Query 021945
Match_columns 305
No_of_seqs 308 out of 1556
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 06:50:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021945.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021945hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00018 AP2 DNA-binding domain 99.8 1E-19 2.2E-24 133.3 7.2 59 31-89 1-61 (61)
2 PF02362 B3: B3 DNA binding do 99.8 2.1E-18 4.6E-23 136.6 11.6 99 164-267 1-99 (100)
3 smart00380 AP2 DNA-binding dom 99.8 1.1E-18 2.4E-23 129.1 8.2 60 32-91 1-62 (64)
4 PHA00280 putative NHN endonucl 99.7 1.2E-16 2.7E-21 132.3 6.5 70 14-84 50-120 (121)
5 PF00847 AP2: AP2 domain; Int 99.1 1.4E-10 3E-15 83.0 5.6 50 31-80 1-56 (56)
6 PF03754 DUF313: Domain of unk 99.0 7.8E-10 1.7E-14 90.9 8.1 79 159-238 19-114 (114)
7 PF09217 EcoRII-N: Restriction 98.3 1.2E-05 2.6E-10 69.0 11.5 92 161-253 7-113 (156)
8 PF10844 DUF2577: Protein of u 79.3 11 0.00024 30.0 7.4 80 159-263 16-97 (100)
9 PF14657 Integrase_AP2: AP2-li 66.0 20 0.00043 24.3 5.1 36 43-78 1-42 (46)
10 PF04014 Antitoxin-MazE: Antid 55.5 19 0.00041 24.4 3.5 27 234-263 14-40 (47)
11 PF09853 DUF2080: Putative tra 55.3 19 0.00042 25.7 3.5 30 157-188 11-42 (53)
12 PHA02601 int integrase; Provis 47.0 27 0.00058 32.7 4.2 42 35-77 2-46 (333)
13 COG3466 ISA1214 Putative trans 43.2 22 0.00047 25.2 2.2 30 157-188 14-43 (52)
14 PF08846 DUF1816: Domain of un 40.7 55 0.0012 24.6 4.1 29 43-71 9-39 (68)
15 PRK09570 rpoH DNA-directed RNA 40.0 42 0.0009 26.0 3.5 32 233-266 44-75 (79)
16 PF05036 SPOR: Sporulation rel 38.9 19 0.00041 25.8 1.5 22 53-74 44-65 (76)
17 PF01191 RNA_pol_Rpb5_C: RNA p 37.6 57 0.0012 24.9 3.9 31 233-265 41-71 (74)
18 PF02261 Asp_decarbox: Asparta 36.4 2.5E+02 0.0054 23.3 9.6 75 163-251 10-89 (116)
19 PRK11347 antitoxin ChpS; Provi 33.8 1.2E+02 0.0026 23.4 5.3 43 215-264 3-45 (83)
20 TIGR02609 doc_partner putative 32.1 99 0.0022 23.1 4.5 33 218-253 4-36 (74)
21 PF13356 DUF4102: Domain of un 32.0 2.2E+02 0.0048 21.6 6.6 37 38-74 29-71 (89)
22 PRK05449 aspartate alpha-decar 31.9 3.1E+02 0.0068 23.1 8.9 77 163-253 10-91 (126)
23 PF14250 AbrB-like: AbrB-like 31.5 1E+02 0.0022 23.4 4.3 40 208-251 24-63 (71)
24 PF05382 Amidase_5: Bacterioph 31.4 34 0.00075 29.4 2.1 35 230-264 63-101 (145)
25 PF03120 DNA_ligase_OB: NAD-de 31.3 33 0.00072 26.7 1.8 21 233-253 42-62 (82)
26 TIGR01643 YD_repeat_2x YD repe 31.0 74 0.0016 20.4 3.3 20 199-218 4-23 (42)
27 cd06919 Asp_decarbox Aspartate 30.1 3.2E+02 0.0068 22.6 8.9 77 163-253 9-90 (111)
28 PRK14699 replication factor A; 29.9 1.1E+02 0.0025 31.3 5.8 64 161-250 70-133 (484)
29 TIGR03784 marine_sortase sorta 29.0 3.4E+02 0.0073 23.8 8.0 31 223-253 90-121 (174)
30 PF06967 Mo-nitro_C: Mo-depend 28.5 47 0.001 25.9 2.2 21 280-300 30-50 (84)
31 TIGR00223 panD L-aspartate-alp 28.1 3.7E+02 0.0079 22.7 8.9 77 163-253 10-91 (126)
32 PF08471 Ribonuc_red_2_N: Clas 27.8 60 0.0013 25.9 2.7 21 57-77 70-90 (93)
33 COG5569 Uncharacterized conser 27.6 56 0.0012 26.4 2.5 24 237-262 80-103 (108)
34 smart00536 AXH domain in Ataxi 27.6 1.7E+02 0.0036 24.3 5.4 27 223-249 76-112 (116)
35 TIGR01439 lp_hng_hel_AbrB loop 27.1 1E+02 0.0022 19.7 3.4 27 233-262 13-39 (43)
36 PRK06461 single-stranded DNA-b 26.9 1.3E+02 0.0028 25.0 4.7 48 201-265 42-90 (129)
37 PRK03760 hypothetical protein; 26.7 1.7E+02 0.0036 24.1 5.3 28 223-251 89-116 (117)
38 PF02643 DUF192: Uncharacteriz 26.3 1.5E+02 0.0033 23.7 5.0 49 200-249 49-106 (108)
39 cd04491 SoSSB_OBF SoSSB_OBF: A 26.2 2.7E+02 0.0059 20.5 7.5 36 199-250 23-58 (82)
40 PF05593 RHS_repeat: RHS Repea 25.7 1.1E+02 0.0024 19.6 3.3 21 198-218 3-23 (38)
41 COG4043 Preprotein translocase 25.6 78 0.0017 25.8 3.0 18 234-251 27-44 (111)
42 cd00801 INT_P4 Bacteriophage P 25.3 1.2E+02 0.0026 28.0 4.8 37 41-77 9-49 (357)
43 COG0272 Lig NAD-dependent DNA 25.2 2.1E+02 0.0046 30.6 6.9 48 234-281 361-408 (667)
44 PF10729 CedA: Cell division a 24.7 1.4E+02 0.003 22.7 3.9 39 30-69 30-68 (80)
45 PF11948 DUF3465: Protein of u 23.4 2.1E+02 0.0045 24.3 5.3 18 236-253 81-98 (131)
46 PRK11507 ribosome-associated p 23.3 77 0.0017 24.0 2.4 24 226-249 38-61 (70)
47 PF12195 End_beta_barrel: Beta 23.3 48 0.001 25.5 1.3 33 235-267 22-55 (83)
48 cd04459 Rho_CSD Rho_CSD: Rho p 23.1 55 0.0012 24.5 1.6 16 234-249 34-49 (68)
49 COG1430 Uncharacterized conser 22.9 1.1E+02 0.0023 25.7 3.5 28 225-253 96-123 (126)
50 COG0197 RplP Ribosomal protein 22.2 1.4E+02 0.003 25.8 4.1 36 44-80 96-131 (146)
51 PRK09798 antitoxin MazE; Provi 21.5 2.6E+02 0.0057 21.5 5.2 42 216-264 5-46 (82)
52 PF01878 EVE: EVE domain; Int 21.3 1.1E+02 0.0024 25.4 3.3 15 239-253 38-52 (143)
53 PF08922 DUF1905: Domain of un 20.7 3.8E+02 0.0082 20.2 7.8 77 164-249 1-78 (80)
54 PF11604 CusF_Ec: Copper bindi 20.6 1.6E+02 0.0034 21.8 3.7 23 235-258 37-59 (70)
55 TIGR00686 phnA alkylphosphonat 20.4 1.1E+02 0.0025 25.0 3.0 15 239-253 49-63 (109)
No 1
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=99.80 E-value=1e-19 Score=133.26 Aligned_cols=59 Identities=54% Similarity=0.945 Sum_probs=56.9
Q ss_pred CceEEeEECCCCeEEEEEEeC--CeEEeecCCCCHHHHHHHHHHHHHhccCCCCCCCCCCC
Q 021945 31 SKYKGVVPQPNGRWGAQIYEK--HQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTS 89 (305)
Q Consensus 31 s~yrGV~~~~~grw~A~I~~~--~k~v~LG~f~t~EeAA~AYD~Aa~~~~G~~a~~NFp~~ 89 (305)
|+|+||+++++|+|+|+|+.+ ++++|||+|+|+||||+|||.|+++++|.++.+|||++
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 789999999899999999999 99999999999999999999999999999999999974
No 2
>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=99.78 E-value=2.1e-18 Score=136.59 Aligned_cols=99 Identities=35% Similarity=0.553 Sum_probs=74.7
Q ss_pred eeeecccCCCCCCceEEeeHHHHHhcCCCcccccCCCeEEEEEeCCCCEEEEEEEEeCCCCceEEeCCcchhhhhcCCCC
Q 021945 164 FEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKA 243 (305)
Q Consensus 164 F~K~Lt~SDv~~~~rL~iPk~~ae~~fP~~~~~~~~g~~l~v~D~~Gk~W~fr~~~~~~~~~yvLt~GW~~FV~~k~Lk~ 243 (305)
|.|+|+++|+...++|.||++++++|... ...++.|.+.|..|+.|.+++++++.+.+++|++||..||++++|++
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~----~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~~ 76 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGN----KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLKE 76 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--T
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCCC----cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCCC
Confidence 88999999999889999999999997211 13568999999999999999999988888999999999999999999
Q ss_pred CCEEEEEecccCCCCeEEEEEEec
Q 021945 244 GDTVSFWRSNVGSNSKLFIDCKLQ 267 (305)
Q Consensus 244 GD~I~F~~~~~~~~~~l~i~~r~~ 267 (305)
||+|+|+...+ ...++.|.+.++
T Consensus 77 GD~~~F~~~~~-~~~~~~v~i~~~ 99 (100)
T PF02362_consen 77 GDVCVFELIGN-SNFTLKVHIFRK 99 (100)
T ss_dssp T-EEEEEE-SS-SCE-EEEEEE--
T ss_pred CCEEEEEEecC-CCceEEEEEEEC
Confidence 99999999862 555557776654
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.77 E-value=1.1e-18 Score=129.11 Aligned_cols=60 Identities=57% Similarity=0.943 Sum_probs=57.4
Q ss_pred ceEEeEECCCCeEEEEEEe--CCeEEeecCCCCHHHHHHHHHHHHHhccCCCCCCCCCCCCC
Q 021945 32 KYKGVVPQPNGRWGAQIYE--KHQRVWLGTFIEEEEAARVYDTAALRFRGQNAITNFRTSLE 91 (305)
Q Consensus 32 ~yrGV~~~~~grw~A~I~~--~~k~v~LG~f~t~EeAA~AYD~Aa~~~~G~~a~~NFp~~~~ 91 (305)
+|+||+++++|||+|+|+. +++++|||+|+|+||||+|||.|+++++|.++.+|||.+.|
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y 62 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLY 62 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccC
Confidence 5899999889999999999 99999999999999999999999999999999999999774
No 4
>PHA00280 putative NHN endonuclease
Probab=99.66 E-value=1.2e-16 Score=132.26 Aligned_cols=70 Identities=19% Similarity=0.142 Sum_probs=64.5
Q ss_pred CCCCcCCcccCCCCCCCCceEEeEECC-CCeEEEEEEeCCeEEeecCCCCHHHHHHHHHHHHHhccCCCCCC
Q 021945 14 HNLSENGIDAESKKLPSSKYKGVVPQP-NGRWGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQNAIT 84 (305)
Q Consensus 14 ~~~~~n~~n~~~~~~~~s~yrGV~~~~-~grw~A~I~~~~k~v~LG~f~t~EeAA~AYD~Aa~~~~G~~a~~ 84 (305)
++.++|..|++.+++|+|||+||++++ .|||+|+|+.+||+++||.|+++|+|+.||+ ++.+|||+++..
T Consensus 50 ~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~ 120 (121)
T PHA00280 50 ALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTAEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF 120 (121)
T ss_pred cCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEECCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence 456899999999999999999999886 8999999999999999999999999999997 778899998853
No 5
>PF00847 AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-related genes transcriptional activator binds to the GCC-box pathogenesis-related promoter element and activates the plant's defence genes. Ethylene, chemically the simplest plant hormone, participates in a number of stress responses and developmental processes: e.g., fruit ripening, inhibition of stem and root elongation, promotion of seed germination and flowering, senescence of leaves and flowers, and sex determination []. DNA sequence elements that confer ethylene responsiveness have been shown to contain two 11bp GCC boxes, which are necessary and sufficient for transcriptional control by ethylene. Ethylene responsive element binding proteins (EREBPs) have now been identified in a variety of plants. The proteins share a similar domain of around 59 amino acids, which interacts directly with the GCC box in the ERE.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3IGM_A 3GCC_A 1GCC_A 2GCC_A.
Probab=99.10 E-value=1.4e-10 Score=83.02 Aligned_cols=50 Identities=42% Similarity=0.508 Sum_probs=45.3
Q ss_pred CceEEeEECC-CCeEEEEEEeC-----CeEEeecCCCCHHHHHHHHHHHHHhccCC
Q 021945 31 SKYKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFIEEEEAARVYDTAALRFRGQ 80 (305)
Q Consensus 31 s~yrGV~~~~-~grw~A~I~~~-----~k~v~LG~f~t~EeAA~AYD~Aa~~~~G~ 80 (305)
|+|+||++++ .++|+|+|+.. ++.++||.|++++||++|++.++.+++|+
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 7899999887 79999999983 49999999999999999999999999874
No 6
>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=99.04 E-value=7.8e-10 Score=90.93 Aligned_cols=79 Identities=27% Similarity=0.544 Sum_probs=65.2
Q ss_pred cceeeeeeecccCCCC-CCceEEeeHHHHHhcCCCcccc-------------cCCCeEEEEEeCCCCEEEEEEEEeCC--
Q 021945 159 PVEFLFEKVLTPSDVG-KLNRMVIPKQQAEKHFALSSEI-------------ASKGLLLNFEDSTQKVWRLRYCYWSS-- 222 (305)
Q Consensus 159 ~~~~lF~K~Lt~SDv~-~~~rL~iPk~~ae~~fP~~~~~-------------~~~g~~l~v~D~~Gk~W~fr~~~~~~-- 222 (305)
....++.|+|+.|||. +++||.||-..+.. ..+|... ...|+.+.+.|..++.|.++++.|.-
T Consensus 19 d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~ 97 (114)
T PF03754_consen 19 DPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGN 97 (114)
T ss_pred CCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccC
Confidence 4588999999999999 78999999777743 2333311 35689999999999999999999965
Q ss_pred -CCceEEeCCcchhhhh
Q 021945 223 -SQSYVLTKGWSRFVKE 238 (305)
Q Consensus 223 -~~~yvLt~GW~~FV~~ 238 (305)
+..|+|..||.++|.+
T Consensus 98 ~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 98 GTSNYVLNSGWNKVVED 114 (114)
T ss_pred CceEEEEEcChHhhccC
Confidence 5789999999999864
No 7
>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=98.28 E-value=1.2e-05 Score=68.97 Aligned_cols=92 Identities=18% Similarity=0.280 Sum_probs=59.4
Q ss_pred eeeeeeecccCCCC----CCceEEeeHHHHHhcCCCcccc--cCCCeEEEEEeCCC--CEEEEEEEEeCC------CCce
Q 021945 161 EFLFEKVLTPSDVG----KLNRMVIPKQQAEKHFALSSEI--ASKGLLLNFEDSTQ--KVWRLRYCYWSS------SQSY 226 (305)
Q Consensus 161 ~~lF~K~Lt~SDv~----~~~rL~iPk~~ae~~fP~~~~~--~~~g~~l~v~D~~G--k~W~fr~~~~~~------~~~y 226 (305)
..+|.|.|++.|++ |+.++.|||..++.+||.+... ..+.+.|.+.+..+ ..|.+|++|.++ +..|
T Consensus 7 ~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE~ 86 (156)
T PF09217_consen 7 WAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNEY 86 (156)
T ss_dssp EEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--EE
T ss_pred eEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCce
Confidence 46899999999999 7889999999999999876643 45679999999877 568899999966 5779
Q ss_pred EEeCCcchhhhhcC-CCCCCEEEEEecc
Q 021945 227 VLTKGWSRFVKEKG-VKAGDTVSFWRSN 253 (305)
Q Consensus 227 vLt~GW~~FV~~k~-Lk~GD~I~F~~~~ 253 (305)
.||. |.....--+ =.+||.++|-...
T Consensus 87 RIT~-~G~~~~~~~~~~tGaL~vlaf~~ 113 (156)
T PF09217_consen 87 RITR-FGRGFPLQNPENTGALLVLAFDP 113 (156)
T ss_dssp EEE----TTSGGG-GGGTT-EEEEEEE-
T ss_pred EEee-ecCCCccCCccccccEEEEEEcc
Confidence 9994 774444333 3689999987444
No 8
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=79.33 E-value=11 Score=30.00 Aligned_cols=80 Identities=18% Similarity=0.241 Sum_probs=44.6
Q ss_pred cceeeeeeecccCCCC--CCceEEeeHHHHHhcCCCcccccCCCeEEEEEeCCCCEEEEEEEEeCCCCceEEeCCcchhh
Q 021945 159 PVEFLFEKVLTPSDVG--KLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFV 236 (305)
Q Consensus 159 ~~~~lF~K~Lt~SDv~--~~~rL~iPk~~ae~~fP~~~~~~~~g~~l~v~D~~Gk~W~fr~~~~~~~~~yvLt~GW~~FV 236 (305)
+...+|-++++++-+. -.++|.||++.+- +|..- ......+.+... ......+ |.
T Consensus 16 p~~i~~G~V~s~~PL~I~i~~~liL~~~~L~--i~~~l--~~~~~~~~~~~~--------------~~~~~~~-----i~ 72 (100)
T PF10844_consen 16 PVDIVIGTVVSVPPLKIKIDQKLILDKDFLI--IPELL--KDYTRDITIEHN--------------SETDNIT-----IT 72 (100)
T ss_pred CceeEEEEEEecccEEEEECCeEEEchHHEE--eehhc--cceEEEEEEecc--------------cccccee-----EE
Confidence 4455899999999855 2335999977552 22211 012222222221 1111110 55
Q ss_pred hhcCCCCCCEEEEEecccCCCCeEEEE
Q 021945 237 KEKGVKAGDTVSFWRSNVGSNSKLFID 263 (305)
Q Consensus 237 ~~k~Lk~GD~I~F~~~~~~~~~~l~i~ 263 (305)
-...|++||.|.+.+.. .+.+++|-
T Consensus 73 ~~~~Lk~GD~V~ll~~~--~gQ~yiVl 97 (100)
T PF10844_consen 73 FTDGLKVGDKVLLLRVQ--GGQKYIVL 97 (100)
T ss_pred EecCCcCCCEEEEEEec--CCCEEEEE
Confidence 66789999999999965 33444443
No 9
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=65.98 E-value=20 Score=24.27 Aligned_cols=36 Identities=14% Similarity=0.246 Sum_probs=27.9
Q ss_pred eEEEEEE-e---CC--eEEeecCCCCHHHHHHHHHHHHHhcc
Q 021945 43 RWGAQIY-E---KH--QRVWLGTFIEEEEAARVYDTAALRFR 78 (305)
Q Consensus 43 rw~A~I~-~---~~--k~v~LG~f~t~EeAA~AYD~Aa~~~~ 78 (305)
+|...|. . .| ++++-+.|.|..||..+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5788884 3 23 67889999999999999888776653
No 10
>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=55.53 E-value=19 Score=24.40 Aligned_cols=27 Identities=26% Similarity=0.422 Sum_probs=21.8
Q ss_pred hhhhhcCCCCCCEEEEEecccCCCCeEEEE
Q 021945 234 RFVKEKGVKAGDTVSFWRSNVGSNSKLFID 263 (305)
Q Consensus 234 ~FV~~k~Lk~GD~I~F~~~~~~~~~~l~i~ 263 (305)
.|.+..+|++||.|.|.-+. +|++.|.
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~---~g~i~i~ 40 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEG---DGKIVIR 40 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEET---TSEEEEE
T ss_pred HHHHHcCCCCCCEEEEEEeC---CCEEEEE
Confidence 78888999999999998876 5565544
No 11
>PF09853 DUF2080: Putative transposon-encoded protein (DUF2080); InterPro: IPR019205 This entry, found in various hypothetical archaeal proteins, has no known function.
Probab=55.27 E-value=19 Score=25.75 Aligned_cols=30 Identities=30% Similarity=0.431 Sum_probs=26.2
Q ss_pred CCcceeeeeeecccCCCCCCceEE--eeHHHHHh
Q 021945 157 ETPVEFLFEKVLTPSDVGKLNRMV--IPKQQAEK 188 (305)
Q Consensus 157 ~~~~~~lF~K~Lt~SDv~~~~rL~--iPk~~ae~ 188 (305)
.+.+...|.++.++. ++.+++. +|++++.+
T Consensus 11 ~~~i~~~~~~~vk~~--Gnsa~v~p~lPkeyiGK 42 (53)
T PF09853_consen 11 PRNIEPTFIGVVKPF--GNSARVYPSLPKEYIGK 42 (53)
T ss_pred eeeEEEEEEEEEEec--CcceeEcCCCChHHcCc
Confidence 467788999999998 8889999 99999865
No 12
>PHA02601 int integrase; Provisional
Probab=46.95 E-value=27 Score=32.71 Aligned_cols=42 Identities=21% Similarity=0.369 Sum_probs=29.2
Q ss_pred EeEECCCCeEEEEEEeC---CeEEeecCCCCHHHHHHHHHHHHHhc
Q 021945 35 GVVPQPNGRWGAQIYEK---HQRVWLGTFIEEEEAARVYDTAALRF 77 (305)
Q Consensus 35 GV~~~~~grw~A~I~~~---~k~v~LG~f~t~EeAA~AYD~Aa~~~ 77 (305)
+|+..++|+|+++++.. |+++.. +|.|..||....+.....+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~~-~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIRK-RFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhhh-hhcCHHHHHHHHHHHHHhc
Confidence 45556688999999864 666653 6999999876655544433
No 13
>COG3466 ISA1214 Putative transposon-encoded protein [Function unknown]
Probab=43.18 E-value=22 Score=25.22 Aligned_cols=30 Identities=37% Similarity=0.579 Sum_probs=25.4
Q ss_pred CCcceeeeeeecccCCCCCCceEEeeHHHHHh
Q 021945 157 ETPVEFLFEKVLTPSDVGKLNRMVIPKQQAEK 188 (305)
Q Consensus 157 ~~~~~~lF~K~Lt~SDv~~~~rL~iPk~~ae~ 188 (305)
..+.+..|+|+.|+- ++.+.+.+||+++..
T Consensus 14 ~~~ve~~~ek~Vtpf--GnsakVdvPK~yiG~ 43 (52)
T COG3466 14 KEEVEVVFEKRVTPF--GNSAKVDVPKRYIGK 43 (52)
T ss_pred chheEEEEEEEEEec--CCcceeeCchHHcCc
Confidence 356788999999997 888899999999853
No 14
>PF08846 DUF1816: Domain of unknown function (DUF1816); InterPro: IPR014945 Q4C9H3 from SWISSPROT is associated with the IPR008213 from INTERPRO domain suggesting this protein could have a role in phycobilisomes.
Probab=40.72 E-value=55 Score=24.63 Aligned_cols=29 Identities=24% Similarity=0.398 Sum_probs=22.6
Q ss_pred eEEEEEEe--CCeEEeecCCCCHHHHHHHHH
Q 021945 43 RWGAQIYE--KHQRVWLGTFIEEEEAARVYD 71 (305)
Q Consensus 43 rw~A~I~~--~~k~v~LG~f~t~EeAA~AYD 71 (305)
-|=++|.- ....+|.|-|++.+||..+.-
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~ 39 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALP 39 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhc
Confidence 35577764 357889999999999997753
No 15
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=40.02 E-value=42 Score=25.98 Aligned_cols=32 Identities=25% Similarity=0.401 Sum_probs=23.6
Q ss_pred chhhhhcCCCCCCEEEEEecccCCCCeEEEEEEe
Q 021945 233 SRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKL 266 (305)
Q Consensus 233 ~~FV~~k~Lk~GD~I~F~~~~~~~~~~l~i~~r~ 266 (305)
...++.-+|+.||+|.+.|.. ...|+ ++-||.
T Consensus 44 DPv~r~~g~k~GdVvkI~R~S-~taG~-~v~YR~ 75 (79)
T PRK09570 44 DPVVKAIGAKPGDVIKIVRKS-PTAGE-AVYYRL 75 (79)
T ss_pred ChhhhhcCCCCCCEEEEEECC-CCCCc-cEEEEE
Confidence 378888899999999999987 23344 355553
No 16
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=38.92 E-value=19 Score=25.77 Aligned_cols=22 Identities=32% Similarity=0.401 Sum_probs=18.0
Q ss_pred eEEeecCCCCHHHHHHHHHHHH
Q 021945 53 QRVWLGTFIEEEEAARVYDTAA 74 (305)
Q Consensus 53 k~v~LG~f~t~EeAA~AYD~Aa 74 (305)
-+|.+|.|++.+||..+.....
T Consensus 44 yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 44 YRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp EEEEECCECTCCHHHHHHHHHH
T ss_pred EEEEECCCCCHHHHHHHHHHHh
Confidence 4788999999999988876555
No 17
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=37.61 E-value=57 Score=24.87 Aligned_cols=31 Identities=19% Similarity=0.431 Sum_probs=21.6
Q ss_pred chhhhhcCCCCCCEEEEEecccCCCCeEEEEEE
Q 021945 233 SRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCK 265 (305)
Q Consensus 233 ~~FV~~k~Lk~GD~I~F~~~~~~~~~~l~i~~r 265 (305)
...++.-+++.||+|.+.|.. ...|+ ++-||
T Consensus 41 DPv~r~~g~k~GdVvkI~R~S-~taG~-~v~YR 71 (74)
T PF01191_consen 41 DPVARYLGAKPGDVVKIIRKS-ETAGE-YVTYR 71 (74)
T ss_dssp SHHHHHTT--TTSEEEEEEEE-TTTSE-EEEEE
T ss_pred ChhhhhcCCCCCCEEEEEecC-CCCCC-cEEEE
Confidence 478899999999999999987 33343 35555
No 18
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=36.42 E-value=2.5e+02 Score=23.32 Aligned_cols=75 Identities=13% Similarity=0.169 Sum_probs=46.5
Q ss_pred eeeeecccCCCCCCceEEeeHHHHHh--cCCCcccccCCCeEEEEEeC-CCCEEEEEEEEeC--CCCceEEeCCcchhhh
Q 021945 163 LFEKVLTPSDVGKLNRMVIPKQQAEK--HFALSSEIASKGLLLNFEDS-TQKVWRLRYCYWS--SSQSYVLTKGWSRFVK 237 (305)
Q Consensus 163 lF~K~Lt~SDv~~~~rL~iPk~~ae~--~fP~~~~~~~~g~~l~v~D~-~Gk~W~fr~~~~~--~~~~yvLt~GW~~FV~ 237 (305)
|-.-++|..|+...+.+.|..+.+++ ++|. -.|.+.+. +|..|.- |.+.. .+..--|.+ .-
T Consensus 10 iHratVT~a~L~Y~GSitID~~Ll~aagi~p~--------E~V~V~Nv~nG~Rf~T-YvI~g~~GSg~I~lNG-----aA 75 (116)
T PF02261_consen 10 IHRATVTEADLNYEGSITIDEDLLDAAGILPY--------EQVQVVNVNNGERFET-YVIPGERGSGVICLNG-----AA 75 (116)
T ss_dssp EEEEE--EEETTSTSCEEEEHHHHHHCT--TT--------BEEEEEETTT--EEEE-EEEEESTTTT-EEEEG-----GG
T ss_pred hcceEEeccccccceeeEECHHHHHHcCCCcC--------CEEEEEECCCCcEEEE-EEEEccCCCcEEEECC-----HH
Confidence 45668899999988999999999986 3333 44888886 6887653 33442 334455554 46
Q ss_pred hcCCCCCCEEEEEe
Q 021945 238 EKGVKAGDTVSFWR 251 (305)
Q Consensus 238 ~k~Lk~GD~I~F~~ 251 (305)
++..++||.|++.-
T Consensus 76 Arl~~~GD~vII~s 89 (116)
T PF02261_consen 76 ARLVQVGDRVIIMS 89 (116)
T ss_dssp GGCS-TT-EEEEEE
T ss_pred HhccCCCCEEEEEE
Confidence 77889999998854
No 19
>PRK11347 antitoxin ChpS; Provisional
Probab=33.80 E-value=1.2e+02 Score=23.41 Aligned_cols=43 Identities=23% Similarity=0.380 Sum_probs=32.7
Q ss_pred EEEEEeCCCCceEEeCCcchhhhhcCCCCCCEEEEEecccCCCCeEEEEE
Q 021945 215 LRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDC 264 (305)
Q Consensus 215 fr~~~~~~~~~yvLt~GW~~FV~~k~Lk~GD~I~F~~~~~~~~~~l~i~~ 264 (305)
...+.|++|.--.|-. .|+++-+|.+||+|.+.-.. +.+.|.-
T Consensus 3 ~~v~kwGNS~~vriPk---~il~~l~l~~G~~v~i~v~~----~~iii~p 45 (83)
T PRK11347 3 ITIKRWGNSAGMVIPN---IVMKELNLQPGQSVEAQVSN----NQLILTP 45 (83)
T ss_pred EEEEEEcCceeEEeCH---HHHHHcCCCCCCEEEEEEEC----CEEEEEE
Confidence 3556788887777774 89999999999999887654 5555543
No 20
>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=32.14 E-value=99 Score=23.13 Aligned_cols=33 Identities=21% Similarity=0.208 Sum_probs=23.1
Q ss_pred EEeCCCCceEEeCCcchhhhhcCCCCCCEEEEEecc
Q 021945 218 CYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSN 253 (305)
Q Consensus 218 ~~~~~~~~yvLt~GW~~FV~~k~Lk~GD~I~F~~~~ 253 (305)
..|++|..-.|- ..++..-+|.+||.|.|.-+.
T Consensus 4 ~k~GNS~~vtIP---k~i~~~lgl~~Gd~v~v~~~~ 36 (74)
T TIGR02609 4 RKVGNSLVVTLP---KEVLESLGLKEGDTLYVDEEE 36 (74)
T ss_pred EEECCeeEEEEC---HHHHHHcCcCCCCEEEEEEEC
Confidence 456544333333 388999999999999886653
No 21
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=32.03 E-value=2.2e+02 Score=21.58 Aligned_cols=37 Identities=22% Similarity=0.230 Sum_probs=23.9
Q ss_pred ECCCC--eEEEEEEeCCe--EEeecCCCC--HHHHHHHHHHHH
Q 021945 38 PQPNG--RWGAQIYEKHQ--RVWLGTFIE--EEEAARVYDTAA 74 (305)
Q Consensus 38 ~~~~g--rw~A~I~~~~k--~v~LG~f~t--~EeAA~AYD~Aa 74 (305)
..++| .|.-+...+|+ ++.||.|.+ .+||........
T Consensus 29 v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~ 71 (89)
T PF13356_consen 29 VTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELR 71 (89)
T ss_dssp E-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHH
T ss_pred EEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHH
Confidence 44543 59988888776 678999976 555554444333
No 22
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=31.90 E-value=3.1e+02 Score=23.08 Aligned_cols=77 Identities=13% Similarity=0.123 Sum_probs=54.4
Q ss_pred eeeeecccCCCCCCceEEeeHHHHHh--cCCCcccccCCCeEEEEEeC-CCCEEEEEEEEeCC--CCceEEeCCcchhhh
Q 021945 163 LFEKVLTPSDVGKLNRMVIPKQQAEK--HFALSSEIASKGLLLNFEDS-TQKVWRLRYCYWSS--SQSYVLTKGWSRFVK 237 (305)
Q Consensus 163 lF~K~Lt~SDv~~~~rL~iPk~~ae~--~fP~~~~~~~~g~~l~v~D~-~Gk~W~fr~~~~~~--~~~yvLt~GW~~FV~ 237 (305)
|-.-++|..|+..-+.+.|..+++++ ++|. -.|.+++. +|..|.- |.+... |..-.|.+ .-
T Consensus 10 iHratVT~a~L~Y~GSitID~~Ll~aagi~p~--------E~V~V~Nv~NG~Rf~T-YvI~g~~GSg~I~lNG-----AA 75 (126)
T PRK05449 10 IHRATVTEADLNYEGSITIDEDLLDAAGILEN--------EKVQIVNVNNGARFET-YVIAGERGSGVICLNG-----AA 75 (126)
T ss_pred ccceEEeccccccceeEEECHHHHHhcCCCCC--------CEEEEEECCCCcEEEE-EEEEcCCCCCEEEeCC-----HH
Confidence 45668899999988999999999986 3333 45788886 6876643 345543 33455554 46
Q ss_pred hcCCCCCCEEEEEecc
Q 021945 238 EKGVKAGDTVSFWRSN 253 (305)
Q Consensus 238 ~k~Lk~GD~I~F~~~~ 253 (305)
++..++||.|++.--.
T Consensus 76 Ar~~~~GD~vII~ay~ 91 (126)
T PRK05449 76 ARLVQVGDLVIIAAYA 91 (126)
T ss_pred HhcCCCCCEEEEEECc
Confidence 7788999999986543
No 23
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=31.52 E-value=1e+02 Score=23.36 Aligned_cols=40 Identities=20% Similarity=0.243 Sum_probs=30.3
Q ss_pred CCCCEEEEEEEEeCCCCceEEeCCcchhhhhcCCCCCCEEEEEe
Q 021945 208 STQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWR 251 (305)
Q Consensus 208 ~~Gk~W~fr~~~~~~~~~yvLt~GW~~FV~~k~Lk~GD~I~F~~ 251 (305)
..|+.=+||.+...++ -+|.+ +.|-+..+|++||++.+--
T Consensus 24 ~~GR~~syr~~Vq~NG--nLLIG--~AYT~~m~L~PGdEFeI~L 63 (71)
T PF14250_consen 24 RRGRKASYRVSVQGNG--NLLIG--SAYTKQMGLKPGDEFEIKL 63 (71)
T ss_pred CCCcCceEEEEEecCC--CEEEc--HHHHHHhCCCCCCEEEEEe
Confidence 4678888887776554 34554 6999999999999987743
No 24
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 This entry is represented by Bacteriophage SFi21, lysin (Cell wall hydrolase; 3.5.1.28 from EC). At least one of proteins in this entry, the Pal protein from the pneumococcal bacteriophage Dp-1 (O03979 from SWISSPROT) has been shown to be an N-acetylmuramoyl-L-alanine amidase []. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside within this domain while a C-terminal domain binds to the choline residues of the cell wall teichoic acids [, ].
Probab=31.42 E-value=34 Score=29.36 Aligned_cols=35 Identities=17% Similarity=0.290 Sum_probs=20.3
Q ss_pred CCcchhhhh--cCCCCCCEEEEEecc--cCCCCeEEEEE
Q 021945 230 KGWSRFVKE--KGVKAGDTVSFWRSN--VGSNSKLFIDC 264 (305)
Q Consensus 230 ~GW~~FV~~--k~Lk~GD~I~F~~~~--~~~~~~l~i~~ 264 (305)
.||..+-.. +.||.||+|++-... .+..|+..|-.
T Consensus 63 ~G~~~I~~~~~~~~q~GDI~I~g~~g~S~G~~GHtgif~ 101 (145)
T PF05382_consen 63 NGFKKISENVDWNLQRGDIFIWGRRGNSAGAGGHTGIFM 101 (145)
T ss_pred CCcEEeccCCcccccCCCEEEEcCCCCCCCCCCeEEEEe
Confidence 344433332 589999999863432 34566655544
No 25
>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=31.34 E-value=33 Score=26.65 Aligned_cols=21 Identities=33% Similarity=0.536 Sum_probs=17.3
Q ss_pred chhhhhcCCCCCCEEEEEecc
Q 021945 233 SRFVKEKGVKAGDTVSFWRSN 253 (305)
Q Consensus 233 ~~FV~~k~Lk~GD~I~F~~~~ 253 (305)
.+|+++++|..||.|.+++..
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raG 62 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAG 62 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEET
T ss_pred HHHHHHcCCCCCCEEEEEECC
Confidence 589999999999999999965
No 26
>TIGR01643 YD_repeat_2x YD repeat (two copies). This model describes two tandem copies of a 21-residue extracellular repeat found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin.
Probab=30.95 E-value=74 Score=20.40 Aligned_cols=20 Identities=25% Similarity=0.247 Sum_probs=16.7
Q ss_pred CCeEEEEEeCCCCEEEEEEE
Q 021945 199 KGLLLNFEDSTQKVWRLRYC 218 (305)
Q Consensus 199 ~g~~l~v~D~~Gk~W~fr~~ 218 (305)
.|..+.+.|..|..|+|.|-
T Consensus 4 ~g~l~~~~~p~G~~~~~~YD 23 (42)
T TIGR01643 4 AGRLTGSTDADGTTTRYTYD 23 (42)
T ss_pred CCCEEEEECCCCCEEEEEEC
Confidence 46778899999999999863
No 27
>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=30.08 E-value=3.2e+02 Score=22.56 Aligned_cols=77 Identities=13% Similarity=0.086 Sum_probs=54.6
Q ss_pred eeeeecccCCCCCCceEEeeHHHHHh--cCCCcccccCCCeEEEEEeC-CCCEEEEEEEEeCC--CCceEEeCCcchhhh
Q 021945 163 LFEKVLTPSDVGKLNRMVIPKQQAEK--HFALSSEIASKGLLLNFEDS-TQKVWRLRYCYWSS--SQSYVLTKGWSRFVK 237 (305)
Q Consensus 163 lF~K~Lt~SDv~~~~rL~iPk~~ae~--~fP~~~~~~~~g~~l~v~D~-~Gk~W~fr~~~~~~--~~~yvLt~GW~~FV~ 237 (305)
|-.-++|..|+...+.+.|..+++++ ++| .-.|.+++. +|..|.- |.+... |..-.|.+ .-
T Consensus 9 iHratVT~a~L~YeGSitID~~Ll~aagi~~--------~E~V~I~Nv~NG~Rf~T-YvI~g~~gSg~I~lNG-----AA 74 (111)
T cd06919 9 IHRATVTEADLNYEGSITIDEDLLEAAGILP--------YEKVLVVNVNNGARFET-YVIPGERGSGVICLNG-----AA 74 (111)
T ss_pred ccceEEeccccccceeEEECHHHHHhcCCCC--------CCEEEEEECCCCcEEEE-EEEEcCCCCCEEEeCC-----HH
Confidence 45668899999988999999999986 333 345888886 6876643 345533 44455554 46
Q ss_pred hcCCCCCCEEEEEecc
Q 021945 238 EKGVKAGDTVSFWRSN 253 (305)
Q Consensus 238 ~k~Lk~GD~I~F~~~~ 253 (305)
++..++||.|++.--.
T Consensus 75 Ar~~~~GD~vII~sy~ 90 (111)
T cd06919 75 ARLGQPGDRVIIMAYA 90 (111)
T ss_pred HhcCCCCCEEEEEECc
Confidence 7788999999986543
No 28
>PRK14699 replication factor A; Provisional
Probab=29.93 E-value=1.1e+02 Score=31.28 Aligned_cols=64 Identities=20% Similarity=0.310 Sum_probs=41.3
Q ss_pred eeeeeeecccCCCCCCceEEeeHHHHHhcCCCcccccCCCeEEEEEeCCCCEEEEEEEEeCCCCceEEeCCcchhhhhcC
Q 021945 161 EFLFEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKG 240 (305)
Q Consensus 161 ~~lF~K~Lt~SDv~~~~rL~iPk~~ae~~fP~~~~~~~~g~~l~v~D~~Gk~W~fr~~~~~~~~~yvLt~GW~~FV~~k~ 240 (305)
.-++.|+|+-+++.. |...+++...-..+.+-|.+|. .+|+.|... .+.+.+-+
T Consensus 70 v~i~~rVl~i~~~r~--------------f~r~dG~~g~v~~~~iaDeTG~---ir~tlW~~~---------a~~~~~g~ 123 (484)
T PRK14699 70 VNFIARVVSVFDTKE--------------FTRNDGTIGRVGNLIVGDETGK---IKLTLWDNM---------ADLIKAGK 123 (484)
T ss_pred EEEEEEEEEecCceE--------------EecCCCCceEEEEEEEecCCCe---EEEEEecCc---------cchhhhcC
Confidence 347888888887765 4333442223356788898894 666666422 23444557
Q ss_pred CCCCCEEEEE
Q 021945 241 VKAGDTVSFW 250 (305)
Q Consensus 241 Lk~GD~I~F~ 250 (305)
|++||+|.+-
T Consensus 124 l~~GDvv~I~ 133 (484)
T PRK14699 124 IKAGQTLQIS 133 (484)
T ss_pred CCCCCEEEEc
Confidence 9999999983
No 29
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=28.98 E-value=3.4e+02 Score=23.82 Aligned_cols=31 Identities=13% Similarity=0.236 Sum_probs=23.1
Q ss_pred CCceEEeCC-cchhhhhcCCCCCCEEEEEecc
Q 021945 223 SQSYVLTKG-WSRFVKEKGVKAGDTVSFWRSN 253 (305)
Q Consensus 223 ~~~yvLt~G-W~~FV~~k~Lk~GD~I~F~~~~ 253 (305)
...++|.+. -..|-.=.+|++||.|.+....
T Consensus 90 ~Gn~VIAGHrdt~F~~L~~L~~GD~I~v~~~~ 121 (174)
T TIGR03784 90 QGNSVIAGHRDTHFAFLQELRPGDVIRLQTPD 121 (174)
T ss_pred CCcEEEEeeCCccCCChhhCCCCCEEEEEECC
Confidence 356777621 2359999999999999997743
No 30
>PF06967 Mo-nitro_C: Mo-dependent nitrogenase C-terminus; InterPro: IPR009717 This entry represents the C terminus (approximately 80 residues) of a number of bacterial Mo-dependent nitrogenases. These are involved in nitrogen fixation in cyanobacteria [].
Probab=28.52 E-value=47 Score=25.91 Aligned_cols=21 Identities=29% Similarity=0.509 Sum_probs=17.8
Q ss_pred cCCCcceeEEEeeeEeecCCC
Q 021945 280 SQVPNIGVVRLFGVNILEDPN 300 (305)
Q Consensus 280 ~~~~~~~~vrlFG~~i~~~~~ 300 (305)
+++|-+|.|.|||-.|..-|-
T Consensus 30 aqCPFERdi~lfGr~l~hIPP 50 (84)
T PF06967_consen 30 AQCPFERDIKLFGRKLFHIPP 50 (84)
T ss_pred CCCCCcceEEECCeeEEecCC
Confidence 468899999999999987664
No 31
>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=28.08 E-value=3.7e+02 Score=22.67 Aligned_cols=77 Identities=13% Similarity=0.135 Sum_probs=54.4
Q ss_pred eeeeecccCCCCCCceEEeeHHHHHh--cCCCcccccCCCeEEEEEeC-CCCEEEEEEEEeCC--CCceEEeCCcchhhh
Q 021945 163 LFEKVLTPSDVGKLNRMVIPKQQAEK--HFALSSEIASKGLLLNFEDS-TQKVWRLRYCYWSS--SQSYVLTKGWSRFVK 237 (305)
Q Consensus 163 lF~K~Lt~SDv~~~~rL~iPk~~ae~--~fP~~~~~~~~g~~l~v~D~-~Gk~W~fr~~~~~~--~~~yvLt~GW~~FV~ 237 (305)
|-.-++|..|+..-+.+.|..+++++ ++|. -.|.++|. +|..|.- |.+.+. |..-.|.+ .-
T Consensus 10 IHratVT~a~L~Y~GSItID~~Lm~aagi~p~--------E~V~V~Nv~NG~Rf~T-YvI~G~~GSg~I~lNG-----AA 75 (126)
T TIGR00223 10 LHRATVTHANLNYEGSITIDEDLLDAAGILEN--------EKVDIVNVNNGKRFST-YAIAGKRGSRIICVNG-----AA 75 (126)
T ss_pred hcceEEeccccccceeEEECHHHHHhcCCCCC--------CEEEEEECCCCcEEEE-EEEEcCCCCCEEEeCC-----HH
Confidence 45668899999988999999999986 3333 45788886 6886653 345543 34455554 46
Q ss_pred hcCCCCCCEEEEEecc
Q 021945 238 EKGVKAGDTVSFWRSN 253 (305)
Q Consensus 238 ~k~Lk~GD~I~F~~~~ 253 (305)
++..++||.|++.--.
T Consensus 76 Arl~~~GD~VII~sy~ 91 (126)
T TIGR00223 76 ARCVSVGDIVIIASYV 91 (126)
T ss_pred HhcCCCCCEEEEEECC
Confidence 7788999999986543
No 32
>PF08471 Ribonuc_red_2_N: Class II vitamin B12-dependent ribonucleotide reductase; InterPro: IPR013678 This domain is found to the N terminus of the ribonucleotide reductase barrel domain (IPR000788 from INTERPRO). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) []. ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0050897 cobalt ion binding, 0055114 oxidation-reduction process
Probab=27.79 E-value=60 Score=25.91 Aligned_cols=21 Identities=33% Similarity=0.482 Sum_probs=17.9
Q ss_pred ecCCCCHHHHHHHHHHHHHhc
Q 021945 57 LGTFIEEEEAARVYDTAALRF 77 (305)
Q Consensus 57 LG~f~t~EeAA~AYD~Aa~~~ 77 (305)
-|+|+|+|+|..=||.....|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 599999999999999877554
No 33
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=27.60 E-value=56 Score=26.44 Aligned_cols=24 Identities=42% Similarity=0.558 Sum_probs=17.6
Q ss_pred hhcCCCCCCEEEEEecccCCCCeEEE
Q 021945 237 KEKGVKAGDTVSFWRSNVGSNSKLFI 262 (305)
Q Consensus 237 ~~k~Lk~GD~I~F~~~~~~~~~~l~i 262 (305)
.-.+||+||.|.|--+. -+|++.+
T Consensus 80 ~lsglKeGdkV~fvfer--v~gk~tv 103 (108)
T COG5569 80 KLSGLKEGDKVEFVFER--VNGKLTV 103 (108)
T ss_pred HhhccccCCcEEEEEEe--eCCEEEE
Confidence 34579999999998876 4565543
No 34
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=27.58 E-value=1.7e+02 Score=24.33 Aligned_cols=27 Identities=26% Similarity=0.357 Sum_probs=20.8
Q ss_pred CCceEEeCCcchhhh----------hcCCCCCCEEEE
Q 021945 223 SQSYVLTKGWSRFVK----------EKGVKAGDTVSF 249 (305)
Q Consensus 223 ~~~yvLt~GW~~FV~----------~k~Lk~GD~I~F 249 (305)
-+-||..+||+-|-= =..|++||+|.-
T Consensus 76 HPfFV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~ 112 (116)
T smart00536 76 HPFFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLS 112 (116)
T ss_pred CCeEEcCccccccChhhhhhhcCCcceecccCCEEec
Confidence 467899999996643 357899999974
No 35
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=27.05 E-value=1e+02 Score=19.72 Aligned_cols=27 Identities=19% Similarity=0.468 Sum_probs=20.8
Q ss_pred chhhhhcCCCCCCEEEEEecccCCCCeEEE
Q 021945 233 SRFVKEKGVKAGDTVSFWRSNVGSNSKLFI 262 (305)
Q Consensus 233 ~~FV~~k~Lk~GD~I~F~~~~~~~~~~l~i 262 (305)
..|.+.-+++.||.|.+.... ++.+.|
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~---~~~l~l 39 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVE---DGEIIL 39 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeC---CCEEEE
Confidence 378999999999999998654 455433
No 36
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=26.93 E-value=1.3e+02 Score=24.96 Aligned_cols=48 Identities=15% Similarity=0.230 Sum_probs=30.8
Q ss_pred eEEEEEeCCCCEEEEEEEEeCCCCceEEeCCcchhhhhcCCCCCCEEEEEecc-cCCCCeEEEEEE
Q 021945 201 LLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSN-VGSNSKLFIDCK 265 (305)
Q Consensus 201 ~~l~v~D~~Gk~W~fr~~~~~~~~~yvLt~GW~~FV~~k~Lk~GD~I~F~~~~-~~~~~~l~i~~r 265 (305)
..+.+.|.+|. .+++.|.. ....|++||+|.+.--. ..-.|.+.+.+-
T Consensus 42 ~~~~l~D~TG~---I~~tlW~~--------------~a~~l~~GdvV~I~na~v~~f~G~lqL~i~ 90 (129)
T PRK06461 42 SEAVVGDETGR---VKLTLWGE--------------QAGSLKEGEVVEIENAWTTLYRGKVQLNVG 90 (129)
T ss_pred EEEEEECCCCE---EEEEEeCC--------------ccccCCCCCEEEEECcEEeeeCCEEEEEEC
Confidence 56788898886 67778854 12468999999997322 123555444443
No 37
>PRK03760 hypothetical protein; Provisional
Probab=26.70 E-value=1.7e+02 Score=24.07 Aligned_cols=28 Identities=14% Similarity=0.323 Sum_probs=20.6
Q ss_pred CCceEEeCCcchhhhhcCCCCCCEEEEEe
Q 021945 223 SQSYVLTKGWSRFVKEKGVKAGDTVSFWR 251 (305)
Q Consensus 223 ~~~yvLt~GW~~FV~~k~Lk~GD~I~F~~ 251 (305)
.-.|+|.-- ...+.+.++++||.|.|-+
T Consensus 89 ~a~~VLEl~-aG~~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 89 PARYIIEGP-VGKIRVLKVEVGDEIEWID 116 (117)
T ss_pred cceEEEEeC-CChHHHcCCCCCCEEEEee
Confidence 456888711 2467899999999998855
No 38
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=26.34 E-value=1.5e+02 Score=23.68 Aligned_cols=49 Identities=27% Similarity=0.366 Sum_probs=27.2
Q ss_pred CeEEEEEeCCCCEEEEEEEEe---------CCCCceEEeCCcchhhhhcCCCCCCEEEE
Q 021945 200 GLLLNFEDSTQKVWRLRYCYW---------SSSQSYVLTKGWSRFVKEKGVKAGDTVSF 249 (305)
Q Consensus 200 g~~l~v~D~~Gk~W~fr~~~~---------~~~~~yvLt~GW~~FV~~k~Lk~GD~I~F 249 (305)
.+.|.+.|.+|++-....-.. ...-.|+|.-. ..++...++++||.|.|
T Consensus 49 pLDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~-aG~~~~~~i~~Gd~v~~ 106 (108)
T PF02643_consen 49 PLDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELP-AGWFEKLGIKVGDRVRI 106 (108)
T ss_dssp -EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEE-TTHHHHHT--TT-EEE-
T ss_pred eEEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcC-CCchhhcCCCCCCEEEe
Confidence 366777777776554443321 12246888731 35789999999999986
No 39
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=26.19 E-value=2.7e+02 Score=20.53 Aligned_cols=36 Identities=22% Similarity=0.338 Sum_probs=26.7
Q ss_pred CCeEEEEEeCCCCEEEEEEEEeCCCCceEEeCCcchhhhhcCCCCCCEEEEE
Q 021945 199 KGLLLNFEDSTQKVWRLRYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFW 250 (305)
Q Consensus 199 ~g~~l~v~D~~Gk~W~fr~~~~~~~~~yvLt~GW~~FV~~k~Lk~GD~I~F~ 250 (305)
.-+.+.+.|..| ..++++|.... ...|++||+|.+.
T Consensus 23 ~~~~~~l~D~TG---~i~~~~W~~~~-------------~~~~~~G~vv~i~ 58 (82)
T cd04491 23 KVQSGLVGDETG---TIRFTLWDEKA-------------ADDLEPGDVVRIE 58 (82)
T ss_pred EEEEEEEECCCC---EEEEEEECchh-------------cccCCCCCEEEEE
Confidence 347888889888 47788885431 4568999999886
No 40
>PF05593 RHS_repeat: RHS Repeat; InterPro: IPR006530 These sequences contain two tandem copies of a 21-residue extracellular repeat that is found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin [, , ].
Probab=25.66 E-value=1.1e+02 Score=19.59 Aligned_cols=21 Identities=24% Similarity=0.355 Sum_probs=16.5
Q ss_pred CCCeEEEEEeCCCCEEEEEEE
Q 021945 198 SKGLLLNFEDSTQKVWRLRYC 218 (305)
Q Consensus 198 ~~g~~l~v~D~~Gk~W~fr~~ 218 (305)
..|..+.+.|..|.+|+|.|-
T Consensus 3 ~~G~l~~~~d~~G~~~~y~YD 23 (38)
T PF05593_consen 3 ANGRLTSVTDPDGRTTRYTYD 23 (38)
T ss_pred CCCCEEEEEcCCCCEEEEEEC
Confidence 356778888999999987753
No 41
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.57 E-value=78 Score=25.77 Aligned_cols=18 Identities=28% Similarity=0.374 Sum_probs=14.6
Q ss_pred hhhhhcCCCCCCEEEEEe
Q 021945 234 RFVKEKGVKAGDTVSFWR 251 (305)
Q Consensus 234 ~FV~~k~Lk~GD~I~F~~ 251 (305)
..-+.++.+.||+|+|-.
T Consensus 27 ~d~krr~ik~GD~IiF~~ 44 (111)
T COG4043 27 ADPKRRQIKPGDKIIFNG 44 (111)
T ss_pred cCHhhcCCCCCCEEEEcC
Confidence 455778999999999954
No 42
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=25.33 E-value=1.2e+02 Score=28.01 Aligned_cols=37 Identities=22% Similarity=0.257 Sum_probs=26.6
Q ss_pred CCeEEEEEEeCCeE--EeecCCC--CHHHHHHHHHHHHHhc
Q 021945 41 NGRWGAQIYEKHQR--VWLGTFI--EEEEAARVYDTAALRF 77 (305)
Q Consensus 41 ~grw~A~I~~~~k~--v~LG~f~--t~EeAA~AYD~Aa~~~ 77 (305)
.+.|..+++.+|++ +.||+|+ +.++|..........+
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~ 49 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALL 49 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHH
Confidence 35699999888764 6689995 6777777666655444
No 43
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=25.22 E-value=2.1e+02 Score=30.59 Aligned_cols=48 Identities=13% Similarity=0.029 Sum_probs=29.7
Q ss_pred hhhhhcCCCCCCEEEEEecccCCCCeEEEEEEeccCCCCCCccccccC
Q 021945 234 RFVKEKGVKAGDTVSFWRSNVGSNSKLFIDCKLQQNGNGSGFEEMQSQ 281 (305)
Q Consensus 234 ~FV~~k~Lk~GD~I~F~~~~~~~~~~l~i~~r~~~~~~~~~~~~~~~~ 281 (305)
+++++++++.||+|++++-.+.=-..+.+-..+|+.....-.-|-.||
T Consensus 361 d~I~rkdIrIGDtV~V~kAGdVIP~V~~Vv~e~R~~~~~~~~~P~~CP 408 (667)
T COG0272 361 DEIKRKDIRIGDTVVVRKAGDVIPQVVGVVLEKRPGNEKPIPFPTHCP 408 (667)
T ss_pred HHHHhcCCCCCCEEEEEecCCCCcceeeeecccCCCCCCCCCCCCCCC
Confidence 889999999999999999653323344444455543332222344444
No 44
>PF10729 CedA: Cell division activator CedA; InterPro: IPR019666 CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet [, ]. ; GO: 0003677 DNA binding, 0051301 cell division; PDB: 2BN8_A 2D35_A.
Probab=24.67 E-value=1.4e+02 Score=22.68 Aligned_cols=39 Identities=21% Similarity=0.152 Sum_probs=26.8
Q ss_pred CCceEEeEECCCCeEEEEEEeCCeEEeecCCCCHHHHHHH
Q 021945 30 SSKYKGVVPQPNGRWGAQIYEKHQRVWLGTFIEEEEAARV 69 (305)
Q Consensus 30 ~s~yrGV~~~~~grw~A~I~~~~k~v~LG~f~t~EeAA~A 69 (305)
--+||-| |.-.|||+|.+.....-..--.|..+|.|-+=
T Consensus 30 ~dgfrdv-w~lrgkyvafvl~ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 30 MDGFRDV-WQLRGKYVAFVLMGEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTTECCE-CCCCCEEEEEEESSS-EEE---BSSHHHHHHH
T ss_pred cccccce-eeeccceEEEEEecchhccCCCcCCcHHHHHH
Confidence 3578888 44459999999887666666788888888754
No 45
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=23.39 E-value=2.1e+02 Score=24.27 Aligned_cols=18 Identities=22% Similarity=0.377 Sum_probs=13.2
Q ss_pred hhhcCCCCCCEEEEEecc
Q 021945 236 VKEKGVKAGDTVSFWRSN 253 (305)
Q Consensus 236 V~~k~Lk~GD~I~F~~~~ 253 (305)
=+-.+|++||.|.|+=+-
T Consensus 81 prip~l~~GD~V~f~GeY 98 (131)
T PF11948_consen 81 PRIPWLQKGDQVEFYGEY 98 (131)
T ss_pred ccCcCcCCCCEEEEEEEE
Confidence 344569999999996543
No 46
>PRK11507 ribosome-associated protein; Provisional
Probab=23.33 E-value=77 Score=23.96 Aligned_cols=24 Identities=38% Similarity=0.340 Sum_probs=19.2
Q ss_pred eEEeCCcchhhhhcCCCCCCEEEE
Q 021945 226 YVLTKGWSRFVKEKGVKAGDTVSF 249 (305)
Q Consensus 226 yvLt~GW~~FV~~k~Lk~GD~I~F 249 (305)
.|+-+|=-..-|.++|+.||+|.|
T Consensus 38 ~V~VNGeve~rRgkKl~~GD~V~~ 61 (70)
T PRK11507 38 QVKVDGAVETRKRCKIVAGQTVSF 61 (70)
T ss_pred ceEECCEEecccCCCCCCCCEEEE
Confidence 344455667888999999999988
No 47
>PF12195 End_beta_barrel: Beta barrel domain of bacteriophage endosialidase; InterPro: IPR024427 This entry represents the beta barrel domain of endosialidases which is nested in a beta propeller domain. This beta barrel domain is approximately 80 amino acids in length and represents one of the two sialic acid binding sites of the enzyme [].; PDB: 1V0E_B 1V0F_E 3JU4_A 3GVL_A 3GVK_B 3GVJ_A.
Probab=23.29 E-value=48 Score=25.54 Aligned_cols=33 Identities=21% Similarity=0.406 Sum_probs=15.3
Q ss_pred hhhhcCCCCCCEEEEEecc-cCCCCeEEEEEEec
Q 021945 235 FVKEKGVKAGDTVSFWRSN-VGSNSKLFIDCKLQ 267 (305)
Q Consensus 235 FV~~k~Lk~GD~I~F~~~~-~~~~~~l~i~~r~~ 267 (305)
-+.+++|.+||.|.|.-.. .+-.|.+.+---+.
T Consensus 22 ~l~~HGl~vGD~VnFsnsa~tGvSG~mTVatVid 55 (83)
T PF12195_consen 22 TLTDHGLFVGDFVNFSNSAVTGVSGNMTVATVID 55 (83)
T ss_dssp E-TT----TT-EEEEES-SSTT--EEEEEEEEEE
T ss_pred EEccCceeecceEEEeccccccccccEEEEEEec
Confidence 3568999999999997755 33455555444333
No 48
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=23.11 E-value=55 Score=24.49 Aligned_cols=16 Identities=25% Similarity=0.347 Sum_probs=14.3
Q ss_pred hhhhhcCCCCCCEEEE
Q 021945 234 RFVKEKGVKAGDTVSF 249 (305)
Q Consensus 234 ~FV~~k~Lk~GD~I~F 249 (305)
..++..+|+.||.|.=
T Consensus 34 ~~Irr~~LR~GD~V~G 49 (68)
T cd04459 34 SQIRRFNLRTGDTVVG 49 (68)
T ss_pred HHHHHhCCCCCCEEEE
Confidence 6899999999999954
No 49
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=22.92 E-value=1.1e+02 Score=25.74 Aligned_cols=28 Identities=32% Similarity=0.518 Sum_probs=21.1
Q ss_pred ceEEeCCcchhhhhcCCCCCCEEEEEecc
Q 021945 225 SYVLTKGWSRFVKEKGVKAGDTVSFWRSN 253 (305)
Q Consensus 225 ~yvLt~GW~~FV~~k~Lk~GD~I~F~~~~ 253 (305)
+|+|.-. ...+...++++||.|.|....
T Consensus 96 ~yvLEl~-~G~~~~~~i~vGd~v~~~~~~ 123 (126)
T COG1430 96 RYVLELP-AGWAARLGIKVGDRVEFRPLG 123 (126)
T ss_pred cEEEEec-CCchhhcCCccCCEEEecccC
Confidence 5999821 346789999999999986543
No 50
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=22.25 E-value=1.4e+02 Score=25.80 Aligned_cols=36 Identities=19% Similarity=0.234 Sum_probs=28.9
Q ss_pred EEEEEEeCCeEEeecCCCCHHHHHHHHHHHHHhccCC
Q 021945 44 WGAQIYEKHQRVWLGTFIEEEEAARVYDTAALRFRGQ 80 (305)
Q Consensus 44 w~A~I~~~~k~v~LG~f~t~EeAA~AYD~Aa~~~~G~ 80 (305)
|.|.|.. |+.++-=...+++.|..|.-+|+.+|=+.
T Consensus 96 waArVkp-G~vlfei~g~~e~~A~EAlr~Aa~KLP~~ 131 (146)
T COG0197 96 WAARVKP-GRVLFEIAGVPEELAREALRRAAAKLPVK 131 (146)
T ss_pred EEEEecC-CcEEEEEecCcHHHHHHHHHHHhhcCCCc
Confidence 9999876 66677667788888999999999887443
No 51
>PRK09798 antitoxin MazE; Provisional
Probab=21.48 E-value=2.6e+02 Score=21.49 Aligned_cols=42 Identities=17% Similarity=0.258 Sum_probs=31.7
Q ss_pred EEEEeCCCCceEEeCCcchhhhhcCCCCCCEEEEEecccCCCCeEEEEE
Q 021945 216 RYCYWSSSQSYVLTKGWSRFVKEKGVKAGDTVSFWRSNVGSNSKLFIDC 264 (305)
Q Consensus 216 r~~~~~~~~~yvLt~GW~~FV~~k~Lk~GD~I~F~~~~~~~~~~l~i~~ 264 (305)
....|++|..-.|-. .|+++-+|..||.|.+.-+ ++++.|.-
T Consensus 5 ~v~KwGNS~~vRIPk---~~l~~l~l~~g~~vei~v~----~~~iiI~p 46 (82)
T PRK09798 5 SVKRWGNSPAVRIPA---TLMQALNLNIDDEVKIDLV----DGKLIIEP 46 (82)
T ss_pred EEEEEcCcceEEcCH---HHHHHcCCCCCCEEEEEEE----CCEEEEEE
Confidence 345777776666653 8999999999999998774 47766554
No 52
>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=21.29 E-value=1.1e+02 Score=25.38 Aligned_cols=15 Identities=47% Similarity=0.769 Sum_probs=10.7
Q ss_pred cCCCCCCEEEEEecc
Q 021945 239 KGVKAGDTVSFWRSN 253 (305)
Q Consensus 239 k~Lk~GD~I~F~~~~ 253 (305)
+.+++||.|+||...
T Consensus 38 ~~mk~GD~vifY~s~ 52 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSG 52 (143)
T ss_dssp HC--TT-EEEEEETS
T ss_pred hcCCCCCEEEEEEcC
Confidence 489999999999976
No 53
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=20.71 E-value=3.8e+02 Score=20.24 Aligned_cols=77 Identities=22% Similarity=0.253 Sum_probs=38.4
Q ss_pred eeeecccCCCCCCceEEeeHHHHHhcCCCcccccCCCeEEEEEeCCCCEEEEEEEEeC-CCCceEEeCCcchhhhhcCCC
Q 021945 164 FEKVLTPSDVGKLNRMVIPKQQAEKHFALSSEIASKGLLLNFEDSTQKVWRLRYCYWS-SSQSYVLTKGWSRFVKEKGVK 242 (305)
Q Consensus 164 F~K~Lt~SDv~~~~rL~iPk~~ae~~fP~~~~~~~~g~~l~v~D~~Gk~W~fr~~~~~-~~~~yvLt~GW~~FV~~k~Lk 242 (305)
|+-+|-+.+-+ -.-+.||.+.++.+-.. + -..+.|.+. .+|..|+- +... ....|+|-=. ....+.-++.
T Consensus 1 F~a~l~~~~~~-~~fv~vP~~v~~~l~~~--~--~g~v~V~~t-I~g~~~~~--sl~p~g~G~~~Lpv~-~~vRk~~g~~ 71 (80)
T PF08922_consen 1 FTATLWKGEGG-WTFVEVPFDVAEELGEG--G--WGRVPVRGT-IDGHPWRT--SLFPMGNGGYILPVK-AAVRKAIGKE 71 (80)
T ss_dssp EEEE-EE-TTS--EEEE--S-HHHHH--S------S-EEEEEE-ETTEEEEE--EEEESSTT-EEEEE--HHHHHHHT--
T ss_pred CeEEEEecCCc-eEEEEeCHHHHHHhccc--c--CCceEEEEE-ECCEEEEE--EEEECCCCCEEEEEc-HHHHHHcCCC
Confidence 44455555433 23578998888874322 0 123445443 35666655 4553 4456777510 4788899999
Q ss_pred CCCEEEE
Q 021945 243 AGDTVSF 249 (305)
Q Consensus 243 ~GD~I~F 249 (305)
+||.|.+
T Consensus 72 ~Gd~V~v 78 (80)
T PF08922_consen 72 AGDTVEV 78 (80)
T ss_dssp TTSEEEE
T ss_pred CCCEEEE
Confidence 9999976
No 54
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=20.62 E-value=1.6e+02 Score=21.80 Aligned_cols=23 Identities=30% Similarity=0.381 Sum_probs=14.9
Q ss_pred hhhhcCCCCCCEEEEEecccCCCC
Q 021945 235 FVKEKGVKAGDTVSFWRSNVGSNS 258 (305)
Q Consensus 235 FV~~k~Lk~GD~I~F~~~~~~~~~ 258 (305)
-+.-.+|++||.|.|.-.. .+++
T Consensus 37 ~~~l~~l~~Gd~V~F~~~~-~~~~ 59 (70)
T PF11604_consen 37 PVDLAGLKPGDKVRFTFER-TDDG 59 (70)
T ss_dssp TSEESS-STT-EEEEEEEE-ETTC
T ss_pred hhhhhcCCCCCEEEEEEEE-CCCC
Confidence 3445789999999998776 3444
No 55
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=20.38 E-value=1.1e+02 Score=25.03 Aligned_cols=15 Identities=20% Similarity=0.275 Sum_probs=12.5
Q ss_pred cCCCCCCEEEEEecc
Q 021945 239 KGVKAGDTVSFWRSN 253 (305)
Q Consensus 239 k~Lk~GD~I~F~~~~ 253 (305)
+-|+.||.|++.++-
T Consensus 49 ~~L~dGDsV~liKDL 63 (109)
T TIGR00686 49 NLLANGDSVILIKDL 63 (109)
T ss_pred CCccCCCEEEEEeec
Confidence 458899999999876
Done!