Query 043633
Match_columns 128
No_of_seqs 103 out of 206
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 06:48:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043633.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043633hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02756 S-methyl-5-thioribose 100.0 2.8E-39 6E-44 269.2 13.5 126 1-126 292-417 (418)
2 PRK12396 5-methylribose kinase 100.0 9.4E-38 2E-42 259.2 13.4 115 1-126 289-403 (409)
3 TIGR01767 MTRK 5-methylthiorib 100.0 2E-37 4.3E-42 254.7 13.6 117 1-127 253-369 (370)
4 PRK09550 mtnK methylthioribose 100.0 4.6E-37 9.9E-42 255.2 13.3 115 2-127 284-398 (401)
5 COG4857 Predicted kinase [Gene 100.0 1.1E-33 2.4E-38 226.9 11.6 116 1-126 290-405 (408)
6 PF08520 DUF1748: Fungal prote 48.2 22 0.00048 22.9 2.7 35 70-107 20-54 (70)
7 PF07599 DUF1563: Protein of u 47.5 37 0.0008 19.6 3.2 14 50-63 21-34 (43)
8 PHA01735 hypothetical protein 35.0 33 0.00073 22.3 1.9 27 57-83 8-35 (76)
9 PF05778 Apo-CIII: Apolipoprot 33.4 14 0.00031 23.8 0.1 22 8-29 47-68 (70)
10 PF14714 KH_dom-like: KH-domai 32.1 32 0.00069 22.4 1.5 21 50-70 55-75 (80)
11 smart00803 TAF TATA box bindin 31.3 74 0.0016 19.9 3.1 21 48-68 29-49 (65)
12 PF14981 FAM165: FAM165 family 28.9 40 0.00087 20.2 1.4 17 57-73 16-32 (51)
13 PF06287 DUF1039: Protein of u 27.3 59 0.0013 20.8 2.1 16 85-100 22-37 (66)
14 PF01730 UreF: UreF; InterPro 27.1 69 0.0015 22.6 2.7 61 50-110 7-74 (146)
15 PRK02999 malate synthase G; Pr 26.4 1.6E+02 0.0034 27.1 5.3 71 52-126 594-664 (726)
16 PF03540 TFIID_30kDa: Transcri 26.3 72 0.0016 19.3 2.3 18 50-67 31-48 (51)
17 KOG1355 Adenylosuccinate synth 23.2 79 0.0017 26.9 2.7 50 14-67 188-239 (455)
18 PF14372 DUF4413: Domain of un 23.0 2.4E+02 0.0052 18.8 5.9 58 8-73 31-88 (101)
19 PF10463 Peptidase_U49: Peptid 23.0 3.3E+02 0.0071 21.1 5.9 59 50-110 3-64 (206)
20 TIGR02498 type_III_ssaH type I 22.2 82 0.0018 20.9 2.1 16 85-100 35-50 (79)
21 PRK15356 type III secretion sy 22.1 85 0.0018 20.6 2.1 16 85-100 23-38 (75)
22 PF08072 BDHCT: BDHCT (NUC031) 21.9 54 0.0012 19.0 1.1 23 83-111 13-35 (41)
23 cd00728 malate_synt_G Malate s 20.8 2E+02 0.0043 26.5 4.8 72 51-126 584-655 (712)
24 COG0002 ArgC Acetylglutamate s 20.5 41 0.00089 28.2 0.5 27 62-89 10-36 (349)
25 PF15119 APOC4: Apolipoprotein 20.2 1.7E+02 0.0037 19.9 3.4 20 43-62 48-67 (99)
No 1
>PLN02756 S-methyl-5-thioribose kinase
Probab=100.00 E-value=2.8e-39 Score=269.16 Aligned_cols=126 Identities=81% Similarity=1.300 Sum_probs=116.7
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCchhhhhCChhhHHHHHHHHHHHHHHHHHhhhHHHHhhhhcCCccc
Q 043633 1 EYKEWILRTIEETWTLFHQKFTALWHQHKDGSGEAYLPEIYNKPELQQLVQEKFMKDLFHDTLGFGAAKMIRRIVGVAHV 80 (128)
Q Consensus 1 ~~~~~ll~~I~~~w~~F~~~F~~lw~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~il~D~~GfAG~e~iRRiiG~A~V 80 (128)
+|++||+++|+++|+.|+++|.++|+++.++....|.+++++++++.++|+++||++||+|++|||||||||||||+|||
T Consensus 292 ~~~~~ll~~i~~~w~~F~~~F~~lw~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~i~~d~~Gfag~e~iRR~vG~A~v 371 (418)
T PLN02756 292 TYKEWILKTIEQTWNLFHKKFTALWDEHKDGSGEAYLPEIYNNPELLQLVQKKYMQDLLHDTLGFGAAKMIRRIVGVAHV 371 (418)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCccchhcccccccccchhhHHHHHHHHHHHHHHHHHhhhHHHhhHhcccccc
Confidence 47999999999999999999999999998643333445678888888999999999999999999999999999999999
Q ss_pred cCCcCCCChhHHHHHHHHHHHHHHHHHHcCcCCCCHHHHHHHHHHh
Q 043633 81 EDFESIKDDSKRATCERQALELAKLLLKERRNFQAITEVVSAIRKL 126 (128)
Q Consensus 81 ~D~~~I~d~~~R~~aer~aL~ig~~li~~r~~~~~i~~~~~~~~~~ 126 (128)
+||++|+|.++|+.|||.+|.+||.||+||++++|++++++++++.
T Consensus 372 ~D~~~I~d~~~R~~~er~al~~g~~li~~~~~~~~~~~~~~~~~~~ 417 (418)
T PLN02756 372 EDFESIEDASKRANCERQALDFAKMLLKERRKFQSIGEVVSAIQQL 417 (418)
T ss_pred cccccCCCHHHHHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999998864
No 2
>PRK12396 5-methylribose kinase; Reviewed
Probab=100.00 E-value=9.4e-38 Score=259.18 Aligned_cols=115 Identities=28% Similarity=0.534 Sum_probs=106.6
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCchhhhhCChhhHHHHHHHHHHHHHHHHHhhhHHHHhhhhcCCccc
Q 043633 1 EYKEWILRTIEETWTLFHQKFTALWHQHKDGSGEAYLPEIYNKPELQQLVQEKFMKDLFHDTLGFGAAKMIRRIVGVAHV 80 (128)
Q Consensus 1 ~~~~~ll~~I~~~w~~F~~~F~~lw~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~il~D~~GfAG~e~iRRiiG~A~V 80 (128)
+|++||+++|+++|+.|.++|.++|++++++ ++.+. ++|+++||++||+|++|||||||||||||+|||
T Consensus 289 ~~~~wll~~i~~~w~~F~~~F~~lw~~~~~~-------~~~~~----~~~~~~~l~~i~~D~~Gfag~e~iRR~vG~Ahv 357 (409)
T PRK12396 289 TYMDWLQSTMVEVIDLFKKKFLDAWDIHVTE-------IMAKE----EGFNEIYLQSVLEDTAAVTGLELIRRIVGLAKV 357 (409)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCcc-------ccccc----HHHHHHHHHHHHHHHHHHhhHHHHHHhcccccc
Confidence 4799999999999999999999999999863 23333 348999999999999999999999999999999
Q ss_pred cCCcCCCChhHHHHHHHHHHHHHHHHHHcCcCCCCHHHHHHHHHHh
Q 043633 81 EDFESIKDDSKRATCERQALELAKLLLKERRNFQAITEVVSAIRKL 126 (128)
Q Consensus 81 ~D~~~I~d~~~R~~aer~aL~ig~~li~~r~~~~~i~~~~~~~~~~ 126 (128)
+||++|+|.++|+.|||.+|.+||.||++|++++|++++++++++.
T Consensus 358 ~D~~~I~D~~~R~~~er~aL~~g~~li~~~~~~~~~~~~~~~~~~~ 403 (409)
T PRK12396 358 KDITCIENEEARARAERICLQVAKKFILRANQYKTGTSFVETLKEQ 403 (409)
T ss_pred cccccCCCHHHHHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999998864
No 3
>TIGR01767 MTRK 5-methylthioribose kinase. This enzyme is involved in the methionine salvage pathway in certain bacteria.
Probab=100.00 E-value=2e-37 Score=254.69 Aligned_cols=117 Identities=28% Similarity=0.564 Sum_probs=106.9
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCchhhhhCChhhHHHHHHHHHHHHHHHHHhhhHHHHhhhhcCCccc
Q 043633 1 EYKEWILRTIEETWTLFHQKFTALWHQHKDGSGEAYLPEIYNKPELQQLVQEKFMKDLFHDTLGFGAAKMIRRIVGVAHV 80 (128)
Q Consensus 1 ~~~~~ll~~I~~~w~~F~~~F~~lw~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~il~D~~GfAG~e~iRRiiG~A~V 80 (128)
+|++||+++|+++|+.|.++|+++|+++++ ++. +.+. ++|+++||++||+|++|||||||||||||+|||
T Consensus 253 ~~~~~ll~~i~~~w~~F~~~F~~lw~~~~~--~~~----~~~~----~~~~~~~l~~i~~d~~Gfag~e~iRR~vG~Ahv 322 (370)
T TIGR01767 253 AMREPLLEHVNQVWETFEETFSELWQKDSL--DMV----YANI----DGYLTDTLSHIWEDAIGFAGCELIRRTIGLAHV 322 (370)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCc--ccc----cccc----HHHHHHHHHHHHHHHHHHhHHHHHHHhcccccC
Confidence 479999999999999999999999999985 222 2233 348999999999999999999999999999999
Q ss_pred cCCcCCCChhHHHHHHHHHHHHHHHHHHcCcCCCCHHHHHHHHHHhc
Q 043633 81 EDFESIKDDSKRATCERQALELAKLLLKERRNFQAITEVVSAIRKLH 127 (128)
Q Consensus 81 ~D~~~I~d~~~R~~aer~aL~ig~~li~~r~~~~~i~~~~~~~~~~~ 127 (128)
+||++|+|.++|+.|||.+|.+|+.||++|++++|+++++++++.+.
T Consensus 323 ~D~~~I~d~~~R~~~er~~l~~g~~li~~~~~~~~~~~~~~~~~~~~ 369 (370)
T TIGR01767 323 ADLDTIVDFAKRIGCKRLALETGRAFIVKRSEIKSIDEVIELFALLV 369 (370)
T ss_pred cccccCCCHHHHHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999988753
No 4
>PRK09550 mtnK methylthioribose kinase; Reviewed
Probab=100.00 E-value=4.6e-37 Score=255.20 Aligned_cols=115 Identities=34% Similarity=0.749 Sum_probs=107.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCchhhhhCChhhHHHHHHHHHHHHHHHHHhhhHHHHhhhhcCCcccc
Q 043633 2 YKEWILRTIEETWTLFHQKFTALWHQHKDGSGEAYLPEIYNKPELQQLVQEKFMKDLFHDTLGFGAAKMIRRIVGVAHVE 81 (128)
Q Consensus 2 ~~~~ll~~I~~~w~~F~~~F~~lw~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~il~D~~GfAG~e~iRRiiG~A~V~ 81 (128)
|++|++++|+++|+.|.++|+++|++++++ + +++.++ |+++||++||+|++|||||||||||||+|||+
T Consensus 284 ~~~~~~~~i~~~w~~f~~~f~~~w~~~~~~--~-----~~~~~~----~~~~~l~~i~~d~~gfag~e~~RR~vG~a~v~ 352 (401)
T PRK09550 284 FREWLLETIEETWSTFAEKFLKLWRKESVD--A-----ALAEEG----YLEAYLQNILRDAVGFAGCELIRRTIGLAHVA 352 (401)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccc--h-----hhhhHH----HHHHHHHHHHHHHHHhhhHHHhhhhccccccc
Confidence 789999999999999999999999999963 3 344444 89999999999999999999999999999999
Q ss_pred CCcCCCChhHHHHHHHHHHHHHHHHHHcCcCCCCHHHHHHHHHHhc
Q 043633 82 DFESIKDDSKRATCERQALELAKLLLKERRNFQAITEVVSAIRKLH 127 (128)
Q Consensus 82 D~~~I~d~~~R~~aer~aL~ig~~li~~r~~~~~i~~~~~~~~~~~ 127 (128)
||++|+|+++|+.|||.+|.+|+.||++|++++|++++++.+++..
T Consensus 353 d~~~i~d~~~r~~~er~~l~~g~~li~~~~~~~~~~~~~~~~~~~~ 398 (401)
T PRK09550 353 DLDTIEDPELRAEAERHALKLGRELILNRDKIASIEDLIALFRQIK 398 (401)
T ss_pred ccccCCCHHHHHHHHHHHHHHHHHHHhhhhhcCCHHHHHHHHHHHh
Confidence 9999999999999999999999999999999999999999998753
No 5
>COG4857 Predicted kinase [General function prediction only]
Probab=100.00 E-value=1.1e-33 Score=226.92 Aligned_cols=116 Identities=31% Similarity=0.725 Sum_probs=107.0
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCchhhhhCChhhHHHHHHHHHHHHHHHHHhhhHHHHhhhhcCCccc
Q 043633 1 EYKEWILRTIEETWTLFHQKFTALWHQHKDGSGEAYLPEIYNKPELQQLVQEKFMKDLFHDTLGFGAAKMIRRIVGVAHV 80 (128)
Q Consensus 1 ~~~~~ll~~I~~~w~~F~~~F~~lw~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~il~D~~GfAG~e~iRRiiG~A~V 80 (128)
++++||+++|.++|.+|.++|+.+|+++.. + .++.+ .++|+++|+.+||+|++|||||||||||+|+|||
T Consensus 290 ~~r~~L~e~i~~iw~~F~e~fs~lW~k~~~--~-----~l~~n---~e~~ld~~i~~I~~d~lgfAG~E~iRRtlGlAhv 359 (408)
T COG4857 290 EMRAYLLECILDIWETFREEFSLLWRKERQ--D-----KLFEN---AEQALDYVIENIWKDSLGFAGIEMIRRTLGLAHV 359 (408)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHH--H-----HHHHh---HHHHHHHHHHHHHHHHhhcchHHHHHHHhhhhhh
Confidence 478999999999999999999999999963 2 35555 2559999999999999999999999999999999
Q ss_pred cCCcCCCChhHHHHHHHHHHHHHHHHHHcCcCCCCHHHHHHHHHHh
Q 043633 81 EDFESIKDDSKRATCERQALELAKLLLKERRNFQAITEVVSAIRKL 126 (128)
Q Consensus 81 ~D~~~I~d~~~R~~aer~aL~ig~~li~~r~~~~~i~~~~~~~~~~ 126 (128)
+||++|.|+++|+.||+.+|..|+.+|++|.+++||.|++++++-+
T Consensus 360 adl~ti~~~dkr~~~e~~al~~g~~~i~kr~~~~si~dv~~l~~ll 405 (408)
T COG4857 360 ADLETIADSDKRAQCEKKALKKGRHMIVKRSEIHSITDVIELAKLL 405 (408)
T ss_pred ccccccCCHHHHhhhHHHHHHHhHHHHhhhhhcccHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999988754
No 6
>PF08520 DUF1748: Fungal protein of unknown function (DUF1748); InterPro: IPR013726 This is a family of fungal proteins of unknown function.
Probab=48.21 E-value=22 Score=22.91 Aligned_cols=35 Identities=23% Similarity=0.328 Sum_probs=27.3
Q ss_pred HhhhhcCCccccCCcCCCChhHHHHHHHHHHHHHHHHH
Q 043633 70 MIRRIVGVAHVEDFESIKDDSKRATCERQALELAKLLL 107 (128)
Q Consensus 70 ~iRRiiG~A~V~D~~~I~d~~~R~~aer~aL~ig~~li 107 (128)
=|||..|+..-.| .|++++.|.-.++- |..|....
T Consensus 20 GirR~TGl~~~~~--~~~n~~~r~~~~~Y-L~~GE~~~ 54 (70)
T PF08520_consen 20 GIRRNTGLTPKLD--KIENKDIRNWIHKY-LNVGEWVF 54 (70)
T ss_pred HHhhccCCccChh--hcCChhHHHHHHHH-cchhHHHH
Confidence 3899999985544 99999999888876 77776654
No 7
>PF07599 DUF1563: Protein of unknown function (DUF1563); InterPro: IPR011457 This is a small family of short hypothetical proteins in Leptospira interrogans.
Probab=47.53 E-value=37 Score=19.57 Aligned_cols=14 Identities=36% Similarity=0.610 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHHH
Q 043633 50 VQEKFMKDLFHDTL 63 (128)
Q Consensus 50 ~~e~~l~~il~D~~ 63 (128)
|+|++|+++|-|+.
T Consensus 21 yve~~lkq~fld~~ 34 (43)
T PF07599_consen 21 YVEYFLKQTFLDSM 34 (43)
T ss_pred HHHHHHHHHHHHHH
Confidence 45555555555543
No 8
>PHA01735 hypothetical protein
Probab=34.98 E-value=33 Score=22.31 Aligned_cols=27 Identities=22% Similarity=0.396 Sum_probs=19.0
Q ss_pred HHHHHHHhhhHHHHhhhhc-CCccccCC
Q 043633 57 DLFHDTLGFGAAKMIRRIV-GVAHVEDF 83 (128)
Q Consensus 57 ~il~D~~GfAG~e~iRRii-G~A~V~D~ 83 (128)
+.|.+--+--.-|++|||. |-|-.+|+
T Consensus 8 e~fs~LH~~lt~El~~RiksgeATtaDL 35 (76)
T PHA01735 8 EQFDELHQLLTNELLSRIKSGEATTADL 35 (76)
T ss_pred HHHHHHHHHHHHHHHHHHhcCcccHHHH
Confidence 3455556666789999998 77766654
No 9
>PF05778 Apo-CIII: Apolipoprotein CIII (Apo-CIII); InterPro: IPR008403 This family consists of several mammalian apolipoprotein CIII (Apo-CIII) sequences. Apolipoprotein C-III is a 79-residue glycoprotein. It is synthesised in the intestine and liver as part of the very low density lipoprotein (VLDL) and the high density lipoprotein (HDL) particles. Owing to its positive correlation with plasma triglyceride (Tg) levels, Apo-CIII is suggested to play a role in Tg metabolism and is therefore of interest regarding atherosclerosis. However, unlike other apolipoproteins such as Apo-AI, Apo E or CII for which many naturally occurring mutations are known, the structure-function relationships of apo C-III remains a subject of debate. One possibility is that apo C-III inhibits lipoprotein lipase (LPL) activity, as shown by in vitro experiments. Another suggestion, is that elevated levels of Apo-CIII displace other apolipoproteins at the lipoprotein surface, modifying their clearance from plasma [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0042157 lipoprotein metabolic process, 0005576 extracellular region; PDB: 2JQ3_A.
Probab=33.42 E-value=14 Score=23.83 Aligned_cols=22 Identities=23% Similarity=0.828 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhc
Q 043633 8 RTIEETWTLFHQKFTALWHQHK 29 (128)
Q Consensus 8 ~~I~~~w~~F~~~F~~lw~~~~ 29 (128)
+.++.-|..|..+|+.+|+..+
T Consensus 47 sslk~Yws~~~gk~s~~wd~~p 68 (70)
T PF05778_consen 47 SSLKDYWSTFKGKFSGFWDSAP 68 (70)
T ss_dssp THHHHHHHHHHHHTTGGGS-SS
T ss_pred HHHHHHHHHHhhhhhcccccCC
Confidence 5678899999999999998755
No 10
>PF14714 KH_dom-like: KH-domain-like of EngA bacterial GTPase enzymes, C-terminal; PDB: 2HJG_A 1MKY_A.
Probab=32.13 E-value=32 Score=22.41 Aligned_cols=21 Identities=10% Similarity=0.542 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHhhhHHHH
Q 043633 50 VQEKFMKDLFHDTLGFGAAKM 70 (128)
Q Consensus 50 ~~e~~l~~il~D~~GfAG~e~ 70 (128)
--..||.+-+++..||-|+-|
T Consensus 55 sY~ryL~n~lRe~f~f~G~Pi 75 (80)
T PF14714_consen 55 SYKRYLENQLREAFGFEGVPI 75 (80)
T ss_dssp HHHHHHHHHHHHHH--TTS--
T ss_pred HHHHHHHHHHHHHCCCCceeE
Confidence 447899999999999999865
No 11
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=31.33 E-value=74 Score=19.88 Aligned_cols=21 Identities=19% Similarity=0.188 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHhhhHH
Q 043633 48 QLVQEKFMKDLFHDTLGFGAA 68 (128)
Q Consensus 48 ~~~~e~~l~~il~D~~GfAG~ 68 (128)
....++++.+|.+|++-|+-.
T Consensus 29 ~~~~e~rl~~i~~~A~k~~~h 49 (65)
T smart00803 29 AEDVEYRIKEIVQEALKFMRH 49 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999754
No 12
>PF14981 FAM165: FAM165 family
Probab=28.87 E-value=40 Score=20.24 Aligned_cols=17 Identities=29% Similarity=0.395 Sum_probs=13.4
Q ss_pred HHHHHHHhhhHHHHhhh
Q 043633 57 DLFHDTLGFGAAKMIRR 73 (128)
Q Consensus 57 ~il~D~~GfAG~e~iRR 73 (128)
..+-=.++|||.+|--|
T Consensus 16 KtlilClaFAgvK~yQ~ 32 (51)
T PF14981_consen 16 KTLILCLAFAGVKMYQR 32 (51)
T ss_pred HHHHHHHHHhhHHHHHH
Confidence 44556899999999866
No 13
>PF06287 DUF1039: Protein of unknown function (DUF1039); InterPro: IPR010437 This family describes a small protein, always smaller than 100 amino acids, encoded in pathogenicity islands for bacterial type III secretion systems in various strains of Yersinia, Salmonella, and enteropathogenic Escherichia coli, as well as Chromobacterium violaceum and Citrobacter rodentium. Although strictly associated with type III secretion systems, this protein seems not yet to have been characterised as part of the apparatus or as an effector protein.
Probab=27.27 E-value=59 Score=20.79 Aligned_cols=16 Identities=44% Similarity=0.671 Sum_probs=13.5
Q ss_pred CCCChhHHHHHHHHHH
Q 043633 85 SIKDDSKRATCERQAL 100 (128)
Q Consensus 85 ~I~d~~~R~~aer~aL 100 (128)
-|+|++.|..||..++
T Consensus 22 Li~D~~~r~~c~alll 37 (66)
T PF06287_consen 22 LIPDEEDRAVCEALLL 37 (66)
T ss_pred hcCCHhHHHHHHHHHH
Confidence 3899999999998844
No 14
>PF01730 UreF: UreF; InterPro: IPR002639 This family consists of the urease accessory protein, UreF. The urease enzyme (urea amidohydrolase) hydrolyses urea into ammonia and carbamic acid []. UreF is proposed to modulate the activation process of urease by eliminating the binding of nickel irons to noncarbamylated protein [].; GO: 0016151 nickel ion binding, 0006807 nitrogen compound metabolic process; PDB: 3SF5_A 3CXN_B 2WGL_A 3O1Q_B.
Probab=27.07 E-value=69 Score=22.64 Aligned_cols=61 Identities=11% Similarity=0.195 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHhhhHHHHhhhhcCCccccCCcCCCChhHHHHH-------HHHHHHHHHHHHHcC
Q 043633 50 VQEKFMKDLFHDTLGFGAAKMIRRIVGVAHVEDFESIKDDSKRATC-------ERQALELAKLLLKER 110 (128)
Q Consensus 50 ~~e~~l~~il~D~~GfAG~e~iRRiiG~A~V~D~~~I~d~~~R~~a-------er~aL~ig~~li~~r 110 (128)
-...||...+...+++.-.-.+.+..-.+.-.|++.+.+-+.+..+ .+....+|+.|+.--
T Consensus 7 ~l~~~l~~~L~~~~~~~d~~~l~~a~~a~~~~d~~~l~~ld~~l~A~~~~~e~R~as~~~G~~ll~~~ 74 (146)
T PF01730_consen 7 SLKDWLRDYLRHGLARFDLPALAAAYRAAKAGDLEALAELDRLLDASKLSRELREASRQMGRALLRLA 74 (146)
T ss_dssp HHHHHHHHHHTTHHHHTHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhHHHhHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHH
Confidence 3578889999989999888888888887777888888777777644 345677888887543
No 15
>PRK02999 malate synthase G; Provisional
Probab=26.45 E-value=1.6e+02 Score=27.14 Aligned_cols=71 Identities=17% Similarity=0.260 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHhhhHHHHhhhhcCCccccCCcCCCChhHHHHHHHHHHHHHHHHHHcCcCCCCHHHHHHHHHHh
Q 043633 52 EKFMKDLFHDTLGFGAAKMIRRIVGVAHVEDFESIKDDSKRATCERQALELAKLLLKERRNFQAITEVVSAIRKL 126 (128)
Q Consensus 52 e~~l~~il~D~~GfAG~e~iRRiiG~A~V~D~~~I~d~~~R~~aer~aL~ig~~li~~r~~~~~i~~~~~~~~~~ 126 (128)
+.=|++=.+=.+||-..= +=+=+|.++|+||..+.=-+.|+.+|...-+|+..|- +..-|-+++.+.++..
T Consensus 594 ~~el~nN~q~iLgYvvrW-ld~GvGcskvpdI~~vgLMEDrATaeISrqqiwnWL~---HG~~~~~qv~~~l~rm 664 (726)
T PRK02999 594 QQELDNNAQGILGYVVRW-VDQGVGCSKVPDIHDVGLMEDRATLRISSQHIANWLR---HGVVTEEQVMESLKRM 664 (726)
T ss_pred HHHHHHHHHHHHHHHHHH-HhcCCCcCccccccccccccchHHHHhHHHHHHHHHH---ccCCCHHHHHHHHHHH
Confidence 334555555666664311 1134799999999954444457777777777776553 3455688888887754
No 16
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=26.33 E-value=72 Score=19.34 Aligned_cols=18 Identities=22% Similarity=0.567 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHhhhH
Q 043633 50 VQEKFMKDLFHDTLGFGA 67 (128)
Q Consensus 50 ~~e~~l~~il~D~~GfAG 67 (128)
.-+.|+.+|..|+..|+-
T Consensus 31 aaQKFisdI~~dA~q~~k 48 (51)
T PF03540_consen 31 AAQKFISDIANDAMQYCK 48 (51)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 568999999999999874
No 17
>KOG1355 consensus Adenylosuccinate synthase [Nucleotide transport and metabolism]
Probab=23.18 E-value=79 Score=26.92 Aligned_cols=50 Identities=18% Similarity=0.146 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHhhhcCCCCCCchhhhhCChhhHHHHHHH--HHHHHHHHHHhhhH
Q 043633 14 WTLFHQKFTALWHQHKDGSGEAYLPEIYNKPELQQLVQEK--FMKDLFHDTLGFGA 67 (128)
Q Consensus 14 w~~F~~~F~~lw~~~~~~~~~~~~~~~~~~~~~~~~~~e~--~l~~il~D~~GfAG 67 (128)
|+.|+++|+.+-..... .||.--+..++-++.|+++ -|+-...|+++|.=
T Consensus 188 ~~~fs~r~k~l~~~~~~----~fp~~e~die~el~~~K~~aekl~p~V~D~V~F~~ 239 (455)
T KOG1355|consen 188 FDEFSERFKVLAEQYKS----RFPTLEIDIEGELARYKGYAEKLKPMVRDTVYFMY 239 (455)
T ss_pred HHHHHHHHHHHHHHHHH----hcCCeEecHHHHHHHHHHHHHhhcchhhchhhhhh
Confidence 99999999999988873 3332223333333334321 24556778877753
No 18
>PF14372 DUF4413: Domain of unknown function (DUF4413)
Probab=22.99 E-value=2.4e+02 Score=18.77 Aligned_cols=58 Identities=16% Similarity=0.242 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCCCCchhhhhCChhhHHHHHHHHHHHHHHHHHhhhHHHHhhh
Q 043633 8 RTIEETWTLFHQKFTALWHQHKDGSGEAYLPEIYNKPELQQLVQEKFMKDLFHDTLGFGAAKMIRR 73 (128)
Q Consensus 8 ~~I~~~w~~F~~~F~~lw~~~~~~~~~~~~~~~~~~~~~~~~~~e~~l~~il~D~~GfAG~e~iRR 73 (128)
..+.++...-.++|.+.|++-.. . +.-+..=+|. |+=.|++-.+....|=-+.+.+.+
T Consensus 31 ~~l~~ma~~M~~KfdKYw~~~~~---~-l~ia~ILDPR----~Kl~~~~~~~~~~~~~~~~~~~~~ 88 (101)
T PF14372_consen 31 PDLKNMAKKMKEKFDKYWKDCNL---L-LAIATILDPR----FKLEFLEFCFSKLYGSDAKEKIEE 88 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHH---H-HHHHHHhchH----HHHHHHHHHHHHHhcchHHHHHHH
Confidence 45677888899999999985542 1 2111111454 445555555555544444444443
No 19
>PF10463 Peptidase_U49: Peptidase U49; InterPro: IPR019504 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This entry contains peptidases belonging to MEROPS peptidase family U49 (Lit peptidase, clan U-). The Lit peptidase from Escherichia coli functions in bacterial cell death in response to infection by Enterobacteria phage T4. Following binding of Gol peptide to domains II and III of elongation factor Tu, the Lit peptidase cleaves domain I of the elongation factor. This prevents binding of guanine nucleotides, shuts down translation and leads to cell death.
Probab=22.96 E-value=3.3e+02 Score=21.06 Aligned_cols=59 Identities=22% Similarity=0.311 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHhhhHHHHhhhhcCCc---cccCCcCCCChhHHHHHHHHHHHHHHHHHHcC
Q 043633 50 VQEKFMKDLFHDTLGFGAAKMIRRIVGVA---HVEDFESIKDDSKRATCERQALELAKLLLKER 110 (128)
Q Consensus 50 ~~e~~l~~il~D~~GfAG~e~iRRiiG~A---~V~D~~~I~d~~~R~~aer~aL~ig~~li~~r 110 (128)
+.+.+|+-+| +.||++..+....+|+. ..-++...-+.+.+.+-..-.+.-++.|+-+.
T Consensus 3 ~~~~~L~~lW--~f~~~~~~~ye~~~~i~~~~~~g~~~~~l~~~~~~~~~~~~~~~a~~ll~~~ 64 (206)
T PF10463_consen 3 FNERFLEYLW--IFGFAAWVLYEENYGIQKPQKDGTLESDLEDEELLQKAMDLFSWARSLLENF 64 (206)
T ss_pred ecHHHHHHHH--HHHHHHHHHHHHHHHHHHHhhcCcccccccchhHHHHHHHHHHHHHHHHHhc
Confidence 3467888888 58999999999944443 34444433347788888888999999999885
No 20
>TIGR02498 type_III_ssaH type III secretion system protein, SsaH family. This family describes a small protein, always smaller than 100 amino acids, encoded in pathogenicity islands for bacterial type III secretion systems in various strains of Yersinia, Salmonella, and enteropathogenic E. coli, as well as Chromobacterium violaceum and Citrobacter rodentium. Although strictly associated with type III secretion systems, this protein seems not yet to have been characterized as part of the apparatus or as an effector protein.
Probab=22.24 E-value=82 Score=20.87 Aligned_cols=16 Identities=38% Similarity=0.549 Sum_probs=13.5
Q ss_pred CCCChhHHHHHHHHHH
Q 043633 85 SIKDDSKRATCERQAL 100 (128)
Q Consensus 85 ~I~d~~~R~~aer~aL 100 (128)
-|+|++.|+.||...|
T Consensus 35 li~D~~~r~vcea~ll 50 (79)
T TIGR02498 35 IIPDKKDRLVCEAILL 50 (79)
T ss_pred ccCCHhHHHHHHHHHH
Confidence 4899999999998844
No 21
>PRK15356 type III secretion system protein SsaH; Provisional
Probab=22.14 E-value=85 Score=20.60 Aligned_cols=16 Identities=19% Similarity=0.283 Sum_probs=13.3
Q ss_pred CCCChhHHHHHHHHHH
Q 043633 85 SIKDDSKRATCERQAL 100 (128)
Q Consensus 85 ~I~d~~~R~~aer~aL 100 (128)
-|+|++.|+.|+...+
T Consensus 23 LIpD~~~r~vC~alll 38 (75)
T PRK15356 23 IVPDKKLQLVCLALLL 38 (75)
T ss_pred hcCCHHHHHHHHHHHH
Confidence 4899999999998743
No 22
>PF08072 BDHCT: BDHCT (NUC031) domain; InterPro: IPR012532 This is a C-terminal domain in Bloom's syndrome DEAD helicase subfamily []. The helicase articipates in DNA replication and repair, exhibiting a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction.; GO: 0003677 DNA binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006260 DNA replication, 0005634 nucleus
Probab=21.91 E-value=54 Score=19.02 Aligned_cols=23 Identities=35% Similarity=0.446 Sum_probs=17.7
Q ss_pred CcCCCChhHHHHHHHHHHHHHHHHHHcCc
Q 043633 83 FESIKDDSKRATCERQALELAKLLLKERR 111 (128)
Q Consensus 83 ~~~I~d~~~R~~aer~aL~ig~~li~~r~ 111 (128)
.|+||+. |-.+|..|.+|+..|+
T Consensus 13 VD~IP~~------eL~aL~CG~eLlqqR~ 35 (41)
T PF08072_consen 13 VDTIPID------ELKALSCGNELLQQRD 35 (41)
T ss_pred HccCcHH------HHHHcchHHHHHHHHH
Confidence 4778754 6678999999998774
No 23
>cd00728 malate_synt_G Malate synthase G (MSG), monomeric enzyme present in some bacteria. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms to derive their carbon requirements from two-carbon compounds, by bypassing the two carboxylation steps of the citric acid cycle.
Probab=20.77 E-value=2e+02 Score=26.46 Aligned_cols=72 Identities=15% Similarity=0.233 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHhhhHHHHhhhhcCCccccCCcCCCChhHHHHHHHHHHHHHHHHHHcCcCCCCHHHHHHHHHHh
Q 043633 51 QEKFMKDLFHDTLGFGAAKMIRRIVGVAHVEDFESIKDDSKRATCERQALELAKLLLKERRNFQAITEVVSAIRKL 126 (128)
Q Consensus 51 ~e~~l~~il~D~~GfAG~e~iRRiiG~A~V~D~~~I~d~~~R~~aer~aL~ig~~li~~r~~~~~i~~~~~~~~~~ 126 (128)
++.=|++=.+=.+||-..= +=+=+|.++|+||..+.=-+.|+.+|...-+|+..|- +..-|-+.+.+.++..
T Consensus 584 i~~el~nN~q~iLgYvvrW-ld~GvGcskvpdI~~vgLMEDrATaeISrqqiwqWl~---Hg~vt~e~v~~~l~rm 655 (712)
T cd00728 584 IQSELDNNVQGILGYVVRW-VDQGIGCSKVPDINNVGLMEDRATLRISSQHIANWLR---HGICTKEQVQESLERM 655 (712)
T ss_pred HHHHHHHHHHHHHHHHHHH-HhcCCCcCcccccccccccCCchhhhhHHHHHHHHHH---ccCCcHHHHHHHHHHH
Confidence 3344555566667774311 1133799999999944434456777777667766543 2335777777777653
No 24
>COG0002 ArgC Acetylglutamate semialdehyde dehydrogenase [Amino acid transport and metabolism]
Probab=20.47 E-value=41 Score=28.17 Aligned_cols=27 Identities=22% Similarity=0.426 Sum_probs=22.8
Q ss_pred HHhhhHHHHhhhhcCCccccCCcCCCCh
Q 043633 62 TLGFGAAKMIRRIVGVAHVEDFESIKDD 89 (128)
Q Consensus 62 ~~GfAG~e~iRRiiG~A~V~D~~~I~d~ 89 (128)
+-||+|.|++|+..+=-+|. +..++..
T Consensus 10 asGYtG~EL~rlL~~Hp~ve-~~~~ss~ 36 (349)
T COG0002 10 ASGYTGLELLRLLAGHPDVE-LILISSR 36 (349)
T ss_pred CCCCcHHHHHHHHhcCCCeE-EEEeech
Confidence 35999999999999998888 7777654
No 25
>PF15119 APOC4: Apolipoprotein C4
Probab=20.25 E-value=1.7e+02 Score=19.93 Aligned_cols=20 Identities=20% Similarity=0.273 Sum_probs=15.1
Q ss_pred ChhhHHHHHHHHHHHHHHHH
Q 043633 43 KPELQQLVQEKFMKDLFHDT 62 (128)
Q Consensus 43 ~~~~~~~~~e~~l~~il~D~ 62 (128)
.+++.++|++.|-.+.|+|-
T Consensus 48 ~p~~~qGFmQTYYdDHLkDL 67 (99)
T PF15119_consen 48 GPSAFQGFMQTYYDDHLKDL 67 (99)
T ss_pred ChHHHHHHHHHHHHHHHhhc
Confidence 45556778898888888873
Done!