Query 038867
Match_columns 721
No_of_seqs 128 out of 363
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 04:06:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038867.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038867hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02362 B3: B3 DNA binding do 99.7 4.1E-16 8.8E-21 133.0 11.5 97 575-678 1-99 (100)
2 PF03754 DUF313: Domain of unk 97.9 1.5E-05 3.2E-10 74.1 5.7 80 569-651 18-114 (114)
3 PF09217 EcoRII-N: Restriction 97.8 5.8E-05 1.2E-09 73.6 7.3 90 572-663 7-110 (156)
4 PHA03308 transcriptional regul 76.0 2 4.2E-05 51.3 2.8 10 60-69 1237-1246(1463)
5 PF15376 DUF4603: Domain of un 60.2 4.7 0.0001 48.8 1.7 34 54-87 149-197 (1286)
6 KOG3018 Malonyl-CoA decarboxyl 55.0 9.1 0.0002 41.6 2.6 58 238-295 210-269 (362)
7 KOG1924 RhoA GTPase effector D 50.7 75 0.0016 39.2 9.2 15 231-246 381-395 (1102)
8 PF04614 Pex19: Pex19 protein 45.4 23 0.0005 37.1 3.7 40 232-271 146-185 (248)
9 PF04014 Antitoxin-MazE: Antid 39.3 46 0.001 26.1 3.7 28 646-674 13-40 (47)
10 PF08610 Pex16: Peroxisomal me 36.9 34 0.00073 37.1 3.5 33 263-295 92-133 (335)
11 TIGR03830 CxxCG_CxxCG_HTH puta 36.7 50 0.0011 29.8 4.0 48 231-278 47-95 (127)
12 PF14097 SpoVAE: Stage V sporu 34.2 30 0.00064 35.5 2.4 29 259-287 11-49 (180)
13 PF03120 DNA_ligase_OB: NAD-de 30.4 70 0.0015 29.0 3.8 33 645-677 41-73 (82)
14 cd06919 Asp_decarbox Aspartate 29.8 2.5E+02 0.0055 27.1 7.5 76 574-664 9-88 (111)
15 PF12095 DUF3571: Protein of u 28.5 64 0.0014 29.6 3.3 35 231-271 26-60 (83)
16 KOG1924 RhoA GTPase effector D 28.3 2.4E+02 0.0052 35.2 8.7 7 99-105 171-177 (1102)
17 PF01878 EVE: EVE domain; Int 28.1 70 0.0015 30.0 3.6 27 652-678 38-64 (143)
18 TIGR01764 excise DNA binding d 27.6 67 0.0015 23.7 2.8 27 263-296 3-29 (49)
19 PF10844 DUF2577: Protein of u 27.5 72 0.0016 29.1 3.5 77 572-673 18-96 (100)
20 KOG4752 Ribosomal protein L41 27.4 33 0.00071 25.2 1.0 11 469-479 5-15 (26)
21 PRK11347 antitoxin ChpS; Provi 27.2 1.4E+02 0.003 26.9 5.1 41 630-676 6-46 (83)
22 TIGR02609 doc_partner putative 26.4 1.5E+02 0.0033 25.7 5.1 39 630-674 4-42 (74)
23 PF06078 DUF937: Bacterial pro 26.3 1.2E+02 0.0027 28.5 4.9 60 232-291 72-132 (137)
24 PF05298 Bombinin: Bombinin; 25.9 23 0.00049 34.3 0.0 48 244-301 29-76 (141)
25 PF09853 DUF2080: Putative tra 24.4 44 0.00095 28.4 1.4 37 561-599 4-42 (53)
26 TIGR00223 panD L-aspartate-alp 23.6 3.8E+02 0.0081 26.5 7.6 76 574-664 10-89 (126)
27 smart00719 Plus3 Short conserv 22.8 44 0.00096 30.8 1.2 17 249-265 2-18 (109)
28 KOG0260 RNA polymerase II, lar 22.7 95 0.0021 39.9 4.2 102 556-667 322-441 (1605)
29 cd00213 S-100 S-100: S-100 dom 22.6 2E+02 0.0043 24.5 5.1 65 231-295 7-87 (88)
30 TIGR02242 tail_TIGR02242 phage 21.9 75 0.0016 30.6 2.7 59 232-291 45-112 (130)
31 COG5297 CelA Cellobiohydrolase 21.4 53 0.0012 37.4 1.7 14 77-90 455-468 (544)
32 cd05829 Sortase_E Sortase E (S 21.3 1.3E+02 0.0028 28.8 4.1 41 637-677 49-97 (144)
33 PF12970 DUF3858: Domain of Un 20.3 68 0.0015 31.0 1.9 33 252-293 79-111 (116)
34 COG2002 AbrB Regulators of sta 20.3 1.6E+02 0.0036 26.2 4.2 27 647-673 21-47 (89)
35 PF01272 GreA_GreB: Transcript 20.1 5.6E+02 0.012 22.0 8.2 66 608-677 8-74 (77)
No 1
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=99.67 E-value=4.1e-16 Score=132.99 Aligned_cols=97 Identities=29% Similarity=0.421 Sum_probs=68.8
Q ss_pred eeeccccCCCCCCCceeecHhHHhhhCCCCcCCCCeEEEEEEcCCCcEEEEEEeeeeeCCCCCCceeec-ChhHHhhhcC
Q 038867 575 LQKVLKQSDVGNLGRIVLPKKEAETHLPELEARDGISIAMEDIGTSRVWNMRYSFRFWPNNKSRMYLLE-NTGDFVKANG 653 (721)
Q Consensus 575 F~KvLT~SDVgklGRLVIPKk~AEa~LP~Ld~~~Gi~L~veDi~tGkvW~FRys~RYW~NnkSRmYLLT-GWsdFVRsKg 653 (721)
|.|+|+++|+.+.++|+||++.+++| .+....++.|.+.|. .|+.|.+++ .++. .++.|+|+ ||.+||++++
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~--~~~~~~~~~v~l~~~-~g~~W~v~~--~~~~--~~~~~~l~~GW~~Fv~~n~ 73 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKH--GGNKRKSREVTLKDP-DGRSWPVKL--KYRK--NSGRYYLTGGWKKFVRDNG 73 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTT--S--SS--CEEEEEET-TTEEEEEEE--EEEC--CTTEEEEETTHHHHHHHCT
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHh--CCCcCCCeEEEEEeC-CCCEEEEEE--EEEc--cCCeEEECCCHHHHHHHcC
Confidence 88999999999999999999999998 222235679999997 899999999 6663 33346666 8999999999
Q ss_pred CCCCCEEEEEEec-CCCeEEEEEEEc
Q 038867 654 LQEGDFIVIYSDV-KCGKYLIRGVKV 678 (721)
Q Consensus 654 LqaGD~IVFyrd~-snGky~IggRR~ 678 (721)
|++||+|+|+... ...++.|.+.|+
T Consensus 74 L~~GD~~~F~~~~~~~~~~~v~i~~~ 99 (100)
T PF02362_consen 74 LKEGDVCVFELIGNSNFTLKVHIFRK 99 (100)
T ss_dssp --TT-EEEEEE-SSSCE-EEEEEE--
T ss_pred CCCCCEEEEEEecCCCceEEEEEEEC
Confidence 9999999999875 344668888764
No 2
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=97.93 E-value=1.5e-05 Score=74.07 Aligned_cols=80 Identities=24% Similarity=0.521 Sum_probs=63.7
Q ss_pred CcccceeeeccccCCCCC-CCceeecHhHHhh--hCCC-----C-------cCCCCeEEEEEEcCCCcEEEEEEeeeeeC
Q 038867 569 KNLRFLLQKVLKQSDVGN-LGRIVLPKKEAET--HLPE-----L-------EARDGISIAMEDIGTSRVWNMRYSFRFWP 633 (721)
Q Consensus 569 k~~~~LF~KvLT~SDVgk-lGRLVIPKk~AEa--~LP~-----L-------d~~~Gi~L~veDi~tGkvW~FRys~RYW~ 633 (721)
.+...++.|+|++|||.. .+||.||...... +|=+ + +...|+.+.+.|. .++.|.+++ |.|.
T Consensus 18 ~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp-~~~~~~m~l--kkW~ 94 (114)
T PF03754_consen 18 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDP-SLRKWTMRL--KKWN 94 (114)
T ss_pred CCCeEEEeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECC-cCcEEEEEE--EEec
Confidence 556899999999999995 7999999877643 2221 1 1246899999998 899999999 9998
Q ss_pred C-CCCCceeec-ChhHHhhh
Q 038867 634 N-NKSRMYLLE-NTGDFVKA 651 (721)
Q Consensus 634 N-nkSRmYLLT-GWsdFVRs 651 (721)
- +..-.|+|. ||.++|++
T Consensus 95 mg~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 95 MGNGTSNYVLNSGWNKVVED 114 (114)
T ss_pred ccCCceEEEEEcChHhhccC
Confidence 7 445679997 89999863
No 3
>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 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 the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.
Probab=97.79 E-value=5.8e-05 Score=73.59 Aligned_cols=90 Identities=19% Similarity=0.262 Sum_probs=58.6
Q ss_pred cceeeeccccCCCCCC----CceeecHhHHhhhCCCCcC----CCCeEEEEEEcCCC-cEEEEEEeeeeeCC----CCCC
Q 038867 572 RFLLQKVLKQSDVGNL----GRIVLPKKEAETHLPELEA----RDGISIAMEDIGTS-RVWNMRYSFRFWPN----NKSR 638 (721)
Q Consensus 572 ~~LF~KvLT~SDVgkl----GRLVIPKk~AEa~LP~Ld~----~~Gi~L~veDi~tG-kvW~FRys~RYW~N----nkSR 638 (721)
...|+|.|++.|++.+ .++.|||..++.+||.+.. +..+.|.+++.++. ..|+||+ +|+.| +.+.
T Consensus 7 ~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~--iYYnn~~~~gTRN 84 (156)
T PF09217_consen 7 WAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRF--IYYNNRLFGGTRN 84 (156)
T ss_dssp EEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEE--EEE-CCCTTSS--
T ss_pred eEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEE--EEEcccccCCCcC
Confidence 4689999999999964 6899999999999988754 45688999997432 5577999 88866 5688
Q ss_pred ceeecChhHHhhhcC-CCCCCEEEEE
Q 038867 639 MYLLENTGDFVKANG-LQEGDFIVIY 663 (721)
Q Consensus 639 mYLLTGWsdFVRsKg-LqaGD~IVFy 663 (721)
.|.||.|+....--+ =.+||.++|-
T Consensus 85 E~RIT~~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 85 EYRITRFGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp EEEEE---TTSGGG-GGGTT-EEEEE
T ss_pred ceEEeeecCCCccCCccccccEEEEE
Confidence 899999888777444 3689998885
No 4
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=76.02 E-value=2 Score=51.33 Aligned_cols=10 Identities=40% Similarity=0.889 Sum_probs=6.7
Q ss_pred cCCCCCCCCc
Q 038867 60 DFPPLPDFPC 69 (721)
Q Consensus 60 dfp~lpdfpc 69 (721)
-.||-||..-
T Consensus 1237 amppcpdlse 1246 (1463)
T PHA03308 1237 AMPPCPDLSE 1246 (1463)
T ss_pred CCCCCCCccc
Confidence 4677777653
No 5
>PF15376 DUF4603: Domain of unknown function (DUF4603)
Probab=60.18 E-value=4.7 Score=48.84 Aligned_cols=34 Identities=50% Similarity=0.757 Sum_probs=24.0
Q ss_pred cccccccCCCCCCCC---------------ccccCCCCCCCcccccccc
Q 038867 54 ASIFYADFPPLPDFP---------------CMSSSSSSSSTPAAVKAIT 87 (721)
Q Consensus 54 ~s~fy~dfp~lpdfp---------------cmsssSssss~p~p~~~~~ 87 (721)
+-++|+-||||-.=| |.-|||||||+-.|..+-|
T Consensus 149 aEmYYeAFPPLsekpVcLqeImtvwNksk~csySsSSSsstap~~stdt 197 (1286)
T PF15376_consen 149 AEMYYEAFPPLSEKPVCLQEIMTVWNKSKVCSYSSSSSSSTAPQTSTDT 197 (1286)
T ss_pred HHHHHHhCCCccccchHHHHHHHHhhcccccccccCcccCCCCCCCCCC
Confidence 457899999999888 7777777766544444433
No 6
>KOG3018 consensus Malonyl-CoA decarboxylase [Carbohydrate transport and metabolism]
Probab=55.00 E-value=9.1 Score=41.63 Aligned_cols=58 Identities=26% Similarity=0.352 Sum_probs=48.8
Q ss_pred HHHHhhcCCCCCChhhh-ccccchhhhHHHHHHHhCCcHHHHHHHHHHH-HHHHHhhhhh
Q 038867 238 FLEWLKSNKETVSAEDL-RNVKIKKSTIECAAKRLGGGKEAMKQLLKLI-LEWVQTNHLQ 295 (721)
Q Consensus 238 F~EWLksNke~iSaeDl-R~iklkrsTIE~Aa~RLGggkeg~kqLLKLI-L~WVq~~hLQ 295 (721)
|+.||-+|-.+-|.+-= +|=|+--+||-.-..+=|+|-|.+..|||+| -||++...|-
T Consensus 210 F~~WLl~~L~sqs~~~~~~nEkv~~~~~sdiSe~~~n~~e~tl~LL~v~s~ew~~se~L~ 269 (362)
T KOG3018|consen 210 FMQWLLSKLSSQSRFAEDFNEKVLLPTLSDISESGSNGMEVTLNLLSVKSCEWATSERLL 269 (362)
T ss_pred HHHHHHHhcccccccchhhhhhhhchhhhhhhhccCccHHHHHHHHhhhcccccccHHHH
Confidence 99999888777665432 8888888999999999999999999999988 5899877653
No 7
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=50.69 E-value=75 Score=39.22 Aligned_cols=15 Identities=40% Similarity=0.470 Sum_probs=7.9
Q ss_pred ChhHHHHHHHHhhcCC
Q 038867 231 SDDLAMVFLEWLKSNK 246 (721)
Q Consensus 231 ~ddl~~vF~EWLksNk 246 (721)
-||+--|| +-|+++-
T Consensus 381 mDd~~~~f-~lL~n~v 395 (1102)
T KOG1924|consen 381 MDDANEVF-ELLANTV 395 (1102)
T ss_pred hccHHHHH-HHHHHhh
Confidence 45555555 4555543
No 8
>PF04614 Pex19: Pex19 protein family; InterPro: IPR006708 Peroxisome(s) form an intracellular compartment, bounded by a typical lipid bilayer membrane. Peroxisome functions are often specialised by organism and cell type; two widely distributed and well-conserved functions are H2O2-based respiration and fatty acid beta-oxidation. Other functions include ether lipid (plasmalogen) synthesis and cholesterol synthesis in animals, the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts. PEX genes encode the machinery ("peroxins") required to assemble the peroxisome. Membrane assembly and maintenance requires three of these (peroxins 3, 16, and 19) and may occur without the import of the matrix (lumen) enzymes. Matrix protein import follows a branched pathway of soluble recycling receptors, with one branch for each class of peroxisome targeting sequence (two are well characterised), and a common trunk for all. At least one of these receptors, Pex5p, enters and exits peroxisomes as it functions. Proliferation of the organelle is regulated by Pex11p. Peroxisome biogenesis is remarkably conserved among eukaryotes. A group of fatal, inherited neuropathologies are recognised as peroxisome biogenesis diseases. ; GO: 0005777 peroxisome; PDB: 2WL8_B 2W85_B.
Probab=45.42 E-value=23 Score=37.09 Aligned_cols=40 Identities=25% Similarity=0.394 Sum_probs=29.7
Q ss_pred hhHHHHHHHHhhcCCCCCChhhhccccchhhhHHHHHHHh
Q 038867 232 DDLAMVFLEWLKSNKETVSAEDLRNVKIKKSTIECAAKRL 271 (721)
Q Consensus 232 ddl~~vF~EWLksNke~iSaeDlR~iklkrsTIE~Aa~RL 271 (721)
-||..-|=+||+.||+.+|+||+-+-+---..|..-...+
T Consensus 146 Kel~~kyP~wL~~n~~~l~~ed~~rY~~Q~~~v~~I~~~f 185 (248)
T PF04614_consen 146 KELRDKYPEWLEENKSKLSAEDYERYEKQYELVKEICAIF 185 (248)
T ss_dssp HHHHHHHHHHHHHHCCCS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhHHHHHhCcCcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4788889999999999999999987765555554444444
No 9
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=39.28 E-value=46 Score=26.14 Aligned_cols=28 Identities=32% Similarity=0.440 Sum_probs=22.0
Q ss_pred hHHhhhcCCCCCCEEEEEEecCCCeEEEE
Q 038867 646 GDFVKANGLQEGDFIVIYSDVKCGKYLIR 674 (721)
Q Consensus 646 sdFVRsKgLqaGD~IVFyrd~snGky~Ig 674 (721)
.+|.++.+|++||.|.|.-+ .+|++.|.
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~-~~g~i~i~ 40 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVE-GDGKIVIR 40 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEE-TTSEEEEE
T ss_pred HHHHHHcCCCCCCEEEEEEe-CCCEEEEE
Confidence 47888999999999999775 35566663
No 10
>PF08610 Pex16: Peroxisomal membrane protein (Pex16); InterPro: IPR013919 Pex16 is a peripheral protein located at the matrix face of the peroxisomal membrane [].
Probab=36.90 E-value=34 Score=37.08 Aligned_cols=33 Identities=36% Similarity=0.535 Sum_probs=27.6
Q ss_pred hHHHHHHHhCCcH---------HHHHHHHHHHHHHHHhhhhh
Q 038867 263 TIECAAKRLGGGK---------EAMKQLLKLILEWVQTNHLQ 295 (721)
Q Consensus 263 TIE~Aa~RLGggk---------eg~kqLLKLIL~WVq~~hLQ 295 (721)
-+|=+|+|+||-+ |++|-+|+|+|=++.+++.+
T Consensus 92 l~Em~A~r~~G~~~rW~vI~~iE~iKa~lRL~Ll~~~~~~~l 133 (335)
T PF08610_consen 92 LVEMAARRKWGEKGRWRVIVLIEAIKAILRLLLLRITKSRML 133 (335)
T ss_pred HHHHHHHHhcCCcceehhHHHHHHHHHHHHHHHHHHhcCCCc
Confidence 4688999999988 99999999999776665554
No 11
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=36.71 E-value=50 Score=29.80 Aligned_cols=48 Identities=21% Similarity=0.367 Sum_probs=39.6
Q ss_pred ChhHHHHHHHHhhcCCCCCChhhhccccchhh-hHHHHHHHhCCcHHHH
Q 038867 231 SDDLAMVFLEWLKSNKETVSAEDLRNVKIKKS-TIECAAKRLGGGKEAM 278 (721)
Q Consensus 231 ~ddl~~vF~EWLksNke~iSaeDlR~iklkrs-TIE~Aa~RLGggkeg~ 278 (721)
.+++.....+=++..+.-++++.||.+|.++- |.+.+|++||.++...
T Consensus 47 ~~~~~~~i~~~~~~~~~~~~~~~i~~~r~~~gltq~~lA~~lg~~~~ti 95 (127)
T TIGR03830 47 SKRNSAALADFYRKVDGLLTPPEIRRIRKKLGLSQREAAELLGGGVNAF 95 (127)
T ss_pred HHHHHHHHHHHHHHccCCcCHHHHHHHHHHcCCCHHHHHHHhCCCHHHH
Confidence 56777777888899999999999999977655 8999999999887543
No 12
>PF14097 SpoVAE: Stage V sporulation protein AE1
Probab=34.18 E-value=30 Score=35.50 Aligned_cols=29 Identities=34% Similarity=0.496 Sum_probs=21.6
Q ss_pred chhhhHHHHHHHhCCc----------HHHHHHHHHHHHH
Q 038867 259 IKKSTIECAAKRLGGG----------KEAMKQLLKLILE 287 (721)
Q Consensus 259 lkrsTIE~Aa~RLGgg----------keg~kqLLKLIL~ 287 (721)
.-|.|||.|||++||= +=.=.||.+||+.
T Consensus 11 ~A~ravE~aa~~iGgRCIS~S~GNPT~lsG~elV~lIk~ 49 (180)
T PF14097_consen 11 YAKRAVEIAAKNIGGRCISQSAGNPTPLSGEELVELIKQ 49 (180)
T ss_pred HHHHHHHHHHHHhCcEEEeccCCCCCcCCHHHHHHHHHh
Confidence 3578999999999972 2233679999973
No 13
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=30.37 E-value=70 Score=28.97 Aligned_cols=33 Identities=18% Similarity=0.246 Sum_probs=21.0
Q ss_pred hhHHhhhcCCCCCCEEEEEEecCCCeEEEEEEE
Q 038867 645 TGDFVKANGLQEGDFIVIYSDVKCGKYLIRGVK 677 (721)
Q Consensus 645 WsdFVRsKgLqaGD~IVFyrd~snGky~IggRR 677 (721)
=.+|+++++|..||.|.++|.+.-=-..++..+
T Consensus 41 N~~~i~~~~i~~Gd~V~V~raGdVIP~I~~vv~ 73 (82)
T PF03120_consen 41 NYDYIKELDIRIGDTVLVTRAGDVIPKIVGVVK 73 (82)
T ss_dssp SHHHHHHTT-BBT-EEEEEEETTTEEEEEEE-G
T ss_pred CHHHHHHcCCCCCCEEEEEECCCccceEeEeeh
Confidence 468999999999999999985321134444443
No 14
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=29.82 E-value=2.5e+02 Score=27.09 Aligned_cols=76 Identities=18% Similarity=0.297 Sum_probs=53.6
Q ss_pred eeeeccccCCCCCCCceeecHhHHhhh--CCCCcCCCCeEEEEEEcCCCcEEEEEEeeeeeCCCC--CCceeecChhHHh
Q 038867 574 LLQKVLKQSDVGNLGRIVLPKKEAETH--LPELEARDGISIAMEDIGTSRVWNMRYSFRFWPNNK--SRMYLLENTGDFV 649 (721)
Q Consensus 574 LF~KvLT~SDVgklGRLVIPKk~AEa~--LP~Ld~~~Gi~L~veDi~tGkvW~FRys~RYW~Nnk--SRmYLLTGWsdFV 649 (721)
+=.-+.|..|+..-|.+.|..+..++- +| .-.|.+.++..|.-|. .|.|. +. |+...|.| .
T Consensus 9 iHratVT~a~L~YeGSitID~~Ll~aagi~~------~E~V~I~Nv~NG~Rf~-TYvI~----g~~gSg~I~lNG----A 73 (111)
T cd06919 9 IHRATVTEADLNYEGSITIDEDLLEAAGILP------YEKVLVVNVNNGARFE-TYVIP----GERGSGVICLNG----A 73 (111)
T ss_pred ccceEEeccccccceeEEECHHHHHhcCCCC------CCEEEEEECCCCcEEE-EEEEE----cCCCCCEEEeCC----H
Confidence 334578999999999999999988863 44 3378888986676332 23222 44 46666666 4
Q ss_pred hhcCCCCCCEEEEEE
Q 038867 650 KANGLQEGDFIVIYS 664 (721)
Q Consensus 650 RsKgLqaGD~IVFyr 664 (721)
-++..+.||.|+|..
T Consensus 74 AAr~~~~GD~vII~s 88 (111)
T cd06919 74 AARLGQPGDRVIIMA 88 (111)
T ss_pred HHhcCCCCCEEEEEE
Confidence 578889999999864
No 15
>PF12095 DUF3571: Protein of unknown function (DUF3571); InterPro: IPR021954 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 85 to 97 amino acids in length. ; PDB: 2KRX_A.
Probab=28.51 E-value=64 Score=29.56 Aligned_cols=35 Identities=29% Similarity=0.512 Sum_probs=27.0
Q ss_pred ChhHHHHHHHHhhcCCCCCChhhhccccchhhhHHHHHHHh
Q 038867 231 SDDLAMVFLEWLKSNKETVSAEDLRNVKIKKSTIECAAKRL 271 (721)
Q Consensus 231 ~ddl~~vF~EWLksNke~iSaeDlR~iklkrsTIE~Aa~RL 271 (721)
.+||-..+-+||.. .+.+ +.||.+ .+|+++||++|
T Consensus 26 ~~Ell~~Lk~~L~~-~~~L-P~dL~~----~~s~~~qa~~L 60 (83)
T PF12095_consen 26 PEELLEKLKEWLQN-QDDL-PPDLAK----FSSVEEQAQYL 60 (83)
T ss_dssp HHHHHHHHHHHHHH-TTTS--HHHHH-------HHHHHHHH
T ss_pred HHHHHHHHHHHHHc-CCCC-CHHHHh----CCCHHHHHHHH
Confidence 68998999999998 7777 888874 58999999987
No 16
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=28.29 E-value=2.4e+02 Score=35.19 Aligned_cols=7 Identities=43% Similarity=0.952 Sum_probs=3.9
Q ss_pred ccccchh
Q 038867 99 SSAASWA 105 (721)
Q Consensus 99 ssaaswa 105 (721)
|-.-||+
T Consensus 171 ~npVSwv 177 (1102)
T KOG1924|consen 171 SNPVSWV 177 (1102)
T ss_pred CCccHHH
Confidence 3446773
No 17
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=28.10 E-value=70 Score=29.97 Aligned_cols=27 Identities=15% Similarity=0.224 Sum_probs=16.5
Q ss_pred cCCCCCCEEEEEEecCCCeEEEEEEEc
Q 038867 652 NGLQEGDFIVIYSDVKCGKYLIRGVKV 678 (721)
Q Consensus 652 KgLqaGD~IVFyrd~snGky~IggRR~ 678 (721)
++++.||.|+||..+..++-++++.++
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V 64 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEV 64 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEE
Confidence 399999999999875234566666555
No 18
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=27.62 E-value=67 Score=23.71 Aligned_cols=27 Identities=30% Similarity=0.443 Sum_probs=19.7
Q ss_pred hHHHHHHHhCCcHHHHHHHHHHHHHHHHhhhhhh
Q 038867 263 TIECAAKRLGGGKEAMKQLLKLILEWVQTNHLQK 296 (721)
Q Consensus 263 TIE~Aa~RLGggkeg~kqLLKLIL~WVq~~hLQk 296 (721)
||+.||+.||=++.- |..||.+..+..
T Consensus 3 t~~e~a~~lgis~~t-------i~~~~~~g~i~~ 29 (49)
T TIGR01764 3 TVEEAAEYLGVSKDT-------VYRLIHEGELPA 29 (49)
T ss_pred CHHHHHHHHCCCHHH-------HHHHHHcCCCCe
Confidence 789999999998865 445566665543
No 19
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=27.54 E-value=72 Score=29.08 Aligned_cols=77 Identities=18% Similarity=0.257 Sum_probs=45.2
Q ss_pred cceeeeccccCCCC--CCCceeecHhHHhhhCCCCcCCCCeEEEEEEcCCCcEEEEEEeeeeeCCCCCCceeecChhHHh
Q 038867 572 RFLLQKVLKQSDVG--NLGRIVLPKKEAETHLPELEARDGISIAMEDIGTSRVWNMRYSFRFWPNNKSRMYLLENTGDFV 649 (721)
Q Consensus 572 ~~LF~KvLT~SDVg--klGRLVIPKk~AEa~LP~Ld~~~Gi~L~veDi~tGkvW~FRys~RYW~NnkSRmYLLTGWsdFV 649 (721)
..+|-|+++.+-+. -.++|+|+++.. +++.+-.+....+.+... ... .. ..|.
T Consensus 18 ~i~~G~V~s~~PL~I~i~~~liL~~~~L--~i~~~l~~~~~~~~~~~~-~~~--------------~~--------~~i~ 72 (100)
T PF10844_consen 18 DIVIGTVVSVPPLKIKIDQKLILDKDFL--IIPELLKDYTRDITIEHN-SET--------------DN--------ITIT 72 (100)
T ss_pred eeEEEEEEecccEEEEECCeEEEchHHE--EeehhccceEEEEEEecc-ccc--------------cc--------eeEE
Confidence 44799999999733 345699988643 344432223233333322 010 00 0155
Q ss_pred hhcCCCCCCEEEEEEecCCCeEEE
Q 038867 650 KANGLQEGDFIVIYSDVKCGKYLI 673 (721)
Q Consensus 650 RsKgLqaGD~IVFyrd~snGky~I 673 (721)
-..+|++||.|.+++.....+|.|
T Consensus 73 ~~~~Lk~GD~V~ll~~~~gQ~yiV 96 (100)
T PF10844_consen 73 FTDGLKVGDKVLLLRVQGGQKYIV 96 (100)
T ss_pred EecCCcCCCEEEEEEecCCCEEEE
Confidence 667999999999998643447776
No 20
>KOG4752 consensus Ribosomal protein L41 [Translation, ribosomal structure and biogenesis]
Probab=27.41 E-value=33 Score=25.17 Aligned_cols=11 Identities=64% Similarity=0.800 Sum_probs=7.6
Q ss_pred HHHHHHHhhhc
Q 038867 469 ARKKRMARQRR 479 (721)
Q Consensus 469 ARKkRMARQRR 479 (721)
=|||||.|-.|
T Consensus 5 wrkkrmrrlkr 15 (26)
T KOG4752|consen 5 WRKKRMRRLKR 15 (26)
T ss_pred HHHHHHHHHHH
Confidence 48888876543
No 21
>PRK11347 antitoxin ChpS; Provisional
Probab=27.18 E-value=1.4e+02 Score=26.87 Aligned_cols=41 Identities=15% Similarity=0.261 Sum_probs=29.1
Q ss_pred eeeCCCCCCceeecChhHHhhhcCCCCCCEEEEEEecCCCeEEEEEE
Q 038867 630 RFWPNNKSRMYLLENTGDFVKANGLQEGDFIVIYSDVKCGKYLIRGV 676 (721)
Q Consensus 630 RYW~NnkSRmYLLTGWsdFVRsKgLqaGD~IVFyrd~snGky~IggR 676 (721)
+-| |.|.-..|- ..|++.-+|.+||.|.+... .|.+.|.-+
T Consensus 6 ~kw--GNS~~vriP--k~il~~l~l~~G~~v~i~v~--~~~iii~p~ 46 (83)
T PRK11347 6 KRW--GNSAGMVIP--NIVMKELNLQPGQSVEAQVS--NNQLILTPI 46 (83)
T ss_pred EEE--cCceeEEeC--HHHHHHcCCCCCCEEEEEEE--CCEEEEEEC
Confidence 668 445434443 58999999999999977653 577777544
No 22
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=26.42 E-value=1.5e+02 Score=25.70 Aligned_cols=39 Identities=21% Similarity=0.353 Sum_probs=28.0
Q ss_pred eeeCCCCCCceeecChhHHhhhcCCCCCCEEEEEEecCCCeEEEE
Q 038867 630 RFWPNNKSRMYLLENTGDFVKANGLQEGDFIVIYSDVKCGKYLIR 674 (721)
Q Consensus 630 RYW~NnkSRmYLLTGWsdFVRsKgLqaGD~IVFyrd~snGky~Ig 674 (721)
+-| |+| +.++==.+++..-+|.+||.|.|... .|.+.|.
T Consensus 4 ~k~--GNS--~~vtIPk~i~~~lgl~~Gd~v~v~~~--~~~iii~ 42 (74)
T TIGR02609 4 RKV--GNS--LVVTLPKEVLESLGLKEGDTLYVDEE--EGGLKLK 42 (74)
T ss_pred EEE--CCe--eEEEECHHHHHHcCcCCCCEEEEEEE--CCEEEEE
Confidence 557 445 44553468999999999999987654 5667764
No 23
>PF06078 DUF937: Bacterial protein of unknown function (DUF937); InterPro: IPR009282 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 1Z67_A.
Probab=26.27 E-value=1.2e+02 Score=28.50 Aligned_cols=60 Identities=22% Similarity=0.304 Sum_probs=41.2
Q ss_pred hhHHHHHHHHhhcC-CCCCChhhhccccchhhhHHHHHHHhCCcHHHHHHHHHHHHHHHHh
Q 038867 232 DDLAMVFLEWLKSN-KETVSAEDLRNVKIKKSTIECAAKRLGGGKEAMKQLLKLILEWVQT 291 (721)
Q Consensus 232 ddl~~vF~EWLksN-ke~iSaeDlR~iklkrsTIE~Aa~RLGggkeg~kqLLKLIL~WVq~ 291 (721)
..+...+..|+-.- -..|+++.|+.|==-...|+.-|+++|-.++..++||-.+|-=|-.
T Consensus 72 ~g~~~~~~sw~~~~~~~~~g~~~l~~lfg~~~~~~~lA~~tGl~~~~~~~lL~~~lP~vv~ 132 (137)
T PF06078_consen 72 AGLGGQVQSWLGQGPNQPIGPEILNSLFGGDDVIQQLAQQTGLSPDSAQQLLAMLLPLVVD 132 (137)
T ss_dssp TT-HHHHHHHH-SS------HHHHHHHH--HHHHHHHHHHHT--HHHHHHHHHHHHHHHHH
T ss_pred CCccHHHHhhccCCCCCCCCHHHHHHHhCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34566788999732 2357999999885359999999999999999999999999866543
No 24
>PF05298 Bombinin: Bombinin; InterPro: IPR007962 This family consists of Bombinin and Maximin proteins from Bombina maxima (Giant fire-bellied toad). Two groups of antimicrobial peptides have been isolated from skin secretions of B. maxima. Peptides in the first group, named maximins 1, 2, 3, 4 and 5, are structurally related to bombinin-like peptides (BLPs). Unlike BLPs, sequence variations in maximins occurred all through the molecules. In addition to the potent antimicrobial activity, cytotoxicity against tumour cells and spermicidal action of maximins, maximin 3 possessed a significant anti-Simian-Human immunodeficiency virus (HIV) activity. Maximins 1 and 3 have been found to be toxic to mice. Peptides in the second group, termed maximins H1, H2, H3 and H4, are homologous with bombinin H peptides [].; GO: 0042742 defense response to bacterium, 0005576 extracellular region; PDB: 2AP7_A.
Probab=25.89 E-value=23 Score=34.34 Aligned_cols=48 Identities=33% Similarity=0.508 Sum_probs=0.0
Q ss_pred cCCCCCChhhhccccchhhhHHHHHHHhCCcHHHHHHHHHHHHHHHHhhhhhhhhhhh
Q 038867 244 SNKETVSAEDLRNVKIKKSTIECAAKRLGGGKEAMKQLLKLILEWVQTNHLQKRRMRE 301 (721)
Q Consensus 244 sNke~iSaeDlR~iklkrsTIE~Aa~RLGggkeg~kqLLKLIL~WVq~~hLQkkR~~~ 301 (721)
|-||-+-.|-||.||= | -++-|||||-+.|-++|-+- .++++.||.-+
T Consensus 29 sqrdvleeeslreirg----I--G~~il~~~Kta~kg~~k~la----~~~~~gkRtAe 76 (141)
T PF05298_consen 29 SQRDVLEEESLREIRG----I--GGKILGGGKTALKGAAKELA----STYANGKRTAE 76 (141)
T ss_dssp ----------------------------------------------------------
T ss_pred hHHhhhhHHhHHHHHh----h--hHHHHHhHHHHHHHHHHHHH----HHHhccccchH
Confidence 4566667788888863 2 46789999999999988643 47889999877
No 25
>PF09853 DUF2080: Putative transposon-encoded protein (DUF2080); InterPro: IPR019205 This entry, found in various hypothetical archaeal proteins, has no known function.
Probab=24.43 E-value=44 Score=28.39 Aligned_cols=37 Identities=27% Similarity=0.522 Sum_probs=31.3
Q ss_pred hccCCCCCCcccceeeeccccCCCCCCCcee--ecHhHHhh
Q 038867 561 RRQGWKPEKNLRFLLQKVLKQSDVGNLGRIV--LPKKEAET 599 (721)
Q Consensus 561 r~qg~k~~k~~~~LF~KvLT~SDVgklGRLV--IPKk~AEa 599 (721)
|+.+|....+....|.++.++. |+.+++. +||++.-+
T Consensus 4 ~k~~w~k~~~i~~~~~~~vk~~--Gnsa~v~p~lPkeyiGK 42 (53)
T PF09853_consen 4 KKKTWRKPRNIEPTFIGVVKPF--GNSARVYPSLPKEYIGK 42 (53)
T ss_pred ecccccceeeEEEEEEEEEEec--CcceeEcCCCChHHcCc
Confidence 5667877788888999999998 8889999 99999744
No 26
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=23.59 E-value=3.8e+02 Score=26.50 Aligned_cols=76 Identities=17% Similarity=0.361 Sum_probs=53.9
Q ss_pred eeeeccccCCCCCCCceeecHhHHhh--hCCCCcCCCCeEEEEEEcCCCcEEEEEEeeeeeCCCC--CCceeecChhHHh
Q 038867 574 LLQKVLKQSDVGNLGRIVLPKKEAET--HLPELEARDGISIAMEDIGTSRVWNMRYSFRFWPNNK--SRMYLLENTGDFV 649 (721)
Q Consensus 574 LF~KvLT~SDVgklGRLVIPKk~AEa--~LP~Ld~~~Gi~L~veDi~tGkvW~FRys~RYW~Nnk--SRmYLLTGWsdFV 649 (721)
+=.-+.|..|+..-|.+.|..+..++ ++|. -.|.+.++..|.-|. .|.|. ++ |+...|.| .
T Consensus 10 IHratVT~a~L~Y~GSItID~~Lm~aagi~p~------E~V~V~Nv~NG~Rf~-TYvI~----G~~GSg~I~lNG----A 74 (126)
T TIGR00223 10 LHRATVTHANLNYEGSITIDEDLLDAAGILEN------EKVDIVNVNNGKRFS-TYAIA----GKRGSRIICVNG----A 74 (126)
T ss_pred hcceEEeccccccceeEEECHHHHHhcCCCCC------CEEEEEECCCCcEEE-EEEEE----cCCCCCEEEeCC----H
Confidence 33457899999999999999998886 3442 378888986776443 23222 44 45666666 4
Q ss_pred hhcCCCCCCEEEEEE
Q 038867 650 KANGLQEGDFIVIYS 664 (721)
Q Consensus 650 RsKgLqaGD~IVFyr 664 (721)
-++..+.||.|+|..
T Consensus 75 AArl~~~GD~VII~s 89 (126)
T TIGR00223 75 AARCVSVGDIVIIAS 89 (126)
T ss_pred HHhcCCCCCEEEEEE
Confidence 578889999999854
No 27
>smart00719 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.
Probab=22.76 E-value=44 Score=30.77 Aligned_cols=17 Identities=18% Similarity=0.516 Sum_probs=11.6
Q ss_pred CChhhhccccchhhhHH
Q 038867 249 VSAEDLRNVKIKKSTIE 265 (721)
Q Consensus 249 iSaeDlR~iklkrsTIE 265 (721)
|+.|||..|+|+|++||
T Consensus 2 ~~l~~l~~i~L~R~~l~ 18 (109)
T smart00719 2 IVFDNLNLLRLRRSLVE 18 (109)
T ss_pred CChHHhheEEEEHHHHH
Confidence 56677777777777655
No 28
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=22.69 E-value=95 Score=39.88 Aligned_cols=102 Identities=18% Similarity=0.248 Sum_probs=71.4
Q ss_pred cchhhhccCCCCCCcccceeeeccccCCCCCCCceeecHhHHhhh-CCCCcC-----------------CCCeEEEEEEc
Q 038867 556 QPASDRRQGWKPEKNLRFLLQKVLKQSDVGNLGRIVLPKKEAETH-LPELEA-----------------RDGISIAMEDI 617 (721)
Q Consensus 556 ~~~~~r~qg~k~~k~~~~LF~KvLT~SDVgklGRLVIPKk~AEa~-LP~Ld~-----------------~~Gi~L~veDi 617 (721)
.+.++|=+|.=.+|..-+.++.|.|..---++.-+-||+.-|..+ ||+... ..|..-.+.|-
T Consensus 322 KgkegriRgnLmGKRvDFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~NidrLqeLV~~g~~~~pgakyiird~ 401 (1605)
T KOG0260|consen 322 KGKEGRIRGNLMGKRVDFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNIDRLQELVRRGLLEHPGAKYIIRDN 401 (1605)
T ss_pred ccccchhhhcccccccCcceeeeecCCCCcchhcccCcHHHHhhccCcceeccccHHHHHHHhhCCCCCCCCcceeeecC
Confidence 566678778878899999999999987766789999999999876 887632 23444455553
Q ss_pred CCCcEEEEEEeeeeeCCCCCCceeecChhHHhhhcCCCCCCEEEEEEecC
Q 038867 618 GTSRVWNMRYSFRFWPNNKSRMYLLENTGDFVKANGLQEGDFIVIYSDVK 667 (721)
Q Consensus 618 ~tGkvW~FRys~RYW~NnkSRmYLLTGWsdFVRsKgLqaGD~IVFyrd~s 667 (721)
|..-..|| - +.++..+|=+||.. +++|+-||+|+|=|-..
T Consensus 402 --G~Ridlr~----~-~~~~d~~Lq~G~kV---eRhl~DGD~VlfNRqPS 441 (1605)
T KOG0260|consen 402 --GDRIDLRY----H-KRAGDIHLQPGYKV---ERHLMDGDVVLFNRQPS 441 (1605)
T ss_pred --CcEEEEee----c-CCccccccccccEE---EEeeccCCEEEEcCCCc
Confidence 65555555 2 22344444447654 57899999998866543
No 29
>cd00213 S-100 S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents th
Probab=22.61 E-value=2e+02 Score=24.49 Aligned_cols=65 Identities=22% Similarity=0.334 Sum_probs=46.4
Q ss_pred ChhHHHHHHHHhh--cCCCCCChhhhcccc---ch--------hhhHHHHHHHh---CCcHHHHHHHHHHHHHHHHhhhh
Q 038867 231 SDDLAMVFLEWLK--SNKETVSAEDLRNVK---IK--------KSTIECAAKRL---GGGKEAMKQLLKLILEWVQTNHL 294 (721)
Q Consensus 231 ~ddl~~vF~EWLk--sNke~iSaeDlR~ik---lk--------rsTIE~Aa~RL---Gggkeg~kqLLKLIL~WVq~~hL 294 (721)
.++|..+|-.+=+ .++..|+.++|+.+- +. ...|+..-+.+ +.|+=...+++.++..++--.||
T Consensus 7 ~~~l~~~F~~~D~~~~~~G~Is~~el~~~l~~~~g~~~~~~~~~~ei~~i~~~~d~~~~g~I~f~eF~~~~~~~~~~~~~ 86 (88)
T cd00213 7 IETIIDVFHKYSGKEGDKDTLSKKELKELLETELPNFLKNQKDPEAVDKIMKDLDVNKDGKVDFQEFLVLIGKLAVACHE 86 (88)
T ss_pred HHHHHHHHHHHhhccCCCCcCcHHHHHHHHHHHhhhhccCCCCHHHHHHHHHHhccCCCCcCcHHHHHHHHHHHHHHHhh
Confidence 4678899999999 788899999999873 11 22233333333 45677778888888888888887
Q ss_pred h
Q 038867 295 Q 295 (721)
Q Consensus 295 Q 295 (721)
|
T Consensus 87 ~ 87 (88)
T cd00213 87 F 87 (88)
T ss_pred h
Confidence 6
No 30
>TIGR02242 tail_TIGR02242 phage tail protein domain. This model describes a region of sequence similarity shared by a number of uncharacterized proteins in bacterial genomes, including Geobacter sulfurreducens PCA, Mesorhizobium loti, Streptomyces coelicolor A3(2), Gloeobacter violaceus PCC 7421, and Myxococcus xanthus. In all cases, the genomic region resembles a phage tail region, based on tentative identifications of neighboring genes. A region of this domain resembles a region of TIGR01634, another phage tail protein model.
Probab=21.95 E-value=75 Score=30.61 Aligned_cols=59 Identities=24% Similarity=0.320 Sum_probs=39.5
Q ss_pred hhHHHHHHHHhhcCCCCCChhhhccccchhhhHHHHHH--HhCCcHHHHHHHHHH-------HHHHHHh
Q 038867 232 DDLAMVFLEWLKSNKETVSAEDLRNVKIKKSTIECAAK--RLGGGKEAMKQLLKL-------ILEWVQT 291 (721)
Q Consensus 232 ddl~~vF~EWLksNke~iSaeDlR~iklkrsTIE~Aa~--RLGggkeg~kqLLKL-------IL~WVq~ 291 (721)
+--+.-||.||-..-. +.-.+==..--||..|..|+. |.=|.+.|+..+|++ |.||-|.
T Consensus 45 ~~~P~~~Lp~LA~w~g-~~~d~~w~~~~kR~~I~~a~~l~r~rGT~~gLr~~l~~~~G~~~~i~E~f~~ 112 (130)
T TIGR02242 45 ETAPAPFLDFLAQWLG-NPFDDELDVPQLRRLVARAADIYRQRGTRLGLRELLRLYLGIEPRIVEPFAS 112 (130)
T ss_pred hhCCHHHHHHHHHHhC-CCCCCCCCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcCCCcEEeeehhc
Confidence 3445568888886533 221122235678888877764 677999999999998 6677654
No 31
>COG5297 CelA Cellobiohydrolase A (1,4-beta-cellobiosidase A) [Carbohydrate transport and metabolism]
Probab=21.36 E-value=53 Score=37.43 Aligned_cols=14 Identities=50% Similarity=0.565 Sum_probs=9.5
Q ss_pred CCCccccccccccc
Q 038867 77 SSTPAAVKAITSSA 90 (721)
Q Consensus 77 ss~p~p~~~~~~s~ 90 (721)
|.+|+|.|-|+++-
T Consensus 455 sp~p~p~~ni~~~i 468 (544)
T COG5297 455 SPNPDPTKNITSSI 468 (544)
T ss_pred CCCCCCccCceeEE
Confidence 34477888887664
No 32
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=21.27 E-value=1.3e+02 Score=28.83 Aligned_cols=41 Identities=15% Similarity=0.293 Sum_probs=27.1
Q ss_pred CCceeecC--hhH-----HhhhcCCCCCCEEEEEEe-cCCCeEEEEEEE
Q 038867 637 SRMYLLEN--TGD-----FVKANGLQEGDFIVIYSD-VKCGKYLIRGVK 677 (721)
Q Consensus 637 SRmYLLTG--Wsd-----FVRsKgLqaGD~IVFyrd-~snGky~IggRR 677 (721)
...++|.| +.. |-+=++|++||.|.+... ...=.|.|...+
T Consensus 49 ~Gn~viaGH~~~~g~~~~F~~L~~l~~GD~I~v~~~~g~~~~Y~V~~~~ 97 (144)
T cd05829 49 KGTAVLAGHVDSRGGPAVFFRLGDLRKGDKVEVTRADGQTATFRVDRVE 97 (144)
T ss_pred CCCEEEEEecCCCCCChhhcchhcCCCCCEEEEEECCCCEEEEEEeEEE
Confidence 45677764 333 999999999999998662 212256665443
No 33
>PF12970 DUF3858: Domain of Unknown Function with PDB structure (DUF3858); InterPro: IPR024544 This domain of unknown function is structurally similar to part of neuropilin-2. The proteins it occurs in have not yet been functionally characterised.; PDB: 3KD4_A.
Probab=20.31 E-value=68 Score=31.05 Aligned_cols=33 Identities=24% Similarity=0.410 Sum_probs=24.2
Q ss_pred hhhccccchhhhHHHHHHHhCCcHHHHHHHHHHHHHHHHhhh
Q 038867 252 EDLRNVKIKKSTIECAAKRLGGGKEAMKQLLKLILEWVQTNH 293 (721)
Q Consensus 252 eDlR~iklkrsTIE~Aa~RLGggkeg~kqLLKLIL~WVq~~h 293 (721)
+=-|+|+|||+-|.=| --+++-.||.||--+++
T Consensus 79 ~V~rsL~L~KqlitPa---------EY~afr~L~~eW~d~~~ 111 (116)
T PF12970_consen 79 KVTRSLELKKQLITPA---------EYPAFRSLMTEWTDVDG 111 (116)
T ss_dssp EEEEEEEE--SEE-HH---------HHHHHHHHHHHHH-GGG
T ss_pred EEEEEEEEeeeeeCch---------hHHHHHHHHHHhccCCC
Confidence 4469999999999887 46789999999998876
No 34
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=20.27 E-value=1.6e+02 Score=26.18 Aligned_cols=27 Identities=30% Similarity=0.550 Sum_probs=21.8
Q ss_pred HHhhhcCCCCCCEEEEEEecCCCeEEE
Q 038867 647 DFVKANGLQEGDFIVIYSDVKCGKYLI 673 (721)
Q Consensus 647 dFVRsKgLqaGD~IVFyrd~snGky~I 673 (721)
..-+.-+|++||.|.|+.+...|++.|
T Consensus 21 eiR~~lgi~~Gd~lei~~~~~~~~ivl 47 (89)
T COG2002 21 EIREALGIKEGDVLEIIVDGDGGRIVL 47 (89)
T ss_pred HHHHHhCCCCCCEEEEEEeCCCCEEEE
Confidence 556778999999999999866677555
No 35
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=20.12 E-value=5.6e+02 Score=21.96 Aligned_cols=66 Identities=12% Similarity=0.020 Sum_probs=39.2
Q ss_pred CCeEEEEEEcCCCcEEEEEEeeeeeCCCCCCceeecChhHHhhh-cCCCCCCEEEEEEecCCCeEEEEEEE
Q 038867 608 DGISIAMEDIGTSRVWNMRYSFRFWPNNKSRMYLLENTGDFVKA-NGLQEGDFIVIYSDVKCGKYLIRGVK 677 (721)
Q Consensus 608 ~Gi~L~veDi~tGkvW~FRys~RYW~NnkSRmYLLTGWsdFVRs-KgLqaGD~IVFyrd~snGky~IggRR 677 (721)
-|-.|.++|.+++..-.|.++.. |. .+...-.++-.+..-++ -+.++||.|.+-- ..|++.+++.+
T Consensus 8 ~Gs~V~l~~~~~~~~~~~~lv~~-~~-~~~~~~~IS~~SPLG~ALlG~~~Gd~v~~~~--~~g~~~~~I~~ 74 (77)
T PF01272_consen 8 IGSTVTLKDLDDGEEETYTLVGP-DE-ADPDNGKISIDSPLGKALLGKKVGDEVEVEL--PGGERKYEILE 74 (77)
T ss_dssp TTEEEEEEETTTTEEEEEEEE-G-GG--BSTSTEEETTSHHHHHHTT-BTT-EEEEEE--TTBEEEEEEEE
T ss_pred eCCEEEEEECCCCCEEEEEEEeE-hH-hCCceeEEEecCHHHHHhcCCCCCCEEEEEe--CCceEEEEEEE
Confidence 35688999976888888877322 32 22222244545555554 5899999998754 46666666654
Done!