Query 038665
Match_columns 171
No_of_seqs 118 out of 761
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 13:22:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038665.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038665hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10343 RNA-binding protein Y 100.0 1.3E-36 2.7E-41 228.5 12.4 90 27-119 1-90 (97)
2 TIGR00253 RNA_bind_YhbY putati 100.0 5.2E-36 1.1E-40 224.2 12.2 91 29-122 1-91 (95)
3 COG1534 Predicted RNA-binding 100.0 7.3E-34 1.6E-38 214.0 11.5 93 28-123 1-93 (97)
4 PF01985 CRS1_YhbY: CRS1 / Yhb 100.0 4.9E-32 1.1E-36 196.6 10.4 84 29-115 1-84 (84)
5 KOG1990 Poly(A)-specific exori 97.4 0.00014 3E-09 68.9 4.4 105 15-122 369-478 (564)
6 KOG1990 Poly(A)-specific exori 95.2 0.021 4.6E-07 54.3 4.1 96 22-122 7-103 (564)
7 PF10369 ALS_ss_C: Small subun 67.2 11 0.00023 26.7 4.0 39 73-113 2-40 (75)
8 COG2390 DeoR Transcriptional r 61.6 33 0.00071 30.9 6.9 55 54-109 34-88 (321)
9 PF11272 DUF3072: Protein of u 58.7 32 0.00069 24.1 5.0 39 27-71 14-52 (57)
10 PF14807 AP4E_app_platf: Adapt 52.7 60 0.0013 24.8 6.1 51 63-113 7-58 (104)
11 PF09180 ProRS-C_1: Prolyl-tRN 49.0 67 0.0015 22.3 5.4 39 63-106 1-39 (68)
12 PF04391 DUF533: Protein of un 44.0 30 0.00065 28.9 3.6 31 28-70 157-187 (188)
13 PF00408 PGM_PMM_IV: Phosphogl 37.2 22 0.00048 24.3 1.5 47 75-123 1-49 (73)
14 PRK05783 hypothetical protein; 35.2 1.2E+02 0.0026 22.4 5.2 45 55-99 12-67 (84)
15 PRK11895 ilvH acetolactate syn 33.1 2.2E+02 0.0048 23.2 6.9 39 73-113 84-122 (161)
16 PRK14864 putative biofilm stre 31.7 1.4E+02 0.003 22.9 5.2 47 69-116 47-104 (104)
17 PRK03031 rnpA ribonuclease P; 30.8 90 0.002 23.8 4.1 42 36-77 74-119 (122)
18 cd02639 R3H_RRM R3H domain of 27.9 63 0.0014 22.4 2.5 22 26-47 23-44 (60)
19 CHL00100 ilvH acetohydroxyacid 27.4 1.4E+02 0.0031 24.6 5.0 40 73-114 84-123 (174)
20 COG1098 VacB Predicted RNA bin 27.0 58 0.0012 26.2 2.5 27 58-84 38-64 (129)
21 TIGR00119 acolac_sm acetolacta 26.5 1.5E+02 0.0033 24.0 4.9 39 73-113 83-121 (157)
22 COG4809 Archaeal ADP-dependent 26.4 1.3E+02 0.0029 28.7 5.0 72 53-124 293-364 (466)
23 cd05797 Ribosomal_L10 Ribosoma 25.9 2.6E+02 0.0057 21.6 6.0 73 35-117 10-84 (157)
24 PF04019 DUF359: Protein of un 25.6 1.9E+02 0.0041 22.5 5.1 52 51-104 39-90 (121)
25 cd08586 PI-PLCc_BcPLC_like Cat 25.5 2.5E+02 0.0053 24.5 6.3 63 57-119 73-152 (279)
26 cd08557 PI-PLCc_bacteria_like 25.2 2.6E+02 0.0057 22.8 6.2 63 57-119 79-161 (271)
27 PF13604 AAA_30: AAA domain; P 25.0 3.7E+02 0.0079 21.6 7.6 68 28-102 1-69 (196)
28 PF12802 MarR_2: MarR family; 23.7 1.5E+02 0.0032 18.8 3.6 55 29-83 3-58 (62)
29 PRK07315 fructose-bisphosphate 23.6 2.1E+02 0.0046 25.2 5.6 58 28-95 187-246 (293)
30 PRK00099 rplJ 50S ribosomal pr 23.0 3.8E+02 0.0082 21.2 6.5 72 35-116 11-84 (172)
31 PRK03459 rnpA ribonuclease P; 22.8 1.4E+02 0.003 23.0 3.9 44 33-76 67-118 (122)
32 PF01075 Glyco_transf_9: Glyco 22.8 2.6E+02 0.0056 22.4 5.6 83 24-108 83-170 (247)
33 PF06296 DUF1044: Protein of u 22.4 1E+02 0.0022 24.2 3.0 38 27-78 83-120 (120)
34 cd03338 TCP1_delta TCP-1 (CTT 22.4 2.3E+02 0.005 26.4 5.8 67 32-107 256-326 (515)
35 PF07997 DUF1694: Protein of u 21.9 1.7E+02 0.0037 22.7 4.2 68 32-103 24-91 (120)
36 PRK15418 transcriptional regul 21.9 4.1E+02 0.0089 23.5 7.1 52 55-107 38-89 (318)
37 PF13601 HTH_34: Winged helix 21.2 1.4E+02 0.0031 21.1 3.4 27 56-82 24-50 (80)
38 COG5238 RNA1 Ran GTPase-activa 21.0 75 0.0016 29.5 2.3 77 35-113 148-228 (388)
39 COG0042 tRNA-dihydrouridine sy 20.7 3E+02 0.0065 24.5 6.0 60 59-118 119-183 (323)
40 COG1846 MarR Transcriptional r 20.6 1.7E+02 0.0036 20.2 3.6 54 29-84 20-74 (126)
41 TIGR02045 P_fruct_ADP ADP-spec 20.4 4.2E+02 0.0091 25.2 7.1 84 33-121 262-345 (446)
No 1
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=100.00 E-value=1.3e-36 Score=228.55 Aligned_cols=90 Identities=33% Similarity=0.544 Sum_probs=87.5
Q ss_pred CCCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeE
Q 038665 27 PKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQ 106 (171)
Q Consensus 27 ~~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~ 106 (171)
|+||++||+|||++||+|+|+ |+|||+||||+|+++|+++|++||||||+|++++++++++++++||+.|+|++||+
T Consensus 1 m~Lt~kqr~~LR~~ah~l~Pv---v~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~ 77 (97)
T PRK10343 1 MNLSTKQKQHLKGLAHPLKPV---VLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQV 77 (97)
T ss_pred CCCCHHHHHHHHHhcCCCCCe---EEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEee
Confidence 679999999999999999995 79999999999999999999999999999999999999999999999999999999
Q ss_pred EccEEEEEcCCCC
Q 038665 107 IGQTVIIYRPSLT 119 (171)
Q Consensus 107 IG~t~ILYR~s~~ 119 (171)
||+++||||++++
T Consensus 78 IG~~~vlYR~~~~ 90 (97)
T PRK10343 78 IGKTLVLYRPTKE 90 (97)
T ss_pred eCcEEEEEecCCC
Confidence 9999999999864
No 2
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=100.00 E-value=5.2e-36 Score=224.21 Aligned_cols=91 Identities=36% Similarity=0.557 Sum_probs=87.7
Q ss_pred CCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEc
Q 038665 29 LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIG 108 (171)
Q Consensus 29 LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG 108 (171)
||++||++||++||+|+|+ |+|||+||||+|+++|+++|++||||||+|++++++|++++|++||+.|||++||+||
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~---v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~iG 77 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPV---VLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQVIG 77 (95)
T ss_pred CCHHHHHHHHHHhCCCCCe---EEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEEc
Confidence 7999999999999999995 7999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEEcCCCCccc
Q 038665 109 QTVIIYRPSLTRMK 122 (171)
Q Consensus 109 ~t~ILYR~s~~~~k 122 (171)
++++|||+++++++
T Consensus 78 ~~~vlYR~~~~~~~ 91 (95)
T TIGR00253 78 KTIVLYRPTKERKI 91 (95)
T ss_pred cEEEEEecCCccCC
Confidence 99999999987543
No 3
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.3e-34 Score=213.96 Aligned_cols=93 Identities=37% Similarity=0.576 Sum_probs=89.7
Q ss_pred CCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEE
Q 038665 28 KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQI 107 (171)
Q Consensus 28 ~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~I 107 (171)
+||++|+++||++||+++|+ |||||+||||+||+||+++|++||||||+|++++.+|++++|+.||+.+||++||+|
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~pi---v~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqvi 77 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPI---VQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQVI 77 (97)
T ss_pred CCcHHHHHHHHHhhccCCce---EEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeeee
Confidence 58999999999999999996 699999999999999999999999999999999999999999999999999999999
Q ss_pred ccEEEEEcCCCCccch
Q 038665 108 GQTVIIYRPSLTRMKL 123 (171)
Q Consensus 108 G~t~ILYR~s~~~~k~ 123 (171)
|+++||||++.++.++
T Consensus 78 G~~~vlyr~~~e~~~i 93 (97)
T COG1534 78 GKTLVLYRESKEKRKI 93 (97)
T ss_pred eeEEEEEecCcccccc
Confidence 9999999988887765
No 4
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.97 E-value=4.9e-32 Score=196.65 Aligned_cols=84 Identities=42% Similarity=0.694 Sum_probs=75.0
Q ss_pred CCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEc
Q 038665 29 LTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIG 108 (171)
Q Consensus 29 LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG 108 (171)
||++|+++||++||+|+|+ |+|||+||||+|+++|+++|++||||||+|++++++|+++++++||+.|||++||+||
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~---v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~iG 77 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPV---VQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQVIG 77 (84)
T ss_dssp --HHHHHHHHHHHTTC--S---EEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEEET
T ss_pred CCHHHHHHHHHHhcCCCCe---EEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEEEC
Confidence 7999999999999999996 6999999999999999999999999999999999999999999999999999999999
Q ss_pred cEEEEEc
Q 038665 109 QTVIIYR 115 (171)
Q Consensus 109 ~t~ILYR 115 (171)
+++||||
T Consensus 78 ~~~vlyR 84 (84)
T PF01985_consen 78 RTIVLYR 84 (84)
T ss_dssp TEEEEEE
T ss_pred CEEEEEC
Confidence 9999998
No 5
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=97.44 E-value=0.00014 Score=68.93 Aligned_cols=105 Identities=22% Similarity=0.309 Sum_probs=91.1
Q ss_pred eccCCCCCCCCCCCCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCCh-hhHHHHHH
Q 038665 15 EVKSPSRSPLPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCP-GELEDVVK 93 (171)
Q Consensus 15 ~~~~~~r~~~~~~~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~-~d~~e~ae 93 (171)
..+.+...+-....+|.+++.+++.++..+++. +..|..|+.++++..++.+|+++|++|+.+..... ....+.+.
T Consensus 369 ~~~~~~~~~~~~e~~t~ee~~~~~k~g~k~~~~---~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~ 445 (564)
T KOG1990|consen 369 DPKIPAELRYDPESITEEERLMLRKVGLKMKRR---LLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYAS 445 (564)
T ss_pred ccccccccccchhhcChHHHHHHHHHHHhhccc---cccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHH
Confidence 345555555566779999999999999999997 59999999999999999999999999999999654 89999999
Q ss_pred HHHHHhCCeEEeEEcc----EEEEEcCCCCccc
Q 038665 94 QLEEATGSAVVSQIGQ----TVIIYRPSLTRMK 122 (171)
Q Consensus 94 ~La~~tgaevVq~IG~----t~ILYR~s~~~~k 122 (171)
.++...|..+|....+ .+++||+......
T Consensus 446 ~le~esg~~~v~~~~~~~~~ai~~yr~k~y~~p 478 (564)
T KOG1990|consen 446 ALERESGGILVSIDKNPKGYAIIAYRGKNYDRP 478 (564)
T ss_pred HHHHHhCCceeeeccCCchhhHHHhhhhhccCC
Confidence 9999999999999954 4799998765544
No 6
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=95.21 E-value=0.021 Score=54.32 Aligned_cols=96 Identities=19% Similarity=0.081 Sum_probs=84.9
Q ss_pred CCCCCCCCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCC
Q 038665 22 SPLPLPKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGS 101 (171)
Q Consensus 22 ~~~~~~~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tga 101 (171)
..+.++.+..++-.+||..+-.+.-. +++.|+|..+++.|.+-|+.+|++.++|.-..-..+....+.+...|++
T Consensus 7 ~~~~~~~~~~~~~~~l~~~~~~~~~~-----~~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~~~~~~~~ 81 (564)
T KOG1990|consen 7 LSLAELTVDEADLRRLRLVATGMTSA-----PWKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEALEMSTGG 81 (564)
T ss_pred hhHHHhhcCHHHHHHHhhhhccceec-----ccccccchhhhHHHHHHHHhhhhhheeeccccchhHHHhhhHhhccCCC
Confidence 56777889999999999999999874 5999999999999999999999999999999888999999999999999
Q ss_pred -eEEeEEccEEEEEcCCCCccc
Q 038665 102 -AVVSQIGQTVIIYRPSLTRMK 122 (171)
Q Consensus 102 -evVq~IG~t~ILYR~s~~~~k 122 (171)
-+||..|-....|++.-...+
T Consensus 82 n~~~~~~g~~~s~~~~~~~~~~ 103 (564)
T KOG1990|consen 82 NFVVWSRGDSISSPEFLCQRSP 103 (564)
T ss_pred ceeeeecCccccCCccceeecc
Confidence 789999999999844443333
No 7
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=67.17 E-value=11 Score=26.73 Aligned_cols=39 Identities=28% Similarity=0.382 Sum_probs=24.2
Q ss_pred CCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEccEEEE
Q 038665 73 NELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVII 113 (171)
Q Consensus 73 hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG~t~IL 113 (171)
+||+=|||.. ...+ ..-..+|++..+|.+|++--+++++
T Consensus 2 rEl~LiKV~~-~~~~-r~ei~~l~~~f~a~ivd~~~~~~ii 40 (75)
T PF10369_consen 2 RELALIKVKA-TPEN-RSEILQLAEIFRARIVDVSPDSIII 40 (75)
T ss_dssp EEEEEEEEE--SCHH-HHHHHHHHHHTT-EEEEEETTEEEE
T ss_pred eEEEEEEEEC-CccC-HHHHHHHHHHhCCEEEEECCCEEEE
Confidence 3444444444 2233 3445678999999999998887766
No 8
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=61.57 E-value=33 Score=30.88 Aligned_cols=55 Identities=16% Similarity=0.253 Sum_probs=46.5
Q ss_pred CCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEcc
Q 038665 54 GKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQ 109 (171)
Q Consensus 54 GK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG~ 109 (171)
-+-|||..++..+=...+..++|||+|. ....+.-++.++|.++.|-.=+.++-.
T Consensus 34 ~~LgiSR~~v~rlL~~Ar~~GiV~I~i~-~~~~~~~~Le~~L~~~fgL~~a~VVp~ 88 (321)
T COG2390 34 ERLGISRATVSRLLAKAREEGIVKISIN-SPVEGCLELEQQLKERFGLKEAIVVPS 88 (321)
T ss_pred HHhCCCHHHHHHHHHHHHHCCeEEEEeC-CCCcchHHHHHHHHHhcCCCeEEEEcC
Confidence 3569999999999999999999999999 556677789999999999886666543
No 9
>PF11272 DUF3072: Protein of unknown function (DUF3072); InterPro: IPR021425 This bacterial family of proteins has no known function.
Probab=58.74 E-value=32 Score=24.10 Aligned_cols=39 Identities=15% Similarity=0.244 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHH
Q 038665 27 PKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLE 71 (171)
Q Consensus 27 ~~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~ 71 (171)
.++|+.|+.||+.+++.-..-+ -.+||-+-..+.-+.|.
T Consensus 14 ePmT~aQ~syL~tL~e~Age~~------~~~LtkaeAs~rId~L~ 52 (57)
T PF11272_consen 14 EPMTGAQASYLKTLSEEAGEPF------PDDLTKAEASERIDELQ 52 (57)
T ss_pred CCCcHHHHHHHHHHHHHhCCCC------CCcccHHHHHHHHHHHH
Confidence 4689999999999999887532 35788765555555444
No 10
>PF14807 AP4E_app_platf: Adaptin AP4 complex epsilon appendage platform
Probab=52.74 E-value=60 Score=24.84 Aligned_cols=51 Identities=18% Similarity=0.215 Sum_probs=41.1
Q ss_pred HHHHHHHHHh-CCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEccEEEE
Q 038665 63 VTSFIETLEA-NELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVII 113 (171)
Q Consensus 63 I~eI~~aL~~-hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG~t~IL 113 (171)
.+|+...|.. ..=.|+++.........++...+.++.+-.+|++||+=.|+
T Consensus 7 TeeFG~~W~s~~~e~k~~l~~~~~~t~~~~l~~l~~~l~lh~VevIg~E~I~ 58 (104)
T PF14807_consen 7 TEEFGQLWLSFSNERKQNLPSSSQRTLPEFLQRLQQKLRLHVVEVIGNEGIF 58 (104)
T ss_pred HHHHHHHHHcCCCeEEEeccccCcCCHHHHHHHHHHhcCceEEEEeCcccee
Confidence 4677777877 44578888766677888999999999999999999996554
No 11
>PF09180 ProRS-C_1: Prolyl-tRNA synthetase, C-terminal; InterPro: IPR016061 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. Prolyl tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This domain is found at the C-terminal in archaeal and eukaryotic enzymes, as well as in certain bacterial ones.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1NJ6_A 1NJ2_A 1NJ5_A 1NJ1_A 1H4T_C 1H4S_A 1HC7_C 1H4Q_B 3IAL_B.
Probab=48.96 E-value=67 Score=22.29 Aligned_cols=39 Identities=18% Similarity=0.331 Sum_probs=29.8
Q ss_pred HHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeE
Q 038665 63 VTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQ 106 (171)
Q Consensus 63 I~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~ 106 (171)
++|+..+|++.++|.+-+-.+ .+-.+.|.+.|||.+--+
T Consensus 1 ~eE~k~~i~~gg~v~~pwcg~-----~ece~~ike~t~at~rci 39 (68)
T PF09180_consen 1 YEEFKEAIEKGGFVLVPWCGD-----EECEEKIKEETGATIRCI 39 (68)
T ss_dssp HHHHHHHHHTSSEEEEEES-S-----HHHHHHHHHHHS-EEEEE
T ss_pred ChHHHHHHhCCCEEEEEccCC-----HHHHHHHHHhcCCcEeEe
Confidence 478999998889999999775 556677888998877554
No 12
>PF04391 DUF533: Protein of unknown function (DUF533); InterPro: IPR007486 Some family members may be secreted or integral membrane proteins.
Probab=44.03 E-value=30 Score=28.94 Aligned_cols=31 Identities=23% Similarity=0.280 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHH
Q 038665 28 KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETL 70 (171)
Q Consensus 28 ~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL 70 (171)
..|..||.||..+|..| ||++.++++|+.+.
T Consensus 157 ~d~~~Er~YL~~LA~aL------------~L~~~lv~~le~~~ 187 (188)
T PF04391_consen 157 VDTFAERAYLDELAQAL------------GLDPDLVAQLEQQA 187 (188)
T ss_pred CCCHHHHHHHHHHHHHh------------CcCHHHHHHHHHHc
Confidence 46899999999999998 56799999998763
No 13
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=37.18 E-value=22 Score=24.33 Aligned_cols=47 Identities=13% Similarity=0.177 Sum_probs=27.1
Q ss_pred eEeEEEcCCChhhHHHHHHHHHH--HhCCeEEeEEccEEEEEcCCCCccch
Q 038665 75 LLKIKIHRTCPGELEDVVKQLEE--ATGSAVVSQIGQTVIIYRPSLTRMKL 123 (171)
Q Consensus 75 LIKVKil~n~~~d~~e~ae~La~--~tgaevVq~IG~t~ILYR~s~~~~k~ 123 (171)
+|++++..... ++.+...... ..++.-+.......++.|+|.+.|+.
T Consensus 1 eIn~~v~~~~~--~~~~~~~~~~~~~~~~~~~~~~dG~~l~vR~SgTEP~i 49 (73)
T PF00408_consen 1 EINVKVKEKKK--IKELEDIFKAESTIDGIKILFEDGWRLLVRPSGTEPKI 49 (73)
T ss_dssp EEEEE-STCCH--TCECHHHHHHHEHHHCEEEEETTEEEEEEEEESSSSEE
T ss_pred CcceEcCCchh--HHHHHHHHhcccccceEEEECCCceEEEEECCCCCceE
Confidence 57777766533 3333333333 45555555554444559999999984
No 14
>PRK05783 hypothetical protein; Provisional
Probab=35.18 E-value=1.2e+02 Score=22.38 Aligned_cols=45 Identities=18% Similarity=0.211 Sum_probs=31.3
Q ss_pred CCCCCHHHHHHHHHHHHhCC-----------eEeEEEcCCChhhHHHHHHHHHHHh
Q 038665 55 KSGVTDGVVTSFIETLEANE-----------LLKIKIHRTCPGELEDVVKQLEEAT 99 (171)
Q Consensus 55 K~GLTe~VI~eI~~aL~~hE-----------LIKVKil~n~~~d~~e~ae~La~~t 99 (171)
|.|+-|--=+.|.++|..++ .+.+.+..++.++..+.++++|+++
T Consensus 12 K~gVlDPqG~aI~~aL~~lg~~~V~~VRvGK~iel~l~~~~~e~a~~~v~~mc~~L 67 (84)
T PRK05783 12 KDSVRDPEGETIQRYVIERYTGNIIEVRAGKYLVFKIEANSPEEAKELALKIAREG 67 (84)
T ss_pred CCCCcCchHHHHHHHHHHcCCCCcceEEeeEEEEEEEcCCCHHHHHHHHHHHHHhc
Confidence 56666666677777776553 3556666666777788888888775
No 15
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=33.10 E-value=2.2e+02 Score=23.17 Aligned_cols=39 Identities=15% Similarity=0.253 Sum_probs=25.7
Q ss_pred CCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEccEEEE
Q 038665 73 NELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVII 113 (171)
Q Consensus 73 hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG~t~IL 113 (171)
+||+=||+..+. .+ ..-+.+|++..+|.+|++--+++++
T Consensus 84 rEl~LiKv~~~~-~~-r~~i~~i~~~f~a~ivdv~~~~~~i 122 (161)
T PRK11895 84 RELALVKVRASG-EN-RAEILRLADIFRAKIVDVTPESLTI 122 (161)
T ss_pred eEEEEEEEECCc-cc-HHHHHHHHHHhCCEEEEecCCEEEE
Confidence 555555554432 23 3456678999999999987666665
No 16
>PRK14864 putative biofilm stress and motility protein A; Provisional
Probab=31.72 E-value=1.4e+02 Score=22.92 Aligned_cols=47 Identities=19% Similarity=0.297 Sum_probs=34.2
Q ss_pred HHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEcc-----------EEEEEcC
Q 038665 69 TLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQ-----------TVIIYRP 116 (171)
Q Consensus 69 aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG~-----------t~ILYR~ 116 (171)
.|.+=+.|-|.+ ..+++|.++...+-|++-||.-.++|.- +++|||+
T Consensus 47 ~lq~iGtVSvs~-~gsp~d~~~~La~KAda~GA~yYrIi~~~e~~~~~~~~atA~iYk~ 104 (104)
T PRK14864 47 GLQKMGTVSALV-RGSPDDAEREIQAKANAAGADYYVIVMVDETVVPGQWYSQAILYRK 104 (104)
T ss_pred CCceeeEEEEec-CCCHHHHHHHHHHHHHHcCCCEEEEEEccccCCCCeEEEEEEEecC
Confidence 455556777774 4567888888888888889988777743 6888873
No 17
>PRK03031 rnpA ribonuclease P; Reviewed
Probab=30.81 E-value=90 Score=23.78 Aligned_cols=42 Identities=10% Similarity=0.156 Sum_probs=29.0
Q ss_pred HHHHhhhhcCCcccceecCCCCCCH----HHHHHHHHHHHhCCeEe
Q 038665 36 ELASYAHSLGKKLKCQLVGKSGVTD----GVVTSFIETLEANELLK 77 (171)
Q Consensus 36 ~LR~~AH~LkP~i~~V~IGK~GLTe----~VI~eI~~aL~~hELIK 77 (171)
.+|...+.|.|-..+|.|.+.|+.+ .+.+++...|+..+|+.
T Consensus 74 ~~R~~~~~l~~g~diVvi~r~~~~~~~~~~l~~~l~~ll~k~~~~~ 119 (122)
T PRK03031 74 ALRQLLPRIAPGWDLVIIVKPTAAECNYEQFLQELEQLLIQAEIIH 119 (122)
T ss_pred HHHHhhhccCCCceEEEEECCCcccCCHHHHHHHHHHHHHHccCcc
Confidence 3344445565543458899999865 77888888888887665
No 18
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=27.90 E-value=63 Score=22.35 Aligned_cols=22 Identities=23% Similarity=0.274 Sum_probs=19.0
Q ss_pred CCCCCHHHHHHHHHhhhhcCCc
Q 038665 26 LPKLTVKEKKELASYAHSLGKK 47 (171)
Q Consensus 26 ~~~LT~kqRk~LR~~AH~LkP~ 47 (171)
+..||+.||+.+-.+||.|.=.
T Consensus 23 p~~ls~~eRriih~la~~lGL~ 44 (60)
T cd02639 23 PSSLSPAERRIVHLLASRLGLN 44 (60)
T ss_pred CCCCCHHHHHHHHHHHHHcCCc
Confidence 3569999999999999999754
No 19
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=27.43 E-value=1.4e+02 Score=24.60 Aligned_cols=40 Identities=20% Similarity=0.254 Sum_probs=25.8
Q ss_pred CCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEccEEEEE
Q 038665 73 NELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIY 114 (171)
Q Consensus 73 hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG~t~ILY 114 (171)
+||+=||+..+ +.++. -+.+|++..+|.+|++--+++++=
T Consensus 84 rEl~LiKv~~~-~~~r~-ei~~~~~~f~a~ivdv~~~~~~ie 123 (174)
T CHL00100 84 RELMLIKINVN-SQTRP-EILEIAQIFRAKVVDLSEESLILE 123 (174)
T ss_pred eEEEEEEEecC-CcCHH-HHHHHHHHhCCEEEEecCCEEEEE
Confidence 55555554443 23443 345688889999999887777653
No 20
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=27.02 E-value=58 Score=26.24 Aligned_cols=27 Identities=22% Similarity=0.412 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHHHHhCCeEeEEEcCCC
Q 038665 58 VTDGVVTSFIETLEANELLKIKIHRTC 84 (171)
Q Consensus 58 LTe~VI~eI~~aL~~hELIKVKil~n~ 84 (171)
|+++++..|++.|.--+=|+|||+.-+
T Consensus 38 Ia~~fVkdI~d~L~vG~eV~vKVl~id 64 (129)
T COG1098 38 IADGFVKDIHDHLKVGQEVKVKVLDID 64 (129)
T ss_pred hhhhhHHhHHHHhcCCCEEEEEEEeec
Confidence 589999999999999999999999843
No 21
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=26.46 E-value=1.5e+02 Score=23.98 Aligned_cols=39 Identities=15% Similarity=0.168 Sum_probs=24.2
Q ss_pred CCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEccEEEE
Q 038665 73 NELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVII 113 (171)
Q Consensus 73 hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG~t~IL 113 (171)
+||+=||+..+ ..++ .-+.+|++..+|.+|++--+++++
T Consensus 83 rEl~LiKv~~~-~~~r-~~i~~i~~~f~a~ivdv~~~~~~i 121 (157)
T TIGR00119 83 RELCLVKVSAP-GEGR-DEIIRLTNIFRGRIVDVSPDSYTV 121 (157)
T ss_pred eEEEEEEEECC-ccCH-HHHHHHHHHhCCEEEEecCCEEEE
Confidence 45544444332 2333 445668889999999986666554
No 22
>COG4809 Archaeal ADP-dependent phosphofructokinase/glucokinase [Carbohydrate transport and metabolism]
Probab=26.38 E-value=1.3e+02 Score=28.74 Aligned_cols=72 Identities=11% Similarity=-0.011 Sum_probs=56.6
Q ss_pred cCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEccEEEEEcCCCCccchH
Q 038665 53 VGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSLTRMKLE 124 (171)
Q Consensus 53 IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG~t~ILYR~s~~~~k~~ 124 (171)
+=.=|+++.=++.+-+.|-.+||-+=-+..+..++.=+-+.+|...+|-+.||+.-.-++||=-.+.+|.-.
T Consensus 293 v~SvGldE~ElA~vl~vlG~~eLa~~I~~~~~~~avieg~~~L~~e~~~e~i~vHT~~y~l~i~~~~npl~~ 364 (466)
T COG4809 293 VYSVGLDEVELANVLNVLGYRELADRIISKDDIEAVIEGAMILLDELGLERIHVHTYGYYLAITKRGNPLSG 364 (466)
T ss_pred hhhcCCCHHHHHHHHHhhChHHHHHhhhccccHHHHHHHHHHHHHhcCccEEEEEEeeEEEEEecCCCcccH
Confidence 344589999999999999999999888888878888899999999999988877755555555555555533
No 23
>cd05797 Ribosomal_L10 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-in
Probab=25.85 E-value=2.6e+02 Score=21.63 Aligned_cols=73 Identities=21% Similarity=0.247 Sum_probs=47.0
Q ss_pred HHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEE--eEEccEEE
Q 038665 35 KELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVV--SQIGQTVI 112 (171)
Q Consensus 35 k~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevV--q~IG~t~I 112 (171)
..|+.....-+- ++.+.-+|+|-+-+.++...|..++ +++++.+|. ++..-.+.|+.+-+ ...|.+++
T Consensus 10 ~~l~~~l~~~~~---v~v~~~~gl~~~~~~~lR~~lr~~~-~~~~V~KNt------L~~~Al~~t~~~~l~~~l~G~~al 79 (157)
T cd05797 10 AELKEKLKEAKS---VVVADYRGLTVAQLTELRKELREAG-VKLKVVKNT------LAKRALEGTGFEDLDDLLKGPTAI 79 (157)
T ss_pred HHHHHHHHhCCE---EEEEecCCCcHHHHHHHHHHHHHcC-CEEEEehhH------HHHHHHhcCCchhhHhhCcCCEEE
Confidence 344445444444 3688889999999999999999886 477777764 22222223332211 34699999
Q ss_pred EEcCC
Q 038665 113 IYRPS 117 (171)
Q Consensus 113 LYR~s 117 (171)
+|=..
T Consensus 80 ~f~~~ 84 (157)
T cd05797 80 AFSEE 84 (157)
T ss_pred EEeCC
Confidence 99643
No 24
>PF04019 DUF359: Protein of unknown function (DUF359); InterPro: IPR007164 This is family of archaebacterial proteins, which are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function.
Probab=25.55 E-value=1.9e+02 Score=22.55 Aligned_cols=52 Identities=17% Similarity=0.210 Sum_probs=40.8
Q ss_pred eecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEE
Q 038665 51 QLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVV 104 (171)
Q Consensus 51 V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevV 104 (171)
|.=-..-||++.++.|..+++..+=+-|.+.+ .+|...+...+..-.|+.++
T Consensus 39 v~NPpG~It~el~~ai~~a~~~~~~~~I~V~G--EEDL~~lPail~aP~gs~V~ 90 (121)
T PF04019_consen 39 VKNPPGTITEELIEAIKKALESGKPVVIFVDG--EEDLAVLPAILYAPEGSVVL 90 (121)
T ss_pred EECCCCcccHHHHHHHHHHHhCCCCEEEEEeC--hHHHHHHHHHHhCCCCCEEE
Confidence 33455779999999999999888888888877 46777777777777676554
No 25
>cd08586 PI-PLCc_BcPLC_like Catalytic domain of Bacillus cereus phosphatidylinositol-specific phospholipases C and similar proteins. This subfamily corresponds to the catalytic domain present in Bacillus cereus phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) and its sequence homologs found in bacteria and eukaryota. Bacterial PI-PLCs participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although their precise physiological function remains unclear, bacterial PI-PLCs may function as virulence factors in some pathogenic bacteria. Bacterial PI-PLCs contain a single TIM-barrel type catalytic domain. Their catalytic mechanism is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This family also includes some uncharacterized eukaryotic homologs, which
Probab=25.53 E-value=2.5e+02 Score=24.45 Aligned_cols=63 Identities=16% Similarity=0.179 Sum_probs=46.8
Q ss_pred CCCHHHHHHHHHHHHhC--CeEeEEEcCCChhh--HHHHHHHHHHHhCCeE-------------EeEEccEEEEEcCCCC
Q 038665 57 GVTDGVVTSFIETLEAN--ELLKIKIHRTCPGE--LEDVVKQLEEATGSAV-------------VSQIGQTVIIYRPSLT 119 (171)
Q Consensus 57 GLTe~VI~eI~~aL~~h--ELIKVKil~n~~~d--~~e~ae~La~~tgaev-------------Vq~IG~t~ILYR~s~~ 119 (171)
+--+.|+.+|..-|++| |+|=+.+......+ .+..++.+.+...... =+.+|.+++|=|-.-.
T Consensus 73 ~~~~dvL~~i~~FL~~nP~E~Vil~l~~e~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~PtLge~RGKIVLl~rf~~~ 152 (279)
T cd08586 73 LTFGDVLNECYSFLDANPSETIIMSLKQEGSGDGNTDSFAEIFKEYLDNYPSYFYYTESKIPTLGEVRGKIVLLRRFDGD 152 (279)
T ss_pred CcHHHHHHHHHHHHHhCCCcEEEEEEEecCCCCCchHHHHHHHHHHHhcccccccccCCCCCchHHhcccEEEEEecCCC
Confidence 44589999999999997 99999998866543 6677777776655443 2567888888775443
No 26
>cd08557 PI-PLCc_bacteria_like Catalytic domain of bacterial phosphatidylinositol-specific phospholipase C and similar proteins. This subfamily corresponds to the catalytic domain present in bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) and their sequence homologs found in eukaryota. Bacterial PI-PLCs participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although their precise physiological function remains unclear, bacterial PI-PLCs may function as virulence factors in some pathogenic bacteria. Bacterial PI-PLCs contain a single TIM-barrel type catalytic domain. Its catalytic mechanism is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. Eukaryotic homologs in this family are named as phosphatidylinositol-specific phospholipase C X
Probab=25.19 E-value=2.6e+02 Score=22.82 Aligned_cols=63 Identities=14% Similarity=0.304 Sum_probs=47.5
Q ss_pred CCCHHHHHHHHHHHHhC--CeEeEEEcCCChh----hHHHHHHHHHHHhCCeEEe-------------EE-ccEEEEEcC
Q 038665 57 GVTDGVVTSFIETLEAN--ELLKIKIHRTCPG----ELEDVVKQLEEATGSAVVS-------------QI-GQTVIIYRP 116 (171)
Q Consensus 57 GLTe~VI~eI~~aL~~h--ELIKVKil~n~~~----d~~e~ae~La~~tgaevVq-------------~I-G~t~ILYR~ 116 (171)
..-+.++++|.+-|++| |.|=+.+...... +...+.+.|.+..|..+.. .+ |+.+|+++.
T Consensus 79 ~~~~~vL~~i~~fl~~~p~E~vil~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~ptL~el~~gK~vi~~~~ 158 (271)
T cd08557 79 QTLEDVLNEVKDFLDAHPSEVVILDLEHEYGGDNGEDHDELDALLRDVLGDPLYRPPVRAGGWPTLGELRAGKRVLLFYF 158 (271)
T ss_pred ccHHHHHHHHHHHHHHCCCcEEEEEEEccCCCcchhhHHHHHHHHHHHhCccccCCccccCCCCcHHHHhcCCeEEEEEC
Confidence 34488999999999995 9999998875432 3678888888888776653 34 888888887
Q ss_pred CCC
Q 038665 117 SLT 119 (171)
Q Consensus 117 s~~ 119 (171)
...
T Consensus 159 ~~~ 161 (271)
T cd08557 159 GGD 161 (271)
T ss_pred CCc
Confidence 654
No 27
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=25.04 E-value=3.7e+02 Score=21.63 Aligned_cols=68 Identities=21% Similarity=0.278 Sum_probs=46.5
Q ss_pred CCCHHHHHHHHHhhhhcCCcccceecCCCCCCH-HHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCe
Q 038665 28 KLTVKEKKELASYAHSLGKKLKCQLVGKSGVTD-GVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSA 102 (171)
Q Consensus 28 ~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe-~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgae 102 (171)
+||..|+..++.+...-+.+ ++..|..|--- .++..+..+|+.++ .+|-+.... ..++..|.+.++..
T Consensus 1 ~L~~~Q~~a~~~~l~~~~~~--~~l~G~aGtGKT~~l~~~~~~~~~~g-~~v~~~apT----~~Aa~~L~~~~~~~ 69 (196)
T PF13604_consen 1 TLNEEQREAVRAILTSGDRV--SVLQGPAGTGKTTLLKALAEALEAAG-KRVIGLAPT----NKAAKELREKTGIE 69 (196)
T ss_dssp -S-HHHHHHHHHHHHCTCSE--EEEEESTTSTHHHHHHHHHHHHHHTT---EEEEESS----HHHHHHHHHHHTS-
T ss_pred CCCHHHHHHHHHHHhcCCeE--EEEEECCCCCHHHHHHHHHHHHHhCC-CeEEEECCc----HHHHHHHHHhhCcc
Confidence 58999999999998776665 35668888533 36777999999998 777777654 34555577777643
No 28
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=23.71 E-value=1.5e+02 Score=18.81 Aligned_cols=55 Identities=22% Similarity=0.365 Sum_probs=40.9
Q ss_pred CCHHHHHHHHHhhhhcCCcc-cceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCC
Q 038665 29 LTVKEKKELASYAHSLGKKL-KCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRT 83 (171)
Q Consensus 29 LT~kqRk~LR~~AH~LkP~i-~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n 83 (171)
||+.|-..|..++++-.+.+ +.-..-.-|++...+..+-..|++.+||.-.-..+
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~ 58 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPG 58 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SS
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCC
Confidence 78889999999998887421 01233456999999999999999999998775543
No 29
>PRK07315 fructose-bisphosphate aldolase; Provisional
Probab=23.62 E-value=2.1e+02 Score=25.20 Aligned_cols=58 Identities=16% Similarity=0.289 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHhhhhc--CCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHH
Q 038665 28 KLTVKEKKELASYAHSL--GKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQL 95 (171)
Q Consensus 28 ~LT~kqRk~LR~~AH~L--kP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~L 95 (171)
.|.-.- |+.+...+ -|+ |.+|.+|++++-+.++ -..+.-||.|......+..+.+.++
T Consensus 187 ~l~~e~---L~~i~~~~~~iPl---VlhGGSGi~~e~~~~~----i~~Gi~KiNv~T~i~~~~~~~~~~~ 246 (293)
T PRK07315 187 GLDLDH---LEKLTEAVPGFPI---VLHGGSGIPDDQIQEA----IKLGVAKVNVNTECQIAFANATRKF 246 (293)
T ss_pred cCCHHH---HHHHHHhccCCCE---EEECCCCCCHHHHHHH----HHcCCCEEEEccHHHHHHHHHHHHH
Confidence 355444 55555555 374 7999999999776554 4678999999876555444444443
No 30
>PRK00099 rplJ 50S ribosomal protein L10; Reviewed
Probab=23.01 E-value=3.8e+02 Score=21.23 Aligned_cols=72 Identities=19% Similarity=0.223 Sum_probs=46.1
Q ss_pred HHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEE--eEEccEEE
Q 038665 35 KELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVV--SQIGQTVI 112 (171)
Q Consensus 35 k~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevV--q~IG~t~I 112 (171)
..|+.....-+. ++.+.-+|+|-+-+.++...|..++ +++++.+|. ++..-.+.++-+-+ ..-|.+++
T Consensus 11 ~~l~~~l~~~~~---v~v~~~~gl~~~~~~~lR~~lr~~~-~~~~V~KNt------L~~~Al~~~~~~~l~~~l~G~~al 80 (172)
T PRK00099 11 AELAEKLKKAQS---AVVADYRGLTVAQMTELRKKLREAG-VEYKVVKNT------LARRALEGTGFEGLDDLLKGPTAI 80 (172)
T ss_pred HHHHHHHHhCCE---EEEEecCCCcHHHHHHHHHHHHHcC-CEEEEehhH------HHHHHHhcCCchhhhhhCcCCeEE
Confidence 344555555554 3578999999999999999999975 356666663 22222222333222 25599999
Q ss_pred EEcC
Q 038665 113 IYRP 116 (171)
Q Consensus 113 LYR~ 116 (171)
+|=.
T Consensus 81 ~fs~ 84 (172)
T PRK00099 81 AFSY 84 (172)
T ss_pred EEeC
Confidence 9953
No 31
>PRK03459 rnpA ribonuclease P; Reviewed
Probab=22.80 E-value=1.4e+02 Score=23.00 Aligned_cols=44 Identities=7% Similarity=0.047 Sum_probs=29.2
Q ss_pred HHHHHHHhhhh----cCCcccceecCCCCCCH----HHHHHHHHHHHhCCeE
Q 038665 33 EKKELASYAHS----LGKKLKCQLVGKSGVTD----GVVTSFIETLEANELL 76 (171)
Q Consensus 33 qRk~LR~~AH~----LkP~i~~V~IGK~GLTe----~VI~eI~~aL~~hELI 76 (171)
=++.||..... +.|-..+|.|++.++.+ .+.+++...|...++.
T Consensus 67 iKR~lRe~~R~~~~~l~~g~D~Viiar~~~~~~~~~~l~~~l~~ll~k~~~~ 118 (122)
T PRK03459 67 VSRRLRHICADIVDQVPETHHVVIRALPGAATASSAELERDVRAGLGKLNRV 118 (122)
T ss_pred HHHHHHHHHHHhhhccCCCcEEEEEECcccccCCHHHHHHHHHHHHHHhccc
Confidence 45555555544 44333468899999864 7788888888876554
No 32
>PF01075 Glyco_transf_9: Glycosyltransferase family 9 (heptosyltransferase); InterPro: IPR002201 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 9 GT9 from CAZY comprises enzymes with two known activity; lipopolysaccharide N-acetylglucosaminyltransferase (2.4.1.56 from EC), heptosyltransferase (2.4 from EC). Heptosyltransferase I is thought to add L-glycero-D-manno-heptose to the inner 3-deoxy-D-manno-octulosonic acid (Kdo) residue of the lipopolysaccharide core []. Heptosyltransferase II is a glycosyltransferase involved in the synthesis of the inner core region of lipopolysaccharide []. Lipopolysaccharide is a major component of the outer leaflet of the outer membrane in Gram-negative bacteria. It is composed of three domains; lipid A, Core oligosaccharide and the O-antigen. These enzymes transfer heptose to the lipopolysaccharide core [].; GO: 0016757 transferase activity, transferring glycosyl groups, 0008152 metabolic process; PDB: 1PSW_A 2H1F_A 2GT1_A 3TOV_A 2H1H_A.
Probab=22.80 E-value=2.6e+02 Score=22.40 Aligned_cols=83 Identities=13% Similarity=0.107 Sum_probs=46.8
Q ss_pred CCCCCCCHHHHHHHHHhhh-hcCCcccceecCCCC----CCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHH
Q 038665 24 LPLPKLTVKEKKELASYAH-SLGKKLKCQLVGKSG----VTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEA 98 (171)
Q Consensus 24 ~~~~~LT~kqRk~LR~~AH-~LkP~i~~V~IGK~G----LTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~ 98 (171)
.+...++..+....+...+ .=+|.+ ++..|..+ .+.+-..++-+.|..+. ..|-+.....++-++.++.+...
T Consensus 83 ~~~l~~~~~~~~~~~~~~~~~~~~~i-~i~~~a~~~~k~wp~e~~~~l~~~l~~~~-~~vvl~g~~~~~~~~~~~~~~~~ 160 (247)
T PF01075_consen 83 KPELPLSEEEEAAARELLKSKDKPYI-GINPGASWPSKRWPAEKWAELIERLKERG-YRVVLLGGPEEQEKEIADQIAAG 160 (247)
T ss_dssp SS----THHHHTTHHTTTT-TTSSEE-EEE---SSGGGS--HHHHHHHHHHHCCCT--EEEE--SSHHHHHHHHHHHHTT
T ss_pred CcCCcCCHHHHHHHHHhhhhccCCeE-EEeecCCCccccCCHHHHHHHHHHHHhhC-ceEEEEccchHHHHHHHHHHHHh
Confidence 3455677777777666665 334555 57777655 56677888888898888 88877776555456777777776
Q ss_pred hCCeEEeEEc
Q 038665 99 TGSAVVSQIG 108 (171)
Q Consensus 99 tgaevVq~IG 108 (171)
....++...|
T Consensus 161 ~~~~~~~~~~ 170 (247)
T PF01075_consen 161 LQNPVINLAG 170 (247)
T ss_dssp HTTTTEEETT
T ss_pred cccceEeecC
Confidence 5533444443
No 33
>PF06296 DUF1044: Protein of unknown function (DUF1044); InterPro: IPR009387 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=22.41 E-value=1e+02 Score=24.17 Aligned_cols=38 Identities=21% Similarity=0.312 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeE
Q 038665 27 PKLTVKEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKI 78 (171)
Q Consensus 27 ~~LT~kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKV 78 (171)
..||.+|++.|+.+|..|-.. |+ ++|+.++...+|+.|
T Consensus 83 ~nis~~El~~lk~la~~l~~~-----------~~---~~l~~~i~~g~l~Ev 120 (120)
T PF06296_consen 83 ANISDKELKALKKLAKELLNL-----------SE---EQLETLIANGELIEV 120 (120)
T ss_pred CCCCHHHHHHHHHHHHHHHHh-----------CH---HHHHHHHHcCCEEeC
Confidence 489999999999999998652 33 567778888888764
No 34
>cd03338 TCP1_delta TCP-1 (CTT or eukaryotic type II) chaperonin family, delta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin.
Probab=22.38 E-value=2.3e+02 Score=26.37 Aligned_cols=67 Identities=15% Similarity=0.272 Sum_probs=41.6
Q ss_pred HHHHHHHHhhhhc---CCcccceecCCCCCCHHHHHH-HHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEE
Q 038665 32 KEKKELASYAHSL---GKKLKCQLVGKSGVTDGVVTS-FIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQI 107 (171)
Q Consensus 32 kqRk~LR~~AH~L---kP~i~~V~IGK~GLTe~VI~e-I~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~I 107 (171)
.|+.+|+.+...+ ++-+ |.+ .+|++.+++.. +.+.|..+.++=|+.. ..+..+.||..|||.++..+
T Consensus 256 ~E~~~i~~~v~~i~~~g~~l--vi~-~~~i~~~~v~~l~~~~l~~~~I~av~~~------~~~~LerIa~~tGa~ii~sl 326 (515)
T cd03338 256 EERKYILNMCKKIKKSGCNV--LLI-QKSILRDAVSDLALHFLAKLKIMVVKDI------EREEIEFICKTIGCKPVASI 326 (515)
T ss_pred HHHHHHHHHHHHHHhcCCCE--EEE-CCCcccccccHHHHHHHHHCCceEEecC------CHHHHHHHHHHHCCEEeccc
Confidence 3455666554433 5542 455 44665555443 3666777888888722 24455779999999999854
No 35
>PF07997 DUF1694: Protein of unknown function (DUF1694); InterPro: IPR012543 This family contains many hypothetical proteins.; PDB: 2OHW_A.
Probab=21.95 E-value=1.7e+02 Score=22.69 Aligned_cols=68 Identities=15% Similarity=0.216 Sum_probs=39.1
Q ss_pred HHHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeE
Q 038665 32 KEKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAV 103 (171)
Q Consensus 32 kqRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaev 103 (171)
+||+||=...-..--.+-.-++...++ ..++..+|+++.=.+++|+++-..+...---.+|.+.|..+
T Consensus 24 Eqr~yLGtfrERV~lalt~~q~~~~~~----~~~~~~~l~~~~~~~l~ing~l~~~~~~~YiklA~~~~~~f 91 (120)
T PF07997_consen 24 EQRRYLGTFRERVILALTKEQVEEPDI----YPEFEQALKDYPNYKLKINGNLDYSFQSKYIKLANKHGIPF 91 (120)
T ss_dssp HHHHTTT--GGGEEEEEEHHHHTSSS------HHHHHHHHC-SSEEEEEETTS-HHHHHHHHHHHHHTT--E
T ss_pred HHHHhcchHHhHhhheecHHHHhChhH----HHHHHHHHhhCCCeEEEEcCCCCHHHHHHHHHHHHHcCCCE
Confidence 356666555444322111124555555 46677778889999999999987777766777888777654
No 36
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=21.94 E-value=4.1e+02 Score=23.47 Aligned_cols=52 Identities=12% Similarity=0.206 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEE
Q 038665 55 KSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQI 107 (171)
Q Consensus 55 K~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~I 107 (171)
+-|+|-..+.-+=..=...++|+|+|.... ....++.++|.++.|-.-+-++
T Consensus 38 ~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~-~~~~~Le~~L~~~fgLk~~iVv 89 (318)
T PRK15418 38 RLGLTRLKVSRLLEKGRQSGIIRVQINSRF-EGCLELENALRQHFSLQHIRVL 89 (318)
T ss_pred HhCCCHHHHHHHHHHHHHcCcEEEEEeCCC-ccHHHHHHHHHHHhCCCEEEEE
Confidence 458888888888888888999999998753 4556799999999986544433
No 37
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=21.15 E-value=1.4e+02 Score=21.09 Aligned_cols=27 Identities=22% Similarity=0.423 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHHHHHhCCeEeEEEcC
Q 038665 56 SGVTDGVVTSFIETLEANELLKIKIHR 82 (171)
Q Consensus 56 ~GLTe~VI~eI~~aL~~hELIKVKil~ 82 (171)
-|+|++.+..-=..|+..++|+++-.-
T Consensus 24 l~lt~g~Ls~hL~~Le~~GyV~~~k~~ 50 (80)
T PF13601_consen 24 LGLTDGNLSKHLKKLEEAGYVEVEKEF 50 (80)
T ss_dssp TT--HHHHHHHHHHHHHTTSEEEEEE-
T ss_pred hCcCHHHHHHHHHHHHHCCCEEEEEec
Confidence 388999999999999999999998544
No 38
>COG5238 RNA1 Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Signal transduction mechanisms / RNA processing and modification]
Probab=20.95 E-value=75 Score=29.46 Aligned_cols=77 Identities=21% Similarity=0.214 Sum_probs=52.7
Q ss_pred HHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEe-EEEcCCC--hhhHHHH-HHHHHHHhCCeEEeEEccE
Q 038665 35 KELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLK-IKIHRTC--PGELEDV-VKQLEEATGSAVVSQIGQT 110 (171)
Q Consensus 35 k~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIK-VKil~n~--~~d~~e~-ae~La~~tgaevVq~IG~t 110 (171)
.++++.|. +|.+.+|.+|++-+.-+-.....-.|+.||.+| ||+.+|. ++-..-+ ..-++-...-++.+.--||
T Consensus 148 a~nKKaa~--kp~Le~vicgrNRlengs~~~~a~~l~sh~~lk~vki~qNgIrpegv~~L~~~gl~y~~~LevLDlqDNt 225 (388)
T COG5238 148 AYNKKAAD--KPKLEVVICGRNRLENGSKELSAALLESHENLKEVKIQQNGIRPEGVTMLAFLGLFYSHSLEVLDLQDNT 225 (388)
T ss_pred HHHhhhcc--CCCceEEEeccchhccCcHHHHHHHHHhhcCceeEEeeecCcCcchhHHHHHHHHHHhCcceeeeccccc
Confidence 44454443 466667899999998888999999999997776 6888875 3323333 3334444556777777777
Q ss_pred EEE
Q 038665 111 VII 113 (171)
Q Consensus 111 ~IL 113 (171)
+.+
T Consensus 226 ft~ 228 (388)
T COG5238 226 FTL 228 (388)
T ss_pred hhh
Confidence 764
No 39
>COG0042 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=20.66 E-value=3e+02 Score=24.48 Aligned_cols=60 Identities=12% Similarity=0.113 Sum_probs=37.0
Q ss_pred CHHHHHHHHHHHHhCC---e--EeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEccEEEEEcCCC
Q 038665 59 TDGVVTSFIETLEANE---L--LKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVIIYRPSL 118 (171)
Q Consensus 59 Te~VI~eI~~aL~~hE---L--IKVKil~n~~~d~~e~ae~La~~tgaevVq~IG~t~ILYR~s~ 118 (171)
+++++.+|-.++...= = ||+++.-...+-....+..+++.+|+..+.+.|+|....-..+
T Consensus 119 ~p~lv~~iv~a~~~av~~iPVTVKiRlG~d~~~~~~~~ia~~~~~~g~~~ltVHgRtr~~~y~~~ 183 (323)
T COG0042 119 NPELLAEIVKAMVEAVGDIPVTVKIRLGWDDDDILALEIARILEDAGADALTVHGRTRAQGYLGP 183 (323)
T ss_pred CHHHHHHHHHHHHHhhCCCCeEEEEecccCcccccHHHHHHHHHhcCCCEEEEecccHHhcCCCc
Confidence 5666777766666644 3 4444444333212344555667789999999999876644433
No 40
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=20.60 E-value=1.7e+02 Score=20.23 Aligned_cols=54 Identities=20% Similarity=0.217 Sum_probs=44.4
Q ss_pred CCHHHHHHHHHhhhhcCCc-ccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCC
Q 038665 29 LTVKEKKELASYAHSLGKK-LKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTC 84 (171)
Q Consensus 29 LT~kqRk~LR~~AH~LkP~-i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~ 84 (171)
||..|-..|..+.+.-... - -..-.-|++.+.+..+-+.|+..+||+-.-..++
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~--~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~D 74 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVK--ELAERLGLDRSTVTRLLKRLEDKGLIERLRDPED 74 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHH--HHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccc
Confidence 8999999999988877663 1 2345679999999999999999999998876654
No 41
>TIGR02045 P_fruct_ADP ADP-specific phosphofructokinase. Phosphofructokinase is a key enzyme of glycolysis. The phosphate group donor for different subtypes of phosphofructokinase can be ATP, ADP, or pyrophosphate. This family consists of ADP-dependent phosphofructokinases. Members are more similar to ADP-dependent glucokinases (excluded from this family) than to other phosphofructokinases.
Probab=20.38 E-value=4.2e+02 Score=25.25 Aligned_cols=84 Identities=14% Similarity=0.085 Sum_probs=59.9
Q ss_pred HHHHHHHhhhhcCCcccceecCCCCCCHHHHHHHHHHHHhCCeEeEEEcCCChhhHHHHHHHHHHHhCCeEEeEEccEEE
Q 038665 33 EKKELASYAHSLGKKLKCQLVGKSGVTDGVVTSFIETLEANELLKIKIHRTCPGELEDVVKQLEEATGSAVVSQIGQTVI 112 (171)
Q Consensus 33 qRk~LR~~AH~LkP~i~~V~IGK~GLTe~VI~eI~~aL~~hELIKVKil~n~~~d~~e~ae~La~~tgaevVq~IG~t~I 112 (171)
.+..++.+.+.+=|. +=--|++|.=+..+-+.|-..+|=.=-+..+..++.-+.+..|.+++|-+.||+.=..++
T Consensus 262 ~~~l~~~i~~~ilp~-----vDSlGMNE~ELa~ll~~lg~~~l~~~i~~~~~i~~vi~a~~~l~~~~~leri~vHT~~y~ 336 (446)
T TIGR02045 262 NREIRKKVVTNIFPH-----VDSVGMDEAEIANVLSVLGYDELSDRIFRYNRIEDLILGAKILLDELNLEVVQVHTIYYI 336 (446)
T ss_pred cHHHHHHHHHhhccc-----cccccCCHHHHHHHHHHhcCCchhhhhhccccHHHHHHHHHHHHHHcCCCEEEEEeccee
Confidence 344555566677774 556689998888888877666665544455677899999999999999988887766666
Q ss_pred EEcCCCCcc
Q 038665 113 IYRPSLTRM 121 (171)
Q Consensus 113 LYR~s~~~~ 121 (171)
+|-...++|
T Consensus 337 l~i~~~~~p 345 (446)
T TIGR02045 337 MYITHADNP 345 (446)
T ss_pred EEEeccCCC
Confidence 666554443
Done!