Query 038271
Match_columns 158
No_of_seqs 137 out of 304
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 09:18:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038271.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038271hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1512 Beta-propeller domains 100.0 1.4E-34 3.1E-39 246.0 14.3 138 9-152 18-168 (271)
2 PF04536 TPM: TLP18.3, Psb32 a 99.8 2E-20 4.4E-25 136.3 10.5 106 33-145 1-119 (119)
3 COG3762 Predicted membrane pro 86.4 0.32 6.8E-06 40.8 1.0 63 80-147 130-193 (213)
4 TIGR02500 type_III_yscD type I 85.2 2.9 6.3E-05 37.5 6.6 76 25-105 304-385 (410)
5 PF08854 DUF1824: Domain of un 76.8 9.6 0.00021 29.6 6.0 71 28-100 10-96 (125)
6 COG1125 OpuBA ABC-type proline 59.8 22 0.00048 31.5 5.4 50 27-84 158-208 (309)
7 PF13728 TraF: F plasmid trans 50.2 99 0.0021 25.4 7.5 61 42-104 138-205 (215)
8 cd06266 RNaseH_typeII Ribonucl 48.3 21 0.00044 28.6 3.1 55 5-61 12-66 (193)
9 PF09967 DUF2201: VWA-like dom 44.0 70 0.0015 24.0 5.3 37 26-62 3-39 (126)
10 COG1136 SalX ABC-type antimicr 41.7 49 0.0011 27.9 4.5 49 7-61 151-200 (226)
11 TIGR02739 TraF type-F conjugat 41.6 1.4E+02 0.0031 25.6 7.4 72 42-117 168-246 (256)
12 PF11768 DUF3312: Protein of u 38.6 50 0.0011 31.6 4.5 67 38-117 18-94 (545)
13 PF13740 ACT_6: ACT domain; PD 37.4 56 0.0012 22.0 3.6 25 35-59 51-75 (76)
14 COG0300 DltE Short-chain dehyd 36.0 55 0.0012 28.2 4.1 70 34-117 35-110 (265)
15 COG1116 TauB ABC-type nitrate/ 35.7 89 0.0019 26.9 5.2 56 27-90 153-209 (248)
16 PRK13703 conjugal pilus assemb 34.7 2.1E+02 0.0045 24.4 7.3 69 44-116 163-238 (248)
17 PF13604 AAA_30: AAA domain; P 32.9 35 0.00076 27.2 2.2 45 20-69 91-135 (196)
18 PRK15043 transcriptional regul 31.6 49 0.0011 28.3 3.0 31 13-44 200-230 (243)
19 PRK13709 conjugal transfer nic 31.1 85 0.0018 34.0 5.2 38 20-61 498-535 (1747)
20 COG0263 ProB Glutamate 5-kinas 30.2 1.8E+02 0.0038 26.7 6.4 67 25-92 16-112 (369)
21 PF03147 FDX-ACB: Ferredoxin-f 29.8 89 0.0019 22.0 3.7 32 27-58 62-94 (94)
22 COG0541 Ffh Signal recognition 29.6 3.2E+02 0.0069 25.7 8.0 90 24-117 184-295 (451)
23 PF05121 GvpK: Gas vesicle pro 29.2 77 0.0017 23.4 3.3 23 31-53 39-61 (88)
24 PF03796 DnaB_C: DnaB-like hel 29.1 1E+02 0.0022 25.2 4.4 38 25-62 133-178 (259)
25 PRK13925 rnhB ribonuclease HII 28.6 59 0.0013 26.7 2.9 55 5-61 22-76 (198)
26 COG0094 RplE Ribosomal protein 28.3 84 0.0018 26.0 3.7 71 12-83 20-90 (180)
27 KOG4648 Uncharacterized conser 28.1 28 0.00061 32.3 1.0 21 118-139 102-122 (536)
28 PF13734 Inhibitor_I69: Spi pr 28.0 1.8E+02 0.004 21.3 5.1 26 79-108 49-75 (96)
29 COG0164 RnhB Ribonuclease HII 27.6 80 0.0017 26.3 3.5 53 5-61 14-66 (199)
30 PF13014 KH_3: KH domain 26.7 70 0.0015 19.2 2.4 18 44-61 11-28 (43)
31 smart00591 RWD domain in RING 26.7 2E+02 0.0044 19.7 5.0 41 12-53 45-87 (107)
32 PF13689 DUF4154: Domain of un 26.2 2.9E+02 0.0062 20.8 6.5 23 42-66 38-62 (145)
33 COG3445 Acid-induced glycyl ra 26.1 36 0.00079 26.1 1.1 29 13-41 86-117 (127)
34 COG0419 SbcC ATPase involved i 26.0 79 0.0017 31.2 3.7 40 22-62 841-881 (908)
35 cd07013 S14_ClpP Caseinolytic 25.2 1.9E+02 0.004 22.5 5.1 50 26-77 1-55 (162)
36 cd02011 TPP_PK Thiamine pyroph 25.1 3.3E+02 0.0072 23.0 6.9 53 71-128 96-156 (227)
37 cd08577 PI-PLCc_GDPD_SF_unchar 25.0 1.5E+02 0.0033 24.6 4.8 32 32-66 177-208 (228)
38 cd01714 ETF_beta The electron 24.7 3.4E+02 0.0073 21.8 6.7 52 12-66 7-62 (202)
39 COG0552 FtsY Signal recognitio 24.0 1.5E+02 0.0031 26.9 4.7 79 26-108 225-328 (340)
40 PF07201 HrpJ: HrpJ-like domai 24.0 17 0.00037 28.1 -1.0 27 31-57 91-117 (166)
41 PF14385 DUF4416: Domain of un 23.3 3.4E+02 0.0073 21.9 6.3 81 13-108 47-130 (164)
42 PRK13434 F0F1 ATP synthase sub 23.3 1.2E+02 0.0027 23.9 3.8 30 30-62 111-140 (184)
43 PF02370 M: M protein repeat; 23.2 1.2E+02 0.0027 16.7 2.6 16 38-53 2-17 (21)
44 TIGR02740 TraF-like TraF-like 23.0 4.6E+02 0.01 22.2 7.4 16 14-29 128-143 (271)
45 cd03238 ABC_UvrA The excision 22.8 2.4E+02 0.0053 22.2 5.4 38 23-61 108-146 (176)
46 PF04339 DUF482: Protein of un 22.5 2.7E+02 0.0059 25.1 6.2 56 29-87 175-256 (370)
47 COG0039 Mdh Malate/lactate deh 22.5 45 0.00099 29.5 1.2 55 13-70 30-85 (313)
48 cd07021 Clp_protease_NfeD_like 22.5 1.3E+02 0.0029 23.9 3.9 35 26-61 2-36 (178)
49 COG2086 FixA Electron transfer 22.2 2.1E+02 0.0046 24.6 5.2 54 33-88 34-88 (260)
50 PRK08474 F0F1 ATP synthase sub 22.2 1.9E+02 0.0041 22.7 4.7 29 30-61 110-138 (176)
51 cd07396 MPP_Nbla03831 Homo sap 22.0 1.8E+02 0.0039 24.0 4.7 33 29-62 155-187 (267)
52 PRK00745 4-oxalocrotonate taut 22.0 2.2E+02 0.0047 18.0 5.2 28 29-56 7-35 (62)
53 PRK13646 cbiO cobalt transport 21.3 1.7E+02 0.0038 24.4 4.5 36 26-61 167-203 (286)
54 COG0687 PotD Spermidine/putres 21.1 1.3E+02 0.0029 25.9 3.9 35 24-67 33-67 (363)
55 PF11062 DUF2863: Protein of u 20.9 1E+02 0.0022 28.4 3.2 54 93-155 236-291 (398)
56 cd07181 RNaseH_typeII_eukaryot 20.8 71 0.0015 26.3 2.0 57 5-61 12-68 (216)
57 PRK13436 F0F1 ATP synthase sub 20.8 1.5E+02 0.0033 23.4 3.8 30 30-62 115-144 (179)
58 cd00394 Clp_protease_like Case 20.3 1.2E+02 0.0026 22.8 3.1 35 27-61 1-35 (161)
59 COG4525 TauB ABC-type taurine 20.1 1.9E+02 0.0041 25.0 4.4 68 31-117 160-227 (259)
60 cd07015 Clp_protease_NfeD Nodu 20.1 1.9E+02 0.0041 23.2 4.3 35 26-61 2-36 (172)
No 1
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=100.00 E-value=1.4e-34 Score=245.96 Aligned_cols=138 Identities=23% Similarity=0.318 Sum_probs=128.5
Q ss_pred hccccccCCCCCCCCCCceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcch-------hhhhhhcCC--
Q 038271 9 EAKVGVNKPELLPREFTSVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPGL-------AIKDFWQVD-- 79 (158)
Q Consensus 9 ~a~~~~~~P~l~P~l~~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~~-------~v~~~W~~~-- 79 (158)
.+..++.-|.+.|.++.||+|+|++||.+++++||++|++||++|+.||+||| +|+|.|. ++||+||+|
T Consensus 18 ~~~~~~a~~~~~p~~~~~V~D~t~~Ls~~e~~~Leq~l~~L~~kt~~QiaVv~--vpSt~g~~IE~ya~rlfd~W~lG~k 95 (271)
T COG1512 18 LAPLLFAEPIPAPTLSQRVTDLTGTLSAAERGALEQQLADLEQKTGAQIAVVT--VPSTGGETIEQYATRLFDKWKLGDK 95 (271)
T ss_pred HHHhhhccccCCCcccceeeeccccCChhhHHHHHHHHHHHHhccCCeEEEEE--ecCCCCCCHHHHHHHHHHhcCCCcc
Confidence 33457888999999999999999999999999999999999999999999999 9999874 889999966
Q ss_pred ---CCeEEEEE-cCCCCceeEEeeccccccCCCHHHHHHHhhccCCcceecccChhHHHHHHHHHHHHHhcCCCCCC
Q 038271 80 ---DRTIVFVA-DPTFGNILNFNVGASVDLDIPRSFWSRLAGKYGNIFYWKEKGEDASIEAAVVAISNCLREPVGPN 152 (158)
Q Consensus 80 ---dg~lLlVa-d~r~~n~l~i~vG~gleg~Lpd~~a~~I~~r~gn~~~fr~~~~~~gi~aav~ai~~~L~ge~~~~ 152 (158)
||+||||| |+| ++|||||||||+.+||+.+.+|++..+. |+||+|+|++||.+++++|.+.+.|||.+.
T Consensus 96 ~~~dGvLLlVa~~dr---~~rIevGyGLEg~ltD~~a~~iIr~~i~-P~fr~gny~~gi~~~id~l~~~l~g~~~~~ 168 (271)
T COG1512 96 AQDDGVLLLVAMNDR---RVRIEVGYGLEGVLTDAQAGRIIRETIA-PAFRDGNYAGGLEAGIDRLVALLAGEPLPS 168 (271)
T ss_pred ccCCCEEEEEEcCCC---eEEEEEecCcccccChHHHHHHHHhhhC-cccccCcHHHHHHHHHHHHHHHHcCCCCCC
Confidence 88999999 887 4899999999999999999999999995 799999999999999999999999999664
No 2
>PF04536 TPM: TLP18.3, Psb32 and MOLO-1 founding proteins of phosphatase; InterPro: IPR007621 This is a family of uncharacterised proteins. They are found in both eukarya and eubacteria. In eubacteria the region is towards the N-terminal of the protein and is accompanied by an N-terminal signal sequence. The C-terminal of eubacterial proteins typically contains one or more putative transmembrane regions. In eukaryotes the region is not accompanied by a signal sequence.; PDB: 3PTJ_A 3PW9_A 3PVH_A 2KPT_A 2KW7_A.
Probab=99.84 E-value=2e-20 Score=136.33 Aligned_cols=106 Identities=28% Similarity=0.493 Sum_probs=88.5
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcch-------hhhhhhcCC-----CCeEEEEE-cCCCCceeEEee
Q 038271 33 FLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPGL-------AIKDFWQVD-----DRTIVFVA-DPTFGNILNFNV 99 (158)
Q Consensus 33 ~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~~-------~v~~~W~~~-----dg~lLlVa-d~r~~n~l~i~v 99 (158)
+||++++++|++.|+++|++||.||+|+| ++++++. ++++.|+++ +|+||+|+ ++| .++|.+
T Consensus 1 iLs~~~~~~l~~~l~~~~~~t~~~i~Vvt--v~~~~~~~~~~~A~~~~~~~~~g~~~~~~gvlilv~~~~r---~~~i~~ 75 (119)
T PF04536_consen 1 ILSQEERERLNQALAKLEKKTGVQIVVVT--VPSLPGQDIEDYAQQLFERWGLGDGECNNGVLILVSKDDR---KVRIET 75 (119)
T ss_dssp -S-HHHHHHHHHHHHHHHHHC--EEEEEE--ESB-TTS-HHHHHHHHHHHHSTTCCCTSSEEEEEEETTTT---EEEEEE
T ss_pred CCCHHHHHHHHHHHHHHHHhhCCEEEEEE--EcCCCCCCHHHHHHHHHHHhCCCCccccCcEEEEEEcCCC---EEEEEE
Confidence 58999999999999999999999999999 8888663 778899965 66677776 766 479999
Q ss_pred ccccccCCCHHHHHHHhhccCCcceecccChhHHHHHHHHHHHHHh
Q 038271 100 GASVDLDIPRSFWSRLAGKYGNIFYWKEKGEDASIEAAVVAISNCL 145 (158)
Q Consensus 100 G~gleg~Lpd~~a~~I~~r~gn~~~fr~~~~~~gi~aav~ai~~~L 145 (158)
|++++..+||..+.+|...+ .|+||+++|++|+..++++|..+|
T Consensus 76 g~~~~~~l~~~~~~~i~~~~--~~~~~~~~~~~g~~~~v~~i~~~L 119 (119)
T PF04536_consen 76 GGGLEERLTDSECESIIDEM--VPYFKDGDYAEGIEAAVDAIAEVL 119 (119)
T ss_dssp -CTCCCCH-HHHHHHHHHHH--HHHHHTT-HHHHHHHHHHHHHHHH
T ss_pred CCchhhcCCHHHHHHHHHHH--HHHHHcCCHHHHHHHHHHHHHhhC
Confidence 99999999999999999999 589999999999999999999886
No 3
>COG3762 Predicted membrane protein [Function unknown]
Probab=86.37 E-value=0.32 Score=40.82 Aligned_cols=63 Identities=10% Similarity=0.222 Sum_probs=53.8
Q ss_pred CCeEEEEE-cCCCCceeEEeeccccccCCCHHHHHHHhhccCCcceecccChhHHHHHHHHHHHHHhcC
Q 038271 80 DRTIVFVA-DPTFGNILNFNVGASVDLDIPRSFWSRLAGKYGNIFYWKEKGEDASIEAAVVAISNCLRE 147 (158)
Q Consensus 80 dg~lLlVa-d~r~~n~l~i~vG~gleg~Lpd~~a~~I~~r~gn~~~fr~~~~~~gi~aav~ai~~~L~g 147 (158)
.|+|+.|+ -++. ..+--..|+....|+.+|.+|-+.-.. .||++.+.+||..|++++.++|+-
T Consensus 130 tGVLIfvs~aeh~---veViAD~GI~a~V~~~~W~~ic~~lta--g~~~~~~adgfveAi~qig~vLA~ 193 (213)
T COG3762 130 TGVLIFVSLAEHR---VEVIADQGIHAYVGQAEWNAICDTLTA--GFRQGAAADGFVEAIGQIGKVLAA 193 (213)
T ss_pred ceeEEeeHHHHHH---HHHHhcccHHhhccHHHHHHHHHHHHH--HHhccchhhHHHHHHHHHHHHHHH
Confidence 89999998 6652 344556999999999999999998753 789999999999999999999964
No 4
>TIGR02500 type_III_yscD type III secretion apparatus protein, YscD/HrpQ family. This family represents a conserved protein of bacterial type III secretion systems. Gene symbols are variable from species to species. Members are designated YscD in Yersinia, HrpQ in Pseudomonas syringae, and EscD in enteropathogenic Escherichia coli. In the Chlamydiae, this model describes the C-terminal 400 residues of a longer protein.
Probab=85.23 E-value=2.9 Score=37.49 Aligned_cols=76 Identities=24% Similarity=0.325 Sum_probs=55.2
Q ss_pred CceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcc------hhhhhhhcCCCCeEEEEEcCCCCceeEEe
Q 038271 25 TSVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPG------LAIKDFWQVDDRTIVFVADPTFGNILNFN 98 (158)
Q Consensus 25 ~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~------~~v~~~W~~~dg~lLlVad~r~~n~l~i~ 98 (158)
..-+-.+|.|++++.+++.+.+++|.++.|.-..+..|+.|.+.+ ..|..+++.+....++++|-+ |+-
T Consensus 304 ~~~i~lsG~l~~~~~~~~~~~l~~f~~~~~~~~~~~~~~~~~~~~~~~~lP~~i~~~~~~g~~~yvvl~dG~-----Rl~ 378 (410)
T TIGR02500 304 GREIALSGQLDSEKRSRLQELLAAFKQRDGVIPDVVLQNIPAADGTSDELPFPVVSISGSGPNPYVVLADGQ-----RLF 378 (410)
T ss_pred CCEEEEEecCCHHHHHHHHHHHHHHHHhCCCCceEEEecCCccccccccCCcceEEEecCCCCCEEEEeCCc-----Eec
Confidence 345667899999999999999999999999633233333664432 366777877777788777776 567
Q ss_pred ecccccc
Q 038271 99 VGASVDL 105 (158)
Q Consensus 99 vG~gleg 105 (158)
+|.-|.+
T Consensus 379 ~G~~l~~ 385 (410)
T TIGR02500 379 VGARLPG 385 (410)
T ss_pred cCCCCCC
Confidence 7766655
No 5
>PF08854 DUF1824: Domain of unknown function (DUF1824); InterPro: IPR014953 This uncharacterised group of proteins are principally found in cyanobacteria. ; PDB: 2Q22_B.
Probab=76.84 E-value=9.6 Score=29.61 Aligned_cols=71 Identities=18% Similarity=0.284 Sum_probs=46.9
Q ss_pred eecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcc-h-hhhhhhc-------------CCCCeEEEEEcCCCC
Q 038271 28 IDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPG-L-AIKDFWQ-------------VDDRTIVFVADPTFG 92 (158)
Q Consensus 28 vD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~-~-~v~~~W~-------------~~dg~lLlVad~r~~ 92 (158)
++.|-.||++++++|-++|..+-..+.|+..=++ =|+... . ++++++. -.+|.+.|=++.+++
T Consensus 10 l~~ap~ls~~~~~~Lr~~L~~~~~~sd~~~lGIc--A~s~~~ai~ALr~~~~alg~~~~~~~~~~~~~GpVfLK~N~~tg 87 (125)
T PF08854_consen 10 LRIAPQLSPSQRKKLRQALRLLASNSDWFTLGIC--APSAEEAIAALRSYEQALGYPPLEPLDSPPIEGPVFLKANQKTG 87 (125)
T ss_dssp -SB-----HHHHHHHHHHHHHHHHTSSEEEEEEE--ESSHHHHHHHHHHHHHHTT------------SSSEEEEEETTT-
T ss_pred ccccccCCHHHHHHHHHHHHHHHhccCceEEEee--cCCHHHHHHHHHHHHHHcCCCccCCCCCCCCCCCEEEEecCCCC
Confidence 3557789999999999999999999999998888 565432 2 5555544 228999999999998
Q ss_pred c-eeEEeec
Q 038271 93 N-ILNFNVG 100 (158)
Q Consensus 93 n-~l~i~vG 100 (158)
+ -++.+.|
T Consensus 88 ~~yv~~y~G 96 (125)
T PF08854_consen 88 SCYVRSYTG 96 (125)
T ss_dssp -EEEEE--S
T ss_pred cEEEeecCC
Confidence 6 3466666
No 6
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=59.82 E-value=22 Score=31.50 Aligned_cols=50 Identities=26% Similarity=0.434 Sum_probs=39.4
Q ss_pred eeec-CCCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcchhhhhhhcCCCCeEE
Q 038271 27 VIDV-AGFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPGLAIKDFWQVDDRTIV 84 (158)
Q Consensus 27 VvD~-A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~~~v~~~W~~~dg~lL 84 (158)
..|. =+.|+|-.+.+|..++.++.++.|.-|++||- ++-|+-+++|+..+
T Consensus 158 LMDEPFgALDpI~R~~lQ~e~~~lq~~l~kTivfVTH--------DidEA~kLadri~v 208 (309)
T COG1125 158 LMDEPFGALDPITRKQLQEEIKELQKELGKTIVFVTH--------DIDEALKLADRIAV 208 (309)
T ss_pred eecCCccccChhhHHHHHHHHHHHHHHhCCEEEEEec--------CHHHHHhhhceEEE
Confidence 4454 47899999999999999999999999999993 34455666655443
No 7
>PF13728 TraF: F plasmid transfer operon protein
Probab=50.16 E-value=99 Score=25.40 Aligned_cols=61 Identities=15% Similarity=0.239 Sum_probs=38.5
Q ss_pred HHHHHHHHHHhcCCeEEEEeee---cCCC----cchhhhhhhcCCCCeEEEEEcCCCCceeEEeeccccc
Q 038271 42 LAQEIADLEKDTGFKLRVLAQN---YPET----PGLAIKDFWQVDDRTIVFVADPTFGNILNFNVGASVD 104 (158)
Q Consensus 42 L~~~L~~lE~~TG~qv~Vlt~~---~p~t----~~~~v~~~W~~~dg~lLlVad~r~~n~l~i~vG~gle 104 (158)
....|..|++++|++|..+..| .|.. ....++..+++..=-.|+++++.+++. ..|++|+-
T Consensus 138 ~~pil~~~~~~yg~~v~~vs~DG~~~~~fp~~~~~~g~~~~l~v~~~Pal~Lv~~~~~~~--~pv~~G~~ 205 (215)
T PF13728_consen 138 QAPILQQFADKYGFSVIPVSLDGRPIPSFPNPRPDPGQAKRLGVKVTPALFLVNPNTKKW--YPVSQGFM 205 (215)
T ss_pred HHHHHHHHHHHhCCEEEEEecCCCCCcCCCCCCCCHHHHHHcCCCcCCEEEEEECCCCeE--EEEeeecC
Confidence 3445778999999999999953 1222 123677788887555556666655444 34566654
No 8
>cd06266 RNaseH_typeII Ribonuclease H type II. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, however, no prokaryotic genome contained the combination of only RNase HI and HIII. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escheri
Probab=48.33 E-value=21 Score=28.60 Aligned_cols=55 Identities=15% Similarity=0.133 Sum_probs=42.0
Q ss_pred ccchhccccccCCCCCCCCCCceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEe
Q 038271 5 VGCSEAKVGVNKPELLPREFTSVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 5 ~~~~~a~~~~~~P~l~P~l~~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt 61 (158)
+||-+.+.+|=.++....+...=+.....||+.++..|-+++.+ ..-++.+.++.
T Consensus 12 ~GPlvva~v~~~~~~~~~l~~~gv~DSK~Lt~~~r~~l~~~I~~--~~~~~~v~~~~ 66 (193)
T cd06266 12 AGPVVAAAVILPKENIEILKILGVKDSKKLSEKKREELFEEIKE--EALAYAIGIIS 66 (193)
T ss_pred chheEEEEEEEchhhcccccccCCCCcccCCHHHHHHHHHHHHh--hCCeEEEEEEC
Confidence 46666666666666666666666778899999999999999988 45667777777
No 9
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=44.00 E-value=70 Score=23.99 Aligned_cols=37 Identities=27% Similarity=0.392 Sum_probs=33.7
Q ss_pred ceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEee
Q 038271 26 SVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQ 62 (158)
Q Consensus 26 ~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~ 62 (158)
-++|..+-+|.++.++.-+++..+-++.+.+|.|+.-
T Consensus 3 vaiDtSGSis~~~l~~fl~ev~~i~~~~~~~v~vi~~ 39 (126)
T PF09967_consen 3 VAIDTSGSISDEELRRFLSEVAGILRRFPAEVHVIQF 39 (126)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHHhCCCCEEEEEE
Confidence 3689999999999999999999999999999999873
No 10
>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
Probab=41.72 E-value=49 Score=27.92 Aligned_cols=49 Identities=18% Similarity=0.403 Sum_probs=39.9
Q ss_pred chhccccccCCCCCCCCCCceeec-CCCCCHHHHHHHHHHHHHHHHhcCCeEEEEe
Q 038271 7 CSEAKVGVNKPELLPREFTSVIDV-AGFLSDGQERRLAQEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 7 ~~~a~~~~~~P~l~P~l~~~VvD~-A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt 61 (158)
+|.|.-.++.|.++ +-|. |+-|++.+...+-..|.++-++.|.-|.++|
T Consensus 151 VAIARAL~~~P~ii------lADEPTgnLD~~t~~~V~~ll~~~~~~~g~tii~VT 200 (226)
T COG1136 151 VAIARALINNPKII------LADEPTGNLDSKTAKEVLELLRELNKERGKTIIMVT 200 (226)
T ss_pred HHHHHHHhcCCCeE------EeeCccccCChHHHHHHHHHHHHHHHhcCCEEEEEc
Confidence 35566666777654 3444 8999999999999999999999999999999
No 11
>TIGR02739 TraF type-F conjugative transfer system pilin assembly protein TraF. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm. Unlike the related protein TrbB (TIGR02738), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. Even more closely related than TrbB is a clade of genes (TIGR02740) which do contain the CXXC motif, but it is unclear whether these genes are involved in type-F conjugation systems per se.
Probab=41.60 E-value=1.4e+02 Score=25.56 Aligned_cols=72 Identities=13% Similarity=0.174 Sum_probs=43.4
Q ss_pred HHHHHHHHHHhcCCeEEEEeeecCCCcc-------hhhhhhhcCCCCeEEEEEcCCCCceeEEeeccccccCCCHHHHHH
Q 038271 42 LAQEIADLEKDTGFKLRVLAQNYPETPG-------LAIKDFWQVDDRTIVFVADPTFGNILNFNVGASVDLDIPRSFWSR 114 (158)
Q Consensus 42 L~~~L~~lE~~TG~qv~Vlt~~~p~t~~-------~~v~~~W~~~dg~lLlVad~r~~n~l~i~vG~gleg~Lpd~~a~~ 114 (158)
+.-.|++|+++.|++|..+..|-...++ ...+.+|++--=-.|+.+++.++.. ..||+|+-.. |++..|
T Consensus 168 ~apil~~fa~~ygi~v~~VS~DG~~~p~fp~~~~d~gqa~~l~v~~~Pal~Lv~~~t~~~--~pv~~G~iS~--deL~~R 243 (256)
T TIGR02739 168 MAPVIQAFAKEYGISVIPISVDGTLIPGLPNSRSDSGQAQHLGVKYFPALYLVNPKSQKM--SPLAYGFISQ--DELKER 243 (256)
T ss_pred HHHHHHHHHHHhCCeEEEEecCCCCCCCCCCccCChHHHHhcCCccCceEEEEECCCCcE--EEEeeccCCH--HHHHHH
Confidence 3445778999999999999842111122 3567788876555566666665544 4566665432 445555
Q ss_pred Hhh
Q 038271 115 LAG 117 (158)
Q Consensus 115 I~~ 117 (158)
|..
T Consensus 244 i~~ 246 (256)
T TIGR02739 244 ILN 246 (256)
T ss_pred HHH
Confidence 443
No 12
>PF11768 DUF3312: Protein of unknown function (DUF3312); InterPro: IPR024511 This is a eukaryotic family of uncharacterised proteins that contain WD40 repeats.
Probab=38.61 E-value=50 Score=31.56 Aligned_cols=67 Identities=10% Similarity=0.135 Sum_probs=54.0
Q ss_pred HHHHHHHHHHHHHHhcCCeEEEEeeecCCCcchhhhhhhc--------CCCCeEEEEE-cCCCCceeEEeeccccccCCC
Q 038271 38 QERRLAQEIADLEKDTGFKLRVLAQNYPETPGLAIKDFWQ--------VDDRTIVFVA-DPTFGNILNFNVGASVDLDIP 108 (158)
Q Consensus 38 ~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~~~v~~~W~--------~~dg~lLlVa-d~r~~n~l~i~vG~gleg~Lp 108 (158)
.=++|...|+++|+.--.--.|.+ +|+ .++|+++-+. +..++.+-+|.+-+-|.|-|+
T Consensus 18 rp~kLRd~LkelEell~~~~~V~~-------------~W~~~~~~qll~snGvlv~i~v~~~~~dle~i~iDk~LvGKL~ 84 (545)
T PF11768_consen 18 RPEKLRDSLKELEELLQNHQCVCC-------------KWKNKHCCQLLFSNGVLVSITVSLSGPDLERIVIDKSLVGKLI 84 (545)
T ss_pred ChHHHHHHHHHHHHHHhhCcEEEE-------------EeccCcEEEEEecCcEEEEEEEecCCCceeEEEEehhhhcccc
Confidence 446888999999998777777777 698 5588888766 888888999999999999999
Q ss_pred -HHHHHHHhh
Q 038271 109 -RSFWSRLAG 117 (158)
Q Consensus 109 -d~~a~~I~~ 117 (158)
|.++..++.
T Consensus 85 ~d~isda~~t 94 (545)
T PF11768_consen 85 SDTISDAVIT 94 (545)
T ss_pred cccccceEec
Confidence 888765554
No 13
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=37.36 E-value=56 Score=22.00 Aligned_cols=25 Identities=20% Similarity=0.482 Sum_probs=21.7
Q ss_pred CHHHHHHHHHHHHHHHHhcCCeEEE
Q 038271 35 SDGQERRLAQEIADLEKDTGFKLRV 59 (158)
Q Consensus 35 s~~~~~~L~~~L~~lE~~TG~qv~V 59 (158)
++...++|++.|+++.++.|-+|.|
T Consensus 51 ~~~~~~~l~~~L~~l~~~~~l~v~v 75 (76)
T PF13740_consen 51 PEDSLERLESALEELAEELGLDVSV 75 (76)
T ss_dssp SHHHHHHHHHHHHHHHHHTT-EEEE
T ss_pred CcccHHHHHHHHHHHHHHCCcEEEE
Confidence 3778899999999999999999886
No 14
>COG0300 DltE Short-chain dehydrogenases of various substrate specificities [General function prediction only]
Probab=36.02 E-value=55 Score=28.20 Aligned_cols=70 Identities=21% Similarity=0.249 Sum_probs=50.0
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcch-hhhhh-----hcCCCCeEEEEEcCCCCceeEEeeccccccCC
Q 038271 34 LSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPGL-AIKDF-----WQVDDRTIVFVADPTFGNILNFNVGASVDLDI 107 (158)
Q Consensus 34 Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~~-~v~~~-----W~~~dg~lLlVad~r~~n~l~i~vG~gleg~L 107 (158)
|..-.+.+|++.-+++|+++|-++.++..|+-++... +|++. |.+| +|| -+.|.|..+..
T Consensus 35 LvaR~~~kL~~la~~l~~~~~v~v~vi~~DLs~~~~~~~l~~~l~~~~~~Id----vLV----------NNAG~g~~g~f 100 (265)
T COG0300 35 LVARREDKLEALAKELEDKTGVEVEVIPADLSDPEALERLEDELKERGGPID----VLV----------NNAGFGTFGPF 100 (265)
T ss_pred EEeCcHHHHHHHHHHHHHhhCceEEEEECcCCChhHHHHHHHHHHhcCCccc----EEE----------ECCCcCCccch
Confidence 4455789999999999999999999999777666553 44433 5544 222 24588888877
Q ss_pred CHHHHHHHhh
Q 038271 108 PRSFWSRLAG 117 (158)
Q Consensus 108 pd~~a~~I~~ 117 (158)
.+.-|+++..
T Consensus 101 ~~~~~~~~~~ 110 (265)
T COG0300 101 LELSLDEEEE 110 (265)
T ss_pred hhCChHHHHH
Confidence 7777775554
No 15
>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=35.70 E-value=89 Score=26.93 Aligned_cols=56 Identities=20% Similarity=0.284 Sum_probs=45.9
Q ss_pred eeec-CCCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcchhhhhhhcCCCCeEEEEEcCC
Q 038271 27 VIDV-AGFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPGLAIKDFWQVDDRTIVFVADPT 90 (158)
Q Consensus 27 VvD~-A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~~~v~~~W~~~dg~lLlVad~r 90 (158)
+.|. =+.|++.++..|.+.|.++-++++.-|.++| -+|.|.=.+.|+++++-.-++
T Consensus 153 LlDEPFgALDalTR~~lq~~l~~lw~~~~~TvllVT--------Hdi~EAv~LsdRivvl~~~P~ 209 (248)
T COG1116 153 LLDEPFGALDALTREELQDELLRLWEETRKTVLLVT--------HDVDEAVYLADRVVVLSNRPG 209 (248)
T ss_pred EEcCCcchhhHHHHHHHHHHHHHHHHhhCCEEEEEe--------CCHHHHHhhhCEEEEecCCCc
Confidence 4555 4689999999999999999999999999999 356677778888777766654
No 16
>PRK13703 conjugal pilus assembly protein TraF; Provisional
Probab=34.74 E-value=2.1e+02 Score=24.45 Aligned_cols=69 Identities=14% Similarity=0.167 Sum_probs=39.7
Q ss_pred HHHHHHHHhcCCeEEEEeee---cCCC----cchhhhhhhcCCCCeEEEEEcCCCCceeEEeeccccccCCCHHHHHHHh
Q 038271 44 QEIADLEKDTGFKLRVLAQN---YPET----PGLAIKDFWQVDDRTIVFVADPTFGNILNFNVGASVDLDIPRSFWSRLA 116 (158)
Q Consensus 44 ~~L~~lE~~TG~qv~Vlt~~---~p~t----~~~~v~~~W~~~dg~lLlVad~r~~n~l~i~vG~gleg~Lpd~~a~~I~ 116 (158)
..|++|+++.|++|..+..| .|+. ++......|++--=--|+++++.++.. +.+|+|+-.. |++..||.
T Consensus 163 Pil~~fa~~yg~~v~~VS~DG~~~p~fp~~~~d~gqa~~l~v~~~PAl~Lv~~~t~~~--~pv~~G~iS~--deL~~Ri~ 238 (248)
T PRK13703 163 QVINDFRDTYGLSVIPVSVDGVINPLLPDSRTDQGQAQRLGVKYFPALMLVDPKSGSV--RPLSYGFITQ--DDLAKRFL 238 (248)
T ss_pred HHHHHHHHHhCCeEEEEecCCCCCCCCCCCccChhHHHhcCCcccceEEEEECCCCcE--EEEeeccCCH--HHHHHHHH
Confidence 45778899999999999952 1222 122445677765333344456665444 3567765432 44444444
No 17
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=32.89 E-value=35 Score=27.15 Aligned_cols=45 Identities=24% Similarity=0.358 Sum_probs=26.5
Q ss_pred CCCCCCceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcc
Q 038271 20 LPREFTSVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPG 69 (158)
Q Consensus 20 ~P~l~~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~ 69 (158)
.++.+-.|||.|++++..+-..|-.... .+|.+|+++- |--.+++
T Consensus 91 ~~~~~vliVDEasmv~~~~~~~ll~~~~----~~~~klilvG-D~~QL~p 135 (196)
T PF13604_consen 91 LPKKDVLIVDEASMVDSRQLARLLRLAK----KSGAKLILVG-DPNQLPP 135 (196)
T ss_dssp -TSTSEEEESSGGG-BHHHHHHHHHHS-----T-T-EEEEEE--TTSHHH
T ss_pred CCcccEEEEecccccCHHHHHHHHHHHH----hcCCEEEEEC-CcchhcC
Confidence 5566789999999999988666554443 3677666655 3434443
No 18
>PRK15043 transcriptional regulator MirA; Provisional
Probab=31.61 E-value=49 Score=28.26 Aligned_cols=31 Identities=19% Similarity=0.220 Sum_probs=25.4
Q ss_pred cccCCCCCCCCCCceeecCCCCCHHHHHHHHH
Q 038271 13 GVNKPELLPREFTSVIDVAGFLSDGQERRLAQ 44 (158)
Q Consensus 13 ~~~~P~l~P~l~~~VvD~A~~Ls~~~~~~L~~ 44 (158)
..-.|++||. .++++=-.+.||+.|+++|++
T Consensus 200 ~~~~pelf~~-~~~~~~~~~~~t~~q~~~~~~ 230 (243)
T PRK15043 200 NQLRPELFEG-RTLLVWCGENRTSAQQQQLTS 230 (243)
T ss_pred cccChhhcCC-CeEEEEeCCCCCHHHHHHHHH
Confidence 3457889998 458999999999999988864
No 19
>PRK13709 conjugal transfer nickase/helicase TraI; Provisional
Probab=31.11 E-value=85 Score=33.98 Aligned_cols=38 Identities=21% Similarity=0.147 Sum_probs=29.5
Q ss_pred CCCCCCceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEe
Q 038271 20 LPREFTSVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 20 ~P~l~~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt 61 (158)
+++-..||||.|++||..+-.+|- +..++.|.||+++=
T Consensus 498 ~~~~~ilIVDEAg~lsar~m~~Ll----~~A~~~~arvVllg 535 (1747)
T PRK13709 498 FTPGSTLIVDQAEKLSLKETLTLL----DGAARHNVQVLILD 535 (1747)
T ss_pred CCCCcEEEEECCCcCCHHHHHHHH----HHHHHhCCEEEEEC
Confidence 345679999999999998877654 56778888877663
No 20
>COG0263 ProB Glutamate 5-kinase [Amino acid transport and metabolism]
Probab=30.22 E-value=1.8e+02 Score=26.67 Aligned_cols=67 Identities=18% Similarity=0.307 Sum_probs=49.6
Q ss_pred CceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEee----------ecCCCcch-------------hh-------hh
Q 038271 25 TSVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQ----------NYPETPGL-------------AI-------KD 74 (158)
Q Consensus 25 ~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~----------~~p~t~~~-------------~v-------~~ 74 (158)
.-++|.++.|+++....|-.++.+|- +.|.||.+|+. ++|..|.. ++ |.
T Consensus 16 s~Lt~~~g~l~~~~l~~l~~~ia~L~-~~G~eVilVSSGAiaaG~~~Lg~~~rp~~l~~kQA~AAVGQ~~Lm~~y~~~f~ 94 (369)
T COG0263 16 SSLTDGTGGLDRSKLEELVRQVAALH-KAGHEVVLVSSGAIAAGRTRLGLPKRPKTLAEKQAAAAVGQVRLMQLYEELFA 94 (369)
T ss_pred ceeeCCCCCcCHHHHHHHHHHHHHHH-hCCCEEEEEccchhhhChhhcCCCCCCcchHHHHHHHHhCHHHHHHHHHHHHH
Confidence 34677799999999999999999995 56999999996 45544421 23 33
Q ss_pred hhcCCCCeEEEEEcCCCC
Q 038271 75 FWQVDDRTIVFVADPTFG 92 (158)
Q Consensus 75 ~W~~~dg~lLlVad~r~~ 92 (158)
..++.-+|+||-.|+...
T Consensus 95 ~~g~~v~QiLLTr~D~~~ 112 (369)
T COG0263 95 RYGIKVGQILLTRDDFSD 112 (369)
T ss_pred hcCCeeeEEEeehhhhhh
Confidence 344668999998866543
No 21
>PF03147 FDX-ACB: Ferredoxin-fold anticodon binding domain; InterPro: IPR005121 Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in the translation of the genetic code by means of covalent attachment of amino acids to their cognate tRNAs. Phenylalanine-tRNA synthetase (PheRS) is known to be among the most complex enzymes of the aaRS family. Bacterial and mitochondrial PheRSs share a ferredoxin-fold anticodon binding (FDX-ACB) domain, which represents a canonical double split alpha+beta motif having no insertions. The FDX-ACB domain displays a typical RNA recognition fold (RRM) (see PDOC00030 from PROSITEDOC) formed by the four-stranded antiparallel beta sheet, with two helices packed against it [, , , , ].; GO: 0000049 tRNA binding, 0000287 magnesium ion binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation, 0008033 tRNA processing; PDB: 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 3PCO_D 2RHS_D 2RHQ_B 2AKW_B 1B70_B ....
Probab=29.75 E-value=89 Score=21.98 Aligned_cols=32 Identities=28% Similarity=0.348 Sum_probs=21.0
Q ss_pred eeecCCCCCHHHHHHHHHHHH-HHHHhcCCeEE
Q 038271 27 VIDVAGFLSDGQERRLAQEIA-DLEKDTGFKLR 58 (158)
Q Consensus 27 VvD~A~~Ls~~~~~~L~~~L~-~lE~~TG~qv~ 58 (158)
.-|..++|+.++..++-+++. +|+++.|.++|
T Consensus 62 ~~~~~~TLt~~ev~~~~~~i~~~l~~~~~~~lR 94 (94)
T PF03147_consen 62 YQSPDRTLTDEEVNEIHDKIIKALEKKLGAELR 94 (94)
T ss_dssp E--SSS---HHHHHHHHHHHHHHHHHTCT-BEE
T ss_pred EECCCCCCCHHHHHHHHHHHHHHHHHHhCcEeC
Confidence 447789999999998877765 67888999887
No 22
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=29.64 E-value=3.2e+02 Score=25.71 Aligned_cols=90 Identities=20% Similarity=0.251 Sum_probs=62.7
Q ss_pred CCceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcch---hhhhhhc--CC-CCeEEEEE--cCCC----
Q 038271 24 FTSVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPGL---AIKDFWQ--VD-DRTIVFVA--DPTF---- 91 (158)
Q Consensus 24 ~~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~~---~v~~~W~--~~-dg~lLlVa--d~r~---- 91 (158)
..-+||.||-|.- ...|-++|+++.+..--.=.++. ++.+-|. .++..+. ++ .|++|-=. |.|.
T Consensus 184 DvvIvDTAGRl~i--de~Lm~El~~Ik~~~~P~E~llV--vDam~GQdA~~~A~aF~e~l~itGvIlTKlDGdaRGGaAL 259 (451)
T COG0541 184 DVVIVDTAGRLHI--DEELMDELKEIKEVINPDETLLV--VDAMIGQDAVNTAKAFNEALGITGVILTKLDGDARGGAAL 259 (451)
T ss_pred CEEEEeCCCcccc--cHHHHHHHHHHHhhcCCCeEEEE--EecccchHHHHHHHHHhhhcCCceEEEEcccCCCcchHHH
Confidence 3468999999875 66789999999887766555566 6777665 3444444 45 56665555 4442
Q ss_pred ------Cc-eeEEeec---cccccCCCHHHHHHHhh
Q 038271 92 ------GN-ILNFNVG---ASVDLDIPRSFWSRLAG 117 (158)
Q Consensus 92 ------~n-~l~i~vG---~gleg~Lpd~~a~~I~~ 117 (158)
+- |-.|-+| ++||..-||-|++||.+
T Consensus 260 S~~~~tg~PIkFiGtGEki~dLE~F~P~R~asRILG 295 (451)
T COG0541 260 SARAITGKPIKFIGTGEKIDDLEPFHPDRFASRILG 295 (451)
T ss_pred hhHHHHCCCeEEEecCCCcccCCCcChHHHHHHhcC
Confidence 22 3355688 67889999999999987
No 23
>PF05121 GvpK: Gas vesicle protein K ; InterPro: IPR007805 Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in liquid to access oxygen and/or light. Proteins containing this domain are involved in the formation of gas vesicles [].; GO: 0031412 gas vesicle organization
Probab=29.24 E-value=77 Score=23.36 Aligned_cols=23 Identities=39% Similarity=0.523 Sum_probs=20.5
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhc
Q 038271 31 AGFLSDGQERRLAQEIADLEKDT 53 (158)
Q Consensus 31 A~~Ls~~~~~~L~~~L~~lE~~T 53 (158)
++.||.+|..+|-..|-.+|++-
T Consensus 39 ~G~Lse~qiErlG~tLm~Le~~~ 61 (88)
T PF05121_consen 39 AGSLSEEQIERLGETLMKLEEAM 61 (88)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHH
Confidence 68999999999999999998763
No 24
>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....
Probab=29.11 E-value=1e+02 Score=25.17 Aligned_cols=38 Identities=21% Similarity=0.320 Sum_probs=32.4
Q ss_pred CceeecCCCCCH--------HHHHHHHHHHHHHHHhcCCeEEEEee
Q 038271 25 TSVIDVAGFLSD--------GQERRLAQEIADLEKDTGFKLRVLAQ 62 (158)
Q Consensus 25 ~~VvD~A~~Ls~--------~~~~~L~~~L~~lE~~TG~qv~Vlt~ 62 (158)
--|||+-+.|++ .+...+..+|+++.++.+--|.+++|
T Consensus 133 ~v~IDyl~ll~~~~~~~~~~~~~~~i~~~Lk~lA~~~~i~vi~~sQ 178 (259)
T PF03796_consen 133 VVFIDYLQLLKSEDSSDNRRQEIGEISRELKALAKELNIPVIALSQ 178 (259)
T ss_dssp EEEEEEGGGSBTSCSSSCCHHHHHHHHHHHHHHHHHHTSEEEEEEE
T ss_pred EEEechHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHcCCeEEEccc
Confidence 457888888766 55667888999999999999999999
No 25
>PRK13925 rnhB ribonuclease HII; Provisional
Probab=28.60 E-value=59 Score=26.67 Aligned_cols=55 Identities=15% Similarity=0.100 Sum_probs=37.0
Q ss_pred ccchhccccccCCCCCCCCCCceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEe
Q 038271 5 VGCSEAKVGVNKPELLPREFTSVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 5 ~~~~~a~~~~~~P~l~P~l~~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt 61 (158)
+||-+++.++=-++..+.+...=++....||+.++.+|-.++.+. ...+.+.++.
T Consensus 22 ~GPmVvaav~~~~~~~~~L~~~gv~DSK~Ls~~~Re~l~~~I~~~--~~~~~i~~i~ 76 (198)
T PRK13925 22 FGPVFAAAVILSEKAEPQLLQAGLTDSKKLSPKRRAQLVPLILTL--ASDWGIGQAS 76 (198)
T ss_pred hHHhEEEEEEEchHhhhhhhhcCCCCcccCCHHHHHHHHHHHHhh--CCcEEEEEEC
Confidence 355555555544444455554557778999999999999988753 3457777766
No 26
>COG0094 RplE Ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=28.34 E-value=84 Score=25.98 Aligned_cols=71 Identities=21% Similarity=0.257 Sum_probs=50.3
Q ss_pred ccccCCCCCCCCCCceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcchhhhhhhcCCCCeE
Q 038271 12 VGVNKPELLPREFTSVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPGLAIKDFWQVDDRTI 83 (158)
Q Consensus 12 ~~~~~P~l~P~l~~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~~~v~~~W~~~dg~l 83 (158)
-.|.+|...|.+..-|+--.-==+..+...|+....+||.=||.+=++--- =-+.++-.|.+.+.+|-.++
T Consensus 20 ~~y~n~M~~P~i~KVvvNmGvGEa~~d~~~l~~A~~~L~~ItGQKPv~tkA-kksia~FkiR~g~pIG~KVT 90 (180)
T COG0094 20 FGYSNPMQVPRIEKVVVNMGVGEAAADGKRLEKAAKDLELITGQKPVITKA-KKSIAGFKIREGMPIGVKVT 90 (180)
T ss_pred hccCCccccceeEEEEEEccchhhhhchHHHHHHHHHHHHHhCCCceeeeh-hcccccccccCCCeeeEEEE
Confidence 368899999999988887655556677899999999999999988655431 22334445555555554443
No 27
>KOG4648 consensus Uncharacterized conserved protein, contains LRR repeats [Function unknown]
Probab=28.08 E-value=28 Score=32.33 Aligned_cols=21 Identities=24% Similarity=0.452 Sum_probs=16.5
Q ss_pred ccCCcceecccChhHHHHHHHH
Q 038271 118 KYGNIFYWKEKGEDASIEAAVV 139 (158)
Q Consensus 118 r~gn~~~fr~~~~~~gi~aav~ 139 (158)
..||. ||+||.|++||.-=..
T Consensus 102 E~GN~-yFKQgKy~EAIDCYs~ 122 (536)
T KOG4648|consen 102 ERGNT-YFKQGKYEEAIDCYST 122 (536)
T ss_pred Hhhhh-hhhccchhHHHHHhhh
Confidence 55997 8999999999864333
No 28
>PF13734 Inhibitor_I69: Spi protease inhibitor; PDB: 1PVJ_A 1DKI_D 2UZJ_A 2JTC_A 4D8E_A 4D8I_A 4D8B_A.
Probab=27.96 E-value=1.8e+02 Score=21.34 Aligned_cols=26 Identities=27% Similarity=0.408 Sum_probs=15.6
Q ss_pred CCCeEEEEE-cCCCCceeEEeeccccccCCC
Q 038271 79 DDRTIVFVA-DPTFGNILNFNVGASVDLDIP 108 (158)
Q Consensus 79 ~dg~lLlVa-d~r~~n~l~i~vG~gleg~Lp 108 (158)
+++-.++|+ |+|.+.+| ||.-+|-+.
T Consensus 49 ~~~GFVIVSgDdr~~~IL----aYS~~G~fd 75 (96)
T PF13734_consen 49 NNKGFVIVSGDDRMGPIL----AYSDEGSFD 75 (96)
T ss_dssp TTS-EEEEESBTTS-SEE----EEESSS---
T ss_pred CCCEEEEEECCCCcccee----EEcCCCCcC
Confidence 677888888 99988775 555555554
No 29
>COG0164 RnhB Ribonuclease HII [DNA replication, recombination, and repair]
Probab=27.64 E-value=80 Score=26.31 Aligned_cols=53 Identities=23% Similarity=0.254 Sum_probs=39.6
Q ss_pred ccchhccccccCCCCCCCCCCceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEe
Q 038271 5 VGCSEAKVGVNKPELLPREFTSVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 5 ~~~~~a~~~~~~P~l~P~l~~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt 61 (158)
+||-+++.++=.|...| ...=++....||+.+|..|-+++. +....|.|.+..
T Consensus 14 ~GPvV~Aavil~~~~~~--~~~Gl~DSKkLs~~kRe~L~~~I~--~~a~~~~v~~~~ 66 (199)
T COG0164 14 AGPVVAAAVILPPDRLP--KKLGLKDSKKLSPKKREELFEEIK--EKALAWGVGIIP 66 (199)
T ss_pred ccceeEEEEEECccccc--cccCccccccCCHHHHHHHHHHHH--hhccEEEEEEcC
Confidence 46777777765565555 223367789999999999999999 677777777766
No 30
>PF13014 KH_3: KH domain
Probab=26.71 E-value=70 Score=19.22 Aligned_cols=18 Identities=22% Similarity=0.536 Sum_probs=15.0
Q ss_pred HHHHHHHHhcCCeEEEEe
Q 038271 44 QEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 44 ~~L~~lE~~TG~qv~Vlt 61 (158)
+.+++++++||.+|.|--
T Consensus 11 ~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 11 STIKEIREETGAKIQIPP 28 (43)
T ss_pred hHHHHHHHHhCcEEEECC
Confidence 458899999999988765
No 31
>smart00591 RWD domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain.
Probab=26.66 E-value=2e+02 Score=19.65 Aligned_cols=41 Identities=27% Similarity=0.413 Sum_probs=30.3
Q ss_pred ccccCCCCCCCCCCceeec--CCCCCHHHHHHHHHHHHHHHHhc
Q 038271 12 VGVNKPELLPREFTSVIDV--AGFLSDGQERRLAQEIADLEKDT 53 (158)
Q Consensus 12 ~~~~~P~l~P~l~~~VvD~--A~~Ls~~~~~~L~~~L~~lE~~T 53 (158)
-.+..|...|.. .+.+.. ..-|+..++.+|.++|.+..++.
T Consensus 45 l~~~~p~~YP~~-~P~i~~~~~~~l~~~~~~~l~~~l~~~~~e~ 87 (107)
T smart00591 45 LQVKLPENYPDE-APPISLLNSEGLSDEQLAELLKKLEEIAEEN 87 (107)
T ss_pred EEEECCCCCCCC-CCCeEEECCCCCCHHHHHHHHHHHHHHHHHh
Confidence 457778888863 444544 34699999999999998877664
No 32
>PF13689 DUF4154: Domain of unknown function (DUF4154)
Probab=26.19 E-value=2.9e+02 Score=20.81 Aligned_cols=23 Identities=22% Similarity=0.362 Sum_probs=16.4
Q ss_pred HHHHHHHHHHhc--CCeEEEEeeecCC
Q 038271 42 LAQEIADLEKDT--GFKLRVLAQNYPE 66 (158)
Q Consensus 42 L~~~L~~lE~~T--G~qv~Vlt~~~p~ 66 (158)
+...|..++.++ |.+|+|.. +.+
T Consensus 38 ~~~~L~~l~~~~~~~~~i~v~~--~~~ 62 (145)
T PF13689_consen 38 FAEALSTLAGKQVGGRPIRVRR--LSS 62 (145)
T ss_pred HHHHHHHhhhcccCCCcEEEEE--CCC
Confidence 446677787665 89999988 543
No 33
>COG3445 Acid-induced glycyl radical enzyme [General function prediction only]
Probab=26.09 E-value=36 Score=26.06 Aligned_cols=29 Identities=31% Similarity=0.359 Sum_probs=23.3
Q ss_pred cccCCCCCCCCCCceeecC---CCCCHHHHHH
Q 038271 13 GVNKPELLPREFTSVIDVA---GFLSDGQERR 41 (158)
Q Consensus 13 ~~~~P~l~P~l~~~VvD~A---~~Ls~~~~~~ 41 (158)
++++|+..|.++-||--+| ..|+|+|...
T Consensus 86 av~~pekypqltirvsgyavrfnsltpeqqrd 117 (127)
T COG3445 86 AVKHPEKYPQLTIRVSGYAVRFNSLTPEQQRD 117 (127)
T ss_pred HhhCcccCCceEEEEeeEEEEeccCCHHHhhh
Confidence 6889999999999998886 4677776543
No 34
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=26.04 E-value=79 Score=31.18 Aligned_cols=40 Identities=23% Similarity=0.343 Sum_probs=36.4
Q ss_pred CCCCceeec-CCCCCHHHHHHHHHHHHHHHHhcCCeEEEEee
Q 038271 22 REFTSVIDV-AGFLSDGQERRLAQEIADLEKDTGFKLRVLAQ 62 (158)
Q Consensus 22 ~l~~~VvD~-A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~ 62 (158)
++..-++|. +++|+++.+.+|-..|.++... |.||.|+|-
T Consensus 841 ~l~~l~LDEpf~~LD~e~l~~l~~~l~~i~~~-~~qiiIISH 881 (908)
T COG0419 841 RLELLFLDEPFGTLDEERLEKLAEILEELLSD-GRQIIIISH 881 (908)
T ss_pred CCCeeEeeCCCCCCCHHHHHHHHHHHHHHHhc-CCeEEEEeC
Confidence 456778898 8999999999999999999999 999999994
No 35
>cd07013 S14_ClpP Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease. Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. Additionally, they are implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of proteas
Probab=25.21 E-value=1.9e+02 Score=22.48 Aligned_cols=50 Identities=22% Similarity=0.113 Sum_probs=35.9
Q ss_pred ceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcc-----hhhhhhhc
Q 038271 26 SVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPG-----LAIKDFWQ 77 (158)
Q Consensus 26 ~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~-----~~v~~~W~ 77 (158)
|++...+.+++..-..+.++|..++++...+-.+|- +.|..| .+|.+..+
T Consensus 1 r~i~i~g~I~~~~~~~~~~~L~~l~~~~~~~~i~l~--InSpGG~v~~~~~i~~~i~ 55 (162)
T cd07013 1 REIMLTGEVEDISANQFAAQLLFLGAVNPEKDIYLY--INSPGGDVFAGMAIYDTIK 55 (162)
T ss_pred CEEEEccEECcHHHHHHHHHHHHHhcCCCCCCEEEE--EECCCCcHHHHHHHHHHHH
Confidence 456677888889999999999999998776666665 444444 25555544
No 36
>cd02011 TPP_PK Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent magnesium ions and TPP for activity.
Probab=25.12 E-value=3.3e+02 Score=22.97 Aligned_cols=53 Identities=15% Similarity=0.301 Sum_probs=27.2
Q ss_pred hhhhhhc-------CCCCeEEEEEcCCCCceeEEeeccccccCCC-HHHHHHHhhccCCcceeccc
Q 038271 71 AIKDFWQ-------VDDRTIVFVADPTFGNILNFNVGASVDLDIP-RSFWSRLAGKYGNIFYWKEK 128 (158)
Q Consensus 71 ~v~~~W~-------~~dg~lLlVad~r~~n~l~i~vG~gleg~Lp-d~~a~~I~~r~gn~~~fr~~ 128 (158)
.++..|+ ..++.+|.|.|.. -..|. +.-....++ +.++.+... ||=.+++=+|
T Consensus 96 ~lA~~W~a~~~~~~~~~~~vLpIld~N---g~~i~-~pt~~~~~~~e~l~~~~~~-yG~~~~~VDG 156 (227)
T cd02011 96 PLATSWHSNKFLNPATDGAVLPILHLN---GYKIS-NPTILARISHEELEALFRG-YGYEPYFVEG 156 (227)
T ss_pred hHHHHHHhhhhhcccccCCeEEEEEcC---CCccc-CCccccccCchhHHHHHHh-CCCceEEECC
Confidence 6778898 3367777777633 23333 222224343 445554444 4444554454
No 37
>cd08577 PI-PLCc_GDPD_SF_unchar3 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues.
Probab=25.01 E-value=1.5e+02 Score=24.58 Aligned_cols=32 Identities=22% Similarity=0.368 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCC
Q 038271 32 GFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPE 66 (158)
Q Consensus 32 ~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~ 66 (158)
+.++.+|+.+|.+..++.-+ .|.++|+=| +|+
T Consensus 177 g~~~~~q~~~l~~~v~~a~~-~Gl~vr~Wt--v~~ 208 (228)
T cd08577 177 GDTPEDEKEKLKSIIDKAHA-RGKKVRFWG--TPD 208 (228)
T ss_pred CCCCHHHHHHHHHHHHHHHH-CCCEEEEEc--cCC
Confidence 67999999999888766555 599999999 776
No 38
>cd01714 ETF_beta The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an alpha and a beta subunit which binds one molecule of FAD per dimer . A similar system also exists in some bacteria. The homologous pair of proteins (FixA/FixB) are essential for nitrogen fixation. The beta subunit protein is distantly related to and forms a heterodimer with the alpha subunit.
Probab=24.73 E-value=3.4e+02 Score=21.80 Aligned_cols=52 Identities=19% Similarity=0.118 Sum_probs=37.4
Q ss_pred ccccCCCCCCCC-CCceeecC---CCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCC
Q 038271 12 VGVNKPELLPRE-FTSVIDVA---GFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPE 66 (158)
Q Consensus 12 ~~~~~P~l~P~l-~~~VvD~A---~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~ 66 (158)
-++.+|+..+.. +++.+|.. ..+++...+.|+ .+..+.++.|.+|.++. ++.
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~vi~e~~~~~l~-ea~~la~~~g~~v~av~--~G~ 62 (202)
T cd01714 7 KQVPDTEEKRVDPDTGTIDREGVPLIINPYDEYAVE-EALRLKEKYGGEVTVVS--MGP 62 (202)
T ss_pred EECcCCcceEEeCCCCcEEcCCCCccCChHhHHHHH-HHHHhhhhcCCEEEEEE--ECC
Confidence 456677666655 57888854 478888888888 55557777888888888 554
No 39
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=24.00 E-value=1.5e+02 Score=26.86 Aligned_cols=79 Identities=24% Similarity=0.185 Sum_probs=57.6
Q ss_pred ceeecCCCCCHHHHHHHHHHHHHHHHhcCCeE------EEEeeecCCCcch------hhhhh-h--------cCC----C
Q 038271 26 SVIDVAGFLSDGQERRLAQEIADLEKDTGFKL------RVLAQNYPETPGL------AIKDF-W--------QVD----D 80 (158)
Q Consensus 26 ~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv------~Vlt~~~p~t~~~------~v~~~-W--------~~~----d 80 (158)
-++|.||-| .+...|-.+|+.+-+=....+ .+|+ ...|-|. ++|.. = |+| -
T Consensus 225 vliDTAGRL--hnk~nLM~EL~KI~rV~~k~~~~ap~e~llv--lDAttGqnal~QAk~F~eav~l~GiIlTKlDgtAKG 300 (340)
T COG0552 225 VLIDTAGRL--HNKKNLMDELKKIVRVIKKDDPDAPHEILLV--LDATTGQNALSQAKIFNEAVGLDGIILTKLDGTAKG 300 (340)
T ss_pred EEEeCcccc--cCchhHHHHHHHHHHHhccccCCCCceEEEE--EEcccChhHHHHHHHHHHhcCCceEEEEecccCCCc
Confidence 478999988 467789999999999888888 4444 5777774 33332 1 133 5
Q ss_pred CeEEEEEcCCCCceeEEeeccccccCCC
Q 038271 81 RTIVFVADPTFGNILNFNVGASVDLDIP 108 (158)
Q Consensus 81 g~lLlVad~r~~n~l~i~vG~gleg~Lp 108 (158)
|++|=+++..+--+..|-+|++++.+.|
T Consensus 301 G~il~I~~~l~~PI~fiGvGE~~~DL~~ 328 (340)
T COG0552 301 GIILSIAYELGIPIKFIGVGEGYDDLRP 328 (340)
T ss_pred ceeeeHHHHhCCCEEEEeCCCChhhccc
Confidence 6666677887777878889999888776
No 40
>PF07201 HrpJ: HrpJ-like domain; InterPro: IPR010812 This entry represents a conserved region approximately 200 residues long within a number of bacterial hypersensitivity response secretion protein HrpJ and similar proteins. HrpJ forms part of a type III secretion system through which, in phytopathogenic bacterial species, virulence factors are thought to be delivered to plant cells []. This entry also includes the InvE invasion protein from Salmonella. This protein is involved in host parasite interactions and mutations in the InvE gene render Salmonella typhimurium non-invasive []. InvE S. typhimurium mutants fail to elicit a rapid Ca2+ increase in cultured cells, an important event in the infection procedure and internalisation of S. typhimurium into epithelial cells []. This family includes bacterial SepL and SsaL proteins. SepL plays an essential role in the infection process of enterohemorrhagic Escherichia coli and is thought to be responsible for the secretion of EspA, EspD, and EspB []. SsaL of Salmonella typhimurium is thought to be a component of the type III secretion system []. ; GO: 0009405 pathogenesis, 0046903 secretion, 0019867 outer membrane; PDB: 1XL3_B 1XKP_A 2VIX_B 2VJ4_B 2VJ5_B.
Probab=24.00 E-value=17 Score=28.11 Aligned_cols=27 Identities=30% Similarity=0.401 Sum_probs=24.7
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhcCCeE
Q 038271 31 AGFLSDGQERRLAQEIADLEKDTGFKL 57 (158)
Q Consensus 31 A~~Ls~~~~~~L~~~L~~lE~~TG~qv 57 (158)
..-+++..+.+|++.|+.|+++.|++|
T Consensus 91 ~~~~~~~~~~~l~~aL~~L~~~~g~~i 117 (166)
T PF07201_consen 91 QRPLSPELRKALEQALAELEAEEGREI 117 (166)
T ss_dssp SSCCGCCHHHHHHHHHHHHHCCCHHHH
T ss_pred cCcccHHHHHHHHHHHHHHHhhchHHH
Confidence 356889999999999999999999998
No 41
>PF14385 DUF4416: Domain of unknown function (DUF4416)
Probab=23.33 E-value=3.4e+02 Score=21.88 Aligned_cols=81 Identities=16% Similarity=0.204 Sum_probs=57.7
Q ss_pred cccCCCCCCCCCCceeecCCCCCHHHHHHHHHHHHHHHHhcCCe--EEEEeeecCCCcchhhhhhhcCCCCeEEEEE-cC
Q 038271 13 GVNKPELLPREFTSVIDVAGFLSDGQERRLAQEIADLEKDTGFK--LRVLAQNYPETPGLAIKDFWQVDDRTIVFVA-DP 89 (158)
Q Consensus 13 ~~~~P~l~P~l~~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~q--v~Vlt~~~p~t~~~~v~~~W~~~dg~lLlVa-d~ 89 (158)
-|-.++.-|++..+++=..+.+++++...+...-.++|++.... =+|=. -|| .+....++|.. .+
T Consensus 47 ~YY~~EmG~~l~r~~~sF~~li~~~~L~~iK~~tn~iE~~~~~~g~R~VNi-----DPG-------Yl~~~~lVLAt~K~ 114 (164)
T PF14385_consen 47 DYYNKEMGPGLKRRFISFKRLIHPEELADIKLETNEIEKEFAKDGKRRVNI-----DPG-------YLTLERLVLATTKN 114 (164)
T ss_pred cccchhcCCCceEEEEEEcccCCHHHHHHHHHHHHHHHHHHHhcCCceEEe-----Cce-------ecccCeEEEEecCC
Confidence 35567888999999999999999999999888888888876442 22222 122 13455566666 77
Q ss_pred CCCceeEEeeccccccCCC
Q 038271 90 TFGNILNFNVGASVDLDIP 108 (158)
Q Consensus 90 r~~n~l~i~vG~gleg~Lp 108 (158)
+++|+ ..|+|+..-++
T Consensus 115 ~~HRI---YL~~GIyaE~t 130 (164)
T PF14385_consen 115 FSHRI---YLGDGIYAELT 130 (164)
T ss_pred CCcce---eccCCEEEEEE
Confidence 77555 99999877553
No 42
>PRK13434 F0F1 ATP synthase subunit delta; Provisional
Probab=23.29 E-value=1.2e+02 Score=23.94 Aligned_cols=30 Identities=10% Similarity=0.032 Sum_probs=23.9
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEee
Q 038271 30 VAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQ 62 (158)
Q Consensus 30 ~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~ 62 (158)
.|..||++|+++|.+.|++ ++|.+|.+-+.
T Consensus 111 sA~~Ls~~q~~~l~~~L~k---~~g~~v~l~~~ 140 (184)
T PRK13434 111 SYPSLEPAQVDKLGSILSE---KFKSEFILEVS 140 (184)
T ss_pred EcCCCCHHHHHHHHHHHHH---HHCCEeEEEee
Confidence 4788999999999887654 78888877663
No 43
>PF02370 M: M protein repeat; InterPro: IPR003345 This short repeat is found in multiple copies in bacterial M proteins. The M proteins bind to IgA and are closely associated with virulence. The M protein has been postulated to be a major group A streptococcal (GAS) virulence factor because of its contribution to the bacterial resistance to opsonophagocytosis [].; PDB: 2KK9_A.
Probab=23.20 E-value=1.2e+02 Score=16.70 Aligned_cols=16 Identities=19% Similarity=0.414 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHhc
Q 038271 38 QERRLAQEIADLEKDT 53 (158)
Q Consensus 38 ~~~~L~~~L~~lE~~T 53 (158)
..+.|++++..||.+.
T Consensus 2 akk~lEa~~qkLe~e~ 17 (21)
T PF02370_consen 2 AKKQLEADHQKLEAEK 17 (21)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHH
Confidence 5678899999888763
No 44
>TIGR02740 TraF-like TraF-like protein. This protein is related to the F-type conjugation system pilus assembly proteins TraF (TIGR02739)and TrbB (TIGR02738) both of which exhibit a thioredoxin fold. The protein represented by this model has the same length and architecture as TraF, but lacks the CXXC-motif found in TrbB and believed to be responsible for the disulfide isomerase activity of that protein.
Probab=22.97 E-value=4.6e+02 Score=22.21 Aligned_cols=16 Identities=19% Similarity=-0.031 Sum_probs=8.7
Q ss_pred ccCCCCCCCCCCceee
Q 038271 14 VNKPELLPREFTSVID 29 (158)
Q Consensus 14 ~~~P~l~P~l~~~VvD 29 (158)
..+|++-..+..++-.
T Consensus 128 ~~~P~Ldy~~~~P~~~ 143 (271)
T TIGR02740 128 WTDPILDETLRRPVST 143 (271)
T ss_pred HhCCCCCccccCCchH
Confidence 4566666655544443
No 45
>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.
Probab=22.77 E-value=2.4e+02 Score=22.21 Aligned_cols=38 Identities=16% Similarity=0.129 Sum_probs=26.3
Q ss_pred CCCceeec-CCCCCHHHHHHHHHHHHHHHHhcCCeEEEEe
Q 038271 23 EFTSVIDV-AGFLSDGQERRLAQEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 23 l~~~VvD~-A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt 61 (158)
.+-.+.|. +.-|++..++.+.+.|+++.+ .|.-|.+++
T Consensus 108 p~llLlDEPt~~LD~~~~~~l~~~l~~~~~-~g~tvIivS 146 (176)
T cd03238 108 GTLFILDEPSTGLHQQDINQLLEVIKGLID-LGNTVILIE 146 (176)
T ss_pred CCEEEEeCCcccCCHHHHHHHHHHHHHHHh-CCCEEEEEe
Confidence 34567776 667888888888888877743 466666666
No 46
>PF04339 DUF482: Protein of unknown function, DUF482; InterPro: IPR007434 This family contains several proteins of uncharacterised function.
Probab=22.50 E-value=2.7e+02 Score=25.11 Aligned_cols=56 Identities=20% Similarity=0.392 Sum_probs=41.7
Q ss_pred ecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcch-----------hhhhhhc---------------CCCCe
Q 038271 29 DVAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPGL-----------AIKDFWQ---------------VDDRT 82 (158)
Q Consensus 29 D~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~~-----------~v~~~W~---------------~~dg~ 82 (158)
|.=..||+..|.++.++.++.+ +.|-++++++ -.+.... ....+|+ .+++.
T Consensus 175 dfLa~Lss~kRk~IRrERr~v~-~~Gi~~~~l~--G~~i~~~~~~~f~~~Y~~Ty~k~~~~~yLt~~FF~~l~~~m~~~~ 251 (370)
T PF04339_consen 175 DFLAALSSRKRKNIRRERRKVA-EQGIRIRTLT--GDEITDEDWDRFYRLYQNTYAKRWGRPYLTREFFEQLAETMPEQV 251 (370)
T ss_pred HHHHHhchhhHHHHHHHHHHHH-HcCCEEEEEe--CCCCCHHHHHHHHHHHHHHHHhhCCChhhcHHHHHHHHHhCcCCE
Confidence 4446799999999999999995 7899999999 4544332 2233455 45888
Q ss_pred EEEEE
Q 038271 83 IVFVA 87 (158)
Q Consensus 83 lLlVa 87 (158)
+|++|
T Consensus 252 ~l~~A 256 (370)
T PF04339_consen 252 VLVVA 256 (370)
T ss_pred EEEEE
Confidence 88888
No 47
>COG0039 Mdh Malate/lactate dehydrogenases [Energy production and conversion]
Probab=22.49 E-value=45 Score=29.47 Aligned_cols=55 Identities=16% Similarity=0.251 Sum_probs=38.4
Q ss_pred cccCCCCCCCCCCceeecCCCCCHHHHH-HHHHHHHHHHHhcCCeEEEEeeecCCCcch
Q 038271 13 GVNKPELLPREFTSVIDVAGFLSDGQER-RLAQEIADLEKDTGFKLRVLAQNYPETPGL 70 (158)
Q Consensus 13 ~~~~P~l~P~l~~~VvD~A~~Ls~~~~~-~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~~ 70 (158)
.||+|+..| .+.+.|..+..+..... .+... .+++.=.|+.|+|+|..+|+-||.
T Consensus 30 LiDi~~~~~--~G~a~DL~~~~~~~~~~~~i~~~-~~y~~~~~aDiVvitAG~prKpGm 85 (313)
T COG0039 30 LIDINEEKA--EGVALDLSHAAAPLGSDVKITGD-GDYEDLKGADIVVITAGVPRKPGM 85 (313)
T ss_pred EEEcccccc--cchhcchhhcchhccCceEEecC-CChhhhcCCCEEEEeCCCCCCCCC
Confidence 366774333 47888888877665332 22222 448888999999999888999994
No 48
>cd07021 Clp_protease_NfeD_like Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentiall
Probab=22.45 E-value=1.3e+02 Score=23.92 Aligned_cols=35 Identities=17% Similarity=0.265 Sum_probs=29.5
Q ss_pred ceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEe
Q 038271 26 SVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 26 ~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt 61 (158)
+|++..+.+++.....|...|++.+++. .+..|+-
T Consensus 2 ~vi~i~g~I~~~~~~~l~~~l~~a~~~~-~~~ivl~ 36 (178)
T cd07021 2 YVIPIEGEIDPGLAAFVERALKEAKEEG-ADAVVLD 36 (178)
T ss_pred EEEEEeeEECHHHHHHHHHHHHHHHhCC-CCeEEEE
Confidence 5888899999999999999999998886 5555555
No 49
>COG2086 FixA Electron transfer flavoprotein, beta subunit [Energy production and conversion]
Probab=22.22 E-value=2.1e+02 Score=24.60 Aligned_cols=54 Identities=13% Similarity=0.162 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcch-hhhhhhcCCCCeEEEEEc
Q 038271 33 FLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPGL-AIKDFWQVDDRTIVFVAD 88 (158)
Q Consensus 33 ~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~~-~v~~~W~~~dg~lLlVad 88 (158)
.+++-.+.++|..++=-|+..|.+|.|+| ++..... .+.+.-..|-...+++.|
T Consensus 34 ~in~~D~~AvEeAlrLke~~~~~eV~vlt--~Gp~~a~~~lr~aLAmGaDraili~d 88 (260)
T COG2086 34 SINPFDLNAVEEALRLKEKGYGGEVTVLT--MGPPQAEEALREALAMGADRAILITD 88 (260)
T ss_pred ccChhhHHHHHHHHHhhccCCCceEEEEE--ecchhhHHHHHHHHhcCCCeEEEEec
Confidence 57899999999999988889999999999 6655443 455545566545555554
No 50
>PRK08474 F0F1 ATP synthase subunit delta; Validated
Probab=22.20 E-value=1.9e+02 Score=22.73 Aligned_cols=29 Identities=14% Similarity=0.245 Sum_probs=22.5
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEe
Q 038271 30 VAGFLSDGQERRLAQEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 30 ~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt 61 (158)
.|..||.+|+++|.+.|++ ++|.+|.+-+
T Consensus 110 SA~~Ls~~q~~~i~~~l~~---~~g~~v~l~~ 138 (176)
T PRK08474 110 SNEKLSEETLKKLEEKLSK---KFNAKIKLKQ 138 (176)
T ss_pred ECccCCHHHHHHHHHHHHH---HhCCeEEEEE
Confidence 3778898888888887765 6888887766
No 51
>cd07396 MPP_Nbla03831 Homo sapiens Nbla03831 and related proteins, metallophosphatase domain. Nbla03831 (also known as LOC56985) is an uncharacterized Homo sapiens protein with a domain that belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.
Probab=22.05 E-value=1.8e+02 Score=23.96 Aligned_cols=33 Identities=21% Similarity=0.359 Sum_probs=26.6
Q ss_pred ecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEee
Q 038271 29 DVAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQ 62 (158)
Q Consensus 29 D~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~ 62 (158)
+..+.|+++|.+-|+++|++.+. ++..+.|++-
T Consensus 155 ~~~G~l~~~Ql~WL~~~L~~~~~-~~~~viV~~H 187 (267)
T cd07396 155 DWNGGIGEEQLQWLRNELQEADA-NGEKVIIFSH 187 (267)
T ss_pred eccCcCCHHHHHHHHHHHHHHHh-cCCeEEEEEe
Confidence 34688999999999999998764 5667777774
No 52
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=22.01 E-value=2.2e+02 Score=17.97 Aligned_cols=28 Identities=21% Similarity=0.224 Sum_probs=21.1
Q ss_pred ecCCCCCHHHHHHHHHHHHH-HHHhcCCe
Q 038271 29 DVAGFLSDGQERRLAQEIAD-LEKDTGFK 56 (158)
Q Consensus 29 D~A~~Ls~~~~~~L~~~L~~-lE~~TG~q 56 (158)
....-.|++|+++|-+.+.+ +.+..|..
T Consensus 7 ~~~~grs~eqk~~l~~~it~~l~~~~~~p 35 (62)
T PRK00745 7 ELFEGRTVEQKRKLVEEITRVTVETLGCP 35 (62)
T ss_pred EEcCCCCHHHHHHHHHHHHHHHHHHcCCC
Confidence 33333699999999999987 77777744
No 53
>PRK13646 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=21.28 E-value=1.7e+02 Score=24.37 Aligned_cols=36 Identities=17% Similarity=0.269 Sum_probs=25.6
Q ss_pred ceeec-CCCCCHHHHHHHHHHHHHHHHhcCCeEEEEe
Q 038271 26 SVIDV-AGFLSDGQERRLAQEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 26 ~VvD~-A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt 61 (158)
.+.|. +.-|++..+..+.+.|.++-++.|..|.++|
T Consensus 167 lllDEPt~~LD~~~~~~l~~~l~~l~~~~g~tvl~vt 203 (286)
T PRK13646 167 IVLDEPTAGLDPQSKRQVMRLLKSLQTDENKTIILVS 203 (286)
T ss_pred EEEECCcccCCHHHHHHHHHHHHHHHHhCCCEEEEEe
Confidence 46666 6677777777777777777666676666666
No 54
>COG0687 PotD Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]
Probab=21.10 E-value=1.3e+02 Score=25.92 Aligned_cols=35 Identities=20% Similarity=0.374 Sum_probs=30.0
Q ss_pred CCceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCC
Q 038271 24 FTSVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPET 67 (158)
Q Consensus 24 ~~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t 67 (158)
+-+|..-.+...++ -++.||++||.+|++-+ +.+.
T Consensus 33 ~l~v~~w~gy~~~~-------~~~~F~k~tGi~V~~~~--~~sn 67 (363)
T COG0687 33 TLNVYNWGGYIDPA-------LLKPFEKETGIKVVYDT--FDSN 67 (363)
T ss_pred EEEEEcccccCCHH-------HHHHHHHHHCCEEEEEe--cCCc
Confidence 35678888888888 89999999999999999 7764
No 55
>PF11062 DUF2863: Protein of unknown function (DUF2863); InterPro: IPR021292 This bacterial family of proteins have no known function.
Probab=20.86 E-value=1e+02 Score=28.41 Aligned_cols=54 Identities=24% Similarity=0.351 Sum_probs=43.7
Q ss_pred ceeEEeeccccccCCCHHHHH--HHhhccCCcceecccChhHHHHHHHHHHHHHhcCCCCCCCCc
Q 038271 93 NILNFNVGASVDLDIPRSFWS--RLAGKYGNIFYWKEKGEDASIEAAVVAISNCLREPVGPNNCS 155 (158)
Q Consensus 93 n~l~i~vG~gleg~Lpd~~a~--~I~~r~gn~~~fr~~~~~~gi~aav~ai~~~L~ge~~~~~~~ 155 (158)
++-++-.|=++|-+|||++.. |-.+|.+.+| +|.+++.-+...|.=+|+.+.++
T Consensus 236 ~l~~lLpGC~~elLlPday~~acR~aD~~~Rp~---------sirAav~~L~~~l~~~~~~LrAv 291 (398)
T PF11062_consen 236 NLAPLLPGCGFELLLPDAYFAACREADRRIRPY---------SIRAAVAYLETALGVPPSDLRAV 291 (398)
T ss_pred hHHHhcCCcchheecchHHHHHHHhhhhhhchH---------HHHHHHHHHHHhhCCChhhceEE
Confidence 344556899999999999977 6677888765 89999999999999888877653
No 56
>cd07181 RNaseH_typeII_eukaryota_like Eukaryotic Ribonuclease HII; putative role in Okazaki fragment removal during replication. Ribonuclease (RNase) HII endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is a type II RNase H that is active during replication and is believed to play a role in removal
Probab=20.82 E-value=71 Score=26.29 Aligned_cols=57 Identities=12% Similarity=0.101 Sum_probs=36.9
Q ss_pred ccchhccccccCCCCCCCCCCceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEe
Q 038271 5 VGCSEAKVGVNKPELLPREFTSVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 5 ~~~~~a~~~~~~P~l~P~l~~~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt 61 (158)
.||-+++.++=-|+....+...=+.....||+.++..|-+++.+.-..-.+.+.++.
T Consensus 12 ~GPlvvaav~~~~~~~~~l~~~gv~DSK~Ls~~~r~~L~~~I~~~~~~~~~~i~~i~ 68 (216)
T cd07181 12 LGPMVYGIAYCPISYEEDLKKLGFADSKTLTEEKREELFKKIKEKSEALGWATRILS 68 (216)
T ss_pred hhhhEEEEEEEchHhhhhhhhcCCCcCCcCCHHHHHHHHHHHHhccccceEEEEEEC
Confidence 355566655544444344444456778899999999999999755323346666666
No 57
>PRK13436 F0F1 ATP synthase subunit delta; Provisional
Probab=20.76 E-value=1.5e+02 Score=23.44 Aligned_cols=30 Identities=20% Similarity=0.251 Sum_probs=23.2
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEee
Q 038271 30 VAGFLSDGQERRLAQEIADLEKDTGFKLRVLAQ 62 (158)
Q Consensus 30 ~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~ 62 (158)
.|..||++++++|.+.| ++++|.+|.+-+.
T Consensus 115 sA~~Ls~~~~~~i~~~l---~~~~g~~v~l~~~ 144 (179)
T PRK13436 115 TTEPLSEVQISRFESKL---SKKLNKKVHLVNK 144 (179)
T ss_pred ecCCCCHHHHHHHHHHH---HHHHCCeEEEEee
Confidence 47889999998887665 6788988876553
No 58
>cd00394 Clp_protease_like Caseinolytic protease (ClpP) is an ATP-dependent protease. Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradec
Probab=20.33 E-value=1.2e+02 Score=22.77 Aligned_cols=35 Identities=34% Similarity=0.379 Sum_probs=28.7
Q ss_pred eeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEe
Q 038271 27 VIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 27 VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt 61 (158)
|+...+.+++.....|.+.|+.++++...+..|+.
T Consensus 1 vi~i~g~I~~~~~~~l~~~l~~a~~d~~~~~ivl~ 35 (161)
T cd00394 1 VIFINGVIEDVSADQLAAQIRFAEADNSVKAIVLE 35 (161)
T ss_pred CEEEEeEEccchHHHHHHHHHHHHhCCCCceEEEE
Confidence 45666778888889999999999998877777777
No 59
>COG4525 TauB ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=20.07 E-value=1.9e+02 Score=25.05 Aligned_cols=68 Identities=22% Similarity=0.385 Sum_probs=48.5
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhcCCeEEEEeeecCCCcchhhhhhhcCCCCeEEEEEcCCCCceeEEeeccccccCCCHH
Q 038271 31 AGFLSDGQERRLAQEIADLEKDTGFKLRVLAQNYPETPGLAIKDFWQVDDRTIVFVADPTFGNILNFNVGASVDLDIPRS 110 (158)
Q Consensus 31 A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt~~~p~t~~~~v~~~W~~~dg~lLlVad~r~~n~l~i~vG~gleg~Lpd~ 110 (158)
=+.|+.-.+.++...|-++.++||.++-++|- .|.|.-.+.+. |+|.++..++++ + .+|-.
T Consensus 160 fgAlDa~tRe~mQelLldlw~~tgk~~lliTH--------~ieEAlflatr--Lvvlsp~pgRvv--------~-~~~~d 220 (259)
T COG4525 160 FGALDALTREQMQELLLDLWQETGKQVLLITH--------DIEEALFLATR--LVVLSPGPGRVV--------E-RLPLD 220 (259)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHhCCeEEEEec--------cHHHHHhhhhe--eEEecCCCceee--------E-ecCCC
Confidence 46788889999999999999999999999993 34445454444 455577766662 2 34445
Q ss_pred HHHHHhh
Q 038271 111 FWSRLAG 117 (158)
Q Consensus 111 ~a~~I~~ 117 (158)
|+.|...
T Consensus 221 f~rR~aa 227 (259)
T COG4525 221 FARRYAA 227 (259)
T ss_pred HHHHhhc
Confidence 7777664
No 60
>cd07015 Clp_protease_NfeD Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cle
Probab=20.07 E-value=1.9e+02 Score=23.16 Aligned_cols=35 Identities=14% Similarity=0.184 Sum_probs=29.1
Q ss_pred ceeecCCCCCHHHHHHHHHHHHHHHHhcCCeEEEEe
Q 038271 26 SVIDVAGFLSDGQERRLAQEIADLEKDTGFKLRVLA 61 (158)
Q Consensus 26 ~VvD~A~~Ls~~~~~~L~~~L~~lE~~TG~qv~Vlt 61 (158)
+|+...+.+++.+...|+..|+.-+++ +.+-.++-
T Consensus 2 ~vi~i~G~I~~~~~~~l~~~l~~A~~~-~~~~i~l~ 36 (172)
T cd07015 2 YVAQIKGQITSYTYDQFDRYITIAEQD-NAEAIIIE 36 (172)
T ss_pred EEEEEeeEECHhHHHHHHHHHHHHhcC-CCCeEEEE
Confidence 688899999999999999999988765 56666665
Done!