Query 037330
Match_columns 84
No_of_seqs 104 out of 215
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 11:05:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037330.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037330hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00148 40S ribosomal protein 100.0 1.8E-37 3.8E-42 233.0 7.3 74 5-78 132-205 (205)
2 KOG3283 40S ribosomal protein 100.0 3.7E-37 8E-42 230.0 6.4 73 7-79 128-200 (200)
3 PF01201 Ribosomal_S8e: Riboso 98.4 6.5E-08 1.4E-12 68.6 -0.1 19 43-61 114-132 (132)
4 COG2007 RPS8A Ribosomal protei 98.0 3.1E-06 6.8E-11 60.6 1.9 36 19-62 89-127 (127)
5 TIGR00307 S8e ribosomal protei 97.9 5.4E-06 1.2E-10 59.1 2.0 21 43-63 107-127 (127)
6 PRK04049 30S ribosomal protein 97.4 8.4E-05 1.8E-09 53.0 2.0 20 44-63 108-127 (127)
7 PTZ00388 40S ribosomal protein 95.9 0.0044 9.5E-08 48.0 1.8 19 43-61 204-222 (223)
8 PF09064 Tme5_EGF_like: Thromb 58.8 5.2 0.00011 23.1 0.9 16 48-63 15-30 (34)
9 PF09012 FeoC: FeoC like trans 49.5 13 0.00028 22.5 1.6 34 28-61 30-65 (69)
10 cd03148 GATase1_EcHsp31_like T 48.8 5.7 0.00012 29.6 -0.0 38 29-66 118-159 (232)
11 PF10878 DUF2672: Protein of u 42.5 14 0.0003 24.2 1.0 14 61-74 26-39 (67)
12 PF00863 Peptidase_C4: Peptida 42.2 10 0.00022 29.3 0.5 18 44-61 144-166 (235)
13 cd03147 GATase1_Ydr533c_like T 41.4 11 0.00023 28.2 0.4 41 29-69 116-161 (231)
14 PF04214 DUF411: Protein of un 41.1 17 0.00037 23.6 1.3 25 53-77 28-52 (70)
15 PF03891 DUF333: Domain of unk 40.1 56 0.0012 19.6 3.4 38 31-70 6-47 (50)
16 cd01422 MGS Methylglyoxal synt 38.2 28 0.00061 23.2 2.1 33 30-62 59-94 (115)
17 PF04083 Abhydro_lipase: Parti 35.6 16 0.00034 22.6 0.5 8 55-62 19-26 (63)
18 PF07313 DUF1460: Protein of u 33.7 23 0.0005 26.9 1.2 25 28-52 145-169 (216)
19 cd01151 GCD Glutaryl-CoA dehyd 26.7 93 0.002 23.7 3.4 31 34-64 118-160 (386)
20 PRK15231 fimbrial adhesin prot 25.3 52 0.0011 24.4 1.8 28 37-64 55-89 (150)
21 KOG3100 Uncharacterized conser 24.5 27 0.0006 27.1 0.2 21 58-79 161-181 (206)
22 PF00415 RCC1: Regulator of ch 24.1 76 0.0016 17.2 2.0 16 39-54 1-16 (51)
23 PF04694 Corona_3: Coronavirus 23.7 41 0.00088 21.6 0.8 13 34-46 28-40 (60)
24 KOG2630 Enolase-phosphatase E- 23.5 47 0.001 26.6 1.3 22 38-60 215-236 (254)
25 PRK05234 mgsA methylglyoxal sy 22.1 72 0.0016 22.3 2.0 32 30-61 64-98 (142)
26 cd01155 ACAD_FadE2 Acyl-CoA de 21.4 1.4E+02 0.003 22.9 3.5 32 33-64 116-160 (394)
27 PRK04155 chaperone protein Hch 21.4 61 0.0013 25.3 1.6 39 29-67 169-211 (287)
28 PF00749 tRNA-synt_1c: tRNA sy 21.3 70 0.0015 24.9 1.9 19 31-49 83-101 (314)
29 cd00049 MH1 MH1 is a small DNA 21.2 1.1E+02 0.0025 21.4 2.8 45 2-50 13-59 (121)
30 PLN02519 isovaleryl-CoA dehydr 20.7 1.4E+02 0.0031 23.0 3.5 31 34-64 134-176 (404)
31 PF08206 OB_RNB: Ribonuclease 20.3 75 0.0016 18.8 1.5 29 33-62 29-57 (58)
No 1
>PTZ00148 40S ribosomal protein S8; Provisional
Probab=100.00 E-value=1.8e-37 Score=233.01 Aligned_cols=74 Identities=61% Similarity=0.924 Sum_probs=70.3
Q ss_pred hhhhhhhhchHHHHHHHHHhccCCCChHHHHHhhcCceeEEEeccCCcccccceeeeccchHHHHHHHHHhhhc
Q 037330 5 PATEEAKKSSHVLRKLEKRQKDRTLDPHIEEQFGSGRLLACIASRPGQCGRADGYILEGKELEFYMKKLQRKKG 78 (84)
Q Consensus 5 ~~~~~kk~Sk~~~kK~~~R~k~~kv~~~L~eqf~~GrllA~IsSRPGQ~GraDGyILEGkELeFY~kki~~kK~ 78 (84)
++.+++++|+++++||+.|+++++||++|+|||.+||||||||||||||||||||||||+||+||+++|++||+
T Consensus 132 ~~~~~~k~s~~~~kk~~~r~~~~~~~~~leeqf~~GrllA~IsSRPGQ~Gr~dGyILEGkEL~FY~kk~~~kK~ 205 (205)
T PTZ00148 132 ENKKAKKKSESLVAKLEVRKKNHKIDKALLEQFQSGRLLARISSRPGQSGRADGYILEGKELEFYLKKLEKKKK 205 (205)
T ss_pred hhhhhhhhhHHHHHHHHHhhhhccccHHHHHHHhhCeEEEEEeCCCCCccceeEEEEecHHHHHHHHHHHhccC
Confidence 34567899999999999999999999999999999999999999999999999999999999999999999873
No 2
>KOG3283 consensus 40S ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.7e-37 Score=229.98 Aligned_cols=73 Identities=66% Similarity=1.101 Sum_probs=70.3
Q ss_pred hhhhhhchHHHHHHHHHhccCCCChHHHHHhhcCceeEEEeccCCcccccceeeeccchHHHHHHHHHhhhcc
Q 037330 7 TEEAKKSSHVLRKLEKRQKDRTLDPHIEEQFGSGRLLACIASRPGQCGRADGYILEGKELEFYMKKLQRKKGK 79 (84)
Q Consensus 7 ~~~kk~Sk~~~kK~~~R~k~~kv~~~L~eqf~~GrllA~IsSRPGQ~GraDGyILEGkELeFY~kki~~kK~k 79 (84)
.+++++|+++++||++|+++++||++|+|||++|||||||+|||||||+||||||||+||+||+++|++||.|
T Consensus 128 ~~~~k~sk~~~rk~~~r~~~a~vds~l~eqF~~GrL~A~isSrpGQ~GradgyileGkEl~FYlrki~~kk~k 200 (200)
T KOG3283|consen 128 ILNKKKSKHVQRKYAERQKNAKVDSSLEEQFAAGRLYACISSRPGQCGRADGYILEGKELEFYLRKIKAKKGK 200 (200)
T ss_pred cccchhhHHHHHHHHHhhccccccHHHHHHHhcCcEEEEEeCCCCcccccceeeeccchhHHHHHHhhhhcCC
Confidence 5678899999999999999999999999999999999999999999999999999999999999999999854
No 3
>PF01201 Ribosomal_S8e: Ribosomal protein S8e; InterPro: IPR022309 A number of eukaryotic and archaeal ribosomal proteins have been grouped based on sequence similarities []. One of these families, S8e, consists of a number of proteins with either about 220 amino acids (in eukaryotes) or about 125 amino acids (in archaea). This entry also contains proteins annotated as NSA2, which are though to be involved in ribosomal biogenesis of the 60S ribosomal subunit, having a role in the quality control of pre-60S particles. They are a component of the pre-66S ribosomal particle. ; PDB: 2KCY_A 2KCP_A 3U5G_I 3U5C_I 2KCO_A 2XZM_2 2XZN_2.
Probab=98.37 E-value=6.5e-08 Score=68.62 Aligned_cols=19 Identities=42% Similarity=0.660 Sum_probs=18.6
Q ss_pred eEEEeccCCcccccceeee
Q 037330 43 LACIASRPGQCGRADGYIL 61 (84)
Q Consensus 43 lA~IsSRPGQ~GraDGyIL 61 (84)
||+|+|||||+|.+|||||
T Consensus 114 ~A~vtSRPGQdG~vnavLl 132 (132)
T PF01201_consen 114 YARVTSRPGQDGVVNAVLL 132 (132)
T ss_dssp EEEEESEHHHHSCEEEEEE
T ss_pred eEEEEeCCCCcceeeEEEC
Confidence 9999999999999999997
No 4
>COG2007 RPS8A Ribosomal protein S8E [Translation, ribosomal structure and biogenesis]
Probab=97.99 E-value=3.1e-06 Score=60.59 Aligned_cols=36 Identities=36% Similarity=0.644 Sum_probs=27.5
Q ss_pred HHHHHh---ccCCCChHHHHHhhcCceeEEEeccCCcccccceeeec
Q 037330 19 KLEKRQ---KDRTLDPHIEEQFGSGRLLACIASRPGQCGRADGYILE 62 (84)
Q Consensus 19 K~~~R~---k~~kv~~~L~eqf~~GrllA~IsSRPGQ~GraDGyILE 62 (84)
-|..|. |.+.|+..+ | ||+|+|||||.|.+++++|+
T Consensus 89 ~y~rrniitKGaiI~t~~------G--~A~VTsRPgQdG~vNavLl~ 127 (127)
T COG2007 89 EYVRRNIITKGAIIETEI------G--YAVVTSRPGQDGVVNAVLLE 127 (127)
T ss_pred HHhhccceecceEEEEee------e--EEEEecCCCccceeEEEEeC
Confidence 355552 445555443 7 99999999999999999996
No 5
>TIGR00307 S8e ribosomal protein S8.e. Archaeal and eukaryotic ribosomal protein S8. This model could easily have been split into two models, one for eukaryotic S8 and one for archaeal S8; eukaryotic forms invariably have in insert of about 80 residues that archaeal forms of S8 do not.
Probab=97.92 E-value=5.4e-06 Score=59.05 Aligned_cols=21 Identities=43% Similarity=0.719 Sum_probs=19.9
Q ss_pred eEEEeccCCcccccceeeecc
Q 037330 43 LACIASRPGQCGRADGYILEG 63 (84)
Q Consensus 43 lA~IsSRPGQ~GraDGyILEG 63 (84)
+|+|+|||||.|.++|++||+
T Consensus 107 ~A~VTsrPgQdG~vNavll~~ 127 (127)
T TIGR00307 107 YARVTSRPGQDGVVNGVLIEE 127 (127)
T ss_pred EEEEecCCCcCceEeEEEecC
Confidence 599999999999999999985
No 6
>PRK04049 30S ribosomal protein S8e; Validated
Probab=97.41 E-value=8.4e-05 Score=53.03 Aligned_cols=20 Identities=40% Similarity=0.644 Sum_probs=18.9
Q ss_pred EEEeccCCcccccceeeecc
Q 037330 44 ACIASRPGQCGRADGYILEG 63 (84)
Q Consensus 44 A~IsSRPGQ~GraDGyILEG 63 (84)
|.|+|||||.|-.+|++||.
T Consensus 108 A~VTSRPGQdG~vNavLi~~ 127 (127)
T PRK04049 108 AKVTSRPGQDGVVNAVLIEE 127 (127)
T ss_pred EEEecCCCcCceEEEEEecC
Confidence 99999999999999999983
No 7
>PTZ00388 40S ribosomal protein S8-like; Provisional
Probab=95.92 E-value=0.0044 Score=48.03 Aligned_cols=19 Identities=21% Similarity=0.373 Sum_probs=18.1
Q ss_pred eEEEeccCCcccccceeee
Q 037330 43 LACIASRPGQCGRADGYIL 61 (84)
Q Consensus 43 lA~IsSRPGQ~GraDGyIL 61 (84)
||.|+|||||.|-.+|++|
T Consensus 204 yAqVTsrPgQDG~VNAVLL 222 (223)
T PTZ00388 204 YAQVTNNPENDGCINAVLL 222 (223)
T ss_pred eEEEecCCCcCceeeEEEe
Confidence 6999999999999999987
No 8
>PF09064 Tme5_EGF_like: Thrombomodulin like fifth domain, EGF-like; InterPro: IPR015149 This domain adopts a fold similar to other EGF domains, with a flat major and a twisted minor beta sheet. Disulphide pairing, however, is not of the usual 1-3, 2-4, 5-6 type; rather 1-2, 3-4, 5-6 pairing is found. Its extended major sheet (strands beta-2 and beta-3 and the connecting loop) projects into thrombin's active site groove. This domain is required for interaction of thrombomodulin with thrombin, and subsequent activation of protein-C []. ; GO: 0004888 transmembrane signaling receptor activity, 0016021 integral to membrane
Probab=58.79 E-value=5.2 Score=23.13 Aligned_cols=16 Identities=50% Similarity=1.020 Sum_probs=13.6
Q ss_pred ccCCcccccceeeecc
Q 037330 48 SRPGQCGRADGYILEG 63 (84)
Q Consensus 48 SRPGQ~GraDGyILEG 63 (84)
.-|+||-=+|||||.-
T Consensus 15 n~~~~C~CPeGyIlde 30 (34)
T PF09064_consen 15 NSPGQCFCPEGYILDE 30 (34)
T ss_pred CCCCceeCCCceEecC
Confidence 4688999999999973
No 9
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=49.47 E-value=13 Score=22.50 Aligned_cols=34 Identities=15% Similarity=0.213 Sum_probs=23.4
Q ss_pred CCChHHHHHhhcCceeEEEeccC--Ccccccceeee
Q 037330 28 TLDPHIEEQFGSGRLLACIASRP--GQCGRADGYIL 61 (84)
Q Consensus 28 kv~~~L~eqf~~GrllA~IsSRP--GQ~GraDGyIL 61 (84)
.|++.|+.-...|++-.+..+.+ |.|+.|++.-.
T Consensus 30 ~ve~mL~~l~~kG~I~~~~~~~~~~~~C~~C~~~~~ 65 (69)
T PF09012_consen 30 AVEAMLEQLIRKGYIRKVDMSSCCGGSCSSCGPASK 65 (69)
T ss_dssp HHHHHHHHHHCCTSCEEEEEE--SSSSSSS-SS---
T ss_pred HHHHHHHHHHHCCcEEEecCCCCCCCCCCCCCCccc
Confidence 47778888999999988877766 78888886543
No 10
>cd03148 GATase1_EcHsp31_like Type 1 glutamine amidotransferase (GATase1)-like domain found in Escherichia coli Hsp31 protein (EcHsp31). Type 1 glutamine amidotransferase (GATase1)-like domain found in Escherichia coli Hsp31 protein (EcHsp31). This group includes proteins similar to EcHsp31. EcHsp31 has chaperone activity. EcHsp31 coordinates a metal ion using a 2-His-1-carboxylate motif present in various ions that use iron as a cofactor such as Carboxypeptidase A. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with a typical GATase1domain, a reactive Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. This Cys together with a different His and, an Asp (rather than a Glu) residue form a different catalytic triad from the typical GATase1 domain. EcHsp31 is a homodimer.
Probab=48.77 E-value=5.7 Score=29.62 Aligned_cols=38 Identities=16% Similarity=0.279 Sum_probs=27.2
Q ss_pred CChHHHHHhhcCceeEEEeccC---Ccccccce-eeeccchH
Q 037330 29 LDPHIEEQFGSGRLLACIASRP---GQCGRADG-YILEGKEL 66 (84)
Q Consensus 29 v~~~L~eqf~~GrllA~IsSRP---GQ~GraDG-yILEGkEL 66 (84)
+-..|.+...+|+++|.||.-| .-.|..|| +||+|+.+
T Consensus 118 l~~ll~~f~~~gK~VaAICHGp~~L~~a~l~~g~~ll~Gk~v 159 (232)
T cd03148 118 VAAALQWAIKNDRFVITLCHGPAAFLAARHGGGKNPLEGYSV 159 (232)
T ss_pred HHHHHHHHHHcCCEEEEECcHHHHHHhccCCCCCeeeCCcEE
Confidence 3355777889999999999988 22355554 77887543
No 11
>PF10878 DUF2672: Protein of unknown function (DUF2672); InterPro: IPR022718 This group of proteins with unknown function appears to be restricted to Rickettsiaceae.
Probab=42.50 E-value=14 Score=24.18 Aligned_cols=14 Identities=50% Similarity=0.933 Sum_probs=11.0
Q ss_pred eccchHHHHHHHHH
Q 037330 61 LEGKELEFYMKKLQ 74 (84)
Q Consensus 61 LEGkELeFY~kki~ 74 (84)
||-+.+.||++||-
T Consensus 26 le~eQ~NFYlkkIi 39 (67)
T PF10878_consen 26 LETEQLNFYLKKII 39 (67)
T ss_pred hhHHHHHHHHHHHH
Confidence 55677999999874
No 12
>PF00863 Peptidase_C4: Peptidase family C4 This family belongs to family C4 of the peptidase classification.; InterPro: IPR001730 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. Nuclear inclusion A (NIA) proteases from potyviruses are cysteine peptidases belong to the MEROPS peptidase family C4 (NIa protease family, clan PA(C)) [, ]. Potyviruses include plant viruses in which the single-stranded RNA encodes a polyprotein with NIA protease activity, where proteolytic cleavage is specific for Gln+Gly sites. The NIA protease acts on the polyprotein, releasing itself by Gln+Gly cleavage at both the N- and C-termini. It further processes the polyprotein by cleavage at five similar sites in the C-terminal half of the sequence. In addition to its C-terminal protease activity, the NIA protease contains an N-terminal domain that has been implicated in the transcription process []. This peptidase is present in the nuclear inclusion protein of potyviruses.; GO: 0008234 cysteine-type peptidase activity, 0006508 proteolysis; PDB: 3MMG_B 1Q31_B 1LVB_A 1LVM_A.
Probab=42.20 E-value=10 Score=29.30 Aligned_cols=18 Identities=39% Similarity=0.842 Sum_probs=7.7
Q ss_pred EEEeccCCccccc-----ceeee
Q 037330 44 ACIASRPGQCGRA-----DGYIL 61 (84)
Q Consensus 44 A~IsSRPGQ~Gra-----DGyIL 61 (84)
=-|++.+|+||-+ ||.|+
T Consensus 144 HwIsTk~G~CG~PlVs~~Dg~IV 166 (235)
T PF00863_consen 144 HWISTKDGDCGLPLVSTKDGKIV 166 (235)
T ss_dssp E-C---TT-TT-EEEETTT--EE
T ss_pred EEecCCCCccCCcEEEcCCCcEE
Confidence 3577899999965 78886
No 13
>cd03147 GATase1_Ydr533c_like Type 1 glutamine amidotransferase (GATase1)-like domain found in Saccharomyces cerevisiae Ydr533c protein. Type 1 glutamine amidotransferase (GATase1)-like domain found in Saccharomyces cerevisiae Ydr533c protein. This group includes proteins similar to S. cerevisiae Ydr533c. Ydr533c is upregulated in response to various stress conditions along with the heat shock family. The catalytic triad typical of GATase1domains is not conserved in this GATase1-like domain. However, in common with a typical GATase1domain, a reactive Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. This Cys together with a different His and Glu residue form a different catalytic triad from the typical GATase1domain. Ydr533c protein is a homodimer.
Probab=41.42 E-value=11 Score=28.18 Aligned_cols=41 Identities=17% Similarity=0.405 Sum_probs=29.7
Q ss_pred CChHHHHHhhcCceeEEEeccCCccccc----ce-eeeccchHHHH
Q 037330 29 LDPHIEEQFGSGRLLACIASRPGQCGRA----DG-YILEGKELEFY 69 (84)
Q Consensus 29 v~~~L~eqf~~GrllA~IsSRPGQ~Gra----DG-yILEGkELeFY 69 (84)
+-..|.+...+|+++|.||.-|.--..+ || .||.|+.+.=|
T Consensus 116 l~~ll~~f~~~gK~iaAIChgp~~L~~a~~~~~g~~ll~Gk~vT~~ 161 (231)
T cd03147 116 LQKIAQQIYANGGVVAAVCHGPAILANLKDPKTGKPLIKGKTVTGF 161 (231)
T ss_pred HHHHHHHHHHcCCEEEEEChHHHHHHhhhcccCCCcccCCCEEEee
Confidence 4456778889999999999988544444 55 78888665433
No 14
>PF04214 DUF411: Protein of unknown function, DUF; InterPro: IPR007332 The function of the members of this bacterial protein family is unknown. Some members may be involved in conferring cation resistance.
Probab=41.13 E-value=17 Score=23.64 Aligned_cols=25 Identities=28% Similarity=0.433 Sum_probs=19.1
Q ss_pred ccccceeeeccchHHHHHHHHHhhh
Q 037330 53 CGRADGYILEGKELEFYMKKLQRKK 77 (84)
Q Consensus 53 ~GraDGyILEGkELeFY~kki~~kK 77 (84)
+...|||++||--..=.+++|-+.|
T Consensus 28 Ta~v~gy~iEGHVPa~~I~~lL~e~ 52 (70)
T PF04214_consen 28 TAVVGGYVIEGHVPADDIKRLLAEK 52 (70)
T ss_pred EEEECCEEEEccCCHHHHHHHHhcC
Confidence 4567899999977777777776655
No 15
>PF03891 DUF333: Domain of unknown function (DUF333); InterPro: IPR005590 This family consists of bacterial proteins whose function has not been characterised.
Probab=40.15 E-value=56 Score=19.60 Aligned_cols=38 Identities=26% Similarity=0.212 Sum_probs=25.1
Q ss_pred hHHHHHhhcCceeEEEeccCC-cc---cccceeeeccchHHHHH
Q 037330 31 PHIEEQFGSGRLLACIASRPG-QC---GRADGYILEGKELEFYM 70 (84)
Q Consensus 31 ~~L~eqf~~GrllA~IsSRPG-Q~---GraDGyILEGkELeFY~ 70 (84)
|+=.-....|--+....+--| |. --+||-..+ |++||.
T Consensus 6 PAs~yC~~~GG~~~~~~~~~G~~~g~C~lpdG~~~~--eW~l~r 47 (50)
T PF03891_consen 6 PASVYCVEQGGKLEIRKQPDGSQVGYCVLPDGRRCE--EWALYR 47 (50)
T ss_pred hHHHHHHHhCCEEEEEEcCCCCeEeEEECCCCCEEe--HHHHhh
Confidence 444445566666666555555 44 567899998 999985
No 16
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=38.20 E-value=28 Score=23.23 Aligned_cols=33 Identities=27% Similarity=0.239 Sum_probs=25.9
Q ss_pred ChHHHHHhhcCceeEEEecc-C-Cccc-ccceeeec
Q 037330 30 DPHIEEQFGSGRLLACIASR-P-GQCG-RADGYILE 62 (84)
Q Consensus 30 ~~~L~eqf~~GrllA~IsSR-P-GQ~G-raDGyILE 62 (84)
++.+.+.+..|.+=.+|... | |+.+ +.||+.|-
T Consensus 59 ~~~i~~~i~~g~i~~VInt~~~~~~~~~~~dg~~iR 94 (115)
T cd01422 59 DQQIGALIAEGEIDAVIFFRDPLTAQPHEPDVKALL 94 (115)
T ss_pred hhHHHHHHHcCceeEEEEcCCCCCCCcccccHHHHH
Confidence 36799999999988888764 4 8777 88987653
No 17
>PF04083 Abhydro_lipase: Partial alpha/beta-hydrolase lipase region; InterPro: IPR006693 The alpha/beta hydrolase fold is common to several hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is similar: an alpha/beta sheet, not barrel, of eight beta-sheets connected by alpha-helices []. This entry represents the N-terminal part of an alpha/beta hydrolase domain found in a number of lipases.; GO: 0006629 lipid metabolic process; PDB: 1K8Q_B 1HLG_B.
Probab=35.62 E-value=16 Score=22.63 Aligned_cols=8 Identities=63% Similarity=1.115 Sum_probs=6.2
Q ss_pred ccceeeec
Q 037330 55 RADGYILE 62 (84)
Q Consensus 55 raDGyILE 62 (84)
-.|||||+
T Consensus 19 T~DGYiL~ 26 (63)
T PF04083_consen 19 TEDGYILT 26 (63)
T ss_dssp -TTSEEEE
T ss_pred eCCCcEEE
Confidence 36999997
No 18
>PF07313 DUF1460: Protein of unknown function (DUF1460); InterPro: IPR010846 This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown.; PDB: 2P1G_B 2IM9_A.
Probab=33.74 E-value=23 Score=26.89 Aligned_cols=25 Identities=16% Similarity=0.381 Sum_probs=18.9
Q ss_pred CCChHHHHHhhcCceeEEEeccCCc
Q 037330 28 TLDPHIEEQFGSGRLLACIASRPGQ 52 (84)
Q Consensus 28 kv~~~L~eqf~~GrllA~IsSRPGQ 52 (84)
.|++.+..++.+|-++|.+++.+|-
T Consensus 145 ~i~~~~~~~i~~GDiI~i~t~~~GL 169 (216)
T PF07313_consen 145 KINDKLLSQIKNGDIIAIVTNIKGL 169 (216)
T ss_dssp HH-CCHHTTS-TT-EEEEEEECTTE
T ss_pred HHhHHHHhcCCCCCEEEEEeCCCCC
Confidence 3466788999999999999999884
No 19
>cd01151 GCD Glutaryl-CoA dehydrogenase. Glutaryl-CoA dehydrogenase (GCD). GCD is an acyl-CoA dehydrogenase, which catalyzes the oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA and carbon dioxide in the catabolism of lysine, hydroxylysine, and tryptophan. It uses electron transfer flavoprotein (ETF) as an electron acceptor. GCD is a homotetramer. GCD deficiency leads to a severe neurological disorder in humans.
Probab=26.72 E-value=93 Score=23.73 Aligned_cols=31 Identities=29% Similarity=0.711 Sum_probs=19.9
Q ss_pred HHHhhcCceeEEEe-ccCCc-c--------c--ccceeeeccc
Q 037330 34 EEQFGSGRLLACIA-SRPGQ-C--------G--RADGYILEGK 64 (84)
Q Consensus 34 ~eqf~~GrllA~Is-SRPGQ-~--------G--raDGyILEGk 64 (84)
...+.+|.+++|++ |-|+- + - ..|||+|.|.
T Consensus 118 l~~l~~G~~~~~~a~tEp~~Gsd~~~~~t~A~~~~~g~~lnG~ 160 (386)
T cd01151 118 LPKLASGELIGCFGLTEPNHGSDPGGMETRARKDGGGYKLNGS 160 (386)
T ss_pred HHHHhCCCeEEEEEecCCCCCCChhhCeEEEEEECCEEEEEEE
Confidence 34578899888775 44531 0 1 1368999984
No 20
>PRK15231 fimbrial adhesin protein SefD; Provisional
Probab=25.34 E-value=52 Score=24.44 Aligned_cols=28 Identities=29% Similarity=0.561 Sum_probs=20.5
Q ss_pred hhcCcee------EEEeccCCccc-ccceeeeccc
Q 037330 37 FGSGRLL------ACIASRPGQCG-RADGYILEGK 64 (84)
Q Consensus 37 f~~Grll------A~IsSRPGQ~G-raDGyILEGk 64 (84)
+.+||+. -.|.||--|.| ++.=|||.|+
T Consensus 55 laTGri~cregfhiwmns~~~q~gg~P~~YIvqGk 89 (150)
T PRK15231 55 IGTGHLFNREGKKILISSSLEKIKNTPGAYIIRGQ 89 (150)
T ss_pred EeeeeEEecCCeEEEEecchhhcCCCccEEEEECC
Confidence 3455554 36788877775 9999999984
No 21
>KOG3100 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.46 E-value=27 Score=27.08 Aligned_cols=21 Identities=38% Similarity=0.762 Sum_probs=15.8
Q ss_pred eeeeccchHHHHHHHHHhhhcc
Q 037330 58 GYILEGKELEFYMKKLQRKKGK 79 (84)
Q Consensus 58 GyILEGkELeFY~kki~~kK~k 79 (84)
|.|+|+.| +||..+|-+|-+|
T Consensus 161 GtIVe~p~-dFYsSRm~kKeRK 181 (206)
T KOG3100|consen 161 GTIVEDPE-DFYSSRMPKKERK 181 (206)
T ss_pred eeeccCHH-HHhhhccchhhHH
Confidence 66899876 8999877766544
No 22
>PF00415 RCC1: Regulator of chromosome condensation (RCC1) repeat; InterPro: IPR000408 The regulator of chromosome condensation (RCC1) [] is a eukaryotic protein which binds to chromatin and interacts with ran, a nuclear GTP-binding protein IPR002041 from INTERPRO, to promote the loss of bound GDP and the uptake of fresh GTP, thus acting as a guanine-nucleotide dissociation stimulator (GDS). The interaction of RCC1 with ran probably plays an important role in the regulation of gene expression. RCC1, known as PRP20 or SRM1 in yeast, pim1 in fission yeast and BJ1 in Drosophila, is a protein that contains seven tandem repeats of a domain of about 50 to 60 amino acids. As shown in the following schematic representation, the repeats make up the major part of the length of the protein. Outside the repeat region, there is just a small N-terminal domain of about 40 to 50 residues and, in the Drosophila protein only, a C-terminal domain of about 130 residues. +----+-------+-------+-------+-------+-------+-------+-------+-------------+ |N-t.|Rpt. 1 |Rpt. 2 |Rpt. 3 |Rpt. 4 |Rpt. 5 |Rpt. 6 |Rpt. 7 | C-terminal | +----+-------+-------+-------+-------+-------+-------+-------+-------------+ The RCC1-type of repeat is also found in the X-linked retinitis pigmentosa GTPase regulator []. The RCC repeats form a beta-propeller structure.; PDB: 3MVD_L 3OF7_A 1I2M_D 1A12_B 3KCI_A 4DNV_B 4DNU_A 4D9S_B 4DNW_A.
Probab=24.14 E-value=76 Score=17.17 Aligned_cols=16 Identities=31% Similarity=0.463 Sum_probs=14.8
Q ss_pred cCceeEEEeccCCccc
Q 037330 39 SGRLLACIASRPGQCG 54 (84)
Q Consensus 39 ~GrllA~IsSRPGQ~G 54 (84)
.|+||++=...-||.|
T Consensus 1 dG~vy~wG~n~~GqLG 16 (51)
T PF00415_consen 1 DGRVYSWGSNDYGQLG 16 (51)
T ss_dssp TSEEEEEEEETTSTTS
T ss_pred CCcEEEEECCCCCCCC
Confidence 4899999999999999
No 23
>PF04694 Corona_3: Coronavirus ORF3 protein; InterPro: IPR006784 This family represents the Coronavirus ORF3 protein, also known as the X2A protein.
Probab=23.66 E-value=41 Score=21.56 Aligned_cols=13 Identities=46% Similarity=1.058 Sum_probs=11.0
Q ss_pred HHHhhcCceeEEE
Q 037330 34 EEQFGSGRLLACI 46 (84)
Q Consensus 34 ~eqf~~GrllA~I 46 (84)
.-.|.+|+|+.||
T Consensus 28 kvef~tgkllVci 40 (60)
T PF04694_consen 28 KVEFKTGKLLVCI 40 (60)
T ss_pred EEEEecCcEEEEE
Confidence 3358999999998
No 24
>KOG2630 consensus Enolase-phosphatase E-1 [Amino acid transport and metabolism]
Probab=23.45 E-value=47 Score=26.55 Aligned_cols=22 Identities=36% Similarity=0.480 Sum_probs=18.6
Q ss_pred hcCceeEEEeccCCcccccceee
Q 037330 38 GSGRLLACIASRPGQCGRADGYI 60 (84)
Q Consensus 38 ~~GrllA~IsSRPGQ~GraDGyI 60 (84)
..| |.|.|.||||-.+-+|+-.
T Consensus 215 ~aG-l~a~l~~rPgna~l~dd~~ 236 (254)
T KOG2630|consen 215 KAG-LQAGLVSRPGNAPLPDDAK 236 (254)
T ss_pred hcc-cceeeeecCCCCCCCcccc
Confidence 345 9999999999999999755
No 25
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=22.07 E-value=72 Score=22.33 Aligned_cols=32 Identities=22% Similarity=0.142 Sum_probs=24.8
Q ss_pred ChHHHHHhhcCceeEEEecc--CCccc-ccceeee
Q 037330 30 DPHIEEQFGSGRLLACIASR--PGQCG-RADGYIL 61 (84)
Q Consensus 30 ~~~L~eqf~~GrllA~IsSR--PGQ~G-raDGyIL 61 (84)
++.+.+.+.+|.+-.+|... -|+-+ ..||+.|
T Consensus 64 ~~~i~~~I~~g~i~lVInt~dp~~~~~~~~D~~~I 98 (142)
T PRK05234 64 DQQIGALIAEGKIDMLIFFRDPLTAQPHDPDVKAL 98 (142)
T ss_pred chhHHHHHHcCceeEEEEecCCCCCCcccchHHHH
Confidence 36689999999999999875 47666 7788543
No 26
>cd01155 ACAD_FadE2 Acyl-CoA dehydrogenases similar to fadE2. FadE2-like Acyl-CoA dehydrogenase (ACAD). Acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACAD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. ACAD's are generally homotetramers and have an active site glutamate at a conserved position.
Probab=21.35 E-value=1.4e+02 Score=22.91 Aligned_cols=32 Identities=22% Similarity=0.495 Sum_probs=19.9
Q ss_pred HHHHhhcCceeEEEe-ccCCcc--------cc----cceeeeccc
Q 037330 33 IEEQFGSGRLLACIA-SRPGQC--------GR----ADGYILEGK 64 (84)
Q Consensus 33 L~eqf~~GrllA~Is-SRPGQ~--------Gr----aDGyILEGk 64 (84)
+...+.+|.+++++. |-|+-. ++ .|||+|.|.
T Consensus 116 ~l~~l~~G~~~~~~a~tE~~~~gsd~~~~~t~a~~~~~g~~LnG~ 160 (394)
T cd01155 116 WLEPLLDGKIRSAFAMTEPDVASSDATNIECSIERDGDDYVINGR 160 (394)
T ss_pred HHHHHhCCCeEEEEEeCCCCCCCCchhhCEEEEEEECCEEEEEEE
Confidence 334566788776655 667532 12 268999984
No 27
>PRK04155 chaperone protein HchA; Provisional
Probab=21.35 E-value=61 Score=25.26 Aligned_cols=39 Identities=15% Similarity=0.339 Sum_probs=26.5
Q ss_pred CChHHHHHhhcCceeEEEeccCC---cccccce-eeeccchHH
Q 037330 29 LDPHIEEQFGSGRLLACIASRPG---QCGRADG-YILEGKELE 67 (84)
Q Consensus 29 v~~~L~eqf~~GrllA~IsSRPG---Q~GraDG-yILEGkELe 67 (84)
+-..|.+.+.+|+++|.||.=|- ..|..|| +||+|+...
T Consensus 169 l~~ll~~~~~~~K~VaAICHGPa~Ll~a~~~~g~~ll~GkkvT 211 (287)
T PRK04155 169 VAAALQWALDNDRFIITLCHGPAALLAAGVDHGDNPLNGYSIC 211 (287)
T ss_pred HHHHHHHHHHcCCEEEEEChHHHHHHHcCCcCCCcccCCCEEe
Confidence 44567778899999999999882 2243333 677775543
No 28
>PF00749 tRNA-synt_1c: tRNA synthetases class I (E and Q), catalytic domain; InterPro: IPR020058 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Glutamyl-tRNA synthetase (6.1.1.17 from EC) is a class Ic synthetase and shows several similarities with glutaminyl-tRNA synthetase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamyl-tRNA synthetase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I synthetases and resembles the corresponding part of Escherichia coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure []. ; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0016876 ligase activity, forming aminoacyl-tRNA and related compounds, 0043039 tRNA aminoacylation, 0005737 cytoplasm; PDB: 2HZ7_A 2CFO_A 4A91_A 1NZJ_A 1N78_A 1G59_C 2CV2_A 2CV1_A 2CV0_B 1GLN_A ....
Probab=21.32 E-value=70 Score=24.90 Aligned_cols=19 Identities=26% Similarity=0.538 Sum_probs=15.8
Q ss_pred hHHHHHhhcCceeEEEecc
Q 037330 31 PHIEEQFGSGRLLACIASR 49 (84)
Q Consensus 31 ~~L~eqf~~GrllA~IsSR 49 (84)
..++..+..|.+|.|.+||
T Consensus 83 ~~~~~L~~~g~aY~C~Csr 101 (314)
T PF00749_consen 83 EAAEKLIDKGKAYPCFCSR 101 (314)
T ss_dssp HHHHHHHHTTSEEEEESEH
T ss_pred HHHHHHhhcCCCccccCCH
Confidence 4566678899999999996
No 29
>cd00049 MH1 MH1 is a small DNA binding domain, binding in an unusal way involving a beta hairpin structure binding to the major groove. MH1 is present in Smad proteins, an important family of proteins involved in TGF-beta signalling and frequent targets of tumorigenic mutations. Also known as Domain A in dwarfin family proteins.
Probab=21.21 E-value=1.1e+02 Score=21.43 Aligned_cols=45 Identities=22% Similarity=0.394 Sum_probs=25.7
Q ss_pred CChhhhhhhhhchHHHHHHHHHhccCCCChHHHHHhh-cCce-eEEEeccC
Q 037330 2 GDAPATEEAKKSSHVLRKLEKRQKDRTLDPHIEEQFG-SGRL-LACIASRP 50 (84)
Q Consensus 2 ~~~~~~~~kk~Sk~~~kK~~~R~k~~kv~~~L~eqf~-~Grl-lA~IsSRP 50 (84)
+|++++..++-..++.+|+.+++ .++. |+..+. .|.- ..||.+.|
T Consensus 13 ~~~~e~~~~k~~~sLlKkLKk~~---~le~-L~~AV~s~g~~~t~CV~i~r 59 (121)
T cd00049 13 GGEEEKWKKKAAESLLKKLKKKI---QLEE-LEDAVESRGGPPTRCVLIPR 59 (121)
T ss_pred CcchHHHHHHHHHHHHHHHhccc---CHHH-HHHHHHcCCCCCCCeEEecc
Confidence 34455555677778888886664 3332 222222 3433 77888865
No 30
>PLN02519 isovaleryl-CoA dehydrogenase
Probab=20.69 E-value=1.4e+02 Score=23.04 Aligned_cols=31 Identities=29% Similarity=0.539 Sum_probs=19.8
Q ss_pred HHHhhcCceeEEEe-ccCCcc-------cc----cceeeeccc
Q 037330 34 EEQFGSGRLLACIA-SRPGQC-------GR----ADGYILEGK 64 (84)
Q Consensus 34 ~eqf~~GrllA~Is-SRPGQ~-------Gr----aDGyILEGk 64 (84)
-..+.+|.+++|+. |-|+-- ++ .|||+|.|.
T Consensus 134 l~~l~~G~~~~~~a~sEp~~gsd~~~~~t~a~~~~~g~~lnG~ 176 (404)
T PLN02519 134 LPKLISGEHVGALAMSEPNSGSDVVSMKCKAERVDGGYVLNGN 176 (404)
T ss_pred HHHHhCCCeeEEEEecCCCcCCCcccceEEEEEeCCEEEEEeE
Confidence 34677898887764 556421 12 279999984
No 31
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=20.27 E-value=75 Score=18.77 Aligned_cols=29 Identities=21% Similarity=0.493 Sum_probs=21.5
Q ss_pred HHHHhhcCceeEEEeccCCcccccceeeec
Q 037330 33 IEEQFGSGRLLACIASRPGQCGRADGYILE 62 (84)
Q Consensus 33 L~eqf~~GrllA~IsSRPGQ~GraDGyILE 62 (84)
|...+..-++++.|.+ |-.-+++.|-|+|
T Consensus 29 l~~A~~gD~V~v~i~~-~~~~~~~eg~vv~ 57 (58)
T PF08206_consen 29 LNGAMDGDKVLVRITP-PSRGKRPEGEVVE 57 (58)
T ss_dssp HTTS-TT-EEEEEEEE-SSSEEEEEEEEEE
T ss_pred HCCCCCCCEEEEEEec-CCCCCCCCEEEEe
Confidence 4445666789999998 8888999998875
Done!