Query psy14677
Match_columns 483
No_of_seqs 321 out of 1662
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 17:50:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14677.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14677hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1882|consensus 100.0 7.5E-43 1.6E-47 338.5 10.3 161 314-474 132-292 (293)
2 KOG1881|consensus 99.8 1.2E-19 2.6E-24 196.3 8.1 141 337-480 138-278 (793)
3 PF00498 FHA: FHA domain; Int 99.7 6.1E-18 1.3E-22 131.2 9.1 68 378-458 1-68 (68)
4 cd00060 FHA Forkhead associate 99.6 1.4E-14 3.1E-19 117.0 12.9 98 356-466 2-100 (102)
5 KOG1880|consensus 99.6 2.8E-15 6.1E-20 150.3 6.5 117 342-469 4-120 (337)
6 PLN02927 antheraxanthin epoxid 99.5 1E-13 2.2E-18 151.5 11.4 101 354-468 532-646 (668)
7 TIGR03354 VI_FHA type VI secre 99.4 1.1E-12 2.4E-17 135.8 12.6 84 368-467 17-104 (396)
8 COG1716 FOG: FHA domain [Signa 99.4 1.1E-12 2.5E-17 118.5 10.3 79 374-468 87-166 (191)
9 smart00240 FHA Forkhead associ 99.2 2.3E-11 5E-16 89.4 6.2 52 378-441 1-52 (52)
10 COG3456 Predicted component of 98.9 5.4E-09 1.2E-13 109.4 8.1 71 376-461 26-99 (430)
11 KOG0615|consensus 98.3 9.6E-07 2.1E-11 93.2 6.3 100 369-471 58-159 (475)
12 TIGR02500 type_III_yscD type I 97.6 0.00031 6.7E-09 73.4 9.2 86 356-460 1-89 (410)
13 KOG0245|consensus 94.8 0.11 2.4E-06 60.7 8.9 81 374-469 475-557 (1221)
14 KOG2293|consensus 94.7 0.081 1.8E-06 58.0 7.4 80 374-466 446-531 (547)
15 TIGR01663 PNK-3'Pase polynucle 94.6 0.15 3.3E-06 55.9 9.1 85 368-468 25-109 (526)
16 KOG1892|consensus 93.2 0.23 4.9E-06 58.1 7.5 96 357-469 358-456 (1629)
17 KOG0241|consensus 79.3 5.1 0.00011 47.6 7.2 84 369-471 462-545 (1714)
18 KOG1882|consensus 76.1 8.9 0.00019 39.4 7.1 34 320-353 105-140 (293)
19 TIGR01642 U2AF_lg U2 snRNP aux 63.5 32 0.00068 36.3 8.3 11 431-441 357-367 (509)
20 KOG0670|consensus 63.1 5 0.00011 45.2 2.4 13 292-304 257-269 (752)
21 smart00363 S4 S4 RNA-binding d 56.4 18 0.00038 25.8 3.6 27 431-459 25-52 (60)
22 PF01479 S4: S4 domain; Inter 56.1 9.4 0.0002 28.0 2.1 23 431-455 25-48 (48)
23 KOG0151|consensus 55.5 8.4 0.00018 44.4 2.6 11 116-126 634-644 (877)
24 COG1188 Ribosome-associated he 55.3 18 0.00039 32.4 4.1 32 434-467 36-67 (100)
25 TIGR02988 YaaA_near_RecF S4 do 53.4 15 0.00032 28.5 2.9 25 432-457 34-58 (59)
26 cd00165 S4 S4/Hsp/ tRNA synthe 49.2 30 0.00065 25.3 3.9 28 431-460 25-53 (70)
27 PRK01777 hypothetical protein; 47.8 19 0.00041 31.5 3.0 30 426-458 45-74 (95)
28 PF02626 AHS2: Allophanate hyd 44.7 27 0.00058 35.6 4.0 38 430-467 53-93 (271)
29 PF13275 S4_2: S4 domain; PDB: 40.6 17 0.00036 30.0 1.5 29 432-461 33-61 (65)
30 TIGR01687 moaD_arch MoaD famil 38.8 30 0.00066 28.4 2.8 26 433-458 57-82 (88)
31 KOG1847|consensus 38.2 29 0.00063 40.0 3.3 30 193-223 694-725 (878)
32 PF10491 Nrf1_DNA-bind: NLS-bi 37.2 15 0.00032 36.8 0.8 20 47-66 110-129 (214)
33 PRK11507 ribosome-associated p 36.0 51 0.0011 27.8 3.7 29 432-461 37-65 (70)
34 cd00754 MoaD Ubiquitin domain 35.5 38 0.00082 26.9 2.8 25 432-458 50-74 (80)
35 smart00797 AHS2 Allophanate hy 34.7 55 0.0012 33.6 4.5 36 432-467 55-93 (280)
36 PRK10348 ribosome-associated h 32.8 69 0.0015 29.9 4.3 35 432-468 34-68 (133)
37 COG2501 S4-like RNA binding pr 31.2 78 0.0017 27.0 4.0 37 420-461 29-65 (73)
38 cd01764 Urm1 Urm1-like ubuitin 31.0 40 0.00086 29.1 2.3 26 434-459 62-89 (94)
39 PF02824 TGS: TGS domain; Int 30.6 35 0.00075 26.9 1.8 24 432-457 35-58 (60)
40 PF14478 DUF4430: Domain of un 28.5 47 0.001 26.6 2.2 12 446-457 56-67 (68)
41 PRK06437 hypothetical protein; 27.5 80 0.0017 25.5 3.4 23 433-457 38-60 (67)
42 cd01666 TGS_DRG_C TGS_DRG_C: 27.1 52 0.0011 27.5 2.4 20 436-457 54-73 (75)
43 TIGR00724 urea_amlyse_rel biot 25.4 98 0.0021 32.4 4.5 38 430-467 75-116 (314)
44 KOG4676|consensus 24.5 73 0.0016 35.0 3.4 9 110-118 156-164 (479)
45 KOG0835|consensus 24.0 73 0.0016 34.2 3.2 11 25-35 46-56 (367)
46 KOG4368|consensus 23.6 91 0.002 35.8 4.0 9 117-125 280-288 (757)
47 COG1984 DUR1 Allophanate hydro 23.5 1.3E+02 0.0027 31.9 4.8 37 430-466 74-113 (314)
48 PF14451 Ub-Mut7C: Mut7-C ubiq 23.5 82 0.0018 26.8 2.9 24 434-459 52-75 (81)
49 cd00565 ThiS ThiaminS ubiquiti 22.2 95 0.0021 24.4 2.9 25 433-457 32-58 (65)
50 PRK06488 sulfur carrier protei 22.0 66 0.0014 25.3 2.0 24 435-458 34-59 (65)
51 TIGR01683 thiS thiamine biosyn 21.6 90 0.002 24.5 2.6 22 436-457 34-57 (64)
52 PF02597 ThiS: ThiS family; I 21.5 56 0.0012 25.6 1.4 26 432-457 44-70 (77)
53 PF11012 DUF2850: Protein of u 20.6 1.7E+02 0.0036 25.3 4.2 38 430-470 22-61 (79)
No 1
>KOG1882|consensus
Probab=100.00 E-value=7.5e-43 Score=338.54 Aligned_cols=161 Identities=68% Similarity=1.150 Sum_probs=155.6
Q ss_pred CCCCCCCCCCCCccccccccccCCceeeccCCCCCCCCCCCceEEEEeeCCCcccEEEecccceeeeccCCCccceeeCC
Q psy14677 314 AQQPKQKPDFGLSGKLTEDTNTYNGVVIKYSEPPDARKPKRRWRLYPFKGDTQLPVLHIHRQSAFLMGRDRKVADIPVDH 393 (483)
Q Consensus 314 ~~~~kekPnF~~SG~LaedsNt~nGVvLkysEPp~Ar~P~~~WrL~VfKGge~~eti~L~~qs~ylIGRd~~~cDIvLdD 393 (483)
+++.+++|+|++||+|++++|++.||+|+|++|++|..|...|+||+|+++..+++++++.+++||+||+..++||.|+|
T Consensus 132 ~~~dke~p~f~lsg~l~E~tn~~~gv~v~y~eppearkP~kRwrLy~fk~~e~l~~l~iHrqs~yL~gRerkIaDi~idh 211 (293)
T KOG1882|consen 132 EPQDKEKPSFELSGALLEDTNRFRGVVVKYNEPPEARKPKKRWRLYPFKCYEVLPVLYIHRQSCYLDGRERKIADIPIDH 211 (293)
T ss_pred CchhccCCchhhchhhhhhhcceeeEEEEecCCchhcCchhheecccccCCcccchheeeeeeeeecCceeeeeccCCCC
Confidence 56788999999999999999999999999999999999999999999999999999999999999999999899999999
Q ss_pred CCcCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCceEecCEEcCCCceEEcCCCCEEEEcCcceEEEEeecCCCC
Q psy14677 394 PSCSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANGTFVNNKKIDPKRYVELLEKDVIKFGFSSREYVLLHEHSKD 473 (483)
Q Consensus 394 PSISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNGTFVNGeRI~p~r~veLkdGDvIrFG~STReYVLl~e~S~d 473 (483)
|+||+|||+|||+.+.++..+|..+..+.+||+||||+||||||+.+|++.+|++|.++|+|+||.++++|||+++.++.
T Consensus 212 pScSKQHaviQyR~v~~~r~dGt~grrvkpYiiDLgS~NgTfLNnk~IepqRYyEL~ekDvlkfgfs~rEyvllhe~s~~ 291 (293)
T KOG1882|consen 212 PSCSKQHAVIQYRLVEFTRADGTVGRRVKPYIIDLGSGNGTFLNNKVIEPQRYYELREKDVLKFGFSSREYVLLHEISMN 291 (293)
T ss_pred ccccccceeeeeeecccccCCCccceeeeeEEEecCCCCcceecCcccCchheeeeecCceeeeccchHHHHHHHhhhcc
Confidence 99999999999999999889999899999999999999999999999999999999999999999999999999998765
Q ss_pred C
Q psy14677 474 S 474 (483)
Q Consensus 474 d 474 (483)
.
T Consensus 292 ~ 292 (293)
T KOG1882|consen 292 V 292 (293)
T ss_pred c
Confidence 4
No 2
>KOG1881|consensus
Probab=99.79 E-value=1.2e-19 Score=196.33 Aligned_cols=141 Identities=28% Similarity=0.434 Sum_probs=124.9
Q ss_pred CceeeccCCCCCCCCCCCceEEEEeeCCCcccEEEecccceeeeccCCCccceeeCCCCcCccceEEEEeecccccCCCC
Q psy14677 337 NGVVIKYSEPPDARKPKRRWRLYPFKGDTQLPVLHIHRQSAFLMGRDRKVADIPVDHPSCSKQHAALQYRLTDYTREDGS 416 (483)
Q Consensus 337 nGVvLkysEPp~Ar~P~~~WrL~VfKGge~~eti~L~~qs~ylIGRd~~~cDIvLdDPSISRqHAvIq~r~~~~~~edG~ 416 (483)
+...+.|..|+|+.+|...+.|.++++|..+.++.|.....|+|||.. .||+.+.||+|||.||+|+|...... +-.
T Consensus 138 pa~~~py~vppw~~P~~~~~~lEvlKeg~iiet~~l~~~~~~~fgr~~-~cD~~~eHpsISr~h~vlQy~~~~~~--~p~ 214 (793)
T KOG1881|consen 138 PAAAAPYEVPPWSGPPAAIFQLEVLKEGAIIETEDLKGAAACLFGRLG-GCDVALEHPSISRFHAVLQYKASGPD--DPC 214 (793)
T ss_pred cCCCCcccCCCCCCCcccchhhhhhccCceeeeeecccceeEEecccC-CCccccccCcccccceeeeccCCCCC--ccc
Confidence 334677999999999999999999999999999999999999999999 79999999999999999999764221 000
Q ss_pred CCceeEEEEEeCCCCCceEecCEEcCCCceEEcCCCCEEEEcCcceEEEEeecCCCCCCCCCCC
Q psy14677 417 KGKRIRLYIIDLESANGTFVNNKKIDPKRYVELLEKDVIKFGFSSREYVLLHEHSKDSDYDDDV 480 (483)
Q Consensus 417 ~~~~vr~yIiDLGSTNGTFVNGeRI~p~r~veLkdGDvIrFG~STReYVLl~e~S~dde~~dd~ 480 (483)
...+..|||.|||||+|||+|..+|++.+|+.+..|++++||.+||.|+|.....+.++++|..
T Consensus 215 ~s~~~g~~i~dlgsThgt~~NK~rvppk~yir~~Vg~v~~fggsTrl~i~Qgp~eD~Epe~dls 278 (793)
T KOG1881|consen 215 ASNGEGWYIYDLGSTHGTFLNKDRVPPKVYIRDRVGHVARFGGSTRLYIFQGPEEDEEPESDLS 278 (793)
T ss_pred cCCCCceEEeeccccccceeccccCCCcchhhhhHHHHHHhcCceEEEEeeCCCcCCCchhhcC
Confidence 1245679999999999999999999999999999999999999999999999998888888764
No 3
>PF00498 FHA: FHA domain; InterPro: IPR000253 The forkhead-associated (FHA) domain [] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands []. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.; GO: 0005515 protein binding; PDB: 1LGQ_B 1LGP_A 2CSW_A 2PIE_A 3FM8_A 3MDB_B 3GQS_B 1UHT_A 1WLN_A 3POA_A ....
Probab=99.75 E-value=6.1e-18 Score=131.18 Aligned_cols=68 Identities=40% Similarity=0.670 Sum_probs=61.3
Q ss_pred eeeccCCCccceeeCCCCcCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCceEecCEEcCCCceEEcCCCCEEEE
Q psy14677 378 FLMGRDRKVADIPVDHPSCSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANGTFVNNKKIDPKRYVELLEKDVIKF 457 (483)
Q Consensus 378 ylIGRd~~~cDIvLdDPSISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNGTFVNGeRI~p~r~veLkdGDvIrF 457 (483)
|+|||++ .|||+|.+++||+.||.|.+... ..|+|+|++|+|||||||++|.++.+++|.+||+|.|
T Consensus 1 ~~iGR~~-~~di~l~~~~iSr~Ha~i~~~~~------------~~~~i~d~~s~ngt~vng~~l~~~~~~~L~~gd~i~~ 67 (68)
T PF00498_consen 1 VTIGRSP-DCDIVLPDPSISRRHARISFDDD------------GQFYIEDLGSTNGTFVNGQRLGPGEPVPLKDGDIIRF 67 (68)
T ss_dssp EEEESST-TSSEEETSTTSSTTSEEEEEETT------------EEEEEEESSSSS-EEETTEEESSTSEEEE-TTEEEEE
T ss_pred CEEcCCC-CCCEEECCHheeeeeeEEEEece------------eeEEEEeCCCCCcEEECCEEcCCCCEEECCCCCEEEc
Confidence 6899997 69999999999999999998741 2699999999999999999999999999999999999
Q ss_pred c
Q psy14677 458 G 458 (483)
Q Consensus 458 G 458 (483)
|
T Consensus 68 G 68 (68)
T PF00498_consen 68 G 68 (68)
T ss_dssp T
T ss_pred C
Confidence 8
No 4
>cd00060 FHA Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. Members of the FHA family include: Dun1, Rad53, Cds1, Mek1, KAPP(kinase-associated protein phosphatase),and Ki-67 (a human nuclear protein related to cell proliferation).
Probab=99.60 E-value=1.4e-14 Score=116.97 Aligned_cols=98 Identities=36% Similarity=0.577 Sum_probs=82.7
Q ss_pred eEEEEeeCCCcccEEEecccceeeeccCCCcc-ceeeCCCCcCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCce
Q psy14677 356 WRLYPFKGDTQLPVLHIHRQSAFLMGRDRKVA-DIPVDHPSCSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANGT 434 (483)
Q Consensus 356 WrL~VfKGge~~eti~L~~qs~ylIGRd~~~c-DIvLdDPSISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNGT 434 (483)
|.|.++.++.....+.|.....++|||+. .| +|.|.++.||+.||.|.+... + .+++.|+.|+|||
T Consensus 2 ~~L~~~~~~~~~~~~~l~~~~~~~iGr~~-~~~~i~l~~~~iS~~H~~i~~~~~------~------~~~~~~~~s~~g~ 68 (102)
T cd00060 2 PRLVVLSGDASGRRYYLDPGGTYTIGRDS-DNCDIVLDDPSVSRRHAVIRYDGD------G------GVVLIDLGSTNGT 68 (102)
T ss_pred eEEEEecCCCceeEEEECCCCeEEECcCC-CcCCEEcCCCCeeCcceEEEEcCC------C------CEEEEECCCCCCe
Confidence 67888877766778888765789999998 57 999999999999999998641 2 5899999999999
Q ss_pred EecCEEcCCCceEEcCCCCEEEEcCcceEEEE
Q psy14677 435 FVNNKKIDPKRYVELLEKDVIKFGFSSREYVL 466 (483)
Q Consensus 435 FVNGeRI~p~r~veLkdGDvIrFG~STReYVL 466 (483)
||||.++..+..+.|..||.|.||.....|.+
T Consensus 69 ~vn~~~~~~~~~~~l~~gd~i~ig~~~~~~~~ 100 (102)
T cd00060 69 FVNGQRVSPGEPVRLRDGDVIRLGNTSISFRF 100 (102)
T ss_pred EECCEECCCCCcEECCCCCEEEECCeEEEEEE
Confidence 99999999877899999999999974444443
No 5
>KOG1880|consensus
Probab=99.56 E-value=2.8e-15 Score=150.27 Aligned_cols=117 Identities=36% Similarity=0.630 Sum_probs=106.9
Q ss_pred ccCCCCCCCCCCCceEEEEeeCCCcccEEEecccceeeeccCCCccceeeCCCCcCccceEEEEeecccccCCCCCCcee
Q psy14677 342 KYSEPPDARKPKRRWRLYPFKGDTQLPVLHIHRQSAFLMGRDRKVADIPVDHPSCSKQHAALQYRLTDYTREDGSKGKRI 421 (483)
Q Consensus 342 kysEPp~Ar~P~~~WrL~VfKGge~~eti~L~~qs~ylIGRd~~~cDIvLdDPSISRqHAvIq~r~~~~~~edG~~~~~v 421 (483)
+|..|.||.+|+.+.+|.+.+++..++.+.+..+.+|+|||....||++|+|.+|||+||.+.|-.. ..
T Consensus 4 ~~~~p~wA~kpp~g~hldv~k~d~li~kl~iddkr~y~Fgrn~q~~df~idh~scSrvhaa~vyhkh-----------l~ 72 (337)
T KOG1880|consen 4 NFDPPSWAGKPPAGLHLDVVKGDKLIQKLIIDDKRRYLFGRNHQTCDFVIDHASCSRVHAALVYHKH-----------LS 72 (337)
T ss_pred cCCCCCcccCCCCCCceeeeecchhHHHHHhhhhhhhhhccCCCccceEeecchhhhhHhhhhhhhc-----------cc
Confidence 5778999999999999999999888887777778899999999999999999999999999988642 23
Q ss_pred EEEEEeCCCCCceEecCEEcCCCceEEcCCCCEEEEcCcceEEEEeec
Q psy14677 422 RLYIIDLESANGTFVNNKKIDPKRYVELLEKDVIKFGFSSREYVLLHE 469 (483)
Q Consensus 422 r~yIiDLGSTNGTFVNGeRI~p~r~veLkdGDvIrFG~STReYVLl~e 469 (483)
.++|+||+|++||||...+|.+..+++|..|..+.||.||+.|.+...
T Consensus 73 ~~~lidl~s~hgtf~g~~rL~~~~p~~l~i~~~~~fgasTr~y~lr~k 120 (337)
T KOG1880|consen 73 RIFLIDLGSTHGTFLGNERLEPHKPVQLEIGSTFHFGASTRIYLLREK 120 (337)
T ss_pred eEEEEEccCCcceeeeeeeeccCCCccccCCceEEEeccceeeeeecc
Confidence 799999999999999999999999999999999999999999988665
No 6
>PLN02927 antheraxanthin epoxidase/zeaxanthin epoxidase
Probab=99.49 E-value=1e-13 Score=151.47 Aligned_cols=101 Identities=24% Similarity=0.473 Sum_probs=82.3
Q ss_pred CceEEEEeeCCC-cccEEEe--cccceeeeccCCCccce-----eeCCCCcCccceEEEEeecccccCCCCCCceeEEEE
Q psy14677 354 RRWRLYPFKGDT-QLPVLHI--HRQSAFLMGRDRKVADI-----PVDHPSCSKQHAALQYRLTDYTREDGSKGKRIRLYI 425 (483)
Q Consensus 354 ~~WrL~VfKGge-~~eti~L--~~qs~ylIGRd~~~cDI-----vLdDPSISRqHAvIq~r~~~~~~edG~~~~~vr~yI 425 (483)
..|.|.+..++. ..+.+.| ..+.+++|||.+ .||+ +|.+|.||+.||.|.+.. | .|||
T Consensus 532 ~~w~l~~~~~~~~~~~~~~l~~~~~~p~~iG~~~-~~~~~~~~i~i~~~~vS~~Ha~i~~~~-------~------~~~~ 597 (668)
T PLN02927 532 GEWYLIPHGDDCCVSETLCLTKDEDQPCIVGSEP-DQDFPGMRIVIPSSQVSKMHARVIYKD-------G------AFFL 597 (668)
T ss_pred CCeEEEecCCCCcccceeeeecCCCCCeEecCCC-CcCCCCceEEecCCccChhHeEEEEEC-------C------EEEE
Confidence 469999986543 3466777 334689999998 6885 999999999999998863 3 6999
Q ss_pred EeCCCCCceEecCEE-----cCCCceEEcCCCCEEEEcCcc-eEEEEee
Q psy14677 426 IDLESANGTFVNNKK-----IDPKRYVELLEKDVIKFGFSS-REYVLLH 468 (483)
Q Consensus 426 iDLGSTNGTFVNGeR-----I~p~r~veLkdGDvIrFG~ST-ReYVLl~ 468 (483)
+||+|||||||||.+ +.++.+..|++||+|.||... ..|.+..
T Consensus 598 ~Dl~S~nGT~v~~~~~~r~~~~p~~~~~l~~~d~I~~g~~~~~~fr~~~ 646 (668)
T PLN02927 598 MDLRSEHGTYVTDNEGRRYRATPNFPARFRSSDIIEFGSDKKAAFRVKV 646 (668)
T ss_pred EECCCCCccEEeCCCCceEecCCCCceEeCCCCEEEeCCCcceeEEEEe
Confidence 999999999998776 567888999999999999853 4466655
No 7
>TIGR03354 VI_FHA type VI secretion system FHA domain protein. Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis, Burkholderia mallei, etc.
Probab=99.42 E-value=1.1e-12 Score=135.76 Aligned_cols=84 Identities=26% Similarity=0.354 Sum_probs=73.0
Q ss_pred cEEEecccceeeeccCCCccceeeCCCC--cCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCceEec--CEEcCC
Q psy14677 368 PVLHIHRQSAFLMGRDRKVADIPVDHPS--CSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANGTFVN--NKKIDP 443 (483)
Q Consensus 368 eti~L~~qs~ylIGRd~~~cDIvLdDPS--ISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNGTFVN--GeRI~p 443 (483)
..+.+.. ..++|||+. .||++|.++. ||+.||.|.+.. | .|+|+|+ |+|||||| |.+|.+
T Consensus 17 ~~~~f~~-~~~~IGR~~-~~d~~l~d~~~~VS~~Ha~I~~~~-------g------~~~l~Dl-StNGT~VN~sg~~l~~ 80 (396)
T TIGR03354 17 AQKTFGT-NGGTIGRSE-DCDWVLPDPERHVSGRHARIRYRD-------G------AYLLTDL-STNGVFLNGSGSPLGR 80 (396)
T ss_pred eEEEECC-CCEEEecCC-CCCEEeCCCCCCcchhhcEEEEEC-------C------EEEEEEC-CCCCeEECCCCCCCCC
Confidence 3566654 568999999 6999999999 999999999862 3 6999999 99999999 899999
Q ss_pred CceEEcCCCCEEEEcCcceEEEEe
Q psy14677 444 KRYVELLEKDVIKFGFSSREYVLL 467 (483)
Q Consensus 444 ~r~veLkdGDvIrFG~STReYVLl 467 (483)
+.++.|.+||+|+||.....+.+-
T Consensus 81 ~~~~~L~~GD~I~iG~~~lrv~~~ 104 (396)
T TIGR03354 81 GNPVRLEQGDRLRLGDYEIRVSLG 104 (396)
T ss_pred CCceEcCCCCEEEECCEEEEEEeC
Confidence 888999999999999987777664
No 8
>COG1716 FOG: FHA domain [Signal transduction mechanisms]
Probab=99.41 E-value=1.1e-12 Score=118.52 Aligned_cols=79 Identities=32% Similarity=0.473 Sum_probs=67.8
Q ss_pred ccceeeeccCCCccceeeCCCCcCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCceEecCEEcCCCceEEcCCCC
Q psy14677 374 RQSAFLMGRDRKVADIPVDHPSCSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANGTFVNNKKIDPKRYVELLEKD 453 (483)
Q Consensus 374 ~qs~ylIGRd~~~cDIvLdDPSISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNGTFVNGeRI~p~r~veLkdGD 453 (483)
....+.|||+. .+++++.++.|||.||.|.+... .++++|++|+|||||||.++.. .+.|.+||
T Consensus 87 ~~~~~tigr~~-~~~i~~~~~~vSR~Ha~l~~~~~-------------~~~~~d~~S~nGt~vn~~~v~~--~~~l~~gd 150 (191)
T COG1716 87 GEPVTTIGRDP-DNDIVLDDDVVSRRHAELRREGN-------------EVFLEDLGSTNGTYVNGEKVRQ--RVLLQDGD 150 (191)
T ss_pred ccceEEeccCC-CCCEEcCCCccccceEEEEEeCC-------------ceEEEECCCCcceEECCeEccC--cEEcCCCC
Confidence 34589999987 69999999999999999988642 5899999999999999999996 47899999
Q ss_pred EEEEcCcce-EEEEee
Q psy14677 454 VIKFGFSSR-EYVLLH 468 (483)
Q Consensus 454 vIrFG~STR-eYVLl~ 468 (483)
+|.||.... .+....
T Consensus 151 ~i~i~~~~~~~~~~~~ 166 (191)
T COG1716 151 VIRLGGTLAERLRIIL 166 (191)
T ss_pred EEEECccceeeEeecc
Confidence 999999877 444433
No 9
>smart00240 FHA Forkhead associated domain. Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain.
Probab=99.22 E-value=2.3e-11 Score=89.44 Aligned_cols=52 Identities=48% Similarity=0.794 Sum_probs=45.5
Q ss_pred eeeccCCCccceeeCCCCcCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCceEecCEEc
Q psy14677 378 FLMGRDRKVADIPVDHPSCSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANGTFVNNKKI 441 (483)
Q Consensus 378 ylIGRd~~~cDIvLdDPSISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNGTFVNGeRI 441 (483)
++|||.+..|+|+|+++.||+.||.|.+.. ++ .|+|.|++|+|||||||++|
T Consensus 1 ~~iGr~~~~~~i~~~~~~vs~~H~~i~~~~------~~------~~~i~d~~s~~gt~vng~~v 52 (52)
T smart00240 1 VTIGRSSEDCDIQLPGPSISRRHAEIVYDG------GG------RFYLIDLGSTNGTFVNGKRI 52 (52)
T ss_pred CEeCCCCCCCCEEeCCCCcchhHcEEEECC------CC------eEEEEECCCCCCeeECCEEC
Confidence 479999845999999999999999998863 12 59999999999999999986
No 10
>COG3456 Predicted component of the type VI protein secretion system, contains a FHA domain [Intracellular trafficking, secretion, and vesicular transport; Signal transduction mechanisms]
Probab=98.86 E-value=5.4e-09 Score=109.37 Aligned_cols=71 Identities=30% Similarity=0.402 Sum_probs=62.3
Q ss_pred ceeeeccCCCccceeeCCC--CcCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCceEecCEEcCCCce-EEcCCC
Q psy14677 376 SAFLMGRDRKVADIPVDHP--SCSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANGTFVNNKKIDPKRY-VELLEK 452 (483)
Q Consensus 376 s~ylIGRd~~~cDIvLdDP--SISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNGTFVNGeRI~p~r~-veLkdG 452 (483)
....|||++ .||..|+|| .||++||.|.++. | .|||.|. |.|||||||..+..+.. ..|..|
T Consensus 26 ~~g~IGrs~-dcdW~i~D~~~~VS~~Hc~I~~~d-------g------~f~L~Dt-S~g~l~VNgs~~~~g~~~~RLqqG 90 (430)
T COG3456 26 GGGVIGRSP-DCDWQIDDPERFVSKQHCTISYRD-------G------GFCLTDT-SNGGLLVNGSDLPLGEGSARLQQG 90 (430)
T ss_pred CCcccccCC-CCCccccCcccccchhheEEEecC-------C------eEEEEec-CCCceeecccccCCCCCccccccC
Confidence 357899999 699999987 6999999999873 4 5999999 79999999999988777 899999
Q ss_pred CEEEEcCcc
Q psy14677 453 DVIKFGFSS 461 (483)
Q Consensus 453 DvIrFG~ST 461 (483)
|+|.||.-.
T Consensus 91 d~i~iG~y~ 99 (430)
T COG3456 91 DEILIGRYI 99 (430)
T ss_pred CEEeeccEE
Confidence 999999543
No 11
>KOG0615|consensus
Probab=98.29 E-value=9.6e-07 Score=93.18 Aligned_cols=100 Identities=22% Similarity=0.309 Sum_probs=74.8
Q ss_pred EEEecccceeeeccCCCccceeeCCCCcCccceEEEEee-ccccc-CCCCCCceeEEEEEeCCCCCceEecCEEcCCCce
Q psy14677 369 VLHIHRQSAFLMGRDRKVADIPVDHPSCSKQHAALQYRL-TDYTR-EDGSKGKRIRLYIIDLESANGTFVNNKKIDPKRY 446 (483)
Q Consensus 369 ti~L~~qs~ylIGRd~~~cDIvLdDPSISRqHAvIq~r~-~~~~~-edG~~~~~vr~yIiDLGSTNGTFVNGeRI~p~r~ 446 (483)
.+.+.. ..|++||+. .||+++..+.+|..|..|.+.. ..+.. ..+...+...+||.|. |+||||||.+.|.++..
T Consensus 58 ~~d~~n-d~f~fGR~~-~~d~~ln~~~~s~~~~~i~~~~~~~~~~f~~dr~~~sn~~y~~Dh-S~nGT~VN~e~i~k~~~ 134 (475)
T KOG0615|consen 58 SIDLAN-DEFTFGRGD-SCDAPLNLNNVSNKHFKILLYNKISKIHFRIDRDKNSNRVYLHDH-SRNGTFVNDEMIGKGLS 134 (475)
T ss_pred cceecc-ceEEecCCC-cccccccCccccccchheeeeeeeeeeeecccCCCccceEEEEec-ccCcccccHhHhhcccc
Confidence 445544 589999997 6999999999999999886541 00000 1112356779999998 99999999999999999
Q ss_pred EEcCCCCEEEEcCcceEEEEeecCC
Q psy14677 447 VELLEKDVIKFGFSSREYVLLHEHS 471 (483)
Q Consensus 447 veLkdGDvIrFG~STReYVLl~e~S 471 (483)
..|++||+|.||.+...-.++.+.|
T Consensus 135 r~lkN~dei~is~p~~~~~v~~~~s 159 (475)
T KOG0615|consen 135 RILKNGDEISISIPALKIFVFEDLS 159 (475)
T ss_pred ccccCCCEEEeccchhheeeeeccc
Confidence 9999999999998754444444333
No 12
>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=97.55 E-value=0.00031 Score=73.35 Aligned_cols=86 Identities=14% Similarity=0.209 Sum_probs=69.7
Q ss_pred eEEEEeeCCCcccEEEecccceeeec-cCCCccceeeCCCCcCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCce
Q psy14677 356 WRLYPFKGDTQLPVLHIHRQSAFLMG-RDRKVADIPVDHPSCSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANGT 434 (483)
Q Consensus 356 WrL~VfKGge~~eti~L~~qs~ylIG-Rd~~~cDIvLdDPSISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNGT 434 (483)
|.|.++.|...+..+.|..+ .++|| ++. .|||+|.++.||+.||.|.+... .+.+.+ +..++
T Consensus 1 ~~lrvl~G~~~G~~~~L~~g-~~~iG~~~~-~~di~L~d~~~~~~h~~l~v~~~-------------~~~l~~--~~~~~ 63 (410)
T TIGR02500 1 WKLRVLSGPHRGAELPLPEG-NLVLGTDAA-DCDIVLSDGGIAAVHVSLHVRLE-------------GVTLAG--AVEPA 63 (410)
T ss_pred CEEEEecCCCCCcEEECCCC-ceEeccCCC-CcEEEeCCCCccchheEEEEcCc-------------eEEEec--CCcce
Confidence 78899999999999999876 49999 887 79999999999999999998631 366665 57789
Q ss_pred EecC--EEcCCCceEEcCCCCEEEEcCc
Q psy14677 435 FVNN--KKIDPKRYVELLEKDVIKFGFS 460 (483)
Q Consensus 435 FVNG--eRI~p~r~veLkdGDvIrFG~S 460 (483)
++|| .....+ ..|..+-.|..|..
T Consensus 64 ~~~g~~~~~~~g--~~l~~~~~l~~g~~ 89 (410)
T TIGR02500 64 WEEGGVLPDEEG--TPLPSGTPLLVAGV 89 (410)
T ss_pred eECCcccccCCC--CccCCCCceeccee
Confidence 9999 555544 45778888888855
No 13
>KOG0245|consensus
Probab=94.75 E-value=0.11 Score=60.67 Aligned_cols=81 Identities=20% Similarity=0.300 Sum_probs=58.9
Q ss_pred ccceeeeccCC--CccceeeCCCCcCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCceEecCEEcCCCceEEcCC
Q psy14677 374 RQSAFLMGRDR--KVADIPVDHPSCSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANGTFVNNKKIDPKRYVELLE 451 (483)
Q Consensus 374 ~qs~ylIGRd~--~~cDIvLdDPSISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNGTFVNGeRI~p~r~veLkd 451 (483)
......|||.. ...||+|..+.|--+||.|.-. +|. .++.+-.-----|||||+.|.. +..|+.
T Consensus 475 keG~TrVG~~~a~~~~DI~LsG~~I~~qHC~i~~~-------~g~-----~~vtl~p~e~aetyVNGk~v~e--p~qL~~ 540 (1221)
T KOG0245|consen 475 KEGETRVGREDASSRQDIVLSGQLIREQHCSIRNE-------GGN-----DVVTLEPCEDAETYVNGKLVTE--PTQLRS 540 (1221)
T ss_pred ccCceecCCCCcccCCceEecchhhhhhceEEEec-------CCC-----ceEEeccCCccceeEccEEcCC--cceecc
Confidence 33568899864 2479999999999999999643 231 2333333234569999999985 689999
Q ss_pred CCEEEEcCcceEEEEeec
Q psy14677 452 KDVIKFGFSSREYVLLHE 469 (483)
Q Consensus 452 GDvIrFG~STReYVLl~e 469 (483)
||.|-||.. -.|.+.+.
T Consensus 541 GdRiilG~~-H~frfn~P 557 (1221)
T KOG0245|consen 541 GDRIILGGN-HVFRFNHP 557 (1221)
T ss_pred CCEEEEcCc-eeEEecCH
Confidence 999999985 45666554
No 14
>KOG2293|consensus
Probab=94.74 E-value=0.081 Score=57.96 Aligned_cols=80 Identities=19% Similarity=0.314 Sum_probs=65.0
Q ss_pred ccceeeeccCCCccceeeC------CCCcCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCceEecCEEcCCCceE
Q psy14677 374 RQSAFLMGRDRKVADIPVD------HPSCSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANGTFVNNKKIDPKRYV 447 (483)
Q Consensus 374 ~qs~ylIGRd~~~cDIvLd------DPSISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNGTFVNGeRI~p~r~v 447 (483)
.+..++|||+...|.|-|+ ..-|||..|.|.... +| .|+|..|| .--.||||.+|..|..+
T Consensus 446 rk~EVtlGRat~d~~VDIDLgkegpatKISRRQa~IkL~n------~G------sF~IkNlG-K~~I~vng~~l~~gq~~ 512 (547)
T KOG2293|consen 446 RKKEVTLGRATGDLKVDIDLGKEGPATKISRRQALIKLKN------DG------SFFIKNLG-KRSILVNGGELDRGQKV 512 (547)
T ss_pred cCcceEeeccCCCcceeeeccccCccceeeccceeEEecc------CC------cEEeccCc-ceeEEeCCccccCCceE
Confidence 4568999999865544443 346999999998764 45 59999995 78899999999999999
Q ss_pred EcCCCCEEEEcCcceEEEE
Q psy14677 448 ELLEKDVIKFGFSSREYVL 466 (483)
Q Consensus 448 eLkdGDvIrFG~STReYVL 466 (483)
.|++.-+|.|-.-++.|.+
T Consensus 513 ~L~~nclveIrg~~FiF~~ 531 (547)
T KOG2293|consen 513 ILKNNCLVEIRGLRFIFEI 531 (547)
T ss_pred EeccCcEEEEccceEEEee
Confidence 9999999999977666644
No 15
>TIGR01663 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase. Note that the EC number for the kinase function is: 2.7.1.78
Probab=94.58 E-value=0.15 Score=55.85 Aligned_cols=85 Identities=20% Similarity=0.278 Sum_probs=68.4
Q ss_pred cEEEecccceeeeccCCCccceeeCCCCcCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCceEecCEEcCCCceE
Q psy14677 368 PVLHIHRQSAFLMGRDRKVADIPVDHPSCSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANGTFVNNKKIDPKRYV 447 (483)
Q Consensus 368 eti~L~~qs~ylIGRd~~~cDIvLdDPSISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNGTFVNGeRI~p~r~v 447 (483)
..++|.. ...+|||+++ -.|.|..|||+...|+.+-. .| .+.+.=||. |-|-|||..|.++..+
T Consensus 25 ~~~~~~~-~~~~~gr~pe---t~i~d~~cs~~qv~l~a~~~-----~~------~v~~k~lg~-np~~~~~~~~~~~~~~ 88 (526)
T TIGR01663 25 HFIHLDA-GALFLGRGPE---TGIRDRKCSKRQIELQADLE-----KA------TVALKQLGV-NPCGTGGLELKPGGEG 88 (526)
T ss_pred CeeccCC-CceEEccCcc---cccchhhhchhhheeeeccc-----Cc------eEEEEEccC-CCcccCceEecCCCee
Confidence 5677765 4577999984 57789999999999986532 23 688888975 9999999999999999
Q ss_pred EcCCCCEEEEcCcceEEEEee
Q psy14677 448 ELLEKDVIKFGFSSREYVLLH 468 (483)
Q Consensus 448 eLkdGDvIrFG~STReYVLl~ 468 (483)
.|++||++.|=+...-|.+..
T Consensus 89 ~l~~g~~l~~v~~~~~~~~~f 109 (526)
T TIGR01663 89 ELGHGDLLEIVNGLHPLTLQF 109 (526)
T ss_pred eecCCCEEEEeccccceeEEe
Confidence 999999999987765554443
No 16
>KOG1892|consensus
Probab=93.24 E-value=0.23 Score=58.07 Aligned_cols=96 Identities=17% Similarity=0.237 Sum_probs=67.5
Q ss_pred EEEEeeCCCcc--cEEEecccceeeeccCCC-ccceeeCCCCcCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCc
Q psy14677 357 RLYPFKGDTQL--PVLHIHRQSAFLMGRDRK-VADIPVDHPSCSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANG 433 (483)
Q Consensus 357 rL~VfKGge~~--eti~L~~qs~ylIGRd~~-~cDIvLdDPSISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNG 433 (483)
.|+.+..+... ..|.|.. +..-+|.+.. .+.|.|..|.|-..||.|.+- +| .+.|.-+.--.-
T Consensus 358 vLve~s~dG~~s~~ri~L~~-~vtEVGs~~~~~~~iqLfGP~IqprHc~it~m-------eG------VvTvTP~~~DA~ 423 (1629)
T KOG1892|consen 358 VLVELSPDGSDSRKRIRLQL-SVTEVGSEKLDDNSIQLFGPGIQPRHCDITNM-------EG------VVTVTPRSMDAE 423 (1629)
T ss_pred EEEEEcCCCCCcceeEEecc-CceeccccccCCcceeeeCCCCCccccchhhc-------cc------eEEecccccchh
Confidence 56555543322 4566654 5677898762 247899999999999999764 34 466666644456
Q ss_pred eEecCEEcCCCceEEcCCCCEEEEcCcceEEEEeec
Q psy14677 434 TFVNNKKIDPKRYVELLEKDVIKFGFSSREYVLLHE 469 (483)
Q Consensus 434 TFVNGeRI~p~r~veLkdGDvIrFG~STReYVLl~e 469 (483)
|||||.+|.. ...|++|+.|+||.+. .|.|...
T Consensus 424 t~VnGh~isq--ttiL~~G~~v~fGa~h-sfkF~ds 456 (1629)
T KOG1892|consen 424 TYVNGHRISQ--TTILQSGMKVQFGASH-SFKFVDS 456 (1629)
T ss_pred hhccceecch--hhhhccCCEEEeccce-eEEecCC
Confidence 9999999985 4689999999999863 4544443
No 17
>KOG0241|consensus
Probab=79.28 E-value=5.1 Score=47.62 Aligned_cols=84 Identities=20% Similarity=0.247 Sum_probs=64.1
Q ss_pred EEEecccceeeeccCCCccceeeCCCCcCccceEEEEeecccccCCCCCCceeEEEEEeCCCCCceEecCEEcCCCceEE
Q psy14677 369 VLHIHRQSAFLMGRDRKVADIPVDHPSCSKQHAALQYRLTDYTREDGSKGKRIRLYIIDLESANGTFVNNKKIDPKRYVE 448 (483)
Q Consensus 369 ti~L~~qs~ylIGRd~~~cDIvLdDPSISRqHAvIq~r~~~~~~edG~~~~~vr~yIiDLGSTNGTFVNGeRI~p~r~ve 448 (483)
.+++. ...+||-.. .-||++..-.|=..||+|.+.. +| .+++.-+-++ -+||||..|.. ..+
T Consensus 462 vyyl~--~~tlig~~~-~~~i~l~glgi~p~h~vidI~~------dg------~l~~~p~~~~-R~~VNGs~v~~--~t~ 523 (1714)
T KOG0241|consen 462 VYYLK--DHTLIGLFK-SQDIQLSGLGIQPKHCVIDIES------DG------ELRLTPLLNA-RSCVNGSLVCS--TTQ 523 (1714)
T ss_pred HHhhc--Cceeecccc-CcceeeecCcccCccceeeecc------CC------cEEecccccc-eeeecCceecc--ccc
Confidence 45553 457899876 6899999999999999998863 44 3888888555 99999999986 478
Q ss_pred cCCCCEEEEcCcceEEEEeecCC
Q psy14677 449 LLEKDVIKFGFSSREYVLLHEHS 471 (483)
Q Consensus 449 LkdGDvIrFG~STReYVLl~e~S 471 (483)
|.+||.|-.|+-. -|.+-....
T Consensus 524 L~~GdRiLwGnnH-FFrvN~PK~ 545 (1714)
T KOG0241|consen 524 LWHGDRILWGNNH-FFRVNLPKR 545 (1714)
T ss_pred cccCceEEecccc-eEEecCccc
Confidence 9999999999764 244444433
No 18
>KOG1882|consensus
Probab=76.12 E-value=8.9 Score=39.40 Aligned_cols=34 Identities=29% Similarity=0.452 Sum_probs=26.4
Q ss_pred CCCCCCcccccccccc--CCceeeccCCCCCCCCCC
Q psy14677 320 KPDFGLSGKLTEDTNT--YNGVVIKYSEPPDARKPK 353 (483)
Q Consensus 320 kPnF~~SG~LaedsNt--~nGVvLkysEPp~Ar~P~ 353 (483)
.++|-+++.+...+|. ..|+.++..+|.++.+|.
T Consensus 105 ~~d~~~~r~~e~~~nn~~k~~~~~k~~~~~dke~p~ 140 (293)
T KOG1882|consen 105 GRDFSNARLRELESNNGGKEGIALKEVEPQDKEKPS 140 (293)
T ss_pred cccccchhhhhhcccccCCccccccccCchhccCCc
Confidence 4567777877777777 568888888898888875
No 19
>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. Members of this subfamily are found in plants, metazoa and fungi.
Probab=63.48 E-value=32 Score=36.32 Aligned_cols=11 Identities=27% Similarity=0.431 Sum_probs=6.2
Q ss_pred CCceEecCEEc
Q psy14677 431 ANGTFVNNKKI 441 (483)
Q Consensus 431 TNGTFVNGeRI 441 (483)
.||+.|+|.+|
T Consensus 357 l~g~~~~~~~l 367 (509)
T TIGR01642 357 LNGKDTGDNKL 367 (509)
T ss_pred cCCCEECCeEE
Confidence 46666666544
No 20
>KOG0670|consensus
Probab=63.08 E-value=5 Score=45.23 Aligned_cols=13 Identities=15% Similarity=0.565 Sum_probs=9.1
Q ss_pred CCCCcccccCccc
Q psy14677 292 CDASDEYEWGRKD 304 (483)
Q Consensus 292 ~dds~~~~wG~~~ 304 (483)
.|......|+.++
T Consensus 257 dd~~~~~~~~s~e 269 (752)
T KOG0670|consen 257 DDIGEKLTWESEE 269 (752)
T ss_pred ccccccccccchh
Confidence 3556678898875
No 21
>smart00363 S4 S4 RNA-binding domain.
Probab=56.39 E-value=18 Score=25.76 Aligned_cols=27 Identities=30% Similarity=0.268 Sum_probs=21.3
Q ss_pred CCceEecCEEc-CCCceEEcCCCCEEEEcC
Q psy14677 431 ANGTFVNNKKI-DPKRYVELLEKDVIKFGF 459 (483)
Q Consensus 431 TNGTFVNGeRI-~p~r~veLkdGDvIrFG~ 459 (483)
.++.+|||..+ .+. ..|..||.|.+-.
T Consensus 25 ~g~i~vng~~~~~~~--~~l~~gd~i~~~~ 52 (60)
T smart00363 25 QGRVKVNGKKVTKPS--YIVKPGDVISVRG 52 (60)
T ss_pred cCCEEECCEEecCCC--eEeCCCCEEEEcc
Confidence 45788999998 543 5789999998864
No 22
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=56.12 E-value=9.4 Score=28.04 Aligned_cols=23 Identities=30% Similarity=0.330 Sum_probs=18.9
Q ss_pred CCceEecCEEcC-CCceEEcCCCCEE
Q psy14677 431 ANGTFVNNKKID-PKRYVELLEKDVI 455 (483)
Q Consensus 431 TNGTFVNGeRI~-p~r~veLkdGDvI 455 (483)
.++.+|||+.+. ++ +.+.+||+|
T Consensus 25 ~g~V~VNg~~v~~~~--~~v~~~d~I 48 (48)
T PF01479_consen 25 QGRVKVNGKVVKDPS--YIVKPGDVI 48 (48)
T ss_dssp TTTEEETTEEESSTT--SBESTTEEE
T ss_pred CCEEEECCEEEcCCC--CCCCCcCCC
Confidence 367899999998 44 578999987
No 23
>KOG0151|consensus
Probab=55.47 E-value=8.4 Score=44.40 Aligned_cols=11 Identities=27% Similarity=0.293 Sum_probs=6.2
Q ss_pred hcccchhhhhc
Q psy14677 116 AQIPNMKRNLK 126 (483)
Q Consensus 116 ~~~~~~~~~~~ 126 (483)
.+||-|..-+-
T Consensus 634 dgipm~~e~~s 644 (877)
T KOG0151|consen 634 DGIPMMVETKS 644 (877)
T ss_pred cCceeeeeecc
Confidence 45676665443
No 24
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=55.32 E-value=18 Score=32.38 Aligned_cols=32 Identities=22% Similarity=0.466 Sum_probs=24.7
Q ss_pred eEecCEEcCCCceEEcCCCCEEEEcCcceEEEEe
Q psy14677 434 TFVNNKKIDPKRYVELLEKDVIKFGFSSREYVLL 467 (483)
Q Consensus 434 TFVNGeRI~p~r~veLkdGDvIrFG~STReYVLl 467 (483)
..|||.++.++ ..++.||+|.|.....+|.+.
T Consensus 36 V~vNG~~aKpS--~~VK~GD~l~i~~~~~~~~v~ 67 (100)
T COG1188 36 VKVNGQRAKPS--KEVKVGDILTIRFGNKEFTVK 67 (100)
T ss_pred EEECCEEcccc--cccCCCCEEEEEeCCcEEEEE
Confidence 56899999876 579999999888765555443
No 25
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=53.38 E-value=15 Score=28.51 Aligned_cols=25 Identities=32% Similarity=0.364 Sum_probs=19.6
Q ss_pred CceEecCEEcCCCceEEcCCCCEEEE
Q psy14677 432 NGTFVNNKKIDPKRYVELLEKDVIKF 457 (483)
Q Consensus 432 NGTFVNGeRI~p~r~veLkdGDvIrF 457 (483)
...+|||..+.. ..+.|..||+|.|
T Consensus 34 G~V~VNg~~~~~-~~~~l~~Gd~v~i 58 (59)
T TIGR02988 34 NEVLVNGELENR-RGKKLYPGDVIEI 58 (59)
T ss_pred CCEEECCEEccC-CCCCCCCCCEEEe
Confidence 568899999843 1368999999986
No 26
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=49.19 E-value=30 Score=25.26 Aligned_cols=28 Identities=25% Similarity=0.325 Sum_probs=21.8
Q ss_pred CCceEecCEEc-CCCceEEcCCCCEEEEcCc
Q psy14677 431 ANGTFVNNKKI-DPKRYVELLEKDVIKFGFS 460 (483)
Q Consensus 431 TNGTFVNGeRI-~p~r~veLkdGDvIrFG~S 460 (483)
.++.+|||+.+ .++ ..|..||+|.+...
T Consensus 25 ~g~V~vn~~~~~~~~--~~v~~~d~i~i~~~ 53 (70)
T cd00165 25 HGHVLVNGKVVTKPS--YKVKPGDVIEVDGK 53 (70)
T ss_pred cCCEEECCEEccCCc--cCcCCCCEEEEcCC
Confidence 46789999998 443 57889999998753
No 27
>PRK01777 hypothetical protein; Validated
Probab=47.77 E-value=19 Score=31.45 Aligned_cols=30 Identities=20% Similarity=0.176 Sum_probs=24.5
Q ss_pred EeCCCCCceEecCEEcCCCceEEcCCCCEEEEc
Q psy14677 426 IDLESANGTFVNNKKIDPKRYVELLEKDVIKFG 458 (483)
Q Consensus 426 iDLGSTNGTFVNGeRI~p~r~veLkdGDvIrFG 458 (483)
+|+ +++-..|||+.+... ..|++||.|.|=
T Consensus 45 i~~-~~~~vgI~Gk~v~~d--~~L~dGDRVeIy 74 (95)
T PRK01777 45 IDL-AKNKVGIYSRPAKLT--DVLRDGDRVEIY 74 (95)
T ss_pred ccc-ccceEEEeCeECCCC--CcCCCCCEEEEe
Confidence 366 678889999999875 589999999874
No 28
>PF02626 AHS2: Allophanate hydrolase subunit 2; InterPro: IPR003778 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 2 of allophanate hydrolase (AHS2) which is found in urea carboxylase.; PDB: 3MML_G 3VA7_A 3OEP_A 3OPF_C 3ORE_B.
Probab=44.65 E-value=27 Score=35.62 Aligned_cols=38 Identities=24% Similarity=0.309 Sum_probs=27.9
Q ss_pred CCCceEecCEEcCCCceEEcCCCCEEEEcCc---ceEEEEe
Q psy14677 430 SANGTFVNNKKIDPKRYVELLEKDVIKFGFS---SREYVLL 467 (483)
Q Consensus 430 STNGTFVNGeRI~p~r~veLkdGDvIrFG~S---TReYVLl 467 (483)
..-.-.|||+.|...+.+.++.||+|+||.. .+.|+-.
T Consensus 53 a~~~~~lng~~~~~~~~~~v~~Gd~L~~~~~~~G~r~YLAv 93 (271)
T PF02626_consen 53 ADFEATLNGKPVPMWQPFLVKAGDVLKFGPPRSGARAYLAV 93 (271)
T ss_dssp SCEEEEETTEEE-TTSEEEE-TT-EEEEEEESSECEEEEEE
T ss_pred CCCceEECCEEccCCEEEEECCCCEEEecCCCCccEEEEEe
Confidence 3445678999999999999999999999965 5667543
No 29
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=40.55 E-value=17 Score=30.01 Aligned_cols=29 Identities=21% Similarity=0.105 Sum_probs=17.1
Q ss_pred CceEecCEEcCCCceEEcCCCCEEEEcCcc
Q psy14677 432 NGTFVNNKKIDPKRYVELLEKDVIKFGFSS 461 (483)
Q Consensus 432 NGTFVNGeRI~p~r~veLkdGDvIrFG~ST 461 (483)
+..+|||+.... +-..|.+||+|.|+...
T Consensus 33 g~V~VNGe~e~r-rg~Kl~~GD~V~~~~~~ 61 (65)
T PF13275_consen 33 GEVKVNGEVETR-RGKKLRPGDVVEIDGEE 61 (65)
T ss_dssp HHHEETTB-----SS----SSEEEEETTEE
T ss_pred CceEECCEEccc-cCCcCCCCCEEEECCEE
Confidence 678999997764 34689999999997654
No 30
>TIGR01687 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable.
Probab=38.82 E-value=30 Score=28.37 Aligned_cols=26 Identities=27% Similarity=0.222 Sum_probs=18.6
Q ss_pred ceEecCEEcCCCceEEcCCCCEEEEc
Q psy14677 433 GTFVNNKKIDPKRYVELLEKDVIKFG 458 (483)
Q Consensus 433 GTFVNGeRI~p~r~veLkdGDvIrFG 458 (483)
-.+|||+.+......+|++||+|.|=
T Consensus 57 ~v~vN~~~v~~~~~~~l~dgdev~i~ 82 (88)
T TIGR01687 57 IILVNGRNVDWGLGTELKDGDVVAIF 82 (88)
T ss_pred EEEECCEecCccCCCCCCCCCEEEEe
Confidence 45677777765433579999999873
No 31
>KOG1847|consensus
Probab=38.22 E-value=29 Score=39.96 Aligned_cols=30 Identities=47% Similarity=0.619 Sum_probs=15.1
Q ss_pred cCCCCCCCCCCccccCC--CCCCCchhhhhhhc
Q psy14677 193 QRPRHEKPHSSDKHRHS--SKTEPSERETKRNR 223 (483)
Q Consensus 193 ~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~r 223 (483)
.|+-|+-.- +-+-||| ||-||+|.+..-.|
T Consensus 694 ~R~l~~~~~-~~~dr~ssksk~ep~ee~k~~~~ 725 (878)
T KOG1847|consen 694 KRHLHKTRY-SSKDRHSSKSKHEPSEEDKYHSR 725 (878)
T ss_pred CCcCccccc-CCCCcccccccCCChhhhhhhhh
Confidence 344444322 2344555 45688876654433
No 32
>PF10491 Nrf1_DNA-bind: NLS-binding and DNA-binding and dimerisation domains of Nrf1; InterPro: IPR019525 Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila []. In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human []. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Q8C4C0 from SWISSPROT, there is also an NLS domain at 88-116, and a DNA binding and dimerisation domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity [].
Probab=37.16 E-value=15 Score=36.82 Aligned_cols=20 Identities=40% Similarity=0.703 Sum_probs=17.3
Q ss_pred eccCCCcccccccchhHHHH
Q psy14677 47 IPFNLPSLFLDGCNLCIELI 66 (483)
Q Consensus 47 ~~~~~~~~~~~~~~~~~~~~ 66 (483)
.-+|||.||.|||..|++-|
T Consensus 110 ~~~~LP~L~~dGiPtsvekm 129 (214)
T PF10491_consen 110 MLSNLPPLFIDGIPTSVEKM 129 (214)
T ss_pred ccccCchHHhcCCCCcHHHh
Confidence 34799999999999999754
No 33
>PRK11507 ribosome-associated protein; Provisional
Probab=36.04 E-value=51 Score=27.76 Aligned_cols=29 Identities=10% Similarity=0.122 Sum_probs=22.8
Q ss_pred CceEecCEEcCCCceEEcCCCCEEEEcCcc
Q psy14677 432 NGTFVNNKKIDPKRYVELLEKDVIKFGFSS 461 (483)
Q Consensus 432 NGTFVNGeRI~p~r~veLkdGDvIrFG~ST 461 (483)
+...|||+.-.. +-..|.+||+|.|+...
T Consensus 37 g~V~VNGeve~r-RgkKl~~GD~V~~~g~~ 65 (70)
T PRK11507 37 GQVKVDGAVETR-KRCKIVAGQTVSFAGHS 65 (70)
T ss_pred CceEECCEEecc-cCCCCCCCCEEEECCEE
Confidence 678899986543 44679999999999753
No 34
>cd00754 MoaD Ubiquitin domain of MoaD-like proteins. MoaD family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that contains the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase, the second major step in Moco biosynthesis. MPT synthase consists of a large (MoeE) and small (MoaD) subunit. The small subunit is inserted into the lare subunit to form the active site. The small subunit, which is structurally similar to ubiquitin, contains a C-terminal thiocarboxylated glycine residue that serves as a sulfur donor for the synthesis of the MPT dithiolene group.
Probab=35.46 E-value=38 Score=26.89 Aligned_cols=25 Identities=16% Similarity=0.046 Sum_probs=19.1
Q ss_pred CceEecCEEcCCCceEEcCCCCEEEEc
Q psy14677 432 NGTFVNNKKIDPKRYVELLEKDVIKFG 458 (483)
Q Consensus 432 NGTFVNGeRI~p~r~veLkdGDvIrFG 458 (483)
--.+|||+.+.. ...|++||.|.|=
T Consensus 50 ~~v~vNg~~v~~--~~~l~~gD~v~i~ 74 (80)
T cd00754 50 VRIAVNGEYVRL--DTPLKDGDEVAII 74 (80)
T ss_pred EEEEECCeEcCC--CcccCCCCEEEEe
Confidence 456778888874 3679999999873
No 35
>smart00797 AHS2 Allophanate hydrolase subunit 2. This domain represents subunit 2 of allophanate hydrolase (AHS2).
Probab=34.69 E-value=55 Score=33.57 Aligned_cols=36 Identities=14% Similarity=0.287 Sum_probs=29.1
Q ss_pred CceEecCEEcCCCceEEcCCCCEEEEcCc---ceEEEEe
Q psy14677 432 NGTFVNNKKIDPKRYVELLEKDVIKFGFS---SREYVLL 467 (483)
Q Consensus 432 NGTFVNGeRI~p~r~veLkdGDvIrFG~S---TReYVLl 467 (483)
-...|||++|.....+.|+.||+|+||.. .|.|+-.
T Consensus 55 ~~~~ln~~~~~~~~~~~v~~Gd~L~~g~~~~G~R~YLAv 93 (280)
T smart00797 55 FPATLDGQPVPPWKPFLVRAGQVLSLGAPKAGARAYLAV 93 (280)
T ss_pred CeeeECCEEcCCCeEEEECCCCEEEeCCCCCccEEEEEE
Confidence 44568999999988899999999999965 5677544
No 36
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=32.77 E-value=69 Score=29.87 Aligned_cols=35 Identities=9% Similarity=0.116 Sum_probs=25.6
Q ss_pred CceEecCEEcCCCceEEcCCCCEEEEcCcceEEEEee
Q psy14677 432 NGTFVNNKKIDPKRYVELLEKDVIKFGFSSREYVLLH 468 (483)
Q Consensus 432 NGTFVNGeRI~p~r~veLkdGDvIrFG~STReYVLl~ 468 (483)
...+|||.+..++ ..+..||+|.|-.....|+|..
T Consensus 34 G~V~vnG~~~Kps--~~V~~gd~l~v~~~~~~~~v~V 68 (133)
T PRK10348 34 GKVHYNGQRSKPS--KIVELNATLTLRQGNDERTVIV 68 (133)
T ss_pred CCEEECCEECCCC--CccCCCCEEEEEECCEEEEEEE
Confidence 4577899997665 5678999998876665665543
No 37
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair]
Probab=31.18 E-value=78 Score=26.99 Aligned_cols=37 Identities=19% Similarity=0.211 Sum_probs=27.5
Q ss_pred eeEEEEEeCCCCCceEecCEEcCCCceEEcCCCCEEEEcCcc
Q psy14677 420 RIRLYIIDLESANGTFVNNKKIDPKRYVELLEKDVIKFGFSS 461 (483)
Q Consensus 420 ~vr~yIiDLGSTNGTFVNGeRI~p~r~veLkdGDvIrFG~ST 461 (483)
.-.+||.| +..+|||+.-.. +-..|..||+|.|..-.
T Consensus 29 ~AK~~i~e----g~V~vNGe~EtR-RgkKlr~gd~V~i~~~~ 65 (73)
T COG2501 29 QAKAFIAE----GEVKVNGEVETR-RGKKLRDGDVVEIPGQR 65 (73)
T ss_pred HHHHHHHC----CeEEECCeeeec-cCCEeecCCEEEECCEE
Confidence 33566654 689999997764 34689999999999653
No 38
>cd01764 Urm1 Urm1-like ubuitin domain. Urm1 (Ubiquitin-Related Modifier1) The Urm1 fold, like those of two closely related proteins MoaD (molybdopterin synthase) and ThiS (sulfur carrier protein), is similar to that of ubiquitin although there is little or no sequence similarity. The C-terminal glycines of Urm1 are conjugated to an E1-like protein Uba4 as part of a novel conjugation system in yeast. The Urm1 fold is found only in eukaryotes.
Probab=30.96 E-value=40 Score=29.10 Aligned_cols=26 Identities=15% Similarity=0.164 Sum_probs=19.3
Q ss_pred eEecCEEcC--CCceEEcCCCCEEEEcC
Q psy14677 434 TFVNNKKID--PKRYVELLEKDVIKFGF 459 (483)
Q Consensus 434 TFVNGeRI~--p~r~veLkdGDvIrFG~ 459 (483)
.+|||..|. .+-.++|++||+|.|=.
T Consensus 62 VlvN~~di~~l~g~~t~L~dgD~v~i~P 89 (94)
T cd01764 62 VLINDTDWELLGEEDYILEDGDHVVFIS 89 (94)
T ss_pred EEECCccccccCCcccCCCCcCEEEEEC
Confidence 457888764 34457899999999843
No 39
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=30.62 E-value=35 Score=26.89 Aligned_cols=24 Identities=25% Similarity=0.311 Sum_probs=18.6
Q ss_pred CceEecCEEcCCCceEEcCCCCEEEE
Q psy14677 432 NGTFVNNKKIDPKRYVELLEKDVIKF 457 (483)
Q Consensus 432 NGTFVNGeRI~p~r~veLkdGDvIrF 457 (483)
-+..|||+.+.-. .+|.+||+|.|
T Consensus 35 ~~A~Vng~~vdl~--~~L~~~d~v~i 58 (60)
T PF02824_consen 35 VAAKVNGQLVDLD--HPLEDGDVVEI 58 (60)
T ss_dssp EEEEETTEEEETT--SBB-SSEEEEE
T ss_pred eEEEEcCEECCCC--CCcCCCCEEEE
Confidence 3566899998875 67999999987
No 40
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=28.46 E-value=47 Score=26.57 Aligned_cols=12 Identities=25% Similarity=0.346 Sum_probs=7.7
Q ss_pred eEEcCCCCEEEE
Q psy14677 446 YVELLEKDVIKF 457 (483)
Q Consensus 446 ~veLkdGDvIrF 457 (483)
.+.|++||.|.|
T Consensus 56 ~~~l~~GD~i~~ 67 (68)
T PF14478_consen 56 SYKLKDGDKITW 67 (68)
T ss_dssp C-B--TTEEEEE
T ss_pred eeEeCCCCEEEe
Confidence 368999999987
No 41
>PRK06437 hypothetical protein; Provisional
Probab=27.46 E-value=80 Score=25.51 Aligned_cols=23 Identities=13% Similarity=0.081 Sum_probs=17.8
Q ss_pred ceEecCEEcCCCceEEcCCCCEEEE
Q psy14677 433 GTFVNNKKIDPKRYVELLEKDVIKF 457 (483)
Q Consensus 433 GTFVNGeRI~p~r~veLkdGDvIrF 457 (483)
...+||..|+. ...|++||.|.|
T Consensus 38 aV~vNg~iv~~--~~~L~dgD~Vei 60 (67)
T PRK06437 38 VVIVNGSPVLE--DHNVKKEDDVLI 60 (67)
T ss_pred EEEECCEECCC--ceEcCCCCEEEE
Confidence 45578888874 368999999987
No 42
>cd01666 TGS_DRG_C TGS_DRG_C: DRG (developmentally regulated GTP-binding protein) represents a family of GTP-binding proteins that includes two members, DRG1 and DRG2. DRG1 and DRG2 have a C-terminal TGS domain (named after the ThrRS, GTPase, and SpoT proteins where it occurs) with a predominantly beta-sheet structure. The function of TGS is unknown but its presence in two types of regulatory proteins (the DRG GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.
Probab=27.10 E-value=52 Score=27.53 Aligned_cols=20 Identities=15% Similarity=0.310 Sum_probs=17.3
Q ss_pred ecCEEcCCCceEEcCCCCEEEE
Q psy14677 436 VNNKKIDPKRYVELLEKDVIKF 457 (483)
Q Consensus 436 VNGeRI~p~r~veLkdGDvIrF 457 (483)
++|++++.. .+|++||+|.|
T Consensus 54 ~~gq~Vgl~--~~L~d~DvVeI 73 (75)
T cd01666 54 HSPQRVGLD--HVLEDEDVVQI 73 (75)
T ss_pred CCCeECCCC--CEecCCCEEEE
Confidence 588999875 68999999987
No 43
>TIGR00724 urea_amlyse_rel biotin-dependent carboxylase uncharacterized domain. Urea amidolyase of Saccharomyces cerevisiae is a 1835 amino acid protein with an amidase domain, a biotin/lipoyl cofactor attachment domain, a carbamoyl-phosphate synthase L chain-like domain, and uncharacterized regions. It has both urea carboxylase and allophanate hydrolase activities. This alignment models a domain that represents uncharacterized prokaryotic proteins of about 300 amino acids, regions of prokaryotic urea carboxylase and of the urea carboxylase region of yeast urea amidolyase, and regions of other biotin-containing proteins.
Probab=25.43 E-value=98 Score=32.43 Aligned_cols=38 Identities=18% Similarity=0.325 Sum_probs=29.9
Q ss_pred CCCceEecCEEcCC-CceEEcCCCCEEEEcCc---ceEEEEe
Q psy14677 430 SANGTFVNNKKIDP-KRYVELLEKDVIKFGFS---SREYVLL 467 (483)
Q Consensus 430 STNGTFVNGeRI~p-~r~veLkdGDvIrFG~S---TReYVLl 467 (483)
-.-...|||++|.. .+.+.++.||+|+||.. .|.|+-.
T Consensus 75 A~~~~~lng~~~~~~~~~~~v~~Gd~L~~g~~~~G~R~YLAv 116 (314)
T TIGR00724 75 ADTDLCLNDGQVIPQWRPYEVKRGQILSLGRLKSGMRGYLAV 116 (314)
T ss_pred CCCcceeCCcccCCCceEEEECCCCEEEeCCCCCccEEEEEE
Confidence 34578899999976 77799999999999965 4666543
No 44
>KOG4676|consensus
Probab=24.51 E-value=73 Score=34.97 Aligned_cols=9 Identities=44% Similarity=0.611 Sum_probs=4.8
Q ss_pred HHhhhhhcc
Q psy14677 110 IQNLTQAQI 118 (483)
Q Consensus 110 ~~~~~~~~~ 118 (483)
.|+|..++|
T Consensus 156 v~sl~~~~~ 164 (479)
T KOG4676|consen 156 VQSLISAAI 164 (479)
T ss_pred hhcchhhhc
Confidence 455555554
No 45
>KOG0835|consensus
Probab=23.95 E-value=73 Score=34.21 Aligned_cols=11 Identities=0% Similarity=0.262 Sum_probs=4.7
Q ss_pred HHHHHhhhhee
Q psy14677 25 SALIRYYQYRC 35 (483)
Q Consensus 25 ~~~~~~~~~~~ 35 (483)
.++|-|+.|.|
T Consensus 46 tgqVLFqRf~~ 56 (367)
T KOG0835|consen 46 TGQVLFQRFCY 56 (367)
T ss_pred HHHHHHHHHHh
Confidence 33444444443
No 46
>KOG4368|consensus
Probab=23.63 E-value=91 Score=35.80 Aligned_cols=9 Identities=33% Similarity=0.781 Sum_probs=3.5
Q ss_pred cccchhhhh
Q psy14677 117 QIPNMKRNL 125 (483)
Q Consensus 117 ~~~~~~~~~ 125 (483)
|||.|.+.+
T Consensus 280 q~~~~e~~~ 288 (757)
T KOG4368|consen 280 QMPQMEAEV 288 (757)
T ss_pred hhHHHHHhh
Confidence 334333333
No 47
>COG1984 DUR1 Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]
Probab=23.53 E-value=1.3e+02 Score=31.94 Aligned_cols=37 Identities=14% Similarity=0.236 Sum_probs=30.7
Q ss_pred CCCceEecCEEcCCCceEEcCCCCEEEEcCc---ceEEEE
Q psy14677 430 SANGTFVNNKKIDPKRYVELLEKDVIKFGFS---SREYVL 466 (483)
Q Consensus 430 STNGTFVNGeRI~p~r~veLkdGDvIrFG~S---TReYVL 466 (483)
..-.-.|||+.|.+...+.++.||+|+||.. .|-|.-
T Consensus 74 ad~~a~ld~~~i~~~~~~~vk~Gq~L~~g~~~~G~R~YLa 113 (314)
T COG1984 74 ADCEATLDGQEVPPWSPYLVKAGQTLKLGRPKQGMRAYLA 113 (314)
T ss_pred CcccceECCEEcCCCceEEccCCCEEEecCCCCcceEEEE
Confidence 3455679999999999999999999999976 466654
No 48
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=23.47 E-value=82 Score=26.79 Aligned_cols=24 Identities=21% Similarity=0.225 Sum_probs=19.4
Q ss_pred eEecCEEcCCCceEEcCCCCEEEEcC
Q psy14677 434 TFVNNKKIDPKRYVELLEKDVIKFGF 459 (483)
Q Consensus 434 TFVNGeRI~p~r~veLkdGDvIrFG~ 459 (483)
.+|||..+... +.|++||.|.+=.
T Consensus 52 i~vNG~~v~~~--~~~~~Gd~v~V~P 75 (81)
T PF14451_consen 52 ILVNGRPVDFD--YRLKDGDRVAVYP 75 (81)
T ss_pred EEECCEECCCc--ccCCCCCEEEEEe
Confidence 56899888875 6899999998753
No 49
>cd00565 ThiS ThiaminS ubiquitin-like sulfur carrier protein. ThiS (ThiaminS) is a sulfur carrier protein involved in thiamin biosynthesis in bacteria. The ThiS fold, like those of two closely related proteins MoaD and Urm1, is similar to that of ubiquitin although there is little or no sequence similarity.
Probab=22.15 E-value=95 Score=24.41 Aligned_cols=25 Identities=16% Similarity=0.213 Sum_probs=17.7
Q ss_pred ceEecCEEcCCCc--eEEcCCCCEEEE
Q psy14677 433 GTFVNNKKIDPKR--YVELLEKDVIKF 457 (483)
Q Consensus 433 GTFVNGeRI~p~r--~veLkdGDvIrF 457 (483)
...|||+-|++.. ...|++||.|.|
T Consensus 32 ~V~vNg~~v~~~~~~~~~L~~gD~V~i 58 (65)
T cd00565 32 AVALNGEIVPRSEWASTPLQDGDRIEI 58 (65)
T ss_pred EEEECCEEcCHHHcCceecCCCCEEEE
Confidence 3457887776531 257999999987
No 50
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=21.99 E-value=66 Score=25.28 Aligned_cols=24 Identities=25% Similarity=0.189 Sum_probs=16.5
Q ss_pred EecCEEcCCCc--eEEcCCCCEEEEc
Q psy14677 435 FVNNKKIDPKR--YVELLEKDVIKFG 458 (483)
Q Consensus 435 FVNGeRI~p~r--~veLkdGDvIrFG 458 (483)
-||++-|++.. .+.|++||.|.|=
T Consensus 34 avN~~iv~~~~~~~~~L~dgD~Ieiv 59 (65)
T PRK06488 34 AVNGELVHKEARAQFVLHEGDRIEIL 59 (65)
T ss_pred EECCEEcCHHHcCccccCCCCEEEEE
Confidence 35666666532 3679999999873
No 51
>TIGR01683 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small thiamine-biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis.
Probab=21.57 E-value=90 Score=24.51 Aligned_cols=22 Identities=27% Similarity=0.356 Sum_probs=16.1
Q ss_pred ecCEEcCCCce--EEcCCCCEEEE
Q psy14677 436 VNNKKIDPKRY--VELLEKDVIKF 457 (483)
Q Consensus 436 VNGeRI~p~r~--veLkdGDvIrF 457 (483)
|||+-|++..+ +.|++||.|.|
T Consensus 34 vN~~iv~~~~~~~~~L~~gD~vei 57 (64)
T TIGR01683 34 VNGEIVPRSEWDDTILKEGDRIEI 57 (64)
T ss_pred ECCEEcCHHHcCceecCCCCEEEE
Confidence 57777765432 57999999987
No 52
>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in Escherichia coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalysed by IscS []. MoaD, a protein involved in sulphur transfer during molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end.; PDB: 1JW9_D 1JWB_D 1JWA_D 3BII_D 1NVI_D 1FMA_D 1FM0_D 2QIE_G 2Q5W_D 2K5P_A ....
Probab=21.45 E-value=56 Score=25.65 Aligned_cols=26 Identities=15% Similarity=0.102 Sum_probs=17.8
Q ss_pred CceEecCEEcCC-CceEEcCCCCEEEE
Q psy14677 432 NGTFVNNKKIDP-KRYVELLEKDVIKF 457 (483)
Q Consensus 432 NGTFVNGeRI~p-~r~veLkdGDvIrF 457 (483)
--.+|||+.+.. .....|++||.|.|
T Consensus 44 ~~v~vN~~~v~~~~~~~~l~~gD~V~i 70 (77)
T PF02597_consen 44 VAVAVNGEIVPDDGLDTPLKDGDEVAI 70 (77)
T ss_dssp EEEEETTEEEGGGTTTSBEETTEEEEE
T ss_pred EEEEECCEEcCCccCCcCcCCCCEEEE
Confidence 345567776665 12267999999987
No 53
>PF11012 DUF2850: Protein of unknown function (DUF2850); InterPro: IPR021271 This family of proteins with unknown function appear to be restricted to Vibrionaceae.
Probab=20.64 E-value=1.7e+02 Score=25.26 Aligned_cols=38 Identities=18% Similarity=0.400 Sum_probs=27.8
Q ss_pred CCCceEecCEEcCCCceEEcCCCCEEE--EcCcceEEEEeecC
Q psy14677 430 SANGTFVNNKKIDPKRYVELLEKDVIK--FGFSSREYVLLHEH 470 (483)
Q Consensus 430 STNGTFVNGeRI~p~r~veLkdGDvIr--FG~STReYVLl~e~ 470 (483)
+..|.|+||..|... +. -+|+.|. .|..++.|.+..+.
T Consensus 22 ~~~GV~~ngrlV~T~--F~-fDG~~l~~~~G~~~~~y~~~~~~ 61 (79)
T PF11012_consen 22 NESGVFRNGRLVATS--FE-FDGKTLEYRTGSGTYRYQISGEN 61 (79)
T ss_pred CCCcEEECCCEEeeE--EE-ECCCEEEEEECCeEEEEEEcCCC
Confidence 679999999999853 22 4777765 47778888776653
Done!