVCEKMRDLVKEWSEEFKKDPSLSLISALYKKLKEEG 140 (462)
T ss_pred cccHHHHHHHHHHHHHHHHHhccCcchhHHHHHHHHHHHcC
Confidence 55666777777777777778888888888888888888876
No 48
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=43.84 E-value=6.7e+02 Score=31.90 Aligned_cols=180 Identities=12% Similarity=0.112 Sum_probs=90.7
Q ss_pred hhccCccccchhhhhhccCCHHHHHHHHHHHhcC--hhhhccCcchh-HHHHHHHHhhCHHHH--HHHHHHHHHHHHHHh
Q 004857 446 KLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQ--VLPLSLQMYGC-RVIQKALEVIELHQK--SQLVLELDGHVMRCV 520 (727)
Q Consensus 446 eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G~--v~~La~h~yGS-rVIQklIe~as~eqr--~~Lv~EL~g~i~~L~ 520 (727)
-.+..+-|..+++|++..+ -.|+....+. -.+-.+.++|+ |+|-.+.+....+.. .++=.-|..|+...+
T Consensus 397 ~~~~~KR~ke~l~k~l~F~-----~~Il~~~~~~~~~~~~~rqkdGAL~~vgsl~~~L~K~s~~~~~mE~flv~hVfP~f 471 (1010)
T KOG1991|consen 397 TTLVSKRGKETLPKILSFI-----VDILTRYKEASPPNKNPRQKDGALRMVGSLASILLKKSPYKSQMEYFLVNHVFPEF 471 (1010)
T ss_pred HHHHHhcchhhhhhHHHHH-----HHHHHhhcccCCCccChhhhhhHHHHHHHHHHHHccCCchHHHHHHHHHHHhhHhh
Confidence 3444555555555555432 1222222222 23445667777 444444444433222 333333567888888
Q ss_pred hcccCchhhhHhhhcC--------ChhHHHHHHHHhhhhHh---hhccCCCCchHHHHHHhhCCcH-HHHHHHHHHHHHH
Q 004857 521 RDQNGNHVIQKCIECV--------PAEKIEFIISAFRGQVA---TLSTHPYGCRVIQRVLEHCSDE-QQGQCIVDEILES 588 (727)
Q Consensus 521 ~D~~GNhVIQklLe~~--------~~e~~~~Ii~~L~~~l~---~Ls~hk~GS~VLQk~Le~~~~~-~~r~~Ll~eI~~~ 588 (727)
++++|--.-+.|--+. .+.....+++.....+. +|.-.--+...+|.++.++... +..+..+..++++
T Consensus 472 ~s~~g~Lrarac~vl~~~~~~df~d~~~l~~ale~t~~~l~~d~~lPV~VeAalALq~fI~~~~~~~e~~~~hvp~~mq~ 551 (1010)
T KOG1991|consen 472 QSPYGYLRARACWVLSQFSSIDFKDPNNLSEALELTHNCLLNDNELPVRVEAALALQSFISNQEQADEKVSAHVPPIMQE 551 (1010)
T ss_pred cCchhHHHHHHHHHHHHHHhccCCChHHHHHHHHHHHHHhccCCcCchhhHHHHHHHHHHhcchhhhhhHhhhhhHHHHH
Confidence 8888865555543321 12222233332222222 1111122566778888887644 3356677788888
Q ss_pred HHHHhhCc---CccHHHHHHHHcCCchh---HHHHHHHHHHHHHHHhc
Q 004857 589 AFALAQDQ---YGNYVTQHVLERGKSYE---RTQILSKLAGKIVQMSQ 630 (727)
Q Consensus 589 l~~La~Dq---~GNyVVQ~lLe~~~~k~---r~~II~~L~g~lveLs~ 630 (727)
+..|++.- --..|+|+++..-.++- -.+++..|...+..+.+
T Consensus 552 lL~L~ne~End~Lt~vme~iV~~fseElsPfA~eL~q~La~~F~k~l~ 599 (1010)
T KOG1991|consen 552 LLKLSNEVENDDLTNVMEKIVCKFSEELSPFAVELCQNLAETFLKVLQ 599 (1010)
T ss_pred HHHHHHhcchhHHHHHHHHHHHHHHHhhchhHHHHHHHHHHHHHHHHh
Confidence 77777543 34557777776543332 23455555555555444
No 49
>COG5240 SEC21 Vesicle coat complex COPI, gamma subunit [Intracellular trafficking and secretion]
Probab=43.33 E-value=4.4e+02 Score=31.74 Aligned_cols=110 Identities=13% Similarity=0.227 Sum_probs=65.9
Q ss_pred HHHHHhhCcC---ccHHHHHHHHcCCchhHHHHHHHHHHHHHHHhcCchHHHHHHH----HHHhCCHHHHHHHHHHHhcC
Q 004857 588 SAFALAQDQY---GNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEK----CLEYGDTAERELLIEEILGQ 660 (727)
Q Consensus 588 ~l~~La~Dq~---GNyVVQ~lLe~~~~k~r~~II~~L~g~lveLs~~K~GS~VVEk----~L~~as~k~Rk~IIkeLl~~ 660 (727)
++..|++|.. ..|.|..+|+.+.++..+.+++.+-..+.+++- -|---+|+. |+.+ +...+.+++-|.
T Consensus 344 evEsLIsd~Nr~IstyAITtLLKTGt~e~idrLv~~I~sfvhD~SD-~FKiI~ida~rsLsl~F--p~k~~s~l~FL~-- 418 (898)
T COG5240 344 EVESLISDENRTISTYAITTLLKTGTEETIDRLVNLIPSFVHDMSD-GFKIIAIDALRSLSLLF--PSKKLSYLDFLG-- 418 (898)
T ss_pred hHHHHhhcccccchHHHHHHHHHcCchhhHHHHHHHHHHHHHhhcc-CceEEeHHHHHHHHhhC--cHHHHHHHHHHH--
Confidence 4566666654 679999999999999988888888776666662 232223332 2222 222333333222
Q ss_pred CCChhHHHhhhcCCChHHHHHHHHhc--CCHHHHHHHHHHHHHhHHHH
Q 004857 661 SEENDNLLVMMKDQYANYVVQKILEK--CNEKLRETLISRIRVHCDAL 706 (727)
Q Consensus 661 ~~~~e~L~~La~DqyGnyVVQklL~~--~d~~~Rk~Ll~~Lk~~l~~L 706 (727)
+.|.+=-.=+|-+|.|..+.+. -+++.|++.++.|+..+++-
T Consensus 419 ----~~L~~eGg~eFK~~~Vdaisd~~~~~p~skEraLe~LC~fIEDc 462 (898)
T COG5240 419 ----SSLLQEGGLEFKKYMVDAISDAMENDPDSKERALEVLCTFIEDC 462 (898)
T ss_pred ----HHHHhcccchHHHHHHHHHHHHHhhCchHHHHHHHHHHHHHhhc
Confidence 1122211223557777777766 35678888888888776654
No 50
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=42.57 E-value=3.1e+02 Score=26.12 Aligned_cols=75 Identities=19% Similarity=0.316 Sum_probs=41.8
Q ss_pred HHHHHHHHHhCCHHHHHHHHH-HHhcCCCChhHHHhhhcCCChHHHHHHHHhcCCHHHHHHHHHHHHHhHHHHhcCCChH
Q 004857 635 SNVVEKCLEYGDTAERELLIE-EILGQSEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGK 713 (727)
Q Consensus 635 S~VVEk~L~~as~k~Rk~IIk-eLl~~~~~~e~L~~La~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk 713 (727)
=.+++.|+..+.......+.. +++ +.|..++.+++..- ..++++++-|..-...++..+.=.
T Consensus 58 L~lLe~~vkNcg~~f~~ev~s~~fl------~~L~~l~~~~~~~~-----------~Vk~kil~li~~W~~~f~~~~~~~ 120 (133)
T smart00288 58 LTLLDACVKNCGSKFHLEVASKEFL------NELVKLIKPKYPLP-----------LVKKRILELIQEWADAFKNDPDLS 120 (133)
T ss_pred HHHHHHHHHHCCHHHHHHHHhHHHH------HHHHHHHcCCCCcH-----------HHHHHHHHHHHHHHHHHcCCCCch
Confidence 367777887777665444433 344 34666777665443 255555555555555565555555
Q ss_pred HHHHHHHHHHhcC
Q 004857 714 HIVARFEQLYGEG 726 (727)
Q Consensus 714 ~Vv~~Lekli~~g 726 (727)
.|.+.-+.+...|
T Consensus 121 ~i~~~y~~L~~~g 133 (133)
T smart00288 121 QIVDVYDLLKKKG 133 (133)
T ss_pred HHHHHHHHHHHCc
Confidence 5555555554433
No 51
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=41.73 E-value=5.7e+02 Score=30.58 Aligned_cols=21 Identities=24% Similarity=0.349 Sum_probs=11.4
Q ss_pred CCHHHHHHHHHHHhcChhhhc
Q 004857 464 GSPDQRKELAEKLVGQVLPLS 484 (727)
Q Consensus 464 gs~eqr~~Ii~~L~G~v~~La 484 (727)
+++..|+.+++.+..++..|.
T Consensus 145 ~de~~Re~~lkFl~~kl~~l~ 165 (556)
T PF05918_consen 145 GDEQVRERALKFLREKLKPLK 165 (556)
T ss_dssp S-HHHHHHHHHHHHHHGGGS-
T ss_pred CchHHHHHHHHHHHHHHhhCc
Confidence 444556666666666655553
No 52
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=38.47 E-value=2.9e+02 Score=26.89 Aligned_cols=32 Identities=13% Similarity=0.082 Sum_probs=18.6
Q ss_pred HHHHHHHHHhHHHHhcC----CChHHHHHHHHHHHh
Q 004857 693 ETLISRIRVHCDALKKY----TYGKHIVARFEQLYG 724 (727)
Q Consensus 693 k~Ll~~Lk~~l~~L~~~----~yGk~Vv~~Lekli~ 724 (727)
...++++...+...... ....++-..++.++.
T Consensus 169 ~~~l~~~~~~~~~~~~~~~~~~~~~r~~~~l~~l~~ 204 (209)
T PF02854_consen 169 PKALDEIFERLQKYANSKKDPNLSSRIRFMLEDLIE 204 (209)
T ss_dssp HHHHHHHHHHHHHHHHHCHSSSSSHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHHH
Confidence 44455555555555443 567777777776654
No 53
>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=37.96 E-value=6.2e+02 Score=28.91 Aligned_cols=9 Identities=44% Similarity=0.685 Sum_probs=3.5
Q ss_pred HHHHHHHHH
Q 004857 691 LRETLISRI 699 (727)
Q Consensus 691 ~Rk~Ll~~L 699 (727)
.++.++..|
T Consensus 356 ~~~~~i~~I 364 (526)
T PF01602_consen 356 FRRELIKAI 364 (526)
T ss_dssp HHHHHHHHH
T ss_pred hhhhHHHHH
Confidence 344443333
No 54
>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=36.19 E-value=7.6e+02 Score=28.86 Aligned_cols=303 Identities=12% Similarity=0.078 Sum_probs=0.0
Q ss_pred ChhhhHHHHHhhccccccchHHhHHHHHHHHh-cCCCccHHHHHhhhcCCHHHHH---HHHHHHhhchhhhccCccccch
Q 004857 381 DSKKHSFLEELKSSNAQKFELSDIAGRIVEFS-VDQHGSRFIQQKLEHCSAEEKV---SVFKEVLPHASKLMTDVFGNYV 456 (727)
Q Consensus 381 d~~r~~LLeeL~~~~~~~~~L~~I~GkIveLa-~dq~gSRvLQ~lLk~~t~Eqr~---~If~EI~~~~~eL~tD~fGn~V 456 (727)
++.+..+|++|.....+.-.|.+++..+.... .+..-.++|=.+|...+.|+.+ .+++.+.....--...+.-.-+
T Consensus 2 ~~~~~~~l~~l~~~~~~~~~L~~l~~~~~~~~~l~~~~~~~lf~~L~~~~~e~v~~~~~iL~~~l~~~~~~~l~~~~~~~ 81 (503)
T PF10508_consen 2 EEWINELLEELSSKAERLEALPELKTELSSSPFLERLPEPVLFDCLNTSNREQVELICDILKRLLSALSPDSLLPQYQPF 81 (503)
T ss_pred chHHHHHHHHHhcccchHHHHHHHHHHHhhhhHHHhchHHHHHHHHhhcChHHHHHHHHHHHHHHhccCHHHHHHHHHHH
Q ss_pred hhhhhccCCHHHHHHHHHHHhcChhhhccCcch-------hHHHHHHHHhhC------HHHHHHHHHHHHHHHHHH--hh
Q 004857 457 IQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYG-------CRVIQKALEVIE------LHQKSQLVLELDGHVMRC--VR 521 (727)
Q Consensus 457 VQKLLe~gs~eqr~~Ii~~L~G~v~~La~h~yG-------SrVIQklIe~as------~eqr~~Lv~EL~g~i~~L--~~ 521 (727)
+++.|.+.++..|...+.. +..++.|..+ ..++..++.+.. .+.-..++..|..+-..+ +.
T Consensus 82 L~~gL~h~~~~Vr~l~l~~----l~~~~~~~~~~~~~~~~~~l~~~i~~~L~~~d~~Va~~A~~~L~~l~~~~~~~~~l~ 157 (503)
T PF10508_consen 82 LQRGLTHPSPKVRRLALKQ----LGRIARHSEGAAQLLVDNELLPLIIQCLRDPDLSVAKAAIKALKKLASHPEGLEQLF 157 (503)
T ss_pred HHHHhcCCCHHHHHHHHHH----HHHHhcCCHHHHHHhcCccHHHHHHHHHcCCcHHHHHHHHHHHHHHhCCchhHHHHh
Q ss_pred cccCchhhhHhhhcCChhHHHHHHHHhhhhH---hhhccCCCCchHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhCcCc
Q 004857 522 DQNGNHVIQKCIECVPAEKIEFIISAFRGQV---ATLSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFALAQDQYG 598 (727)
Q Consensus 522 D~~GNhVIQklLe~~~~e~~~~Ii~~L~~~l---~~Ls~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~G 598 (727)
+.+.-..+..++.......|-.+++.+..-. .+.+.--..+-++..++....+++ -.+--...+-+..|+..+.|
T Consensus 158 ~~~~~~~L~~l~~~~~~~vR~Rv~el~v~i~~~S~~~~~~~~~sgll~~ll~eL~~dD--iLvqlnalell~~La~~~~g 235 (503)
T PF10508_consen 158 DSNLLSKLKSLMSQSSDIVRCRVYELLVEIASHSPEAAEAVVNSGLLDLLLKELDSDD--ILVQLNALELLSELAETPHG 235 (503)
T ss_pred CcchHHHHHHHHhccCHHHHHHHHHHHHHHHhcCHHHHHHHHhccHHHHHHHHhcCcc--HHHHHHHHHHHHHHHcChhH
Q ss_pred cH------HHHHHHHcCCchhHHH-----HHHHHHHHHHHHhc-------CchHHH--HHHHHHHhCCHHHHHHHHHHHh
Q 004857 599 NY------VTQHVLERGKSYERTQ-----ILSKLAGKIVQMSQ-------HKYASN--VVEKCLEYGDTAERELLIEEIL 658 (727)
Q Consensus 599 Ny------VVQ~lLe~~~~k~r~~-----II~~L~g~lveLs~-------~K~GS~--VVEk~L~~as~k~Rk~IIkeLl 658 (727)
.. |++++.+.......+. ++-.+...+..|+. ..|..- .+..+++..+...+...++.+-
T Consensus 236 ~~yL~~~gi~~~L~~~l~~~~~dp~~~~~~l~g~~~f~g~la~~~~~~v~~~~p~~~~~l~~~~~s~d~~~~~~A~dtlg 315 (503)
T PF10508_consen 236 LQYLEQQGIFDKLSNLLQDSEEDPRLSSLLLPGRMKFFGNLARVSPQEVLELYPAFLERLFSMLESQDPTIREVAFDTLG 315 (503)
T ss_pred HHHHHhCCHHHHHHHHHhccccCCcccchhhhhHHHHHHHHHhcChHHHHHHHHHHHHHHHHHhCCCChhHHHHHHHHHH
Q ss_pred cCCCChhHHHhhhcCCChHHHHHHHHhcCCHHHHHHHHHHHHHhH
Q 004857 659 GQSEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVHC 703 (727)
Q Consensus 659 ~~~~~~e~L~~La~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~~l 703 (727)
.++...-|..+| ........+.++..+-...
T Consensus 316 ----------~igst~~G~~~L----~~~~~~~~~~~l~~~~~~~ 346 (503)
T PF10508_consen 316 ----------QIGSTVEGKQLL----LQKQGPAMKHVLKAIGDAI 346 (503)
T ss_pred ----------HHhCCHHHHHHH----HhhcchHHHHHHHHHHHHh
No 55
>PF11510 FA_FANCE: Fanconi Anaemia group E protein FANCE; InterPro: IPR021025 Fanconi Anaemia (FA) is a cancer predisposition disorder characterised by chromosome fragility and hypersensitivity to genotoxic agents that suggest defects in the molecular mechanisms of DNA damage signalling and repair. In response to DNA damage, the FA core complex monoubiquitinates the FANCD2 protein. This ubiquitination targets FANCD2 to nuclear foci where it interacts with a variety of DNA repair proteins. The FA group E protein (FANCE) has an important role in DNA repair, functioning as the FANCD2-binding protein in the FA core complex []. This entry represents the C-terminal domain of FANCE, which consists predominantly of helices and does not contain any beta-strands. This domain folds in a continuous right-handed solenoidal pattern from its N terminus to its C terminus. ; PDB: 2ILR_A.
Probab=36.10 E-value=3e+02 Score=29.69 Aligned_cols=22 Identities=18% Similarity=0.176 Sum_probs=15.0
Q ss_pred HHHHhhhcCCHHHHHHHHHHHh
Q 004857 420 FIQQKLEHCSAEEKVSVFKEVL 441 (727)
Q Consensus 420 vLQ~lLk~~t~Eqr~~If~EI~ 441 (727)
..=+.|-.+++.|.+.+++++.
T Consensus 39 ~~lq~L~~csp~q~e~lc~~L~ 60 (263)
T PF11510_consen 39 SELQFLNECSPSQVEMLCSQLQ 60 (263)
T ss_dssp HHHHGGGG--HHHHHHHHHHHT
T ss_pred HHHHHHHhCCHHHHHHHHHHhC
Confidence 3445567789999999998875
No 56
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=35.90 E-value=6.4e+02 Score=30.26 Aligned_cols=11 Identities=18% Similarity=0.492 Sum_probs=5.6
Q ss_pred hhhcCCChHHH
Q 004857 669 VMMKDQYANYV 679 (727)
Q Consensus 669 ~La~DqyGnyV 679 (727)
++.++.||..|
T Consensus 242 ~~~~~~y~~~~ 252 (757)
T KOG4368|consen 242 ATLINEYSSVV 252 (757)
T ss_pred HHHHhhhhHHH
Confidence 44455666543
No 57
>PF14666 RICTOR_M: Rapamycin-insensitive companion of mTOR, middle domain
Probab=35.78 E-value=1.6e+02 Score=30.93 Aligned_cols=39 Identities=18% Similarity=0.241 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHhcCchHHHHHHHHHHhCCHHHHHHH
Q 004857 614 RTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELL 653 (727)
Q Consensus 614 r~~II~~L~g~lveLs~~K~GS~VVEk~L~~as~k~Rk~I 653 (727)
++.++..+...+ +...+...-.++.++|..++...|...
T Consensus 178 ~~~l~klil~~L-DY~~~~~~R~iLsKaLt~~s~~iRl~a 216 (226)
T PF14666_consen 178 RDDLLKLILSSL-DYSVDGHPRIILSKALTSGSESIRLYA 216 (226)
T ss_pred hHHHHHHHHhhC-CCCCccHHHHHHHHHHhcCCHHHHHHH
Confidence 344444444444 455566666777778877777766543
No 58
>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=35.13 E-value=3.6e+02 Score=30.19 Aligned_cols=48 Identities=19% Similarity=0.027 Sum_probs=27.9
Q ss_pred ccHHHHHHHHcCCchhHHHHHHHHHHHHHHHhcCchHHHHHHHHHHhCC
Q 004857 598 GNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGD 646 (727)
Q Consensus 598 GNyVVQ~lLe~~~~k~r~~II~~L~g~lveLs~~K~GS~VVEk~L~~as 646 (727)
-..++..++.. ....|...+..+.+-...+..++.-++.+..+++...
T Consensus 177 ~~~l~~~l~~~-~k~ir~~a~~l~~~~~~~l~~~~~~s~~~~~~~~~~~ 224 (372)
T PF12231_consen 177 FPILFPDLLSS-AKDIRTKAISLLLEAKKCLGPNKELSKSVLEDLQRSL 224 (372)
T ss_pred HHHHHHHHhhc-chHHHHHHHHHHHHHHHHhChhHHHHHHHHHHhcccc
Confidence 34566666654 3344444555554444555667777777777777543
No 59
>PF08625 Utp13: Utp13 specific WD40 associated domain; InterPro: IPR013934 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp13 is a nucleolar protein and component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA []. Upt13 is also a component of the Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome []. Components of the Pwp2 complex are: Utp1 (Pwp2), Utp6, Utp12 (Dip2), Utp13, Utp18, and Utp21. The relationship between the Pwp2 complex and the t-Utps complex [] that also associates with the 5' end of nascent pre-18S rRNA is unclear. ; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=35.12 E-value=4.3e+02 Score=25.68 Aligned_cols=108 Identities=17% Similarity=0.202 Sum_probs=60.2
Q ss_pred HHHHHHcCCchhHHHHHHHHHHHHHHHhcCchHHHHHHHHHHhCCHHHHHHHHHHHhcCCCChhHHHhhhcCCC----hH
Q 004857 602 TQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQY----AN 677 (727)
Q Consensus 602 VQ~lLe~~~~k~r~~II~~L~g~lveLs~~K~GS~VVEk~L~~as~k~Rk~IIkeLl~~~~~~e~L~~La~Dqy----Gn 677 (727)
+.-.|+...|...-.|++.+.. ..--.+..|+..++.++..-+.++...+++-+. .+-++.- |+
T Consensus 17 l~LAl~L~~P~~ll~i~~~~~~--~~~~~~~~g~~~l~~~i~~L~~~~l~~LL~~ir----------~WNTNsr~~~vAQ 84 (141)
T PF08625_consen 17 LRLALKLDHPFRLLKILKDLLE--TEEDEDSIGSEELDEVIKKLDDEQLEKLLRFIR----------DWNTNSRTSHVAQ 84 (141)
T ss_pred HHHHHhcCCcHHHHHHHHHHHh--cccccccchHHHHHHHHHhcCHHHHHHHHHHHH----------HhhcccccHHHHH
Confidence 4444555556655555555543 111223347788888888877777666555544 3334333 45
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHHHhHHHHhcCCChHHHHHHHHHHHh
Q 004857 678 YVVQKILEKCNEKLRETLISRIRVHCDALKKYTYGKHIVARFEQLYG 724 (727)
Q Consensus 678 yVVQklL~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~Lekli~ 724 (727)
.|+-.+|...+.+....+ ..++..++.|. +|..+=..++++++.
T Consensus 85 ~vL~~il~~~~~~~L~~~-~~~~~~le~li--pYteRH~~Rl~~L~q 128 (141)
T PF08625_consen 85 RVLNAILKSHPPEELLKI-PGLKEILEALI--PYTERHFQRLDRLLQ 128 (141)
T ss_pred HHHHHHHHhCCHHHHHcc-ccHHHHHHHHh--hhHHHHHHHHHHHHH
Confidence 555556655555542222 24666666666 465666666776654
No 60
>PF09770 PAT1: Topoisomerase II-associated protein PAT1; InterPro: IPR019167 Proteins in this entry are necessary for accurate chromosome transmission during cell division []. ; PDB: 2XER_C 2XES_B 2XEQ_D.
Probab=34.75 E-value=30 Score=42.73 Aligned_cols=41 Identities=15% Similarity=0.196 Sum_probs=31.4
Q ss_pred chhhhccCccccchhhhhhccCCHHHHHHHHHHHhcChhhh
Q 004857 443 HASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPL 483 (727)
Q Consensus 443 ~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G~v~~L 483 (727)
.|+.++.-.=|..+|-++|.+.+.+++..|+..|..++..|
T Consensus 576 ~fi~~ls~~KGkkll~R~~~~l~~~q~~~il~~i~~~l~~l 616 (808)
T PF09770_consen 576 PFISILSVRKGKKLLPRIFPFLSQEQRLTILTMIFRHLDQL 616 (808)
T ss_dssp HHHHHTTSHHHHHHHHHHGGGS-HHHHHHHHHHHHHTH---
T ss_pred cceEEEeeCChheeHHhhhhhCChhHHHHHHHHHHHHhhhh
Confidence 46788888888999999999999998888888887777444
No 61
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=34.28 E-value=9e+02 Score=29.11 Aligned_cols=81 Identities=12% Similarity=0.192 Sum_probs=41.2
Q ss_pred HHhhCCcHHHHHHHHHHHHHHHHHHhhCcC----ccHHHHHHHHcCCchhHHHHHHHHHHHHHHHhcCchHHHHHHHHHH
Q 004857 568 VLEHCSDEQQGQCIVDEILESAFALAQDQY----GNYVTQHVLERGKSYERTQILSKLAGKIVQMSQHKYASNVVEKCLE 643 (727)
Q Consensus 568 ~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~----GNyVVQ~lLe~~~~k~r~~II~~L~g~lveLs~~K~GS~VVEk~L~ 643 (727)
+|+.|..+..++.|+..++..+..=+.+-+ --|+|-.++-||..++-+.++..|...++ --.|+.
T Consensus 129 ~f~~~~s~~~~e~~~~~l~n~~~~~~~~~~lrlh~~ylind~~~hcqrk~~~~~~~~l~~~v~-----------~~yc~~ 197 (757)
T KOG4368|consen 129 MFSNAKSPPHCELMAGHLRNRITADGAHFELRLHLIYLINDVLHHCQRKQARELLAALQKVVV-----------PIYCTS 197 (757)
T ss_pred hhhcCCCchHHHHHHHHHHhhhcccccchhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhH-----------HHHHhh
Confidence 456666554444444333332221111111 12556666677877777777777765443 233555
Q ss_pred h-CCHHHHHHHHHHHhc
Q 004857 644 Y-GDTAERELLIEEILG 659 (727)
Q Consensus 644 ~-as~k~Rk~IIkeLl~ 659 (727)
+ +..+++..++..|++
T Consensus 198 ~~~~~e~~~~~~~~ll~ 214 (757)
T KOG4368|consen 198 FLAVEEDKQQKIARLLQ 214 (757)
T ss_pred hhhhHhHHHHHHHHHHH
Confidence 4 334555666666664
No 62
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=34.18 E-value=1.3e+02 Score=34.65 Aligned_cols=39 Identities=21% Similarity=0.124 Sum_probs=17.5
Q ss_pred CCCCCCCCCCCcchhhhhhcc--cccchhHHHHHHHHHhhh
Q 004857 56 RIDDTNSKNAGLEDVASVSAA--SQSDVSRAESRMRKKQEE 94 (727)
Q Consensus 56 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~ 94 (727)
+-.+..+|-.+.-|+-.--+. -.-|+..||.|+.|||..
T Consensus 298 lkq~kGsDASn~~DeE~p~~e~dfSDDEkEaeak~~kKQrk 338 (483)
T KOG2236|consen 298 LKQGKGSDASNRYDEEIPPREQDFSDDEKEAEAKQMKKQRK 338 (483)
T ss_pred hhhcccccccccccccCChhhhccchHHHHHHHHHHHHHhh
Confidence 334445555555554332111 112344556666655443
No 63
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=32.92 E-value=7.2e+02 Score=27.56 Aligned_cols=53 Identities=11% Similarity=0.068 Sum_probs=24.9
Q ss_pred hhcCCHHHHHHHHHHHhhchhhhccCcccc-chhhhhhcc-CCHHHHHHHHHHHh
Q 004857 425 LEHCSAEEKVSVFKEVLPHASKLMTDVFGN-YVIQKFFEH-GSPDQRKELAEKLV 477 (727)
Q Consensus 425 Lk~~t~Eqr~~If~EI~~~~~eL~tD~fGn-~VVQKLLe~-gs~eqr~~Ii~~L~ 477 (727)
|+.-++++.+.|++|+...+..-..-..|. -.++++|+. ..++.-..|++.+.
T Consensus 47 l~~v~~~~~~~vl~eF~~~~~~~~~~~~g~~~~~~~~L~~alg~~~a~~il~~i~ 101 (334)
T PRK07194 47 LSGIKVDQARQVLQRFFDDYREQSGINGASRSYLQRTLNKALGGDIAKSLINSIY 101 (334)
T ss_pred CCCCCHHHHHHHHHHHHHHHHhcCCcccchHHHHHHHHHHHcCHHHHHHHHHHHh
Confidence 344566666666666655543322222121 233444433 24445555555544
No 64
>COG2733 Predicted membrane protein [Function unknown]
Probab=32.52 E-value=8.1e+02 Score=28.08 Aligned_cols=45 Identities=7% Similarity=0.169 Sum_probs=24.4
Q ss_pred HHHHHHHHhcCCCccHHHHHhhhcCCHHHHHHHHHHHhhchhhhccCc
Q 004857 404 IAGRIVEFSVDQHGSRFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDV 451 (727)
Q Consensus 404 I~GkIveLa~dq~gSRvLQ~lLk~~t~Eqr~~If~EI~~~~~eL~tD~ 451 (727)
+..++-++-.++-..++|.+++... -.+.|++++...+.....+.
T Consensus 155 v~~~i~e~~~~~~~~~vL~~l~~d~---r~q~l~D~~~~~L~r~~~~~ 199 (415)
T COG2733 155 VIRAIAEVYLGPTAGRVLESLTADD---RHQALLDKLIDRLIRWLLND 199 (415)
T ss_pred HHHHHhcccccchHHHHHHHHHhcc---cHHHHHHHHHHHHHHHhhhh
Confidence 3344445555666667776666432 22567777666555444443
No 65
>TIGR00400 mgtE Mg2+ transporter (mgtE). This family of prokaryotic proteins models a class of Mg++ transporter first described in Bacillus firmus. May form a homodimer.
Probab=30.55 E-value=2e+02 Score=33.02 Aligned_cols=14 Identities=14% Similarity=0.223 Sum_probs=6.5
Q ss_pred HHHHHHhhCHHHHH
Q 004857 493 IQKALEVIELHQKS 506 (727)
Q Consensus 493 IQklIe~as~eqr~ 506 (727)
.++++...+++++.
T Consensus 107 ~~~lL~~l~~~er~ 120 (449)
T TIGR00400 107 VQQLLASSTEEERK 120 (449)
T ss_pred HHHHHHcCCHHHHH
Confidence 34444445554443
No 66
>PF14666 RICTOR_M: Rapamycin-insensitive companion of mTOR, middle domain
Probab=30.53 E-value=2.3e+02 Score=29.72 Aligned_cols=75 Identities=20% Similarity=0.163 Sum_probs=52.7
Q ss_pred HHHHHHHhcCchHHHHHHH--HHH----hCCHHHHHHHHHHHhcCCCChhHHHhhhcCCChHHHHHHHHhcCCHHHHHHH
Q 004857 622 AGKIVQMSQHKYASNVVEK--CLE----YGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQKILEKCNEKLRETL 695 (727)
Q Consensus 622 ~g~lveLs~~K~GS~VVEk--~L~----~as~k~Rk~IIkeLl~~~~~~e~L~~La~DqyGnyVVQklL~~~d~~~Rk~L 695 (727)
-.-+-.|+.++.|-.++|+ ++. ..+.+.+..+++-++.. .....+....-++.++|...++..|...
T Consensus 144 f~~IG~lS~~~~Gl~lLe~~~if~~l~~i~~~~~~~~l~klil~~-------LDY~~~~~~R~iLsKaLt~~s~~iRl~a 216 (226)
T PF14666_consen 144 FLFIGVLSSTPNGLKLLERWNIFTMLYHIFSLSSRDDLLKLILSS-------LDYSVDGHPRIILSKALTSGSESIRLYA 216 (226)
T ss_pred HHHHHHHhCChhHHHHHHHCCHHHHHHHHHccCchHHHHHHHHhh-------CCCCCccHHHHHHHHHHhcCCHHHHHHH
Confidence 3446678899999888886 222 23344556666666653 2456678889999999999999988877
Q ss_pred HHHHHHhH
Q 004857 696 ISRIRVHC 703 (727)
Q Consensus 696 l~~Lk~~l 703 (727)
.+.|+..+
T Consensus 217 T~~L~~ll 224 (226)
T PF14666_consen 217 TKHLRVLL 224 (226)
T ss_pred HHHHHHHh
Confidence 77666543
No 67
>COG4399 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.07 E-value=8.8e+02 Score=27.40 Aligned_cols=9 Identities=22% Similarity=0.497 Sum_probs=4.2
Q ss_pred HHHHHhhhc
Q 004857 419 RFIQQKLEH 427 (727)
Q Consensus 419 RvLQ~lLk~ 427 (727)
+++|++++.
T Consensus 94 ~~lqk~lk~ 102 (376)
T COG4399 94 QLLQKLLKS 102 (376)
T ss_pred HHHHHHHHh
Confidence 344555543
No 68
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=28.72 E-value=2.6e+02 Score=34.87 Aligned_cols=28 Identities=7% Similarity=-0.151 Sum_probs=14.4
Q ss_pred CCHHHHHHHHHHHHHhHHHHhcCCChHH
Q 004857 687 CNEKLRETLISRIRVHCDALKKYTYGKH 714 (727)
Q Consensus 687 ~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk~ 714 (727)
.+.++...+++.+..-..+|...+.-+.
T Consensus 319 ~s~~~l~~~~qi~l~g~~el~~ap~~~~ 346 (830)
T PRK07003 319 LSPEQVQLFYQIATVGRGELGLAPDEYA 346 (830)
T ss_pred CCHHHHHHHHHHHHhHHHHhhcCCCHHH
Confidence 3444445555555555566655544443
No 69
>KOG1059 consensus Vesicle coat complex AP-3, delta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.99 E-value=1.3e+03 Score=28.82 Aligned_cols=25 Identities=24% Similarity=0.389 Sum_probs=21.6
Q ss_pred HHhhchhhhccCccccchhhhhhcc
Q 004857 439 EVLPHASKLMTDVFGNYVIQKFFEH 463 (727)
Q Consensus 439 EI~~~~~eL~tD~fGn~VVQKLLe~ 463 (727)
.+.|.+.+|+++.--|+++-|+|+.
T Consensus 218 ~LAP~ffkllttSsNNWmLIKiiKL 242 (877)
T KOG1059|consen 218 QLAPLFYKLLVTSSNNWVLIKLLKL 242 (877)
T ss_pred cccHHHHHHHhccCCCeehHHHHHH
Confidence 4567889999999999999998865
No 70
>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=27.83 E-value=8e+02 Score=26.51 Aligned_cols=24 Identities=17% Similarity=0.375 Sum_probs=13.2
Q ss_pred CCccccccCCCcccCChhhhHHHHHhhc
Q 004857 366 GWQGQRTFEGQRTFEDSKKHSFLEELKS 393 (727)
Q Consensus 366 ~W~~~r~~~~~~~~~d~~r~~LLeeL~~ 393 (727)
.|++..+.. +=.++-..++..+.+
T Consensus 16 ~W~~~~ra~----~is~~~~~~ik~~~~ 39 (312)
T PF03224_consen 16 PWDGYVRAG----LISEEDLSLIKKLDK 39 (312)
T ss_dssp -HHHHHHTT----SS-HHHHHHHHHHHH
T ss_pred CHHHHHHhC----CCCHHHHHHHHHHHC
Confidence 588887655 333444556666543
No 71
>PLN03218 maturation of RBCL 1; Provisional
Probab=27.75 E-value=1.4e+03 Score=29.49 Aligned_cols=22 Identities=5% Similarity=0.155 Sum_probs=11.6
Q ss_pred HHHHhhhcCCHHHHHHHHHHHh
Q 004857 420 FIQQKLEHCSAEEKVSVFKEVL 441 (727)
Q Consensus 420 vLQ~lLk~~t~Eqr~~If~EI~ 441 (727)
++..+++.+..++-..+|+++.
T Consensus 376 ~y~~l~r~G~l~eAl~Lfd~M~ 397 (1060)
T PLN03218 376 AYNRLLRDGRIKDCIDLLEDME 397 (1060)
T ss_pred HHHHHHHCcCHHHHHHHHHHHH
Confidence 3344445555555555666554
No 72
>COG1536 FliG Flagellar motor switch protein [Cell motility and secretion]
Probab=26.77 E-value=9.4e+02 Score=26.96 Aligned_cols=61 Identities=11% Similarity=0.113 Sum_probs=34.8
Q ss_pred HHHHHHHHHHhCCHHHHHHHHHHHhcCCCChhHHHhhhcCCChHHHHHHHHhcCCHHHHHHHHHHHHHh
Q 004857 634 ASNVVEKCLEYGDTAERELLIEEILGQSEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRVH 702 (727)
Q Consensus 634 GS~VVEk~L~~as~k~Rk~IIkeLl~~~~~~e~L~~La~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~~ 702 (727)
....+-..|.-++++.|++|++.+. .+..+|.++..+...- +...-.++.++.|+..++..
T Consensus 263 ~~~~La~aLkg~~~~lrekilsnms------kR~~e~i~~el~~~gp--i~~~dve~aq~~il~~~r~l 323 (339)
T COG1536 263 DKEDLAIALKGASEELREKILSNMS------KRAAEMLKEELEFLGP--VRLSDVETAQKAILNIVRRL 323 (339)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHhcc------HHHHHHHHHHhhccCC--ccHHHHHHHHHHHHHHHHHH
Confidence 4455666666777777777777774 3466666665543332 11122334566677666543
No 73
>KOG4347 consensus GTPase-activating protein VRP [General function prediction only]
Probab=26.20 E-value=9.7e+02 Score=29.16 Aligned_cols=166 Identities=13% Similarity=0.131 Sum_probs=74.4
Q ss_pred cchhhhhhccCCHHHHHHHHHHHhcChh--hhccCcchhHHHHHHHHhhCHHHHHHHHHHH--------------HHHHH
Q 004857 454 NYVIQKFFEHGSPDQRKELAEKLVGQVL--PLSLQMYGCRVIQKALEVIELHQKSQLVLEL--------------DGHVM 517 (727)
Q Consensus 454 n~VVQKLLe~gs~eqr~~Ii~~L~G~v~--~La~h~yGSrVIQklIe~as~eqr~~Lv~EL--------------~g~i~ 517 (727)
|-|+-.++-++.+|+--.++..+..... .-+...+|.-|-|..++.+-...--.+.+.+ ..-+.
T Consensus 291 NIV~s~lll~~~EEeafwll~~lce~~ip~yys~~vvGtliDQ~vfe~lve~~lP~l~~~~~~l~~l~~Vsl~WFlslFl 370 (671)
T KOG4347|consen 291 NIVGSELLLFCKEEEAFWLLSKLCEIYIPDYYSKTVVGTLIDQSVFEELVEDTLPVLGEHLAVLGQLSTVSLSWFLSLFL 370 (671)
T ss_pred HHHHHhhhhhhccchHHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHhhhHHHHHhhhhcccceEeeHHHHHHHH
Confidence 4556666666666665555555543322 2355567777777666543222111111111 11122
Q ss_pred HHhhcccCchhhhHhhhcCChhHHHHHHHHhhhhHhhhccCCC---CchHHHHHHhhCCcHHH------HHHHHHHHHHH
Q 004857 518 RCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQVATLSTHPY---GCRVIQRVLEHCSDEQQ------GQCIVDEILES 588 (727)
Q Consensus 518 ~L~~D~~GNhVIQklLe~~~~e~~~~Ii~~L~~~l~~Ls~hk~---GS~VLQk~Le~~~~~~~------r~~Ll~eI~~~ 588 (727)
.++.=.++.+++..++-.++.-..+.=++.++.+...++..+- .--|+.+++++..+... +..-++ .+.
T Consensus 371 s~m~le~a~~ilD~FF~eG~rvlFqiaLail~~N~~~il~~~dDge~~~vl~~y~~~i~~~~~~~~~~~~~~~~~--i~~ 448 (671)
T KOG4347|consen 371 SLMPLEYAVRILDCFFYEGPRVLFQIALAILKQNAERILSATDDGEAMMVLGNYFDSIYNGDYPDESDHASDSIE--IQD 448 (671)
T ss_pred HHcchHHHHHHHhhhhhcccHHHHHHHHHHHHhhHHHhcccCCchHHHHHHHHHHHhccCCCCCccccchhhhhH--HHH
Confidence 3333344444444433344443444434444444444433222 22455566665433221 001111 333
Q ss_pred HHHHhhCcCccHHHHHHHHcCCchhHHHHHHHHH
Q 004857 589 AFALAQDQYGNYVTQHVLERGKSYERTQILSKLA 622 (727)
Q Consensus 589 l~~La~Dq~GNyVVQ~lLe~~~~k~r~~II~~L~ 622 (727)
+..-+-..|| .+-+.++++...+.|..++..|.
T Consensus 449 Ll~~ay~kFg-~it~e~ie~~R~K~r~~v~q~le 481 (671)
T KOG4347|consen 449 LLATAYEKFG-DITDELIEHLRKKHRLGVLQSLE 481 (671)
T ss_pred HHHHHHHHhc-cchHHHHHHHHHHHHHHHHHHHh
Confidence 3344444555 45555666655566665555553
No 74
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=25.92 E-value=3.8e+02 Score=25.60 Aligned_cols=36 Identities=17% Similarity=0.291 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhHHHHhcCCChHHHHHHHHHHHhcC
Q 004857 691 LRETLISRIRVHCDALKKYTYGKHIVARFEQLYGEG 726 (727)
Q Consensus 691 ~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~Lekli~~g 726 (727)
+|+++++.|..=-..+...+.-+.|.+..+.+...|
T Consensus 105 Vk~k~l~ll~~W~~~f~~~~~~~~i~~~y~~Lk~~G 140 (140)
T PF00790_consen 105 VKEKILELLQEWAEAFKSDPELSLIQDTYKRLKRKG 140 (140)
T ss_dssp HHHHHHHHHHHHHHHTTTSTTGHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHCCCCCchHHHHHHHHHHHCc
Confidence 788888888888888888888888888888887776
No 75
>KOG1992 consensus Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=25.86 E-value=1.7e+02 Score=36.20 Aligned_cols=61 Identities=18% Similarity=0.269 Sum_probs=31.9
Q ss_pred cHHHHHhhhcCCHHHH-HHHHHHHhhchh----hhccCccccchhhhhhccCCHHHHHHHHHHHhc
Q 004857 418 SRFIQQKLEHCSAEEK-VSVFKEVLPHAS----KLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVG 478 (727)
Q Consensus 418 SRvLQ~lLk~~t~Eqr-~~If~EI~~~~~----eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G 478 (727)
.|++|..|+.+...-. ..-+.-|.+.+- .=+.|.+|=++++.++++.+......-++.+.+
T Consensus 701 vrLl~aflk~g~~~~~~~~~l~~iLGifqkLiaSka~Dh~GF~LLn~i~~~~~~~~~~py~k~i~~ 766 (960)
T KOG1992|consen 701 VRLLQAFLKTGSQIVEAADKLSGILGIFQKLIASKANDHHGFYLLNTIIESIPPNELAPYMKQIFG 766 (960)
T ss_pred HHHHHHHHhcCchhhcccccchhHHHHHHHHhcCcccchhHHHHHHHHHhcCCHhhhhHHHHHHHH
Confidence 3666666666653322 111222333333 334567777777777777776655444444433
No 76
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=25.57 E-value=1.9e+02 Score=28.07 Aligned_cols=33 Identities=9% Similarity=0.294 Sum_probs=22.0
Q ss_pred hHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhC
Q 004857 563 RVIQRVLEHCSDEQQGQCIVDEILESAFALAQD 595 (727)
Q Consensus 563 ~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~D 595 (727)
.+++.|+++|+........-.++++.+..++.+
T Consensus 63 ~LLe~~vkNCG~~fh~evas~~fl~~l~~l~~~ 95 (142)
T cd03569 63 LLLESCVKNCGTHFHDEVASREFMDELKDLIKT 95 (142)
T ss_pred HHHHHHHHHCCHHHHHHHhhHHHHHHHHHHHcc
Confidence 467888888876655444445666666666665
No 77
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=25.19 E-value=8.6e+02 Score=26.00 Aligned_cols=29 Identities=21% Similarity=0.161 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHhcCchHHHHHHHHHHh
Q 004857 614 RTQILSKLAGKIVQMSQHKYASNVVEKCLEY 644 (727)
Q Consensus 614 r~~II~~L~g~lveLs~~K~GS~VVEk~L~~ 644 (727)
++.+-..|+..+. +...|+..++.-+++.
T Consensus 188 ~edLk~~L~~cl~--s~~~fa~~~~p~LleK 216 (262)
T PF14500_consen 188 REDLKRALRNCLS--STPLFAPFAFPLLLEK 216 (262)
T ss_pred HHHHHHHHHHHhc--CcHhhHHHHHHHHHHH
Confidence 4555555555443 4566666666666655
No 78
>PF11510 FA_FANCE: Fanconi Anaemia group E protein FANCE; InterPro: IPR021025 Fanconi Anaemia (FA) is a cancer predisposition disorder characterised by chromosome fragility and hypersensitivity to genotoxic agents that suggest defects in the molecular mechanisms of DNA damage signalling and repair. In response to DNA damage, the FA core complex monoubiquitinates the FANCD2 protein. This ubiquitination targets FANCD2 to nuclear foci where it interacts with a variety of DNA repair proteins. The FA group E protein (FANCE) has an important role in DNA repair, functioning as the FANCD2-binding protein in the FA core complex []. This entry represents the C-terminal domain of FANCE, which consists predominantly of helices and does not contain any beta-strands. This domain folds in a continuous right-handed solenoidal pattern from its N terminus to its C terminus. ; PDB: 2ILR_A.
Probab=24.62 E-value=9.1e+02 Score=26.10 Aligned_cols=114 Identities=14% Similarity=0.211 Sum_probs=43.7
Q ss_pred HHHHHHHHHhhcccCchhhhHhhhcCChhHHHHHHHHhhhhH-hhhccCCCCchHHHHHH-hhCCcHHHHHHHHHHHHHH
Q 004857 511 ELDGHVMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRGQV-ATLSTHPYGCRVIQRVL-EHCSDEQQGQCIVDEILES 588 (727)
Q Consensus 511 EL~g~i~~L~~D~~GNhVIQklLe~~~~e~~~~Ii~~L~~~l-~~Ls~hk~GS~VLQk~L-e~~~~~~~r~~Ll~eI~~~ 588 (727)
-+.+++..+ +.-+++++...+..+-...-..+++.+..-+ ..-...+.=+-+|-+++ +.|-.++.+..++..+.
T Consensus 95 l~LpkilsL--~~~ASR~L~sal~~f~k~~p~~~~~all~PlL~~~~~g~~Q~eLl~rlvk~~~l~p~~~~l~l~~~L-- 170 (263)
T PF11510_consen 95 LFLPKILSL--EEPASRLLVSALTSFCKKYPRPVCEALLVPLLQAPGLGPPQCELLCRLVKKECLEPDHRLLLLRQIL-- 170 (263)
T ss_dssp HHHHHHHH---SS---HHHHHHHHHHHHHSHHHHHHHHHHHHHHSTT--HHHHHHHHHHHH-TTS-HHHHHHHHHHHH--
T ss_pred HHHHHHHhc--CCCccHHHHHHHHHHHHhCcHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccCCHHHHHHHHHHHH--
Confidence 355666666 3445555555444322233233333322111 11111222345666777 56665655555555444
Q ss_pred HHHHhhCcCccHHHHHHHHcCCch---hHHHHHHHHHHHHHHHhc
Q 004857 589 AFALAQDQYGNYVTQHVLERGKSY---ERTQILSKLAGKIVQMSQ 630 (727)
Q Consensus 589 l~~La~Dq~GNyVVQ~lLe~~~~k---~r~~II~~L~g~lveLs~ 630 (727)
.+.-+..--.|+|.+|+...+- .-..+++.|.+.-..++.
T Consensus 171 --~~~W~E~~~~Vlq~lL~~k~~l~~~~~~~l~~~L~~~a~~~sk 213 (263)
T PF11510_consen 171 --ELVWNEETFLVLQSLLERKVELSQELFSLLVELLCEQAPQFSK 213 (263)
T ss_dssp --HS---HHHHHHHHHHHTT-----HHHHHHHHHHHH--------
T ss_pred --hCcCcHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhhHhhhc
Confidence 2333333445888998876432 223344555444333333
No 79
>PTZ00429 beta-adaptin; Provisional
Probab=23.71 E-value=1.5e+03 Score=28.21 Aligned_cols=259 Identities=9% Similarity=0.172 Sum_probs=0.0
Q ss_pred HHHHhhhcCCHHHHHHHHHHHhhchhhhccCccccchhh------hhhccCCHHHHHHHHHHHhcChhhhcc-CcchhHH
Q 004857 420 FIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQ------KFFEHGSPDQRKELAEKLVGQVLPLSL-QMYGCRV 492 (727)
Q Consensus 420 vLQ~lLk~~t~Eqr~~If~EI~~~~~eL~tD~fGn~VVQ------KLLe~gs~eqr~~Ii~~L~G~v~~La~-h~yGSrV 492 (727)
+|+-+..+...+..+ ...|...+.....+....-|+. .+..++.++....++..+..-++.|.. ...-.+|
T Consensus 239 IL~lL~~y~P~~~~e--~~~il~~l~~~Lq~~N~AVVl~Aik~il~l~~~~~~~~~~~~~~rl~~pLv~L~ss~~eiqyv 316 (746)
T PTZ00429 239 ILELLAAQRPSDKES--AETLLTRVLPRMSHQNPAVVMGAIKVVANLASRCSQELIERCTVRVNTALLTLSRRDAETQYI 316 (746)
T ss_pred HHHHHHhcCCCCcHH--HHHHHHHHHHHhcCCCHHHHHHHHHHHHHhcCcCCHHHHHHHHHHHHHHHHHhhCCCccHHHH
Q ss_pred HHHHHHhhCHHHHHHHHHHHHHH-----------------HHHHhhcccCchhhhHhhhcCChhHHHHHHHHhhh-hHhh
Q 004857 493 IQKALEVIELHQKSQLVLELDGH-----------------VMRCVRDQNGNHVIQKCIECVPAEKIEFIISAFRG-QVAT 554 (727)
Q Consensus 493 IQklIe~as~eqr~~Lv~EL~g~-----------------i~~L~~D~~GNhVIQklLe~~~~e~~~~Ii~~L~~-~l~~ 554 (727)
+-+.|..+-......+..++.-- +..|+.+.|...|+..+.++......++..+.++. ....
T Consensus 317 aLr~I~~i~~~~P~lf~~~~~~Ff~~~~Dp~yIK~~KLeIL~~Lane~Nv~~IL~EL~eYa~d~D~ef~r~aIrAIg~lA 396 (746)
T PTZ00429 317 VCKNIHALLVIFPNLLRTNLDSFYVRYSDPPFVKLEKLRLLLKLVTPSVAPEILKELAEYASGVDMVFVVEVVRAIASLA 396 (746)
T ss_pred HHHHHHHHHHHCHHHHHHHHHhhhcccCCcHHHHHHHHHHHHHHcCcccHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHH
Q ss_pred hccCCCCchHHHHHHhhCCcHHHHHHHHHHHHHHHHHHhhCcCccHHHHHHH-----HcCCchhHHHHHHHHHHHHHHHh
Q 004857 555 LSTHPYGCRVIQRVLEHCSDEQQGQCIVDEILESAFALAQDQYGNYVTQHVL-----ERGKSYERTQILSKLAGKIVQMS 629 (727)
Q Consensus 555 Ls~hk~GS~VLQk~Le~~~~~~~r~~Ll~eI~~~l~~La~Dq~GNyVVQ~lL-----e~~~~k~r~~II~~L~g~lveLs 629 (727)
+........+|..+++..... ..++.+....+..+.+..-..+++..++ +...+.+-+.-+=-+.|.+.+..
T Consensus 397 ~k~~~~a~~cV~~Ll~ll~~~---~~~v~e~i~vik~IlrkyP~~~il~~L~~~~~~~~i~e~~AKaaiiWILGEy~~~I 473 (746)
T PTZ00429 397 IKVDSVAPDCANLLLQIVDRR---PELLPQVVTAAKDIVRKYPELLMLDTLVTDYGADEVVEEEAKVSLLWMLGEYCDFI 473 (746)
T ss_pred HhChHHHHHHHHHHHHHhcCC---chhHHHHHHHHHHHHHHCccHHHHHHHHHhhcccccccHHHHHHHHHHHHhhHhhH
Q ss_pred cCchHHHHHHHHHHh---CCHHHHHHHHHHHhcCCCChhHHHhhhcCCC-----hHHHHHHHHhcCCH-HHHHH
Q 004857 630 QHKYASNVVEKCLEY---GDTAERELLIEEILGQSEENDNLLVMMKDQY-----ANYVVQKILEKCNE-KLRET 694 (727)
Q Consensus 630 ~~K~GS~VVEk~L~~---as~k~Rk~IIkeLl~~~~~~e~L~~La~Dqy-----GnyVVQklL~~~d~-~~Rk~ 694 (727)
.+ +-.+++.+++. -+...|-.++....+ -....+- =.+|++++.+..++ +.|.+
T Consensus 474 ~~--a~~~L~~~i~~f~~E~~~VqlqlLta~vK---------lfl~~p~~~~~~l~~vL~~~t~~~~d~DVRDR 536 (746)
T PTZ00429 474 EN--GKDIIQRFIDTIMEHEQRVQLAILSAAVK---------MFLRDPQGMEPQLNRVLETVTTHSDDPDVRDR 536 (746)
T ss_pred hh--HHHHHHHHHhhhccCCHHHHHHHHHHHHH---------HHhcCcHHHHHHHHHHHHHHHhcCCChhHHHH
No 80
>PF12069 DUF3549: Protein of unknown function (DUF3549); InterPro: IPR021936 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 340 amino acids in length. This protein has a conserved LDE sequence motif.
Probab=23.67 E-value=1.1e+03 Score=26.57 Aligned_cols=29 Identities=10% Similarity=0.121 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHhhchhhhccCccccchhh
Q 004857 430 AEEKVSVFKEVLPHASKLMTDVFGNYVIQ 458 (727)
Q Consensus 430 ~Eqr~~If~EI~~~~~eL~tD~fGn~VVQ 458 (727)
.++|-.+|..+...-+.+-.+.|--++.+
T Consensus 125 ~~~klA~fhA~v~~~L~~p~S~yye~a~~ 153 (340)
T PF12069_consen 125 SQEKLAMFHAQVRAQLGQPASQYYEHAQA 153 (340)
T ss_pred ChHHHHHHHHHHHHHcCCCcchhHHHHHH
Confidence 45566666666666666666665555544
No 81
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=23.45 E-value=1.4e+03 Score=30.53 Aligned_cols=39 Identities=15% Similarity=0.130 Sum_probs=26.7
Q ss_pred HHHHHHhcCCCcc----HHHHHhhhcCCHHHHHHHHHHHhhch
Q 004857 406 GRIVEFSVDQHGS----RFIQQKLEHCSAEEKVSVFKEVLPHA 444 (727)
Q Consensus 406 GkIveLa~dq~gS----RvLQ~lLk~~t~Eqr~~If~EI~~~~ 444 (727)
.....+-.+++.| +.|+..|+.+..|.-.+|+++.++.+
T Consensus 1446 DferlvrssPNSSi~WI~YMaf~LelsEiekAR~iaerAL~tI 1488 (1710)
T KOG1070|consen 1446 DFERLVRSSPNSSILWIRYMAFHLELSEIEKARKIAERALKTI 1488 (1710)
T ss_pred HHHHHHhcCCCcchHHHHHHHHHhhhhhhHHHHHHHHHHhhhC
Confidence 4444556677777 45677777777777788888766543
No 82
>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=23.40 E-value=1.1e+03 Score=26.75 Aligned_cols=37 Identities=5% Similarity=0.049 Sum_probs=19.6
Q ss_pred CHHHHHHHHHHHHHhHHHHhcCCChHHHHHHHHHHHh
Q 004857 688 NEKLRETLISRIRVHCDALKKYTYGKHIVARFEQLYG 724 (727)
Q Consensus 688 d~~~Rk~Ll~~Lk~~l~~L~~~~yGk~Vv~~Lekli~ 724 (727)
++..|..++..+.+-....-.......|+..++++..
T Consensus 467 ~~~vk~~ilt~~~Kl~~~~~~~~~~~~i~~~~~~~~~ 503 (526)
T PF01602_consen 467 SPEVKLQILTALAKLFKRNPENEVQNEILQFLLSLAT 503 (526)
T ss_dssp HHHHHHHHHHHHHHHHHHSCSTTHHHHHHHHHHCHHH
T ss_pred cHHHHHHHHHHHHHHHhhCCchhhHHHHHHHHHHHhc
Confidence 3446666666555544332221234477777776655
No 83
>KOG1820 consensus Microtubule-associated protein [Cytoskeleton]
Probab=23.28 E-value=3.7e+02 Score=33.65 Aligned_cols=113 Identities=13% Similarity=0.150 Sum_probs=68.4
Q ss_pred HHHHHHHHHHHHHHHhhCcCccHHHHHHH---HcCCchhHHHHHHHHHHHHHHHh---cCchHHH-HHHHHHHhC---CH
Q 004857 578 GQCIVDEILESAFALAQDQYGNYVTQHVL---ERGKSYERTQILSKLAGKIVQMS---QHKYASN-VVEKCLEYG---DT 647 (727)
Q Consensus 578 r~~Ll~eI~~~l~~La~Dq~GNyVVQ~lL---e~~~~k~r~~II~~L~g~lveLs---~~K~GS~-VVEk~L~~a---s~ 647 (727)
+..+++.+...+...+....-..+...++ .+.++..+.++...+...+..+- ..++..+ ++..|+.+. +.
T Consensus 349 k~~l~d~l~~~~d~~~ns~~l~~~~~~I~e~lk~knp~~k~~~~~~l~r~~~~~~~~~~~~~t~~~l~p~~~~~~~D~~~ 428 (815)
T KOG1820|consen 349 KSELRDALLKALDAILNSTPLSKMSEAILEALKGKNPQIKGECLLLLDRKLRKLGPKTVEKETVKTLVPHLIKHINDTDK 428 (815)
T ss_pred cHHHHHHHHHHHHHHHhcccHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHhhcCCcCcchhhHHHHhHHHhhhccCCcH
Confidence 45567777776666666444444555554 45567777776655544443332 4444443 556666664 34
Q ss_pred HHHHHHHHHHhcCCCChhHHHhhhcCCChHHHHHHHHhcCCHHHHHHHHHHHHH
Q 004857 648 AERELLIEEILGQSEENDNLLVMMKDQYANYVVQKILEKCNEKLRETLISRIRV 701 (727)
Q Consensus 648 k~Rk~IIkeLl~~~~~~e~L~~La~DqyGnyVVQklL~~~d~~~Rk~Ll~~Lk~ 701 (727)
..|+.-.+.+.+ ...-+|--|+.++|...++..+..+.+.+++
T Consensus 429 ~VR~Aa~e~~~~-----------v~k~~Ge~~~~k~L~~~~~~~~~~~~E~~~p 471 (815)
T KOG1820|consen 429 DVRKAALEAVAA-----------VMKVHGEEVFKKLLKDLDKQDIKPKEEKLKP 471 (815)
T ss_pred HHHHHHHHHHHH-----------HHHHhhHHHHHHHHHhhccchhhhhhhhccc
Confidence 455555444442 3455788899999988877777777777777
No 84
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=23.04 E-value=1.3e+03 Score=29.02 Aligned_cols=29 Identities=3% Similarity=-0.054 Sum_probs=19.1
Q ss_pred hcCCHHHHHHHHHHHHHhHHHHhcCCChH
Q 004857 685 EKCNEKLRETLISRIRVHCDALKKYTYGK 713 (727)
Q Consensus 685 ~~~d~~~Rk~Ll~~Lk~~l~~L~~~~yGk 713 (727)
...+......+++.|..-+..++.+..=+
T Consensus 324 ~~~s~~~L~r~ie~l~ea~~~lrgn~npr 352 (824)
T PRK07764 324 QRLGPAELTRAADVVNDGLTEMRGATSPR 352 (824)
T ss_pred HhCCHHHHHHHHHHHHHHHHHHhhCCCcH
Confidence 33455666777777777777777665544
No 85
>TIGR00400 mgtE Mg2+ transporter (mgtE). This family of prokaryotic proteins models a class of Mg++ transporter first described in Bacillus firmus. May form a homodimer.
Probab=22.53 E-value=2.1e+02 Score=32.91 Aligned_cols=60 Identities=10% Similarity=0.140 Sum_probs=31.3
Q ss_pred HHHHHhhhcCCHHHHHHHHHHHhhchhhhccCccccchhhhhhccCCHHHHHHHHHHHhc
Q 004857 419 RFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVG 478 (727)
Q Consensus 419 RvLQ~lLk~~t~Eqr~~If~EI~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G 478 (727)
..++..|+...+.+...+++++.+.-.............-.+|++.+++.+..+++.+..
T Consensus 21 ~~l~~~l~~~~~~dia~~l~~l~~~~~~~~~~~l~~~~~a~vl~~l~~~~~~~ll~~l~~ 80 (449)
T TIGR00400 21 SKIKEKFLKXQPXDIAEALKRLPGTELILLYRFLPKKIAVDTFSNLDQSTQNKLLNSFTN 80 (449)
T ss_pred HHHHHHHhcCCHHHHHHHHHhCCHHHHHHHHHhCChhhHHHHHHcCCHHHHHHHHHhCCH
Confidence 344555555555555555555544322222222233344556777777777777766643
No 86
>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=22.38 E-value=8.1e+02 Score=26.25 Aligned_cols=84 Identities=14% Similarity=0.137 Sum_probs=46.5
Q ss_pred cCCHHHHHHHHHHHhhchhhhccCc------cccchhhhhhccCCHHHHHHHHHHHhcChhhhccCcch-hHHHHHHHHh
Q 004857 427 HCSAEEKVSVFKEVLPHASKLMTDV------FGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYG-CRVIQKALEV 499 (727)
Q Consensus 427 ~~t~Eqr~~If~EI~~~~~eL~tD~------fGn~VVQKLLe~gs~eqr~~Ii~~L~G~v~~La~h~yG-SrVIQklIe~ 499 (727)
..+.......+.-+.|-++.|+-|. -|-.++..+++.+.... -.....+| ..|++.++..
T Consensus 107 ~~~~~~i~~~~~liiP~iL~llDD~~~~~K~~G~~lL~~ll~~~~~~~-------------~~~L~~tGl~~v~~~al~~ 173 (282)
T PF10521_consen 107 QLDRPWISQHWPLIIPPILNLLDDYSPEIKIQGCQLLHHLLEKVPAAE-------------WDILRRTGLFSVFEDALFP 173 (282)
T ss_pred cCCcchHHHhhhHHHhhHHHHhcCCCHHHHHHHHHHHHHHHHhCChhh-------------hHHHHHcChHHHHHHHHHH
Confidence 5555666677777777777777774 34455555555554433 00112222 3455555532
Q ss_pred h--------CHHHHHHHHHHHHHHHHHHhhcc
Q 004857 500 I--------ELHQKSQLVLELDGHVMRCVRDQ 523 (727)
Q Consensus 500 a--------s~eqr~~Lv~EL~g~i~~L~~D~ 523 (727)
+ +.++...++.+.++.+..|+.-.
T Consensus 174 ~L~~LP~~tp~~~s~~Ll~~ay~~L~~L~~~~ 205 (282)
T PF10521_consen 174 CLYYLPPITPEDESLELLQAAYPALLSLLKTQ 205 (282)
T ss_pred HhhcCCCCCCchhhHHHHHHHHHHHHHHHHhh
Confidence 1 13555667777777777776543
No 87
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=22.12 E-value=1.4e+03 Score=27.44 Aligned_cols=58 Identities=12% Similarity=0.075 Sum_probs=29.2
Q ss_pred HHHHHhhhcCCHHHHHHHHHHHhhchhhhccCccccchhhhhhccCCHHHHHHHHHHHh
Q 004857 419 RFIQQKLEHCSAEEKVSVFKEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLV 477 (727)
Q Consensus 419 RvLQ~lLk~~t~Eqr~~If~EI~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~ 477 (727)
.+|..+.+....+.-..++.++...-+.. ...-.|.++.-+.+.+..+.-..+++.+.
T Consensus 128 ~ll~a~~~~~~~~~a~~l~~~m~~~g~~~-~~~~~n~Li~~y~k~g~~~~A~~lf~~m~ 185 (697)
T PLN03081 128 ALVEACIALKSIRCVKAVYWHVESSGFEP-DQYMMNRVLLMHVKCGMLIDARRLFDEMP 185 (697)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHhCCCc-chHHHHHHHHHHhcCCCHHHHHHHHhcCC
Confidence 34555555555555556665554432221 12223455555555566665566665553
No 88
>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=21.82 E-value=1e+03 Score=25.54 Aligned_cols=53 Identities=17% Similarity=0.183 Sum_probs=32.9
Q ss_pred chhHHHHHHHH-hhCHHHHHHHHHHHHHHHHHHhhcc------cCchhhhHhhhcCChhH
Q 004857 488 YGCRVIQKALE-VIELHQKSQLVLELDGHVMRCVRDQ------NGNHVIQKCIECVPAEK 540 (727)
Q Consensus 488 yGSrVIQklIe-~as~eqr~~Lv~EL~g~i~~L~~D~------~GNhVIQklLe~~~~e~ 540 (727)
+++.++.-++. ..+.....+.+.-+.+-+..++-|. .|..+++++++..+...
T Consensus 95 ~~~~~l~w~v~~~~~~~~i~~~~~liiP~iL~llDD~~~~~K~~G~~lL~~ll~~~~~~~ 154 (282)
T PF10521_consen 95 LASHVLSWIVLSQLDRPWISQHWPLIIPPILNLLDDYSPEIKIQGCQLLHHLLEKVPAAE 154 (282)
T ss_pred ccHHHHHHHHHhcCCcchHHHhhhHHHhhHHHHhcCCCHHHHHHHHHHHHHHHHhCChhh
Confidence 44567777766 5555555555666667777777664 35666677777665544
No 89
>PF05794 Tcp11: T-complex protein 11; InterPro: IPR008862 This family consists of several eukaryotic T-complex protein 11 (Tcp11) related sequences. Tcp11 is only expressed in fertile adult mammalian testes and is thought to be important in sperm function and fertility. The family also contains the Saccharomyces cerevisiae Sok1 protein which is known to suppress cyclic AMP-dependent protein kinase mutants [].
Probab=21.19 E-value=3.5e+02 Score=30.72 Aligned_cols=29 Identities=14% Similarity=0.197 Sum_probs=14.6
Q ss_pred CccHHHHHHHHcCCchhHHHHHHHHHHHHH
Q 004857 597 YGNYVTQHVLERGKSYERTQILSKLAGKIV 626 (727)
Q Consensus 597 ~GNyVVQ~lLe~~~~k~r~~II~~L~g~lv 626 (727)
+..|++..+-++|.|- |++.++.+...+.
T Consensus 100 l~~~i~~~l~~~CAP~-RD~~v~~l~~~~~ 128 (441)
T PF05794_consen 100 LARFIISLLKKLCAPM-RDEEVKALVEKIE 128 (441)
T ss_pred HHHHHHHHHHHhCCCC-CcHHHHHHHHHHH
Confidence 3456666666666543 2334455544443
No 90
>KOG0166 consensus Karyopherin (importin) alpha [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.15 E-value=1.4e+03 Score=27.09 Aligned_cols=82 Identities=16% Similarity=0.169 Sum_probs=43.0
Q ss_pred hccCcchhHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhhcccCchhhhHh-----hhcCChhHHHHHHHH-hhhhHhhhc
Q 004857 483 LSLQMYGCRVIQKALEVIELHQKSQLVLELDGHVMRCVRDQNGNHVIQKC-----IECVPAEKIEFIISA-FRGQVATLS 556 (727)
Q Consensus 483 La~h~yGSrVIQklIe~as~eqr~~Lv~EL~g~i~~L~~D~~GNhVIQkl-----Le~~~~e~~~~Ii~~-L~~~l~~Ls 556 (727)
+++++...++|-.+....++.--..-+.++.+-+..|+.+..-.-+...| |.-++.+.++.+++. +..+++++.
T Consensus 209 ~~~lRn~tW~LsNlcrgk~P~P~~~~v~~iLp~L~~ll~~~D~~Vl~Da~WAlsyLsdg~ne~iq~vi~~gvv~~LV~lL 288 (514)
T KOG0166|consen 209 LSMLRNATWTLSNLCRGKNPSPPFDVVAPILPALLRLLHSTDEEVLTDACWALSYLTDGSNEKIQMVIDAGVVPRLVDLL 288 (514)
T ss_pred hHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCChHHHHHHHHccchHHHHHHH
Confidence 44555566666666654433222333455555666666555444332222 112456666666654 566777777
Q ss_pred cCCCCchH
Q 004857 557 THPYGCRV 564 (727)
Q Consensus 557 ~hk~GS~V 564 (727)
.|.-+.-+
T Consensus 289 ~~~~~~v~ 296 (514)
T KOG0166|consen 289 GHSSPKVV 296 (514)
T ss_pred cCCCcccc
Confidence 77665433
No 91
>KOG1060 consensus Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.01 E-value=1.7e+03 Score=27.99 Aligned_cols=86 Identities=13% Similarity=0.188 Sum_probs=40.1
Q ss_pred CchhHHHHHHHHHHHHHHHhcCchHHHHHHHHHHhCCHH--HHHHHHHHHhcCCCChhHHHhhhcCCCh------HHHHH
Q 004857 610 KSYERTQILSKLAGKIVQMSQHKYASNVVEKCLEYGDTA--ERELLIEEILGQSEENDNLLVMMKDQYA------NYVVQ 681 (727)
Q Consensus 610 ~~k~r~~II~~L~g~lveLs~~K~GS~VVEk~L~~as~k--~Rk~IIkeLl~~~~~~e~L~~La~DqyG------nyVVQ 681 (727)
++.....|++.|.-.+. .....|++-.|+.+=+++... ....-++. |+.|+.+.-. --||+
T Consensus 386 ~esni~~ILrE~q~YI~-s~d~~faa~aV~AiGrCA~~~~sv~~tCL~g----------Lv~Llsshde~Vv~eaV~vIk 454 (968)
T KOG1060|consen 386 NESNISEILRELQTYIK-SSDRSFAAAAVKAIGRCASRIGSVTDTCLNG----------LVQLLSSHDELVVAEAVVVIK 454 (968)
T ss_pred hhccHHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHHhhCchhhHHHHH----------HHHHHhcccchhHHHHHHHHH
Confidence 33444556555554433 233357777777766654321 11222222 3333333332 23344
Q ss_pred HHHhcCCHHHHHHHHHHHHHhHHHHh
Q 004857 682 KILEKCNEKLRETLISRIRVHCDALK 707 (727)
Q Consensus 682 klL~~~d~~~Rk~Ll~~Lk~~l~~L~ 707 (727)
++++ .++.....|+..|-..+..+.
T Consensus 455 ~Llq-~~p~~h~~ii~~La~lldti~ 479 (968)
T KOG1060|consen 455 RLLQ-KDPAEHLEILFQLARLLDTIL 479 (968)
T ss_pred HHHh-hChHHHHHHHHHHHHHhhhhh
Confidence 4443 355555556666655555544
No 92
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=20.36 E-value=3.6e+02 Score=26.18 Aligned_cols=14 Identities=7% Similarity=0.230 Sum_probs=7.0
Q ss_pred cchhHHHHHHHHhh
Q 004857 487 MYGCRVIQKALEVI 500 (727)
Q Consensus 487 ~yGSrVIQklIe~a 500 (727)
.++..+++.+.+..
T Consensus 70 ~f~~~ll~~~~~~f 83 (209)
T PF02854_consen 70 EFRSLLLNRCQEEF 83 (209)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHH
Confidence 44555555555433
No 93
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=20.24 E-value=7.8e+02 Score=30.75 Aligned_cols=47 Identities=17% Similarity=0.217 Sum_probs=22.1
Q ss_pred HHHhhchhhhccCccccchhhhhhccCCHHHHHHHHHHHhcChhhhc
Q 004857 438 KEVLPHASKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLS 484 (727)
Q Consensus 438 ~EI~~~~~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G~v~~La 484 (727)
+||+--++++-.+....-+||.|+.+.++.....-+.+++.....|+
T Consensus 716 eeik~~ILevne~vLse~~iqnLik~lPe~E~l~~L~e~Kaeye~l~ 762 (1102)
T KOG1924|consen 716 EEIKNVILEVNEDVLSESMIQNLIKHLPEQEQLNKLSELKAEYEDLP 762 (1102)
T ss_pred HHHHHHHhhccHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence 34444444444444555556666666554333333344444444443
No 94
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=20.08 E-value=1.1e+03 Score=29.74 Aligned_cols=48 Identities=8% Similarity=-0.022 Sum_probs=39.2
Q ss_pred hhhccCccccchhhhhhccCCHHHHHHHHHHHhcChhhhccCcchhHH
Q 004857 445 SKLMTDVFGNYVIQKFFEHGSPDQRKELAEKLVGQVLPLSLQMYGCRV 492 (727)
Q Consensus 445 ~eL~tD~fGn~VVQKLLe~gs~eqr~~Ii~~L~G~v~~La~h~yGSrV 492 (727)
++.+.+-.+++-.|-||.|--......+.+.|..|+-.+..|.+.++-
T Consensus 172 lE~lY~~ia~~aFqFCLkYqRktEFRrLCe~LR~HL~~i~k~~nq~~~ 219 (988)
T KOG2072|consen 172 LEALYHDIARKAFQFCLKYQRKTEFRRLCELLRMHLDNINKHQNQSTR 219 (988)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhccCcC
Confidence 466666777788888888888888899999999999999988887643
Done!