Query psy17504
Match_columns 196
No_of_seqs 322 out of 1722
Neff 7.5
Searched_HMMs 46136
Date Sat Aug 17 00:15:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17504.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17504hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4577|consensus 99.8 8E-21 1.7E-25 157.3 5.3 112 1-195 100-212 (383)
2 KOG0484|consensus 99.2 5E-12 1.1E-16 90.5 2.2 49 147-195 14-62 (125)
3 TIGR01565 homeo_ZF_HD homeobox 99.1 1.4E-10 3E-15 75.6 3.3 45 151-195 2-50 (58)
4 KOG2251|consensus 99.0 2.1E-10 4.5E-15 92.6 3.1 51 146-196 33-83 (228)
5 KOG0490|consensus 99.0 5E-10 1.1E-14 91.6 4.2 47 149-195 59-105 (235)
6 PF00412 LIM: LIM domain; Int 98.9 1.3E-11 2.9E-16 80.0 -4.8 51 3-54 8-58 (58)
7 KOG0850|consensus 98.9 7E-10 1.5E-14 90.0 2.8 52 144-195 116-167 (245)
8 KOG0488|consensus 98.9 1.9E-09 4.2E-14 92.5 3.9 50 146-195 168-217 (309)
9 KOG0843|consensus 98.8 2.4E-09 5.2E-14 83.9 2.9 48 148-195 100-147 (197)
10 KOG0489|consensus 98.8 3.2E-09 7E-14 89.3 2.8 48 148-195 157-204 (261)
11 KOG0485|consensus 98.8 3.9E-09 8.5E-14 85.0 3.1 48 148-195 102-149 (268)
12 KOG0494|consensus 98.8 4.9E-09 1.1E-13 86.5 3.0 47 149-195 140-186 (332)
13 KOG0842|consensus 98.7 5.1E-09 1.1E-13 89.1 2.9 49 147-195 150-198 (307)
14 KOG1701|consensus 98.7 3E-09 6.5E-14 93.0 1.2 51 2-53 283-333 (468)
15 KOG0486|consensus 98.7 7.6E-09 1.6E-13 87.4 3.5 50 146-195 108-157 (351)
16 PF00046 Homeobox: Homeobox do 98.7 5.8E-09 1.2E-13 67.4 1.9 46 151-196 1-46 (57)
17 KOG1701|consensus 98.6 1.2E-08 2.5E-13 89.4 0.7 50 6-56 345-395 (468)
18 smart00389 HOX Homeodomain. DN 98.6 5E-08 1.1E-12 62.5 3.1 45 152-196 2-46 (56)
19 KOG0493|consensus 98.5 7.2E-08 1.6E-12 79.7 3.4 45 151-195 247-291 (342)
20 cd00086 homeodomain Homeodomai 98.4 1.9E-07 4.2E-12 60.2 3.0 45 152-196 2-46 (59)
21 KOG0492|consensus 98.3 2.1E-07 4.5E-12 74.7 2.2 49 147-195 141-189 (246)
22 KOG0490|consensus 98.3 1E-06 2.2E-11 72.0 5.8 130 2-195 68-198 (235)
23 KOG0487|consensus 98.3 3E-07 6.5E-12 78.4 1.7 50 146-195 231-280 (308)
24 KOG2272|consensus 98.2 4.9E-07 1.1E-11 74.6 1.8 54 2-56 21-74 (332)
25 KOG0848|consensus 98.1 1.1E-06 2.3E-11 73.1 2.0 48 148-195 197-244 (317)
26 KOG0491|consensus 98.1 1.1E-06 2.4E-11 68.1 1.5 47 149-195 99-145 (194)
27 KOG4577|consensus 98.1 1.4E-06 3.1E-11 73.0 1.6 50 6-57 45-94 (383)
28 KOG0849|consensus 98.0 4.7E-06 1E-10 73.1 3.1 50 146-195 172-221 (354)
29 KOG0844|consensus 97.9 8.2E-06 1.8E-10 69.1 3.5 49 147-195 178-226 (408)
30 KOG2272|consensus 97.9 3.3E-06 7.2E-11 69.7 0.3 49 6-55 206-254 (332)
31 COG5576 Homeodomain-containing 97.6 5.1E-05 1.1E-09 59.2 3.6 46 150-195 51-96 (156)
32 KOG1703|consensus 97.6 1.3E-05 2.7E-10 73.0 0.2 49 6-55 374-422 (479)
33 KOG3802|consensus 97.6 3.8E-05 8.2E-10 67.3 3.0 47 149-195 293-339 (398)
34 KOG1044|consensus 97.5 2E-05 4.4E-10 71.7 -1.0 45 9-55 148-192 (670)
35 KOG2252|consensus 97.3 0.00015 3.3E-09 65.8 3.0 49 148-196 418-466 (558)
36 smart00132 LIM Zinc-binding do 97.3 1.1E-05 2.4E-10 47.3 -3.1 29 3-31 9-37 (39)
37 KOG1044|consensus 96.9 0.00016 3.4E-09 66.0 -1.1 46 8-53 29-74 (670)
38 KOG1702|consensus 96.8 0.00046 9.9E-09 55.7 1.0 49 4-54 15-63 (264)
39 KOG1168|consensus 96.3 0.0022 4.7E-08 54.3 2.1 47 149-195 308-354 (385)
40 KOG1700|consensus 96.3 0.0015 3.3E-08 52.9 1.1 45 12-57 126-170 (200)
41 KOG0483|consensus 96.3 0.0036 7.8E-08 50.6 3.1 40 156-195 56-95 (198)
42 KOG0847|consensus 96.1 0.003 6.6E-08 51.5 1.6 48 148-195 165-212 (288)
43 PF05920 Homeobox_KN: Homeobox 95.7 0.0058 1.3E-07 36.7 1.3 26 171-196 7-32 (40)
44 KOG1700|consensus 95.3 0.0098 2.1E-07 48.2 1.8 48 5-54 19-66 (200)
45 KOG0775|consensus 93.7 0.062 1.3E-06 45.3 3.0 38 159-196 185-222 (304)
46 KOG0774|consensus 91.8 0.18 3.8E-06 42.4 3.3 47 150-196 188-237 (334)
47 KOG1146|consensus 89.3 0.36 7.7E-06 48.7 3.4 49 147-195 900-948 (1406)
48 KOG1703|consensus 87.8 0.085 1.8E-06 48.2 -1.8 48 8-56 317-364 (479)
49 PF04967 HTH_10: HTH DNA bindi 84.4 1.2 2.7E-05 28.3 2.8 38 157-194 1-40 (53)
50 PF11569 Homez: Homeodomain le 75.5 2.4 5.1E-05 27.3 1.9 34 162-195 10-43 (56)
51 PF04218 CENP-B_N: CENP-B N-te 73.6 3.5 7.7E-05 25.9 2.4 40 151-195 1-40 (53)
52 COG1645 Uncharacterized Zn-fin 73.0 1.6 3.5E-05 33.0 0.8 23 23-51 30-52 (131)
53 COG3413 Predicted DNA binding 68.5 4.6 0.0001 32.7 2.7 39 156-194 155-195 (215)
54 PF11781 RRN7: RNA polymerase 67.7 2.1 4.6E-05 24.9 0.4 24 22-50 9-32 (36)
55 PRK00420 hypothetical protein; 63.6 2.9 6.4E-05 30.8 0.5 25 22-51 24-48 (112)
56 PF14471 DUF4428: Domain of un 61.5 2.8 6E-05 26.4 0.1 30 23-53 1-30 (51)
57 PF06677 Auto_anti-p27: Sjogre 52.2 6.8 0.00015 23.5 0.7 28 17-49 13-40 (41)
58 PF04570 DUF581: Protein of un 50.1 8.3 0.00018 25.0 0.9 28 23-50 18-46 (58)
59 COG4847 Uncharacterized protei 46.0 5.8 0.00013 28.3 -0.3 30 21-53 6-35 (103)
60 PF08280 HTH_Mga: M protein tr 44.4 13 0.00027 23.7 1.1 32 161-196 7-38 (59)
61 COG4357 Zinc finger domain con 41.3 4.2 9E-05 29.1 -1.6 34 16-50 57-90 (105)
62 COG4367 Uncharacterized protei 41.2 19 0.00041 25.4 1.6 39 157-195 3-41 (97)
63 PF10367 Vps39_2: Vacuolar sor 40.0 14 0.0003 25.9 0.9 26 23-49 80-106 (109)
64 PF04545 Sigma70_r4: Sigma-70, 39.8 34 0.00074 20.6 2.5 34 157-195 5-38 (50)
65 PF13834 DUF4193: Domain of un 39.1 10 0.00023 27.2 0.1 10 40-49 89-98 (99)
66 PRK12495 hypothetical protein; 36.6 29 0.00064 28.6 2.3 32 16-53 37-68 (226)
67 KOG0773|consensus 35.3 20 0.00044 31.0 1.3 46 151-196 240-288 (342)
68 PF12855 Ecl1: Life-span regul 33.5 19 0.0004 21.9 0.5 24 24-52 9-32 (43)
69 smart00504 Ubox Modified RING 31.9 20 0.00043 22.5 0.5 32 22-55 2-33 (63)
70 PF13936 HTH_38: Helix-turn-he 31.2 50 0.0011 19.6 2.2 36 155-195 3-38 (44)
71 PF10764 Gin: Inhibitor of sig 30.7 21 0.00046 21.9 0.5 31 23-56 1-31 (46)
72 PF02069 Metallothio_Pro: Prok 28.0 29 0.00063 21.9 0.8 27 23-50 9-35 (52)
73 PF06971 Put_DNA-bind_N: Putat 27.7 29 0.00063 21.7 0.7 18 179-196 30-47 (50)
74 PF12874 zf-met: Zinc-finger o 26.6 20 0.00042 18.2 -0.2 11 22-32 1-11 (25)
75 PF02796 HTH_7: Helix-turn-hel 25.2 79 0.0017 18.7 2.4 34 157-195 6-39 (45)
76 PF08279 HTH_11: HTH domain; 24.6 46 0.001 20.3 1.3 19 178-196 16-34 (55)
77 PRK00085 recO DNA repair prote 24.4 32 0.0007 28.1 0.7 30 20-50 148-177 (247)
78 PF09943 DUF2175: Uncharacteri 24.1 23 0.00051 25.5 -0.2 22 22-43 3-24 (101)
79 PF13730 HTH_36: Helix-turn-he 23.3 73 0.0016 19.3 2.0 21 176-196 24-44 (55)
80 KOG3623|consensus 23.0 78 0.0017 30.9 2.9 34 162-195 568-601 (1007)
81 PF08880 QLQ: QLQ; InterPro: 22.9 47 0.001 19.3 1.0 14 156-169 2-15 (37)
82 PRK13558 bacterio-opsin activa 22.7 74 0.0016 29.8 2.8 41 154-194 605-647 (665)
83 PF10078 DUF2316: Uncharacteri 22.6 31 0.00068 24.3 0.2 28 164-195 14-41 (89)
84 PF13945 NST1: Salt tolerance 22.3 54 0.0012 26.4 1.5 24 7-31 128-151 (190)
85 PF12824 MRP-L20: Mitochondria 22.3 1E+02 0.0022 24.2 3.0 39 154-194 83-121 (164)
86 TIGR03879 near_KaiC_dom probab 22.0 22 0.00048 24.1 -0.6 29 168-196 23-51 (73)
No 1
>KOG4577|consensus
Probab=99.82 E-value=8e-21 Score=157.29 Aligned_cols=112 Identities=36% Similarity=0.670 Sum_probs=95.8
Q ss_pred CCCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCcccc-ccceeeeccchhhhhhccccCcccccCCCCCCCCCCCCcc
Q psy17504 1 MGISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGM-RDEMIYCRPHYEILRHRDYCGSAEIEQPMSPRPAPWQPTT 79 (196)
Q Consensus 1 ~~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~-~~~~~~C~~~y~~~~~~~~~~~~~~~~~~~p~~~~~~~~~ 79 (196)
+||.|+..|.+|.+.+||+.||.|++|+++|.+|++|++ .++++.|+.||+....-..
T Consensus 100 ~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~--------------------- 158 (383)
T KOG4577|consen 100 EGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC--------------------- 158 (383)
T ss_pred CCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc---------------------
Confidence 589999999999999999999999999999999999965 6789999999986532100
Q ss_pred cccCCcccccccccCCCCCccccccceeeccccchhhhccCCccccccccccccCCCCCCCCCccccccccchhhcccch
Q psy17504 80 VQKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLEMLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKH 159 (196)
Q Consensus 80 ~~~g~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gs~~~~~~k~rR~RT~ft~ 159 (196)
. .+++ + ...||+||++|+
T Consensus 159 --------------------------------~-----------------~l~g--d-----------~~nKRPRTTItA 176 (383)
T KOG4577|consen 159 --------------------------------N-----------------ELEG--D-----------ASNKRPRTTITA 176 (383)
T ss_pred --------------------------------c-----------------cccc--c-----------cccCCCcceeeH
Confidence 0 0111 0 124789999999
Q ss_pred hhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 160 HQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 160 ~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
.||+.|+.+|...+.|.++.||+|+..+||..++||
T Consensus 177 KqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQ 212 (383)
T KOG4577|consen 177 KQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQ 212 (383)
T ss_pred HHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehh
Confidence 999999999999999999999999999999999997
No 2
>KOG0484|consensus
Probab=99.21 E-value=5e-12 Score=90.54 Aligned_cols=49 Identities=27% Similarity=0.483 Sum_probs=47.0
Q ss_pred ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
++|.||.||+||..||.+||+.|...||||+..|++||.++.|++..||
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQ 62 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQ 62 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHH
Confidence 4678999999999999999999999999999999999999999999987
No 3
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.05 E-value=1.4e-10 Score=75.56 Aligned_cols=45 Identities=20% Similarity=0.434 Sum_probs=43.8
Q ss_pred chhhcccchhhHhhhhhhhcccCC----CChHHHHHHHHHhCcchhhhc
Q psy17504 151 KRMRTSFKHHQLRTMKSYFNINQN----PDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 151 rR~RT~ft~~Ql~~L~~~F~~~~~----p~~~~r~~La~~lgL~~~~Vq 195 (196)
||.||.||.+|+..|+..|+.++| |+..++++||..|||++++||
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvK 50 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFK 50 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHee
Confidence 789999999999999999999999 999999999999999999987
No 4
>KOG2251|consensus
Probab=99.00 E-value=2.1e-10 Score=92.56 Aligned_cols=51 Identities=29% Similarity=0.420 Sum_probs=48.3
Q ss_pred cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504 146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~ 196 (196)
..+|.||.||+||..||++||..|.+.+|||..+||+||.+|+|++.+||.
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqV 83 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQV 83 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhh
Confidence 457889999999999999999999999999999999999999999999983
No 5
>KOG0490|consensus
Probab=98.96 E-value=5e-10 Score=91.59 Aligned_cols=47 Identities=19% Similarity=0.076 Sum_probs=45.0
Q ss_pred ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
+.||.||.|+..|+.+|+++|+++|||+...|+.||..+++++..||
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVq 105 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQ 105 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeee
Confidence 56889999999999999999999999999999999999999999987
No 6
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=98.94 E-value=1.3e-11 Score=80.03 Aligned_cols=51 Identities=35% Similarity=0.716 Sum_probs=42.9
Q ss_pred CChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhh
Q psy17504 3 ISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR 54 (196)
Q Consensus 3 i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~ 54 (196)
|.+.+.++++.++.||..||+|..|++.|..+. |.+.++++||+.||..+|
T Consensus 8 I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 8 IYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGD-FYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp ESSSSEEEEETTEEEETTTSBETTTTCBTTTSS-EEEETTEEEEHHHHHHHT
T ss_pred ccCcEEEEEeCCcEEEccccccCCCCCccCCCe-eEeECCEEECHHHHhhhC
Confidence 445556667899999999999999999996555 888899999999998764
No 7
>KOG0850|consensus
Probab=98.90 E-value=7e-10 Score=89.95 Aligned_cols=52 Identities=19% Similarity=0.299 Sum_probs=49.7
Q ss_pred cccccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 144 VHSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 144 ~~~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
+++.||.|+.||+|+..||..|.+.|++.+|+-..+|.+||..|||+..|||
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVK 167 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVK 167 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhh
Confidence 4578899999999999999999999999999999999999999999999997
No 8
>KOG0488|consensus
Probab=98.85 E-value=1.9e-09 Score=92.51 Aligned_cols=50 Identities=24% Similarity=0.410 Sum_probs=47.6
Q ss_pred cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
..||+|+.||+||..||.+||..|+++.|++..+|.+||++|||+..|||
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVK 217 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVK 217 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHH
Confidence 44788889999999999999999999999999999999999999999997
No 9
>KOG0843|consensus
Probab=98.81 E-value=2.4e-09 Score=83.93 Aligned_cols=48 Identities=38% Similarity=0.436 Sum_probs=46.3
Q ss_pred cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
.|.||.||+||.+||..||.+|+.++|....+|++||+.|+|++.|||
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVk 147 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVK 147 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhh
Confidence 378999999999999999999999999999999999999999999997
No 10
>KOG0489|consensus
Probab=98.78 E-value=3.2e-09 Score=89.29 Aligned_cols=48 Identities=25% Similarity=0.388 Sum_probs=46.2
Q ss_pred cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
.+.||.||.||..||.+||..|+.|+|+++..|.+||..|.|+|+|||
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIK 204 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIK 204 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHH
Confidence 467899999999999999999999999999999999999999999997
No 11
>KOG0485|consensus
Probab=98.78 E-value=3.9e-09 Score=84.99 Aligned_cols=48 Identities=23% Similarity=0.360 Sum_probs=45.2
Q ss_pred cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
.++||.||+|+..|+..||..|+..+|++..+|..||++|.|+|.|||
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVK 149 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVK 149 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhh
Confidence 355679999999999999999999999999999999999999999997
No 12
>KOG0494|consensus
Probab=98.75 E-value=4.9e-09 Score=86.46 Aligned_cols=47 Identities=30% Similarity=0.427 Sum_probs=43.4
Q ss_pred ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
|+|+-||+||..||.+||..|...+|||...|+-||.+|.|++.+||
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIq 186 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQ 186 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhh
Confidence 34444999999999999999999999999999999999999999986
No 13
>KOG0842|consensus
Probab=98.74 E-value=5.1e-09 Score=89.11 Aligned_cols=49 Identities=16% Similarity=0.296 Sum_probs=46.2
Q ss_pred ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
.+++||.|..|+..|..+||+.|..++|+++.+||+||..|.||++|||
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVK 198 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVK 198 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchhee
Confidence 4566778999999999999999999999999999999999999999997
No 14
>KOG1701|consensus
Probab=98.73 E-value=3e-09 Score=93.02 Aligned_cols=51 Identities=35% Similarity=0.653 Sum_probs=46.9
Q ss_pred CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhh
Q psy17504 2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53 (196)
Q Consensus 2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~ 53 (196)
+|...+...+|++.+||+.||+|.+|+++| .|..|+..++++||+.+|+..
T Consensus 283 ~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L-~Gq~FY~v~~k~~CE~cyq~t 333 (468)
T KOG1701|consen 283 TVSGQGLAVEAMDQLFHVQCFTCRTCRRQL-AGQSFYQVDGKPYCEGCYQDT 333 (468)
T ss_pred cccCcchHHHHhhhhhcccceehHhhhhhh-ccccccccCCcccchHHHHHH
Confidence 567778889999999999999999999999 799999999999999999754
No 15
>KOG0486|consensus
Probab=98.73 E-value=7.6e-09 Score=87.38 Aligned_cols=50 Identities=26% Similarity=0.439 Sum_probs=47.0
Q ss_pred cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
+.+|+||.||.||.+||++||..|++|.||+...||+||..++|++..|+
T Consensus 108 ki~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvr 157 (351)
T KOG0486|consen 108 KISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVR 157 (351)
T ss_pred hhhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhh
Confidence 34588999999999999999999999999999999999999999999886
No 16
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=98.72 E-value=5.8e-09 Score=67.42 Aligned_cols=46 Identities=37% Similarity=0.681 Sum_probs=43.6
Q ss_pred chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~ 196 (196)
||.|+.||.+|+..|+..|..++||+...++.||..+||+..+|++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~ 46 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKN 46 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhcccccccccccccccccccccccc
Confidence 5689999999999999999999999999999999999999999973
No 17
>KOG1701|consensus
Probab=98.59 E-value=1.2e-08 Score=89.42 Aligned_cols=50 Identities=28% Similarity=0.632 Sum_probs=46.0
Q ss_pred HHHHHHHHhHHHhhhhhhhhhhcceeccCCccccc-cceeeeccchhhhhhc
Q psy17504 6 SELVMRARDLVFHLHCFTCISCGILLTKGDLFGMR-DEMIYCRPHYEILRHR 56 (196)
Q Consensus 6 ~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~-~~~~~C~~~y~~~~~~ 56 (196)
.|+++||.++.||..||+|++|++-| .|..|.+. ++++||-.||+..|+.
T Consensus 345 ~d~iLrA~GkayHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~kfAP 395 (468)
T KOG1701|consen 345 MDRILRALGKAYHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKKFAP 395 (468)
T ss_pred HHHHHHhcccccCCCceEEEEecccc-CCccccccCCCceeeehhhhhhcCc
Confidence 58999999999999999999999999 78999886 6799999999999864
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.57 E-value=5e-08 Score=62.52 Aligned_cols=45 Identities=38% Similarity=0.547 Sum_probs=42.5
Q ss_pred hhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504 152 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 152 R~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~ 196 (196)
+.|+.|+..|+..|+..|..++||+...+..||..+||+..+|++
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~ 46 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKV 46 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 567889999999999999999999999999999999999999974
No 19
>KOG0493|consensus
Probab=98.51 E-value=7.2e-08 Score=79.71 Aligned_cols=45 Identities=33% Similarity=0.490 Sum_probs=43.6
Q ss_pred chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
||+||.||.+||..|++.|+.|+|+....|.+||+.|+|.+.|||
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIK 291 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIK 291 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhh
Confidence 588999999999999999999999999999999999999999986
No 20
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=98.42 E-value=1.9e-07 Score=60.19 Aligned_cols=45 Identities=31% Similarity=0.519 Sum_probs=42.4
Q ss_pred hhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504 152 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 152 R~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~ 196 (196)
+.|+.|+..|+..|+..|..++||+..+++.||..+||++.+|++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~ 46 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKI 46 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 467899999999999999999999999999999999999999974
No 21
>KOG0492|consensus
Probab=98.35 E-value=2.1e-07 Score=74.66 Aligned_cols=49 Identities=18% Similarity=0.325 Sum_probs=45.8
Q ss_pred ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
.+..|++||.||..||..||+.|...+|+++.+|.+++..|.|++.|||
T Consensus 141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVK 189 (246)
T KOG0492|consen 141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVK 189 (246)
T ss_pred cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhhee
Confidence 3455778999999999999999999999999999999999999999997
No 22
>KOG0490|consensus
Probab=98.32 E-value=1e-06 Score=72.01 Aligned_cols=130 Identities=34% Similarity=0.440 Sum_probs=92.3
Q ss_pred CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccc-eeeeccchhhhhhccccCcccccCCCCCCCCCCCCccc
Q psy17504 2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDE-MIYCRPHYEILRHRDYCGSAEIEQPMSPRPAPWQPTTV 80 (196)
Q Consensus 2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~-~~~C~~~y~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~ 80 (196)
.|...|+|+++...+ |.-||.|..|...+..++++.+... +.+|..++...... ... .+.+ ..
T Consensus 68 ~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~--~~~-----~~~~--~~------ 131 (235)
T KOG0490|consen 68 TISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPL--PEG-----ENLP--DL------ 131 (235)
T ss_pred CcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccc--ccc-----ccCC--CC------
Confidence 467889999999999 9999999999999989999988765 88888887654200 000 0000 00
Q ss_pred ccCCcccccccccCCCCCccccccceeeccccchhhhccCCccccccccccccCCCCCCCCCccccccccchhhcccchh
Q psy17504 81 QKGRPRKRKLSVDSPTPPSEDINANVMRIPSTTLEMLHSGDLSSSMESLSYESGAGNSSPGSGVHSHQRTKRMRTSFKHH 160 (196)
Q Consensus 81 ~~g~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gs~~~~~~k~rR~RT~ft~~ 160 (196)
..+.. . . . ..+. ... .....+.++.||.++..
T Consensus 132 -------------~~~~~-----~-~--~--------------------~~~~----~~~---~~~~~~~~~~~~~~~~~ 163 (235)
T KOG0490|consen 132 -------------SGTAP-----P-S--A--------------------SRDK----LDK---GPSNKKPRRPRTTFTEN 163 (235)
T ss_pred -------------CCCCC-----c-c--c--------------------cccc----ccc---CCCccccCCCccccccc
Confidence 00000 0 0 0 0000 000 01234678899999999
Q ss_pred hHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 161 QLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 161 Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
|+..+...|...++|+...+++|+..+++++.+||
T Consensus 164 ~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q 198 (235)
T KOG0490|consen 164 QLEVLETVFRATPKPDADDREQLAEETGLSERVIQ 198 (235)
T ss_pred hhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhh
Confidence 99999999999999999999999999999999886
No 23
>KOG0487|consensus
Probab=98.27 E-value=3e-07 Score=78.42 Aligned_cols=50 Identities=20% Similarity=0.327 Sum_probs=46.7
Q ss_pred cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
..++.|++|-.||..|+.+||+.|..|.|+....|.+|++.|+|+++|||
T Consensus 231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVK 280 (308)
T KOG0487|consen 231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVK 280 (308)
T ss_pred cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhhee
Confidence 34677788999999999999999999999999999999999999999997
No 24
>KOG2272|consensus
Probab=98.22 E-value=4.9e-07 Score=74.58 Aligned_cols=54 Identities=20% Similarity=0.509 Sum_probs=48.6
Q ss_pred CCChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504 2 GISSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR 56 (196)
Q Consensus 2 ~i~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~ 56 (196)
|+.++|.++...+.+||..||.|+.|-.++ ++..|+--+|+.||+.||+.|+++
T Consensus 21 gF~~~e~~vns~ge~wH~~CFvCAQCf~pf-~~g~~~efEgRkYCEhDF~~LfaP 74 (332)
T KOG2272|consen 21 GFEPAEKIVNSNGELWHEQCFVCAQCFRPF-PDGIFYEFEGRKYCEHDFHVLFAP 74 (332)
T ss_pred cCCchhhhhccCchhhHHHHHHHHHhcCcC-CCceeEEecCcccccccchhhhch
Confidence 678999999999999999999999999999 566666679999999999999874
No 25
>KOG0848|consensus
Probab=98.13 E-value=1.1e-06 Score=73.11 Aligned_cols=48 Identities=21% Similarity=0.363 Sum_probs=44.1
Q ss_pred cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
+.+-+.|.+||..|+.+||..|..++|+.+..+.+||..|+|+|||||
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVK 244 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVK 244 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhh
Confidence 333457999999999999999999999999999999999999999997
No 26
>KOG0491|consensus
Probab=98.10 E-value=1.1e-06 Score=68.12 Aligned_cols=47 Identities=23% Similarity=0.374 Sum_probs=44.5
Q ss_pred ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
++++.||+|+..||..|+..|+.+.|++..+|.+||..|+|++.|||
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVK 145 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVK 145 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHH
Confidence 45668999999999999999999999999999999999999999997
No 27
>KOG4577|consensus
Probab=98.07 E-value=1.4e-06 Score=73.04 Aligned_cols=50 Identities=20% Similarity=0.455 Sum_probs=45.9
Q ss_pred HHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhcc
Q psy17504 6 SELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRD 57 (196)
Q Consensus 6 ~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~~ 57 (196)
..+|+++.++.||-.|..|..|..+| ++.+..+++.+||++||-+.|++.
T Consensus 45 DrFilKvl~R~wHs~CLkCs~C~~qL--~drCFsR~~s~yCkedFfKrfGTK 94 (383)
T KOG4577|consen 45 DRFILKVLDRHWHSSCLKCSDCHDQL--ADRCFSREGSVYCKEDFFKRFGTK 94 (383)
T ss_pred HHHHHHHHhhhhhhhhcchhhhhhHH--HHHHhhcCCceeehHHHHHHhCCc
Confidence 45899999999999999999999999 788888999999999999998754
No 28
>KOG0849|consensus
Probab=97.97 E-value=4.7e-06 Score=73.06 Aligned_cols=50 Identities=32% Similarity=0.460 Sum_probs=46.6
Q ss_pred cccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 146 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 146 ~~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
..++.+|.||+|+..|+..|+..|++++||+...|++||.+++|++..|+
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riq 221 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQ 221 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHH
Confidence 45677888999999999999999999999999999999999999998876
No 29
>KOG0844|consensus
Probab=97.92 E-value=8.2e-06 Score=69.05 Aligned_cols=49 Identities=18% Similarity=0.299 Sum_probs=46.2
Q ss_pred ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
.-+-||.||.||.+|+-.||+.|-+..|.++..|-+||..|+|+|..||
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIK 226 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIK 226 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceee
Confidence 3567899999999999999999999999999999999999999999886
No 30
>KOG2272|consensus
Probab=97.87 E-value=3.3e-06 Score=69.74 Aligned_cols=49 Identities=27% Similarity=0.478 Sum_probs=45.8
Q ss_pred HHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504 6 SELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH 55 (196)
Q Consensus 6 ~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~ 55 (196)
.+.|+.|+++.||+.-|.|++|.+++ -|...+.+.|..||+.||.+|++
T Consensus 206 eervi~amgKhWHveHFvCa~CekPF-lGHrHYEkkGlaYCe~h~~qLfG 254 (332)
T KOG2272|consen 206 EERVIFAMGKHWHVEHFVCAKCEKPF-LGHRHYEKKGLAYCETHYHQLFG 254 (332)
T ss_pred HHHHHHHhccccchhheeehhcCCcc-cchhhhhhcCchhHHHHHHHHhh
Confidence 57899999999999999999999998 68888889999999999999985
No 31
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=97.64 E-value=5.1e-05 Score=59.16 Aligned_cols=46 Identities=22% Similarity=0.281 Sum_probs=41.7
Q ss_pred cchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 150 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 150 ~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
.++.|+..|..|+..|++.|++++||+...|..|+..++|+++-||
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVq 96 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQ 96 (156)
T ss_pred CcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhh
Confidence 4455666689999999999999999999999999999999999887
No 32
>KOG1703|consensus
Probab=97.63 E-value=1.3e-05 Score=73.05 Aligned_cols=49 Identities=35% Similarity=0.566 Sum_probs=43.0
Q ss_pred HHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504 6 SELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH 55 (196)
Q Consensus 6 ~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~ 55 (196)
.+-+|.|.+..||..||.|..|.+.| .+..|++.++.+||..||..++.
T Consensus 374 ~~~~v~a~~~~wH~~cf~C~~C~~~~-~~~~~~~~~~~pyce~~~~~~~~ 422 (479)
T KOG1703|consen 374 LEEGVCALGRLWHPECFVCADCGKPL-KNSSFFESDGEPYCEDHYKKLFT 422 (479)
T ss_pred HHhHhhhccCeechhceeeecccCCC-CCCcccccCCccchhhhHhhhcc
Confidence 35577888999999999999998888 67788889999999999999885
No 33
>KOG3802|consensus
Probab=97.62 E-value=3.8e-05 Score=67.28 Aligned_cols=47 Identities=23% Similarity=0.426 Sum_probs=44.9
Q ss_pred ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
|+||+||.|....+..||..|.+|+.|+..+...||.+|+|.+.||+
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVR 339 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVR 339 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEE
Confidence 66779999999999999999999999999999999999999999986
No 34
>KOG1044|consensus
Probab=97.45 E-value=2e-05 Score=71.71 Aligned_cols=45 Identities=29% Similarity=0.635 Sum_probs=38.7
Q ss_pred HHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504 9 VMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH 55 (196)
Q Consensus 9 v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~ 55 (196)
++-|.++.||+.||.|..|...| . .+|...++.+||..||+..|.
T Consensus 148 ~llald~qwhv~cfkc~~c~~vL-~-gey~skdg~pyce~dy~~~fg 192 (670)
T KOG1044|consen 148 ALLALDKQWHVSCFKCKSCSAVL-N-GEYMSKDGVPYCEKDYQAKFG 192 (670)
T ss_pred eeeeeccceeeeeeehhhhcccc-c-ceeeccCCCcchhhhhhhhcC
Confidence 44578999999999999999999 3 467778999999999988764
No 35
>KOG2252|consensus
Probab=97.32 E-value=0.00015 Score=65.82 Aligned_cols=49 Identities=27% Similarity=0.375 Sum_probs=45.7
Q ss_pred cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504 148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~ 196 (196)
-+.||+|.+||..|...|...|..+++|+..+.+.|+++|+|....|.|
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~N 466 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVIN 466 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHH
Confidence 4567789999999999999999999999999999999999999998875
No 36
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=97.29 E-value=1.1e-05 Score=47.26 Aligned_cols=29 Identities=48% Similarity=0.902 Sum_probs=23.6
Q ss_pred CChHHHHHHHHhHHHhhhhhhhhhhccee
Q psy17504 3 ISSSELVMRARDLVFHLHCFTCISCGILL 31 (196)
Q Consensus 3 i~~~~~v~~a~~~~~H~~CF~C~~C~~~L 31 (196)
|...+.++.+.+..||..||.|..|++.|
T Consensus 9 i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L 37 (39)
T smart00132 9 IRGGELVLRALGKVWHPECFKCSKCGKPL 37 (39)
T ss_pred ccCCcEEEEeCCccccccCCCCcccCCcC
Confidence 33334566778899999999999999988
No 37
>KOG1044|consensus
Probab=96.89 E-value=0.00016 Score=66.01 Aligned_cols=46 Identities=30% Similarity=0.689 Sum_probs=39.2
Q ss_pred HHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhh
Q psy17504 8 LVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53 (196)
Q Consensus 8 ~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~ 53 (196)
-|+|+.++.||+.||.|..|++.|..|..|.-.+..+||-.++...
T Consensus 29 evlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~ 74 (670)
T KOG1044|consen 29 EVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAF 74 (670)
T ss_pred ceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhh
Confidence 3788999999999999999999998888888767799998666543
No 38
>KOG1702|consensus
Probab=96.81 E-value=0.00046 Score=55.69 Aligned_cols=49 Identities=35% Similarity=0.663 Sum_probs=36.3
Q ss_pred ChHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhh
Q psy17504 4 SSSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR 54 (196)
Q Consensus 4 ~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~ 54 (196)
.|.|.| +..+++||..||.|.+|+..|.-- .|--.+.++||..||....
T Consensus 15 YPvE~v-~cldk~whk~cfkce~c~mtlnmK-nyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 15 YPVEEV-KCLDKVWHKQCFKCEVCGMTLNMK-NYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred ccHHHH-hhHHHHHHHHhheeeeccCChhhh-hccccccCCCcCcccccce
Confidence 345544 568899999999999999988432 2222477999999997543
No 39
>KOG1168|consensus
Probab=96.32 E-value=0.0022 Score=54.28 Aligned_cols=47 Identities=30% Similarity=0.569 Sum_probs=43.3
Q ss_pred ccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 149 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 149 k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
-+||+||.+-.-..+.||.+|..++.|+......||++|+|.+.+|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVR 354 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 354 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEE
Confidence 35678999999999999999999999999999999999999998875
No 40
>KOG1700|consensus
Probab=96.32 E-value=0.0015 Score=52.93 Aligned_cols=45 Identities=29% Similarity=0.721 Sum_probs=37.4
Q ss_pred HHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhcc
Q psy17504 12 ARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHRD 57 (196)
Q Consensus 12 a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~~ 57 (196)
+.+..||+.||.|..|+..|..+ .|....+.+||..++..++.+.
T Consensus 126 ~~~~~~hk~cfrc~~~~~~ls~~-~~~~~~g~l~~~~~~~~~~~~~ 170 (200)
T KOG1700|consen 126 GNGLEFHKSCFRCTHCGKKLSPK-NYAALEGVLYCKHHFAQLFKGK 170 (200)
T ss_pred hhhhhhhhhheeecccccccCCc-chhhcCCccccchhhheeecCC
Confidence 57889999999999999999654 5666789999999998876543
No 41
>KOG0483|consensus
Probab=96.29 E-value=0.0036 Score=50.62 Aligned_cols=40 Identities=20% Similarity=0.381 Sum_probs=38.0
Q ss_pred ccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 156 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 156 ~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
.|+.+|+..||..|+.+.++....+..||..|||.++||.
T Consensus 56 Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVa 95 (198)
T KOG0483|consen 56 RLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVA 95 (198)
T ss_pred cccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHH
Confidence 4799999999999999999999999999999999999984
No 42
>KOG0847|consensus
Probab=96.07 E-value=0.003 Score=51.46 Aligned_cols=48 Identities=23% Similarity=0.365 Sum_probs=44.2
Q ss_pred cccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 148 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 148 ~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
.+++-.|.+|+-.|+..|+..|+..+|+-...|.+||..+|+++.+|+
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvk 212 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVK 212 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHH
Confidence 455667889999999999999999999999999999999999999985
No 43
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=95.66 E-value=0.0058 Score=36.69 Aligned_cols=26 Identities=35% Similarity=0.613 Sum_probs=20.7
Q ss_pred ccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504 171 INQNPDAKDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 171 ~~~~p~~~~r~~La~~lgL~~~~Vq~ 196 (196)
.++||+..+++.||..+||+..||.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~ 32 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISN 32 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence 37999999999999999999999863
No 44
>KOG1700|consensus
Probab=95.27 E-value=0.0098 Score=48.22 Aligned_cols=48 Identities=25% Similarity=0.416 Sum_probs=36.6
Q ss_pred hHHHHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhh
Q psy17504 5 SSELVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILR 54 (196)
Q Consensus 5 ~~~~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~ 54 (196)
..+++. ..+..||..||.|..|.+.|..+ .+...++.+||+.+|-.++
T Consensus 19 ~~e~~~-~~g~~~hk~c~~c~~~~k~l~~~-~~~~~e~~~yc~~~~~~~~ 66 (200)
T KOG1700|consen 19 FVEKVQ-KDGVDFHKECFKCEKCKKTLTLS-GYSEHEGVPYCKNCHVAQF 66 (200)
T ss_pred HHHHHh-ccCcchhhhHHhccccccccccc-cccccccccccccchHhhh
Confidence 444554 66889999999999999999554 4555899999999544444
No 45
>KOG0775|consensus
Probab=93.68 E-value=0.062 Score=45.30 Aligned_cols=38 Identities=21% Similarity=0.441 Sum_probs=32.8
Q ss_pred hhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504 159 HHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 159 ~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~ 196 (196)
+.-...|+..|..++||....+.+||+.|||+..||-|
T Consensus 185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsN 222 (304)
T KOG0775|consen 185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSN 222 (304)
T ss_pred HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhh
Confidence 33446788899999999999999999999999999854
No 46
>KOG0774|consensus
Probab=91.84 E-value=0.18 Score=42.39 Aligned_cols=47 Identities=21% Similarity=0.445 Sum_probs=41.3
Q ss_pred cchhhcccchhhHhhhhhhhc---ccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504 150 TKRMRTSFKHHQLRTMKSYFN---INQNPDAKDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 150 ~rR~RT~ft~~Ql~~L~~~F~---~~~~p~~~~r~~La~~lgL~~~~Vq~ 196 (196)
.||+|-.|+..--+.|..+|. .|+||+-..+++||.+-+++..||-|
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsn 237 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSN 237 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhcc
Confidence 367788899999999999985 58999999999999999999988753
No 47
>KOG1146|consensus
Probab=89.32 E-value=0.36 Score=48.65 Aligned_cols=49 Identities=27% Similarity=0.443 Sum_probs=44.8
Q ss_pred ccccchhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 147 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 147 ~~k~rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
.-.+|+.||.++..||..|...|....||...+.|.|...++++.++|+
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~ 948 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQ 948 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhH
Confidence 3455778999999999999999999999999999999999999999985
No 48
>KOG1703|consensus
Probab=87.75 E-value=0.085 Score=48.21 Aligned_cols=48 Identities=23% Similarity=0.376 Sum_probs=39.1
Q ss_pred HHHHHHhHHHhhhhhhhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504 8 LVMRARDLVFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR 56 (196)
Q Consensus 8 ~v~~a~~~~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~ 56 (196)
.++.+.+..||..+|.|.+|...+..+. |...+|.+||..+|...+..
T Consensus 317 ~~i~~~~~~~h~~~~~c~~~~~~~~~~~-~~~~~g~~~c~~~~~~~~~p 364 (479)
T KOG1703|consen 317 KVIVALGKEWHPEHFSCEVCAIVILDGG-PRELDGKILCHECFHAPFRP 364 (479)
T ss_pred eeEeeccccccccceeeccccccccCCC-ccccCCCccHHHHHHHhhCc
Confidence 3455788999999999999999995554 46678999999999887654
No 49
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=84.38 E-value=1.2 Score=28.27 Aligned_cols=38 Identities=24% Similarity=0.427 Sum_probs=31.3
Q ss_pred cchhhHhhhhhhhcccCC--CChHHHHHHHHHhCcchhhh
Q psy17504 157 FKHHQLRTMKSYFNINQN--PDAKDLKQLAQKTGLSKRVL 194 (196)
Q Consensus 157 ft~~Ql~~L~~~F~~~~~--p~~~~r~~La~~lgL~~~~V 194 (196)
+|..|++.|..+++.-.| |-...-.+||..+|+++..|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 478899999999987776 66667789999999998654
No 50
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=75.48 E-value=2.4 Score=27.33 Aligned_cols=34 Identities=18% Similarity=0.453 Sum_probs=24.7
Q ss_pred HhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 162 LRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 162 l~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
++.|+.+|...+++.-.....|..+++|+..+|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr 43 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVR 43 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHH
Confidence 3558999999999999999999999999999986
No 51
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=73.59 E-value=3.5 Score=25.92 Aligned_cols=40 Identities=18% Similarity=0.295 Sum_probs=28.4
Q ss_pred chhhcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 151 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 151 rR~RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
||.|..+|-.+-..+-..++... ....||..+|++..+|.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~ 40 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVS 40 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHH
Confidence 46788899998888887887765 56789999999998874
No 52
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=73.04 E-value=1.6 Score=33.00 Aligned_cols=23 Identities=30% Similarity=0.689 Sum_probs=19.2
Q ss_pred hhhhhcceeccCCccccccceeeeccchh
Q psy17504 23 TCISCGILLTKGDLFGMRDEMIYCRPHYE 51 (196)
Q Consensus 23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y~ 51 (196)
.|-.|+.+| |- .+|.+||..|=.
T Consensus 30 hCp~Cg~PL-----F~-KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL-----FR-KDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc-----ee-eCCeEECCCCCc
Confidence 488999999 44 899999999853
No 53
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=68.50 E-value=4.6 Score=32.67 Aligned_cols=39 Identities=28% Similarity=0.479 Sum_probs=33.4
Q ss_pred ccchhhHhhhhhhhcccCC--CChHHHHHHHHHhCcchhhh
Q psy17504 156 SFKHHQLRTMKSYFNINQN--PDAKDLKQLAQKTGLSKRVL 194 (196)
Q Consensus 156 ~ft~~Ql~~L~~~F~~~~~--p~~~~r~~La~~lgL~~~~V 194 (196)
.+|..|++.|..+|..-.| |-...-.+||..+|+++..+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 6999999999999997775 66667789999999998754
No 54
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=67.70 E-value=2.1 Score=24.92 Aligned_cols=24 Identities=29% Similarity=0.506 Sum_probs=17.9
Q ss_pred hhhhhhcceeccCCccccccceeeeccch
Q psy17504 22 FTCISCGILLTKGDLFGMRDEMIYCRPHY 50 (196)
Q Consensus 22 F~C~~C~~~L~~G~~f~~~~~~~~C~~~y 50 (196)
+.|.+|+.. .|...+|..||..+-
T Consensus 9 ~~C~~C~~~-----~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 9 EPCPVCGSR-----WFYSDDGFYYCDRCG 32 (36)
T ss_pred CcCCCCCCe-----EeEccCCEEEhhhCc
Confidence 348888865 367789999997653
No 55
>PRK00420 hypothetical protein; Validated
Probab=63.58 E-value=2.9 Score=30.77 Aligned_cols=25 Identities=32% Similarity=0.727 Sum_probs=20.0
Q ss_pred hhhhhhcceeccCCccccccceeeeccchh
Q psy17504 22 FTCISCGILLTKGDLFGMRDEMIYCRPHYE 51 (196)
Q Consensus 22 F~C~~C~~~L~~G~~f~~~~~~~~C~~~y~ 51 (196)
-.|-+|+.+| |.+.+|..||..|-.
T Consensus 24 ~~CP~Cg~pL-----f~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPL-----FELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcc-----eecCCCceECCCCCC
Confidence 5688999887 556899999998843
No 56
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=61.53 E-value=2.8 Score=26.39 Aligned_cols=30 Identities=23% Similarity=0.495 Sum_probs=22.4
Q ss_pred hhhhhcceeccCCccccccceeeeccchhhh
Q psy17504 23 TCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53 (196)
Q Consensus 23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~ 53 (196)
.|.+|+..+..=..|-+.+| .+|..|+..+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 48999998833223556788 7999999887
No 57
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=52.17 E-value=6.8 Score=23.50 Aligned_cols=28 Identities=29% Similarity=0.579 Sum_probs=18.8
Q ss_pred HhhhhhhhhhhcceeccCCccccccceeeeccc
Q psy17504 17 FHLHCFTCISCGILLTKGDLFGMRDEMIYCRPH 49 (196)
Q Consensus 17 ~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~ 49 (196)
|-.---.|..|+.+| |..+++++||-.|
T Consensus 13 ~~ML~~~Cp~C~~PL-----~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 13 WTMLDEHCPDCGTPL-----MRDKDGKIYCVSC 40 (41)
T ss_pred HhHhcCccCCCCCee-----EEecCCCEECCCC
Confidence 333344678888888 2346888999765
No 58
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=50.10 E-value=8.3 Score=24.98 Aligned_cols=28 Identities=21% Similarity=0.578 Sum_probs=21.1
Q ss_pred hhhhhcceeccCC-ccccccceeeeccch
Q psy17504 23 TCISCGILLTKGD-LFGMRDEMIYCRPHY 50 (196)
Q Consensus 23 ~C~~C~~~L~~G~-~f~~~~~~~~C~~~y 50 (196)
.|..|++.|..|. .|..+..+.+|....
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~EC 46 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSEEC 46 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccHHH
Confidence 4788999997554 666677889997654
No 59
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=46.02 E-value=5.8 Score=28.29 Aligned_cols=30 Identities=30% Similarity=0.616 Sum_probs=21.3
Q ss_pred hhhhhhhcceeccCCccccccceeeeccchhhh
Q psy17504 21 CFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53 (196)
Q Consensus 21 CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~ 53 (196)
=|.|.+|+..+..|..|.+.... ..||.-+
T Consensus 6 ewkC~VCg~~iieGqkFTF~~kG---sVH~eCl 35 (103)
T COG4847 6 EWKCYVCGGTIIEGQKFTFTKKG---SVHYECL 35 (103)
T ss_pred eeeEeeeCCEeeeccEEEEeeCC---cchHHHH
Confidence 47899999999999999764321 3455544
No 60
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=44.45 E-value=13 Score=23.74 Aligned_cols=32 Identities=31% Similarity=0.468 Sum_probs=22.0
Q ss_pred hHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504 161 QLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 161 Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq~ 196 (196)
|+..|+-.+. +.+... .+||..++++++.|++
T Consensus 7 q~~Ll~~L~~-~~~~~~---~ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 7 QLKLLELLLK-NKWITL---KELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHH-HTSBBH---HHHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHc-CCCCcH---HHHHHHHCCCHHHHHH
Confidence 5566666666 555533 3899999999998874
No 61
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=41.27 E-value=4.2 Score=29.11 Aligned_cols=34 Identities=26% Similarity=0.586 Sum_probs=20.6
Q ss_pred HHhhhhhhhhhhcceeccCCccccccceeeeccch
Q psy17504 16 VFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50 (196)
Q Consensus 16 ~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y 50 (196)
.|+..|..|.+|.+.| +-.+|.+...-+||...|
T Consensus 57 ~~~~~~iiCGvC~~~L-T~~EY~~~~~Cp~C~spF 90 (105)
T COG4357 57 EFNPKAIICGVCRKLL-TRAEYGMCGSCPYCQSPF 90 (105)
T ss_pred hcCCccEEhhhhhhhh-hHHHHhhcCCCCCcCCCC
Confidence 4566666777777766 445555555556665544
No 62
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.17 E-value=19 Score=25.41 Aligned_cols=39 Identities=13% Similarity=0.072 Sum_probs=26.7
Q ss_pred cchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 157 FKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 157 ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
++.+|.+.-+..|+.|--.+....+++|..++.++-.|+
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 445555555556666655666777889999999886654
No 63
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=40.04 E-value=14 Score=25.89 Aligned_cols=26 Identities=19% Similarity=0.330 Sum_probs=16.3
Q ss_pred hhhhhcceeccCCccc-cccceeeeccc
Q psy17504 23 TCISCGILLTKGDLFG-MRDEMIYCRPH 49 (196)
Q Consensus 23 ~C~~C~~~L~~G~~f~-~~~~~~~C~~~ 49 (196)
.|.+|+++|.. ..|. +.+|.++-..|
T Consensus 80 ~C~vC~k~l~~-~~f~~~p~~~v~H~~C 106 (109)
T PF10367_consen 80 KCSVCGKPLGN-SVFVVFPCGHVVHYSC 106 (109)
T ss_pred CccCcCCcCCC-ceEEEeCCCeEEeccc
Confidence 39999999954 4443 34566554444
No 64
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=39.83 E-value=34 Score=20.58 Aligned_cols=34 Identities=12% Similarity=0.372 Sum_probs=23.8
Q ss_pred cchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 157 FKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 157 ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
++..+...|...|. ....-.++|..+|++...|+
T Consensus 5 L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~ 38 (50)
T PF04545_consen 5 LPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVR 38 (50)
T ss_dssp S-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHH
T ss_pred CCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHH
Confidence 55667777777772 22356789999999998875
No 65
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=39.06 E-value=10 Score=27.19 Aligned_cols=10 Identities=30% Similarity=0.551 Sum_probs=6.4
Q ss_pred ccceeeeccc
Q psy17504 40 RDEMIYCRPH 49 (196)
Q Consensus 40 ~~~~~~C~~~ 49 (196)
.+|.+||..|
T Consensus 89 ~~g~~iC~DC 98 (99)
T PF13834_consen 89 KDGQPICRDC 98 (99)
T ss_pred cCCCEecccc
Confidence 4567777665
No 66
>PRK12495 hypothetical protein; Provisional
Probab=36.58 E-value=29 Score=28.58 Aligned_cols=32 Identities=19% Similarity=0.350 Sum_probs=23.9
Q ss_pred HHhhhhhhhhhhcceeccCCccccccceeeeccchhhh
Q psy17504 16 VFHLHCFTCISCGILLTKGDLFGMRDEMIYCRPHYEIL 53 (196)
Q Consensus 16 ~~H~~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~ 53 (196)
..-..-|.|..|+.+| |.+ .|.++|..|-...
T Consensus 37 gatmsa~hC~~CG~PI-----pa~-pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 37 GATMTNAHCDECGDPI-----FRH-DGQEFCPTCQQPV 68 (226)
T ss_pred hcccchhhcccccCcc-----cCC-CCeeECCCCCCcc
Confidence 3456678899999998 233 8999998886543
No 67
>KOG0773|consensus
Probab=35.32 E-value=20 Score=31.01 Aligned_cols=46 Identities=22% Similarity=0.445 Sum_probs=33.6
Q ss_pred chhhcccchhhHhhhhhh-hc--ccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504 151 KRMRTSFKHHQLRTMKSY-FN--INQNPDAKDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 151 rR~RT~ft~~Ql~~L~~~-F~--~~~~p~~~~r~~La~~lgL~~~~Vq~ 196 (196)
.|.+..+.......|+.. |+ ..+||....+..||.++||+..||-|
T Consensus 240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~N 288 (342)
T KOG0773|consen 240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSN 288 (342)
T ss_pred CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCc
Confidence 334446666666666644 22 26899999999999999999998864
No 68
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=33.49 E-value=19 Score=21.87 Aligned_cols=24 Identities=25% Similarity=0.679 Sum_probs=16.7
Q ss_pred hhhhcceeccCCccccccceeeeccchhh
Q psy17504 24 CISCGILLTKGDLFGMRDEMIYCRPHYEI 52 (196)
Q Consensus 24 C~~C~~~L~~G~~f~~~~~~~~C~~~y~~ 52 (196)
|.+|.+++.. ..++.+||..-...
T Consensus 9 C~~Cdk~~~~-----~~~~~lYCSe~Cr~ 32 (43)
T PF12855_consen 9 CIVCDKQIDP-----PDDGSLYCSEECRL 32 (43)
T ss_pred HHHhhccccC-----CCCCccccCHHHHh
Confidence 7788888732 45788999765543
No 69
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=31.94 E-value=20 Score=22.52 Aligned_cols=32 Identities=19% Similarity=0.130 Sum_probs=24.2
Q ss_pred hhhhhhcceeccCCccccccceeeeccchhhhhh
Q psy17504 22 FTCISCGILLTKGDLFGMRDEMIYCRPHYEILRH 55 (196)
Q Consensus 22 F~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~ 55 (196)
|.|.+|...+. +......|.+||+.+......
T Consensus 2 ~~Cpi~~~~~~--~Pv~~~~G~v~~~~~i~~~~~ 33 (63)
T smart00504 2 FLCPISLEVMK--DPVILPSGQTYERRAIEKWLL 33 (63)
T ss_pred cCCcCCCCcCC--CCEECCCCCEEeHHHHHHHHH
Confidence 57899998883 345556789999999877654
No 70
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.24 E-value=50 Score=19.63 Aligned_cols=36 Identities=8% Similarity=0.305 Sum_probs=16.6
Q ss_pred cccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 155 TSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 155 T~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
..+|..|...++...+.. ....+||..+|.+...|-
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~ 38 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVS 38 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHH
Confidence 356777777777666533 355679999999988763
No 71
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=30.70 E-value=21 Score=21.88 Aligned_cols=31 Identities=19% Similarity=0.288 Sum_probs=22.8
Q ss_pred hhhhhcceeccCCccccccceeeeccchhhhhhc
Q psy17504 23 TCISCGILLTKGDLFGMRDEMIYCRPHYEILRHR 56 (196)
Q Consensus 23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y~~~~~~ 56 (196)
+|.+|++....| ....+.++|..|=..+...
T Consensus 1 ~CiiC~~~~~~G---I~I~~~fIC~~CE~~iv~~ 31 (46)
T PF10764_consen 1 KCIICGKEKEEG---IHIYGKFICSDCEKEIVNT 31 (46)
T ss_pred CeEeCCCcCCCC---EEEECeEehHHHHHHhccC
Confidence 478899887554 4457899999997776543
No 72
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=28.00 E-value=29 Score=21.94 Aligned_cols=27 Identities=22% Similarity=0.528 Sum_probs=14.6
Q ss_pred hhhhhcceeccCCccccccceeeeccch
Q psy17504 23 TCISCGILLTKGDLFGMRDEMIYCRPHY 50 (196)
Q Consensus 23 ~C~~C~~~L~~G~~f~~~~~~~~C~~~y 50 (196)
.|..|...+.. .+-.+++|+.||...-
T Consensus 9 aC~~C~C~V~~-~~Ai~~dGk~YCS~aC 35 (52)
T PF02069_consen 9 ACPSCSCVVSE-EEAIQKDGKYYCSEAC 35 (52)
T ss_dssp SSTT----B-T-TTSEESSS-EESSHHH
T ss_pred cCCCCEeEECc-hHhHHhCCEeeecHHH
Confidence 36778887743 4556689999997654
No 73
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=27.70 E-value=29 Score=21.66 Aligned_cols=18 Identities=17% Similarity=0.377 Sum_probs=13.6
Q ss_pred HHHHHHHHhCcchhhhcC
Q psy17504 179 DLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 179 ~r~~La~~lgL~~~~Vq~ 196 (196)
--.+||..+|++..||++
T Consensus 30 SS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 30 SSQELAEALGITPAQVRK 47 (50)
T ss_dssp -HHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHHCCCHHHhcc
Confidence 445899999999999974
No 74
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=26.65 E-value=20 Score=18.21 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=8.4
Q ss_pred hhhhhhcceec
Q psy17504 22 FTCISCGILLT 32 (196)
Q Consensus 22 F~C~~C~~~L~ 32 (196)
|.|.+|++.+.
T Consensus 1 ~~C~~C~~~f~ 11 (25)
T PF12874_consen 1 FYCDICNKSFS 11 (25)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCCcC
Confidence 57888888773
No 75
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=25.21 E-value=79 Score=18.74 Aligned_cols=34 Identities=15% Similarity=0.390 Sum_probs=22.1
Q ss_pred cchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 157 FKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 157 ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
++.+|.+.+...+... ....++|..+|++...|.
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~Tvy 39 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVY 39 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHH
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHH
Confidence 5565666666666544 356689999999988764
No 76
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=24.60 E-value=46 Score=20.26 Aligned_cols=19 Identities=32% Similarity=0.566 Sum_probs=14.1
Q ss_pred HHHHHHHHHhCcchhhhcC
Q psy17504 178 KDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 178 ~~r~~La~~lgL~~~~Vq~ 196 (196)
..-.+||..++++.+.|++
T Consensus 16 it~~eLa~~l~vS~rTi~~ 34 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRR 34 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHH
T ss_pred cCHHHHHHHhCCCHHHHHH
Confidence 3456899999999998863
No 77
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=24.45 E-value=32 Score=28.06 Aligned_cols=30 Identities=17% Similarity=0.250 Sum_probs=23.1
Q ss_pred hhhhhhhhcceeccCCccccccceeeeccch
Q psy17504 20 HCFTCISCGILLTKGDLFGMRDEMIYCRPHY 50 (196)
Q Consensus 20 ~CF~C~~C~~~L~~G~~f~~~~~~~~C~~~y 50 (196)
.-..|..|++.+. ...|.+.+|.++|..|.
T Consensus 148 ~l~~C~~Cg~~~~-~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 148 DLDHCAVCGAPGD-HRYFSPKEGGAVCSECG 177 (247)
T ss_pred chhhHhcCCCCCC-ceEEecccCCccccccc
Confidence 3347999999873 44667789999999885
No 78
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=24.08 E-value=23 Score=25.54 Aligned_cols=22 Identities=27% Similarity=0.690 Sum_probs=17.8
Q ss_pred hhhhhhcceeccCCccccccce
Q psy17504 22 FTCISCGILLTKGDLFGMRDEM 43 (196)
Q Consensus 22 F~C~~C~~~L~~G~~f~~~~~~ 43 (196)
++|.+|+..+..|.-|.+..+.
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG 24 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKG 24 (101)
T ss_pred eEEEecCCeeeecceEEEecCC
Confidence 5799999999899988765443
No 79
>PF13730 HTH_36: Helix-turn-helix domain
Probab=23.29 E-value=73 Score=19.32 Aligned_cols=21 Identities=29% Similarity=0.381 Sum_probs=16.5
Q ss_pred ChHHHHHHHHHhCcchhhhcC
Q psy17504 176 DAKDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 176 ~~~~r~~La~~lgL~~~~Vq~ 196 (196)
..+-.+.||..+|++.+.|++
T Consensus 24 ~~pS~~~la~~~g~s~~Tv~~ 44 (55)
T PF13730_consen 24 CFPSQETLAKDLGVSRRTVQR 44 (55)
T ss_pred CCcCHHHHHHHHCcCHHHHHH
Confidence 444677899999999988863
No 80
>KOG3623|consensus
Probab=23.03 E-value=78 Score=30.92 Aligned_cols=34 Identities=29% Similarity=0.592 Sum_probs=31.5
Q ss_pred HhhhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 162 LRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 162 l~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
+..|+.+|..|.+|...+...+|..+||+.++||
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk 601 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVK 601 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHH
Confidence 5678889999999999999999999999999987
No 81
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=22.89 E-value=47 Score=19.35 Aligned_cols=14 Identities=21% Similarity=0.468 Sum_probs=11.6
Q ss_pred ccchhhHhhhhhhh
Q psy17504 156 SFKHHQLRTMKSYF 169 (196)
Q Consensus 156 ~ft~~Ql~~L~~~F 169 (196)
.||..|+.+|+.-.
T Consensus 2 ~FT~~Ql~~L~~Qi 15 (37)
T PF08880_consen 2 PFTPAQLQELRAQI 15 (37)
T ss_pred CCCHHHHHHHHHHH
Confidence 68999999998653
No 82
>PRK13558 bacterio-opsin activator; Provisional
Probab=22.72 E-value=74 Score=29.79 Aligned_cols=41 Identities=17% Similarity=0.330 Sum_probs=35.1
Q ss_pred hcccchhhHhhhhhhhcccCC--CChHHHHHHHHHhCcchhhh
Q psy17504 154 RTSFKHHQLRTMKSYFNINQN--PDAKDLKQLAQKTGLSKRVL 194 (196)
Q Consensus 154 RT~ft~~Ql~~L~~~F~~~~~--p~~~~r~~La~~lgL~~~~V 194 (196)
...+|..|.+.|+.++..-.| |-...-++||..+|++...+
T Consensus 605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~ 647 (665)
T PRK13558 605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTF 647 (665)
T ss_pred hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 357999999999999998886 77777889999999998654
No 83
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=22.60 E-value=31 Score=24.30 Aligned_cols=28 Identities=25% Similarity=0.430 Sum_probs=19.2
Q ss_pred hhhhhhcccCCCChHHHHHHHHHhCcchhhhc
Q psy17504 164 TMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 195 (196)
Q Consensus 164 ~L~~~F~~~~~p~~~~r~~La~~lgL~~~~Vq 195 (196)
+|...|.... ...+.+|..++++...|+
T Consensus 14 ELq~nf~~~~----ls~~~ia~dL~~s~~~le 41 (89)
T PF10078_consen 14 ELQANFELSG----LSLEQIAADLGTSPEHLE 41 (89)
T ss_pred HHHHHHHHcC----CCHHHHHHHhCCCHHHHH
Confidence 4555555444 456788999999887765
No 84
>PF13945 NST1: Salt tolerance down-regulator
Probab=22.29 E-value=54 Score=26.41 Aligned_cols=24 Identities=25% Similarity=0.479 Sum_probs=15.7
Q ss_pred HHHHHHHhHHHhhhhhhhhhhccee
Q psy17504 7 ELVMRARDLVFHLHCFTCISCGILL 31 (196)
Q Consensus 7 ~~v~~a~~~~~H~~CF~C~~C~~~L 31 (196)
|.||+-+...-+..| .|.+|++.-
T Consensus 128 e~VLkkmKeqq~h~C-~C~vCgr~~ 151 (190)
T PF13945_consen 128 EAVLKKMKEQQKHSC-SCSVCGRKR 151 (190)
T ss_pred HHHHHHHHHHhccCc-ccHHHhchh
Confidence 456666555554456 699999864
No 85
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=22.28 E-value=1e+02 Score=24.17 Aligned_cols=39 Identities=15% Similarity=0.225 Sum_probs=31.9
Q ss_pred hcccchhhHhhhhhhhcccCCCChHHHHHHHHHhCcchhhh
Q psy17504 154 RTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 194 (196)
Q Consensus 154 RT~ft~~Ql~~L~~~F~~~~~p~~~~r~~La~~lgL~~~~V 194 (196)
...+|.+++.++.+.-..+ |....+..||.++|++..-|
T Consensus 83 ~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV 121 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFV 121 (164)
T ss_pred cccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHH
Confidence 4689999999998776655 66788999999999987654
No 86
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=22.02 E-value=22 Score=24.06 Aligned_cols=29 Identities=14% Similarity=0.302 Sum_probs=21.2
Q ss_pred hhcccCCCChHHHHHHHHHhCcchhhhcC
Q psy17504 168 YFNINQNPDAKDLKQLAQKTGLSKRVLQN 196 (196)
Q Consensus 168 ~F~~~~~p~~~~r~~La~~lgL~~~~Vq~ 196 (196)
.|...+|.......+||..+|+++..|++
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~ 51 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRN 51 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHH
Confidence 34444555556778999999999988863
Done!