Query psy11691
Match_columns 271
No_of_seqs 223 out of 1161
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 16:25:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11691.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11691hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2272|consensus 99.6 9.4E-17 2E-21 146.9 -2.0 109 91-214 69-182 (332)
2 KOG1701|consensus 99.5 7.2E-16 1.6E-20 149.0 -1.5 102 94-200 273-377 (468)
3 KOG1044|consensus 99.4 6.4E-14 1.4E-18 139.5 2.2 122 12-159 69-195 (670)
4 PF00412 LIM: LIM domain; Int 99.4 1.8E-13 4E-18 96.9 1.9 57 98-155 1-58 (58)
5 KOG1701|consensus 99.2 2.3E-12 5E-17 124.9 0.0 99 96-196 335-440 (468)
6 KOG1703|consensus 99.0 6.2E-11 1.3E-15 117.3 -0.2 95 93-189 361-456 (479)
7 KOG4577|consensus 99.0 8.3E-12 1.8E-16 116.4 -6.6 103 94-210 32-135 (383)
8 KOG2272|consensus 98.9 1.2E-10 2.5E-15 107.2 -1.9 94 95-190 12-106 (332)
9 KOG1700|consensus 98.9 3.8E-10 8.2E-15 100.6 0.9 108 9-152 53-164 (200)
10 COG0722 AroG 3-deoxy-D-arabino 98.7 2.1E-09 4.5E-14 101.7 0.3 56 182-237 12-68 (351)
11 KOG1702|consensus 98.6 1.5E-09 3.2E-14 97.6 -3.5 60 96-156 5-64 (264)
12 smart00132 LIM Zinc-binding do 98.6 2.8E-08 6.1E-13 64.2 2.6 37 97-133 1-38 (39)
13 KOG1700|consensus 98.6 7.6E-09 1.6E-13 92.2 -0.3 60 95-155 7-66 (200)
14 KOG1703|consensus 98.5 2.3E-08 4.9E-13 99.2 1.5 92 94-187 302-393 (479)
15 TIGR00034 aroFGH phospho-2-deh 98.4 7.8E-08 1.7E-12 92.1 0.2 54 183-236 8-62 (344)
16 PRK12756 phospho-2-dehydro-3-d 98.4 7.9E-08 1.7E-12 92.1 0.2 55 183-237 12-67 (348)
17 PRK12755 phospho-2-dehydro-3-d 98.3 1E-07 2.2E-12 91.5 0.2 56 182-237 13-69 (353)
18 PRK12822 phospho-2-dehydro-3-d 98.3 1.2E-07 2.7E-12 90.9 0.2 54 183-236 13-67 (356)
19 PRK09261 phospho-2-dehydro-3-d 98.2 2.5E-07 5.4E-12 88.9 0.3 54 183-236 13-67 (349)
20 KOG1044|consensus 98.2 1.2E-06 2.7E-11 88.2 4.1 79 96-187 17-95 (670)
21 KOG4577|consensus 97.8 3.7E-06 7.9E-11 79.1 -1.2 62 95-156 92-155 (383)
22 PF00793 DAHP_synth_1: DAHP sy 96.6 0.0009 2E-08 62.4 1.8 23 214-236 8-30 (270)
23 smart00132 LIM Zinc-binding do 89.5 0.31 6.7E-06 30.7 2.2 19 171-189 15-33 (39)
24 PRK13398 3-deoxy-7-phosphohept 88.8 0.25 5.4E-06 46.1 1.9 20 217-237 23-42 (266)
25 PRK13396 3-deoxy-7-phosphohept 87.9 0.29 6.3E-06 47.6 1.8 25 213-237 92-116 (352)
26 KOG0490|consensus 85.5 0.15 3.3E-06 44.7 -1.4 51 101-153 2-54 (235)
27 PF00412 LIM: LIM domain; Int 85.1 0.58 1.3E-05 32.5 1.7 16 173-188 16-31 (58)
28 PF09943 DUF2175: Uncharacteri 81.5 0.67 1.5E-05 37.7 0.9 31 97-127 4-35 (101)
29 PF10367 Vps39_2: Vacuolar sor 75.3 2.2 4.7E-05 33.0 2.1 31 94-124 77-108 (109)
30 PF10367 Vps39_2: Vacuolar sor 73.3 3.1 6.7E-05 32.1 2.5 29 124-152 80-108 (109)
31 PF11781 RRN7: RNA polymerase 71.9 2.9 6.2E-05 27.8 1.7 25 123-152 9-33 (36)
32 PRK08673 3-deoxy-7-phosphohept 66.8 3.4 7.3E-05 40.0 1.8 25 220-244 91-123 (335)
33 PF14446 Prok-RING_1: Prokaryo 63.2 4.7 0.0001 29.4 1.5 37 95-131 5-50 (54)
34 PF08394 Arc_trans_TRASH: Arch 57.2 7.3 0.00016 26.3 1.5 27 98-125 1-29 (37)
35 PF14471 DUF4428: Domain of un 51.8 3.8 8.3E-05 29.1 -0.5 30 124-154 1-30 (51)
36 COG2191 Formylmethanofuran deh 51.7 7.8 0.00017 35.3 1.3 31 123-154 173-203 (206)
37 PRK00807 50S ribosomal protein 47.4 15 0.00034 26.2 2.0 32 96-130 2-36 (52)
38 COG4802 FtrB Ferredoxin-thiore 46.0 8 0.00017 31.8 0.4 30 213-242 52-81 (110)
39 PF13240 zinc_ribbon_2: zinc-r 44.9 11 0.00024 22.5 0.8 8 125-132 2-9 (23)
40 PF04502 DUF572: Family of unk 41.8 20 0.00043 34.3 2.5 42 93-134 38-89 (324)
41 COG4847 Uncharacterized protei 41.5 13 0.00027 30.3 0.9 36 96-131 7-43 (103)
42 COG1645 Uncharacterized Zn-fin 36.1 24 0.00051 30.1 1.8 23 124-152 30-52 (131)
43 TIGR01361 DAHP_synth_Bsub phos 35.3 23 0.0005 32.8 1.7 16 221-236 24-39 (260)
44 PF05502 Dynactin_p62: Dynacti 34.5 21 0.00045 36.2 1.4 40 95-135 26-65 (483)
45 cd00162 RING RING-finger (Real 31.3 25 0.00054 21.9 1.0 26 98-123 2-27 (45)
46 KOG1829|consensus 29.6 20 0.00044 37.4 0.4 39 121-160 339-382 (580)
47 TIGR02098 MJ0042_CXXC MJ0042 f 29.4 22 0.00047 23.0 0.4 31 97-132 4-35 (38)
48 PF12674 Zn_ribbon_2: Putative 29.2 20 0.00044 27.8 0.3 30 124-153 2-35 (81)
49 PF13834 DUF4193: Domain of un 28.9 22 0.00047 29.0 0.4 28 123-150 71-98 (99)
50 PF06677 Auto_anti-p27: Sjogre 27.9 46 0.001 22.7 1.8 21 125-150 20-40 (41)
51 PF00645 zf-PARP: Poly(ADP-rib 27.6 34 0.00074 25.6 1.3 14 96-109 8-21 (82)
52 PF07754 DUF1610: Domain of un 27.0 41 0.00089 20.6 1.3 7 99-105 2-8 (24)
53 PF13248 zf-ribbon_3: zinc-rib 26.9 40 0.00087 20.4 1.2 8 98-105 5-12 (26)
54 PRK14890 putative Zn-ribbon RN 26.5 46 0.001 24.7 1.7 14 96-109 8-21 (59)
55 KOG3579|consensus 26.1 1.5E+02 0.0033 28.7 5.5 32 96-127 269-300 (352)
56 PRK06266 transcription initiat 25.6 25 0.00053 31.0 0.2 31 96-134 118-148 (178)
57 TIGR00373 conserved hypothetic 25.1 22 0.00048 30.6 -0.2 31 96-134 110-140 (158)
58 PF08271 TF_Zn_Ribbon: TFIIB z 25.0 65 0.0014 21.5 2.1 27 123-152 1-27 (43)
59 PF08746 zf-RING-like: RING-li 24.5 23 0.0005 24.1 -0.1 27 98-124 1-29 (43)
60 PHA03357 Alkaline exonuclease; 24.0 1.2E+02 0.0025 23.8 3.5 25 26-50 7-32 (81)
61 PF11331 DUF3133: Protein of u 23.6 21 0.00046 25.1 -0.5 35 96-132 7-41 (46)
62 PLN03033 2-dehydro-3-deoxyphos 23.6 50 0.0011 31.7 1.8 19 218-236 12-30 (290)
63 COG1571 Predicted DNA-binding 22.4 50 0.0011 33.2 1.7 35 94-138 349-383 (421)
64 PRK12595 bifunctional 3-deoxy- 21.8 51 0.0011 32.2 1.5 17 221-237 117-133 (360)
65 PF13639 zf-RING_2: Ring finge 21.5 40 0.00087 22.2 0.5 28 97-124 2-31 (44)
66 PRK14873 primosome assembly pr 20.5 98 0.0021 32.7 3.4 25 124-152 394-418 (665)
67 PRK00420 hypothetical protein; 20.4 71 0.0015 26.4 1.9 25 123-152 24-48 (112)
68 cd00472 Ribosomal_L24e_L24 Rib 20.2 66 0.0014 23.3 1.4 25 95-119 3-30 (54)
No 1
>KOG2272|consensus
Probab=99.58 E-value=9.4e-17 Score=146.89 Aligned_cols=109 Identities=21% Similarity=0.413 Sum_probs=97.7
Q ss_pred CCcCCCcccccCceeecceeEEeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCCCcccccCC-----CCCCC
Q psy11691 91 GSLKLNSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPDEEERSLTD-----PLRSS 165 (271)
Q Consensus 91 g~~~s~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~~~~I~~-----rc~~~ 165 (271)
-+.+++.|+.|+++| .++.|.+++.+||+.||+|..|++.|.+..|+.. .|+.+|..|.++..+.+.+ +|++.
T Consensus 69 ~~LfaPcC~kC~EFi-iGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rn-qgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~ 146 (332)
T KOG2272|consen 69 HVLFAPCCGKCGEFI-IGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRN-QGRALCRECNQKEKAKGRGRYVCQKCHAH 146 (332)
T ss_pred hhhhchhhcccccch-hhHHHHhhccccCcccchhHHHHHHHhhhhhHhh-cchHHhhhhhhhhcccccceeehhhhhhh
Confidence 345789999999999 7999999999999999999999999999999885 7999999999988776654 48887
Q ss_pred CCCCCceeecCccccCCCCCCCCCCcccCCCCCCccccchhcchhhhhh
Q psy11691 166 DRPDGHHAIGDDRYHAELNSDKSTNLLTDSEPSTHCDSNLVTASVESTN 214 (271)
Q Consensus 166 ~~~~~~I~~gg~~YH~ecFs~ks~~ll~d~~p~~~c~~~~~~~~~e~~~ 214 (271)
++. +++++.|++||++||+ ++.|.++|++++||.-.
T Consensus 147 iD~-~~l~fr~d~yH~yHFk------------Ct~C~keL~sdaRevk~ 182 (332)
T KOG2272|consen 147 IDE-QPLTFRGDPYHPYHFK------------CTTCGKELTSDAREVKG 182 (332)
T ss_pred ccc-ccccccCCCCCcccee------------cccccccccchhhhhcc
Confidence 776 7899999999999999 99999999999998654
No 2
>KOG1701|consensus
Probab=99.53 E-value=7.2e-16 Score=148.96 Aligned_cols=102 Identities=24% Similarity=0.390 Sum_probs=82.0
Q ss_pred CCCcccccCceeecce-eEEeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCCCcccccCCCCCCCCCC--CC
Q psy11691 94 KLNSCSLCGEKVYLAQ-RFAFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPDEEERSLTDPLRSSDRP--DG 170 (271)
Q Consensus 94 ~s~kCa~Cgk~V~~~E-rI~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~~~~I~~rc~~~~~~--~~ 170 (271)
+...|.+|+|.|+..+ .+.||+++||..||+|..|+++|....||.. |+++||+.||+... ++|..+.+. +.
T Consensus 273 ~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v-~~k~~CE~cyq~tl----ekC~~Cg~~I~d~ 347 (468)
T KOG1701|consen 273 YFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQV-DGKPYCEGCYQDTL----EKCNKCGEPIMDR 347 (468)
T ss_pred hhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhcccccccc-CCcccchHHHHHHH----HHHhhhhhHHHHH
Confidence 4568999999996444 3889999999999999999999999999997 79999999999653 333322221 12
Q ss_pred ceeecCccccCCCCCCCCCCcccCCCCCCc
Q psy11691 171 HHAIGDDRYHAELNSDKSTNLLTDSEPSTH 200 (271)
Q Consensus 171 ~I~~gg~~YH~ecFs~ks~~ll~d~~p~~~ 200 (271)
.+++.|+.||++||.|..|+-..|.||++.
T Consensus 348 iLrA~GkayHp~CF~Cv~C~r~ldgipFtv 377 (468)
T KOG1701|consen 348 ILRALGKAYHPGCFTCVVCARCLDGIPFTV 377 (468)
T ss_pred HHHhcccccCCCceEEEEeccccCCccccc
Confidence 345889999999999998888888888753
No 3
>KOG1044|consensus
Probab=99.41 E-value=6.4e-14 Score=139.52 Aligned_cols=122 Identities=23% Similarity=0.371 Sum_probs=88.7
Q ss_pred hhhhhccCCccccccccC---Ccccc--ccccccCCCccCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy11691 12 HYQRSYLGGAVVNALDFG---SGVAA--ARYLFHSIDLGDQLTNSNTDNPLSLPGVDVPQKTTSPAHREPGAPRAPSQPP 86 (271)
Q Consensus 12 ~~~~~~~~~~~~~~~g~g---~~~g~--~~~~~~s~d~g~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~ps~~~ 86 (271)
+=||-|+.|+||+++|.. .++.| +|.+|. .|+.+++++. +.+... -....+. .|.
T Consensus 69 ~~c~~~~~gevvsa~gktyh~~cf~cs~ck~pf~---~g~~vt~~gk-~~~c~~-------------c~~~~~~---~p~ 128 (670)
T KOG1044|consen 69 DDCRAFVEGEVVSTLGKTYHPKCFSCSTCKSPFK---SGDKVTFSGK-ECLCQT-------------CSQPMPV---SPA 128 (670)
T ss_pred cchhhhccceeEecccceeccccceecccCCCCC---CCCeeeecch-hhhhhh-------------hcCcccC---Ccc
Confidence 559999999999999987 33333 455777 7889988773 211100 0111111 112
Q ss_pred CCCCCCcCCCcccccCceeecceeEEeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCCCcccccC
Q psy11691 87 STLPGSLKLNSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPDEEERSLT 159 (271)
Q Consensus 87 ~~~~g~~~s~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~~~~I~ 159 (271)
.. .....|++|++.|..++.+.|+++.||..||+|..|+..|.+ .|..+ ||.+||+.||++.|...+
T Consensus 129 ~~----~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~sk-dg~pyce~dy~~~fgvkc 195 (670)
T KOG1044|consen 129 ES----YGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSK-DGVPYCEKDYQAKFGVKC 195 (670)
T ss_pred cc----cCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeecc-CCCcchhhhhhhhcCeeh
Confidence 11 124679999999999999999999999999999999999977 56664 799999999998886433
No 4
>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=99.37 E-value=1.8e-13 Score=96.94 Aligned_cols=57 Identities=28% Similarity=0.706 Sum_probs=51.2
Q ss_pred ccccCceeecceeE-EeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCCCcc
Q psy11691 98 CSLCGEKVYLAQRF-AFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPDEEE 155 (271)
Q Consensus 98 Ca~Cgk~V~~~ErI-~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~~ 155 (271)
|++|++.|...+.+ .++|+.||++||+|..|++.|..+.|+.. ++.+||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEK-DGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEE-TTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeE-CCEEECHHHHhhhC
Confidence 88999999877775 69999999999999999999999998886 79999999997643
No 5
>KOG1701|consensus
Probab=99.20 E-value=2.3e-12 Score=124.89 Aligned_cols=99 Identities=21% Similarity=0.345 Sum_probs=81.8
Q ss_pred CcccccCceeeccee-EEeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCCCcccccCCCCCCCCCC----CC
Q psy11691 96 NSCSLCGEKVYLAQR-FAFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPDEEERSLTDPLRSSDRP----DG 170 (271)
Q Consensus 96 ~kCa~Cgk~V~~~Er-I~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~~~~I~~rc~~~~~~----~~ 170 (271)
.+|..|++.| .|+ +.|+|+.||..||+|..|.+.|++..|....++++||..||.++|++.+..|..-|-+ ++
T Consensus 335 ekC~~Cg~~I--~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~e 412 (468)
T KOG1701|consen 335 EKCNKCGEPI--MDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDE 412 (468)
T ss_pred HHHhhhhhHH--HHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcc
Confidence 5688899998 454 6799999999999999999999999998766899999999999998877666554432 22
Q ss_pred c--eeecCccccCCCCCCCCCCcccCCC
Q psy11691 171 H--HAIGDDRYHAELNSDKSTNLLTDSE 196 (271)
Q Consensus 171 ~--I~~gg~~YH~ecFs~ks~~ll~d~~ 196 (271)
. |.+++..||.+|..|..|.++...+
T Consensus 413 tvRvvamdr~fHv~CY~CEDCg~~LS~e 440 (468)
T KOG1701|consen 413 TVRVVAMDRDFHVNCYKCEDCGLLLSSE 440 (468)
T ss_pred eEEEEEccccccccceehhhcCcccccc
Confidence 2 4579999999999999888877633
No 6
>KOG1703|consensus
Probab=98.99 E-value=6.2e-11 Score=117.29 Aligned_cols=95 Identities=19% Similarity=0.301 Sum_probs=76.0
Q ss_pred cCCCcccccCceeecceeEEeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCCCcccccCCCCCC-CCCCCCc
Q psy11691 93 LKLNSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPDEEERSLTDPLRS-SDRPDGH 171 (271)
Q Consensus 93 ~~s~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~~~~I~~rc~~-~~~~~~~ 171 (271)
.+++.|.+|++.| .++.|.+.++.||++||.|..|++.|....|+.. ++.+||+.||.+.+..+..-|.- ....+..
T Consensus 361 ~~~p~C~~C~~~i-~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~-~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ 438 (479)
T KOG1703|consen 361 PFRPNCKRCLLPI-LEEGVCALGRLWHPECFVCADCGKPLKNSSFFES-DGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQ 438 (479)
T ss_pred hhCccccccCCch-HHhHhhhccCeechhceeeecccCCCCCCccccc-CCccchhhhHhhhccccchhccchhHhhhhH
Confidence 3578999999999 6788889999999999999999999999999986 89999999999887644321211 1112345
Q ss_pred eeecCccccCCCCCCCCC
Q psy11691 172 HAIGDDRYHAELNSDKST 189 (271)
Q Consensus 172 I~~gg~~YH~ecFs~ks~ 189 (271)
|.+.|..||..||.|.-+
T Consensus 439 ie~~~~~~h~~~F~c~~c 456 (479)
T KOG1703|consen 439 IEADGSPFHGDCFRCANC 456 (479)
T ss_pred hhccCccccccceehhhh
Confidence 678899999999996543
No 7
>KOG4577|consensus
Probab=98.98 E-value=8.3e-12 Score=116.37 Aligned_cols=103 Identities=18% Similarity=0.283 Sum_probs=84.3
Q ss_pred CCCcccccCceeecceeEEeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCCCcccccCCCCCCCCCCCCcee
Q psy11691 94 KLNSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPDEEERSLTDPLRSSDRPDGHHA 173 (271)
Q Consensus 94 ~s~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~~~~I~~rc~~~~~~~~~I~ 173 (271)
+.++|++|.+.|...-.+.++++.||..|++|..|..+|...-|.. ++..||+..+-++|...+..|...+-+...|+
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFsR--~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVR 109 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFSR--EGSVYCKEDFFKRFGTKCSACQEGIPPTQVVR 109 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhhc--CCceeehHHHHHHhCCcchhhcCCCChHHHHH
Confidence 4589999999994333357999999999999999999999876654 69999999999998887777877787776664
Q ss_pred -ecCccccCCCCCCCCCCcccCCCCCCccccchhcchh
Q psy11691 174 -IGDDRYHAELNSDKSTNLLTDSEPSTHCDSNLVTASV 210 (271)
Q Consensus 174 -~gg~~YH~ecFs~ks~~ll~d~~p~~~c~~~~~~~~~ 210 (271)
+.+..||.+||- |.-|..+|+|+-+
T Consensus 110 kAqd~VYHl~CF~------------C~iC~R~L~TGdE 135 (383)
T KOG4577|consen 110 KAQDFVYHLHCFA------------CFICKRQLATGDE 135 (383)
T ss_pred Hhhcceeehhhhh------------hHhhhcccccCCe
Confidence 778899999999 6667777766654
No 8
>KOG2272|consensus
Probab=98.90 E-value=1.2e-10 Score=107.24 Aligned_cols=94 Identities=19% Similarity=0.210 Sum_probs=81.1
Q ss_pred CCcccccCceeeccee-EEeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCCCcccccCCCCCCCCCCCCcee
Q psy11691 95 LNSCSLCGEKVYLAQR-FAFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPDEEERSLTDPLRSSDRPDGHHA 173 (271)
Q Consensus 95 s~kCa~Cgk~V~~~Er-I~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~~~~I~~rc~~~~~~~~~I~ 173 (271)
+-.|.+|.....+.|. +...|.+||..||.|++|-.+|..+.|++. +|+.||+..+...|+|-..+|...+. |+.|.
T Consensus 12 ~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~ef-EgRkYCEhDF~~LfaPcC~kC~EFii-GrVik 89 (332)
T KOG2272|consen 12 NMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEF-EGRKYCEHDFHVLFAPCCGKCGEFII-GRVIK 89 (332)
T ss_pred HHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEe-cCcccccccchhhhchhhcccccchh-hHHHH
Confidence 4569999999888887 567899999999999999999999999998 69999999999999998887777654 45677
Q ss_pred ecCccccCCCCCCCCCC
Q psy11691 174 IGDDRYHAELNSDKSTN 190 (271)
Q Consensus 174 ~gg~~YH~ecFs~ks~~ 190 (271)
+++.+||+.||.|.-++
T Consensus 90 amnnSwHp~CF~Cd~Cn 106 (332)
T KOG2272|consen 90 AMNNSWHPACFRCDLCN 106 (332)
T ss_pred hhccccCcccchhHHHH
Confidence 89999999999964433
No 9
>KOG1700|consensus
Probab=98.89 E-value=3.8e-10 Score=100.56 Aligned_cols=108 Identities=20% Similarity=0.366 Sum_probs=77.2
Q ss_pred CcchhhhhccCCcc-ccccccCCc---cccccccccCCCccCccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy11691 9 HHKHYQRSYLGGAV-VNALDFGSG---VAAARYLFHSIDLGDQLTNSNTDNPLSLPGVDVPQKTTSPAHREPGAPRAPSQ 84 (271)
Q Consensus 9 ~~~~~~~~~~~~~~-~~~~g~g~~---~g~~~~~~~s~d~g~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~ps~ 84 (271)
+-..||+.+++-++ ++++|||.| ++. +.+|.++....... +.+
T Consensus 53 e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~----------------------------~~~ 99 (200)
T KOG1700|consen 53 EGVPYCKNCHVAQFGPKGGGFGKGFQKAGG-----LGKDGKSLNESKPN----------------------------QSA 99 (200)
T ss_pred ccccccccchHhhhCcccccccccccccCC-----CCcccccccccccc----------------------------cch
Confidence 34689999887777 999999998 444 55552222222110 001
Q ss_pred CCCCCCCCcCCCcccccCceeecceeEEeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCC
Q psy11691 85 PPSTLPGSLKLNSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPD 152 (271)
Q Consensus 85 ~~~~~~g~~~s~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~ 152 (271)
......| ....|..|.+.||+.|.+...+..||+.||+|..|+..|+.++|...+ +.+||..++.
T Consensus 100 ~~~~~~g--~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~-g~l~~~~~~~ 164 (200)
T KOG1700|consen 100 KFQVFAG--EKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALE-GVLYCKHHFA 164 (200)
T ss_pred hHHhhhc--cccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcC-Cccccchhhh
Confidence 1111112 247899999999999999999999999999999999999999998864 6666655444
No 10
>COG0722 AroG 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]
Probab=98.73 E-value=2.1e-09 Score=101.72 Aligned_cols=56 Identities=14% Similarity=0.229 Sum_probs=45.2
Q ss_pred CCCCCCCCCcccCCCCCCccc-cchhcchhhhhhcccCCCCCceEEecCCccCchhh
Q psy11691 182 ELNSDKSTNLLTDSEPSTHCD-SNLVTASVESTNMERNMDNDDLNILNKCTTDDDKV 237 (271)
Q Consensus 182 ecFs~ks~~ll~d~~p~~~c~-~~~~~~~~e~~~~~~~~d~~~~~i~~~c~~~~~~~ 237 (271)
+..++..+..|..+.|.+.-. +++...|++..+|+.|.|||+|+||||||||||+-
T Consensus 12 ~~~~l~~p~~l~~~~pls~~~~~~v~~~R~~i~~Il~G~DdRLlvViGPCSiHD~~A 68 (351)
T COG0722 12 EIDPLITPAELKAEFPLSDEAAETVAQSRKEIEDILHGEDDRLLVVIGPCSIHDPEA 68 (351)
T ss_pred cccCCCCHHHHHHhCCCCHHHHHHHHHHHHHHHHHhcCCCCcEEEEEeCCccCCHHH
Confidence 445566677788888885555 55556666999999999999999999999999974
No 11
>KOG1702|consensus
Probab=98.64 E-value=1.5e-09 Score=97.56 Aligned_cols=60 Identities=22% Similarity=0.427 Sum_probs=55.0
Q ss_pred CcccccCceeecceeEEeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCCCccc
Q psy11691 96 NSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPDEEER 156 (271)
Q Consensus 96 ~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~~~ 156 (271)
..|..|++.||+.|++..+++.||+.||+|..|+.+|+..+|... |.++||..+|....+
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy-~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGY-DKKPYCNPHYPKQVA 64 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhcccc-ccCCCcCccccccee
Confidence 458899999999999999999999999999999999999999875 789999999987654
No 12
>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=98.60 E-value=2.8e-08 Score=64.19 Aligned_cols=37 Identities=27% Similarity=0.728 Sum_probs=33.4
Q ss_pred cccccCceeecc-eeEEeeCceeccccccccccCCccC
Q psy11691 97 SCSLCGEKVYLA-QRFAFNARLFHRTCFKCARCQSQLT 133 (271)
Q Consensus 97 kCa~Cgk~V~~~-ErI~a~gk~wH~~CFrC~~C~k~L~ 133 (271)
+|.+|++.|... ..+.+.++.||.+||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 599999999876 5678999999999999999999985
No 13
>KOG1700|consensus
Probab=98.59 E-value=7.6e-09 Score=92.25 Aligned_cols=60 Identities=30% Similarity=0.703 Sum_probs=55.1
Q ss_pred CCcccccCceeecceeEEeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCCCcc
Q psy11691 95 LNSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPDEEE 155 (271)
Q Consensus 95 s~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~~ 155 (271)
..+|..|++.||.++++...|..||+.||+|..|.+.|...++... ++.+||+.||...+
T Consensus 7 ~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~-e~~~yc~~~~~~~~ 66 (200)
T KOG1700|consen 7 TDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEH-EGVPYCKNCHVAQF 66 (200)
T ss_pred cchhhhccCcchHHHHHhccCcchhhhHHhcccccccccccccccc-ccccccccchHhhh
Confidence 4789999999999999999999999999999999999999999986 79999999875554
No 14
>KOG1703|consensus
Probab=98.54 E-value=2.3e-08 Score=99.17 Aligned_cols=92 Identities=15% Similarity=0.165 Sum_probs=77.6
Q ss_pred CCCcccccCceeecceeEEeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCCCcccccCCCCCCCCCCCCcee
Q psy11691 94 KLNSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPDEEERSLTDPLRSSDRPDGHHA 173 (271)
Q Consensus 94 ~s~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~~~~I~~rc~~~~~~~~~I~ 173 (271)
+.+.|..|...|...+.+.++++.||+.+|.|..|+..+..+.|... +|.+||..||...+.+.+.+|...+.. +.|.
T Consensus 302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~-~g~~~c~~~~~~~~~p~C~~C~~~i~~-~~v~ 379 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPREL-DGKILCHECFHAPFRPNCKRCLLPILE-EGVC 379 (479)
T ss_pred ccccccccccCcccceeEeeccccccccceeeccccccccCCCcccc-CCCccHHHHHHHhhCccccccCCchHH-hHhh
Confidence 45899999999954377899999999999999999999999888664 799999999999888888877765553 3444
Q ss_pred ecCccccCCCCCCC
Q psy11691 174 IGDDRYHAELNSDK 187 (271)
Q Consensus 174 ~gg~~YH~ecFs~k 187 (271)
+.+..||++||.|.
T Consensus 380 a~~~~wH~~cf~C~ 393 (479)
T KOG1703|consen 380 ALGRLWHPECFVCA 393 (479)
T ss_pred hccCeechhceeee
Confidence 55899999999975
No 15
>TIGR00034 aroFGH phospho-2-dehydro-3-deoxyheptonate aldolase.
Probab=98.37 E-value=7.8e-08 Score=92.13 Aligned_cols=54 Identities=15% Similarity=0.241 Sum_probs=46.3
Q ss_pred CCCCCCCCcccCCCCC-CccccchhcchhhhhhcccCCCCCceEEecCCccCchh
Q psy11691 183 LNSDKSTNLLTDSEPS-THCDSNLVTASVESTNMERNMDNDDLNILNKCTTDDDK 236 (271)
Q Consensus 183 cFs~ks~~ll~d~~p~-~~c~~~~~~~~~e~~~~~~~~d~~~~~i~~~c~~~~~~ 236 (271)
..++.++..|.++.|. ..-..++...|.+..+|++|.|+|+|+|+|||||||++
T Consensus 8 ~~~l~~p~~l~~~~Pl~~~~~~~v~~~R~~i~~Il~g~d~rllvIvGPCSIhd~~ 62 (344)
T TIGR00034 8 IDELLTPAELAAKFPLTPKQAANVAQSRQEIADIIAGKDDRLLVVIGPCSIHDPE 62 (344)
T ss_pred cccCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHhcCCCCCeEEEecCCCCCCHH
Confidence 4456677888888888 55667888888899999999999999999999999986
No 16
>PRK12756 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional
Probab=98.36 E-value=7.9e-08 Score=92.06 Aligned_cols=55 Identities=15% Similarity=0.202 Sum_probs=46.9
Q ss_pred CCCCCCCCcccCCCCC-CccccchhcchhhhhhcccCCCCCceEEecCCccCchhh
Q psy11691 183 LNSDKSTNLLTDSEPS-THCDSNLVTASVESTNMERNMDNDDLNILNKCTTDDDKV 237 (271)
Q Consensus 183 cFs~ks~~ll~d~~p~-~~c~~~~~~~~~e~~~~~~~~d~~~~~i~~~c~~~~~~~ 237 (271)
..++.++..|.++.|. ..-..++...|.+..+|++|+|||+|+|+|||||||++-
T Consensus 12 ~~~L~~P~~l~~~~Pl~~~~~~~v~~~R~~I~~Il~g~d~rllvIvGPCSIhd~~~ 67 (348)
T PRK12756 12 IESLITPAELASEYPITPDVADHVTDSRRRIEKILNGEDPRLLVIIGPCSIHDTDA 67 (348)
T ss_pred cccCCCHHHHHHhCCCCHHHHHHHHHHHHHHHHHhcCCCCceEEEecCCcCCCHHH
Confidence 4456778888888888 555577788888999999999999999999999999874
No 17
>PRK12755 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional
Probab=98.33 E-value=1e-07 Score=91.54 Aligned_cols=56 Identities=11% Similarity=0.181 Sum_probs=47.5
Q ss_pred CCCCCCCCCcccCCCCC-CccccchhcchhhhhhcccCCCCCceEEecCCccCchhh
Q psy11691 182 ELNSDKSTNLLTDSEPS-THCDSNLVTASVESTNMERNMDNDDLNILNKCTTDDDKV 237 (271)
Q Consensus 182 ecFs~ks~~ll~d~~p~-~~c~~~~~~~~~e~~~~~~~~d~~~~~i~~~c~~~~~~~ 237 (271)
...++.++..|.++.|. ..-..++...|.+..+|++|.|||+|+|+|||||||++-
T Consensus 13 ~~~~l~~p~~l~~~~P~~~~~~~~v~~~R~~i~~Il~g~d~rllvI~GPCSI~d~~~ 69 (353)
T PRK12755 13 AEQPLITPEELKAELPLSEAAQAQVAASRQAIADILHGRDDRLLVVVGPCSIHDPEA 69 (353)
T ss_pred ccccCCCHHHHHHhCCCCHHHHHHHHHHHHHHHHHhcCCCCCeEEEeCCCCCCCHHH
Confidence 34556778888888888 556677888888999999999999999999999999973
No 18
>PRK12822 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional
Probab=98.31 E-value=1.2e-07 Score=90.94 Aligned_cols=54 Identities=17% Similarity=0.189 Sum_probs=45.6
Q ss_pred CCCCCCCCcccCCCCC-CccccchhcchhhhhhcccCCCCCceEEecCCccCchh
Q psy11691 183 LNSDKSTNLLTDSEPS-THCDSNLVTASVESTNMERNMDNDDLNILNKCTTDDDK 236 (271)
Q Consensus 183 cFs~ks~~ll~d~~p~-~~c~~~~~~~~~e~~~~~~~~d~~~~~i~~~c~~~~~~ 236 (271)
..++.++..|.++.|. ..-..++...|++..+|++|+|||+|+|+|||||||++
T Consensus 13 ~~~L~~P~~l~~~~Pl~~~~~~~v~~~R~~I~~Il~g~d~rllvIvGPCSIhd~~ 67 (356)
T PRK12822 13 CGSLPSVAEILKEIPCSEETETWISQQRQDIRNILLGKDPRLLVIIGPCSIHDPQ 67 (356)
T ss_pred cccCCCHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCeEEEEcCCcCCCHH
Confidence 3446677778888888 55557788888899999999999999999999999986
No 19
>PRK09261 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated
Probab=98.23 E-value=2.5e-07 Score=88.91 Aligned_cols=54 Identities=17% Similarity=0.254 Sum_probs=47.0
Q ss_pred CCCCCCCCcccCCCCC-CccccchhcchhhhhhcccCCCCCceEEecCCccCchh
Q psy11691 183 LNSDKSTNLLTDSEPS-THCDSNLVTASVESTNMERNMDNDDLNILNKCTTDDDK 236 (271)
Q Consensus 183 cFs~ks~~ll~d~~p~-~~c~~~~~~~~~e~~~~~~~~d~~~~~i~~~c~~~~~~ 236 (271)
..++.++.-|.++.|. ..-..++...|.+..+|++|.|+|+|+|+|||||||++
T Consensus 13 ~~~l~~p~~l~~~~p~~~~~~~~v~~~R~~i~~Il~g~d~rllvI~GPCSIed~e 67 (349)
T PRK09261 13 IKPLIPPAELKEELPLTEEAAETVARSRKEIHNILHGKDDRLLVVVGPCSIHDPK 67 (349)
T ss_pred cccCCCHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCeEEEEcCCcCCCHH
Confidence 5567778888888888 55567788888899999999999999999999999997
No 20
>KOG1044|consensus
Probab=98.18 E-value=1.2e-06 Score=88.24 Aligned_cols=79 Identities=19% Similarity=0.326 Sum_probs=64.7
Q ss_pred CcccccCceeecceeEEeeCceeccccccccccCCccCCcCeeecCCCeeeccCCCCCcccccCCCCCCCCCCCCceeec
Q psy11691 96 NSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTCINAYETHTGQFCCEVCPDEEERSLTDPLRSSDRPDGHHAIG 175 (271)
Q Consensus 96 ~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~~~~I~~rc~~~~~~~~~I~~g 175 (271)
-.|..|++.- .+|++.+.++.||..||.|.+|++.|..+.|+...+.+.||.. .|...++ ++.|.+.
T Consensus 17 i~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~-----------~c~~~~~-gevvsa~ 83 (670)
T KOG1044|consen 17 IKCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTD-----------DCRAFVE-GEVVSTL 83 (670)
T ss_pred eehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccceeeccc-----------chhhhcc-ceeEecc
Confidence 5799999998 5999999999999999999999999999999987656777751 1222222 3577889
Q ss_pred CccccCCCCCCC
Q psy11691 176 DDRYHAELNSDK 187 (271)
Q Consensus 176 g~~YH~ecFs~k 187 (271)
|..||+.||.|.
T Consensus 84 gktyh~~cf~cs 95 (670)
T KOG1044|consen 84 GKTYHPKCFSCS 95 (670)
T ss_pred cceeccccceec
Confidence 999999999974
No 21
>KOG4577|consensus
Probab=97.76 E-value=3.7e-06 Score=79.11 Aligned_cols=62 Identities=23% Similarity=0.441 Sum_probs=53.8
Q ss_pred CCcccccCceeecceeE-EeeCceeccccccccccCCccCCc-CeeecCCCeeeccCCCCCccc
Q psy11691 95 LNSCSLCGEKVYLAQRF-AFNARLFHRTCFKCARCQSQLTCI-NAYETHTGQFCCEVCPDEEER 156 (271)
Q Consensus 95 s~kCa~Cgk~V~~~ErI-~a~gk~wH~~CFrC~~C~k~L~s~-~f~~~~dG~~yCk~CY~~~~~ 156 (271)
..+|..|.+.|.+.+.| .+.+..||..||-|..|+++|+.+ .||..+|.+.+|+..|+...+
T Consensus 92 GTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~ 155 (383)
T KOG4577|consen 92 GTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQ 155 (383)
T ss_pred CCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHh
Confidence 47899999999888876 588999999999999999999987 577778999999998875543
No 22
>PF00793 DAHP_synth_1: DAHP synthetase I family; InterPro: IPR006218 Members of the 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthetase family catalyse the first step in aromatic amino acid biosynthesis from chorismate. Class I includes bacterial and yeast enzymes; class II includes higher plants and various microorganisms (see IPR002480 from INTERPRO) []. The first step in the common pathway leading to the biosynthesis of aromatic compounds is the stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP). This reaction is catalyzed by DAHP synthase, a metal-activated enzyme, which in microorganisms is the target for negative-feedback regulation by pathway intermediates or by end products. In Escherichia coli there are three DAHP synthetase isoforms, each specifically inhibited by one of the three aromatic amino acids. The crystal structure of the phenylalanine-regulated form of DAHP synthetase shows the fold as is a (beta/alpha)8 barrel with several additional beta strands and alpha helices []. ; GO: 0009058 biosynthetic process; PDB: 3FS2_B 3STF_B 3FYP_D 3QQ1_A 3QPZ_C 3FYO_D 3STC_A 2QKF_D 3STE_C 3QQ0_A ....
Probab=96.63 E-value=0.0009 Score=62.41 Aligned_cols=23 Identities=17% Similarity=0.343 Sum_probs=19.9
Q ss_pred hcccCCCCCceEEecCCccCchh
Q psy11691 214 NMERNMDNDDLNILNKCTTDDDK 236 (271)
Q Consensus 214 ~~~~~~d~~~~~i~~~c~~~~~~ 236 (271)
+|+.|.|+|+++|+|||||||.+
T Consensus 8 ~i~~G~~~~l~viaGPCsies~e 30 (270)
T PF00793_consen 8 DILIGKDKRLLVIAGPCSIESEE 30 (270)
T ss_dssp TEEETTTSSEEEEEEESB-S-HH
T ss_pred CeEecCCCceEEEEECCccCCHH
Confidence 89999999999999999999965
No 23
>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=89.46 E-value=0.31 Score=30.73 Aligned_cols=19 Identities=11% Similarity=-0.087 Sum_probs=14.5
Q ss_pred ceeecCccccCCCCCCCCC
Q psy11691 171 HHAIGDDRYHAELNSDKST 189 (271)
Q Consensus 171 ~I~~gg~~YH~ecFs~ks~ 189 (271)
.+.+++..||++||.|..+
T Consensus 15 ~~~~~~~~~H~~Cf~C~~C 33 (39)
T smart00132 15 VLRALGKVWHPECFKCSKC 33 (39)
T ss_pred EEEeCCccccccCCCCccc
Confidence 4456788999999995543
No 24
>PRK13398 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=88.77 E-value=0.25 Score=46.08 Aligned_cols=20 Identities=10% Similarity=0.346 Sum_probs=16.3
Q ss_pred cCCCCCceEEecCCccCchhh
Q psy11691 217 RNMDNDDLNILNKCTTDDDKV 237 (271)
Q Consensus 217 ~~~d~~~~~i~~~c~~~~~~~ 237 (271)
-|-+ |+++|.|||||||.+.
T Consensus 23 ~g~~-~~~~iaGPCsie~~~~ 42 (266)
T PRK13398 23 IGGE-EKIIIAGPCAVESEEQ 42 (266)
T ss_pred EcCC-CEEEEEeCCcCCCHHH
Confidence 3444 9999999999999764
No 25
>PRK13396 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=87.90 E-value=0.29 Score=47.63 Aligned_cols=25 Identities=4% Similarity=0.252 Sum_probs=21.7
Q ss_pred hhcccCCCCCceEEecCCccCchhh
Q psy11691 213 TNMERNMDNDDLNILNKCTTDDDKV 237 (271)
Q Consensus 213 ~~~~~~~d~~~~~i~~~c~~~~~~~ 237 (271)
.++.-|-|+++++|.|||||||.+-
T Consensus 92 ~~v~iGg~~~l~vIAGPCsIEs~eq 116 (352)
T PRK13396 92 GPVPFGENHPVVVVAGPCSVENEEM 116 (352)
T ss_pred CCeEecCCCeEEEEEeCCcccCHHH
Confidence 4577888999999999999999873
No 26
>KOG0490|consensus
Probab=85.51 E-value=0.15 Score=44.68 Aligned_cols=51 Identities=24% Similarity=0.526 Sum_probs=39.4
Q ss_pred cCceeecceeEEeeCceeccccccccccCCccC--CcCeeecCCCeeeccCCCCC
Q psy11691 101 CGEKVYLAQRFAFNARLFHRTCFKCARCQSQLT--CINAYETHTGQFCCEVCPDE 153 (271)
Q Consensus 101 Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~--s~~f~~~~dG~~yCk~CY~~ 153 (271)
|+..|.....+...+..||..|..|..|...|. ...| .. +|..||...|..
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~g~~~~~~d~~~ 54 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCF-SK-DGSIYCKRDYQR 54 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcc-cC-CCcccccccchh
Confidence 566664333455669999999999999999998 4334 33 799999999987
No 27
>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=85.08 E-value=0.58 Score=32.48 Aligned_cols=16 Identities=13% Similarity=-0.014 Sum_probs=13.1
Q ss_pred eecCccccCCCCCCCC
Q psy11691 173 AIGDDRYHAELNSDKS 188 (271)
Q Consensus 173 ~~gg~~YH~ecFs~ks 188 (271)
.++|..||++||.|..
T Consensus 16 ~~~~~~~H~~Cf~C~~ 31 (58)
T PF00412_consen 16 KAMGKFWHPECFKCSK 31 (58)
T ss_dssp EETTEEEETTTSBETT
T ss_pred EeCCcEEEccccccCC
Confidence 4888999999999543
No 28
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=81.48 E-value=0.67 Score=37.72 Aligned_cols=31 Identities=32% Similarity=0.789 Sum_probs=25.8
Q ss_pred cccccCceeecceeEEe-eCceeccccccccc
Q psy11691 97 SCSLCGEKVYLAQRFAF-NARLFHRTCFKCAR 127 (271)
Q Consensus 97 kCa~Cgk~V~~~ErI~a-~gk~wH~~CFrC~~ 127 (271)
+|..|++.|+.+|..++ .+..-|-+||+=..
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 69999999999998775 35889999997443
No 29
>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=75.25 E-value=2.2 Score=32.97 Aligned_cols=31 Identities=23% Similarity=0.475 Sum_probs=20.1
Q ss_pred CCCcccccCceeecceeEE-eeCceecccccc
Q psy11691 94 KLNSCSLCGEKVYLAQRFA-FNARLFHRTCFK 124 (271)
Q Consensus 94 ~s~kCa~Cgk~V~~~ErI~-a~gk~wH~~CFr 124 (271)
....|+.|++.+.....+. -.|..+|..|++
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 3466888888885433332 346778888864
No 30
>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=73.30 E-value=3.1 Score=32.10 Aligned_cols=29 Identities=21% Similarity=0.283 Sum_probs=24.0
Q ss_pred cccccCCccCCcCeeecCCCeeeccCCCC
Q psy11691 124 KCARCQSQLTCINAYETHTGQFCCEVCPD 152 (271)
Q Consensus 124 rC~~C~k~L~s~~f~~~~dG~~yCk~CY~ 152 (271)
.|..|++.|....|....+|..+...|..
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 59999999999888777778888877765
No 31
>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=71.88 E-value=2.9 Score=27.77 Aligned_cols=25 Identities=28% Similarity=0.708 Sum_probs=18.2
Q ss_pred ccccccCCccCCcCeeecCCCeeeccCCCC
Q psy11691 123 FKCARCQSQLTCINAYETHTGQFCCEVCPD 152 (271)
Q Consensus 123 FrC~~C~k~L~s~~f~~~~dG~~yCk~CY~ 152 (271)
+.|.+|+.. .|.. +||.+||..|..
T Consensus 9 ~~C~~C~~~----~~~~-~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYS-DDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEc-cCCEEEhhhCce
Confidence 458888865 2333 589999988865
No 32
>PRK08673 3-deoxy-7-phosphoheptulonate synthase; Reviewed
Probab=66.83 E-value=3.4 Score=40.02 Aligned_cols=25 Identities=16% Similarity=0.380 Sum_probs=20.8
Q ss_pred CCCceEEecCCccCch--------hhhhcccce
Q psy11691 220 DNDDLNILNKCTTDDD--------KVNSVQNSI 244 (271)
Q Consensus 220 d~~~~~i~~~c~~~~~--------~~~~~~~~~ 244 (271)
|+++++|.||||++|. .|+++..++
T Consensus 91 ~~~~~~IAGPCsiEs~e~~~~~A~~lk~~ga~~ 123 (335)
T PRK08673 91 GGKPVVIAGPCSVESEEQILEIARAVKEAGAQI 123 (335)
T ss_pred CCceEEEEecCccCCHHHHHHHHHHHHHhchhh
Confidence 7899999999999998 677666654
No 33
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=63.16 E-value=4.7 Score=29.37 Aligned_cols=37 Identities=24% Similarity=0.623 Sum_probs=25.5
Q ss_pred CCcccccCceeeccee-EE--eeCceeccccc----cccc--cCCc
Q psy11691 95 LNSCSLCGEKVYLAQR-FA--FNARLFHRTCF----KCAR--CQSQ 131 (271)
Q Consensus 95 s~kCa~Cgk~V~~~Er-I~--a~gk~wH~~CF----rC~~--C~k~ 131 (271)
..+|..|++.|..++- |. .-+..||++|. .|.. |+..
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~ 50 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTG 50 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCC
Confidence 4789999999965553 33 34789999997 4555 5443
No 34
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=57.21 E-value=7.3 Score=26.27 Aligned_cols=27 Identities=19% Similarity=0.701 Sum_probs=18.8
Q ss_pred ccccCceeeccee--EEeeCceeccccccc
Q psy11691 98 CSLCGEKVYLAQR--FAFNARLFHRTCFKC 125 (271)
Q Consensus 98 Ca~Cgk~V~~~Er--I~a~gk~wH~~CFrC 125 (271)
|.-||+.|. ++- +...++.||--|-.|
T Consensus 1 Cd~CG~~I~-~eP~~~k~~~~~y~fCC~tC 29 (37)
T PF08394_consen 1 CDYCGGEIT-GEPIVVKIGNKVYYFCCPTC 29 (37)
T ss_pred CCccCCccc-CCEEEEEECCeEEEEECHHH
Confidence 678999984 453 567889998555444
No 35
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=51.83 E-value=3.8 Score=29.13 Aligned_cols=30 Identities=23% Similarity=0.700 Sum_probs=21.8
Q ss_pred cccccCCccCCcCeeecCCCeeeccCCCCCc
Q psy11691 124 KCARCQSQLTCINAYETHTGQFCCEVCPDEE 154 (271)
Q Consensus 124 rC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~ 154 (271)
.|..|+..+..-.-+...|| +.|..|+.+.
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 48888888876543444678 7999999853
No 36
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=51.65 E-value=7.8 Score=35.30 Aligned_cols=31 Identities=19% Similarity=0.575 Sum_probs=19.2
Q ss_pred ccccccCCccCCcCeeecCCCeeeccCCCCCc
Q psy11691 123 FKCARCQSQLTCINAYETHTGQFCCEVCPDEE 154 (271)
Q Consensus 123 FrC~~C~k~L~s~~f~~~~dG~~yCk~CY~~~ 154 (271)
-+|.+|+...-...-.. .+|+++|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~-~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVV-LNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhh-cCCceecccccccc
Confidence 46666665544322222 37889999999854
No 37
>PRK00807 50S ribosomal protein L24e; Validated
Probab=47.36 E-value=15 Score=26.15 Aligned_cols=32 Identities=19% Similarity=0.610 Sum_probs=22.8
Q ss_pred CcccccCceeeccee---EEeeCceeccccccccccCC
Q psy11691 96 NSCSLCGEKVYLAQR---FAFNARLFHRTCFKCARCQS 130 (271)
Q Consensus 96 ~kCa~Cgk~V~~~Er---I~a~gk~wH~~CFrC~~C~k 130 (271)
..|..||..|++++- +..+|+.|. |.+..|.+
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~---Fcs~KC~~ 36 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILY---FCSSKCEK 36 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEE---EeCHHHHH
Confidence 469999999997774 456788887 44445543
No 38
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=46.04 E-value=8 Score=31.80 Aligned_cols=30 Identities=17% Similarity=0.397 Sum_probs=25.9
Q ss_pred hhcccCCCCCceEEecCCccCchhhhhccc
Q psy11691 213 TNMERNMDNDDLNILNKCTTDDDKVNSVQN 242 (271)
Q Consensus 213 ~~~~~~~d~~~~~i~~~c~~~~~~~~~~~~ 242 (271)
|++..|+-+++..||=||-.|||+++.-.+
T Consensus 52 CRl~~g~eeedk~ivCPCvy~~ddi~e~g~ 81 (110)
T COG4802 52 CRLVTGKEEEDKDIVCPCVYRDDDIREYGE 81 (110)
T ss_pred eecccCCHHHhhceeccCcCCccchhhhCc
Confidence 677888888888899999999999987655
No 39
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=44.91 E-value=11 Score=22.53 Aligned_cols=8 Identities=25% Similarity=1.173 Sum_probs=3.6
Q ss_pred ccccCCcc
Q psy11691 125 CARCQSQL 132 (271)
Q Consensus 125 C~~C~k~L 132 (271)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 44444444
No 40
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=41.81 E-value=20 Score=34.31 Aligned_cols=42 Identities=29% Similarity=0.541 Sum_probs=30.4
Q ss_pred cCCCcccccCceeecceeEEee-----C-----ceeccccccccccCCccCC
Q psy11691 93 LKLNSCSLCGEKVYLAQRFAFN-----A-----RLFHRTCFKCARCQSQLTC 134 (271)
Q Consensus 93 ~~s~kCa~Cgk~V~~~ErI~a~-----g-----k~wH~~CFrC~~C~k~L~s 134 (271)
.|+-.|..|+.+||.|-+..+. + -...+=-|+|..|...+.-
T Consensus 38 Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~~ 89 (324)
T PF04502_consen 38 PFNIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIEF 89 (324)
T ss_pred CccCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEee
Confidence 4678999999999988875432 2 3334446789999887743
No 41
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=41.53 E-value=13 Score=30.30 Aligned_cols=36 Identities=22% Similarity=0.556 Sum_probs=26.8
Q ss_pred CcccccCceeecceeEEe-eCceeccccccccccCCc
Q psy11691 96 NSCSLCGEKVYLAQRFAF-NARLFHRTCFKCARCQSQ 131 (271)
Q Consensus 96 ~kCa~Cgk~V~~~ErI~a-~gk~wH~~CFrC~~C~k~ 131 (271)
-+|..|++.|..+|+.++ ....-|-+||-=..-++.
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~ 43 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKP 43 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCc
Confidence 579999999988888764 356788888865555544
No 42
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=36.15 E-value=24 Score=30.10 Aligned_cols=23 Identities=30% Similarity=0.818 Sum_probs=17.4
Q ss_pred cccccCCccCCcCeeecCCCeeeccCCCC
Q psy11691 124 KCARCQSQLTCINAYETHTGQFCCEVCPD 152 (271)
Q Consensus 124 rC~~C~k~L~s~~f~~~~dG~~yCk~CY~ 152 (271)
-|..|+.+| |- .+|.+||..|-.
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 377888887 33 379999999873
No 43
>TIGR01361 DAHP_synth_Bsub phospho-2-dehydro-3-deoxyheptonate aldolase. The member of this family from Synechocystis PCC 6803, CcmA, was shown to be essential for carboxysome formation. However, no other candidate for this enzyme is present in that species, chorismate biosynthesis does occur, other species having this protein lack carboxysomes but appear to make chorismate, and a requirement of CcmA for carboxysome formation does not prohibit a role in chorismate biosynthesis.
Probab=35.31 E-value=23 Score=32.84 Aligned_cols=16 Identities=13% Similarity=0.490 Sum_probs=13.8
Q ss_pred CCceEEecCCccCchh
Q psy11691 221 NDDLNILNKCTTDDDK 236 (271)
Q Consensus 221 ~~~~~i~~~c~~~~~~ 236 (271)
+.+++|.|||+|+|.+
T Consensus 24 ~~~~~IAGpc~ie~~~ 39 (260)
T TIGR01361 24 GSPIVIAGPCSVESEE 39 (260)
T ss_pred CcEEEEEeCCccCCHH
Confidence 3388899999999988
No 44
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=34.48 E-value=21 Score=36.21 Aligned_cols=40 Identities=25% Similarity=0.394 Sum_probs=30.8
Q ss_pred CCcccccCceeecceeEEeeCceeccccccccccCCccCCc
Q psy11691 95 LNSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTCI 135 (271)
Q Consensus 95 s~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s~ 135 (271)
+.-|+.|..-+-.. .+...+..-.++||.|-.|..+|...
T Consensus 26 ~~yCp~CL~~~p~~-e~~~~~nrC~r~Cf~CP~C~~~L~~~ 65 (483)
T PF05502_consen 26 SYYCPNCLFEVPSS-EARSEKNRCSRNCFDCPICFSPLSVR 65 (483)
T ss_pred eeECccccccCChh-hheeccceeccccccCCCCCCcceeE
Confidence 46699998777333 35566777888999999999999774
No 45
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=31.31 E-value=25 Score=21.89 Aligned_cols=26 Identities=23% Similarity=0.531 Sum_probs=13.1
Q ss_pred ccccCceeecceeEEeeCceeccccc
Q psy11691 98 CSLCGEKVYLAQRFAFNARLFHRTCF 123 (271)
Q Consensus 98 Ca~Cgk~V~~~ErI~a~gk~wH~~CF 123 (271)
|..|.+.+...-.+..-+..||..|+
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~ 27 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCI 27 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHH
Confidence 66666655111112224666766666
No 46
>KOG1829|consensus
Probab=29.63 E-value=20 Score=37.35 Aligned_cols=39 Identities=18% Similarity=0.535 Sum_probs=28.1
Q ss_pred ccccccccCCccCCcC-----eeecCCCeeeccCCCCCcccccCC
Q psy11691 121 TCFKCARCQSQLTCIN-----AYETHTGQFCCEVCPDEEERSLTD 160 (271)
Q Consensus 121 ~CFrC~~C~k~L~s~~-----f~~~~dG~~yCk~CY~~~~~~I~~ 160 (271)
.=|+|+.|+.+|+... |... .|.+||..|+......|-+
T Consensus 339 Q~~~CAgC~~~i~~~~~~~~R~C~y-~G~y~C~~Ch~~~~svIPA 382 (580)
T KOG1829|consen 339 QNFRCAGCGHTIGPDLEQRPRLCRY-LGKYFCDCCHQNDKSVIPA 382 (580)
T ss_pred cCceecccCCCcccccccchhHhhh-hhhhhCchhcccCcccccc
Confidence 4589999999998532 2344 5899999999877655543
No 47
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=29.37 E-value=22 Score=22.98 Aligned_cols=31 Identities=16% Similarity=0.521 Sum_probs=17.6
Q ss_pred cccccCceeecce-eEEeeCceeccccccccccCCcc
Q psy11691 97 SCSLCGEKVYLAQ-RFAFNARLFHRTCFKCARCQSQL 132 (271)
Q Consensus 97 kCa~Cgk~V~~~E-rI~a~gk~wH~~CFrC~~C~k~L 132 (271)
.|+.|+..+...+ .+...+. -++|..|+..|
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~-----~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGG-----KVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCC-----EEECCCCCCEE
Confidence 4788887664433 2322222 36777777665
No 48
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=29.22 E-value=20 Score=27.79 Aligned_cols=30 Identities=20% Similarity=0.447 Sum_probs=20.9
Q ss_pred cccccCCccCCcCeeec-CC---CeeeccCCCCC
Q psy11691 124 KCARCQSQLTCINAYET-HT---GQFCCEVCPDE 153 (271)
Q Consensus 124 rC~~C~k~L~s~~f~~~-~d---G~~yCk~CY~~ 153 (271)
.|..|+.+|.....+.+ .| ..-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 48889999988763322 12 35699999984
No 49
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=28.91 E-value=22 Score=28.97 Aligned_cols=28 Identities=25% Similarity=0.497 Sum_probs=16.9
Q ss_pred ccccccCCccCCcCeeecCCCeeeccCC
Q psy11691 123 FKCARCQSQLTCINAYETHTGQFCCEVC 150 (271)
Q Consensus 123 FrC~~C~k~L~s~~f~~~~dG~~yCk~C 150 (271)
|.|..|-.--+.......++|.++|..|
T Consensus 71 FTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 71 FTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred eeeeeeeeEechhhhccccCCCEecccc
Confidence 7777774333332222224789999888
No 50
>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=27.93 E-value=46 Score=22.73 Aligned_cols=21 Identities=29% Similarity=0.896 Sum_probs=11.8
Q ss_pred ccccCCccCCcCeeecCCCeeeccCC
Q psy11691 125 CARCQSQLTCINAYETHTGQFCCEVC 150 (271)
Q Consensus 125 C~~C~k~L~s~~f~~~~dG~~yCk~C 150 (271)
|..|+.+|-. . ++|+.||..|
T Consensus 20 Cp~C~~PL~~----~-k~g~~~Cv~C 40 (41)
T PF06677_consen 20 CPDCGTPLMR----D-KDGKIYCVSC 40 (41)
T ss_pred cCCCCCeeEE----e-cCCCEECCCC
Confidence 4456655532 2 3567777665
No 51
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=27.58 E-value=34 Score=25.64 Aligned_cols=14 Identities=21% Similarity=0.544 Sum_probs=11.0
Q ss_pred CcccccCceeecce
Q psy11691 96 NSCSLCGEKVYLAQ 109 (271)
Q Consensus 96 ~kCa~Cgk~V~~~E 109 (271)
..|..|++.|.-++
T Consensus 8 a~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 8 AKCKGCKKKIAKGE 21 (82)
T ss_dssp EBETTTSCBE-TTS
T ss_pred ccCcccCCcCCCCC
Confidence 57999999997666
No 52
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=26.97 E-value=41 Score=20.62 Aligned_cols=7 Identities=29% Similarity=0.971 Sum_probs=2.8
Q ss_pred cccCcee
Q psy11691 99 SLCGEKV 105 (271)
Q Consensus 99 a~Cgk~V 105 (271)
..|+..|
T Consensus 2 ~sC~~~i 8 (24)
T PF07754_consen 2 TSCGRPI 8 (24)
T ss_pred ccCCCcc
Confidence 3344433
No 53
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=26.89 E-value=40 Score=20.41 Aligned_cols=8 Identities=38% Similarity=1.302 Sum_probs=3.6
Q ss_pred ccccCcee
Q psy11691 98 CSLCGEKV 105 (271)
Q Consensus 98 Ca~Cgk~V 105 (271)
|..|+..|
T Consensus 5 Cp~Cg~~~ 12 (26)
T PF13248_consen 5 CPNCGAEI 12 (26)
T ss_pred CcccCCcC
Confidence 44444433
No 54
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=26.46 E-value=46 Score=24.69 Aligned_cols=14 Identities=21% Similarity=0.629 Sum_probs=8.8
Q ss_pred CcccccCceeecce
Q psy11691 96 NSCSLCGEKVYLAQ 109 (271)
Q Consensus 96 ~kCa~Cgk~V~~~E 109 (271)
++|..|+..|.+.+
T Consensus 8 ~~CtSCg~~i~~~~ 21 (59)
T PRK14890 8 PKCTSCGIEIAPRE 21 (59)
T ss_pred ccccCCCCcccCCC
Confidence 45777777765444
No 55
>KOG3579|consensus
Probab=26.15 E-value=1.5e+02 Score=28.73 Aligned_cols=32 Identities=28% Similarity=0.606 Sum_probs=19.9
Q ss_pred CcccccCceeecceeEEeeCceeccccccccc
Q psy11691 96 NSCSLCGEKVYLAQRFAFNARLFHRTCFKCAR 127 (271)
Q Consensus 96 ~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~ 127 (271)
-.|..|++.+...-+|..-.-.-|+=||-|..
T Consensus 269 LcCTLC~ERLEDTHFVQCPSVp~HKFCFPCSR 300 (352)
T KOG3579|consen 269 LCCTLCHERLEDTHFVQCPSVPSHKFCFPCSR 300 (352)
T ss_pred eeehhhhhhhccCceeecCCCcccceecccCH
Confidence 44666776665555566666666666666653
No 56
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=25.63 E-value=25 Score=30.99 Aligned_cols=31 Identities=19% Similarity=0.489 Sum_probs=22.5
Q ss_pred CcccccCceeecceeEEeeCceeccccccccccCCccCC
Q psy11691 96 NSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTC 134 (271)
Q Consensus 96 ~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s 134 (271)
-.|+.|+..+...|.+. .=|.|..|+..|.-
T Consensus 118 Y~Cp~C~~rytf~eA~~--------~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 118 FFCPNCHIRFTFDEAME--------YGFRCPQCGEMLEE 148 (178)
T ss_pred EECCCCCcEEeHHHHhh--------cCCcCCCCCCCCee
Confidence 56999987775555432 24999999999854
No 57
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=25.12 E-value=22 Score=30.58 Aligned_cols=31 Identities=19% Similarity=0.421 Sum_probs=22.8
Q ss_pred CcccccCceeecceeEEeeCceeccccccccccCCccCC
Q psy11691 96 NSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTC 134 (271)
Q Consensus 96 ~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s 134 (271)
-.|+.|+..+...|.+. .=|.|..|+..|.-
T Consensus 110 Y~Cp~c~~r~tf~eA~~--------~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 110 FICPNMCVRFTFNEAME--------LNFTCPRCGAMLDY 140 (158)
T ss_pred EECCCCCcEeeHHHHHH--------cCCcCCCCCCEeee
Confidence 56999997775555443 24999999999854
No 58
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=25.00 E-value=65 Score=21.52 Aligned_cols=27 Identities=26% Similarity=0.725 Sum_probs=16.4
Q ss_pred ccccccCCccCCcCeeecCCCeeeccCCCC
Q psy11691 123 FKCARCQSQLTCINAYETHTGQFCCEVCPD 152 (271)
Q Consensus 123 FrC~~C~k~L~s~~f~~~~dG~~yCk~CY~ 152 (271)
|+|..|+... -......|.++|..|-.
T Consensus 1 m~Cp~Cg~~~---~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 1 MKCPNCGSKE---IVFDPERGELVCPNCGL 27 (43)
T ss_dssp ESBTTTSSSE---EEEETTTTEEEETTT-B
T ss_pred CCCcCCcCCc---eEEcCCCCeEECCCCCC
Confidence 4677777643 12333458888988854
No 59
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=24.53 E-value=23 Score=24.12 Aligned_cols=27 Identities=37% Similarity=0.607 Sum_probs=13.6
Q ss_pred ccccCceeecceeEE--eeCceecccccc
Q psy11691 98 CSLCGEKVYLAQRFA--FNARLFHRTCFK 124 (271)
Q Consensus 98 Ca~Cgk~V~~~ErI~--a~gk~wH~~CFr 124 (271)
|..|.+.|..+++-. -=+-.||..||.
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~ 29 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFK 29 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHH
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHH
Confidence 677888887676543 234569998884
No 60
>PHA03357 Alkaline exonuclease; Provisional
Probab=24.02 E-value=1.2e+02 Score=23.78 Aligned_cols=25 Identities=20% Similarity=0.052 Sum_probs=16.4
Q ss_pred cccCCccc-cccccccCCCccCcccc
Q psy11691 26 LDFGSGVA-AARYLFHSIDLGDQLTN 50 (271)
Q Consensus 26 ~g~g~~~g-~~~~~~~s~d~g~~~~~ 50 (271)
||-||=-+ |+|+-.|-|-+||.|..
T Consensus 7 ~g~gg~C~~CkR~N~LvT~sGetvaL 32 (81)
T PHA03357 7 SGRGGICGLCKRYNELVTCDGETLAL 32 (81)
T ss_pred ccCCceechhcccCeEEecCCcEEEe
Confidence 44444333 34888888888998874
No 61
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=23.63 E-value=21 Score=25.15 Aligned_cols=35 Identities=26% Similarity=0.621 Sum_probs=24.1
Q ss_pred CcccccCceeecceeEEeeCceeccccccccccCCcc
Q psy11691 96 NSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQL 132 (271)
Q Consensus 96 ~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L 132 (271)
-.|..|.+.+..-.......+..|+ ++|..|+..|
T Consensus 7 v~C~~C~~lLqlP~~~~~~~k~~~k--lrCGaCs~vl 41 (46)
T PF11331_consen 7 VVCSSCFELLQLPAKFSLSKKNQQK--LRCGACSEVL 41 (46)
T ss_pred eECccHHHHHcCCCccCCCccceeE--EeCCCCceeE
Confidence 3588888877655555555555555 7888888766
No 62
>PLN03033 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=23.61 E-value=50 Score=31.69 Aligned_cols=19 Identities=0% Similarity=0.013 Sum_probs=15.3
Q ss_pred CCCCCceEEecCCccCchh
Q psy11691 218 NMDNDDLNILNKCTTDDDK 236 (271)
Q Consensus 218 ~~d~~~~~i~~~c~~~~~~ 236 (271)
|-+..+++|-|||+|-+.+
T Consensus 12 ~~~~~~~lIAGPC~iEs~e 30 (290)
T PLN03033 12 KAAEPFFLLAGPNVIESEE 30 (290)
T ss_pred CCCCCeEEEecCChhcCHH
Confidence 3456688999999999976
No 63
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=22.41 E-value=50 Score=33.19 Aligned_cols=35 Identities=20% Similarity=0.453 Sum_probs=21.8
Q ss_pred CCCcccccCceeecceeEEeeCceeccccccccccCCccCCcCee
Q psy11691 94 KLNSCSLCGEKVYLAQRFAFNARLFHRTCFKCARCQSQLTCINAY 138 (271)
Q Consensus 94 ~s~kCa~Cgk~V~~~ErI~a~gk~wH~~CFrC~~C~k~L~s~~f~ 138 (271)
..++|..||... ...|+. -|||.+|+.......+.
T Consensus 349 ~~p~Cp~Cg~~m------~S~G~~----g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 349 VNPVCPRCGGRM------KSAGRN----GFRCKKCGTRARETLIK 383 (421)
T ss_pred cCCCCCccCCch------hhcCCC----CcccccccccCCccccc
Confidence 357788887654 333433 47888888777665443
No 64
>PRK12595 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed
Probab=21.84 E-value=51 Score=32.18 Aligned_cols=17 Identities=12% Similarity=0.339 Sum_probs=13.2
Q ss_pred CCceEEecCCccCchhh
Q psy11691 221 NDDLNILNKCTTDDDKV 237 (271)
Q Consensus 221 ~~~~~i~~~c~~~~~~~ 237 (271)
+..++|+|||++++.+.
T Consensus 117 ~~~~~iaGpc~iE~~~~ 133 (360)
T PRK12595 117 GNQSFIFGPCSVESYEQ 133 (360)
T ss_pred CCeeeEEecccccCHHH
Confidence 45677889999998653
No 65
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=21.48 E-value=40 Score=22.21 Aligned_cols=28 Identities=29% Similarity=0.691 Sum_probs=18.1
Q ss_pred cccccCceeecceeEEe--eCceecccccc
Q psy11691 97 SCSLCGEKVYLAQRFAF--NARLFHRTCFK 124 (271)
Q Consensus 97 kCa~Cgk~V~~~ErI~a--~gk~wH~~CFr 124 (271)
.|+-|.+.+...+.+.. =+..||.+|+.
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~ 31 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIK 31 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHH
Confidence 47778877754454332 36788888763
No 66
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.49 E-value=98 Score=32.75 Aligned_cols=25 Identities=24% Similarity=0.565 Sum_probs=12.2
Q ss_pred cccccCCccCCcCeeecCCCeeeccCCCC
Q psy11691 124 KCARCQSQLTCINAYETHTGQFCCEVCPD 152 (271)
Q Consensus 124 rC~~C~k~L~s~~f~~~~dG~~yCk~CY~ 152 (271)
+|..|+..|. |.. ..+...|.-|..
T Consensus 394 ~C~~C~~~L~---~h~-~~~~l~Ch~CG~ 418 (665)
T PRK14873 394 RCRHCTGPLG---LPS-AGGTPRCRWCGR 418 (665)
T ss_pred ECCCCCCcee---Eec-CCCeeECCCCcC
Confidence 4555555552 221 234555666644
No 67
>PRK00420 hypothetical protein; Validated
Probab=20.42 E-value=71 Score=26.45 Aligned_cols=25 Identities=24% Similarity=0.432 Sum_probs=16.3
Q ss_pred ccccccCCccCCcCeeecCCCeeeccCCCC
Q psy11691 123 FKCARCQSQLTCINAYETHTGQFCCEVCPD 152 (271)
Q Consensus 123 FrC~~C~k~L~s~~f~~~~dG~~yCk~CY~ 152 (271)
-.|..|+.+|-. . .+|..||..|-.
T Consensus 24 ~~CP~Cg~pLf~----l-k~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFE----L-KDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCccee----c-CCCceECCCCCC
Confidence 356677766622 1 368888888776
No 68
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=20.15 E-value=66 Score=23.28 Aligned_cols=25 Identities=28% Similarity=0.727 Sum_probs=18.9
Q ss_pred CCcccccCceeeccee---EEeeCceec
Q psy11691 95 LNSCSLCGEKVYLAQR---FAFNARLFH 119 (271)
Q Consensus 95 s~kCa~Cgk~V~~~Er---I~a~gk~wH 119 (271)
...|..|+..||++.. |..+|+.++
T Consensus 3 ~~~C~f~g~~I~PG~G~~~Vr~Dgkv~~ 30 (54)
T cd00472 3 TEKCSFCGYKIYPGHGKMYVRNDGKVFR 30 (54)
T ss_pred EEEecCcCCeecCCCccEEEecCCCEEE
Confidence 4679999999998874 455677665
Done!