Query 023958
Match_columns 275
No_of_seqs 46 out of 48
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:52:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023958.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023958hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5665 NOT5 CCR4-NOT transcri 67.6 27 0.00059 35.7 8.2 80 85-168 113-195 (548)
2 PF07136 DUF1385: Protein of u 60.4 5.2 0.00011 37.4 1.7 58 123-196 98-155 (236)
3 PRK10328 DNA binding protein, 58.1 35 0.00076 29.3 6.2 29 84-112 6-42 (134)
4 PF04508 Pox_A_type_inc: Viral 52.9 15 0.00033 23.2 2.4 22 8-29 1-22 (23)
5 PRK10947 global DNA-binding tr 48.8 75 0.0016 27.4 6.7 41 84-124 6-54 (135)
6 PF04000 Sas10_Utp3: Sas10/Utp 44.5 1.3E+02 0.0027 22.2 8.5 62 86-147 2-77 (85)
7 PF02108 FliH: Flagellar assem 37.0 1.4E+02 0.0031 23.3 6.3 72 89-165 7-79 (128)
8 PRK04325 hypothetical protein; 34.4 2.2E+02 0.0047 22.0 7.0 47 89-135 7-56 (74)
9 PRK00846 hypothetical protein; 32.8 2.5E+02 0.0054 22.2 7.0 48 89-136 11-61 (77)
10 PF04102 SlyX: SlyX; InterPro 31.4 2.3E+02 0.0049 21.3 6.4 46 91-136 4-52 (69)
11 PRK00736 hypothetical protein; 31.3 2.3E+02 0.0051 21.4 6.5 45 91-135 5-52 (68)
12 KOG2150 CCR4-NOT transcription 29.6 1.3E+02 0.0028 31.9 6.1 47 85-135 123-169 (575)
13 smart00502 BBC B-Box C-termina 28.3 2.7E+02 0.0059 21.2 7.8 61 88-148 18-82 (127)
14 PF08946 Osmo_CC: Osmosensory 27.9 1.1E+02 0.0025 22.3 3.8 39 80-131 3-41 (46)
15 PRK10361 DNA recombination pro 27.6 3.5E+02 0.0075 28.0 8.7 51 81-131 50-100 (475)
16 PF12761 End3: Actin cytoskele 26.4 1.3E+02 0.0027 27.8 4.8 38 82-123 158-195 (195)
17 PRK10227 DNA-binding transcrip 26.3 2.3E+02 0.0049 23.8 6.1 39 108-146 85-126 (135)
18 PF08654 DASH_Dad2: DASH compl 26.2 2.8E+02 0.0061 22.8 6.4 53 81-142 11-78 (103)
19 PF02954 HTH_8: Bacterial regu 26.0 1.8E+02 0.0038 19.5 4.4 22 114-135 21-42 (42)
20 PF10076 DUF2313: Uncharacteri 25.9 2.2E+02 0.0049 24.3 6.1 77 79-155 24-106 (179)
21 PRK00295 hypothetical protein; 24.0 3.2E+02 0.007 20.7 6.8 43 92-134 6-51 (68)
22 PRK04406 hypothetical protein; 23.8 3.5E+02 0.0076 21.0 7.4 48 88-135 8-58 (75)
23 PF10577 UPF0560: Uncharacteri 23.6 1.1E+02 0.0024 33.6 4.4 27 207-234 274-300 (807)
24 COG5481 Uncharacterized conser 23.5 3.6E+02 0.0078 21.0 7.3 29 6-34 5-33 (67)
25 cd04784 HTH_CadR-PbrR Helix-Tu 22.8 2.3E+02 0.0049 23.1 5.3 41 104-144 81-125 (127)
26 PF05549 Allexi_40kDa: Allexiv 22.5 2.5E+02 0.0054 27.2 6.1 52 81-132 75-134 (271)
27 TIGR02051 MerR Hg(II)-responsi 22.5 1.6E+02 0.0035 24.0 4.4 34 104-137 78-111 (124)
28 PRK02793 phi X174 lysis protei 22.2 3.6E+02 0.0079 20.6 6.8 46 90-135 7-55 (72)
29 KOG4835 DNA-binding protein C1 21.2 5.8E+02 0.013 22.6 8.5 60 86-146 15-83 (144)
No 1
>COG5665 NOT5 CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=67.60 E-value=27 Score=35.65 Aligned_cols=80 Identities=23% Similarity=0.386 Sum_probs=60.5
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHhHHHHHH-HHHHHHHhHHHHHhhhh--ccCCchhHHHHHHHhhhcCccccccccC
Q 023958 85 SLNAIRTALENLEDQLEVLHTVQTNQRAEKDA-AIARLEQSRIVLAMRLS--EHHGKKHKVIEEALAFVGDVQDAARFIS 161 (275)
Q Consensus 85 sL~aIRdALE~LE~QL~~lq~lQ~qQr~ERda-ALarLEqSR~~L~~rl~--e~~Gk~~~VI~Ea~af~ge~~~~~~~vs 161 (275)
...-|.+|||.||.||+...+-..--|.||.. -++.|| .++.||. +.-....+-|.|-.-|-=|..++--|++
T Consensus 113 ~i~~i~~~~~el~~q~e~~ea~e~e~~~erh~~h~~~le----~i~~~l~n~~~~pe~v~~~q~di~yyve~~~~~df~e 188 (548)
T COG5665 113 QVLFIHDCLDELQKQLEQYEAQENEEQTERHEFHIANLE----NILKKLQNNEMDPEPVEEFQDDIKYYVENNDDPDFIE 188 (548)
T ss_pred ceehHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH----HHHHHHhccCCChhhHHHHHHHHHHHhhcCCCcchhh
Confidence 45679999999999999998877777888854 345554 3445554 3456667778888888778888888999
Q ss_pred CCCcCCC
Q 023958 162 PDNLYGS 168 (275)
Q Consensus 162 pd~lyg~ 168 (275)
-|.+|.-
T Consensus 189 ~~~~y~~ 195 (548)
T COG5665 189 YDTIYED 195 (548)
T ss_pred hhhHHHh
Confidence 9999975
No 2
>PF07136 DUF1385: Protein of unknown function (DUF1385); InterPro: IPR010787 This family contains a number of hypothetical bacterial proteins of unknown function approximately 300 residues in length. Some family members are predicted to be metal-dependent.
Probab=60.38 E-value=5.2 Score=37.41 Aligned_cols=58 Identities=26% Similarity=0.216 Sum_probs=41.1
Q ss_pred HhHHHHHhhhhccCCchhHHHHHHHhhhcCccccccccCCCCcCCCCCCCCCCCCCCCCCCcCcchhHhhhhhh
Q 023958 123 QSRIVLAMRLSEHHGKKHKVIEEALAFVGDVQDAARFISPDNLYGSPVSPSGQNFAAPEGRMCNGLIHALISSF 196 (275)
Q Consensus 123 qSR~~L~~rl~e~~Gk~~~VI~Ea~af~ge~~~~~~~vspd~lyg~~~s~sg~N~~~~~~~~sN~l~~~~~ss~ 196 (275)
-|+..-+.|+-+|||-+|++|. .++++.=.+++++... +.-+++=|+||+.-++..|+
T Consensus 98 is~~~dI~Rvf~YHGAEHK~I~--------~yE~g~~Ltvenvrk~--------sr~HpRCGTsFl~~vl~vsI 155 (236)
T PF07136_consen 98 ISRMKDIKRVFQYHGAEHKVIN--------CYEAGEELTVENVRKY--------SRLHPRCGTSFLLIVLIVSI 155 (236)
T ss_pred HHhhHHHHHHHHHcchhhhhHH--------hhcCCCCCCHHHHHhc--------CCcCCCcchhHHHHHHHHHH
Confidence 3666678899999999999994 3455555577777442 22346678999987776553
No 3
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=58.11 E-value=35 Score=29.34 Aligned_cols=29 Identities=41% Similarity=0.635 Sum_probs=21.2
Q ss_pred HHHHHHHH--------HHHhHHHHHHHHHHHHHHhHH
Q 023958 84 KSLNAIRT--------ALENLEDQLEVLHTVQTNQRA 112 (275)
Q Consensus 84 rsL~aIRd--------ALE~LE~QL~~lq~lQ~qQr~ 112 (275)
+.|..||. .||.||+-|+-|..|-...+.
T Consensus 6 k~l~n~R~lra~~re~~~e~Lee~~ekl~~vv~er~~ 42 (134)
T PRK10328 6 QSLNNIRTLRAMAREFSIDVLEEMLEKFRVVTKERRE 42 (134)
T ss_pred HHHhhHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHH
Confidence 66777776 489999999999866544333
No 4
>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family [].; GO: 0016032 viral reproduction
Probab=52.94 E-value=15 Score=23.18 Aligned_cols=22 Identities=27% Similarity=0.424 Sum_probs=19.0
Q ss_pred hHHHHHHHHHHHHHhhHHHHHH
Q 023958 8 DEIEAVLEKIWDLHDKLSDAIH 29 (275)
Q Consensus 8 eeie~VLerawdLhdKlSdaI~ 29 (275)
+|+...=.||.||-.+|++|..
T Consensus 1 ~E~~rlr~rI~dLer~L~~C~~ 22 (23)
T PF04508_consen 1 REMNRLRNRISDLERQLSECRR 22 (23)
T ss_pred ChHHHHHHHHHHHHHHHHHHhc
Confidence 3677888999999999999974
No 5
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=48.81 E-value=75 Score=27.38 Aligned_cols=41 Identities=49% Similarity=0.626 Sum_probs=33.3
Q ss_pred HHHHHHHH--------HHHhHHHHHHHHHHHHHHhHHHHHHHHHHHHHh
Q 023958 84 KSLNAIRT--------ALENLEDQLEVLHTVQTNQRAEKDAAIARLEQS 124 (275)
Q Consensus 84 rsL~aIRd--------ALE~LE~QL~~lq~lQ~qQr~ERdaALarLEqS 124 (275)
+.|..||. .||.||+-|+-|..+-...+.|-.+..+++++-
T Consensus 6 k~l~niR~lra~~re~~~e~Lee~~ekl~~vv~er~ee~~~~~~~~~er 54 (135)
T PRK10947 6 KILNNIRTLRAQARECTLETLEEMLEKLEVVVNERREEESAAAAEVEER 54 (135)
T ss_pred HHHHhHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56777776 489999999999999888888877777777664
No 6
>PF04000 Sas10_Utp3: Sas10/Utp3/C1D family; InterPro: IPR007146 This family contains Utp3 and LCP5 which are components of the U3 ribonucleoprotein complex []. It also includes the Homo sapiens (Human) C1D protein and Saccharomyces cerevisiae (Baker's yeast) YHR081W (rrp47), an exosome-associated protein required for the 3' processing of stable RNAs [] and Sas10 which has been identified as a regulator of chromatin silencing []. This entry also includes the human protein Neuroguidin, an initiation factor 4E (eIF4E)-binding protein [].
Probab=44.49 E-value=1.3e+02 Score=22.21 Aligned_cols=62 Identities=21% Similarity=0.299 Sum_probs=47.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHH--------------HhHHHHHHHHHHHHHhHHHHHhhhhccCCchhHHHHHHH
Q 023958 86 LNAIRTALENLEDQLEVLHTVQT--------------NQRAEKDAAIARLEQSRIVLAMRLSEHHGKKHKVIEEAL 147 (275)
Q Consensus 86 L~aIRdALE~LE~QL~~lq~lQ~--------------qQr~ERdaALarLEqSR~~L~~rl~e~~Gk~~~VI~Ea~ 147 (275)
|..|.++++++++.+.-|+.... =.++.-+..++=+-.+=-.++.|+.+..-.++.|++|..
T Consensus 2 l~~l~~~l~~~~~~l~~l~~~~~~~~~~~l~~~~g~sl~~~K~~~llaY~~~~~~~~~lk~~g~~~~~hpv~~~L~ 77 (85)
T PF04000_consen 2 LKELSESLDEVEESLQPLLEKVKEEKEEELSPSDGISLLQAKNQLLLAYIINLLFYMYLKLSGVDPKDHPVMKELV 77 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHhccCCCcccccHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCChHHHHHH
Confidence 45678889999999888875443 334455666777777777788999999999999999875
No 7
>PF02108 FliH: Flagellar assembly protein FliH; InterPro: IPR018035 This entry represents a region found in the flagellar assembly protein FliH, as well as in type III secretion system protein HrpE. Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export []. The sequence of fliH has been deduced and shown to encode a protein of molecular mass of 25,782 Da. Bacterial HrpE proteins are belived to function on the type III secretion system, specifically the secretion of HrpZ (harpinPss) [].
Probab=37.04 E-value=1.4e+02 Score=23.26 Aligned_cols=72 Identities=25% Similarity=0.327 Sum_probs=35.7
Q ss_pred HHHHHHhHHHHHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHhhhhccCCchhHHHHHHH-hhhcCccccccccCCCCc
Q 023958 89 IRTALENLEDQLEVLHTVQTNQRAEKDAAIARLEQSRIVLAMRLSEHHGKKHKVIEEAL-AFVGDVQDAARFISPDNL 165 (275)
Q Consensus 89 IRdALE~LE~QL~~lq~lQ~qQr~ERdaALarLEqSR~~L~~rl~e~~Gk~~~VI~Ea~-af~ge~~~~~~~vspd~l 165 (275)
+..+++.++.++.-+.. +++.+.+--=+.=.++++-..+....-.=..+|.+|+ ....+...---.++|+|+
T Consensus 7 l~~~~~~~~~~~~~~~~-----~~~~~l~~l~~~iae~vi~~~l~~~~~~i~~~i~~al~~~~~~~~~v~I~v~p~d~ 79 (128)
T PF02108_consen 7 LEQLLEELEEALQELLE-----ELEQELVELALAIAEKVIGRELEEDPEAILNLIREALQELPRDEEKVTIRVHPDDY 79 (128)
T ss_pred HHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhhccCCCeEEEECHHHH
Confidence 34445555555554422 2333333333344556666566554444456677777 555544433333555544
No 8
>PRK04325 hypothetical protein; Provisional
Probab=34.40 E-value=2.2e+02 Score=21.96 Aligned_cols=47 Identities=15% Similarity=0.208 Sum_probs=30.4
Q ss_pred HHHHHHhHHHHHHHHHHHH---HHhHHHHHHHHHHHHHhHHHHHhhhhcc
Q 023958 89 IRTALENLEDQLEVLHTVQ---TNQRAEKDAAIARLEQSRIVLAMRLSEH 135 (275)
Q Consensus 89 IRdALE~LE~QL~~lq~lQ---~qQr~ERdaALarLEqSR~~L~~rl~e~ 135 (275)
+-+-+++||-.|.|....- +..-++.+.-|.+|+.-=..|..||++-
T Consensus 7 ~e~Ri~~LE~klAfQE~tIe~LN~vv~~Qq~~I~~L~~ql~~L~~rl~~~ 56 (74)
T PRK04325 7 MEDRITELEIQLAFQEDLIDGLNATVARQQQTLDLLQAQLRLLYQQMRDA 56 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3344899999999886322 3334444555677776666677788773
No 9
>PRK00846 hypothetical protein; Provisional
Probab=32.81 E-value=2.5e+02 Score=22.23 Aligned_cols=48 Identities=19% Similarity=0.126 Sum_probs=34.3
Q ss_pred HHHHHHhHHHHHHHHHHHH---HHhHHHHHHHHHHHHHhHHHHHhhhhccC
Q 023958 89 IRTALENLEDQLEVLHTVQ---TNQRAEKDAAIARLEQSRIVLAMRLSEHH 136 (275)
Q Consensus 89 IRdALE~LE~QL~~lq~lQ---~qQr~ERdaALarLEqSR~~L~~rl~e~~ 136 (275)
+-+-|++||-+|+|....- ++.-++....|.+|.+-=..|..||++..
T Consensus 11 le~Ri~~LE~rlAfQe~tIe~LN~~v~~qq~~I~~L~~ql~~L~~rL~~~~ 61 (77)
T PRK00846 11 LEARLVELETRLSFQEQALTELSEALADARLTGARNAELIRHLLEDLGKVR 61 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4456888999988876432 44555666778888877778888888754
No 10
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=31.40 E-value=2.3e+02 Score=21.32 Aligned_cols=46 Identities=26% Similarity=0.312 Sum_probs=29.2
Q ss_pred HHHHhHHHHHHHHHHHH---HHhHHHHHHHHHHHHHhHHHHHhhhhccC
Q 023958 91 TALENLEDQLEVLHTVQ---TNQRAEKDAAIARLEQSRIVLAMRLSEHH 136 (275)
Q Consensus 91 dALE~LE~QL~~lq~lQ---~qQr~ERdaALarLEqSR~~L~~rl~e~~ 136 (275)
+-|++||..|+|+...- +..-++.+.-|.+|++-=..|..||++..
T Consensus 4 ~Ri~~LE~~la~qe~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~ 52 (69)
T PF04102_consen 4 ERIEELEIKLAFQEDTIEELNDVVTEQQRQIDRLQRQLRLLRERLRELE 52 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-----
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 56788888888886332 33444556667888888888888988754
No 11
>PRK00736 hypothetical protein; Provisional
Probab=31.26 E-value=2.3e+02 Score=21.42 Aligned_cols=45 Identities=18% Similarity=0.165 Sum_probs=29.9
Q ss_pred HHHHhHHHHHHHHHHHH---HHhHHHHHHHHHHHHHhHHHHHhhhhcc
Q 023958 91 TALENLEDQLEVLHTVQ---TNQRAEKDAAIARLEQSRIVLAMRLSEH 135 (275)
Q Consensus 91 dALE~LE~QL~~lq~lQ---~qQr~ERdaALarLEqSR~~L~~rl~e~ 135 (275)
+-+++||-+|.|....- +..-++.+..|.+|..-=..|..||++.
T Consensus 5 ~Ri~~LE~klafqe~tie~Ln~~v~~Qq~~i~~L~~ql~~L~~rl~~~ 52 (68)
T PRK00736 5 ERLTELEIRVAEQEKTIEELSDQLAEQWKTVEQMRKKLDALTERFLSL 52 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34888999998886322 3344455556677776666777888773
No 12
>KOG2150 consensus CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=29.63 E-value=1.3e+02 Score=31.93 Aligned_cols=47 Identities=21% Similarity=0.398 Sum_probs=39.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHhhhhcc
Q 023958 85 SLNAIRTALENLEDQLEVLHTVQTNQRAEKDAAIARLEQSRIVLAMRLSEH 135 (275)
Q Consensus 85 sL~aIRdALE~LE~QL~~lq~lQ~qQr~ERdaALarLEqSR~~L~~rl~e~ 135 (275)
.--=|-+.++.||.|++.|+. +.+||.....|.-+--.-|+.|+-..
T Consensus 123 ~~~wi~~~ideLe~q~d~~ea----~~~e~~~erh~~H~~~lEliLr~L~N 169 (575)
T KOG2150|consen 123 TMDWISNQIDELERQVDSFEA----EELERFIERHRWHQQKLELILRLLDN 169 (575)
T ss_pred HHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 455689999999999999999 88899988888888888888887543
No 13
>smart00502 BBC B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains
Probab=28.27 E-value=2.7e+02 Score=21.21 Aligned_cols=61 Identities=25% Similarity=0.318 Sum_probs=32.1
Q ss_pred HHHHHHHhHHHHHHHHH----HHHHHhHHHHHHHHHHHHHhHHHHHhhhhccCCchhHHHHHHHh
Q 023958 88 AIRTALENLEDQLEVLH----TVQTNQRAEKDAAIARLEQSRIVLAMRLSEHHGKKHKVIEEALA 148 (275)
Q Consensus 88 aIRdALE~LE~QL~~lq----~lQ~qQr~ERdaALarLEqSR~~L~~rl~e~~Gk~~~VI~Ea~a 148 (275)
.|.+++..|++...-++ .+..+=..+=+..+.-|++.+..|+.+|...+-.+...+++-..
T Consensus 18 ~~~~~~~~l~~~~~~l~~~~~~~~~~I~~~f~~l~~~L~~~e~~ll~~l~~~~~~~~~~l~~q~~ 82 (127)
T smart00502 18 ELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQKENKLKVLEQQLE 82 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444332 33333344445556666666666666666666555555554443
No 14
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=27.88 E-value=1.1e+02 Score=22.32 Aligned_cols=39 Identities=36% Similarity=0.447 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHhh
Q 023958 80 IQEAKSLNAIRTALENLEDQLEVLHTVQTNQRAEKDAAIARLEQSRIVLAMR 131 (275)
Q Consensus 80 ~~EarsL~aIRdALE~LE~QL~~lq~lQ~qQr~ERdaALarLEqSR~~L~~r 131 (275)
.+||+.|+ +.+-++.|.-.+-+ |+-|++||+-|..|+.+
T Consensus 3 ~~EAkelL--qe~~d~IEqkiedi-----------d~qIaeLe~KR~~Lv~q 41 (46)
T PF08946_consen 3 RAEAKELL--QEHYDNIEQKIEDI-----------DEQIAELEAKRQRLVDQ 41 (46)
T ss_dssp --------------THHHHHHHHH-----------HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHH--HHHHHhHHHhHHHH-----------HHHHHHHHHHHHHHHHh
Confidence 35777664 23444444333322 45567888888877765
No 15
>PRK10361 DNA recombination protein RmuC; Provisional
Probab=27.63 E-value=3.5e+02 Score=28.04 Aligned_cols=51 Identities=18% Similarity=0.249 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHhHHHHHHHHHHHHHhHHHHHhh
Q 023958 81 QEAKSLNAIRTALENLEDQLEVLHTVQTNQRAEKDAAIARLEQSRIVLAMR 131 (275)
Q Consensus 81 ~EarsL~aIRdALE~LE~QL~~lq~lQ~qQr~ERdaALarLEqSR~~L~~r 131 (275)
++...+......++.++.+|..++...+.++++....-+++|+-|....+|
T Consensus 50 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~l~~~le~~~~~~~ek 100 (475)
T PRK10361 50 QQITQSEHWRAECELLNNEVRSLQSINTSLEADLREVTTRMEAAQQHADDK 100 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444555555555566666655554444444444444444444433333
No 16
>PF12761 End3: Actin cytoskeleton-regulatory complex protein END3
Probab=26.39 E-value=1.3e+02 Score=27.78 Aligned_cols=38 Identities=26% Similarity=0.497 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 023958 82 EAKSLNAIRTALENLEDQLEVLHTVQTNQRAEKDAAIARLEQ 123 (275)
Q Consensus 82 EarsL~aIRdALE~LE~QL~~lq~lQ~qQr~ERdaALarLEq 123 (275)
....|..||+=|+.+|.|...|+... ..|...|..|.|
T Consensus 158 ~~~~l~~v~~Dl~~ie~QV~~Le~~L----~~k~~eL~~L~q 195 (195)
T PF12761_consen 158 SGKNLKSVREDLDTIEEQVDGLESHL----SSKKQELQQLRQ 195 (195)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHhcC
Confidence 34468899999999999999988765 345555666543
No 17
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=26.26 E-value=2.3e+02 Score=23.83 Aligned_cols=39 Identities=23% Similarity=0.216 Sum_probs=28.2
Q ss_pred HHhHHHHHHHHHHHHHhHHHHHhhhhccCC---chhHHHHHH
Q 023958 108 TNQRAEKDAAIARLEQSRIVLAMRLSEHHG---KKHKVIEEA 146 (275)
Q Consensus 108 ~qQr~ERdaALarLEqSR~~L~~rl~e~~G---k~~~VI~Ea 146 (275)
.+|..+=++-|++|++.|..|...+..+.+ .+|.++++.
T Consensus 85 ~~~~~~l~~~i~~L~~~~~~L~~~~~~~~~~~~~~c~~~~~l 126 (135)
T PRK10227 85 LEKVAEIERHIEELQSMRDQLLALANACPGDDSADCPIIENL 126 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcHHHHH
Confidence 456667777889999999998888877654 356666653
No 18
>PF08654 DASH_Dad2: DASH complex subunit Dad2; InterPro: IPR013963 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ].
Probab=26.16 E-value=2.8e+02 Score=22.83 Aligned_cols=53 Identities=21% Similarity=0.263 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHH---------------HHHHHHhHHHHHHHHHHHHHhHHHHHhhhhccCCchhHH
Q 023958 81 QEAKSLNAIRTALENLEDQLEVL---------------HTVQTNQRAEKDAAIARLEQSRIVLAMRLSEHHGKKHKV 142 (275)
Q Consensus 81 ~EarsL~aIRdALE~LE~QL~~l---------------q~lQ~qQr~ERdaALarLEqSR~~L~~rl~e~~Gk~~~V 142 (275)
.|-..|-.||+.-..|-.||+.| ..+.+||-.=|-.-+|. .+|..|...++++
T Consensus 11 ~ELe~L~~l~~lS~~L~~qle~L~~kl~~m~dg~e~Va~Vl~NW~nV~r~Is~AS---------~~l~~~~~~~~~~ 78 (103)
T PF08654_consen 11 AELEALKQLRDLSADLASQLEALSEKLETMADGAEAVASVLANWQNVFRAISMAS---------LSLAKYSEGDYEE 78 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHhHHHHHHHHHHHH---------hhhhhcccccccc
Confidence 57778888888755555555555 26788888888777775 6777777766654
No 19
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=25.98 E-value=1.8e+02 Score=19.55 Aligned_cols=22 Identities=27% Similarity=0.137 Sum_probs=16.4
Q ss_pred HHHHHHHHHHhHHHHHhhhhcc
Q 023958 114 KDAAIARLEQSRIVLAMRLSEH 135 (275)
Q Consensus 114 RdaALarLEqSR~~L~~rl~e~ 135 (275)
+..|=..|.=||..|-.||++|
T Consensus 21 ~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 21 VSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHC
T ss_pred HHHHHHHHCCCHHHHHHHHHhC
Confidence 4456677888999999998876
No 20
>PF10076 DUF2313: Uncharacterized protein conserved in bacteria (DUF2313); InterPro: IPR018755 Members of this family of proteins comprise various hypothetical and putative bacteriophage tail proteins, including Gp48 from Bacteriophage Mu and other Mu-like prophages such as FluMu.
Probab=25.93 E-value=2.2e+02 Score=24.33 Aligned_cols=77 Identities=17% Similarity=0.125 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhHHHHHHHH-----HHHHHhHHHHHhhhhccCCchhHHHHHHHhhhcC-
Q 023958 79 AIQEAKSLNAIRTALENLEDQLEVLHTVQTNQRAEKDAAI-----ARLEQSRIVLAMRLSEHHGKKHKVIEEALAFVGD- 152 (275)
Q Consensus 79 ~~~EarsL~aIRdALE~LE~QL~~lq~lQ~qQr~ERdaAL-----arLEqSR~~L~~rl~e~~Gk~~~VI~Ea~af~ge- 152 (275)
...|+..|-.+.++.++|.+|+-.-.+...=.+.||.--| .-||+-|..++.|+..--|-....+.+.++-+|.
T Consensus 24 ~~a~~~el~~~~~~~~~l~~e~f~~Tat~~L~~wE~~lgi~~~~~~tle~RR~~i~~k~~~~~~~T~~~l~~~a~~~G~~ 103 (179)
T PF10076_consen 24 LEAEGPELDRLDDRADDLLDEQFPSTATWGLPRWERMLGIPPNPTDTLEERRARILAKLNSKGPYTIAYLEQLANSLGYG 103 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHccCCcCHHHHHHHHHHhCCC
Confidence 4468889999999999999999888877777777776554 3689999999999999888899999998888886
Q ss_pred ccc
Q 023958 153 VQD 155 (275)
Q Consensus 153 ~~~ 155 (275)
.++
T Consensus 104 ~v~ 106 (179)
T PF10076_consen 104 NVE 106 (179)
T ss_pred CEE
Confidence 444
No 21
>PRK00295 hypothetical protein; Provisional
Probab=23.98 E-value=3.2e+02 Score=20.65 Aligned_cols=43 Identities=21% Similarity=0.244 Sum_probs=28.5
Q ss_pred HHHhHHHHHHHHHHH---HHHhHHHHHHHHHHHHHhHHHHHhhhhc
Q 023958 92 ALENLEDQLEVLHTV---QTNQRAEKDAAIARLEQSRIVLAMRLSE 134 (275)
Q Consensus 92 ALE~LE~QL~~lq~l---Q~qQr~ERdaALarLEqSR~~L~~rl~e 134 (275)
-+++||-++.|.... .+..-++.+.-|.+|+.-=..|..||++
T Consensus 6 Ri~~LE~kla~qE~tie~Ln~~v~~Qq~~I~~L~~ql~~L~~rl~~ 51 (68)
T PRK00295 6 RVTELESRQAFQDDTIQALNDVLVEQQRVIERLQLQMAALIKRQEE 51 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 488999999888632 2334445555566777666667778776
No 22
>PRK04406 hypothetical protein; Provisional
Probab=23.75 E-value=3.5e+02 Score=20.98 Aligned_cols=48 Identities=10% Similarity=0.210 Sum_probs=30.3
Q ss_pred HHHHHHHhHHHHHHHHHHHH---HHhHHHHHHHHHHHHHhHHHHHhhhhcc
Q 023958 88 AIRTALENLEDQLEVLHTVQ---TNQRAEKDAAIARLEQSRIVLAMRLSEH 135 (275)
Q Consensus 88 aIRdALE~LE~QL~~lq~lQ---~qQr~ERdaALarLEqSR~~L~~rl~e~ 135 (275)
.+-+-+++||-+|.|....- +..-++.+.-|.+|..-=..|..||++.
T Consensus 8 ~le~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~~ql~~L~~rl~~~ 58 (75)
T PRK04406 8 QLEERINDLECQLAFQEQTIEELNDALSQQQLLITKMQDQMKYVVGKVKNM 58 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 35567889999999886332 3333444445566665555666777763
No 23
>PF10577 UPF0560: Uncharacterised protein family UPF0560; InterPro: IPR018890 This family of proteins has no known function.
Probab=23.61 E-value=1.1e+02 Score=33.64 Aligned_cols=27 Identities=22% Similarity=0.338 Sum_probs=22.6
Q ss_pred hhhhhhHHHHHHHHHHHHHHHHhhhhhc
Q 023958 207 QVGGILSNAAIVAVSMIALLHLHQAAYK 234 (275)
Q Consensus 207 ~~gG~lgnaav~aVsmva~LqLhq~a~~ 234 (275)
++.++||-+++++++.+++| ||.|-+.
T Consensus 274 fLl~ILG~~~livl~lL~vL-l~yCrrk 300 (807)
T PF10577_consen 274 FLLAILGGTALIVLILLCVL-LCYCRRK 300 (807)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHhhhcc
Confidence 46899999999999999999 7777443
No 24
>COG5481 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]
Probab=23.51 E-value=3.6e+02 Score=21.01 Aligned_cols=29 Identities=24% Similarity=0.381 Sum_probs=25.5
Q ss_pred cHhHHHHHHHHHHHHHhhHHHHHHHhhhh
Q 023958 6 EIDEIEAVLEKIWDLHDKLSDAIHSISRT 34 (275)
Q Consensus 6 e~eeie~VLerawdLhdKlSdaI~~~s~s 34 (275)
+..||+.-++|...=|.-+-++|.+....
T Consensus 5 dqaeirl~~arLrqeH~D~DaaInAmi~~ 33 (67)
T COG5481 5 DQAEIRLTLARLRQEHADFDAAINAMIAT 33 (67)
T ss_pred cHHHHHHHHHHHHHHHhhHHHHHHHHHHh
Confidence 57899999999999999999999987553
No 25
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.80 E-value=2.3e+02 Score=23.05 Aligned_cols=41 Identities=17% Similarity=0.195 Sum_probs=25.5
Q ss_pred HHHHHHhHHHHHHHHHHHHHhHHHHHhhhhccCC----chhHHHH
Q 023958 104 HTVQTNQRAEKDAAIARLEQSRIVLAMRLSEHHG----KKHKVIE 144 (275)
Q Consensus 104 q~lQ~qQr~ERdaALarLEqSR~~L~~rl~e~~G----k~~~VI~ 144 (275)
..+-.+|..+=+.-|++|++.+..|-..+..+.+ .+|.+++
T Consensus 81 ~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~~~~~~~~~~c~~~~ 125 (127)
T cd04784 81 NALIDEHLAHVRARIAELQALEKQLQALRERCDGARTIEECGILQ 125 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCCchhh
Confidence 3444555566666777888888777766666554 3455444
No 26
>PF05549 Allexi_40kDa: Allexivirus 40kDa protein; InterPro: IPR008398 This family of sequences contains the 40 kDa polypeptides from garlic viruses (Allexiviruses), which do not resemble any other plant virus gene products reported so far []. Rod-shaped flexuous viruses have been isolated from garlic plants, Allium sativum. Infection by this virus creates typical mosaic symptoms. The core-like sequence of a zinc finger protein preceded by a cluster of basic amino acid residues shows similarities to the corresponding 12K proteins of the potexviruses and carlaviruses []. Viral epidemics by allexiviruses are also known to be caused by aphids and eriophyid mites (Aceria tulipae) carrying Potyviruses, Carlaviruses, and Allexiviruses [].
Probab=22.53 E-value=2.5e+02 Score=27.23 Aligned_cols=52 Identities=27% Similarity=0.425 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHhHHHH------H--HHHHHHHHhHHHHHhhh
Q 023958 81 QEAKSLNAIRTALENLEDQLEVLHTVQTNQRAEK------D--AAIARLEQSRIVLAMRL 132 (275)
Q Consensus 81 ~EarsL~aIRdALE~LE~QL~~lq~lQ~qQr~ER------d--aALarLEqSR~~L~~rl 132 (275)
.+.--|..|||++-.|-.-++-++.++++++..- + .-|+-||.+=..|-.||
T Consensus 75 s~~t~ls~~r~~~~tL~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~iet~L~~lh~kl 134 (271)
T PF05549_consen 75 SQGTPLSRIRDALRTLTRLLDSIHSVEQKSELSANTPSSSKLLKKLASIETSLESLHIKL 134 (271)
T ss_pred hhcchHHHHHHHHHHHHhhHHHHHHHHHHHhcccCCccchhHHHHHHHHHhHHHHHHHHH
Confidence 3777899999999999999999999998877632 3 23455555544444443
No 27
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=22.51 E-value=1.6e+02 Score=24.03 Aligned_cols=34 Identities=15% Similarity=0.105 Sum_probs=22.9
Q ss_pred HHHHHHhHHHHHHHHHHHHHhHHHHHhhhhccCC
Q 023958 104 HTVQTNQRAEKDAAIARLEQSRIVLAMRLSEHHG 137 (275)
Q Consensus 104 q~lQ~qQr~ERdaALarLEqSR~~L~~rl~e~~G 137 (275)
..+-.+|..+=+.-+++|++.+..|-..++.+..
T Consensus 78 ~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~~~~ 111 (124)
T TIGR02051 78 YELASRKLKSVQAKMADLLRIERLLEELLEQCPA 111 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccC
Confidence 3344455566666777888888888777777653
No 28
>PRK02793 phi X174 lysis protein; Provisional
Probab=22.19 E-value=3.6e+02 Score=20.60 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=29.1
Q ss_pred HHHHHhHHHHHHHHHHHH---HHhHHHHHHHHHHHHHhHHHHHhhhhcc
Q 023958 90 RTALENLEDQLEVLHTVQ---TNQRAEKDAAIARLEQSRIVLAMRLSEH 135 (275)
Q Consensus 90 RdALE~LE~QL~~lq~lQ---~qQr~ERdaALarLEqSR~~L~~rl~e~ 135 (275)
-+-|.+||-+|.|....- +..-++.+..|.+|+.-=..|..||++-
T Consensus 7 e~Ri~~LE~~lafQe~tIe~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~ 55 (72)
T PRK02793 7 EARLAELESRLAFQEITIEELNVTVTAHEMEMAKLRDHLRLLTEKLKAS 55 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 356788999988886332 3333444455667766666677777763
No 29
>KOG4835 consensus DNA-binding protein C1D involved in regulation of double-strand break repair [Replication, recombination and repair]
Probab=21.21 E-value=5.8e+02 Score=22.60 Aligned_cols=60 Identities=27% Similarity=0.305 Sum_probs=43.0
Q ss_pred HHHHHHHHHhHHHHH---------HHHHHHHHHhHHHHHHHHHHHHHhHHHHHhhhhccCCchhHHHHHH
Q 023958 86 LNAIRTALENLEDQL---------EVLHTVQTNQRAEKDAAIARLEQSRIVLAMRLSEHHGKKHKVIEEA 146 (275)
Q Consensus 86 L~aIRdALE~LE~QL---------~~lq~lQ~qQr~ERdaALarLEqSR~~L~~rl~e~~Gk~~~VI~Ea 146 (275)
|+.--++|++|+.+| ++++.++ -+||-=|..++-+=-|=-.+-.+++.--.+++.|.+|.
T Consensus 15 ln~f~~~l~~l~~~le~~~s~~e~e~l~sl~-~EqAKld~~~~ya~~sl~~~~l~~kG~da~dh~V~~EL 83 (144)
T KOG4835|consen 15 LNKFLDNLEELKPPLEDMESISELEELRSLL-LEQAKLDLTLAYAINSLFWSFLKLKGVDASDHPVLQEL 83 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccchHHHHH
Confidence 444445555555444 4566777 77888888888887777777788888888888888876
Done!