Query 025821
Match_columns 247
No_of_seqs 108 out of 126
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 09:57:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025821.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025821hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05212 DUF707: Protein of un 100.0 2.9E-87 6.3E-92 609.9 13.5 172 70-243 4-175 (294)
2 PF12996 DUF3880: DUF based on 66.2 5.1 0.00011 30.0 2.3 25 179-213 13-37 (79)
3 PF12621 DUF3779: Phosphate me 62.7 10 0.00022 29.7 3.5 53 173-230 33-87 (95)
4 PF14538 Raptor_N: Raptor N-te 56.5 6.2 0.00013 33.6 1.4 46 137-194 91-144 (154)
5 PF09451 ATG27: Autophagy-rela 51.8 16 0.00035 33.1 3.4 27 18-44 201-227 (268)
6 PRK05325 hypothetical protein; 35.7 24 0.00052 34.8 2.0 28 122-151 296-325 (401)
7 PF07976 Phe_hydrox_dim: Pheno 33.7 83 0.0018 26.7 4.7 71 77-156 34-124 (169)
8 PF13778 DUF4174: Domain of un 33.7 31 0.00068 27.7 2.1 39 121-159 63-103 (118)
9 PF07862 Nif11: Nitrogen fixat 33.2 32 0.0007 23.4 1.8 21 200-220 27-47 (49)
10 PF04285 DUF444: Protein of un 32.4 30 0.00064 34.4 2.0 29 122-152 320-350 (421)
11 PF15018 InaF-motif: TRP-inter 32.1 17 0.00037 25.1 0.3 9 186-194 27-35 (38)
12 PRK10927 essential cell divisi 31.4 40 0.00087 32.6 2.7 26 22-47 34-59 (319)
13 PF09665 RE_Alw26IDE: Type II 29.8 28 0.00061 35.5 1.4 28 174-202 362-393 (511)
14 TIGR02877 spore_yhbH sporulati 28.8 40 0.00086 33.2 2.2 27 123-151 277-305 (371)
15 PRK13863 type IV secretion sys 26.4 59 0.0013 32.8 2.9 82 108-216 83-178 (446)
16 TIGR03798 ocin_TIGR03798 bacte 23.3 22 0.00047 25.7 -0.5 24 200-223 25-48 (64)
17 PF12431 CitT: Transcriptional 22.1 60 0.0013 20.9 1.4 7 77-83 21-27 (30)
18 PRK12757 cell division protein 22.0 56 0.0012 30.6 1.8 22 25-46 2-23 (256)
19 PRK05637 anthranilate synthase 20.9 88 0.0019 27.4 2.7 48 134-182 136-189 (208)
No 1
>PF05212 DUF707: Protein of unknown function (DUF707); InterPro: IPR007877 This family consists of uncharacterised proteins from Arabidopsis thaliana.
Probab=100.00 E-value=2.9e-87 Score=609.86 Aligned_cols=172 Identities=66% Similarity=1.163 Sum_probs=169.4
Q ss_pred cCCCCCCCCCCCCceecCCCCccccCCCCCCCCCCCCCCCceEEEEeccccccchhHHhhhcCCCCeEEEEEEecCcccc
Q 025821 70 QCRLPGTEALPEGIVSKTSNLEMRPLWSSPSKLNNQRPPMNLLAIAAGIKQKKIVDQIVRKFPSKDFVVMLFHYDGVVDE 149 (247)
Q Consensus 70 q~~p~GsE~LP~GIV~~tSDlelr~LWg~p~~~~~~~~~k~Lla~~VGikqK~~Vd~~V~KF~~~nF~imLFHYDG~vd~ 149 (247)
||+|+|+|+||+|||+++||||||||||+|+++. ..++|||||||||+|||++||++|+|| ++||+||||||||+||+
T Consensus 4 ~~~p~g~e~Lp~giv~~~sd~~~r~lw~~p~~~~-~~~~k~Lla~~VG~kqk~~vd~~v~Kf-~~nF~i~LfhYDg~vd~ 81 (294)
T PF05212_consen 4 PCNPRGAERLPPGIVVRESDLELRPLWGNPSEDL-PKKPKYLLAMTVGIKQKDNVDAIVKKF-SDNFDIMLFHYDGRVDE 81 (294)
T ss_pred CCCCCccccCCCCccccCCCceeeecCCCccccc-cCCCceEEEEEecHHHHhhhhHHHhhh-ccCceEEEEEecCCcCc
Confidence 8999999999999999999999999999999885 678999999999999999999999999 99999999999999999
Q ss_pred ccccccccceeEEEEecccchhhhcccCCcccccceeeEEEeecccccCCCChhhhHHHHhhhCcccccCccCCCCCcee
Q 025821 150 WKDLVWADRAIHVSAANQTKWWFAKRFLHPDIVAEYNYIFLWDEDIGVENFNPRRYLSIVKDEGLEISQPALDPVKSEVH 229 (247)
Q Consensus 150 W~d~eWs~~aIHvsa~~QtKWWfAKRFLHPdiVa~YeYiFlWDEDlgve~F~~~~Yl~Ivk~~gLeISQPaLd~~~~~~h 229 (247)
|+|||||++||||+|+|||||||||||||||||++||||||||||||||||||+|||+|||+|||||||||||+++|++|
T Consensus 82 w~~~~ws~~aiHv~~~kqtKww~akrfLHPdiv~~YdYiflwDeDL~vd~f~~~ry~~Ivk~~gLeISQPALd~~~~~~~ 161 (294)
T PF05212_consen 82 WDDFEWSDRAIHVSARKQTKWWFAKRFLHPDIVAPYDYIFLWDEDLGVDHFDINRYFEIVKKEGLEISQPALDPDSSEIH 161 (294)
T ss_pred hhhcccccceEEEEeccceEEeehhhhcChhhhccceeEEecCCccCcCcCCHHHHHHHHHHhCCcccCcccCCCCceee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeecCCccccc
Q 025821 230 HPITARRRNSKAHR 243 (247)
Q Consensus 230 ~~iT~R~~~~~vHr 243 (247)
|+||+|+++++|||
T Consensus 162 ~~iT~R~~~~~vhr 175 (294)
T PF05212_consen 162 HPITKRRPDSEVHR 175 (294)
T ss_pred eeEEeecCCceeEe
Confidence 99999999999998
No 2
>PF12996 DUF3880: DUF based on E. rectale Gene description (DUF3880); InterPro: IPR024542 This entry represents proteins of unknown function. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=66.16 E-value=5.1 Score=29.97 Aligned_cols=25 Identities=28% Similarity=0.668 Sum_probs=18.4
Q ss_pred cccccceeeEEEeecccccCCCChhhhHHHHhhhC
Q 025821 179 PDIVAEYNYIFLWDEDIGVENFNPRRYLSIVKDEG 213 (247)
Q Consensus 179 PdiVa~YeYiFlWDEDlgve~F~~~~Yl~Ivk~~g 213 (247)
..+...|+|||+||++ .++-.|+.|
T Consensus 13 ~~i~~~~~~iFt~D~~----------~~~~~~~~G 37 (79)
T PF12996_consen 13 YSIANSYDYIFTFDRS----------FVEEYRNLG 37 (79)
T ss_pred hhhCCCCCEEEEECHH----------HHHHHHHcC
Confidence 3677899999999975 345555666
No 3
>PF12621 DUF3779: Phosphate metabolism protein ; InterPro: IPR022257 This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with PF02714 from PFAM. There are two completely conserved residues (W and D) that may be functionally important. This family is likely to be involved in phosphate metabolism however there is little accompanying literature to confirm this.
Probab=62.75 E-value=10 Score=29.70 Aligned_cols=53 Identities=26% Similarity=0.475 Sum_probs=45.0
Q ss_pred hcccCCcccccceeeEEEeecccccCCCChhhhHHHHhhhCcccccCc--cCCCCCceee
Q 025821 173 AKRFLHPDIVAEYNYIFLWDEDIGVENFNPRRYLSIVKDEGLEISQPA--LDPVKSEVHH 230 (247)
Q Consensus 173 AKRFLHPdiVa~YeYiFlWDEDlgve~F~~~~Yl~Ivk~~gLeISQPa--Ld~~~~~~h~ 230 (247)
..-|+||.+-++--.|-|--.++||- +.=++-.++.|++||.-+ ||. +|.+.|
T Consensus 33 ~~ay~~Pa~~~~~P~lWIP~D~~GvS----~~ei~~~~~~~v~~Sd~gA~lde-kgkv~~ 87 (95)
T PF12621_consen 33 KHAYLHPAVSAPQPILWIPRDPLGVS----RQEIEETRKVGVPISDEGATLDE-KGKVVW 87 (95)
T ss_pred HhccCCHhHcCCCCeEEeecCCCCCC----HHHHHHhhcCCeEEECCCeEEcc-CCCEEE
Confidence 46799999999999999999999994 466778889999999887 776 577877
No 4
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=56.46 E-value=6.2 Score=33.63 Aligned_cols=46 Identities=26% Similarity=0.520 Sum_probs=27.5
Q ss_pred EEEEEEecCccccccccccccceeEEEEecccchhhhcccCCccccccee--------eEEEeecc
Q 025821 137 VVMLFHYDGVVDEWKDLVWADRAIHVSAANQTKWWFAKRFLHPDIVAEYN--------YIFLWDED 194 (247)
Q Consensus 137 ~imLFHYDG~vd~W~d~eWs~~aIHvsa~~QtKWWfAKRFLHPdiVa~Ye--------YiFlWDED 194 (247)
.=+||||-|. .++. -..+..=|-|-|.+-.-.-+.-|| =||+||++
T Consensus 91 ~RvLFHYnGh-----GvP~-------Pt~~GeIw~f~~~~tqyip~si~dL~~~lg~Psi~V~DC~ 144 (154)
T PF14538_consen 91 ERVLFHYNGH-----GVPR-------PTENGEIWVFNKNYTQYIPLSIYDLQSWLGSPSIYVFDCS 144 (154)
T ss_pred ceEEEEECCC-----CCCC-------CCCCCeEEEEcCCCCcceEEEHHHHHHhcCCCEEEEEECC
Confidence 7899999992 1111 112233477777775444444444 47899987
No 5
>PF09451 ATG27: Autophagy-related protein 27; InterPro: IPR018939 Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. There are more than 25 AuTophaGy-related (ATG) genes that are essential for autophagy, although it is still not known how the autophagosome is made. Atg9 is a potential membrane carrier to deliver lipids that are used to form the vesicle. Atg27 is another transmembrane protein, and is a cycling protein []. It acts as an effector of VPS34 phosphatidylinositol 3-phosphate kinase signalling and regulates the cytoplasm to vacuole transport (Cvt) vesicle formation. It is also required for autophagy-dependent cycling of ATG9.
Probab=51.85 E-value=16 Score=33.12 Aligned_cols=27 Identities=26% Similarity=0.315 Sum_probs=18.8
Q ss_pred cchhhhhHHHHHHHHHhhhcceeeech
Q 025821 18 SCLCSLFIAAALICSVYFIGSSFVAKE 44 (247)
Q Consensus 18 ~~~~~~~~~~~li~~~~fig~~~~t~~ 44 (247)
+++..+|+++.|..++|||++++.-..
T Consensus 201 g~f~wl~i~~~l~~~~Y~i~g~~~n~~ 227 (268)
T PF09451_consen 201 GFFTWLFIILFLFLAAYLIFGSWYNYN 227 (268)
T ss_pred cHHHHHHHHHHHHHHHHhhhhhheeec
Confidence 344567777777778899988876543
No 6
>PRK05325 hypothetical protein; Provisional
Probab=35.72 E-value=24 Score=34.85 Aligned_cols=28 Identities=29% Similarity=0.812 Sum_probs=24.0
Q ss_pred cchhHHhhh-cCCCCeEEEEEEe-cCcccccc
Q 025821 122 KIVDQIVRK-FPSKDFVVMLFHY-DGVVDEWK 151 (247)
Q Consensus 122 ~~Vd~~V~K-F~~~nF~imLFHY-DG~vd~W~ 151 (247)
+.++.||++ |+.+.+.|..||. || |.|.
T Consensus 296 ~l~~eIi~~rYpp~~wNIY~f~aSDG--DNw~ 325 (401)
T PRK05325 296 KLALEIIEERYPPAEWNIYAFQASDG--DNWS 325 (401)
T ss_pred HHHHHHHHhhCCHhHCeeEEEEcccC--CCcC
Confidence 456788885 9999999999997 88 8887
No 7
>PF07976 Phe_hydrox_dim: Phenol hydroxylase, C-terminal dimerisation domain ; InterPro: IPR012941 Phenol hydroxylase is a homodimer which hydroxylates phenol to catechol, or similar products. The enzyme is comprised of three domains. The first two domains form the active site. The third domain, this domain, is involved in forming the dimerisation interface. The domain adopts a thioredoxin-like fold [].; PDB: 2DKH_A 2DKI_A 1PN0_A 1FOH_D.
Probab=33.70 E-value=83 Score=26.70 Aligned_cols=71 Identities=18% Similarity=0.240 Sum_probs=40.9
Q ss_pred CCCCCCceecCCCCccccCCCCCCCCCCCCCC-CceEEEEecccccc---chh----------HHhhhcCCC------Ce
Q 025821 77 EALPEGIVSKTSNLEMRPLWSSPSKLNNQRPP-MNLLAIAAGIKQKK---IVD----------QIVRKFPSK------DF 136 (247)
Q Consensus 77 E~LP~GIV~~tSDlelr~LWg~p~~~~~~~~~-k~Lla~~VGikqK~---~Vd----------~~V~KF~~~------nF 136 (247)
++||+.-|.+-+|-....|- +..+... =.++.++=-+.+-+ .++ .++++|... -|
T Consensus 34 ~Rlp~~~v~r~aD~~p~~l~-----~~l~sdGrfri~vFagd~~~~~~~~~l~~l~~~L~~~~s~~~r~~~~~~~~~s~~ 108 (169)
T PF07976_consen 34 RRLPSAKVVRHADGNPVHLQ-----DDLPSDGRFRILVFAGDISLPEQLSRLSALADYLESPSSFLSRFTPKDRDPDSVF 108 (169)
T ss_dssp CB----EEEETTTTEEEEGG-----GG--SSS-EEEEEEEETTTTCHCCCHHHHHHHHHHSTTSHHHHHSBTTS-TTSSE
T ss_pred cccCCceEEEEcCCCChhHh-----hhcccCCCEEEEEEeCCCccchhHHHHHHHHHHHHhcchHHHhcCCCCCCCCCee
Confidence 37999999999997776663 3223233 36777775554433 233 456677653 39
Q ss_pred EEEEEEecCccccccccccc
Q 025821 137 VVMLFHYDGVVDEWKDLVWA 156 (247)
Q Consensus 137 ~imLFHYDG~vd~W~d~eWs 156 (247)
+++|+| -..++++||.
T Consensus 109 ~~~~I~----~~~~~~~e~~ 124 (169)
T PF07976_consen 109 DVLLIH----SSPRDEVELF 124 (169)
T ss_dssp EEEEEE----SS-CCCS-GG
T ss_pred EEEEEe----cCCCCceeHH
Confidence 999999 3568888885
No 8
>PF13778 DUF4174: Domain of unknown function (DUF4174)
Probab=33.66 E-value=31 Score=27.72 Aligned_cols=39 Identities=15% Similarity=0.148 Sum_probs=31.2
Q ss_pred ccchhHHhhhcC--CCCeEEEEEEecCccccccccccccce
Q 025821 121 KKIVDQIVRKFP--SKDFVVMLFHYDGVVDEWKDLVWADRA 159 (247)
Q Consensus 121 K~~Vd~~V~KF~--~~nF~imLFHYDG~vd~W~d~eWs~~a 159 (247)
...+..+-++|- .++|+++|.-.||.|-.+..-+|+-++
T Consensus 63 ~~~~~~lr~~l~~~~~~f~~vLiGKDG~vK~r~~~p~~~~~ 103 (118)
T PF13778_consen 63 PEDIQALRKRLRIPPGGFTVVLIGKDGGVKLRWPEPIDPEE 103 (118)
T ss_pred HHHHHHHHHHhCCCCCceEEEEEeCCCcEEEecCCCCCHHH
Confidence 345678888886 789999999999999988777776443
No 9
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=33.24 E-value=32 Score=23.37 Aligned_cols=21 Identities=14% Similarity=0.520 Sum_probs=18.2
Q ss_pred CChhhhHHHHhhhCcccccCc
Q 025821 200 FNPRRYLSIVKDEGLEISQPA 220 (247)
Q Consensus 200 F~~~~Yl~Ivk~~gLeISQPa 220 (247)
-++++.++|++++|.++|.--
T Consensus 27 ~~~~e~~~lA~~~Gy~ft~~e 47 (49)
T PF07862_consen 27 QNPEEVVALAREAGYDFTEEE 47 (49)
T ss_pred CCHHHHHHHHHHcCCCCCHHH
Confidence 389999999999999998643
No 10
>PF04285 DUF444: Protein of unknown function (DUF444); InterPro: IPR006698 This entry is represented by Thermus phage phiYS40, Orf56. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches [].
Probab=32.42 E-value=30 Score=34.38 Aligned_cols=29 Identities=31% Similarity=0.885 Sum_probs=24.1
Q ss_pred cchhHHhhh-cCCCCeEEEEEEe-cCccccccc
Q 025821 122 KIVDQIVRK-FPSKDFVVMLFHY-DGVVDEWKD 152 (247)
Q Consensus 122 ~~Vd~~V~K-F~~~nF~imLFHY-DG~vd~W~d 152 (247)
+.++.||++ |+.+++.|..||. || |.|.+
T Consensus 320 ~l~~~ii~erypp~~wNiY~~~~SDG--DN~~~ 350 (421)
T PF04285_consen 320 ELALEIIEERYPPSDWNIYVFHASDG--DNWSS 350 (421)
T ss_pred HHHHHHHHhhCChhhceeeeEEcccC--ccccC
Confidence 346778885 9999999999997 88 88863
No 11
>PF15018 InaF-motif: TRP-interacting helix
Probab=32.05 E-value=17 Score=25.12 Aligned_cols=9 Identities=67% Similarity=1.571 Sum_probs=5.7
Q ss_pred eeEEEeecc
Q 025821 186 NYIFLWDED 194 (247)
Q Consensus 186 eYiFlWDED 194 (247)
=|+|+||.+
T Consensus 27 YY~f~W~p~ 35 (38)
T PF15018_consen 27 YYIFFWDPD 35 (38)
T ss_pred HHheeeCCC
Confidence 367777654
No 12
>PRK10927 essential cell division protein FtsN; Provisional
Probab=31.37 E-value=40 Score=32.62 Aligned_cols=26 Identities=27% Similarity=0.408 Sum_probs=19.1
Q ss_pred hhhHHHHHHHHHhhhcceeeechhhh
Q 025821 22 SLFIAAALICSVYFIGSSFVAKENKE 47 (247)
Q Consensus 22 ~~~~~~~li~~~~fig~~~~t~~~ke 47 (247)
..+.++++.+++.|||+.|..++.|.
T Consensus 34 ~~m~alAvavlv~fiGGLyFith~k~ 59 (319)
T PRK10927 34 PAMVAIAAAVLVTFIGGLYFITHHKK 59 (319)
T ss_pred hHHHHHHHHHHHHHhhheEEEecCCC
Confidence 44566666778889999988888753
No 13
>PF09665 RE_Alw26IDE: Type II restriction endonuclease (RE_Alw26IDE); InterPro: IPR014328 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
Probab=29.82 E-value=28 Score=35.52 Aligned_cols=28 Identities=29% Similarity=0.542 Sum_probs=20.6
Q ss_pred cccCCcccccceeeEE--Eeecc--cccCCCCh
Q 025821 174 KRFLHPDIVAEYNYIF--LWDED--IGVENFNP 202 (247)
Q Consensus 174 KRFLHPdiVa~YeYiF--lWDED--lgve~F~~ 202 (247)
--||||.. |.|+|.| +|-++ +...++.+
T Consensus 362 ~t~L~~~Y-a~y~y~Fe~~~~~~~~~~~~~i~~ 393 (511)
T PF09665_consen 362 ATFLKPEY-ANYDYTFEGLNISNHLTQYKSIYK 393 (511)
T ss_pred HHHhchhh-hhccceeccccccccccccccccc
Confidence 46899999 8999999 55555 45455554
No 14
>TIGR02877 spore_yhbH sporulation protein YhbH. This protein family, typified by YhbH in Bacillus subtilis, is found in nearly every endospore-forming bacterium and in no other genome (but note that the trusted cutoff score is set high to exclude a single high-scoring sequence from Nitrosococcus oceani ATCC 19707, which is classified in the Gammaproteobacteria). The gene in Bacillus subtilis was shown to be in the regulon of the sporulation sigma factor, sigma-E, and its mutation was shown to create a sporulation defect.
Probab=28.81 E-value=40 Score=33.17 Aligned_cols=27 Identities=22% Similarity=0.594 Sum_probs=22.9
Q ss_pred chhHHhh-hcCCCCeEEEEEEe-cCcccccc
Q 025821 123 IVDQIVR-KFPSKDFVVMLFHY-DGVVDEWK 151 (247)
Q Consensus 123 ~Vd~~V~-KF~~~nF~imLFHY-DG~vd~W~ 151 (247)
....||+ +|+++.+.|..||. || |.|.
T Consensus 277 l~~eII~~rYpp~~wNIY~f~aSDG--DNw~ 305 (371)
T TIGR02877 277 KALEIIDERYNPARYNIYAFHFSDG--DNLT 305 (371)
T ss_pred HHHHHHHhhCChhhCeeEEEEcccC--CCcc
Confidence 3566776 69999999999998 88 8887
No 15
>PRK13863 type IV secretion system T-DNA border endonuclease VirD2; Provisional
Probab=26.42 E-value=59 Score=32.78 Aligned_cols=82 Identities=16% Similarity=0.253 Sum_probs=50.8
Q ss_pred CCceEEEEeccccccchhH----HhhhcCCC----Ce-EEEEEEecCccccccccccccceeEEEEe---cccchhhhcc
Q 025821 108 PMNLLAIAAGIKQKKIVDQ----IVRKFPSK----DF-VVMLFHYDGVVDEWKDLVWADRAIHVSAA---NQTKWWFAKR 175 (247)
Q Consensus 108 ~k~Lla~~VGikqK~~Vd~----~V~KF~~~----nF-~imLFHYDG~vd~W~d~eWs~~aIHvsa~---~QtKWWfAKR 175 (247)
..-+|.|+.|..+.+..++ +-++|++. +| -|+-||-|-- .--+||++. +--|=|
T Consensus 83 ~NIVLSMPaGTd~eAVrdAARefA~E~FgsG~~G~~~dYV~AlH~D~d----------HPHVHLvVnrRd~~G~~~---- 148 (446)
T PRK13863 83 THIIVSFPAGTSQVAAYAASREWAAEMFGSGAGGGRYNYLTAFHIDRD----------HPHLHVVVNRRELLGHGW---- 148 (446)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHhCCCCCCCceeEEEEEecCCC----------CCeEEEEEEeecCCCCce----
Confidence 3468999999777766552 34566542 44 3678997761 456899887 444423
Q ss_pred cCCcccccceeeEEEe--ecccccCCCChhhhHHHHhhhCccc
Q 025821 176 FLHPDIVAEYNYIFLW--DEDIGVENFNPRRYLSIVKDEGLEI 216 (247)
Q Consensus 176 FLHPdiVa~YeYiFlW--DEDlgve~F~~~~Yl~Ivk~~gLeI 216 (247)
+.|+ ..|+.++.+ -+.|-++.+++|++.
T Consensus 149 ------------lri~~rk~dlNld~~-Re~FAE~LRe~GIea 178 (446)
T PRK13863 149 ------------LKISRRHPQLNYDAL-RIKMAEISLRHGIVL 178 (446)
T ss_pred ------------eeecCCCccccHHHH-HHHHHHHHHhcCcee
Confidence 2233 223322222 367999999999985
No 16
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=23.32 E-value=22 Score=25.75 Aligned_cols=24 Identities=25% Similarity=0.473 Sum_probs=20.9
Q ss_pred CChhhhHHHHhhhCcccccCccCC
Q 025821 200 FNPRRYLSIVKDEGLEISQPALDP 223 (247)
Q Consensus 200 F~~~~Yl~Ivk~~gLeISQPaLd~ 223 (247)
=++++.++|++++|.+||.--|+.
T Consensus 25 ~~~e~~~~lA~~~Gf~ft~~el~~ 48 (64)
T TIGR03798 25 EDPEDRVAIAKEAGFEFTGEDLKE 48 (64)
T ss_pred CCHHHHHHHHHHcCCCCCHHHHHH
Confidence 368999999999999999887764
No 17
>PF12431 CitT: Transcriptional regulator
Probab=22.10 E-value=60 Score=20.89 Aligned_cols=7 Identities=71% Similarity=1.255 Sum_probs=6.2
Q ss_pred CCCCCCc
Q 025821 77 EALPEGI 83 (247)
Q Consensus 77 E~LP~GI 83 (247)
++||.||
T Consensus 21 ~~LPKGI 27 (30)
T PF12431_consen 21 ERLPKGI 27 (30)
T ss_pred cCCCCCc
Confidence 7799998
No 18
>PRK12757 cell division protein FtsN; Provisional
Probab=22.04 E-value=56 Score=30.60 Aligned_cols=22 Identities=36% Similarity=0.529 Sum_probs=16.5
Q ss_pred HHHHHHHHHhhhcceeeechhh
Q 025821 25 IAAALICSVYFIGSSFVAKENK 46 (247)
Q Consensus 25 ~~~~li~~~~fig~~~~t~~~k 46 (247)
.++++.+++.|||+.|..++.|
T Consensus 2 ~alava~lv~f~gGLyfi~h~k 23 (256)
T PRK12757 2 VALAVAVLVTFIGGLYFITHNK 23 (256)
T ss_pred HHHHHHHHHHHhhheEEEecCC
Confidence 4566677788899888887764
No 19
>PRK05637 anthranilate synthase component II; Provisional
Probab=20.89 E-value=88 Score=27.42 Aligned_cols=48 Identities=21% Similarity=0.306 Sum_probs=32.8
Q ss_pred CCeEEEEEEecCcc---ccccccccccc---eeEEEEecccchhhhcccCCcccc
Q 025821 134 KDFVVMLFHYDGVV---DEWKDLVWADR---AIHVSAANQTKWWFAKRFLHPDIV 182 (247)
Q Consensus 134 ~nF~imLFHYDG~v---d~W~d~eWs~~---aIHvsa~~QtKWWfAKRFLHPdiV 182 (247)
+.|.|..+|-|..+ ++..-+.||+. .+-.++..+.+..|+=.| ||+++
T Consensus 136 ~~~~V~~~H~~~v~~lp~~~~vlA~s~~~~~~v~~a~~~~~~~~~GvQf-HPE~~ 189 (208)
T PRK05637 136 RKVPIARYHSLGCVVAPDGMESLGTCSSEIGPVIMAAETTDGKAIGLQF-HPESV 189 (208)
T ss_pred CceEEEEechhhhhcCCCCeEEEEEecCCCCCEEEEEEECCCCEEEEEe-CCccC
Confidence 45788999988764 33445667654 244455667778888888 88875
Done!