Query 019261
Match_columns 343
No_of_seqs 181 out of 491
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 08:01:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019261.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019261hhsearch_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 99.9 6.7E-21 1.5E-25 151.8 12.1 99 99-208 1-99 (100)
2 PF03754 DUF313: Domain of unk 98.6 3.6E-08 7.7E-13 84.1 5.4 87 93-180 18-114 (114)
3 PF09217 EcoRII-N: Restriction 98.1 1.5E-05 3.2E-10 71.5 8.2 94 94-193 5-111 (156)
4 PF06507 Auxin_resp: Auxin res 93.8 0.015 3.2E-07 47.4 -0.4 35 219-259 1-36 (83)
5 PRK11347 antitoxin ChpS; Provi 57.6 42 0.00091 27.3 6.3 44 157-206 3-46 (83)
6 PF02261 Asp_decarbox: Asparta 54.4 1.5E+02 0.0032 26.0 9.4 77 96-193 8-89 (116)
7 PF04014 Antitoxin-MazE: Antid 54.1 21 0.00046 25.3 3.6 37 163-204 4-40 (47)
8 PF08922 DUF1905: Domain of un 53.7 1E+02 0.0022 24.5 7.9 79 99-192 1-79 (80)
9 PRK06461 single-stranded DNA-b 51.4 60 0.0013 27.9 6.7 34 142-192 41-74 (129)
10 cd06919 Asp_decarbox Aspartate 50.0 1.6E+02 0.0035 25.7 8.9 77 96-193 7-88 (111)
11 TIGR00223 panD L-aspartate-alp 49.5 1.5E+02 0.0032 26.4 8.8 77 96-193 8-89 (126)
12 PF10844 DUF2577: Protein of u 49.1 44 0.00095 27.7 5.3 26 177-203 71-96 (100)
13 PRK05449 aspartate alpha-decar 48.3 1.6E+02 0.0035 26.1 8.8 76 97-193 9-89 (126)
14 PRK09798 antitoxin MazE; Provi 47.6 79 0.0017 25.6 6.4 43 158-206 5-47 (82)
15 TIGR02609 doc_partner putative 45.0 61 0.0013 25.4 5.2 43 160-210 4-46 (74)
16 PRK09838 periplasmic copper-bi 43.9 42 0.0009 29.0 4.5 27 181-207 87-113 (115)
17 smart00536 AXH domain in Ataxi 41.9 13 0.00028 32.5 1.0 27 166-192 77-113 (116)
18 PF11604 CusF_Ec: Copper bindi 41.1 46 0.00099 25.9 4.0 27 181-207 41-68 (70)
19 TIGR01439 lp_hng_hel_AbrB loop 40.0 59 0.0013 21.9 4.0 27 175-203 13-39 (43)
20 PF02643 DUF192: Uncharacteriz 37.0 79 0.0017 26.4 5.1 50 142-192 49-107 (108)
21 cd04491 SoSSB_OBF SoSSB_OBF: A 35.1 1.7E+02 0.0037 22.5 6.4 50 142-207 24-75 (82)
22 PRK03760 hypothetical protein; 35.0 83 0.0018 27.0 5.0 26 165-193 89-116 (117)
23 cd04451 S1_IF1 S1_IF1: Transla 33.9 1.8E+02 0.0039 21.7 6.1 15 181-195 39-53 (64)
24 PF03120 DNA_ligase_OB: NAD-de 33.1 33 0.00072 28.0 2.1 20 175-194 42-61 (82)
25 PF08517 AXH: Ataxin-1 and HBP 32.5 9.8 0.00021 33.0 -1.1 26 166-191 76-111 (115)
26 PRK09937 stationary phase/star 31.6 1.7E+02 0.0037 23.1 5.9 34 175-208 32-67 (74)
27 cd02775 MopB_CT Molybdopterin- 28.5 1.1E+02 0.0025 23.6 4.5 36 176-214 30-65 (101)
28 cd04458 CSP_CDS Cold-Shock Pro 27.5 2.5E+02 0.0055 20.6 6.7 25 175-199 31-57 (65)
29 PF14250 AbrB-like: AbrB-like 27.3 1.8E+02 0.0039 23.5 5.3 43 149-195 23-65 (71)
30 cd06555 ASCH_PF0470_like ASC-1 26.7 83 0.0018 27.0 3.5 29 181-210 30-58 (109)
31 PF12195 End_beta_barrel: Beta 26.6 36 0.00078 28.0 1.2 18 178-195 23-40 (83)
32 cd02792 MopB_CT_Formate-Dh-Na- 24.6 1.4E+02 0.0031 24.2 4.5 38 176-216 42-79 (122)
33 cd04485 DnaE_OBF DnaE_OBF: A s 24.5 2.8E+02 0.006 20.1 5.8 52 143-207 21-73 (84)
34 PF01878 EVE: EVE domain; Int 24.3 89 0.0019 26.7 3.4 27 181-208 38-64 (143)
35 TIGR01643 YD_repeat_2x YD repe 24.0 1.2E+02 0.0025 20.4 3.3 20 142-161 5-24 (42)
36 cd04498 hPOT1_OB2 hPOT1_OB2: A 23.5 99 0.0022 27.1 3.5 17 175-193 71-87 (123)
37 cd02779 MopB_CT_Arsenite-Ox Th 23.2 1.5E+02 0.0033 24.2 4.4 38 176-216 40-77 (115)
38 COG5569 Uncharacterized conser 22.4 91 0.002 26.9 2.9 24 179-203 80-103 (108)
39 COG2002 AbrB Regulators of sta 21.9 1.5E+02 0.0033 23.9 4.1 33 176-211 21-53 (89)
40 KOG3408 U1-like Zn-finger-cont 21.9 29 0.00062 30.8 -0.1 13 323-335 55-68 (129)
41 cd02786 MopB_CT_3 The MopB_CT_ 21.7 1.7E+02 0.0036 23.7 4.3 38 176-216 38-75 (116)
42 PRK09974 putative regulator Pr 21.5 1.8E+02 0.0038 25.3 4.6 33 175-211 24-56 (111)
43 PRK09570 rpoH DNA-directed RNA 20.9 1.2E+02 0.0026 24.8 3.2 25 176-200 45-69 (79)
44 cd00508 MopB_CT_Fdh-Nap-like T 20.8 1.9E+02 0.0042 23.1 4.5 38 176-216 42-79 (120)
45 PLN03148 Blue copper-like prot 20.1 1.2E+02 0.0025 28.0 3.4 18 178-195 41-58 (167)
46 PF04970 LRAT: Lecithin retino 20.0 68 0.0015 26.8 1.8 18 177-194 1-18 (125)
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=99.85 E-value=6.7e-21 Score=151.82 Aligned_cols=99 Identities=34% Similarity=0.564 Sum_probs=75.6
Q ss_pred EEEecccCCCCCCCcEEeehhhHhhcCCCCCCCCCCCCCCCCCceEEEEEcCCCCeEEEEEEEecCCCceEEccChHHHH
Q 019261 99 FEKPLTPSDVGKLNRLVIPKQHAEKYFPLGGGGADLGSSSSDKGLLLSFEDESGKCWRFRYSYWNSSQSYVLTKGWSRYV 178 (343)
Q Consensus 99 F~K~LT~SDVs~~gRLvIPK~~AE~~fP~l~~s~d~~~~~~~~gi~L~v~D~~Gk~W~FR~sywnssrryvLT~GWs~FV 178 (343)
|.|+|+++|+...++|.||+++++++... +..++.+.++|..|++|.+++++++.+.+++|++||.+||
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~-----------~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv 69 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGN-----------KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFV 69 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHH
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCCC-----------cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHH
Confidence 89999999999889999999999998211 1235678999999999999999998888899999999999
Q ss_pred hhcCCCCCCEEEEEEeeCCCCcEEEEEEEc
Q 019261 179 KEKRLDAGDVILFERHRTDSERLFIGWRRR 208 (343)
Q Consensus 179 kdK~LkaGD~VvF~r~~~~~g~L~IgIRR~ 208 (343)
++|+|++||+|+|++..+...++.|.|.|+
T Consensus 70 ~~n~L~~GD~~~F~~~~~~~~~~~v~i~~~ 99 (100)
T PF02362_consen 70 RDNGLKEGDVCVFELIGNSNFTLKVHIFRK 99 (100)
T ss_dssp HHCT--TT-EEEEEE-SSSCE-EEEEEE--
T ss_pred HHcCCCCCCEEEEEEecCCCceEEEEEEEC
Confidence 999999999999999864455679999986
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=98.65 E-value=3.6e-08 Score=84.14 Aligned_cols=87 Identities=25% Similarity=0.497 Sum_probs=66.1
Q ss_pred cCccceEEEecccCCCC-CCCcEEeehhhHhh--cCCCCCCCCCC----CCCCCCCceEEEEEcCCCCeEEEEEEEecC-
Q 019261 93 LEKEPMFEKPLTPSDVG-KLNRLVIPKQHAEK--YFPLGGGGADL----GSSSSDKGLLLSFEDESGKCWRFRYSYWNS- 164 (343)
Q Consensus 93 ~~k~~lF~K~LT~SDVs-~~gRLvIPK~~AE~--~fP~l~~s~d~----~~~~~~~gi~L~v~D~~Gk~W~FR~sywns- 164 (343)
.+...+++|+|+.|||. .++||+||...... +|-..+. +.+ .......|+.+.+.|..++.|..+++.|..
T Consensus 18 ~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~-~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg 96 (114)
T PF03754_consen 18 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEK-RIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMG 96 (114)
T ss_pred CCCeEEEeeeecccCCCCCCceeeccHHHhcccccCCHHHH-HHHHHhhccCcccCCceEEEECCcCcEEEEEEEEeccc
Confidence 34578999999999998 67899999988744 2322111 001 012346789999999999999999999965
Q ss_pred --CCceEEccChHHHHhh
Q 019261 165 --SQSYVLTKGWSRYVKE 180 (343)
Q Consensus 165 --srryvLT~GWs~FVkd 180 (343)
...|+|.+||.++|++
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 4689999999999874
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=98.07 E-value=1.5e-05 Score=71.48 Aligned_cols=94 Identities=21% Similarity=0.351 Sum_probs=58.5
Q ss_pred CccceEEEecccCCCCCC----CcEEeehhhHhhcCCCCCCCCCCCCCCCCCceEEEEEcCCC--CeEEEEEEEecC---
Q 019261 94 EKEPMFEKPLTPSDVGKL----NRLVIPKQHAEKYFPLGGGGADLGSSSSDKGLLLSFEDESG--KCWRFRYSYWNS--- 164 (343)
Q Consensus 94 ~k~~lF~K~LT~SDVs~~----gRLvIPK~~AE~~fP~l~~s~d~~~~~~~~gi~L~v~D~~G--k~W~FR~sywns--- 164 (343)
....+|+|.|++.|++.. .++.|||..++.+||.+.... ..++.+.|.+++..+ ..|+||++|.|+
T Consensus 5 ~~~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~-----~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~ 79 (156)
T PF09217_consen 5 DSWAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTK-----EENPDIWLKARWQSHFVTDSQVRFIYYNNRLF 79 (156)
T ss_dssp SSEEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSS-----SSS-EEEEEEEETTTT---EEEEEEEE-CCCT
T ss_pred cceEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCccc-----ccCCceeEEEEECCCCccceeEEEEEEccccc
Confidence 345689999999999843 479999999999998866531 134578888888877 679999999987
Q ss_pred ---CCceEEccChHHHHhhcC-CCCCCEEEEEE
Q 019261 165 ---SQSYVLTKGWSRYVKEKR-LDAGDVILFER 193 (343)
Q Consensus 165 ---srryvLT~GWs~FVkdK~-LkaGD~VvF~r 193 (343)
...|.||. |.....--+ =.+||.++|.-
T Consensus 80 ~gTRNE~RIT~-~G~~~~~~~~~~tGaL~vlaf 111 (156)
T PF09217_consen 80 GGTRNEYRITR-FGRGFPLQNPENTGALLVLAF 111 (156)
T ss_dssp TSS--EEEEE----TTSGGG-GGGTT-EEEEEE
T ss_pred CCCcCceEEee-ecCCCccCCccccccEEEEEE
Confidence 35589964 775444222 25799888873
No 4
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=93.81 E-value=0.015 Score=47.41 Aligned_cols=35 Identities=29% Similarity=0.352 Sum_probs=29.0
Q ss_pred ccccccCCCCCCCcccCCCCCCCCCCCCCCCCc-cccccccc
Q 019261 219 AGGAAAGGCGWPRGLYPNHPYPVDVAHGHGVSA-PLYQHAGS 259 (343)
Q Consensus 219 ~~~~~~~~~~f~~v~y~~~~~ps~~~~~~~~~~-~~~~~Ag~ 259 (343)
|+++++++++| .|+|+||+.+++| |.+ .+|..|..
T Consensus 1 A~~aa~~~~~F-~V~Y~PRa~~sEF-----VV~~~k~~~al~ 36 (83)
T PF06507_consen 1 AAHAAATGSPF-EVFYYPRASPSEF-----VVPASKYDKALN 36 (83)
T ss_pred ChhHhhcCCeE-EEEECCCCCCcce-----EEEHHHHHHHhc
Confidence 56889999999 7999999999999 555 67777744
No 5
>PRK11347 antitoxin ChpS; Provisional
Probab=57.58 E-value=42 Score=27.26 Aligned_cols=44 Identities=18% Similarity=0.286 Sum_probs=34.3
Q ss_pred EEEEEecCCCceEEccChHHHHhhcCCCCCCEEEEEEeeCCCCcEEEEEE
Q 019261 157 FRYSYWNSSQSYVLTKGWSRYVKEKRLDAGDVILFERHRTDSERLFIGWR 206 (343)
Q Consensus 157 FR~sywnssrryvLT~GWs~FVkdK~LkaGD~VvF~r~~~~~g~L~IgIR 206 (343)
.+.+.|++|..-.|.+ .|++.-+|.+||.|.+.... +.+.|.-.
T Consensus 3 ~~v~kwGNS~~vriPk---~il~~l~l~~G~~v~i~v~~---~~iii~p~ 46 (83)
T PRK11347 3 ITIKRWGNSAGMVIPN---IVMKELNLQPGQSVEAQVSN---NQLILTPI 46 (83)
T ss_pred EEEEEEcCceeEEeCH---HHHHHcCCCCCCEEEEEEEC---CEEEEEEC
Confidence 3566788888888865 89999999999999988873 45666443
No 6
>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=54.44 E-value=1.5e+02 Score=26.04 Aligned_cols=77 Identities=13% Similarity=0.234 Sum_probs=47.5
Q ss_pred cceEEEecccCCCCCCCcEEeehhhHhh--cCCCCCCCCCCCCCCCCCceEEEEEcC-CCCeEEEEEEEec--CCCceEE
Q 019261 96 EPMFEKPLTPSDVGKLNRLVIPKQHAEK--YFPLGGGGADLGSSSSDKGLLLSFEDE-SGKCWRFRYSYWN--SSQSYVL 170 (343)
Q Consensus 96 ~~lF~K~LT~SDVs~~gRLvIPK~~AE~--~fP~l~~s~d~~~~~~~~gi~L~v~D~-~Gk~W~FR~sywn--ssrryvL 170 (343)
..+=..+.|..|+...|.+.|..+..+. ++|.. .+.+.+. +|..|.- |.+.+ .|+.-.|
T Consensus 8 sKiHratVT~a~L~Y~GSitID~~Ll~aagi~p~E---------------~V~V~Nv~nG~Rf~T-YvI~g~~GSg~I~l 71 (116)
T PF02261_consen 8 SKIHRATVTEADLNYEGSITIDEDLLDAAGILPYE---------------QVQVVNVNNGERFET-YVIPGERGSGVICL 71 (116)
T ss_dssp EEEEEEE--EEETTSTSCEEEEHHHHHHCT--TTB---------------EEEEEETTT--EEEE-EEEEESTTTT-EEE
T ss_pred hhhcceEEeccccccceeeEECHHHHHHcCCCcCC---------------EEEEEECCCCcEEEE-EEEEccCCCcEEEE
Confidence 3455678999999999999999999876 34432 3567775 6887775 33432 2355666
Q ss_pred ccChHHHHhhcCCCCCCEEEEEE
Q 019261 171 TKGWSRYVKEKRLDAGDVILFER 193 (343)
Q Consensus 171 T~GWs~FVkdK~LkaGD~VvF~r 193 (343)
.+ .-++..++||.|+++-
T Consensus 72 NG-----aAArl~~~GD~vII~s 89 (116)
T PF02261_consen 72 NG-----AAARLVQVGDRVIIMS 89 (116)
T ss_dssp EG-----GGGGCS-TT-EEEEEE
T ss_pred CC-----HHHhccCCCCEEEEEE
Confidence 55 5677889999999854
No 7
>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=54.09 E-value=21 Score=25.34 Aligned_cols=37 Identities=16% Similarity=0.240 Sum_probs=25.4
Q ss_pred cCCCceEEccChHHHHhhcCCCCCCEEEEEEeeCCCCcEEEE
Q 019261 163 NSSQSYVLTKGWSRYVKEKRLDAGDVILFERHRTDSERLFIG 204 (343)
Q Consensus 163 nssrryvLT~GWs~FVkdK~LkaGD~VvF~r~~~~~g~L~Ig 204 (343)
+++..-.|- ..|.+..+|++||.|.|.-.. ++++.|.
T Consensus 4 g~s~~v~iP---k~~~~~l~l~~Gd~v~i~~~~--~g~i~i~ 40 (47)
T PF04014_consen 4 GNSGQVTIP---KEIREKLGLKPGDEVEIEVEG--DGKIVIR 40 (47)
T ss_dssp TTCSEEEE----HHHHHHTTSSTTTEEEEEEET--TSEEEEE
T ss_pred CCCceEECC---HHHHHHcCCCCCCEEEEEEeC--CCEEEEE
Confidence 334444443 477888899999999999884 3466553
No 8
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=53.70 E-value=1e+02 Score=24.49 Aligned_cols=79 Identities=20% Similarity=0.162 Sum_probs=41.1
Q ss_pred EEEecccCCCCCCCcEEeehhhHhhcCCCCCCCCCCCCCCCCCceEEEEEcCCCCeEEEEEEEecCCCceEEccChHHHH
Q 019261 99 FEKPLTPSDVGKLNRLVIPKQHAEKYFPLGGGGADLGSSSSDKGLLLSFEDESGKCWRFRYSYWNSSQSYVLTKGWSRYV 178 (343)
Q Consensus 99 F~K~LT~SDVs~~gRLvIPK~~AE~~fP~l~~s~d~~~~~~~~gi~L~v~D~~Gk~W~FR~sywnssrryvLT~GWs~FV 178 (343)
|..+|-+..-+. --+.||.+.++.+-.. + ...+.+.+. ..|.+|+-...- .....|+|-= =....
T Consensus 1 F~a~l~~~~~~~-~fv~vP~~v~~~l~~~-~----------~g~v~V~~t-I~g~~~~~sl~p-~g~G~~~Lpv-~~~vR 65 (80)
T PF08922_consen 1 FTATLWKGEGGW-TFVEVPFDVAEELGEG-G----------WGRVPVRGT-IDGHPWRTSLFP-MGNGGYILPV-KAAVR 65 (80)
T ss_dssp EEEE-EE-TTS--EEEE--S-HHHHH--S-------------S-EEEEEE-ETTEEEEEEEEE-SSTT-EEEEE--HHHH
T ss_pred CeEEEEecCCce-EEEEeCHHHHHHhccc-c----------CCceEEEEE-ECCEEEEEEEEE-CCCCCEEEEE-cHHHH
Confidence 555666554432 2467999999887433 1 123444443 467788775544 2345676622 15788
Q ss_pred hhcCCCCCCEEEEE
Q 019261 179 KEKRLDAGDVILFE 192 (343)
Q Consensus 179 kdK~LkaGD~VvF~ 192 (343)
++-++.+||.|.+.
T Consensus 66 k~~g~~~Gd~V~v~ 79 (80)
T PF08922_consen 66 KAIGKEAGDTVEVT 79 (80)
T ss_dssp HHHT--TTSEEEEE
T ss_pred HHcCCCCCCEEEEE
Confidence 88999999999875
No 9
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=51.36 E-value=60 Score=27.95 Aligned_cols=34 Identities=24% Similarity=0.474 Sum_probs=25.9
Q ss_pred ceEEEEEcCCCCeEEEEEEEecCCCceEEccChHHHHhhcCCCCCCEEEEE
Q 019261 142 GLLLSFEDESGKCWRFRYSYWNSSQSYVLTKGWSRYVKEKRLDAGDVILFE 192 (343)
Q Consensus 142 gi~L~v~D~~Gk~W~FR~sywnssrryvLT~GWs~FVkdK~LkaGD~VvF~ 192 (343)
-..+.+.|..|. ++++.|+. .+..|++||+|.+.
T Consensus 41 v~~~~l~D~TG~---I~~tlW~~--------------~a~~l~~GdvV~I~ 74 (129)
T PRK06461 41 ISEAVVGDETGR---VKLTLWGE--------------QAGSLKEGEVVEIE 74 (129)
T ss_pred EEEEEEECCCCE---EEEEEeCC--------------ccccCCCCCEEEEE
Confidence 346778899996 67778854 23468999999997
No 10
>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=50.05 E-value=1.6e+02 Score=25.65 Aligned_cols=77 Identities=14% Similarity=0.191 Sum_probs=54.9
Q ss_pred cceEEEecccCCCCCCCcEEeehhhHhh--cCCCCCCCCCCCCCCCCCceEEEEEcC-CCCeEEEEEEEec--CCCceEE
Q 019261 96 EPMFEKPLTPSDVGKLNRLVIPKQHAEK--YFPLGGGGADLGSSSSDKGLLLSFEDE-SGKCWRFRYSYWN--SSQSYVL 170 (343)
Q Consensus 96 ~~lF~K~LT~SDVs~~gRLvIPK~~AE~--~fP~l~~s~d~~~~~~~~gi~L~v~D~-~Gk~W~FR~sywn--ssrryvL 170 (343)
..+=..+.|..|+...|.+.|..+..+. ++|.. .+.++|. +|..|.- |.+.+ .|+.-.|
T Consensus 7 sKiHratVT~a~L~YeGSitID~~Ll~aagi~~~E---------------~V~I~Nv~NG~Rf~T-YvI~g~~gSg~I~l 70 (111)
T cd06919 7 SKIHRATVTEADLNYEGSITIDEDLLEAAGILPYE---------------KVLVVNVNNGARFET-YVIPGERGSGVICL 70 (111)
T ss_pred hcccceEEeccccccceeEEECHHHHHhcCCCCCC---------------EEEEEECCCCcEEEE-EEEEcCCCCCEEEe
Confidence 3455678899999998999999998876 34432 3567776 6887765 44443 3455666
Q ss_pred ccChHHHHhhcCCCCCCEEEEEE
Q 019261 171 TKGWSRYVKEKRLDAGDVILFER 193 (343)
Q Consensus 171 T~GWs~FVkdK~LkaGD~VvF~r 193 (343)
.+ .-++..+.||.|++.-
T Consensus 71 NG-----AAAr~~~~GD~vII~s 88 (111)
T cd06919 71 NG-----AAARLGQPGDRVIIMA 88 (111)
T ss_pred CC-----HHHhcCCCCCEEEEEE
Confidence 55 5677789999999865
No 11
>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=49.48 E-value=1.5e+02 Score=26.38 Aligned_cols=77 Identities=10% Similarity=0.220 Sum_probs=55.1
Q ss_pred cceEEEecccCCCCCCCcEEeehhhHhh--cCCCCCCCCCCCCCCCCCceEEEEEcC-CCCeEEEEEEEecC--CCceEE
Q 019261 96 EPMFEKPLTPSDVGKLNRLVIPKQHAEK--YFPLGGGGADLGSSSSDKGLLLSFEDE-SGKCWRFRYSYWNS--SQSYVL 170 (343)
Q Consensus 96 ~~lF~K~LT~SDVs~~gRLvIPK~~AE~--~fP~l~~s~d~~~~~~~~gi~L~v~D~-~Gk~W~FR~sywns--srryvL 170 (343)
..+=..+.|..|+...|.+.|..+..+. ++|.. .+.+.|. +|..|.- |.+.+. |+.-.|
T Consensus 8 sKIHratVT~a~L~Y~GSItID~~Lm~aagi~p~E---------------~V~V~Nv~NG~Rf~T-YvI~G~~GSg~I~l 71 (126)
T TIGR00223 8 GKLHRATVTHANLNYEGSITIDEDLLDAAGILENE---------------KVDIVNVNNGKRFST-YAIAGKRGSRIICV 71 (126)
T ss_pred hhhcceEEeccccccceeEEECHHHHHhcCCCCCC---------------EEEEEECCCCcEEEE-EEEEcCCCCCEEEe
Confidence 3455678899999988999999998876 34442 3567776 6887775 444433 455666
Q ss_pred ccChHHHHhhcCCCCCCEEEEEE
Q 019261 171 TKGWSRYVKEKRLDAGDVILFER 193 (343)
Q Consensus 171 T~GWs~FVkdK~LkaGD~VvF~r 193 (343)
.+ .-++..++||.|+++-
T Consensus 72 NG-----AAArl~~~GD~VII~s 89 (126)
T TIGR00223 72 NG-----AAARCVSVGDIVIIAS 89 (126)
T ss_pred CC-----HHHhcCCCCCEEEEEE
Confidence 55 5677789999999865
No 12
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=49.09 E-value=44 Score=27.68 Aligned_cols=26 Identities=19% Similarity=0.374 Sum_probs=19.6
Q ss_pred HHhhcCCCCCCEEEEEEeeCCCCcEEE
Q 019261 177 YVKEKRLDAGDVILFERHRTDSERLFI 203 (343)
Q Consensus 177 FVkdK~LkaGD~VvF~r~~~~~g~L~I 203 (343)
|.-...|++||.|...+.. +|.+|+|
T Consensus 71 i~~~~~Lk~GD~V~ll~~~-~gQ~yiV 96 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQ-GGQKYIV 96 (100)
T ss_pred EEEecCCcCCCEEEEEEec-CCCEEEE
Confidence 5556789999999999975 2445555
No 13
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=48.27 E-value=1.6e+02 Score=26.12 Aligned_cols=76 Identities=12% Similarity=0.211 Sum_probs=54.5
Q ss_pred ceEEEecccCCCCCCCcEEeehhhHhh--cCCCCCCCCCCCCCCCCCceEEEEEcC-CCCeEEEEEEEecC--CCceEEc
Q 019261 97 PMFEKPLTPSDVGKLNRLVIPKQHAEK--YFPLGGGGADLGSSSSDKGLLLSFEDE-SGKCWRFRYSYWNS--SQSYVLT 171 (343)
Q Consensus 97 ~lF~K~LT~SDVs~~gRLvIPK~~AE~--~fP~l~~s~d~~~~~~~~gi~L~v~D~-~Gk~W~FR~sywns--srryvLT 171 (343)
.+=..+.|..|+...|.+.|..+..++ ++|.. .+.+++. +|..|.- |.+.+. |+.-.|.
T Consensus 9 KiHratVT~a~L~Y~GSitID~~Ll~aagi~p~E---------------~V~V~Nv~NG~Rf~T-YvI~g~~GSg~I~lN 72 (126)
T PRK05449 9 KIHRATVTEADLNYEGSITIDEDLLDAAGILENE---------------KVQIVNVNNGARFET-YVIAGERGSGVICLN 72 (126)
T ss_pred cccceEEeccccccceeEEECHHHHHhcCCCCCC---------------EEEEEECCCCcEEEE-EEEEcCCCCCEEEeC
Confidence 455678899999988999999999877 34442 3567776 6887764 444433 4556665
Q ss_pred cChHHHHhhcCCCCCCEEEEEE
Q 019261 172 KGWSRYVKEKRLDAGDVILFER 193 (343)
Q Consensus 172 ~GWs~FVkdK~LkaGD~VvF~r 193 (343)
+ .-++..+.||.|++.-
T Consensus 73 G-----AAAr~~~~GD~vII~a 89 (126)
T PRK05449 73 G-----AAARLVQVGDLVIIAA 89 (126)
T ss_pred C-----HHHhcCCCCCEEEEEE
Confidence 5 5677889999999865
No 14
>PRK09798 antitoxin MazE; Provisional
Probab=47.55 E-value=79 Score=25.63 Aligned_cols=43 Identities=14% Similarity=0.223 Sum_probs=33.6
Q ss_pred EEEEecCCCceEEccChHHHHhhcCCCCCCEEEEEEeeCCCCcEEEEEE
Q 019261 158 RYSYWNSSQSYVLTKGWSRYVKEKRLDAGDVILFERHRTDSERLFIGWR 206 (343)
Q Consensus 158 R~sywnssrryvLT~GWs~FVkdK~LkaGD~VvF~r~~~~~g~L~IgIR 206 (343)
+...|++|..-.|-+ .|+++-+|..||.|.+... ++++.|.-.
T Consensus 5 ~v~KwGNS~~vRIPk---~~l~~l~l~~g~~vei~v~---~~~iiI~p~ 47 (82)
T PRK09798 5 SVKRWGNSPAVRIPA---TLMQALNLNIDDEVKIDLV---DGKLIIEPV 47 (82)
T ss_pred EEEEEcCcceEEcCH---HHHHHcCCCCCCEEEEEEE---CCEEEEEEC
Confidence 356788888777754 8999999999999999886 467776443
No 15
>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=45.01 E-value=61 Score=25.44 Aligned_cols=43 Identities=19% Similarity=0.234 Sum_probs=29.8
Q ss_pred EEecCCCceEEccChHHHHhhcCCCCCCEEEEEEeeCCCCcEEEEEEEcCC
Q 019261 160 SYWNSSQSYVLTKGWSRYVKEKRLDAGDVILFERHRTDSERLFIGWRRRGA 210 (343)
Q Consensus 160 sywnssrryvLT~GWs~FVkdK~LkaGD~VvF~r~~~~~g~L~IgIRR~~~ 210 (343)
..|++|..-.|-+ .++..-+|..||.|.|... ++.+.| ++...
T Consensus 4 ~k~GNS~~vtIPk---~i~~~lgl~~Gd~v~v~~~---~~~iii--~~~~~ 46 (74)
T TIGR02609 4 RKVGNSLVVTLPK---EVLESLGLKEGDTLYVDEE---EGGLKL--KRFDE 46 (74)
T ss_pred EEECCeeEEEECH---HHHHHcCcCCCCEEEEEEE---CCEEEE--EECCC
Confidence 4577665556654 7788999999999988766 345655 44443
No 16
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=43.89 E-value=42 Score=28.97 Aligned_cols=27 Identities=15% Similarity=0.263 Sum_probs=20.6
Q ss_pred cCCCCCCEEEEEEeeCCCCcEEEEEEE
Q 019261 181 KRLDAGDVILFERHRTDSERLFIGWRR 207 (343)
Q Consensus 181 K~LkaGD~VvF~r~~~~~g~L~IgIRR 207 (343)
++|++||.|.|.....+++-+.+.|+.
T Consensus 87 ~~lk~G~~V~F~~~~~~~~~~i~~i~~ 113 (115)
T PRK09838 87 SEIKTGDKVAFNFVQQGNLSLLQDIKV 113 (115)
T ss_pred ccCCCCCEEEEEEEEcCCcEEEEEEee
Confidence 479999999998766555666677765
No 17
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=41.93 E-value=13 Score=32.50 Aligned_cols=27 Identities=37% Similarity=0.466 Sum_probs=21.2
Q ss_pred CceEEccChHHHH----------hhcCCCCCCEEEEE
Q 019261 166 QSYVLTKGWSRYV----------KEKRLDAGDVILFE 192 (343)
Q Consensus 166 rryvLT~GWs~FV----------kdK~LkaGD~VvF~ 192 (343)
.-||..+||+.|- .-..|.+||+|+-.
T Consensus 77 PfFV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~l 113 (116)
T smart00536 77 PFFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLSL 113 (116)
T ss_pred CeEEcCccccccChhhhhhhcCCcceecccCCEEecc
Confidence 5688899999885 34678999999853
No 18
>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=41.06 E-value=46 Score=25.86 Aligned_cols=27 Identities=26% Similarity=0.347 Sum_probs=17.3
Q ss_pred cCCCCCCEEEEEEeeCCCCcE-EEEEEE
Q 019261 181 KRLDAGDVILFERHRTDSERL-FIGWRR 207 (343)
Q Consensus 181 K~LkaGD~VvF~r~~~~~g~L-~IgIRR 207 (343)
.+|++||.|.|.-...+++.+ ...|++
T Consensus 41 ~~l~~Gd~V~F~~~~~~~~~~~I~~i~~ 68 (70)
T PF11604_consen 41 AGLKPGDKVRFTFERTDDGSYVITAIEP 68 (70)
T ss_dssp SS-STT-EEEEEEEEETTCEEEEEEEEE
T ss_pred hcCCCCCEEEEEEEECCCCcEEEEEEEE
Confidence 569999999998877655534 444544
No 19
>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=40.03 E-value=59 Score=21.87 Aligned_cols=27 Identities=15% Similarity=0.225 Sum_probs=21.5
Q ss_pred HHHHhhcCCCCCCEEEEEEeeCCCCcEEE
Q 019261 175 SRYVKEKRLDAGDVILFERHRTDSERLFI 203 (343)
Q Consensus 175 s~FVkdK~LkaGD~VvF~r~~~~~g~L~I 203 (343)
..|.+.-+++.||.|.+.... ++.+.|
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~--~~~l~l 39 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVE--DGEIIL 39 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeC--CCEEEE
Confidence 478999999999999999764 345544
No 20
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=36.99 E-value=79 Score=26.37 Aligned_cols=50 Identities=22% Similarity=0.431 Sum_probs=28.5
Q ss_pred ceEEEEEcCCCCeEEEEEEE--e-------cCCCceEEccChHHHHhhcCCCCCCEEEEE
Q 019261 142 GLLLSFEDESGKCWRFRYSY--W-------NSSQSYVLTKGWSRYVKEKRLDAGDVILFE 192 (343)
Q Consensus 142 gi~L~v~D~~Gk~W~FR~sy--w-------nssrryvLT~GWs~FVkdK~LkaGD~VvF~ 192 (343)
.+.+.+.|.+|+.-...... | ..+-+|+|.-. ..++...+|++||.|.|.
T Consensus 49 pLDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~-aG~~~~~~i~~Gd~v~~~ 107 (108)
T PF02643_consen 49 PLDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELP-AGWFEKLGIKVGDRVRIE 107 (108)
T ss_dssp -EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEE-TTHHHHHT--TT-EEE--
T ss_pred eEEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcC-CCchhhcCCCCCCEEEec
Confidence 36677788888766555443 1 12246888542 456789999999999874
No 21
>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=35.14 E-value=1.7e+02 Score=22.48 Aligned_cols=50 Identities=26% Similarity=0.434 Sum_probs=32.0
Q ss_pred ceEEEEEcCCCCeEEEEEEEecCCCceEEccChHHHHhhcCCCCCCEEEEEEe--eCCCCcEEEEEEE
Q 019261 142 GLLLSFEDESGKCWRFRYSYWNSSQSYVLTKGWSRYVKEKRLDAGDVILFERH--RTDSERLFIGWRR 207 (343)
Q Consensus 142 gi~L~v~D~~Gk~W~FR~sywnssrryvLT~GWs~FVkdK~LkaGD~VvF~r~--~~~~g~L~IgIRR 207 (343)
-+.+.+.|..| ..++++|+..- ...|++||+|.+.-. ..-.+.+.+.+.+
T Consensus 24 ~~~~~l~D~TG---~i~~~~W~~~~-------------~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~ 75 (82)
T cd04491 24 VQSGLVGDETG---TIRFTLWDEKA-------------ADDLEPGDVVRIENAYVREFNGRLELSVGK 75 (82)
T ss_pred EEEEEEECCCC---EEEEEEECchh-------------cccCCCCCEEEEEeEEEEecCCcEEEEeCC
Confidence 45778889988 47888885421 456899999988721 1123445555443
No 22
>PRK03760 hypothetical protein; Provisional
Probab=35.05 E-value=83 Score=26.98 Aligned_cols=26 Identities=19% Similarity=0.456 Sum_probs=20.1
Q ss_pred CCceEE--ccChHHHHhhcCCCCCCEEEEEE
Q 019261 165 SQSYVL--TKGWSRYVKEKRLDAGDVILFER 193 (343)
Q Consensus 165 srryvL--T~GWs~FVkdK~LkaGD~VvF~r 193 (343)
+-+|+| ..|| +.+.++++||.|.|.+
T Consensus 89 ~a~~VLEl~aG~---~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 89 PARYIIEGPVGK---IRVLKVEVGDEIEWID 116 (117)
T ss_pred cceEEEEeCCCh---HHHcCCCCCCEEEEee
Confidence 455787 4555 6689999999999876
No 23
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=33.92 E-value=1.8e+02 Score=21.75 Aligned_cols=15 Identities=27% Similarity=0.277 Sum_probs=12.1
Q ss_pred cCCCCCCEEEEEEee
Q 019261 181 KRLDAGDVILFERHR 195 (343)
Q Consensus 181 K~LkaGD~VvF~r~~ 195 (343)
..+.+||.|.|....
T Consensus 39 ~~~~vGD~V~~~~~~ 53 (64)
T cd04451 39 IRILPGDRVKVELSP 53 (64)
T ss_pred cccCCCCEEEEEEee
Confidence 348999999999653
No 24
>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=33.05 E-value=33 Score=28.03 Aligned_cols=20 Identities=35% Similarity=0.619 Sum_probs=17.0
Q ss_pred HHHHhhcCCCCCCEEEEEEe
Q 019261 175 SRYVKEKRLDAGDVILFERH 194 (343)
Q Consensus 175 s~FVkdK~LkaGD~VvF~r~ 194 (343)
.+|+++++|..||.|.++|.
T Consensus 42 ~~~i~~~~i~~Gd~V~V~ra 61 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRA 61 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEE
T ss_pred HHHHHHcCCCCCCEEEEEEC
Confidence 68999999999999999997
No 25
>PF08517 AXH: Ataxin-1 and HBP1 module (AXH); InterPro: IPR013723 AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1)[]. ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression []. ; GO: 0005488 binding; PDB: 1OA8_C 3QVE_C 1V06_A.
Probab=32.49 E-value=9.8 Score=33.03 Aligned_cols=26 Identities=38% Similarity=0.590 Sum_probs=16.2
Q ss_pred CceEEccChHHHH----------hhcCCCCCCEEEE
Q 019261 166 QSYVLTKGWSRYV----------KEKRLDAGDVILF 191 (343)
Q Consensus 166 rryvLT~GWs~FV----------kdK~LkaGD~VvF 191 (343)
.-||..+||+-|- .-+.|.+||+|+-
T Consensus 76 PFFV~gkGWsS~~P~~T~~~ygL~C~~L~vGDvCl~ 111 (115)
T PF08517_consen 76 PFFVKGKGWSSCNPSLTVQLYGLPCRQLQVGDVCLS 111 (115)
T ss_dssp EEEETTTEEEESSHHHHHHHHTS--EE--TT-EEEE
T ss_pred ceEEeCCcccccCcchhceecCCcccccccCCEEec
Confidence 4577789998763 3467899999974
No 26
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=31.60 E-value=1.7e+02 Score=23.15 Aligned_cols=34 Identities=18% Similarity=0.154 Sum_probs=25.2
Q ss_pred HHHHhh--cCCCCCCEEEEEEeeCCCCcEEEEEEEc
Q 019261 175 SRYVKE--KRLDAGDVILFERHRTDSERLFIGWRRR 208 (343)
Q Consensus 175 s~FVkd--K~LkaGD~VvF~r~~~~~g~L~IgIRR~ 208 (343)
+.|..+ +.|++||.|.|.......|.--+.|+..
T Consensus 32 s~i~~~g~~~l~~G~~V~f~~~~~~~G~~A~~V~~~ 67 (74)
T PRK09937 32 STIQMDGYRTLKAGQSVQFDVHQGPKGNHASVIVPV 67 (74)
T ss_pred eeccccCCCCCCCCCEEEEEEEECCCCceeeEEEEC
Confidence 455544 6899999999998876667666666655
No 27
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=28.52 E-value=1.1e+02 Score=23.57 Aligned_cols=36 Identities=8% Similarity=0.135 Sum_probs=26.7
Q ss_pred HHHhhcCCCCCCEEEEEEeeCCCCcEEEEEEEcCCCCcc
Q 019261 176 RYVKEKRLDAGDVILFERHRTDSERLFIGWRRRGATAVA 214 (343)
Q Consensus 176 ~FVkdK~LkaGD~VvF~r~~~~~g~L~IgIRR~~~~~~~ 214 (343)
+-++..+|+.||.|.+... .+++.+.++.....++.
T Consensus 30 ~da~~lgl~~Gd~v~v~~~---~g~~~~~v~~~~~v~~g 65 (101)
T cd02775 30 EDAAALGIKDGDLVRVESR---RGSVVLRAKVTDGVPPG 65 (101)
T ss_pred HHHHHcCCCCCCEEEEEcC---CcEEEEEEEECCCcCCC
Confidence 4567889999999999865 46777777776654433
No 28
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=27.53 E-value=2.5e+02 Score=20.64 Aligned_cols=25 Identities=28% Similarity=0.430 Sum_probs=19.5
Q ss_pred HHHHhh--cCCCCCCEEEEEEeeCCCC
Q 019261 175 SRYVKE--KRLDAGDVILFERHRTDSE 199 (343)
Q Consensus 175 s~FVkd--K~LkaGD~VvF~r~~~~~g 199 (343)
+.+... ..|++||.|.|......++
T Consensus 31 ~~~~~~~~~~~~~G~~V~f~~~~~~~g 57 (65)
T cd04458 31 SALEGDGFRSLEEGDRVEFELEEGDKG 57 (65)
T ss_pred hHhhccCCCcCCCCCEEEEEEEECCCC
Confidence 666665 7899999999998875443
No 29
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=27.35 E-value=1.8e+02 Score=23.52 Aligned_cols=43 Identities=26% Similarity=0.344 Sum_probs=33.6
Q ss_pred cCCCCeEEEEEEEecCCCceEEccChHHHHhhcCCCCCCEEEEEEee
Q 019261 149 DESGKCWRFRYSYWNSSQSYVLTKGWSRYVKEKRLDAGDVILFERHR 195 (343)
Q Consensus 149 D~~Gk~W~FR~sywnssrryvLT~GWs~FVkdK~LkaGD~VvF~r~~ 195 (343)
+..|+.=.||.+..+++. +|-+ +.|-+..+|+.||...+...+
T Consensus 23 ~~~GR~~syr~~Vq~NGn--LLIG--~AYT~~m~L~PGdEFeI~Lgr 65 (71)
T PF14250_consen 23 GRRGRKASYRVSVQGNGN--LLIG--SAYTKQMGLKPGDEFEIKLGR 65 (71)
T ss_pred CCCCcCceEEEEEecCCC--EEEc--HHHHHHhCCCCCCEEEEEeCc
Confidence 457888888888876553 4445 799999999999998887654
No 30
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=26.68 E-value=83 Score=26.97 Aligned_cols=29 Identities=24% Similarity=0.401 Sum_probs=19.9
Q ss_pred cCCCCCCEEEEEEeeCCCCcEEEEEEEcCC
Q 019261 181 KRLDAGDVILFERHRTDSERLFIGWRRRGA 210 (343)
Q Consensus 181 K~LkaGD~VvF~r~~~~~g~L~IgIRR~~~ 210 (343)
+++++||.|+|.-..+ +..+.+.|-.-.+
T Consensus 30 ~~ikvGD~I~f~~~~~-~~~l~v~V~~i~~ 58 (109)
T cd06555 30 QQIKVGDKILFNDLDT-GQQLLVKVVDIRK 58 (109)
T ss_pred hcCCCCCEEEEEEcCC-CcEEEEEEEEEEe
Confidence 5789999999987643 4456665554443
No 31
>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=26.57 E-value=36 Score=28.01 Aligned_cols=18 Identities=22% Similarity=0.409 Sum_probs=9.3
Q ss_pred HhhcCCCCCCEEEEEEee
Q 019261 178 VKEKRLDAGDVILFERHR 195 (343)
Q Consensus 178 VkdK~LkaGD~VvF~r~~ 195 (343)
+-+++|.+||.|.|.-..
T Consensus 23 l~~HGl~vGD~VnFsnsa 40 (83)
T PF12195_consen 23 LTDHGLFVGDFVNFSNSA 40 (83)
T ss_dssp -TT----TT-EEEEES-S
T ss_pred EccCceeecceEEEeccc
Confidence 568999999999998653
No 32
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=24.62 E-value=1.4e+02 Score=24.18 Aligned_cols=38 Identities=11% Similarity=0.173 Sum_probs=28.2
Q ss_pred HHHhhcCCCCCCEEEEEEeeCCCCcEEEEEEEcCCCCccch
Q 019261 176 RYVKEKRLDAGDVILFERHRTDSERLFIGWRRRGATAVAQV 216 (343)
Q Consensus 176 ~FVkdK~LkaGD~VvF~r~~~~~g~L~IgIRR~~~~~~~~v 216 (343)
+=+++.+|+.||.|.+.-. .|++.+.++-.....+..|
T Consensus 42 ~dA~~lgi~~Gd~V~v~s~---~G~~~~~v~v~~~i~~g~v 79 (122)
T cd02792 42 ELAAERGIKNGDMVWVSSP---RGKIKVKALVTDRVKPHEV 79 (122)
T ss_pred HHHHHcCCCCCCEEEEEcC---CceEEEEEEECCCcCCCEE
Confidence 3477889999999988865 4678877777766655544
No 33
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=24.49 E-value=2.8e+02 Score=20.08 Aligned_cols=52 Identities=17% Similarity=0.305 Sum_probs=33.2
Q ss_pred eEEEEEcCCCCeEEEEEEEecCCCceEEccChHHHHhhcCCCCCCEEEEEEeeC-CCCcEEEEEEE
Q 019261 143 LLLSFEDESGKCWRFRYSYWNSSQSYVLTKGWSRYVKEKRLDAGDVILFERHRT-DSERLFIGWRR 207 (343)
Q Consensus 143 i~L~v~D~~Gk~W~FR~sywnssrryvLT~GWs~FVkdK~LkaGD~VvF~r~~~-~~g~L~IgIRR 207 (343)
+.+.+.|..|. +.+.+|+ ..|..+ ...|+.|..|++.-.-. .++.+.+.+++
T Consensus 21 ~~~~l~D~tg~---~~~~~f~--------~~~~~~--~~~l~~g~~v~v~G~v~~~~~~~~l~~~~ 73 (84)
T cd04485 21 AFVTLEDLTGS---IEVVVFP--------ETYEKY--RDLLKEDALLLVEGKVERRDGGLRLIAER 73 (84)
T ss_pred EEEEEEeCCCe---EEEEECH--------HHHHHH--HHHhcCCCEEEEEEEEEecCCceEEEeec
Confidence 56778888887 6777773 234444 45788999998865432 13445555553
No 34
>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=24.32 E-value=89 Score=26.69 Aligned_cols=27 Identities=26% Similarity=0.393 Sum_probs=15.8
Q ss_pred cCCCCCCEEEEEEeeCCCCcEEEEEEEc
Q 019261 181 KRLDAGDVILFERHRTDSERLFIGWRRR 208 (343)
Q Consensus 181 K~LkaGD~VvF~r~~~~~g~L~IgIRR~ 208 (343)
++++.||.|+||... +..+-++|+=+-
T Consensus 38 ~~mk~GD~vifY~s~-~~~~~ivai~~V 64 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSG-CKERGIVAIGEV 64 (143)
T ss_dssp HC--TT-EEEEEETS-SSS-EEEEEEEE
T ss_pred hcCCCCCEEEEEEcC-CCCCEEEEEEEE
Confidence 499999999999985 233555555543
No 35
>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=24.03 E-value=1.2e+02 Score=20.39 Aligned_cols=20 Identities=30% Similarity=0.471 Sum_probs=16.1
Q ss_pred ceEEEEEcCCCCeEEEEEEE
Q 019261 142 GLLLSFEDESGKCWRFRYSY 161 (343)
Q Consensus 142 gi~L~v~D~~Gk~W~FR~sy 161 (343)
+..+.+.|..|..|+|.|--
T Consensus 5 g~l~~~~~p~G~~~~~~YD~ 24 (42)
T TIGR01643 5 GRLTGSTDADGTTTRYTYDA 24 (42)
T ss_pred CCEEEEECCCCCEEEEEECC
Confidence 45678899999999998643
No 36
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=23.49 E-value=99 Score=27.09 Aligned_cols=17 Identities=24% Similarity=0.366 Sum_probs=14.0
Q ss_pred HHHHhhcCCCCCCEEEEEE
Q 019261 175 SRYVKEKRLDAGDVILFER 193 (343)
Q Consensus 175 s~FVkdK~LkaGD~VvF~r 193 (343)
..|+|+ ||+||.|.++=
T Consensus 71 ~~~ar~--lK~GdfV~L~N 87 (123)
T cd04498 71 VELAKS--LKPGDFVRIYN 87 (123)
T ss_pred HHHHhh--CCCCCEEEEEE
Confidence 467888 99999999863
No 37
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=23.15 E-value=1.5e+02 Score=24.24 Aligned_cols=38 Identities=13% Similarity=0.011 Sum_probs=28.1
Q ss_pred HHHhhcCCCCCCEEEEEEeeCCCCcEEEEEEEcCCCCccch
Q 019261 176 RYVKEKRLDAGDVILFERHRTDSERLFIGWRRRGATAVAQV 216 (343)
Q Consensus 176 ~FVkdK~LkaGD~VvF~r~~~~~g~L~IgIRR~~~~~~~~v 216 (343)
+=+++.+|+.||.|.++-.. |++.+.++-..+..+..|
T Consensus 40 ~dA~~lgi~~Gd~V~v~s~~---G~i~~~~~~~~~i~~g~v 77 (115)
T cd02779 40 EDAKREGLKNGDLVEVYNDY---GSTTAMAYVTNTVKPGQT 77 (115)
T ss_pred HHHHHcCCCCCCEEEEEeCC---EEEEEEEEECCCcCCCeE
Confidence 45788999999999988663 577777777666554443
No 38
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=22.39 E-value=91 Score=26.91 Aligned_cols=24 Identities=29% Similarity=0.398 Sum_probs=17.2
Q ss_pred hhcCCCCCCEEEEEEeeCCCCcEEE
Q 019261 179 KEKRLDAGDVILFERHRTDSERLFI 203 (343)
Q Consensus 179 kdK~LkaGD~VvF~r~~~~~g~L~I 203 (343)
+=.+|++||.|.|--++. +|++.|
T Consensus 80 ~lsglKeGdkV~fvferv-~gk~tv 103 (108)
T COG5569 80 KLSGLKEGDKVEFVFERV-NGKLTV 103 (108)
T ss_pred HhhccccCCcEEEEEEee-CCEEEE
Confidence 345799999999877764 455544
No 39
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=21.88 E-value=1.5e+02 Score=23.85 Aligned_cols=33 Identities=18% Similarity=0.223 Sum_probs=24.0
Q ss_pred HHHhhcCCCCCCEEEEEEeeCCCCcEEEEEEEcCCC
Q 019261 176 RYVKEKRLDAGDVILFERHRTDSERLFIGWRRRGAT 211 (343)
Q Consensus 176 ~FVkdK~LkaGD~VvF~r~~~~~g~L~IgIRR~~~~ 211 (343)
.+-+.-+|++||.|.|+... ++++ |-++|....
T Consensus 21 eiR~~lgi~~Gd~lei~~~~-~~~~--ivl~k~~~~ 53 (89)
T COG2002 21 EIREALGIKEGDVLEIIVDG-DGGR--IVLKKYKPA 53 (89)
T ss_pred HHHHHhCCCCCCEEEEEEeC-CCCE--EEEEECCcc
Confidence 45567899999999999985 2355 455776643
No 40
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=21.86 E-value=29 Score=30.81 Aligned_cols=13 Identities=46% Similarity=0.912 Sum_probs=10.2
Q ss_pred eeeeeee-eeecce
Q 019261 323 VGQFNCL-CYRHGV 335 (343)
Q Consensus 323 ~~~~~~~-~~~~~~ 335 (343)
.|||+|+ |-||=+
T Consensus 55 ~GqfyCi~CaRyFi 68 (129)
T KOG3408|consen 55 GGQFYCIECARYFI 68 (129)
T ss_pred Cceeehhhhhhhhc
Confidence 5999995 888754
No 41
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=21.69 E-value=1.7e+02 Score=23.68 Aligned_cols=38 Identities=11% Similarity=0.158 Sum_probs=26.9
Q ss_pred HHHhhcCCCCCCEEEEEEeeCCCCcEEEEEEEcCCCCccch
Q 019261 176 RYVKEKRLDAGDVILFERHRTDSERLFIGWRRRGATAVAQV 216 (343)
Q Consensus 176 ~FVkdK~LkaGD~VvF~r~~~~~g~L~IgIRR~~~~~~~~v 216 (343)
+=+++.+|+.||.|.++-.. |++.+.++-.....+..|
T Consensus 38 ~dA~~lgi~~Gd~V~v~s~~---G~~~~~v~~~~~i~~g~v 75 (116)
T cd02786 38 ADAAARGIADGDLVVVFNDR---GSVTLRAKVTDDVPPGVV 75 (116)
T ss_pred HHHHHcCCCCCCEEEEEcCC---eEEEEEEEECCCCCCCEE
Confidence 45678999999999888653 667777766665544433
No 42
>PRK09974 putative regulator PrlF; Provisional
Probab=21.49 E-value=1.8e+02 Score=25.31 Aligned_cols=33 Identities=27% Similarity=0.342 Sum_probs=23.5
Q ss_pred HHHHhhcCCCCCCEEEEEEeeCCCCcEEEEEEEcCCC
Q 019261 175 SRYVKEKRLDAGDVILFERHRTDSERLFIGWRRRGAT 211 (343)
Q Consensus 175 s~FVkdK~LkaGD~VvF~r~~~~~g~L~IgIRR~~~~ 211 (343)
....+.-+|+.||.|.|.... +|++.| +|....
T Consensus 24 k~IR~~Lgl~~GdkI~f~i~~--dG~V~i--~~~~~~ 56 (111)
T PRK09974 24 APVRKALKLKKRDSIHYEILP--GGQVFI--CRLGDE 56 (111)
T ss_pred HHHHHHcCCCCCCEEEEEEeC--CCEEEE--EECCCC
Confidence 467788899999999998764 455654 455433
No 43
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=20.89 E-value=1.2e+02 Score=24.81 Aligned_cols=25 Identities=28% Similarity=0.304 Sum_probs=20.1
Q ss_pred HHHhhcCCCCCCEEEEEEeeCCCCc
Q 019261 176 RYVKEKRLDAGDVILFERHRTDSER 200 (343)
Q Consensus 176 ~FVkdK~LkaGD~VvF~r~~~~~g~ 200 (343)
..++.-+|+.||+|-+.|.....|+
T Consensus 45 Pv~r~~g~k~GdVvkI~R~S~taG~ 69 (79)
T PRK09570 45 PVVKAIGAKPGDVIKIVRKSPTAGE 69 (79)
T ss_pred hhhhhcCCCCCCEEEEEECCCCCCc
Confidence 5677779999999999998655554
No 44
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=20.82 E-value=1.9e+02 Score=23.10 Aligned_cols=38 Identities=11% Similarity=0.134 Sum_probs=27.2
Q ss_pred HHHhhcCCCCCCEEEEEEeeCCCCcEEEEEEEcCCCCccch
Q 019261 176 RYVKEKRLDAGDVILFERHRTDSERLFIGWRRRGATAVAQV 216 (343)
Q Consensus 176 ~FVkdK~LkaGD~VvF~r~~~~~g~L~IgIRR~~~~~~~~v 216 (343)
+=+++.+|+.||.|.++-. .|++.+.++-.....+..|
T Consensus 42 ~dA~~lgi~~Gd~V~v~~~---~G~~~~~v~~~~~i~~g~v 79 (120)
T cd00508 42 EDAARLGIKDGDLVRVSSR---RGSVVVRARVTDRVRPGTV 79 (120)
T ss_pred HHHHHcCCCCCCEEEEEeC---CEEEEEEEEECCCcCCCEE
Confidence 4577889999999999865 3577777776665544433
No 45
>PLN03148 Blue copper-like protein; Provisional
Probab=20.11 E-value=1.2e+02 Score=28.01 Aligned_cols=18 Identities=22% Similarity=0.499 Sum_probs=15.2
Q ss_pred HhhcCCCCCCEEEEEEee
Q 019261 178 VKEKRLDAGDVILFERHR 195 (343)
Q Consensus 178 VkdK~LkaGD~VvF~r~~ 195 (343)
...|+.++||+++|.-..
T Consensus 41 A~~k~F~VGD~LvF~Y~~ 58 (167)
T PLN03148 41 ANNQTFYVGDLISFRYQK 58 (167)
T ss_pred hcCCCCccCCEEEEEecC
Confidence 467899999999998764
No 46
>PF04970 LRAT: Lecithin retinol acyltransferase; InterPro: IPR007053 This entry represents a conserved sequence region found in proteins from viruses, bacteria and eukaryotes. It contains a well-conserved NCEHF motif, though its function in these proteins is unknown.; PDB: 2KYT_A 4DOT_A 4FA0_A.
Probab=20.02 E-value=68 Score=26.83 Aligned_cols=18 Identities=39% Similarity=0.578 Sum_probs=9.3
Q ss_pred HHhhcCCCCCCEEEEEEe
Q 019261 177 YVKEKRLDAGDVILFERH 194 (343)
Q Consensus 177 FVkdK~LkaGD~VvF~r~ 194 (343)
|-..++|+.||.|.|.|.
T Consensus 1 ~~~~~~~~~GD~I~~~r~ 18 (125)
T PF04970_consen 1 FKDKKRLKPGDHIEVPRG 18 (125)
T ss_dssp -----S--TT-EEEEEET
T ss_pred CCcccCCCCCCEEEEecC
Confidence 446789999999999986
Done!