Query psy12656
Match_columns 291
No_of_seqs 190 out of 1010
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 16:10:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12656.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12656hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00084 rpl19 ribosomal prote 100.0 1E-42 2.2E-47 289.4 12.7 113 63-180 4-117 (117)
2 PRK05338 rplS 50S ribosomal pr 100.0 1.6E-42 3.4E-47 287.9 11.6 113 65-182 2-115 (116)
3 TIGR01024 rplS_bact ribosomal 100.0 4.4E-42 9.5E-47 284.2 12.2 110 65-179 2-112 (113)
4 KOG1698|consensus 100.0 1.3E-41 2.8E-46 303.1 13.6 146 44-191 56-201 (201)
5 PF01245 Ribosomal_L19: Riboso 100.0 5.8E-42 1.3E-46 283.1 10.5 111 64-179 1-112 (113)
6 COG0335 RplS Ribosomal protein 100.0 1.6E-41 3.5E-46 280.6 11.4 110 65-179 4-114 (115)
7 smart00743 Agenet Tudor-like d 80.9 9.2 0.0002 27.4 6.6 49 86-142 2-50 (61)
8 PF05641 Agenet: Agenet domain 77.4 7.1 0.00015 29.2 5.3 38 87-129 1-38 (68)
9 cd01737 LSm16_N LSm16 belongs 67.5 10 0.00022 29.3 4.0 48 89-141 5-54 (62)
10 COG2139 RPL21A Ribosomal prote 54.0 17 0.00036 30.4 3.4 41 84-124 30-74 (98)
11 PRK01191 rpl24p 50S ribosomal 46.6 59 0.0013 27.9 5.8 59 86-152 45-105 (120)
12 TIGR03170 flgA_cterm flagella 45.2 65 0.0014 26.0 5.7 49 83-136 62-110 (122)
13 smart00739 KOW KOW (Kyprides, 44.3 57 0.0012 19.5 4.0 27 86-118 1-27 (28)
14 PF03888 MucB_RseB: MucB/RseB 39.0 1E+02 0.0022 29.3 6.7 56 105-167 9-64 (285)
15 TIGR01080 rplX_A_E ribosomal p 38.6 94 0.002 26.3 5.7 58 86-151 41-100 (114)
16 PF12701 LSM14: Scd6-like Sm d 38.4 1E+02 0.0023 25.2 5.8 39 88-134 6-45 (96)
17 TIGR00405 L26e_arch ribosomal 38.4 1.6E+02 0.0034 24.8 7.1 37 85-127 85-121 (145)
18 cd08544 Reeler Reeler, the N-t 37.6 69 0.0015 26.4 4.8 31 86-120 29-59 (135)
19 PF12969 DUF3857: Domain of Un 36.4 61 0.0013 27.0 4.3 20 82-101 85-104 (177)
20 PRK03999 translation initiatio 35.1 56 0.0012 27.8 3.9 57 82-143 6-62 (129)
21 PF13144 SAF_2: SAF-like 34.3 1.2E+02 0.0026 26.5 5.9 47 82-133 135-181 (196)
22 PRK04183 glutamyl-tRNA(Gln) am 34.1 67 0.0014 32.6 4.9 57 86-157 2-58 (419)
23 PF14438 SM-ATX: Ataxin 2 SM d 32.7 1.2E+02 0.0025 23.0 4.9 36 88-129 10-45 (77)
24 PRK04306 50S ribosomal protein 31.0 64 0.0014 26.8 3.5 42 86-127 34-79 (98)
25 COG0250 NusG Transcription ant 30.5 2.1E+02 0.0046 25.7 7.0 46 64-119 105-150 (178)
26 PF02765 POT1: Telomeric singl 30.4 54 0.0012 27.7 3.1 47 83-137 69-117 (146)
27 COG1566 EmrA Multidrug resista 28.8 1.5E+02 0.0032 29.5 6.2 58 81-141 253-319 (352)
28 PF02211 NHase_beta: Nitrile h 28.7 59 0.0013 30.3 3.2 37 82-118 130-170 (222)
29 PF08776 VASP_tetra: VASP tetr 28.6 52 0.0011 23.4 2.2 15 257-271 9-23 (40)
30 PRK09455 rseB anti-sigma E fac 28.4 2E+02 0.0043 28.1 6.9 50 105-157 40-89 (319)
31 cd06462 Peptidase_S24_S26 The 27.5 1.4E+02 0.0031 21.4 4.6 44 84-135 11-54 (84)
32 cd04497 hPOT1_OB1_like hPOT1_O 26.6 1E+02 0.0022 25.9 4.1 46 82-134 64-109 (138)
33 PRK07018 flgA flagellar basal 25.3 1.8E+02 0.0039 26.7 5.7 47 83-134 173-219 (235)
34 cd01288 FabZ FabZ is a 17kD be 24.9 1.1E+02 0.0024 24.1 3.8 28 86-113 87-114 (131)
35 PF00717 Peptidase_S24: Peptid 24.8 1.2E+02 0.0027 21.4 3.8 50 84-141 8-57 (70)
36 TIGR01956 NusG_myco NusG famil 24.6 2.3E+02 0.0049 27.4 6.4 50 84-139 203-252 (258)
37 PRK08571 rpl14p 50S ribosomal 24.5 2E+02 0.0043 25.1 5.5 34 84-117 44-77 (132)
38 PRK05609 nusG transcription an 24.2 4E+02 0.0087 22.8 7.4 49 85-141 125-173 (181)
39 PTZ00054 60S ribosomal protein 23.1 2.1E+02 0.0046 25.1 5.4 34 84-117 51-84 (139)
40 KOG3409|consensus 23.0 1.3E+02 0.0029 27.8 4.3 15 83-97 119-133 (193)
41 PF00238 Ribosomal_L14: Riboso 22.8 1.9E+02 0.0041 24.5 5.0 36 83-118 29-67 (122)
42 TIGR00008 infA translation ini 22.4 66 0.0014 25.0 2.0 23 84-106 42-65 (68)
43 PF11717 Tudor-knot: RNA bindi 22.3 2.4E+02 0.0052 20.2 4.8 36 87-128 1-36 (55)
44 COG0361 InfA Translation initi 22.2 71 0.0015 25.4 2.1 23 84-106 44-67 (75)
45 PF01157 Ribosomal_L21e: Ribos 21.9 3.4E+02 0.0074 22.5 6.1 53 86-140 32-88 (99)
46 COG5235 RFA2 Single-stranded D 21.8 1.4E+02 0.0031 28.4 4.4 31 108-141 70-101 (258)
47 PF02014 Reeler: Reeler domain 21.6 72 0.0016 26.3 2.2 30 85-118 28-57 (132)
48 PF07238 PilZ: PilZ domain; I 21.6 1.8E+02 0.0039 21.2 4.2 32 86-119 44-75 (102)
49 TIGR03673 rpl14p_arch 50S ribo 21.1 2.5E+02 0.0053 24.4 5.4 33 85-117 44-76 (131)
50 PF11302 DUF3104: Protein of u 20.8 3.5E+02 0.0075 21.6 5.7 50 84-133 3-57 (75)
51 PF12961 DUF3850: Domain of Un 20.8 1.2E+02 0.0027 23.9 3.2 27 85-117 27-53 (72)
52 PRK12617 flgA flagellar basal 20.6 2.3E+02 0.0049 26.2 5.4 48 85-137 154-201 (214)
53 cd00493 FabA_FabZ FabA/Z, beta 20.2 1.3E+02 0.0027 23.6 3.2 30 86-115 88-117 (131)
No 1
>CHL00084 rpl19 ribosomal protein L19
Probab=100.00 E-value=1e-42 Score=289.43 Aligned_cols=113 Identities=22% Similarity=0.390 Sum_probs=109.1
Q ss_pred HHHHHHHHHHHHhhhhccCCCCCCcCCCCEEEEEeeecC-CCCccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEEe
Q psy12656 63 RNQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYD 141 (291)
Q Consensus 63 ~~~Li~~LE~e~m~~rr~~~diPeF~vGDiV~Vt~~i~e-~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~Fp 141 (291)
.++|++.+|.+++. .++|+|+|||||+|++.+.| +|+|+|.|+|+||+++|+|+++||||||+++|+|||++||
T Consensus 4 ~~~~i~~~~~~~~~-----~~~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki~~gvGVEr~fp 78 (117)
T CHL00084 4 LQQLVKEIESEFLK-----KNLPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKVFQGIGVERVFL 78 (117)
T ss_pred HHHHHHHHHHHHhh-----cCCCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEeccCccEEEEEe
Confidence 56899999999997 69999999999999999999 8999999999999999999999999999999999999999
Q ss_pred ecCCccceEEEeeecccccccccccccCCCCcccccCCC
Q psy12656 142 MYDPTIHNITVLRLEKRLDDDLLYLRDALPQYSTFPFDM 180 (291)
Q Consensus 142 LySP~I~kIeVlr~gKvRRAKLYYLRd~~gK~srik~~m 180 (291)
+|||.|++|||+++||+|||||||||++.||+|+|++.+
T Consensus 79 l~SP~I~~IeV~r~gkvRRAKLyYLR~~~gKaarike~~ 117 (117)
T CHL00084 79 LHSPKLASIEVLRRSKVRRAKLYYLRNRVGKAARLKQKF 117 (117)
T ss_pred cCCCccceEEEEEeCccchheeEEeccCcChhheeeccC
Confidence 999999999999999999999999999999999999853
No 2
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=100.00 E-value=1.6e-42 Score=287.93 Aligned_cols=113 Identities=24% Similarity=0.413 Sum_probs=108.7
Q ss_pred HHHHHHHHHHhhhhccCCCCCCcCCCCEEEEEeeecC-CCCccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEEeec
Q psy12656 65 QVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDMY 143 (291)
Q Consensus 65 ~Li~~LE~e~m~~rr~~~diPeF~vGDiV~Vt~~i~e-~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~FpLy 143 (291)
++++.+|++++. .++|+|++||||+|++.+.| +++|+|.|+|+||+++|+|+++||||||+++|+|||++||||
T Consensus 2 ~~i~~~~~~~~~-----~~~p~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki~~gvGVEr~fpl~ 76 (116)
T PRK05338 2 NLIKEIEAEQLR-----KDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTFPLH 76 (116)
T ss_pred cHHHHHHHHHhh-----cCCCCcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEcccCccEEEEecCC
Confidence 588999999997 69999999999999999999 899999999999999999999999999999999999999999
Q ss_pred CCccceEEEeeecccccccccccccCCCCcccccCCCCc
Q psy12656 144 DPTIHNITVLRLEKRLDDDLLYLRDALPQYSTFPFDMEP 182 (291)
Q Consensus 144 SP~I~kIeVlr~gKvRRAKLYYLRd~~gK~srik~~m~p 182 (291)
||.|++|||+++||+||||||||||+.||+|+|++...+
T Consensus 77 SP~I~~IeV~r~gkvRRAKLyYLR~~~gK~arike~~~~ 115 (116)
T PRK05338 77 SPRIDSIEVVRRGKVRRAKLYYLRELRGKAARIKERRDA 115 (116)
T ss_pred CCcccEEEEEEecccchhheeeeccCcchhheeeeeccC
Confidence 999999999999999999999999999999999997643
No 3
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=100.00 E-value=4.4e-42 Score=284.18 Aligned_cols=110 Identities=24% Similarity=0.422 Sum_probs=106.7
Q ss_pred HHHHHHHHHHhhhhccCCCCCCcCCCCEEEEEeeecC-CCCccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEEeec
Q psy12656 65 QVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDMY 143 (291)
Q Consensus 65 ~Li~~LE~e~m~~rr~~~diPeF~vGDiV~Vt~~i~e-~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~FpLy 143 (291)
++++.+|++++. .++|+|++||+|+|++.+.| +++|+|.|+|+||+++|+|+++||||||+++|+|||++||+|
T Consensus 2 ~~i~~~e~~~~~-----~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i~~gvGVEr~fpl~ 76 (113)
T TIGR01024 2 NLIKQIEQEQLK-----KDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKISYGVGVERIFPLH 76 (113)
T ss_pred cHHHHHHHHHhh-----cCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEeccCccEEEEEEcC
Confidence 478999999987 69999999999999999999 999999999999999999999999999999999999999999
Q ss_pred CCccceEEEeeecccccccccccccCCCCcccccCC
Q psy12656 144 DPTIHNITVLRLEKRLDDDLLYLRDALPQYSTFPFD 179 (291)
Q Consensus 144 SP~I~kIeVlr~gKvRRAKLYYLRd~~gK~srik~~ 179 (291)
||.|++|+|+++||+||||||||||+.||+|++++.
T Consensus 77 SP~I~~IeVl~~~kvrRaKLyYLR~~~gK~arike~ 112 (113)
T TIGR01024 77 SPNIDSIEVVRRGKVRRAKLYYLRERRGKAARIKER 112 (113)
T ss_pred CCccceEEEEEeCccchhheeeeccCcchhheeeec
Confidence 999999999999999999999999999999999974
No 4
>KOG1698|consensus
Probab=100.00 E-value=1.3e-41 Score=303.09 Aligned_cols=146 Identities=45% Similarity=0.748 Sum_probs=140.4
Q ss_pred CCCccccccccCCChhhhhHHHHHHHHHHHHhhhhccCCCCCCcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcce
Q psy12656 44 PQENRFMYQEFLPDPELKFRNQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRH 123 (291)
Q Consensus 44 p~~~r~~~pef~P~p~~~~~~~Li~~LE~e~m~~rr~~~diPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~s 123 (291)
++..++.||+|+|.+.. ...+++.||+++|+.++..+++|+|++||||+|++.+++++.+++.|.||||.+++.|+++
T Consensus 56 ~~~~~~~~~~f~~~~~~--~~~~~e~Ldr~a~~~rr~~r~iPe~~~G~Iv~V~s~~p~~k~k~s~f~Gi~I~R~~~Gl~a 133 (201)
T KOG1698|consen 56 SPCVVEQYPEFLPLRKV--AKRIMEILDRQAVLERRKVRDIPEFKVGSIVRVTSEDPENKRKVSRFKGICIRRRNAGLNA 133 (201)
T ss_pred CccccccCcccccchhH--HHHHHHhhCHHHHHHHHhcccCCccccccEEEEEecCCccCCceeEEEEEEEEecccCCcc
Confidence 56688999999999955 4579999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEeeeCceeEEEEEeecCCccceEEEeeecccccccccccccCCCCcccccCCCCcccCCCCCCc
Q psy12656 124 EFVLRNVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRDALPQYSTFPFDMEPEYLLDGAPV 191 (291)
Q Consensus 124 TFtLRnvi~gvGVEr~FpLySP~I~kIeVlr~gKvRRAKLYYLRd~~gK~srik~~m~p~~~~~~~~v 191 (291)
||+|||+++|+|||.+||||||+|++|+|++..|++||+||||||+.+++++|+++|+|..+++|.+|
T Consensus 134 tf~LRnvIagvGVEi~~pLYsP~IkeI~Vlk~~k~rra~LyYLRd~lp~lstfd~~m~~~~~~~~~~~ 201 (201)
T KOG1698|consen 134 TFLLRNVIAGVGVEIVFPLYSPNIKEIKVLKLEKRRRAKLYYLRDALPELSTFDANMRPKKEENGHKV 201 (201)
T ss_pred eEEeeehhhCceeEEEEeccCCCeeEEEEechhhcccchhhhhhccccccCchhhccccccccCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999875
No 5
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 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 [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=100.00 E-value=5.8e-42 Score=283.07 Aligned_cols=111 Identities=32% Similarity=0.525 Sum_probs=106.9
Q ss_pred HHHHHHHHHHHhhhhccCCCCCCcCCCCEEEEEeeecC-CCCccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEEee
Q psy12656 64 NQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDM 142 (291)
Q Consensus 64 ~~Li~~LE~e~m~~rr~~~diPeF~vGDiV~Vt~~i~e-~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~FpL 142 (291)
++|++.+|++++. .++|+|++||+|+|++.+.| +++|+|.|+|+||+++++|+++||||||+++|+|||++|+|
T Consensus 1 ~~~i~~~e~~~~~-----~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~~~g~gVE~~f~l 75 (113)
T PF01245_consen 1 MNLIEEVEREQIK-----KDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNISQGVGVERVFPL 75 (113)
T ss_dssp -HHHHHHHHTTCS-----SSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEEETTEEEEEEEET
T ss_pred ChHHHHHHHHHhh-----cCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEEecCccEEEEEEc
Confidence 4789999999886 79999999999999999998 89999999999999999999999999999999999999999
Q ss_pred cCCccceEEEeeecccccccccccccCCCCcccccCC
Q psy12656 143 YDPTIHNITVLRLEKRLDDDLLYLRDALPQYSTFPFD 179 (291)
Q Consensus 143 ySP~I~kIeVlr~gKvRRAKLYYLRd~~gK~srik~~ 179 (291)
|||.|++|+|++++++||||||||||+.||+|+|++.
T Consensus 76 ~SP~I~~IeV~~~~kvrRaKLyYLR~~~gK~arike~ 112 (113)
T PF01245_consen 76 YSPLIKSIEVLRRGKVRRAKLYYLRDRKGKAARIKEK 112 (113)
T ss_dssp TSTTEEEEEEEEEBECSSSSTGGGGCTTSHHHHHHBT
T ss_pred CCCCeEEEEEEEecccchhhhhhhhcCccchhhhccc
Confidence 9999999999999999999999999999999999875
No 6
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-41 Score=280.63 Aligned_cols=110 Identities=25% Similarity=0.428 Sum_probs=107.1
Q ss_pred HHHHHHHHHHhhhhccCCCCCCcCCCCEEEEEeeecC-CCCccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEEeec
Q psy12656 65 QVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDMY 143 (291)
Q Consensus 65 ~Li~~LE~e~m~~rr~~~diPeF~vGDiV~Vt~~i~e-~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~FpLy 143 (291)
.+++.||++|+. .++|+|+|||+|+|++++.| +++|+|.|+|+||+++|+|+++|||||++++|+|||++||+|
T Consensus 4 ~~i~~le~~q~~-----~~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRkis~G~GVEr~Fp~~ 78 (115)
T COG0335 4 PIIQQLEQEQIK-----KDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVFPLH 78 (115)
T ss_pred HHHHHHHHHHHH-----hhCCCCCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEEeecCceEEEEeecC
Confidence 589999999998 58999999999999999999 999999999999999999999999999999999999999999
Q ss_pred CCccceEEEeeecccccccccccccCCCCcccccCC
Q psy12656 144 DPTIHNITVLRLEKRLDDDLLYLRDALPQYSTFPFD 179 (291)
Q Consensus 144 SP~I~kIeVlr~gKvRRAKLYYLRd~~gK~srik~~ 179 (291)
||.|++|||+++|+||||||||||++.||+++|++.
T Consensus 79 SP~Ie~IeV~rrGkVRRAKLYYLR~~~GKaArIke~ 114 (115)
T COG0335 79 SPLIESIEVVRRGKVRRAKLYYLRERRGKAARIKEK 114 (115)
T ss_pred CCceeEEEEEecCceeeeeeEeeecccccceeeeec
Confidence 999999999999999999999999999999999875
No 7
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=80.89 E-value=9.2 Score=27.44 Aligned_cols=49 Identities=12% Similarity=0.190 Sum_probs=36.1
Q ss_pred CcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEEee
Q psy12656 86 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDM 142 (291)
Q Consensus 86 eF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~FpL 142 (291)
.|.+||.|.|.... .-.=|.|+|++..+ +..|.|+-.-.+.|-+..|+.
T Consensus 2 ~~~~G~~Ve~~~~~-----~~~W~~a~V~~~~~---~~~~~V~~~~~~~~~~e~v~~ 50 (61)
T smart00743 2 DFKKGDRVEVFSKE-----EDSWWEAVVTKVLG---DGKYLVRYLTESEPLKETVDW 50 (61)
T ss_pred CcCCCCEEEEEECC-----CCEEEEEEEEEECC---CCEEEEEECCCCcccEEEEeH
Confidence 68999999999854 24589999999877 445888765444666666653
No 8
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=77.40 E-value=7.1 Score=29.22 Aligned_cols=38 Identities=13% Similarity=0.212 Sum_probs=25.4
Q ss_pred cCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEe
Q psy12656 87 FFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRN 129 (291)
Q Consensus 87 F~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRn 129 (291)
|++||.|.|..... .-+-.=|.|+|+...+.+ ++.|+-
T Consensus 1 F~~G~~VEV~s~e~--g~~gaWf~a~V~~~~~~~---~~~V~Y 38 (68)
T PF05641_consen 1 FKKGDEVEVSSDED--GFRGAWFPATVLKENGDD---KYLVEY 38 (68)
T ss_dssp --TT-EEEEEE-SB--TT--EEEEEEEEEEETT----EEEEEE
T ss_pred CCCCCEEEEEEcCC--CCCcEEEEEEEEEeCCCc---EEEEEE
Confidence 78999999987554 347889999999998876 777765
No 9
>cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=67.52 E-value=10 Score=29.26 Aligned_cols=48 Identities=21% Similarity=0.332 Sum_probs=34.0
Q ss_pred CCCEEEEEeeecCCCCccccEEEEEEEEecCC--cceeEEEEeeeCceeEEEEEe
Q psy12656 89 VGSILSVTSADKHDPNKTRKFVGICIQKRYCG--LRHEFVLRNVVDNLGIEIAYD 141 (291)
Q Consensus 89 vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~G--l~sTFtLRnvi~gvGVEr~Fp 141 (291)
.|+.|.++-.. -+-.|+|+|.++.... +.-+|-+||=+...-+|.+|.
T Consensus 5 iGs~VSI~C~~-----~lGVyQG~i~~V~~~~qTI~l~~~~~ngik~~~~EVt~~ 54 (62)
T cd01737 5 LGSIVSINCGE-----TLGVYQGLVSAVDQESQTISLAFPFHNGVKCLVPEVTFR 54 (62)
T ss_pred cceEEEEecCC-----ceEEEEEEEEEeCccceEEEEeecccCCccccCceEEEE
Confidence 68888888754 3779999999988755 444555555566666777764
No 10
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=53.97 E-value=17 Score=30.36 Aligned_cols=41 Identities=12% Similarity=0.145 Sum_probs=30.9
Q ss_pred CCCcCCCCEEEEEeeecC----CCCccccEEEEEEEEecCCccee
Q psy12656 84 IPSFFVGSILSVTSADKH----DPNKTRKFVGICIQKRYCGLRHE 124 (291)
Q Consensus 84 iPeF~vGDiV~Vt~~i~e----~K~R~q~F~GivIarr~~Gl~sT 124 (291)
+-+|.+||.|.+.+.-.- --.|.|-.+|+|++.+++...-.
T Consensus 30 l~ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~ 74 (98)
T COG2139 30 LQEYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVE 74 (98)
T ss_pred HhhccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEE
Confidence 448999999998876433 34688899999999998654433
No 11
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=46.65 E-value=59 Score=27.89 Aligned_cols=59 Identities=12% Similarity=0.073 Sum_probs=36.5
Q ss_pred CcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEe--eeCceeEEEEEeecCCccceEEE
Q psy12656 86 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRN--VVDNLGIEIAYDMYDPTIHNITV 152 (291)
Q Consensus 86 eF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRn--vi~gvGVEr~FpLySP~I~kIeV 152 (291)
.++.||.|.|..=. .|+ =+|.|+.+....- .++|-+ +....|+|+-+|+|.-.|.=+..
T Consensus 45 ~IkkGD~V~VisG~--~KG----k~GkV~~V~~~~~--~V~VeGvn~~k~~G~~~e~pIh~SNV~l~~l 105 (120)
T PRK01191 45 PVRKGDTVKVMRGD--FKG----EEGKVVEVDLKRG--RIYVEGVTVKKADGTEVPRPIHPSNVMITKL 105 (120)
T ss_pred eEeCCCEEEEeecC--CCC----ceEEEEEEEcCCC--EEEEeCcEEECCCCeEEEcccchhHeEEEeC
Confidence 59999999997532 233 2488888743221 233322 23346789999999877654443
No 12
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=45.20 E-value=65 Score=25.99 Aligned_cols=49 Identities=10% Similarity=-0.063 Sum_probs=35.3
Q ss_pred CCCCcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCceeE
Q psy12656 83 DIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGI 136 (291)
Q Consensus 83 diPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGV 136 (291)
..+-++-||.|.|.+.... =...-...|..+.+++.++.|||...|-=|
T Consensus 62 ~~~~V~~G~~V~i~~~~~~-----~~i~~~g~Al~~g~~G~~I~V~N~~s~k~i 110 (122)
T TIGR03170 62 PPWLVKRGDTVTVIARGGG-----LSVTTEGKALEDGAVGDQIRVRNLSSGKII 110 (122)
T ss_pred CccEEcCCCEEEEEEecCC-----EEEEEEEEEccccCCCCEEEEEECCCCCEE
Confidence 5678999999999997662 122333456677889999999997655433
No 13
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=44.33 E-value=57 Score=19.48 Aligned_cols=27 Identities=22% Similarity=0.261 Sum_probs=19.1
Q ss_pred CcCCCCEEEEEeeecCCCCccccEEEEEEEEec
Q psy12656 86 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRY 118 (291)
Q Consensus 86 eF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~ 118 (291)
.|.+||.|.|+-= ...-+.|+++.+.+
T Consensus 1 ~~~~G~~V~I~~G------~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAG------PFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeEC------CCCCcEEEEEEEcC
Confidence 3789999999862 34456788877654
No 14
>PF03888 MucB_RseB: MucB/RseB family; InterPro: IPR005588 The members of this family are regulators of the anti-sigma E protein RseD.; PDB: 2P4B_B 2V42_B 2V43_A 3M4W_A.
Probab=38.99 E-value=1e+02 Score=29.29 Aligned_cols=56 Identities=14% Similarity=0.150 Sum_probs=41.2
Q ss_pred ccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEEeecCCccceEEEeeecccccccccccc
Q psy12656 105 KTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLR 167 (291)
Q Consensus 105 R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~FpLySP~I~kIeVlr~gKvRRAKLYYLR 167 (291)
+.+.|+|+.+-.+|..+.+.=.++.+.+|.-.|+...|..|.. ||+|++. .++|+-
T Consensus 9 ~~lnY~g~fv~~~~~~~~s~ri~H~~~~~~e~ErL~~LdG~~r---eviR~~d----~v~~~~ 64 (285)
T PF03888_consen 9 RQLNYEGTFVYQRGGQMESMRIRHAVDDGGEYERLESLDGPPR---EVIRRGD----EVSCFE 64 (285)
T ss_dssp HHSEEEEEEEEEETTEEEEEEEEEEEETTEEEEEEEE-SSS-----EEEEETT----EEEEE-
T ss_pred HhCCeEEEEEEEeCCeEEEEEEEEEeeCCEEEEEEEecCCCcE---EEEEECC----EEEEEc
Confidence 5679999999999887766666666678888999999999874 7887764 455544
No 15
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=38.62 E-value=94 Score=26.34 Aligned_cols=58 Identities=10% Similarity=0.091 Sum_probs=35.0
Q ss_pred CcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEee--eCceeEEEEEeecCCccceEE
Q psy12656 86 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNV--VDNLGIEIAYDMYDPTIHNIT 151 (291)
Q Consensus 86 eF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnv--i~gvGVEr~FpLySP~I~kIe 151 (291)
.++.||.|.|..=. ..--+|.|+.+..... .+.|-.+ ....|+|.-.|+|.-.|+=+.
T Consensus 41 ~IkkGD~V~Vi~Gk------~KGk~GkV~~V~~~~~--~V~Vegvn~~k~~G~~~e~pIh~SnV~l~~ 100 (114)
T TIGR01080 41 PVRKGDKVRIMRGD------FKGHEGKVSKVDLKRY--RIYVEGVTKEKVNGTEVPVPIHPSNVMITK 100 (114)
T ss_pred eeecCCEEEEecCC------CCCCEEEEEEEEcCCC--EEEEcCeEEECCCCeEEEeeechHHeEEEe
Confidence 69999999997522 2235688888764332 2222221 123367888888876665443
No 16
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=38.41 E-value=1e+02 Score=25.20 Aligned_cols=39 Identities=23% Similarity=0.307 Sum_probs=31.0
Q ss_pred CCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeee-Cce
Q psy12656 88 FVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVV-DNL 134 (291)
Q Consensus 88 ~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi-~gv 134 (291)
+.|+.|.+..... -+|+|++..+.. -++|++|+|+. .|+
T Consensus 6 ~IGs~ISlisk~~------iRYeG~L~~Id~--~~sTItL~nVr~~Gt 45 (96)
T PF12701_consen 6 YIGSKISLISKSD------IRYEGILYSIDT--EDSTITLKNVRSFGT 45 (96)
T ss_dssp CTTCEEEEEETTT------EEEEEEEEEEET--TTTEEEEEEEEETTE
T ss_pred ccCCEEEEEECCC------cEEEEEEEEEcC--CCCEEEeeeeeecCc
Confidence 5799999887654 489999999875 46899999983 554
No 17
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=38.40 E-value=1.6e+02 Score=24.75 Aligned_cols=37 Identities=16% Similarity=0.062 Sum_probs=27.0
Q ss_pred CCcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEE
Q psy12656 85 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVL 127 (291)
Q Consensus 85 PeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtL 127 (291)
..|.+||.|+|.- +=.+-|+|+++...+.....++.|
T Consensus 85 ~~~~~Gd~V~I~~------GPf~G~~g~v~~~d~~k~~v~v~l 121 (145)
T TIGR00405 85 ESIKKGDIVEIIS------GPFKGERAKVIRVDESKEEVTLEL 121 (145)
T ss_pred cccCCCCEEEEee------cCCCCCeEEEEEEcCCCCEEEEEE
Confidence 4599999999975 346789999999876544444443
No 18
>cd08544 Reeler Reeler, the N-terminal domain of reelin, F-spondin, and a variety of other proteins. This domain is found at the N-terminus of F-spondin, a protein attached to the extracellular matrix, which plays roles in neuronal development and vascular remodelling. The F-spondin reeler domain has been reported to bind heparin. The reeler domain is also found at the N-terminus of reelin, an extracellular glycoprotein involved in the development of the brain cortex, and in a variety of other eukaryotic proteins with different domain architectures, including the animal ferric-chelate reductase 1 or stromal cell-derived receptor 2, a member of the cytochrome B561 family, which reduces ferric iron before its transport from the endosome to the cytoplasm. Also included is the insect putative defense protein 1, which is expressed upon bacterial infection and appears to contain a single reeler domain.
Probab=37.60 E-value=69 Score=26.38 Aligned_cols=31 Identities=26% Similarity=0.385 Sum_probs=26.7
Q ss_pred CcCCCCEEEEEeeecCCCCccccEEEEEEEEecCC
Q psy12656 86 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCG 120 (291)
Q Consensus 86 eF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~G 120 (291)
.+.+|+.+.|++..... ..|.|..|.-+..+
T Consensus 29 ~y~pG~~~~Vtl~~~~~----~~F~GF~lqAr~~~ 59 (135)
T cd08544 29 SYVPGETYTVTLSGSSP----SPFRGFLLQARDAS 59 (135)
T ss_pred EECCCCEEEEEEECCCC----CceeEEEEEEEcCC
Confidence 79999999999988743 79999999987755
No 19
>PF12969 DUF3857: Domain of Unknown Function with PDB structure (DUF3857); InterPro: IPR024618 This domain is based on the first domain of the PDB structure 3KD4 (residues 1-228). It is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase, despite lack of any significant sequence similarity. The domain is N-terminal to a transglutaminase domain, which is found in many proteins known to have transglutaminase activity. The function of this domain is unknown. ; PDB: 3KD4_A.
Probab=36.39 E-value=61 Score=26.98 Aligned_cols=20 Identities=25% Similarity=0.376 Sum_probs=13.3
Q ss_pred CCCCCcCCCCEEEEEeeecC
Q psy12656 82 IDIPSFFVGSILSVTSADKH 101 (291)
Q Consensus 82 ~diPeF~vGDiV~Vt~~i~e 101 (291)
..+|.+++||+|...+.+..
T Consensus 85 ~~~p~v~~GdiIe~~y~~~~ 104 (177)
T PF12969_consen 85 FAFPDVRVGDIIEYSYTIKS 104 (177)
T ss_dssp EE--S--TT-EEEEEEEEEE
T ss_pred EEcCCCCCCcEEEEEEEEEe
Confidence 68999999999999999875
No 20
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=35.14 E-value=56 Score=27.81 Aligned_cols=57 Identities=12% Similarity=0.127 Sum_probs=34.5
Q ss_pred CCCCCcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEEeec
Q psy12656 82 IDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDMY 143 (291)
Q Consensus 82 ~diPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~FpLy 143 (291)
...++|+.|++|... . ....+..++-.--+++| +-...+.+||+..|.=+|.+|+-.
T Consensus 6 ~~~~~lrkG~~i~~~---g-~p~~V~~~~~~kpGkhg-~a~vr~k~knL~tG~~~e~~~~s~ 62 (129)
T PRK03999 6 VEVGELKEGSYVVID---G-EPCKIVEISKSKPGKHG-SAKARIVAIGIFDGQKRSLVQPVD 62 (129)
T ss_pred ccHHHccCCCEEEEC---C-EEEEEEEEEeecCCCCC-cEEEEEEEEECCCCCEEEEEecCC
Confidence 467799999999542 1 11122222222122212 225678899999999999999753
No 21
>PF13144 SAF_2: SAF-like
Probab=34.26 E-value=1.2e+02 Score=26.49 Aligned_cols=47 Identities=13% Similarity=0.044 Sum_probs=34.6
Q ss_pred CCCCCcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCc
Q psy12656 82 IDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDN 133 (291)
Q Consensus 82 ~diPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~g 133 (291)
...|.++-||.|.|.+.... =..+--.+|..+..+|.++.|+|...|
T Consensus 135 ~~~~~V~~G~~V~v~~~~g~-----i~i~~~g~Al~~G~~G~~I~V~N~~S~ 181 (196)
T PF13144_consen 135 EPPPLVKRGDIVTVIARSGG-----ISISTEGKALEDGALGDTIRVKNLSSG 181 (196)
T ss_pred ccceecCCCCEEEEEEEeCC-----EEEEEEEEEccCCCCCCEEEEEECCCC
Confidence 35578999999999987762 122333466677889999999997654
No 22
>PRK04183 glutamyl-tRNA(Gln) amidotransferase subunit D; Validated
Probab=34.08 E-value=67 Score=32.55 Aligned_cols=57 Identities=26% Similarity=0.301 Sum_probs=36.7
Q ss_pred CcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEEeecCCccceEEEeeecc
Q psy12656 86 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDMYDPTIHNITVLRLEK 157 (291)
Q Consensus 86 eF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~FpLySP~I~kIeVlr~gK 157 (291)
.+.+||.|+|.... ..|+|++|-... +-.-.+.|.|= .++||.. -.|.+||++..+.
T Consensus 2 ~~~~gd~v~~~~~~-------~~~~g~~~p~~~-~~~~~~kl~~g-yn~g~~~------~~~~~~~~~~~~~ 58 (419)
T PRK04183 2 GMEVGDRVRVEKDD-------VVYEGILMPSYE-DDHIVIKLDNG-YNIGIDI------DKIAEIELLEKGE 58 (419)
T ss_pred CCCCCCEEEEEECC-------eEEEEEEecCCC-CCEEEEEcCCC-ceeeecc------ccccceEEccccc
Confidence 36789999997754 599999997665 21223334332 3366653 2467788887654
No 23
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=32.67 E-value=1.2e+02 Score=22.98 Aligned_cols=36 Identities=22% Similarity=0.302 Sum_probs=24.1
Q ss_pred CCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEe
Q psy12656 88 FVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRN 129 (291)
Q Consensus 88 ~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRn 129 (291)
-+|..|.|++.+.. .|+||.-+..-.+-+..+.|+.
T Consensus 10 lvG~~V~V~~~~G~------~yeGif~s~s~~~~~~~vvLk~ 45 (77)
T PF14438_consen 10 LVGQTVEVTTKNGS------VYEGIFHSASPESNEFDVVLKM 45 (77)
T ss_dssp TTTSEEEEEETTS-------EEEEEEEEE-T---T--EEEEE
T ss_pred CcCCEEEEEECCCC------EEEEEEEeCCCcccceeEEEEe
Confidence 47999999999884 8999999877654456666654
No 24
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=30.97 E-value=64 Score=26.77 Aligned_cols=42 Identities=14% Similarity=0.045 Sum_probs=30.4
Q ss_pred CcCCCCEEEEEeeecCC----CCccccEEEEEEEEecCCcceeEEE
Q psy12656 86 SFFVGSILSVTSADKHD----PNKTRKFVGICIQKRYCGLRHEFVL 127 (291)
Q Consensus 86 eF~vGDiV~Vt~~i~e~----K~R~q~F~GivIarr~~Gl~sTFtL 127 (291)
+|++||+|.|...-.-- -.+.+--.|.|+.++++...-.+.+
T Consensus 34 ~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v~v 79 (98)
T PRK04306 34 EFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEVKD 79 (98)
T ss_pred hccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEEEE
Confidence 69999999997764432 3566777899999988766555433
No 25
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=30.47 E-value=2.1e+02 Score=25.67 Aligned_cols=46 Identities=11% Similarity=0.002 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHhhhhccCCCCCCcCCCCEEEEEeeecCCCCccccEEEEEEEEecC
Q psy12656 64 NQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYC 119 (291)
Q Consensus 64 ~~Li~~LE~e~m~~rr~~~diPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~ 119 (291)
++++..++...-. ......|.+||.|+|.- +=+..|.|.|+...+.
T Consensus 105 ~~~l~~~~~~~~~----~~~~~~~e~Gd~VrI~~------GpFa~f~g~V~evd~e 150 (178)
T COG0250 105 EHILGFLEEEVAP----KKPKVDFEPGDVVRIID------GPFAGFKAKVEEVDEE 150 (178)
T ss_pred HHHHhhccccccC----CcccccCCCCCEEEEec------cCCCCccEEEEEEcCc
Confidence 3455566544222 24566899999999964 3345699999998764
No 26
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=30.42 E-value=54 Score=27.75 Aligned_cols=47 Identities=11% Similarity=0.158 Sum_probs=31.5
Q ss_pred CCCCcCC-CCEEEEE-eeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCceeEE
Q psy12656 83 DIPSFFV-GSILSVT-SADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIE 137 (291)
Q Consensus 83 diPeF~v-GDiV~Vt-~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVE 137 (291)
.+|.+.. ||||.++ ++ +|.|.|-..+..+.+-+++|.|= ..++.|..
T Consensus 69 ~LP~v~~~GDii~l~r~k-------v~~~~~~~~~~~~~~~~ss~~vf-~~~~~~~~ 117 (146)
T PF02765_consen 69 SLPNVKSVGDIIRLRRVK-------VQSYNGKPQGLSNSTSNSSWAVF-SSGGSGAP 117 (146)
T ss_dssp HSCTTCSTTHEEEEEEEE-------EEEETTEEEEEEECECTEEEEEE-CTSSTTTC
T ss_pred HCCCCCCCCCEEEEEEEE-------EEEECCEEEEEecCCCcEEEEEE-ecCCCCCC
Confidence 4688888 9999888 44 45777776676666666777764 23444443
No 27
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=28.83 E-value=1.5e+02 Score=29.52 Aligned_cols=58 Identities=16% Similarity=0.071 Sum_probs=43.4
Q ss_pred CCCCCCcCCCCEEEEEeeecCCCCccccEEEEEEEEec-CC--------cceeEEEEeeeCceeEEEEEe
Q psy12656 81 VIDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRY-CG--------LRHEFVLRNVVDNLGIEIAYD 141 (291)
Q Consensus 81 ~~diPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~-~G--------l~sTFtLRnvi~gvGVEr~Fp 141 (291)
..++..+++|+-+.|++...... ..|.|+|-++.. .| .+.|+..=++++.+.|.+.|.
T Consensus 253 ETqL~~~r~Gq~a~I~~da~~~~---~~~~G~v~~i~~~tg~~fsllp~~natgN~tkvvQRvPVrI~ld 319 (352)
T COG1566 253 ETQLARVRPGQPAEITLDAYPGN---GVVEGIVEGIAPATGSAFSLLPAQNATGNWTKVVQRVPVRIELD 319 (352)
T ss_pred eeecCcccCCCeEEEEEEcCCCc---eEEEEEEEEecCCcccccccCCCccCCCCEEEEEEeeeEEEEec
Confidence 46788999999999999876422 889999999863 22 245555567888888877764
No 28
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=28.67 E-value=59 Score=30.33 Aligned_cols=37 Identities=16% Similarity=0.200 Sum_probs=19.6
Q ss_pred CCCCCcCCCCEEEEEeeecCCCCccccE----EEEEEEEec
Q psy12656 82 IDIPSFFVGSILSVTSADKHDPNKTRKF----VGICIQKRY 118 (291)
Q Consensus 82 ~diPeF~vGDiV~Vt~~i~e~K~R~q~F----~GivIarr~ 118 (291)
-.-|.|.+||.|+|.-..+..-.|+..| +|+|....+
T Consensus 130 ~~~~~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~~g 170 (222)
T PF02211_consen 130 DAPPRFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERVHG 170 (222)
T ss_dssp SSS-SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEEEE
T ss_pred CCCCCCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEEec
Confidence 3577999999999987766666666655 688887654
No 29
>PF08776 VASP_tetra: VASP tetramerisation domain; InterPro: IPR014885 Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure []. ; PDB: 1USE_A 1USD_A.
Probab=28.65 E-value=52 Score=23.43 Aligned_cols=15 Identities=40% Similarity=0.645 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHhhhh
Q psy12656 257 QEEIFSEVFSELHQL 271 (291)
Q Consensus 257 ~~~i~~e~~~~~~~~ 271 (291)
+++|++||..+||++
T Consensus 9 KqEIL~EvrkEl~K~ 23 (40)
T PF08776_consen 9 KQEILEEVRKELQKV 23 (40)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 347999999999875
No 30
>PRK09455 rseB anti-sigma E factor; Provisional
Probab=28.42 E-value=2e+02 Score=28.05 Aligned_cols=50 Identities=12% Similarity=0.090 Sum_probs=38.0
Q ss_pred ccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEEeecCCccceEEEeeecc
Q psy12656 105 KTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYDMYDPTIHNITVLRLEK 157 (291)
Q Consensus 105 R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~FpLySP~I~kIeVlr~gK 157 (291)
+.+.|+|+.+-.+|.++.+.=.+.-+.+|.=.|+.-.|..|. .||+|++.
T Consensus 40 ~~lnY~g~fV~~~~~~i~s~ri~H~~~~~~e~erL~~LdG~~---rEviR~~d 89 (319)
T PRK09455 40 QSLNYELSFINITKQGIESLRYRHARLDNKPLAQLLQMDGPR---REIIQRGN 89 (319)
T ss_pred HhCCeEEEEEEEeCCeEEEEEEEEEEeCCEEEEEEEecCCCc---eEEEEECC
Confidence 357999999999987765554455556777799999999886 47888764
No 31
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=27.54 E-value=1.4e+02 Score=21.43 Aligned_cols=44 Identities=20% Similarity=0.251 Sum_probs=28.0
Q ss_pred CCCcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCcee
Q psy12656 84 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLG 135 (291)
Q Consensus 84 iPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvG 135 (291)
.|.|..||+|-|.-... ..-.|-++.....| ..+++|++....+
T Consensus 11 ~P~i~~gd~v~i~~~~~------~~~~G~iv~~~~~~--~~~~ikrl~~~~~ 54 (84)
T cd06462 11 EPTIPDGDLVLVDKSSY------EPKRGDIVVFRLPG--GELTVKRVIGLPG 54 (84)
T ss_pred cCcccCCCEEEEEecCC------CCcCCEEEEEEcCC--CcEEEEEEEEECC
Confidence 47799999999875433 23345444444444 5688888876653
No 32
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=26.64 E-value=1e+02 Score=25.92 Aligned_cols=46 Identities=15% Similarity=0.138 Sum_probs=31.8
Q ss_pred CCCCCcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCce
Q psy12656 82 IDIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNL 134 (291)
Q Consensus 82 ~diPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gv 134 (291)
..+|.+.+||+|.++=. ++|.|.|-..+..+. -.++|-|=+-..+.
T Consensus 64 ~~LP~v~~GDVIll~~~------kv~~~~g~~~~~~~~-~~ss~avf~~~~~~ 109 (138)
T cd04497 64 ESLPIVKVGDIILLRRV------KIQSYNGKPQGISND-RGSSWAVFRGDDGV 109 (138)
T ss_pred hhCCCCCCCCEEEEEEE------EEEEECCceEEEECC-CceeEEEEcCCCCC
Confidence 36888899999998753 367888888887665 45667663333333
No 33
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=25.27 E-value=1.8e+02 Score=26.71 Aligned_cols=47 Identities=9% Similarity=-0.007 Sum_probs=33.7
Q ss_pred CCCCcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCce
Q psy12656 83 DIPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNL 134 (291)
Q Consensus 83 diPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gv 134 (291)
..+-++-||.|.|.+.... =...--..|..+.+++.++.|||...|-
T Consensus 173 ~~~~V~~G~~V~i~~~~g~-----~~i~~~G~Al~~G~~Gd~IrVrN~~Sgk 219 (235)
T PRK07018 173 QAWVVCKGQTVSIIARGDG-----FSVKTEGEALNDGAVGQQIRVRNMASGQ 219 (235)
T ss_pred CccEeCCCCEEEEEEecCC-----EEEEEEEEEcCCCCCCCeEEEEECCCCC
Confidence 5568999999999987651 1122333556678899999999976554
No 34
>cd01288 FabZ FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid biosynthesis pathway.
Probab=24.88 E-value=1.1e+02 Score=24.12 Aligned_cols=28 Identities=18% Similarity=0.093 Sum_probs=20.9
Q ss_pred CcCCCCEEEEEeeecCCCCccccEEEEE
Q psy12656 86 SFFVGSILSVTSADKHDPNKTRKFVGIC 113 (291)
Q Consensus 86 eF~vGDiV~Vt~~i~e~K~R~q~F~Giv 113 (291)
...+||+|.+.+.+.+..++.-.|.+.+
T Consensus 87 pv~pgd~l~i~~~v~~~~~~~~~~~~~~ 114 (131)
T cd01288 87 PVVPGDQLILEVELLKLRRGIGKFKGKA 114 (131)
T ss_pred ccCCCCEEEEEEEEEEeeCCEEEEEEEE
Confidence 3668999999998887556666666665
No 35
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=24.84 E-value=1.2e+02 Score=21.43 Aligned_cols=50 Identities=18% Similarity=0.165 Sum_probs=26.6
Q ss_pred CCCcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEEe
Q psy12656 84 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYD 141 (291)
Q Consensus 84 iPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~Fp 141 (291)
.|.|..||+|-|.-... .+.-..|++...+.+ ..+++++....|=-..+.
T Consensus 8 ~P~i~~Gd~v~v~~~~~-----~~~gdivv~~~~~~~---~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 8 EPTIKDGDIVLVDPSSE-----PKDGDIVVVKIDGDE---ELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp GGTSSTTEEEEEEETS--------TTSEEEEEETTEE---SEEEEEEEEETTEEEEE-
T ss_pred ccCeeCCCEEEEEEcCC-----CccCeEEEEEECCce---eeEEEEEEEeCCCEEEEe
Confidence 48899999999885442 222223333333322 578888874444333333
No 36
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=24.65 E-value=2.3e+02 Score=27.36 Aligned_cols=50 Identities=10% Similarity=0.185 Sum_probs=31.8
Q ss_pred CCCcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCceeEEEE
Q psy12656 84 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIA 139 (291)
Q Consensus 84 iPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~ 139 (291)
.+.|.+||.|+|+- +=.+-|+|+|+......-...+.|-=.-..+-||.-
T Consensus 203 ~~~f~vGd~VrI~d------GPF~GfeG~I~eid~~k~Rv~VlV~IfGR~TpVeL~ 252 (258)
T TIGR01956 203 LSKFRVGNFVKIVD------GPFKGIVGKIKKIDQEKKKAIVEVEILGKSVDVDLN 252 (258)
T ss_pred ccCCCCCCEEEEEe------cCCCCcEEEEEEEeCCCCEEEEEEEecCCcEEEEEc
Confidence 45699999999976 346799999999875433344444222233345443
No 37
>PRK08571 rpl14p 50S ribosomal protein L14P; Reviewed
Probab=24.51 E-value=2e+02 Score=25.07 Aligned_cols=34 Identities=15% Similarity=0.325 Sum_probs=27.5
Q ss_pred CCCcCCCCEEEEEeeecCCCCccccEEEEEEEEe
Q psy12656 84 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKR 117 (291)
Q Consensus 84 iPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr 117 (291)
+|.-.+||+|.|.++......|-+.+.|||+..+
T Consensus 44 ~~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtk 77 (132)
T PRK08571 44 LPKAGVGDMVVVSVKKGTPEMRKQVLRAVVVRQR 77 (132)
T ss_pred CCccccCCEEEEEEEECCCcccCCEeEEEEEEec
Confidence 4678899999999987664456689999999854
No 38
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=24.16 E-value=4e+02 Score=22.81 Aligned_cols=49 Identities=14% Similarity=0.184 Sum_probs=31.5
Q ss_pred CCcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEEe
Q psy12656 85 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAYD 141 (291)
Q Consensus 85 PeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~Fp 141 (291)
..|.+||.|+|+- +=.+-|+|+|....+.. ...+|.=-+.|..+...+.
T Consensus 125 ~~~~~Gd~VrI~~------GPf~G~~g~v~~i~~~~--~r~~v~l~~~G~~~~v~l~ 173 (181)
T PRK05609 125 VDFEVGEMVRVID------GPFADFNGTVEEVDYEK--SKLKVLVSIFGRETPVELE 173 (181)
T ss_pred cCCCCCCEEEEec------cCCCCCEEEEEEEeCCC--CEEEEEEEECCCceEEEEc
Confidence 4699999999973 34678999999986433 2344443455555444433
No 39
>PTZ00054 60S ribosomal protein L23; Provisional
Probab=23.06 E-value=2.1e+02 Score=25.15 Aligned_cols=34 Identities=18% Similarity=0.329 Sum_probs=27.8
Q ss_pred CCCcCCCCEEEEEeeecCCCCccccEEEEEEEEe
Q psy12656 84 IPSFFVGSILSVTSADKHDPNKTRKFVGICIQKR 117 (291)
Q Consensus 84 iPeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr 117 (291)
+|.-.+||+|.|.++....-.+-+.+.|||+..+
T Consensus 51 ~~~a~iGD~IvvsVKk~~p~~kg~V~kAVIVRtK 84 (139)
T PTZ00054 51 LPSASLGDMVLATVKKGKPELRKKVLNAVIIRQR 84 (139)
T ss_pred CcccccCCEEEEEEEECCCcccCCEeeEEEEEEC
Confidence 3678899999999987765556699999999854
No 40
>KOG3409|consensus
Probab=22.95 E-value=1.3e+02 Score=27.81 Aligned_cols=15 Identities=27% Similarity=0.224 Sum_probs=11.3
Q ss_pred CCCCcCCCCEEEEEe
Q psy12656 83 DIPSFFVGSILSVTS 97 (291)
Q Consensus 83 diPeF~vGDiV~Vt~ 97 (291)
-+-.|+|||||.-.+
T Consensus 119 v~ksFrPgDiVlAkV 133 (193)
T KOG3409|consen 119 VYKSFRPGDIVLAKV 133 (193)
T ss_pred hhhccCCCcEEEEEE
Confidence 445799999997654
No 41
>PF00238 Ribosomal_L14: Ribosomal protein L14p/L23e; InterPro: IPR000218 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 [, ]. Ribosomal protein L14 is one of the proteins from the large ribosomal subunit. In eubacteria, L14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities []. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins []. L14 is a protein of 119 to 137 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_M 4A1C_J 4A1E_J 4A1A_J 4A17_J 1VSP_I 3D5D_O 1VSA_I 3MRZ_K 3F1F_O ....
Probab=22.78 E-value=1.9e+02 Score=24.48 Aligned_cols=36 Identities=14% Similarity=0.206 Sum_probs=26.0
Q ss_pred CCCCcCCCCEEEEEeeecC---CCCccccEEEEEEEEec
Q psy12656 83 DIPSFFVGSILSVTSADKH---DPNKTRKFVGICIQKRY 118 (291)
Q Consensus 83 diPeF~vGDiV~Vt~~i~e---~K~R~q~F~GivIarr~ 118 (291)
..+--.+||+|.|.+.... .-.+-+.+.|+|+..+.
T Consensus 29 ~~~~a~vGD~I~vsVkk~~~~~~vkkg~v~~avIVrtk~ 67 (122)
T PF00238_consen 29 RRKYASVGDIIVVSVKKGRPKSKVKKGQVYKAVIVRTKK 67 (122)
T ss_dssp TTSEE-TTSEEEEEEEEE-SSSSSTTTEEEEEEEEECSS
T ss_pred CccccccceEEEEEEeecccCccccccceEEEEEEEEeE
Confidence 4556789999999997763 33455889999999553
No 42
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=22.39 E-value=66 Score=24.99 Aligned_cols=23 Identities=9% Similarity=0.091 Sum_probs=16.9
Q ss_pred CCCcCCCCEEEEEeeecC-CCCcc
Q psy12656 84 IPSFFVGSILSVTSADKH-DPNKT 106 (291)
Q Consensus 84 iPeF~vGDiV~Vt~~i~e-~K~R~ 106 (291)
.-.+.+||.|.|.++.-. +++|+
T Consensus 42 rI~I~~GD~V~Ve~spyd~tkgrI 65 (68)
T TIGR00008 42 YIRILPGDKVKVELSPYDLTRGRI 65 (68)
T ss_pred cEEECCCCEEEEEECcccCCcEeE
Confidence 335899999999988765 55443
No 43
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=22.33 E-value=2.4e+02 Score=20.21 Aligned_cols=36 Identities=17% Similarity=0.159 Sum_probs=25.4
Q ss_pred cCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEE
Q psy12656 87 FFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLR 128 (291)
Q Consensus 87 F~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLR 128 (291)
|.+|+.|-+.... -+.+.+-|+.++..+-...|.|.
T Consensus 1 ~~vG~~v~~~~~~------~~~y~A~I~~~r~~~~~~~YyVH 36 (55)
T PF11717_consen 1 FEVGEKVLCKYKD------GQWYEAKILDIREKNGEPEYYVH 36 (55)
T ss_dssp --TTEEEEEEETT------TEEEEEEEEEEEECTTCEEEEEE
T ss_pred CCcCCEEEEEECC------CcEEEEEEEEEEecCCCEEEEEE
Confidence 6789999998822 46899999998876555555553
No 44
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=22.18 E-value=71 Score=25.39 Aligned_cols=23 Identities=9% Similarity=0.114 Sum_probs=17.2
Q ss_pred CCCcCCCCEEEEEeeecC-CCCcc
Q psy12656 84 IPSFFVGSILSVTSADKH-DPNKT 106 (291)
Q Consensus 84 iPeF~vGDiV~Vt~~i~e-~K~R~ 106 (291)
.-.+.+||+|.|....-. ++.|+
T Consensus 44 ~i~I~~GD~V~Ve~~~~d~~kg~I 67 (75)
T COG0361 44 RIRILPGDVVLVELSPYDLTKGRI 67 (75)
T ss_pred eEEeCCCCEEEEEecccccccccE
Confidence 336899999999998765 55554
No 45
>PF01157 Ribosomal_L21e: Ribosomal protein L21e; InterPro: IPR001147 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 [, ]. L21E family contains proteins from a number of eukaryotic and archaebacterial organisms which include; mammalian L2, Entamoeba histolytica L21, Caenorhabditis elegans L21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) L21E (URP1) and Haloarcula marismortui HL31.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_U 1S1I_Q 3O58_T 3IZS_U 3O5H_T 1Q82_R 1KQS_P 3CCJ_Q 3CCQ_Q 1VQ5_Q ....
Probab=21.87 E-value=3.4e+02 Score=22.52 Aligned_cols=53 Identities=9% Similarity=0.008 Sum_probs=26.6
Q ss_pred CcCCCCEEEEEeeecCCC----CccccEEEEEEEEecCCcceeEEEEeeeCceeEEEEE
Q psy12656 86 SFFVGSILSVTSADKHDP----NKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAY 140 (291)
Q Consensus 86 eF~vGDiV~Vt~~i~e~K----~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVEr~F 140 (291)
.|++||.|.|...-.--+ .+.+==.|.|..+.....+-.+.+ -+.+-+++..+
T Consensus 32 ~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~~G~~~~~--~v~~~~~~K~i 88 (99)
T PF01157_consen 32 EYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGARGVAYNK--QVKDRIKEKRI 88 (99)
T ss_dssp ---TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSCEEEEEEE--ECSSSCEEEEE
T ss_pred HccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCceEEEEEE--EecCCcccEEE
Confidence 699999999987654433 455556888887665555444443 23444444444
No 46
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=21.84 E-value=1.4e+02 Score=28.45 Aligned_cols=31 Identities=29% Similarity=0.497 Sum_probs=26.6
Q ss_pred cEEEEEEEEecCCcceeEEEEeeeCcee-EEEEEe
Q psy12656 108 KFVGICIQKRYCGLRHEFVLRNVVDNLG-IEIAYD 141 (291)
Q Consensus 108 ~F~GivIarr~~Gl~sTFtLRnvi~gvG-VEr~Fp 141 (291)
.|.|+|-.++-.-.|+.|++ -+|+| ||.+|-
T Consensus 70 ~fVGvvrni~~~ttn~~~~i---EDGTG~Ievr~W 101 (258)
T COG5235 70 QFVGVVRNIKTSTTNSMFVI---EDGTGSIEVRFW 101 (258)
T ss_pred EEEEEEEeeeecccceEEEE---ecCCceEEEEec
Confidence 79999999998888999986 68999 787764
No 47
>PF02014 Reeler: Reeler domain Schematic picture including Reeler domain; InterPro: IPR002861 Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cyto-architecture of the central nervous system. The product of the reeler gene in mouse is reelin,a large extracellular protein secreted by pioneer neurons that coordinates cell positioning during neurodevelopment []. F-spondin and mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Both F-spondin and mindin promote adhesion and outgrowth of hippocampal embryonic neurons and bind to a putative receptor(s) expressed on both hippocampal and sensory neurons []. This domain of unknown function is found at the N terminus of reelin and F-spondin.; PDB: 2ZOT_B 2ZOU_B 3COO_A.
Probab=21.62 E-value=72 Score=26.30 Aligned_cols=30 Identities=27% Similarity=0.376 Sum_probs=23.2
Q ss_pred CCcCCCCEEEEEeeecCCCCccccEEEEEEEEec
Q psy12656 85 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKRY 118 (291)
Q Consensus 85 PeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~ 118 (291)
..+.+|+.+.|++ +......|.|..|.-+.
T Consensus 28 ~~y~pg~~~~Vtl----~~~~~~~F~GFllqAr~ 57 (132)
T PF02014_consen 28 SSYEPGQTYTVTL----SSSGSSSFRGFLLQARD 57 (132)
T ss_dssp SSB-TTBEEEEEE----EETTTEEBSEEEEEEEE
T ss_pred CeEcCCCEEEEEE----ECCCCCceeEEEEEEEe
Confidence 3689999999999 23446799999999664
No 48
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=21.60 E-value=1.8e+02 Score=21.21 Aligned_cols=32 Identities=6% Similarity=-0.041 Sum_probs=23.0
Q ss_pred CcCCCCEEEEEeeecCCCCccccEEEEEEEEecC
Q psy12656 86 SFFVGSILSVTSADKHDPNKTRKFVGICIQKRYC 119 (291)
Q Consensus 86 eF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~ 119 (291)
.+.+||.|.|.+.......-. +.|.|+...+.
T Consensus 44 ~~~~~~~v~l~~~~~~~~~~~--~~~~V~~~~~~ 75 (102)
T PF07238_consen 44 PLEPGDRVRLSFSLPGGGFPI--VTGRVVRIQKD 75 (102)
T ss_dssp G--TTSEEEEEEECTTTSCEE--EEEEEEEEEEE
T ss_pred CCCCCCEEEEEEEeCCCCeeE--EEEEEEEEECC
Confidence 789999999999777533322 99999998765
No 49
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=21.05 E-value=2.5e+02 Score=24.45 Aligned_cols=33 Identities=18% Similarity=0.360 Sum_probs=26.6
Q ss_pred CCcCCCCEEEEEeeecCCCCccccEEEEEEEEe
Q psy12656 85 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKR 117 (291)
Q Consensus 85 PeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr 117 (291)
+.-.+||+|.|.++......+-+.+.|||+..+
T Consensus 44 ~~a~iGD~IvvsVK~~~p~~kg~v~kAVIVRtk 76 (131)
T TIGR03673 44 PCAGVGDMVVVSVKKGTPEMRKQVFKAVVVRQR 76 (131)
T ss_pred CccccCCEEEEEEEECCccccCCEeEEEEEEeC
Confidence 667899999999987664456689999999854
No 50
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=20.84 E-value=3.5e+02 Score=21.63 Aligned_cols=50 Identities=14% Similarity=0.118 Sum_probs=35.4
Q ss_pred CCCcCCCCEEEEEeeecC-CCCccccEEEEEEEEecC----CcceeEEEEeeeCc
Q psy12656 84 IPSFFVGSILSVTSADKH-DPNKTRKFVGICIQKRYC----GLRHEFVLRNVVDN 133 (291)
Q Consensus 84 iPeF~vGDiV~Vt~~i~e-~K~R~q~F~GivIarr~~----Gl~sTFtLRnvi~g 133 (291)
+..+++||+|-|.-.... ......-..|-||...+. -..|=|.+=++=.|
T Consensus 3 FL~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~~~tlFQVadVDtG 57 (75)
T PF11302_consen 3 FLSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPKVPTLFQVADVDTG 57 (75)
T ss_pred ccccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCCCCceEEEEEccCC
Confidence 456899999999766522 344557889999987653 24566888887555
No 51
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=20.78 E-value=1.2e+02 Score=23.89 Aligned_cols=27 Identities=30% Similarity=0.458 Sum_probs=19.7
Q ss_pred CCcCCCCEEEEEeeecCCCCccccEEEEEEEEe
Q psy12656 85 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKR 117 (291)
Q Consensus 85 PeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr 117 (291)
=+|++||++...-.... .|.|-.+..+
T Consensus 27 Rdf~VGD~L~L~E~~~~------~YTGr~~~~~ 53 (72)
T PF12961_consen 27 RDFQVGDILVLREWDNG------EYTGREIEAE 53 (72)
T ss_pred CCCCCCCEEEEEEecCC------CccccEEEEE
Confidence 37999999998776542 6777766643
No 52
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.62 E-value=2.3e+02 Score=26.21 Aligned_cols=48 Identities=10% Similarity=0.074 Sum_probs=32.5
Q ss_pred CCcCCCCEEEEEeeecCCCCccccEEEEEEEEecCCcceeEEEEeeeCceeEE
Q psy12656 85 PSFFVGSILSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIE 137 (291)
Q Consensus 85 PeF~vGDiV~Vt~~i~e~K~R~q~F~GivIarr~~Gl~sTFtLRnvi~gvGVE 137 (291)
+-++-||.|.|.+.... =.=.-+| .|..+.+.+..+.|||...|.=|+
T Consensus 154 ~lV~rG~~V~I~a~~~g---~~Vs~~G--~AL~~G~~Ge~IrVrN~~SgrvV~ 201 (214)
T PRK12617 154 RLVRRGDTVPLVSRNGG---LEVRMSG--RALSDAGENERVSVENSSSRRVVQ 201 (214)
T ss_pred ceEcCCCEEEEEEecCC---EEEEEEE--EEccCCCCCCEEEEEECCCCCEEE
Confidence 36899999999987661 0011223 334567889999999977665554
No 53
>cd00493 FabA_FabZ FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation. The third step of the elongation cycle, the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, is catalyzed by FabA or FabZ. FabA is bifunctional and catalyzes an additional isomerization reaction of trans-2-acyl-ACP to cis-3-acyl-ACP, an essential reaction to unsaturated fatty acid synthesis. FabZ is the primary dehydratase that participates in the elongation cycles of saturated as well as unsaturated fatty acid biosynthesis, whereas FabA is more active in the dehydration of beta-hydroxydecanoyl-ACP. The FabA structure is homodimeric with two independent active sites located at the dimer interface.
Probab=20.15 E-value=1.3e+02 Score=23.62 Aligned_cols=30 Identities=17% Similarity=0.122 Sum_probs=22.2
Q ss_pred CcCCCCEEEEEeeecCCCCccccEEEEEEE
Q psy12656 86 SFFVGSILSVTSADKHDPNKTRKFVGICIQ 115 (291)
Q Consensus 86 eF~vGDiV~Vt~~i~e~K~R~q~F~GivIa 115 (291)
..++||+|.+++.+.+..+....|.|.+..
T Consensus 88 ~v~pgd~l~i~~~i~~~~~~~~~~~~~~~~ 117 (131)
T cd00493 88 PVLPGDTLTLEVELLKVRRGLGKFDGRAYV 117 (131)
T ss_pred CcCCCCEEEEEEEEEEeeCCEEEEEEEEEE
Confidence 467999999999888755566666666553
Done!