Query 027998
Match_columns 215
No_of_seqs 223 out of 929
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 04:42:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027998.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027998hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3272 Predicted coiled-coil 100.0 2.1E-63 4.6E-68 419.9 16.9 206 1-215 1-207 (207)
2 PF05670 DUF814: Domain of unk 100.0 6.5E-30 1.4E-34 193.2 10.0 89 4-99 1-90 (90)
3 COG1293 Predicted RNA-binding 99.9 6.4E-25 1.4E-29 212.3 11.9 106 11-121 447-553 (564)
4 KOG2030 Predicted RNA-binding 99.5 3.4E-14 7.4E-19 140.6 8.8 94 3-103 497-592 (911)
5 KOG4691 Uncharacterized conser 78.7 6.6 0.00014 34.5 6.2 41 143-183 123-163 (227)
6 KOG0407 40S ribosomal protein 75.7 15 0.00032 29.8 6.9 61 18-78 5-73 (139)
7 PF07946 DUF1682: Protein of u 70.9 9.9 0.00021 34.9 5.6 23 42-69 157-179 (321)
8 KOG0163 Myosin class VI heavy 55.2 24 0.00052 37.1 5.5 14 23-36 782-795 (1259)
9 TIGR02544 III_secr_YscJ type I 54.6 32 0.0007 29.5 5.5 61 32-97 130-191 (193)
10 PF03460 NIR_SIR_ferr: Nitrite 52.5 26 0.00056 24.2 3.9 39 48-97 11-49 (69)
11 PF13025 DUF3886: Protein of u 49.1 93 0.002 22.9 6.4 13 182-194 54-66 (70)
12 KOG1029 Endocytic adaptor prot 47.4 15 0.00034 38.4 2.7 15 61-75 245-259 (1118)
13 PF07946 DUF1682: Protein of u 45.9 66 0.0014 29.5 6.5 7 136-142 249-255 (321)
14 PF06936 Selenoprotein_S: Sele 43.7 76 0.0016 27.5 6.1 19 139-157 73-91 (190)
15 PRK00247 putative inner membra 42.0 59 0.0013 31.6 5.6 23 147-169 336-358 (429)
16 KOG2963 RNA-binding protein re 40.9 60 0.0013 31.1 5.4 14 100-113 300-313 (405)
17 COG3553 Uncharacterized protei 38.2 1.5E+02 0.0033 23.1 6.3 63 63-133 10-72 (96)
18 PTZ00399 cysteinyl-tRNA-synthe 33.2 98 0.0021 31.4 5.9 8 184-191 592-599 (651)
19 cd04863 MtLigD_Pol_like MtLigD 29.7 67 0.0014 28.7 3.6 59 36-94 137-202 (231)
20 PF14943 MRP-S26: Mitochondria 28.7 2.1E+02 0.0045 24.3 6.3 19 143-161 88-106 (170)
21 TIGR02435 CobG precorrin-3B sy 28.7 1.4E+02 0.0031 27.9 5.8 52 39-101 249-300 (390)
22 PF12220 U1snRNP70_N: U1 small 27.5 99 0.0021 23.3 3.8 12 126-137 41-52 (94)
23 KOG4364 Chromatin assembly fac 27.3 1.5E+02 0.0033 30.8 5.9 12 42-53 159-170 (811)
24 PRK12756 phospho-2-dehydro-3-d 27.2 1.8E+02 0.0038 27.7 6.1 49 38-93 219-267 (348)
25 PRK12822 phospho-2-dehydro-3-d 27.0 1.8E+02 0.0039 27.7 6.1 77 37-122 219-302 (356)
26 cd04862 PaeLigD_Pol_like PaeLi 26.8 79 0.0017 28.2 3.5 58 36-94 133-198 (227)
27 cd04864 LigD_Pol_like_1 LigD_P 26.4 80 0.0017 28.1 3.5 59 36-95 134-200 (228)
28 KOG1029 Endocytic adaptor prot 26.2 1.6E+02 0.0034 31.4 5.9 12 104-115 308-319 (1118)
29 PRK06007 fliF flagellar MS-rin 24.4 1.7E+02 0.0037 29.0 5.8 64 31-98 157-221 (542)
30 KOG1144 Translation initiation 24.2 1.7E+02 0.0037 31.1 5.8 7 23-29 110-116 (1064)
31 cd04861 LigD_Pol_like LigD_Pol 23.4 1E+02 0.0022 27.5 3.6 59 36-94 133-198 (227)
32 KOG4364 Chromatin assembly fac 23.0 1.6E+02 0.0034 30.6 5.2 8 127-134 247-254 (811)
33 PRK07193 fliF flagellar MS-rin 23.0 1.7E+02 0.0037 29.2 5.5 66 31-100 160-227 (552)
34 cd04866 LigD_Pol_like_3 LigD_P 22.3 1.1E+02 0.0023 27.3 3.5 58 36-94 128-194 (223)
35 PTZ00397 macrophage migration 22.2 3.6E+02 0.0078 20.5 6.2 57 35-95 47-104 (116)
36 PRK15348 type III secretion sy 21.6 2.7E+02 0.0059 25.0 6.0 56 39-99 137-192 (249)
37 PTZ00399 cysteinyl-tRNA-synthe 20.8 3.1E+02 0.0067 27.9 6.9 10 143-152 553-562 (651)
38 PRK04203 rpl1P 50S ribosomal p 20.7 2.4E+02 0.0051 24.4 5.3 52 62-113 2-54 (215)
39 TIGR02778 ligD_pol DNA polymer 20.5 1.2E+02 0.0027 27.2 3.6 59 36-94 149-214 (245)
40 KOG1144 Translation initiation 20.1 2.3E+02 0.005 30.2 5.7 9 127-135 218-226 (1064)
41 cd04865 LigD_Pol_like_2 LigD_P 20.1 1.3E+02 0.0028 26.9 3.5 57 37-94 135-199 (228)
42 TIGR00206 fliF flagellar basal 20.1 2.2E+02 0.0049 28.3 5.6 65 31-99 157-222 (555)
No 1
>KOG3272 consensus Predicted coiled-coil protein [General function prediction only]
Probab=100.00 E-value=2.1e-63 Score=419.85 Aligned_cols=206 Identities=67% Similarity=1.019 Sum_probs=199.8
Q ss_pred CEEEEEecccCCCeEEEEeCChhhhHHHHHhcCCCcEEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhccc
Q 027998 1 MVFYFKARPEAGDYTIFMGLDKYENEELIKYGFPEDIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQ 80 (215)
Q Consensus 1 Mv~~f~s~~~~~g~~I~vGRn~~ENe~L~k~a~~~DlWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~k 80 (215)
|||||.|..+.++++||+|+++++|++||+|+||+|+|||+++++|||||||+.+|+++++||.++|.+||||++++||+
T Consensus 1 mv~~~~s~~t~~~~~i~mg~dk~en~~lIk~g~~e~Vwfhv~~~sS~hvyl~l~~~qtiddip~~vL~DC~QLvKaNSIQ 80 (207)
T KOG3272|consen 1 MVFYFKSNPTEPPYMIYMGKDKFENEELIKWGWPEDVWFHVDKLSSAHVYLRLREGQTIDDIPEFVLEDCAQLVKANSIQ 80 (207)
T ss_pred CceEeccccCCCCeeEEEeecccchhHHHHcCCccceEEEeecccccceeeeecCCCCcccccHHHHHHHHHHHHhcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCceEEEEEeccceecCCCCCcceEEEcCceEEEEEecccccHHHHHHhhccceeeC-cchHHHHHHHHHHHHHHHH
Q 027998 81 GNKVNNIDVVYTPWANLKKTASMDVGQVGFHNPKMVRTVKVEKRINEIVNRLNKTKVERK-PDLKAEREAANAAERAERK 159 (215)
Q Consensus 81 g~k~~~V~V~YT~~knvkK~~~~~~G~V~f~~~k~v~~v~v~~~~~~ivnrl~ktk~e~~-~d~~~~~~~~~~~~~~~~k 159 (215)
|+|+++|+|+||||+||+|+++|.||||+||+.+.|+++.+++|.|+|||||+||++|.+ |||+++||.+++++|.+.+
T Consensus 81 G~Kmnnv~VvYT~w~NLKKt~~M~~Gqv~fh~~k~vr~~~~~~r~Nei~NrL~kTkve~~~~d~~~lrEard~~er~e~k 160 (207)
T KOG3272|consen 81 GNKMNNVEVVYTPWSNLKKTADMDVGQVGFHSTKQVRRIVVEKRINEIVNRLAKTKVERFKPDFAALREARDAKERQEIK 160 (207)
T ss_pred cccccceeEEechhHhhcccCCCCcccccchhhhheeeeeecchHHHHHHHHhhhhHhhcchhHHHHHHHHhhhhhhhHH
Confidence 999999999999999999999999999999999999999999999999999999999988 9999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCchhhhhhhccccchhhcccccccccccCCCC
Q 027998 160 LQLRDKKRREEMERLEKERQAEVRSYKGLMVAEKMTSNKQIASESKSLQELEEDFM 215 (215)
Q Consensus 160 ~~~~~~~~~e~~~~~~~~~~~~~~~Y~~l~~~~~~~~~~~~~~~~~~~~~~~ddfm 215 (215)
+..+|++.+|+++..++.++++++||.++|+.| |+++.+. ++ +||||
T Consensus 161 ~~~~Er~~rekee~l~k~~k~e~rsy~~~~k~e-~~~d~d~-------~~-sddfm 207 (207)
T KOG3272|consen 161 KIEQERSKREKEEMLWKEEKAELRSYISLMKDE-MRDDMDL-------GN-SDDFM 207 (207)
T ss_pred HHHHhhhhHHHHHHHhHHHHHHhhhhhccchhh-hhcccCc-------cc-ccccC
Confidence 999999999999999999999999999999999 7777652 23 89999
No 2
>PF05670 DUF814: Domain of unknown function (DUF814); InterPro: IPR008532 This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from O34693 from SWISSPROT where the N-terminal region is involved in this activity []. Hence the activity of this C-terminal domain is unknown. This domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important.
Probab=99.96 E-value=6.5e-30 Score=193.21 Aligned_cols=89 Identities=36% Similarity=0.578 Sum_probs=80.1
Q ss_pred EEEecccCCCeEEEEeCChhhhHHH-HHhcCCCcEEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhccccc
Q 027998 4 YFKARPEAGDYTIFMGLDKYENEEL-IKYGFPEDIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGN 82 (215)
Q Consensus 4 ~f~s~~~~~g~~I~vGRn~~ENe~L-~k~a~~~DlWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~kg~ 82 (215)
||+| ++|++|+||||+.|||.| ++++.++|||||++++||||||||++++ +.++++|++||+||++||+.++
T Consensus 1 wF~s---~~g~~i~vGrn~~eNe~L~~k~~~~~D~wfH~~~~pg~hvil~~~~~----~~~~~~l~~AA~laa~~Ska~~ 73 (90)
T PF05670_consen 1 WFIS---SDGFKIIVGRNAKENEMLTKKYARPNDLWFHADDFPGPHVILRNNPG----DEPPPTLQEAAQLAASYSKAWK 73 (90)
T ss_pred CEEe---cCCeEEEEeCCHHHHHHHHHHhhhhcceeEeccCCCCCEEEEECCCC----ccchHHHHHHHHHHHHhCHhhc
Confidence 4555 489999999999999999 8999999999999999999999999865 3445599999999999995478
Q ss_pred CCCceEEEEEeccceec
Q 027998 83 KVNNIDVVYTPWANLKK 99 (215)
Q Consensus 83 k~~~V~V~YT~~knvkK 99 (215)
+...|.|+||+++||+|
T Consensus 74 ~~~~v~V~yt~~k~v~K 90 (90)
T PF05670_consen 74 KGEKVEVDYTQGKYVKK 90 (90)
T ss_pred cCCCeEEEEeehHhccC
Confidence 89999999999999997
No 3
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription]
Probab=99.92 E-value=6.4e-25 Score=212.29 Aligned_cols=106 Identities=27% Similarity=0.447 Sum_probs=99.3
Q ss_pred CCCeEEEEeCChhhhHHH-HHhcCCCcEEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhcccccCCCceEE
Q 027998 11 AGDYTIFMGLDKYENEEL-IKYGFPEDIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDV 89 (215)
Q Consensus 11 ~~g~~I~vGRn~~ENe~L-~k~a~~~DlWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~kg~k~~~V~V 89 (215)
++|+.|++|||+.|||.| .+++.++|+|||++++|||||+|+++ |. ++|+++|.+||+||++|| +|++++.|.|
T Consensus 447 s~Gf~vi~Grna~qNe~l~~k~~~~~DlwfHa~~~~gshvvik~~-~~---~~~e~ti~eAA~~Aa~~S-ka~~~~~v~v 521 (564)
T COG1293 447 SDGFLVIGGRNAKQNEELVKKYAEKDDLWFHADDIPGSHVVIKTE-GK---EPSEETILEAAQLAASYS-KAWKSGLVPV 521 (564)
T ss_pred cCCeEEEEecCcccchHHHHhhcccCcEEEEccCCCCCeEEEeCC-CC---CCChHHHHHHHHHHHHhc-hHhhcCCCce
Confidence 579999999999999999 79999999999999999999999986 32 799999999999999999 5999999999
Q ss_pred EEEeccceecCCCCCcceEEEcCceEEEEEec
Q 027998 90 VYTPWANLKKTASMDVGQVGFHNPKMVRTVKV 121 (215)
Q Consensus 90 ~YT~~knvkK~~~~~~G~V~f~~~k~v~~v~v 121 (215)
+||.++++++++++++|+|+|.+.++|+.-+.
T Consensus 522 d~t~vk~vqv~K~a~~G~vl~~g~~~I~~k~~ 553 (564)
T COG1293 522 DYTWVKPVQVPKGAKSGEVLYKGQKTIRGKRD 553 (564)
T ss_pred EEEEEcccccCCCCCCceEEecCcEEEEEccc
Confidence 99999999999999999999999999876544
No 4
>KOG2030 consensus Predicted RNA-binding protein [General function prediction only]
Probab=99.51 E-value=3.4e-14 Score=140.63 Aligned_cols=94 Identities=23% Similarity=0.325 Sum_probs=82.1
Q ss_pred EEEEecccCCCeEEEEeCChhhhHHH-HHhcCCCcEEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhcccc
Q 027998 3 FYFKARPEAGDYTIFMGLDKYENEEL-IKYGFPEDIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQG 81 (215)
Q Consensus 3 ~~f~s~~~~~g~~I~vGRn~~ENe~L-~k~a~~~DlWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~kg 81 (215)
.||.| |+||+|++|||+.|||.| -+|..|+||+||++-..+|||||++++++ ++|+.+|.+|+.+|.+|| ++
T Consensus 497 ~wFiS---SEg~LVi~GrdaqQnEllvkky~~~~DiY~had~~gaSsviIkN~~~~---eipp~TL~eAg~ma~~~S-~a 569 (911)
T KOG2030|consen 497 HWFIS---SEGYLVIGGRDAQQNELLVKKYLEPGDIYVHADLHGASSVIIKNPPKT---EIPPKTLEEAGSMALCYS-KA 569 (911)
T ss_pred eEEEe---cCcEEEEcCCChhhhhHHHHhhCCCCCeEEecccCCCceEEEeCCCCC---CCChhhHHHHHHHHhHHh-hh
Confidence 35666 699999999999999999 59999999999999999999999998774 899999999999999999 58
Q ss_pred cCCCce-EEEEEeccceecCCCC
Q 027998 82 NKVNNI-DVVYTPWANLKKTASM 103 (215)
Q Consensus 82 ~k~~~V-~V~YT~~knvkK~~~~ 103 (215)
|...-| ..-|+...+|+|+.+.
T Consensus 570 WdakvvssaWwv~~dqVSKtapt 592 (911)
T KOG2030|consen 570 WDAKVVSSAWWVYPDQVSKTAPT 592 (911)
T ss_pred hcccccccceEEecccccccCCC
Confidence 865433 3448889999998874
No 5
>KOG4691 consensus Uncharacterized conserved protein [Function unknown]
Probab=78.73 E-value=6.6 Score=34.51 Aligned_cols=41 Identities=27% Similarity=0.259 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 027998 143 LKAEREAANAAERAERKLQLRDKKRREEMERLEKERQAEVR 183 (215)
Q Consensus 143 ~~~~~~~~~~~~~~~~k~~~~~~~~~e~~~~~~~~~~~~~~ 183 (215)
+.++|.+|+++.++++++...+.-..+.++.++++++++.+
T Consensus 123 ~~~~R~~Rla~~~~E~~~~i~ee~~~~~e~~~a~k~qae~e 163 (227)
T KOG4691|consen 123 LHELRIARLAQEEREQEQRIAEEQARKAEEVQAWKQQAERE 163 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56678888888888888887777777777777888776643
No 6
>KOG0407 consensus 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=75.74 E-value=15 Score=29.76 Aligned_cols=61 Identities=25% Similarity=0.281 Sum_probs=44.7
Q ss_pred EeCChhhhHHHH----HhcCCCcEEEEecCCCCcEEEEEeCCCCC----CCCCCHHHHHHHHHHHHHhc
Q 027998 18 MGLDKYENEELI----KYGFPEDIWFHVDKMSSAHVYLRLHKGQT----IDDISEGVLEDCAQLVKANS 78 (215)
Q Consensus 18 vGRn~~ENe~L~----k~a~~~DlWFHv~~~pGaHViLR~~~g~~----~~~ipe~~L~~AAqLaa~~S 78 (215)
+|--..+++.++ -++.-+|-|.|+-|++|.-.|+|...|+. -++-++-.-..|||=++.-+
T Consensus 5 lg~q~~e~~~vfgvahi~asfndtfvhitdlsg~eti~rvtggmkvkadrdesspyaamlaaqdva~kc 73 (139)
T KOG0407|consen 5 LGPQVREGEQVFGVAHIFASFNDTFVHVTDLSGKETIVRVTGGMKVKADRDESSPYAAMLAAQDVAAKC 73 (139)
T ss_pred ccchhcccceeeeEEEEEeecccceEEEeccCCceEEEEecCCeEEecccccCChHHHHHHHHHHHHHH
Confidence 445556667664 36778999999999999999999997762 23455666667777777666
No 7
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=70.92 E-value=9.9 Score=34.86 Aligned_cols=23 Identities=13% Similarity=0.296 Sum_probs=15.2
Q ss_pred cCCCCcEEEEEeCCCCCCCCCCHHHHHH
Q 027998 42 DKMSSAHVYLRLHKGQTIDDISEGVLED 69 (215)
Q Consensus 42 ~~~pGaHViLR~~~g~~~~~ipe~~L~~ 69 (215)
.++|..+|++--. .++++.+|..
T Consensus 157 ~~Lp~~~~vmsEs-----~e~~~~il~~ 179 (321)
T PF07946_consen 157 PKLPESLVVMSES-----NEVTDFILTP 179 (321)
T ss_pred cCCCcceEEEEcc-----HhHHHHHhCh
Confidence 4788888888633 2566666663
No 8
>KOG0163 consensus Myosin class VI heavy chain [Cytoskeleton]
Probab=55.24 E-value=24 Score=37.08 Aligned_cols=14 Identities=14% Similarity=0.200 Sum_probs=7.2
Q ss_pred hhhHHHHHhcCCCc
Q 027998 23 YENEELIKYGFPED 36 (215)
Q Consensus 23 ~ENe~L~k~a~~~D 36 (215)
.=|++|+.-.|..-
T Consensus 782 kVn~WLv~sRWkk~ 795 (1259)
T KOG0163|consen 782 KVNKWLVRSRWKKS 795 (1259)
T ss_pred HHHHHHHHhHHHHh
Confidence 34666655444443
No 9
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=54.63 E-value=32 Score=29.45 Aligned_cols=61 Identities=31% Similarity=0.427 Sum_probs=42.0
Q ss_pred cCCCc-EEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhcccccCCCceEEEEEeccce
Q 027998 32 GFPED-IWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYTPWANL 97 (215)
Q Consensus 32 a~~~D-lWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~kg~k~~~V~V~YT~~knv 97 (215)
+.|++ ++.--..-|+|-|+|+..+|. .++. .+.--..|+ +.|..+-+.++|+|+-.||..+
T Consensus 130 ~~P~~~~f~~~~~~~sASV~l~~~~g~---~l~~-qv~~I~~LV-a~SV~~L~~enVtVv~~~~~~~ 191 (193)
T TIGR02544 130 VLPENDNNGRPKKPSSASVFIKYRPGL---NLDA-LIPKIKRLV-ANSIPGLDYDNVSVVLVPAEER 191 (193)
T ss_pred ECCCCCcccccCCCCcEEEEEEeCCCC---CcHH-HHHHHHHHH-HHhcCCCCccceEEEEeccccc
Confidence 34444 444445678999999999875 3343 444444454 4777788999999999998753
No 10
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=52.51 E-value=26 Score=24.24 Aligned_cols=39 Identities=26% Similarity=0.276 Sum_probs=28.7
Q ss_pred EEEEEeCCCCCCCCCCHHHHHHHHHHHHHhcccccCCCceEEEEEeccce
Q 027998 48 HVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYTPWANL 97 (215)
Q Consensus 48 HViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~kg~k~~~V~V~YT~~knv 97 (215)
+|-++.+.| .++.+.+...|++|..|+. -.|..|++.||
T Consensus 11 ~v~~~~~~G----~i~~~~l~~la~ia~~yg~-------~~irlT~~Q~l 49 (69)
T PF03460_consen 11 MVRIRIPGG----RISAEQLRALAEIAEKYGD-------GEIRLTTRQNL 49 (69)
T ss_dssp EEEEB-GGG----EEEHHHHHHHHHHHHHHST-------SEEEEETTSCE
T ss_pred EEEEeCCCE----EECHHHHHHHHHHHHHhCC-------CeEEECCCCeE
Confidence 677888777 5899999999999998883 24445665554
No 11
>PF13025 DUF3886: Protein of unknown function (DUF3886)
Probab=49.13 E-value=93 Score=22.93 Aligned_cols=13 Identities=15% Similarity=0.437 Sum_probs=11.2
Q ss_pred hcCchhhhhhhcc
Q 027998 182 VRSYKGLMVAEKM 194 (215)
Q Consensus 182 ~~~Y~~l~~~~~~ 194 (215)
-.|+..|+.+++|
T Consensus 54 nksFeELL~eS~l 66 (70)
T PF13025_consen 54 NKSFEELLNESEL 66 (70)
T ss_pred hcCHHHHHhcccC
Confidence 6799999988877
No 12
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=47.39 E-value=15 Score=38.36 Aligned_cols=15 Identities=13% Similarity=0.186 Sum_probs=8.6
Q ss_pred CCCHHHHHHHHHHHH
Q 027998 61 DISEGVLEDCAQLVK 75 (215)
Q Consensus 61 ~ipe~~L~~AAqLaa 75 (215)
.+.-+....|.-|+-
T Consensus 245 kL~~dEfilam~lie 259 (1118)
T KOG1029|consen 245 KLSADEFILAMHLIE 259 (1118)
T ss_pred cccHHHHHHHHHHHH
Confidence 356666666665553
No 13
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=45.93 E-value=66 Score=29.46 Aligned_cols=7 Identities=14% Similarity=0.582 Sum_probs=3.0
Q ss_pred ceeeCcc
Q 027998 136 KVERKPD 142 (215)
Q Consensus 136 k~e~~~d 142 (215)
+....|+
T Consensus 249 ~~~l~~e 255 (321)
T PF07946_consen 249 RFKLSPE 255 (321)
T ss_pred eeeeCHH
Confidence 4444444
No 14
>PF06936 Selenoprotein_S: Selenoprotein S (SelS); InterPro: IPR009703 This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. These proteins are involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins which participate in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner []. They probably serve as a linker between DER1, which mediates the retro-translocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination.; GO: 0008430 selenium binding, 0006886 intracellular protein transport, 0030176 integral to endoplasmic reticulum membrane; PDB: 2Q2F_A.
Probab=43.75 E-value=76 Score=27.45 Aligned_cols=19 Identities=32% Similarity=0.520 Sum_probs=10.6
Q ss_pred eCcchHHHHHHHHHHHHHH
Q 027998 139 RKPDLKAEREAANAAERAE 157 (215)
Q Consensus 139 ~~~d~~~~~~~~~~~~~~~ 157 (215)
..||....+++.....|++
T Consensus 73 ~dpd~v~~rqEa~eaAR~R 91 (190)
T PF06936_consen 73 KDPDVVVRRQEAMEAARRR 91 (190)
T ss_dssp TSHHHHHHHHHHHHHHHHH
T ss_pred cChhHHHHHHHHHHHHHHH
Confidence 5677665555555444443
No 15
>PRK00247 putative inner membrane protein translocase component YidC; Validated
Probab=41.97 E-value=59 Score=31.57 Aligned_cols=23 Identities=22% Similarity=0.332 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 027998 147 REAANAAERAERKLQLRDKKRRE 169 (215)
Q Consensus 147 ~~~~~~~~~~~~k~~~~~~~~~e 169 (215)
+.++.+++..++|+..+++++++
T Consensus 336 ~~~~~~~~k~~~k~~~~~~~~~~ 358 (429)
T PRK00247 336 RTAEKNEAKARKKEIAQKRRAAE 358 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333444444444444444443
No 16
>KOG2963 consensus RNA-binding protein required for 60S ribosomal subunit biogenesis [Translation, ribosomal structure and biogenesis]
Probab=40.95 E-value=60 Score=31.07 Aligned_cols=14 Identities=21% Similarity=0.375 Sum_probs=10.1
Q ss_pred CCCCCcceEEEcCc
Q 027998 100 TASMDVGQVGFHNP 113 (215)
Q Consensus 100 ~~~~~~G~V~f~~~ 113 (215)
..|...|.|.||..
T Consensus 300 eEGi~~GkVlyH~h 313 (405)
T KOG2963|consen 300 EEGICEGKVLYHEH 313 (405)
T ss_pred eccccccceEEeeh
Confidence 44667788888876
No 17
>COG3553 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.19 E-value=1.5e+02 Score=23.08 Aligned_cols=63 Identities=19% Similarity=0.176 Sum_probs=42.4
Q ss_pred CHHHHHHHHHHHHHhcccccCCCceEEEEEeccceecCCCCCcceEEEcCceEEEEEecccccHHHHHHhh
Q 027998 63 SEGVLEDCAQLVKANSIQGNKVNNIDVVYTPWANLKKTASMDVGQVGFHNPKMVRTVKVEKRINEIVNRLN 133 (215)
Q Consensus 63 pe~~L~~AAqLaa~~S~kg~k~~~V~V~YT~~knvkK~~~~~~G~V~f~~~k~v~~v~v~~~~~~ivnrl~ 133 (215)
++......-|||++++- +++|-|+|-.-----+ ..|.++.....-...+.|.+.+..-|-+|.
T Consensus 10 TehaarYl~qLckHwah------Kf~ve~~p~~g~idl~--~~~~~~l~a~a~~L~i~v~~d~e~~lA~le 72 (96)
T COG3553 10 TEHAARYLQQLCKHWAH------KFPVEFDPTHGTIDLP--VLGTLTLDADAQTLTIVVEADEEQNLARLE 72 (96)
T ss_pred hHHHHHHHHHHHHHhhc------cCCceECCCcceeecC--ccceEEeecCCCEEEEEeccchhhhHHHHH
Confidence 46677888899999984 4888899865332222 266777666666667778777655555554
No 18
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=33.19 E-value=98 Score=31.42 Aligned_cols=8 Identities=0% Similarity=-0.106 Sum_probs=4.9
Q ss_pred Cchhhhhh
Q 027998 184 SYKGLMVA 191 (215)
Q Consensus 184 ~Y~~l~~~ 191 (215)
+=.++|..
T Consensus 592 ~p~~~f~~ 599 (651)
T PTZ00399 592 PPAEFFKR 599 (651)
T ss_pred CHHHHhhh
Confidence 45566765
No 19
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=29.69 E-value=67 Score=28.69 Aligned_cols=59 Identities=12% Similarity=0.119 Sum_probs=34.5
Q ss_pred cEEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhc-------ccccCCCceEEEEEec
Q 027998 36 DIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANS-------IQGNKVNNIDVVYTPW 94 (215)
Q Consensus 36 DlWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S-------~kg~k~~~V~V~YT~~ 94 (215)
.-|.-..+-.|-|||+.+.++.+|+++-.-....|..|++.+- .+.+-.++|-|+|.+-
T Consensus 137 ~s~~KTSG~kGlHV~vPl~~~~~~~~vr~fa~~~A~~l~~~~P~~~t~~~~k~~R~grvfiDylqN 202 (231)
T cd04863 137 ASFPKTSGSKGLHLYVPLDGPVSSDQTKEFAKALARELEREHPDLVVSRMTKSLRAGKVFVDWSQN 202 (231)
T ss_pred ccceECCCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhhHhhHhhCCCcEEEECccC
Confidence 4477788888999999998765444333223333333333321 1233457888888653
No 20
>PF14943 MRP-S26: Mitochondrial ribosome subunit S26
Probab=28.71 E-value=2.1e+02 Score=24.31 Aligned_cols=19 Identities=37% Similarity=0.405 Sum_probs=10.4
Q ss_pred hHHHHHHHHHHHHHHHHHH
Q 027998 143 LKAEREAANAAERAERKLQ 161 (215)
Q Consensus 143 ~~~~~~~~~~~~~~~~k~~ 161 (215)
+...|++|++.++.+.+..
T Consensus 88 ~~~~Re~Rl~~e~e~~~~~ 106 (170)
T PF14943_consen 88 IAELREERLAKEREEREEE 106 (170)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4455666666655554444
No 21
>TIGR02435 CobG precorrin-3B synthase. An iron-sulfur protein. An oxygen atom from dioxygen is incorporated into the macrocycle at C-20. In the aerobic cobalamin biosythesis pathway, four enzymes are involved in the conversion of precorrin-3A to precorrin-6A. The first of the four steps is carried out by EC 1.14.13.83, precorrin-3B synthase (CobG), yielding precorrin-3B as the product. This is followed by three methylation reactions, which introduce a methyl group at C-17 (CobJ; EC 2.1.1.131), C-11 (CobM; EC 2.1.1.133) and C-1 (CobF; EC 2.1.1.152) of the macrocycle, giving rise to precorrin-4, precorrin-5 and precorrin-6A, respectively.
Probab=28.66 E-value=1.4e+02 Score=27.87 Aligned_cols=52 Identities=25% Similarity=0.286 Sum_probs=36.4
Q ss_pred EEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhcccccCCCceEEEEEeccceecCC
Q 027998 39 FHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYTPWANLKKTA 101 (215)
Q Consensus 39 FHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~kg~k~~~V~V~YT~~knvkK~~ 101 (215)
+|..+-.|-.|-++.+.| .++.+.+...|.+|..|.. -.|..|+|.||-=+.
T Consensus 249 ~~~q~~~~~~v~~~~p~G----~i~~~~l~~la~ia~~~g~-------~~irlT~~Q~l~i~~ 300 (390)
T TIGR02435 249 LHPQGDAGVTLGAGLALG----QLTAAQLRGLAQLAQALGD-------GDLRLTPWRALLVLG 300 (390)
T ss_pred eeecCCCCeEEEEecCcc----ccCHHHHHHHHHHHHHhCC-------CeEEEcCCcceEEcC
Confidence 344444565556677777 6999999999999998862 346678887775543
No 22
>PF12220 U1snRNP70_N: U1 small nuclear ribonucleoprotein of 70kDa MW N terminal; InterPro: IPR022023 This domain is found in eukaryotes. This domain is about 90 amino acids in length. This domain is found associated with PF00076 from PFAM. This domain is part of U1 snRNP, which is the pre-mRNA binding protein of the penta-snRNP spliceosome complex. It extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition.
Probab=27.54 E-value=99 Score=23.35 Aligned_cols=12 Identities=8% Similarity=0.191 Sum_probs=7.1
Q ss_pred HHHHHHhhccce
Q 027998 126 NEIVNRLNKTKV 137 (215)
Q Consensus 126 ~~ivnrl~ktk~ 137 (215)
.+.|+.+.....
T Consensus 41 s~~l~~~~~~~~ 52 (94)
T PF12220_consen 41 SQYLSEFEDYKD 52 (94)
T ss_pred HHHHHHHhcccc
Confidence 566666665554
No 23
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=27.32 E-value=1.5e+02 Score=30.77 Aligned_cols=12 Identities=42% Similarity=0.293 Sum_probs=5.3
Q ss_pred cCCCCcEEEEEe
Q 027998 42 DKMSSAHVYLRL 53 (215)
Q Consensus 42 ~~~pGaHViLR~ 53 (215)
..-++.-|||..
T Consensus 159 ~~~~s~~vVl~~ 170 (811)
T KOG4364|consen 159 IMPSSVRVVLKL 170 (811)
T ss_pred cCCCcchhHHhh
Confidence 333444455543
No 24
>PRK12756 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional
Probab=27.22 E-value=1.8e+02 Score=27.68 Aligned_cols=49 Identities=8% Similarity=0.121 Sum_probs=33.5
Q ss_pred EEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhcccccCCCceEEEEEe
Q 027998 38 WFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYTP 93 (215)
Q Consensus 38 WFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~kg~k~~~V~V~YT~ 93 (215)
.+|..+-|-+|||||... ..+...+.+..|+..-+. ..-...|-|+...
T Consensus 219 iv~T~GN~~~HvILRGg~---~PNY~~~~v~~a~~~l~~----~~l~~~imVDcSH 267 (348)
T PRK12756 219 IYQTSGNPYGHIIMRGGK---KPNYHAEDIAAACDTLRE----FDLPEHLVVDFSH 267 (348)
T ss_pred EEEcCCCCCeEEEeeCCC---CCCCCHHHHHHHHHHHHH----CCCCCcEEEECCC
Confidence 468888999999999643 347778888887766553 2234566666543
No 25
>PRK12822 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional
Probab=27.01 E-value=1.8e+02 Score=27.73 Aligned_cols=77 Identities=16% Similarity=0.103 Sum_probs=46.2
Q ss_pred EEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhcccccCCCceEEEEEeccceecCCCC-------CcceEE
Q 027998 37 IWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYTPWANLKKTASM-------DVGQVG 109 (215)
Q Consensus 37 lWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~kg~k~~~V~V~YT~~knvkK~~~~-------~~G~V~ 109 (215)
..+|..+-|-+|||||... ..+...+.+..|..+-...- -...|-|+.... |-.|...- -..|+.
T Consensus 219 aiv~T~GN~~~HvILRGg~---~PNY~~~~v~~a~~~l~~~~----l~~~vmVDcSH~-NS~K~~~~Q~~V~~~v~~q~~ 290 (356)
T PRK12822 219 STLLSDGNPHGHIILRGGR---EPNYGLSDVTKASKLLHDEG----LNHRLIIDCSHG-NSQKVAKNQISVARELCDQLK 290 (356)
T ss_pred EEEEcCCCCCceEEEeCCC---CCCCCHHHHHHHHHHHHHCC----CCCcEEEECCCc-cCCCCHHHHHHHHHHHHHHHH
Confidence 4578888899999999543 34677888888877665433 335677665443 33333221 234444
Q ss_pred EcCceEEEEEecc
Q 027998 110 FHNPKMVRTVKVE 122 (215)
Q Consensus 110 f~~~k~v~~v~v~ 122 (215)
.....|..++++
T Consensus 291 -~g~~~I~GvMiE 302 (356)
T PRK12822 291 -EGEGAIAGVMVE 302 (356)
T ss_pred -CCCCeEEEEEEe
Confidence 333447777764
No 26
>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nu
Probab=26.77 E-value=79 Score=28.17 Aligned_cols=58 Identities=16% Similarity=0.168 Sum_probs=34.7
Q ss_pred cEEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHh--------cccccCCCceEEEEEec
Q 027998 36 DIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKAN--------SIQGNKVNNIDVVYTPW 94 (215)
Q Consensus 36 DlWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~--------S~kg~k~~~V~V~YT~~ 94 (215)
.-|.-..+-.|-|||+.+.++.+|+++-.-.-..|..|++.+ ++ .+-.++|-|+|.+-
T Consensus 133 ~~~~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~lA~~l~~~~P~~~t~~~~k-~~R~gkvfiDylqN 198 (227)
T cd04862 133 ESFVKTSGGKGLHVVVPLAPRAGWDEVKAFAKALAQHLARTNPDRFVATMGK-AKRVGKIFIDYLRN 198 (227)
T ss_pred ccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhHHhhH-HhCCCcEEEECccC
Confidence 456777788899999999875444333322333333333332 22 34467899998763
No 27
>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=26.36 E-value=80 Score=28.15 Aligned_cols=59 Identities=15% Similarity=0.109 Sum_probs=34.3
Q ss_pred cEEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHH--------hcccccCCCceEEEEEecc
Q 027998 36 DIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKA--------NSIQGNKVNNIDVVYTPWA 95 (215)
Q Consensus 36 DlWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~--------~S~kg~k~~~V~V~YT~~k 95 (215)
.-|.-..+-.|-|||+.+.++.+++++-.-....|-.|+.. .++ .+-.++|-|+|.+-.
T Consensus 134 ~~f~KTSG~kGlHv~vPl~~~~~~~~~r~fa~~lA~~l~~~~P~~~t~~~~k-~~R~grvfiDylqN~ 200 (228)
T cd04864 134 PSFVKTTGSRGFHVVVPLDGRGDFDDVRAFAAEAADALAKRDPDLLTTEARK-AKRGDRVFLDIGRNA 200 (228)
T ss_pred ccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhHHhhH-HhCCCcEEEECccCC
Confidence 34677778889999999987654432222222223333222 222 334678999987643
No 28
>KOG1029 consensus Endocytic adaptor protein intersectin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=26.22 E-value=1.6e+02 Score=31.36 Aligned_cols=12 Identities=17% Similarity=0.199 Sum_probs=8.8
Q ss_pred CcceEEEcCceE
Q 027998 104 DVGQVGFHNPKM 115 (215)
Q Consensus 104 ~~G~V~f~~~k~ 115 (215)
-||+|+|.+-+.
T Consensus 308 lP~~~TFEDKrk 319 (1118)
T KOG1029|consen 308 LPAPVTFEDKRK 319 (1118)
T ss_pred CCCCcchhhhhH
Confidence 578888887653
No 29
>PRK06007 fliF flagellar MS-ring protein; Reviewed
Probab=24.41 E-value=1.7e+02 Score=28.98 Aligned_cols=64 Identities=22% Similarity=0.352 Sum_probs=48.9
Q ss_pred hcCCC-cEEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhcccccCCCceEEEEEecccee
Q 027998 31 YGFPE-DIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYTPWANLK 98 (215)
Q Consensus 31 ~a~~~-DlWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~kg~k~~~V~V~YT~~knvk 98 (215)
++-|+ .+|..-..-|+|-|+|++.+|. .++++.+.--..|++ .|..|-+..+|+|+=+...-|.
T Consensus 157 l~lP~~s~F~~~~~~~tASV~l~l~~g~---~L~~~qV~aI~~LVA-~sVpgL~~enVtVvD~~G~lLs 221 (542)
T PRK06007 157 LALPKESVFVREQQPPSASVVLTLKPGR---ALDPEQVKAIVHLVA-SAVPGLKPENVTIVDQNGRLLS 221 (542)
T ss_pred EECCCCccccccCCCCcEEEEEeccCCC---CCCHHHHHHHHHHHH-hccCCCCccceEEEcCCCCCcc
Confidence 34455 4555666779999999999885 688899988888887 4546888899999876666665
No 30
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=24.23 E-value=1.7e+02 Score=31.09 Aligned_cols=7 Identities=14% Similarity=0.363 Sum_probs=3.4
Q ss_pred hhhHHHH
Q 027998 23 YENEELI 29 (215)
Q Consensus 23 ~ENe~L~ 29 (215)
.+++.|+
T Consensus 110 ~d~dkll 116 (1064)
T KOG1144|consen 110 DDLDKLL 116 (1064)
T ss_pred cchHHHh
Confidence 3455554
No 31
>cd04861 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase do
Probab=23.43 E-value=1e+02 Score=27.50 Aligned_cols=59 Identities=17% Similarity=0.142 Sum_probs=34.8
Q ss_pred cEEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhc-------ccccCCCceEEEEEec
Q 027998 36 DIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANS-------IQGNKVNNIDVVYTPW 94 (215)
Q Consensus 36 DlWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S-------~kg~k~~~V~V~YT~~ 94 (215)
.-|.-..+-.|-|||+.+.++.+|+++-.-.-..|-.|+..+- .+.+-.++|-|+|.+-
T Consensus 133 ~~f~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~iA~~l~~~~P~~~t~~~~k~~R~grvfiDy~qN 198 (227)
T cd04861 133 ESFPKTSGGKGLHVYVPLAPRYTWDEVRAFAKALARELARRLPDLFTAEMAKAKRGGKIFVDYLQN 198 (227)
T ss_pred ccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhhHhhHHhCCCCEEEECccC
Confidence 3467777888899999998765444333323333333333322 0244568888888654
No 32
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=23.04 E-value=1.6e+02 Score=30.63 Aligned_cols=8 Identities=25% Similarity=0.484 Sum_probs=3.3
Q ss_pred HHHHHhhc
Q 027998 127 EIVNRLNK 134 (215)
Q Consensus 127 ~ivnrl~k 134 (215)
.+.+.+.|
T Consensus 247 l~~KQ~rk 254 (811)
T KOG4364|consen 247 LLLKQLRK 254 (811)
T ss_pred HHHHHHHH
Confidence 34444443
No 33
>PRK07193 fliF flagellar MS-ring protein; Reviewed
Probab=22.99 E-value=1.7e+02 Score=29.18 Aligned_cols=66 Identities=32% Similarity=0.362 Sum_probs=49.5
Q ss_pred hcCCCcEEEEe--cCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhcccccCCCceEEEEEeccceecC
Q 027998 31 YGFPEDIWFHV--DKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYTPWANLKKT 100 (215)
Q Consensus 31 ~a~~~DlWFHv--~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~kg~k~~~V~V~YT~~knvkK~ 100 (215)
++-|++=-|-. ..-|+|-|+|++.+|. .++++-+.-...|++ .|..|-+.++|+|+=+...-|...
T Consensus 160 LalPe~s~F~~~~~~~~sASV~l~l~~g~---~Ls~~QV~aI~~LVA-~SVpgL~penVtVvD~~G~lLs~~ 227 (552)
T PRK07193 160 LAIPKSSSFVRQDPELPSASVVLRLKPGQ---KLSPEQVEAIVNLVA-GSVPGLKPANVSVVDQHGNLLSAG 227 (552)
T ss_pred EEcCCCCcccccCCCCCCeEEEEecCCCC---CCCHHHHHHHHHHHH-HhcCCCCccceEEEcCCCCcccCC
Confidence 45666544433 3689999999999886 688888888888876 455688899999987777666643
No 34
>cd04866 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=22.34 E-value=1.1e+02 Score=27.26 Aligned_cols=58 Identities=16% Similarity=0.098 Sum_probs=34.1
Q ss_pred cEEEEecCCCCcEEEEEeC-CCCCCCCCCHHHHHHHHHHHHH--------hcccccCCCceEEEEEec
Q 027998 36 DIWFHVDKMSSAHVYLRLH-KGQTIDDISEGVLEDCAQLVKA--------NSIQGNKVNNIDVVYTPW 94 (215)
Q Consensus 36 DlWFHv~~~pGaHViLR~~-~g~~~~~ipe~~L~~AAqLaa~--------~S~kg~k~~~V~V~YT~~ 94 (215)
.-|.-..+-.|-|||+.+. ++.+|+.+-.-....|..|+.. .++ +.-.++|-|+|.+-
T Consensus 128 ~~f~KTSG~kGlHV~vPl~~~~~~~~~~r~fa~~iA~~l~~~~P~~~t~~~~k-~~R~gkVfiDylqN 194 (223)
T cd04866 128 TSFVKTSGNKGLQVYIPLPDNKFTYDETRLFTEFIAEYLCQQFPELFTTERLK-KNRHNRLYLDYVQH 194 (223)
T ss_pred ccceEccCCCeEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHCchhhhHHhhH-HhCCCCEEEECccC
Confidence 4567778888999999998 6544433332233333333322 232 34467888888654
No 35
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=22.17 E-value=3.6e+02 Score=20.50 Aligned_cols=57 Identities=11% Similarity=0.053 Sum_probs=37.8
Q ss_pred CcEEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhccc-ccCCCceEEEEEecc
Q 027998 35 EDIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQ-GNKVNNIDVVYTPWA 95 (215)
Q Consensus 35 ~DlWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~k-g~k~~~V~V~YT~~k 95 (215)
.+++|...+-|.+.|=|..-.|. -++.-...++.|+..-+.. |-..+.|.|.|+...
T Consensus 47 ~~m~f~g~~~p~a~v~i~~~g~~----~~e~k~~l~~~i~~~l~~~lgi~~~rv~I~f~~~~ 104 (116)
T PTZ00397 47 KHMRFGGSHDGCCFVRVTSIGGI----SRSNNSSIAAAITKILASHLKVKSERVYIEFKDCS 104 (116)
T ss_pred ceEEECCCCCceEEEEEEEecCC----CHHHHHHHHHHHHHHHHHHhCcCcccEEEEEEECC
Confidence 45777766677777777765442 2455666677777766631 557888999988754
No 36
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=21.63 E-value=2.7e+02 Score=25.02 Aligned_cols=56 Identities=14% Similarity=0.061 Sum_probs=38.0
Q ss_pred EEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhcccccCCCceEEEEEeccceec
Q 027998 39 FHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYTPWANLKK 99 (215)
Q Consensus 39 FHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~kg~k~~~V~V~YT~~knvkK 99 (215)
|--..-|+|-|+|+..+|. +.+..+.+-+-..++|..|-+-++|+|+-+|+..-.-
T Consensus 137 ~~~~~~asASV~I~~~~~~-----~~~~~~v~I~~LVA~SV~gL~~enVTVvd~~~~~~~~ 192 (249)
T PRK15348 137 GSNASPSSVAVFIKYSPQV-----NMEAFRVKIKDLIEMSIPGLQYSKISILMQPAEFRMV 192 (249)
T ss_pred ccCCCCccEEEEEEeCCCC-----ChHHHHHHHHHHHHHhcCCCCccceEEEecCCccccC
Confidence 4455667899999998763 3333322344444577778899999999999655443
No 37
>PTZ00399 cysteinyl-tRNA-synthetase; Provisional
Probab=20.79 E-value=3.1e+02 Score=27.91 Aligned_cols=10 Identities=40% Similarity=0.591 Sum_probs=4.6
Q ss_pred hHHHHHHHHH
Q 027998 143 LKAEREAANA 152 (215)
Q Consensus 143 ~~~~~~~~~~ 152 (215)
|..+|+++..
T Consensus 553 ~~~~~~~~~~ 562 (651)
T PTZ00399 553 LQREKEEKEA 562 (651)
T ss_pred HHHHHHHHHH
Confidence 4455544433
No 38
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed
Probab=20.73 E-value=2.4e+02 Score=24.44 Aligned_cols=52 Identities=13% Similarity=0.140 Sum_probs=38.4
Q ss_pred CCHHHHHHHHHHHHHhcccccCCCceEEEEEec-cceecCCCCCcceEEEcCc
Q 027998 62 ISEGVLEDCAQLVKANSIQGNKVNNIDVVYTPW-ANLKKTASMDVGQVGFHNP 113 (215)
Q Consensus 62 ipe~~L~~AAqLaa~~S~kg~k~~~V~V~YT~~-knvkK~~~~~~G~V~f~~~ 113 (215)
++.+.|.+|.++++.+++..+....|+|..+.+ =+.+|+...-.|.|.+-+.
T Consensus 2 ~~~~~~~eai~~~k~~~~~~kf~esvel~v~Lk~id~~k~~~~irg~i~LP~~ 54 (215)
T PRK04203 2 MDREKIEEAVKEALEEAPKRNFTQSVDLIVNLKDIDLKKPENRIDEEVVLPHG 54 (215)
T ss_pred CcHHHHHHHHHHHHHhcccCCCCceEEEEEEecCCCCCccCceeeEEEECCCC
Confidence 467889999999998764466788899999873 3556655556777765444
No 39
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=20.45 E-value=1.2e+02 Score=27.25 Aligned_cols=59 Identities=19% Similarity=0.211 Sum_probs=33.5
Q ss_pred cEEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhc-------ccccCCCceEEEEEec
Q 027998 36 DIWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANS-------IQGNKVNNIDVVYTPW 94 (215)
Q Consensus 36 DlWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S-------~kg~k~~~V~V~YT~~ 94 (215)
.-|.-..+-.|-|||+.+.+..+++++-.-....|-.|+..+- .+.+-.++|-|+|.+-
T Consensus 149 ~~f~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~iA~~l~~~~Pd~~t~~~~k~~R~gkvfiDylqN 214 (245)
T TIGR02778 149 ESFVKTSGGKGLHVYVPLRPTLSWDEVKDFAKALAQALAQQMPDRFTAEMSKKNRVGKIFVDYLRN 214 (245)
T ss_pred ccceEccCCCeEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCchhhhhHhhHHhCCCCEEEECccC
Confidence 4577778888999999998754433222222222333332221 0233467888888654
No 40
>KOG1144 consensus Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis]
Probab=20.12 E-value=2.3e+02 Score=30.22 Aligned_cols=9 Identities=22% Similarity=0.298 Sum_probs=3.5
Q ss_pred HHHHHhhcc
Q 027998 127 EIVNRLNKT 135 (215)
Q Consensus 127 ~ivnrl~kt 135 (215)
++-..|.+.
T Consensus 218 ~~qe~La~~ 226 (1064)
T KOG1144|consen 218 AMQEALAKR 226 (1064)
T ss_pred HHHHHHHHH
Confidence 333344443
No 41
>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=20.08 E-value=1.3e+02 Score=26.88 Aligned_cols=57 Identities=7% Similarity=0.051 Sum_probs=32.8
Q ss_pred EEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHH--------hcccccCCCceEEEEEec
Q 027998 37 IWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKA--------NSIQGNKVNNIDVVYTPW 94 (215)
Q Consensus 37 lWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~--------~S~kg~k~~~V~V~YT~~ 94 (215)
-|.-..+-.|-|||+.+.++.+|+++-.-.-..|..|+.. .++ .+-.++|-|+|.+-
T Consensus 135 sf~KTSG~kGlHv~vPl~~~~~~~~~r~fa~~iA~~l~~~~P~~~t~~~~k-~~R~grvfiDylqN 199 (228)
T cd04865 135 GYPKTSGARGLHIYVPIAPRYTFEEVRRFAELLAREVERRLPDLATTERWK-KERGGRVYLDYLQN 199 (228)
T ss_pred cceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhhHhhH-HhCCCCEEEECccC
Confidence 4667778888999999987544432222222223333322 222 34467888888654
No 42
>TIGR00206 fliF flagellar basal-body M-ring protein/flagellar hook-basal body protein (fliF). Component of the M (cytoplasmic associated) ring, one of four rings (L,P,S,M) which make up the flagellar hook-basal body which is a major portion of the flagellar organelle. Although the basic structure of the flagella appears to be similar for all bacteria, additional rings and structures surrounding the basal body have been observed for some bacteria (eg Vibrio cholerae and Treponema pallidum).
Probab=20.05 E-value=2.2e+02 Score=28.31 Aligned_cols=65 Identities=25% Similarity=0.409 Sum_probs=49.4
Q ss_pred hcCCCc-EEEEecCCCCcEEEEEeCCCCCCCCCCHHHHHHHHHHHHHhcccccCCCceEEEEEeccceec
Q 027998 31 YGFPED-IWFHVDKMSSAHVYLRLHKGQTIDDISEGVLEDCAQLVKANSIQGNKVNNIDVVYTPWANLKK 99 (215)
Q Consensus 31 ~a~~~D-lWFHv~~~pGaHViLR~~~g~~~~~ipe~~L~~AAqLaa~~S~kg~k~~~V~V~YT~~knvkK 99 (215)
++-|++ +|..-..-|+|-|+|++.+|. .++++-+.--..|++ .|..|-+.++|+|+=+...-|..
T Consensus 157 LalPe~s~F~~~~~~~tASV~l~l~~g~---~L~~~QV~aI~~LVA-~SVpgL~~enVtVvDq~G~lLs~ 222 (555)
T TIGR00206 157 LAMPKDALFVEEQEPPSASVRLTLRPGS---DLDTNQIEGLVHLIS-YAVPGLESDNIAIVDQNGTILND 222 (555)
T ss_pred EECCCCCccccCCCCCCEEEEEecCCCC---CCCHHHHHHHHHHHH-hhcCCCCccceEEEcCCCCCccC
Confidence 345554 555556778999999999885 678888888888887 45568889999998777776664
Done!