Query 033200
Match_columns 125
No_of_seqs 45 out of 47
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 11:02:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033200.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033200hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13551 HTH_29: Winged helix- 79.2 3.9 8.4E-05 26.7 3.8 37 82-118 1-40 (112)
2 PF10281 Ish1: Putative stress 78.1 2.8 6.1E-05 24.8 2.7 26 92-117 8-37 (38)
3 PF13384 HTH_23: Homeodomain-l 76.4 4.4 9.6E-05 23.9 3.2 39 80-118 5-45 (50)
4 PF13518 HTH_28: Helix-turn-he 70.8 8.2 0.00018 22.5 3.4 28 92-119 14-41 (52)
5 TIGR01446 DnaD_dom DnaD and ph 67.6 11 0.00025 23.9 3.8 42 79-120 6-48 (73)
6 TIGR03321 alt_F1F0_F0_B altern 63.3 18 0.00038 28.6 4.9 47 66-119 130-177 (246)
7 COG1647 Esterase/lipase [Gener 61.9 12 0.00025 31.6 3.8 78 27-119 96-178 (243)
8 smart00351 PAX Paired Box doma 60.5 17 0.00036 26.1 3.9 41 79-119 20-62 (125)
9 PF00382 TFIIB: Transcription 57.3 16 0.00035 23.2 3.1 24 93-116 1-24 (71)
10 PF01527 HTH_Tnp_1: Transposas 57.0 18 0.00039 22.6 3.3 34 82-115 12-48 (76)
11 cd00001 PTS_IIB_man PTS_IIB, P 52.1 9.8 0.00021 28.6 1.7 37 88-124 11-58 (151)
12 PF03830 PTSIIB_sorb: PTS syst 51.7 8.1 0.00018 29.0 1.2 37 88-124 12-59 (151)
13 TIGR00854 pts-sorbose PTS syst 51.7 10 0.00022 28.6 1.7 37 88-124 12-59 (151)
14 PRK09756 PTS system N-acetylga 49.5 11 0.00025 28.6 1.7 37 88-124 16-64 (158)
15 COG1405 SUA7 Transcription ini 48.5 28 0.00062 29.1 4.0 34 89-122 194-230 (285)
16 PRK11425 PTS system N-acetylga 46.9 13 0.00029 28.2 1.7 37 88-124 14-61 (157)
17 PRK15088 PTS system mannose-sp 46.6 16 0.00034 30.7 2.3 37 88-124 175-222 (322)
18 PRK14474 F0F1 ATP synthase sub 45.4 44 0.00096 26.9 4.5 45 66-118 130-175 (250)
19 PF03447 NAD_binding_3: Homose 44.5 16 0.00034 24.8 1.6 21 103-123 96-116 (117)
20 PF11387 DUF2795: Protein of u 44.1 15 0.00033 22.7 1.4 16 104-119 7-22 (44)
21 TIGR01764 excise DNA binding d 43.0 34 0.00074 19.0 2.7 20 93-112 4-23 (49)
22 TIGR03855 NAD_NadX aspartate d 36.9 53 0.0012 26.2 3.8 36 87-122 48-93 (229)
23 PF01408 GFO_IDH_MocA: Oxidore 36.8 68 0.0015 21.0 3.7 35 87-121 73-116 (120)
24 cd04762 HTH_MerR-trunc Helix-T 36.4 50 0.0011 18.1 2.6 21 93-113 3-23 (49)
25 PF13730 HTH_36: Helix-turn-he 35.8 69 0.0015 19.0 3.3 26 93-118 28-53 (55)
26 PF07961 MBA1: MBA1-like prote 35.3 34 0.00073 28.2 2.5 37 63-99 53-90 (235)
27 PF08035 Op_neuropeptide: Opio 35.1 21 0.00045 21.9 0.9 15 63-77 14-28 (31)
28 PF13591 MerR_2: MerR HTH fami 34.7 44 0.00095 22.6 2.6 20 93-112 3-22 (84)
29 PF06109 HlyE: Haemolysin E (H 34.6 43 0.00094 28.7 3.1 29 74-102 134-162 (299)
30 PF14502 HTH_41: Helix-turn-he 34.1 67 0.0014 21.1 3.2 27 92-118 8-34 (48)
31 KOG1405 4-aminobutyrate aminot 32.7 14 0.0003 33.8 -0.2 37 77-122 414-450 (484)
32 PHA00781 hypothetical protein 31.7 78 0.0017 21.8 3.4 38 80-117 14-57 (59)
33 TIGR00443 hisZ_biosyn_reg ATP 31.7 64 0.0014 26.0 3.5 26 89-114 151-176 (314)
34 PF02617 ClpS: ATP-dependent C 31.4 75 0.0016 21.1 3.3 31 90-120 20-50 (82)
35 PF11281 DUF3083: Protein of u 30.5 22 0.00047 31.1 0.7 21 90-111 286-306 (316)
36 cd07313 terB_like_2 tellurium 30.4 91 0.002 20.6 3.5 29 88-116 19-48 (104)
37 PF12728 HTH_17: Helix-turn-he 30.3 66 0.0014 19.0 2.6 20 93-112 4-23 (51)
38 TIGR01565 homeo_ZF_HD homeobox 28.4 31 0.00068 22.8 1.0 22 88-109 30-51 (58)
39 PF14555 UBA_4: UBA-like domai 27.8 81 0.0018 18.8 2.7 23 91-113 2-24 (43)
40 PF11372 DUF3173: Domain of un 27.8 54 0.0012 22.2 2.1 19 99-117 11-29 (59)
41 PF08328 ASL_C: Adenylosuccina 27.3 67 0.0015 24.4 2.7 48 64-113 58-109 (115)
42 smart00422 HTH_MERR helix_turn 27.0 78 0.0017 19.2 2.6 19 93-111 3-21 (70)
43 PRK12292 hisZ ATP phosphoribos 26.7 85 0.0018 26.2 3.5 27 89-115 162-188 (391)
44 cd04761 HTH_MerR-SF Helix-Turn 24.5 1E+02 0.0022 17.5 2.6 19 93-111 3-21 (49)
45 PF02993 MCPVI: Minor capsid p 23.8 26 0.00057 29.3 0.0 82 4-87 18-111 (238)
46 cd06892 PX_SNX5_like The phosp 23.7 1.6E+02 0.0036 22.7 4.3 46 51-96 77-122 (141)
47 PF07862 Nif11: Nitrogen fixat 23.5 1.4E+02 0.003 18.0 3.2 29 93-121 6-43 (49)
48 PF08281 Sigma70_r4_2: Sigma-7 23.2 1.3E+02 0.0028 17.7 3.0 26 91-116 27-52 (54)
49 PF13411 MerR_1: MerR HTH fami 23.0 1.1E+02 0.0024 18.7 2.7 20 93-112 3-22 (69)
50 PF13393 tRNA-synt_His: Histid 23.0 80 0.0017 24.7 2.5 27 89-115 153-179 (311)
51 smart00420 HTH_DEOR helix_turn 22.7 1.5E+02 0.0033 16.4 3.4 27 92-118 16-42 (53)
52 PRK05255 hypothetical protein; 22.6 1.3E+02 0.0028 23.8 3.7 55 63-117 86-149 (171)
53 PRK10265 chaperone-modulator p 22.0 98 0.0021 21.7 2.6 21 92-112 9-29 (101)
54 TIGR01220 Pmev_kin_Gr_pos phos 21.5 2E+02 0.0043 23.9 4.7 50 69-119 261-312 (358)
55 PF12802 MarR_2: MarR family; 21.5 1.8E+02 0.004 17.1 3.4 27 92-118 23-49 (62)
56 COG2390 DeoR Transcriptional r 21.0 1.1E+02 0.0024 26.0 3.2 25 94-118 30-54 (321)
57 PRK15418 transcriptional regul 20.7 1.2E+02 0.0026 25.1 3.2 26 93-118 32-57 (318)
58 PF13875 DUF4202: Domain of un 20.5 2.5E+02 0.0055 22.7 4.9 46 73-118 72-117 (185)
59 PF08102 Antimicrobial_7: Scor 20.5 2E+02 0.0042 18.8 3.5 38 62-103 4-42 (43)
60 PF05119 Terminase_4: Phage te 20.0 1.1E+02 0.0024 20.1 2.4 24 90-113 70-93 (100)
No 1
>PF13551 HTH_29: Winged helix-turn helix
Probab=79.20 E-value=3.9 Score=26.70 Aligned_cols=37 Identities=16% Similarity=0.383 Sum_probs=29.7
Q ss_pred hhhHHHHhHH---HHHHHHHHhCCChhhhhhHHHHHHHcC
Q 033200 82 RGKAIALHSQ---VITEFCKSIGADAKQRQGLIRLAKKNG 118 (125)
Q Consensus 82 RGKaIaLHSQ---vIt~FC~~iG~d~k~RQ~LIRlAk~NG 118 (125)
|.+++.++.+ .+.++|+.+|++..+-.++++...+.|
T Consensus 1 R~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 1 RAQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred CHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 4455555443 589999999999999999999988777
No 2
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=78.10 E-value=2.8 Score=24.83 Aligned_cols=26 Identities=38% Similarity=0.526 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCChh----hhhhHHHHHHHc
Q 033200 92 VITEFCKSIGADAK----QRQGLIRLAKKN 117 (125)
Q Consensus 92 vIt~FC~~iG~d~k----~RQ~LIRlAk~N 117 (125)
=+++|.+.-|+... .|..|+.+||+|
T Consensus 8 ~L~~wL~~~gi~~~~~~~~rd~Ll~~~k~~ 37 (38)
T PF10281_consen 8 DLKSWLKSHGIPVPKSAKTRDELLKLAKKN 37 (38)
T ss_pred HHHHHHHHcCCCCCCCCCCHHHHHHHHHHh
Confidence 36788888888765 799999999987
No 3
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=76.44 E-value=4.4 Score=23.86 Aligned_cols=39 Identities=23% Similarity=0.344 Sum_probs=23.3
Q ss_pred hhhhhHHHHhHH--HHHHHHHHhCCChhhhhhHHHHHHHcC
Q 033200 80 QFRGKAIALHSQ--VITEFCKSIGADAKQRQGLIRLAKKNG 118 (125)
Q Consensus 80 klRGKaIaLHSQ--vIt~FC~~iG~d~k~RQ~LIRlAk~NG 118 (125)
+.|-.+|-++.+ -+.+.|+.+|++..+-.++++.-++.|
T Consensus 5 ~~R~~ii~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 5 ERRAQIIRLLREGWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp -----HHHHHHHT--HHHHHHHHTS-HHHHHHHHT------
T ss_pred hHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 346677777774 789999999999999999999888776
No 4
>PF13518 HTH_28: Helix-turn-helix domain
Probab=70.76 E-value=8.2 Score=22.45 Aligned_cols=28 Identities=14% Similarity=0.261 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCChhhhhhHHHHHHHcCc
Q 033200 92 VITEFCKSIGADAKQRQGLIRLAKKNGE 119 (125)
Q Consensus 92 vIt~FC~~iG~d~k~RQ~LIRlAk~NG~ 119 (125)
-+.+.|+.+|++..+-..+++.-+++|.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 5788999999999999999999999884
No 5
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=67.62 E-value=11 Score=23.91 Aligned_cols=42 Identities=10% Similarity=0.119 Sum_probs=33.6
Q ss_pred hhhhh-hHHHHhHHHHHHHHHHhCCChhhhhhHHHHHHHcCcc
Q 033200 79 NQFRG-KAIALHSQVITEFCKSIGADAKQRQGLIRLAKKNGER 120 (125)
Q Consensus 79 NklRG-KaIaLHSQvIt~FC~~iG~d~k~RQ~LIRlAk~NG~k 120 (125)
.+.=| ..-+...+.|.++|+..|.++..-..+|+.|.++|++
T Consensus 6 e~~~gr~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~~~~~~ 48 (73)
T TIGR01446 6 EENFGRMLSPFEMEDLKYWLDEFGNSPELIKEALKEAVSNNKA 48 (73)
T ss_pred HHHhCCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCC
Confidence 34444 3345889999999999999999999999999887653
No 6
>TIGR03321 alt_F1F0_F0_B alternate F1F0 ATPase, F0 subunit B. CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
Probab=63.30 E-value=18 Score=28.61 Aligned_cols=47 Identities=13% Similarity=0.352 Sum_probs=35.4
Q ss_pred hhHHHhhhccchhhhhhhhHHHHhHHHHHHHHHHh-CCChhhhhhHHHHHHHcCc
Q 033200 66 VVLTRNIIGKKRFNQFRGKAIALHSQVITEFCKSI-GADAKQRQGLIRLAKKNGE 119 (125)
Q Consensus 66 Vv~~r~ilG~krfNklRGKaIaLHSQvIt~FC~~i-G~d~k~RQ~LIRlAk~NG~ 119 (125)
|-+++.+|++ .++. ..|.++|.+|++.+ ..+..+|+.|-+.+..+|.
T Consensus 130 ~~~A~kil~~-~~d~------~~~~~lid~~i~~l~~l~~~~~~~l~~~~~~~~~ 177 (246)
T TIGR03321 130 FAIARKVLTD-LADT------DLEERMVDVFVQRLRTLDPDEKAALAEALADSGN 177 (246)
T ss_pred HHHHHHHHHH-hcCh------HHHHHHHHHHHHHhhcCCHHHHHHHHHHHhCCCC
Confidence 4556677763 3333 78999999999999 4566779999888887774
No 7
>COG1647 Esterase/lipase [General function prediction only]
Probab=61.93 E-value=12 Score=31.64 Aligned_cols=78 Identities=21% Similarity=0.209 Sum_probs=46.9
Q ss_pred CcchhhhhhccCC---cccCCccccCCCccCCCCCCccchhhhhHHHhhh--ccchhhhhhhhHHHHhHHHHHHHHHHhC
Q 033200 27 GEEYRMLARSVPN---VRVARPIRMQPMMGNINEGKGIFAPVVVLTRNII--GKKRFNQFRGKAIALHSQVITEFCKSIG 101 (125)
Q Consensus 27 ge~~~~l~~~vp~---~~~~~p~r~~~~m~n~~~~~G~FaPlVv~~r~il--G~krfNklRGKaIaLHSQvIt~FC~~iG 101 (125)
|-=-..|+.+.|. |+...|. |+.+...+..|++-++|+.= =.+-+++++-.-=++|...+
T Consensus 96 Gv~alkla~~~p~K~iv~m~a~~-------~~k~~~~iie~~l~y~~~~kk~e~k~~e~~~~e~~~~~~~~~-------- 160 (243)
T COG1647 96 GVFALKLAYHYPPKKIVPMCAPV-------NVKSWRIIIEGLLEYFRNAKKYEGKDQEQIDKEMKSYKDTPM-------- 160 (243)
T ss_pred hHHHHHHHhhCCccceeeecCCc-------ccccchhhhHHHHHHHHHhhhccCCCHHHHHHHHHHhhcchH--------
Confidence 4333456666654 4444443 23456789999999986642 12334555554444444333
Q ss_pred CChhhhhhHHHHHHHcCc
Q 033200 102 ADAKQRQGLIRLAKKNGE 119 (125)
Q Consensus 102 ~d~k~RQ~LIRlAk~NG~ 119 (125)
...++.|.+|+.|++|=+
T Consensus 161 ~~~~~~~~~i~~~~~~~~ 178 (243)
T COG1647 161 TTTAQLKKLIKDARRSLD 178 (243)
T ss_pred HHHHHHHHHHHHHHhhhh
Confidence 345788999999998744
No 8
>smart00351 PAX Paired Box domain.
Probab=60.48 E-value=17 Score=26.15 Aligned_cols=41 Identities=7% Similarity=0.126 Sum_probs=34.3
Q ss_pred hhhhhhHHHHhHH--HHHHHHHHhCCChhhhhhHHHHHHHcCc
Q 033200 79 NQFRGKAIALHSQ--VITEFCKSIGADAKQRQGLIRLAKKNGE 119 (125)
Q Consensus 79 NklRGKaIaLHSQ--vIt~FC~~iG~d~k~RQ~LIRlAk~NG~ 119 (125)
..+|-++|.+|.+ -+.+.|+.+|+...+-..+|+..++.|.
T Consensus 20 ~~~R~riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~ 62 (125)
T smart00351 20 DEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGS 62 (125)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCC
Confidence 3478888888744 4789999999999999999999988774
No 9
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=57.28 E-value=16 Score=23.23 Aligned_cols=24 Identities=25% Similarity=0.462 Sum_probs=16.3
Q ss_pred HHHHHHHhCCChhhhhhHHHHHHH
Q 033200 93 ITEFCKSIGADAKQRQGLIRLAKK 116 (125)
Q Consensus 93 It~FC~~iG~d~k~RQ~LIRlAk~ 116 (125)
|+.||+.++++...++.-.+++++
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~ 24 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKK 24 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHH
Confidence 789999999998777665555443
No 10
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=57.00 E-value=18 Score=22.58 Aligned_cols=34 Identities=9% Similarity=0.134 Sum_probs=26.0
Q ss_pred hhhHHHHh---HHHHHHHHHHhCCChhhhhhHHHHHH
Q 033200 82 RGKAIALH---SQVITEFCKSIGADAKQRQGLIRLAK 115 (125)
Q Consensus 82 RGKaIaLH---SQvIt~FC~~iG~d~k~RQ~LIRlAk 115 (125)
+-.+|..+ -..|.++|+..|+++.+=.++++..+
T Consensus 12 K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 12 KLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 34444444 24689999999999999999999997
No 11
>cd00001 PTS_IIB_man PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. The active site histidine receives a phosphate group from the IIA subunit and transfers it to the substrate.
Probab=52.11 E-value=9.8 Score=28.58 Aligned_cols=37 Identities=32% Similarity=0.568 Sum_probs=31.3
Q ss_pred HhHHHHHHHHHHhCCC-----------hhhhhhHHHHHHHcCcccccc
Q 033200 88 LHSQVITEFCKSIGAD-----------AKQRQGLIRLAKKNGERLGFL 124 (125)
Q Consensus 88 LHSQvIt~FC~~iG~d-----------~k~RQ~LIRlAk~NG~kLGfL 124 (125)
+|-||++.+++.++++ .+.+|.+++.|+=.|-|+-++
T Consensus 11 IHGQV~~~W~~~~~~~~IvVvdD~~A~D~~~k~~l~ma~P~gvk~~i~ 58 (151)
T cd00001 11 IHGQVATTWTKELNANRIIVVNDEVANDELRKTLLKLAAPPGVKLRIF 58 (151)
T ss_pred hhhHhhhhhhcccCCCEEEEEcccccCCHHHHHHHHhhCCCCCeEEEE
Confidence 6999999999999975 458999999999888777654
No 12
>PF03830 PTSIIB_sorb: PTS system sorbose subfamily IIB component; InterPro: IPR004720 Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families: It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This entry is specific for the IIB components of this family of PTS transporters [].; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0005737 cytoplasm; PDB: 3LFJ_B 1BLE_A 3P3V_B 1NRZ_C 3EYE_A 1VSQ_C 2JZH_A 2JZN_C 2JZO_D.
Probab=51.66 E-value=8.1 Score=28.95 Aligned_cols=37 Identities=24% Similarity=0.494 Sum_probs=31.7
Q ss_pred HhHHHHHHHHHHhCCC-----------hhhhhhHHHHHHHcCcccccc
Q 033200 88 LHSQVITEFCKSIGAD-----------AKQRQGLIRLAKKNGERLGFL 124 (125)
Q Consensus 88 LHSQvIt~FC~~iG~d-----------~k~RQ~LIRlAk~NG~kLGfL 124 (125)
+|-||++.+++.++++ .+.+|.+++.|.=.|-++-++
T Consensus 12 IHGQV~~~W~~~~~~~~IiVvdD~~A~D~~~k~~l~ma~P~gvk~~i~ 59 (151)
T PF03830_consen 12 IHGQVATAWVKKLNANRIIVVDDEVANDPFQKMILKMAAPAGVKLSIF 59 (151)
T ss_dssp SCTTHHHHHHHHHTTSEEEEE-HHHHHSHHHHHHHHHTSHTTSEEEEE
T ss_pred eeeeeeEEEhhhcccCEEEEECHHHhcCHHHHHHHHHhhcCCCceEEE
Confidence 6999999999999986 578999999998888777654
No 13
>TIGR00854 pts-sorbose PTS system, mannose/fructose/sorbose family, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIB components of this family of PTS transporters.
Probab=51.66 E-value=10 Score=28.60 Aligned_cols=37 Identities=32% Similarity=0.519 Sum_probs=31.7
Q ss_pred HhHHHHHHHHHHhCCC-----------hhhhhhHHHHHHHcCcccccc
Q 033200 88 LHSQVITEFCKSIGAD-----------AKQRQGLIRLAKKNGERLGFL 124 (125)
Q Consensus 88 LHSQvIt~FC~~iG~d-----------~k~RQ~LIRlAk~NG~kLGfL 124 (125)
+|-||++.+++.++++ .+.+|.+++.|.=.|-|+-|+
T Consensus 12 IHGQV~~~W~~~~~~~~IiVvdD~~A~D~~~k~~lkma~P~gvk~~i~ 59 (151)
T TIGR00854 12 IHGQVGTTWTKVAGANRIIVVNDDVANDEVRQTLMGIVAPTGFKVRFV 59 (151)
T ss_pred hhhHhhhhhhcccCCCEEEEEcccccCCHHHHHHHHhhCCCCCEEEEE
Confidence 6999999999999974 458999999999888887664
No 14
>PRK09756 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=49.52 E-value=11 Score=28.57 Aligned_cols=37 Identities=27% Similarity=0.458 Sum_probs=30.8
Q ss_pred HhHHHHHHHHHHhCCC-----------hhhhhhHHHHHH-HcCcccccc
Q 033200 88 LHSQVITEFCKSIGAD-----------AKQRQGLIRLAK-KNGERLGFL 124 (125)
Q Consensus 88 LHSQvIt~FC~~iG~d-----------~k~RQ~LIRlAk-~NG~kLGfL 124 (125)
+|-||++.+++.++++ .+.||.+++.|. -.|-++.++
T Consensus 16 IHGQV~~~W~~~~~~~~IiVvdD~vA~D~~~k~~lkma~~P~gvk~~i~ 64 (158)
T PRK09756 16 VHGQVGVTWTSTIGANLLVVVDDVVANDDIQQKLMGITAETYGFGIRFF 64 (158)
T ss_pred hhHHHHHhhhcccCCCEEEEEcchhcCCHHHHHHHHhcCCCCCCEEEEE
Confidence 6999999999999975 458999999988 677777654
No 15
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=48.50 E-value=28 Score=29.08 Aligned_cols=34 Identities=26% Similarity=0.459 Sum_probs=26.4
Q ss_pred hHHHHHHHHHHhCCChhhh---hhHHHHHHHcCcccc
Q 033200 89 HSQVITEFCKSIGADAKQR---QGLIRLAKKNGERLG 122 (125)
Q Consensus 89 HSQvIt~FC~~iG~d~k~R---Q~LIRlAk~NG~kLG 122 (125)
=++.|..||+.+|++...+ +.|+++|++.|..-|
T Consensus 194 p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~G 230 (285)
T COG1405 194 PSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAG 230 (285)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccC
Confidence 3678999999999997654 467788888877654
No 16
>PRK11425 PTS system N-acetylgalactosamine-specific transporter subunit IIB; Provisional
Probab=46.92 E-value=13 Score=28.19 Aligned_cols=37 Identities=24% Similarity=0.392 Sum_probs=31.4
Q ss_pred HhHHHHHHHHHHhCCC-----------hhhhhhHHHHHHHcCcccccc
Q 033200 88 LHSQVITEFCKSIGAD-----------AKQRQGLIRLAKKNGERLGFL 124 (125)
Q Consensus 88 LHSQvIt~FC~~iG~d-----------~k~RQ~LIRlAk~NG~kLGfL 124 (125)
+|-||++..++.++++ ...++.+++.|+=.|-|+-++
T Consensus 14 IHGQV~~~W~~~~~~~~IvVvdD~~A~D~~~k~~l~ma~P~gvk~~i~ 61 (157)
T PRK11425 14 IHGQVGVQWVGFAGANLVLVANDEVAEDPVQQNLMEMVLAEGIAVRFW 61 (157)
T ss_pred hhHHhhhhhhcccCCCEEEEEcchhcCCHHHHHHHHhhCCCCCeEEEE
Confidence 6999999999999975 458999999999888877654
No 17
>PRK15088 PTS system mannose-specific transporter subunits IIAB; Provisional
Probab=46.63 E-value=16 Score=30.70 Aligned_cols=37 Identities=22% Similarity=0.314 Sum_probs=32.1
Q ss_pred HhHHHHHHHHHHhCCC-----------hhhhhhHHHHHHHcCcccccc
Q 033200 88 LHSQVITEFCKSIGAD-----------AKQRQGLIRLAKKNGERLGFL 124 (125)
Q Consensus 88 LHSQvIt~FC~~iG~d-----------~k~RQ~LIRlAk~NG~kLGfL 124 (125)
+|-||++.+++.++++ ...+|.+++.|+=.|-|+.++
T Consensus 175 IHGQV~~~W~~~~~~~~IiVvdD~vA~D~~~k~~lk~A~P~gvk~~i~ 222 (322)
T PRK15088 175 IHGQVATRWTKETNVSRIIVVSDEVAADTVRKTLLTQVAPPGVTAHVV 222 (322)
T ss_pred hhHHHHHHHhhccCCCEEEEeCccccCCHHHHHHHHhcCCCCCeEEEE
Confidence 6999999999999975 458999999999888887664
No 18
>PRK14474 F0F1 ATP synthase subunit B; Provisional
Probab=45.38 E-value=44 Score=26.92 Aligned_cols=45 Identities=20% Similarity=0.282 Sum_probs=31.8
Q ss_pred hhHHHhhhccchhhhhhhhHHHHhHHHHHHHHHHhC-CChhhhhhHHHHHHHcC
Q 033200 66 VVLTRNIIGKKRFNQFRGKAIALHSQVITEFCKSIG-ADAKQRQGLIRLAKKNG 118 (125)
Q Consensus 66 Vv~~r~ilG~krfNklRGKaIaLHSQvIt~FC~~iG-~d~k~RQ~LIRlAk~NG 118 (125)
|-+++.+|++. +|. .+|.++|..||+.++ .|..+|+.|-+. ..++
T Consensus 130 ~~~A~kiL~~~-~d~------~~~~~lid~~i~~l~~l~~~~r~~l~~~-~~~~ 175 (250)
T PRK14474 130 VKIIRAALADL-ANA------TLEQQIVGIFIARLEHLSEAERQALANS-NTTP 175 (250)
T ss_pred HHHHHHHHHhh-cCH------HHHHHHHHHHHHHhcccCHHHHHHHHhh-hcCC
Confidence 45566666642 233 789999999999995 566779988766 4443
No 19
>PF03447 NAD_binding_3: Homoserine dehydrogenase, NAD binding domain; InterPro: IPR005106 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see []. Homoserine dehydrogenase (1.1.1.3 from EC) catalyses the third step in the aspartate pathway; theNAD(P)-dependent reduction of aspartate beta-semialdehyde into homoserine [, ]. Homoserine is an intermediate in the biosynthesis of threonine, isoleucine, and methionine. The enzyme can be found in a monofunctional form, in some bacteria and yeast, or a bifunctional form consisting of an N-terminal aspartokinase domain and a C-terminal homoserine dehydrogenase domain, as found in bacteria such as Escherichia coli and in plants. Structural analysis of the yeast monofunctional enzyme (P31116 from SWISSPROT) indicates that the enzyme is a dimer composed of three distinct regions; an N-terminal nucleotide-binding domain, a short central dimerisation region, and a C-terminal catalytic domain []. The N-terminal domain forms a modified Rossman fold, while the catalytic domain forms a novel alpha-beta mixed sheet. This entry represents the NAD(P)-binding domain of aspartate and homoserine dehydrogenase. Asparate dehydrogenase (1.4.1.21 from EC) is strictly specific for L-aspartate as substrate and catalyses the first step in NAD biosynthesis from aspartate. The enzyme has a higher affinity for NAD+ than NADP+ []. Note that the C terminus of the protein contributes a helix to this domain that is not covered by this model.; GO: 0016491 oxidoreductase activity, 0050661 NADP binding, 0055114 oxidation-reduction process; PDB: 3ING_A 3MTJ_A 3DO5_A 3JSA_A 3C8M_A 1J5P_A 1H2H_A 2EJW_E 1TVE_A 1EBU_D ....
Probab=44.52 E-value=16 Score=24.79 Aligned_cols=21 Identities=33% Similarity=0.445 Sum_probs=17.4
Q ss_pred ChhhhhhHHHHHHHcCccccc
Q 033200 103 DAKQRQGLIRLAKKNGERLGF 123 (125)
Q Consensus 103 d~k~RQ~LIRlAk~NG~kLGf 123 (125)
|....+.|.++|++||.++-|
T Consensus 96 ~~~~~~~L~~~A~~~g~~~~~ 116 (117)
T PF03447_consen 96 DEALYEELREAARKNGVRIYY 116 (117)
T ss_dssp SHHHHHHHHHHHHHHT-EEEE
T ss_pred hHHHHHHHHHHHHHcCCEEEe
Confidence 568999999999999988754
No 20
>PF11387 DUF2795: Protein of unknown function (DUF2795); InterPro: IPR021527 This family of proteins has no known function.
Probab=44.08 E-value=15 Score=22.71 Aligned_cols=16 Identities=31% Similarity=0.661 Sum_probs=13.6
Q ss_pred hhhhhhHHHHHHHcCc
Q 033200 104 AKQRQGLIRLAKKNGE 119 (125)
Q Consensus 104 ~k~RQ~LIRlAk~NG~ 119 (125)
+-.|+.||+.|++||-
T Consensus 7 Pa~k~~Lv~~A~~~gA 22 (44)
T PF11387_consen 7 PADKDELVRHARRNGA 22 (44)
T ss_pred CCCHHHHHHHHHHcCC
Confidence 4568999999999984
No 21
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=42.96 E-value=34 Score=19.03 Aligned_cols=20 Identities=20% Similarity=0.303 Sum_probs=16.8
Q ss_pred HHHHHHHhCCChhhhhhHHH
Q 033200 93 ITEFCKSIGADAKQRQGLIR 112 (125)
Q Consensus 93 It~FC~~iG~d~k~RQ~LIR 112 (125)
+.|.|+.+|++...-.++++
T Consensus 4 ~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 68999999999888777775
No 22
>TIGR03855 NAD_NadX aspartate dehydrogenase. Members of this protein family are L-aspartate dehydrogenase, as shown for the NADP-dependent enzyme TM_1643 of Thermotoga maritima. Members lack homology to NadB, the aspartate oxidase (EC 1.4.3.16) of most mesophilic bacteria (described by TIGR00551), which this enzyme replaces in the generation of oxaloacetate from aspartate for the NAD biosynthetic pathway. All members of the seed alignment are found adjacent to other genes of NAD biosynthesis, although other uses of L-aspartate dehydrogenase may occur.
Probab=36.91 E-value=53 Score=26.19 Aligned_cols=36 Identities=25% Similarity=0.384 Sum_probs=27.8
Q ss_pred HHhHHHHHHHHH--------HhCC--ChhhhhhHHHHHHHcCcccc
Q 033200 87 ALHSQVITEFCK--------SIGA--DAKQRQGLIRLAKKNGERLG 122 (125)
Q Consensus 87 aLHSQvIt~FC~--------~iG~--d~k~RQ~LIRlAk~NG~kLG 122 (125)
..|.+++....+ +.|+ |....+.|+++|+++|.+|-
T Consensus 48 ~~H~e~a~~aL~aGkhVl~~s~gAlad~e~~~~l~~aA~~~g~~l~ 93 (229)
T TIGR03855 48 EAVKEYAEKILKNGKDLLIMSVGALADRELRERLREVARSSGRKVY 93 (229)
T ss_pred HHHHHHHHHHHHCCCCEEEECCcccCCHHHHHHHHHHHHhcCCEEE
Confidence 467777666544 4665 77899999999999999874
No 23
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=36.82 E-value=68 Score=21.02 Aligned_cols=35 Identities=14% Similarity=0.355 Sum_probs=30.7
Q ss_pred HHhHHHHHHHHHH---------hCCChhhhhhHHHHHHHcCccc
Q 033200 87 ALHSQVITEFCKS---------IGADAKQRQGLIRLAKKNGERL 121 (125)
Q Consensus 87 aLHSQvIt~FC~~---------iG~d~k~RQ~LIRlAk~NG~kL 121 (125)
..|.+++.+..+. +..+..+=+.|+++|+++|.++
T Consensus 73 ~~h~~~~~~~l~~g~~v~~EKP~~~~~~~~~~l~~~a~~~~~~~ 116 (120)
T PF01408_consen 73 SSHAEIAKKALEAGKHVLVEKPLALTLEEAEELVEAAKEKGVKV 116 (120)
T ss_dssp GGHHHHHHHHHHTTSEEEEESSSSSSHHHHHHHHHHHHHHTSCE
T ss_pred cchHHHHHHHHHcCCEEEEEcCCcCCHHHHHHHHHHHHHhCCEE
Confidence 6799999998865 6789999999999999999875
No 24
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=36.40 E-value=50 Score=18.07 Aligned_cols=21 Identities=10% Similarity=0.183 Sum_probs=16.4
Q ss_pred HHHHHHHhCCChhhhhhHHHH
Q 033200 93 ITEFCKSIGADAKQRQGLIRL 113 (125)
Q Consensus 93 It~FC~~iG~d~k~RQ~LIRl 113 (125)
+.|.|+.+|++...-..+++.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 578999999998777776653
No 25
>PF13730 HTH_36: Helix-turn-helix domain
Probab=35.84 E-value=69 Score=19.02 Aligned_cols=26 Identities=19% Similarity=0.350 Sum_probs=22.3
Q ss_pred HHHHHHHhCCChhhhhhHHHHHHHcC
Q 033200 93 ITEFCKSIGADAKQRQGLIRLAKKNG 118 (125)
Q Consensus 93 It~FC~~iG~d~k~RQ~LIRlAk~NG 118 (125)
+...++.+|+...+-++.|+.-++.|
T Consensus 28 ~~~la~~~g~s~~Tv~~~i~~L~~~G 53 (55)
T PF13730_consen 28 QETLAKDLGVSRRTVQRAIKELEEKG 53 (55)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCc
Confidence 67889999999999999988877765
No 26
>PF07961 MBA1: MBA1-like protein; InterPro: IPR024621 Mba1 is an inner membrane protein that is part of the mitochondrial protein export machinery [, ]. It binds to the large subunit of mitochondrial ribosomes and cooperates with the C-terminal ribosome-binding domain of Oxa1, which is a central component of the insertion machinery of the inner membrane. In the absence of both Mba1 and the C terminus of Oxa1, mitochondrial translation products fail to be properly inserted into the inner membrane and serve as substrates of the matrix chaperone Hsp70 []. It is proposed that Mba1 functions as a ribosome receptor that cooperates with Oxa1 in the positioning of the ribosome exit site to the insertion machinery of the inner membrane [].
Probab=35.28 E-value=34 Score=28.21 Aligned_cols=37 Identities=32% Similarity=0.468 Sum_probs=30.5
Q ss_pred hhhhhHHHhhhc-cchhhhhhhhHHHHhHHHHHHHHHH
Q 033200 63 APVVVLTRNIIG-KKRFNQFRGKAIALHSQVITEFCKS 99 (125)
Q Consensus 63 aPlVv~~r~ilG-~krfNklRGKaIaLHSQvIt~FC~~ 99 (125)
.=-|+..|.-.| +.+||..+-+||.+|.++=+.|++.
T Consensus 53 t~~i~~fr~~~g~k~~f~~wk~~AiE~yv~~NkaFA~~ 90 (235)
T PF07961_consen 53 TVSIAKFRRQTGKKPRFNEWKNKAIELYVQMNKAFAAG 90 (235)
T ss_pred hheeeehhhhcCCCCchhHHHHHHHHHHHHHHHHHHhc
Confidence 334555677788 7799999999999999999999864
No 27
>PF08035 Op_neuropeptide: Opioids neuropeptide; InterPro: IPR013532 Pro-opiomelanocortin is present in high levels in the pituitary and is processed into 3 major peptide families: adrenocorticotrophin (ACTH); alpha-, beta- and gamma-melanocyte- stimulating hormones (MSH); and beta-endorphin []. ACTH regulates the synthesis and release of glucocorticoids and, to some extent, aldosterone in the adrenal cortex. It is synthesised and released in response to corticotrophin-releasing factor at times of stress (i.e. heat, cold, infection, etc.), its release leading to increased metabolism. The action of MSH in man is poorly understood, but it may be involved in temperature regulation []. Full activity of ACTH resides in the first 20 N-terminal amino acids, the first 13 of which are identical to alpha-MSH [, ]. This region corresponds to the conserved YGG motif that is found in a wide variety of opioid neuropeptides such as enkephalin
Probab=35.14 E-value=21 Score=21.85 Aligned_cols=15 Identities=40% Similarity=0.611 Sum_probs=13.0
Q ss_pred hhhhhHHHhhhccch
Q 033200 63 APVVVLTRNIIGKKR 77 (125)
Q Consensus 63 aPlVv~~r~ilG~kr 77 (125)
.|||-+.||+|.++.
T Consensus 14 ~PLvtlfkn~i~k~~ 28 (31)
T PF08035_consen 14 KPLVTLFKNVIIKES 28 (31)
T ss_pred CchHHHHHHHHhhcc
Confidence 699999999998753
No 28
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=34.72 E-value=44 Score=22.58 Aligned_cols=20 Identities=25% Similarity=0.657 Sum_probs=16.7
Q ss_pred HHHHHHHhCCChhhhhhHHH
Q 033200 93 ITEFCKSIGADAKQRQGLIR 112 (125)
Q Consensus 93 It~FC~~iG~d~k~RQ~LIR 112 (125)
+++||...|+++..-+.|+.
T Consensus 3 ~~e~~~~~~i~~~~l~~lve 22 (84)
T PF13591_consen 3 LEEFCEACGIEPEFLRELVE 22 (84)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 68999999999988776654
No 29
>PF06109 HlyE: Haemolysin E (HlyE); InterPro: IPR010356 This family consists of several enterobacterial haemolysin (HlyE) proteins. Haemolysin E (HlyE) is a novel pore-forming toxin of Escherichia coli, Salmonella typhi, and Shigella flexneri. HlyE is unrelated to the well characterised pore-forming E. coli haemolysins of the RTX family, haemolysin A (HlyA), and the enterohaemolysin encoded by the plasmid borne ehxA gene of E. coli 0157. However, it is evident that expression of HlyE in the absence of the RTX toxins is sufficient to give a haemolytic phenotype in E. coli. HlyE is a protein of 34 kDa that is expressed during anaerobic growth of E. coli. Anaerobic expression is controlled by the transcription factor, FNR, such that, upon ingestion and entry into the anaerobic mammalian intestine, HlyE is produced and may then contribute to the colonisation of the host [].; PDB: 2WCD_P 1QOY_A.
Probab=34.62 E-value=43 Score=28.69 Aligned_cols=29 Identities=34% Similarity=0.510 Sum_probs=24.8
Q ss_pred ccchhhhhhhhHHHHhHHHHHHHHHHhCC
Q 033200 74 GKKRFNQFRGKAIALHSQVITEFCKSIGA 102 (125)
Q Consensus 74 G~krfNklRGKaIaLHSQvIt~FC~~iG~ 102 (125)
....||.--||.|+|.||.-++|-+...-
T Consensus 134 ssqsfn~asgkl~aldsql~ndf~eks~y 162 (299)
T PF06109_consen 134 SSQSFNNASGKLIALDSQLTNDFSEKSSY 162 (299)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhcccccceeeehhhhhcchhHHHHH
Confidence 45679999999999999999999886543
No 30
>PF14502 HTH_41: Helix-turn-helix domain
Probab=34.07 E-value=67 Score=21.08 Aligned_cols=27 Identities=22% Similarity=0.503 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCChhhhhhHHHHHHHcC
Q 033200 92 VITEFCKSIGADAKQRQGLIRLAKKNG 118 (125)
Q Consensus 92 vIt~FC~~iG~d~k~RQ~LIRlAk~NG 118 (125)
.|.|+.+.+++..-.-|+-++.-+++|
T Consensus 8 tI~e~~~~~~vs~GtiQ~Alk~Le~~g 34 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNALKFLEENG 34 (48)
T ss_pred CHHHHHHHhCcchhHHHHHHHHHHHCC
Confidence 589999999999999999999999887
No 31
>KOG1405 consensus 4-aminobutyrate aminotransferase [Amino acid transport and metabolism]
Probab=32.73 E-value=14 Score=33.83 Aligned_cols=37 Identities=32% Similarity=0.505 Sum_probs=30.0
Q ss_pred hhhhhhhhHHHHhHHHHHHHHHHhCCChhhhhhHHHHHHHcCcccc
Q 033200 77 RFNQFRGKAIALHSQVITEFCKSIGADAKQRQGLIRLAKKNGERLG 122 (125)
Q Consensus 77 rfNklRGKaIaLHSQvIt~FC~~iG~d~k~RQ~LIRlAk~NG~kLG 122 (125)
.||++||+. .||.+==-+.+.|..+|..||-||--+|
T Consensus 414 ~~~~~RGrG---------TF~a~d~ps~~~Rdk~i~~~~~nGv~~G 450 (484)
T KOG1405|consen 414 KINNLRGRG---------TFIAWDCPSGSIRDKLILIARLNGVNLG 450 (484)
T ss_pred hhhcccccc---------eEEEEeCCChHHHHHHHHHHHHcCceec
Confidence 467777754 4777777788999999999999998776
No 32
>PHA00781 hypothetical protein
Probab=31.72 E-value=78 Score=21.77 Aligned_cols=38 Identities=26% Similarity=0.395 Sum_probs=27.1
Q ss_pred hhhhhHHHHhHHHHHHH------HHHhCCChhhhhhHHHHHHHc
Q 033200 80 QFRGKAIALHSQVITEF------CKSIGADAKQRQGLIRLAKKN 117 (125)
Q Consensus 80 klRGKaIaLHSQvIt~F------C~~iG~d~k~RQ~LIRlAk~N 117 (125)
++-+..--.--.+|-++ |+.+|.=.-.+|.||.-||..
T Consensus 14 ~~t~EL~eRl~svIH~YDGEISl~EAvG~LEllK~~LIe~~k~~ 57 (59)
T PHA00781 14 PITQELYERLESVIHDYDGEISLCEAIGTLELLKQSLIEGAKES 57 (59)
T ss_pred cchHHHHHHHHHHHHHhcccchHHHHHhHHHHHHHHHHHHHhhc
Confidence 33344333344566554 999999999999999999864
No 33
>TIGR00443 hisZ_biosyn_reg ATP phosphoribosyltransferase, regulatory subunit. Apparant second copies of histidyl-tRNA synthetase, found in Bacillus subtilis, Synechocystis sp., Aquifex aeolicus, and others, are in fact a regulatory subunit of ATP phosphoribosyltransferase, and usually encoded by a gene adjacent to that encoding the catalytic subunit.
Probab=31.68 E-value=64 Score=25.97 Aligned_cols=26 Identities=15% Similarity=0.284 Sum_probs=23.9
Q ss_pred hHHHHHHHHHHhCCChhhhhhHHHHH
Q 033200 89 HSQVITEFCKSIGADAKQRQGLIRLA 114 (125)
Q Consensus 89 HSQvIt~FC~~iG~d~k~RQ~LIRlA 114 (125)
|.++++.+|+.+|++..+|+.|.+.-
T Consensus 151 ~~~il~~il~~~~~~~~~~~~l~~~l 176 (314)
T TIGR00443 151 HVGLVRALLEEAGLPEEAREALREAL 176 (314)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 99999999999999999999888754
No 34
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=31.42 E-value=75 Score=21.08 Aligned_cols=31 Identities=19% Similarity=0.329 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhCCChhhhhhHHHHHHHcCcc
Q 033200 90 SQVITEFCKSIGADAKQRQGLIRLAKKNGER 120 (125)
Q Consensus 90 SQvIt~FC~~iG~d~k~RQ~LIRlAk~NG~k 120 (125)
.|||..+.+.+|.+..+=..+.-.++.+|+-
T Consensus 20 ~~Vi~~L~~~~~~s~~~A~~~a~~v~~~G~a 50 (82)
T PF02617_consen 20 EQVIDVLRRVFGCSEEQARQIAMEVHREGRA 50 (82)
T ss_dssp HHHHHHHHHHC---HHHHHHHHHHHHHHSEE
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHhHcCCE
Confidence 5899999999999999999999999999974
No 35
>PF11281 DUF3083: Protein of unknown function (DUF3083); InterPro: IPR021433 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=30.51 E-value=22 Score=31.13 Aligned_cols=21 Identities=33% Similarity=0.626 Sum_probs=17.3
Q ss_pred HHHHHHHHHHhCCChhhhhhHH
Q 033200 90 SQVITEFCKSIGADAKQRQGLI 111 (125)
Q Consensus 90 SQvIt~FC~~iG~d~k~RQ~LI 111 (125)
-+.|.+||+.+++| ++||.||
T Consensus 286 E~Al~~~~~el~i~-~er~dl~ 306 (316)
T PF11281_consen 286 EDALRSFADELDID-KERQDLI 306 (316)
T ss_pred HHHHHHHHHHhCCC-cccceeE
Confidence 46788999999999 7787765
No 36
>cd07313 terB_like_2 tellurium resistance terB-like protein, subgroup 2. This family includes several uncharacterized bacterial proteins. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
Probab=30.43 E-value=91 Score=20.59 Aligned_cols=29 Identities=21% Similarity=0.271 Sum_probs=20.9
Q ss_pred HhHHHHHHHHHH-hCCChhhhhhHHHHHHH
Q 033200 88 LHSQVITEFCKS-IGADAKQRQGLIRLAKK 116 (125)
Q Consensus 88 LHSQvIt~FC~~-iG~d~k~RQ~LIRlAk~ 116 (125)
-.-+.|.+++.. .|.+..++..+++.++.
T Consensus 19 ~E~~~i~~~l~~~~~l~~~~~~~l~~~~~~ 48 (104)
T cd07313 19 EERAAIDRLLAERFGLDAEEAAELLAEAEA 48 (104)
T ss_pred HHHHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 445667777666 58888888888877765
No 37
>PF12728 HTH_17: Helix-turn-helix domain
Probab=30.29 E-value=66 Score=18.95 Aligned_cols=20 Identities=20% Similarity=0.268 Sum_probs=16.1
Q ss_pred HHHHHHHhCCChhhhhhHHH
Q 033200 93 ITEFCKSIGADAKQRQGLIR 112 (125)
Q Consensus 93 It~FC~~iG~d~k~RQ~LIR 112 (125)
++|.|+.+|++..+-..+++
T Consensus 4 ~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 57899999999887666664
No 38
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=28.41 E-value=31 Score=22.81 Aligned_cols=22 Identities=27% Similarity=0.475 Sum_probs=17.6
Q ss_pred HhHHHHHHHHHHhCCChhhhhh
Q 033200 88 LHSQVITEFCKSIGADAKQRQG 109 (125)
Q Consensus 88 LHSQvIt~FC~~iG~d~k~RQ~ 109 (125)
...+.+.+||..+|++..+-|-
T Consensus 30 ~~~~~r~~la~~lgl~~~vvKV 51 (58)
T TIGR01565 30 KRREEVREFCEEIGVTRKVFKV 51 (58)
T ss_pred CCHHHHHHHHHHhCCCHHHeee
Confidence 4567899999999999776553
No 39
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=27.82 E-value=81 Score=18.77 Aligned_cols=23 Identities=22% Similarity=0.310 Sum_probs=16.8
Q ss_pred HHHHHHHHHhCCChhhhhhHHHH
Q 033200 91 QVITEFCKSIGADAKQRQGLIRL 113 (125)
Q Consensus 91 QvIt~FC~~iG~d~k~RQ~LIRl 113 (125)
+.|.+||.-.|++..+=+.+.+.
T Consensus 2 e~i~~F~~iTg~~~~~A~~~L~~ 24 (43)
T PF14555_consen 2 EKIAQFMSITGADEDVAIQYLEA 24 (43)
T ss_dssp HHHHHHHHHH-SSHHHHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHHH
Confidence 57999999999988666655543
No 40
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=27.76 E-value=54 Score=22.20 Aligned_cols=19 Identities=26% Similarity=0.370 Sum_probs=16.7
Q ss_pred HhCCChhhhhhHHHHHHHc
Q 033200 99 SIGADAKQRQGLIRLAKKN 117 (125)
Q Consensus 99 ~iG~d~k~RQ~LIRlAk~N 117 (125)
.+|....|-+++||.||.+
T Consensus 11 ~lGf~~~tA~~IIrqAK~~ 29 (59)
T PF11372_consen 11 ELGFSESTARDIIRQAKAL 29 (59)
T ss_pred HcCCCHHHHHHHHHHHHHH
Confidence 3599999999999999983
No 41
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=27.25 E-value=67 Score=24.37 Aligned_cols=48 Identities=23% Similarity=0.423 Sum_probs=29.7
Q ss_pred hhhhHHHhhhccchhhhh----hhhHHHHhHHHHHHHHHHhCCChhhhhhHHHH
Q 033200 64 PVVVLTRNIIGKKRFNQF----RGKAIALHSQVITEFCKSIGADAKQRQGLIRL 113 (125)
Q Consensus 64 PlVv~~r~ilG~krfNkl----RGKaIaLHSQvIt~FC~~iG~d~k~RQ~LIRl 113 (125)
||=.+.|.-==.+.+.+| |||.| -.+.+.+|.+.+.++...++.|..+
T Consensus 58 pIQTvmRr~g~~~pYE~LK~lTRg~~i--t~~~l~~fI~~L~ip~~~k~~L~~l 109 (115)
T PF08328_consen 58 PIQTVMRRYGIPNPYEKLKELTRGKKI--TKEDLREFIESLDIPEEAKARLLAL 109 (115)
T ss_dssp HHHHHHHHTT-SSHHHHHHHHHTTS-----HHHHHHHHHTSSS-HHHHHHHHH-
T ss_pred HHHHHHHHcCCCCHHHHHHHHHcCCCC--CHHHHHHHHHhCCCCHHHHHHHHhc
Confidence 444444432223444443 89955 5688999999999999999998765
No 42
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=27.05 E-value=78 Score=19.24 Aligned_cols=19 Identities=21% Similarity=0.177 Sum_probs=14.7
Q ss_pred HHHHHHHhCCChhhhhhHH
Q 033200 93 ITEFCKSIGADAKQRQGLI 111 (125)
Q Consensus 93 It~FC~~iG~d~k~RQ~LI 111 (125)
++++|+.+|+++++-+.+.
T Consensus 3 ~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 6889999999987755554
No 43
>PRK12292 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=26.74 E-value=85 Score=26.23 Aligned_cols=27 Identities=15% Similarity=0.204 Sum_probs=24.1
Q ss_pred hHHHHHHHHHHhCCChhhhhhHHHHHH
Q 033200 89 HSQVITEFCKSIGADAKQRQGLIRLAK 115 (125)
Q Consensus 89 HSQvIt~FC~~iG~d~k~RQ~LIRlAk 115 (125)
|.+++..+++.+|++..+|+.+.+.-.
T Consensus 162 ~~~i~~~il~~~~~~~~~~~~l~~~l~ 188 (391)
T PRK12292 162 HVGLFRALLEAAGLSEELEEVLRRALA 188 (391)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 999999999999999999988877554
No 44
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.52 E-value=1e+02 Score=17.49 Aligned_cols=19 Identities=21% Similarity=0.172 Sum_probs=14.7
Q ss_pred HHHHHHHhCCChhhhhhHH
Q 033200 93 ITEFCKSIGADAKQRQGLI 111 (125)
Q Consensus 93 It~FC~~iG~d~k~RQ~LI 111 (125)
+.++|+.+|++..+-..++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYE 21 (49)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 6789999999987655554
No 45
>PF02993 MCPVI: Minor capsid protein VI; InterPro: IPR004243 This minor capsid protein may act as a link between the external capsid and the internal DNA-protein core. Residues at the C-terminal end of the protein may act as a protease cofactor leading to activation of the adenovirus proteinase [].; GO: 0019028 viral capsid; PDB: 1AVP_B.
Probab=23.76 E-value=26 Score=29.32 Aligned_cols=82 Identities=20% Similarity=0.328 Sum_probs=0.0
Q ss_pred ceeeccccCcc-c-cCCCCccccccCcchhhhhhccCC----cccCCccccCC----CccCCCC--CCccchhhhhHHHh
Q 033200 4 TSVCVAGLSSS-F-HGSWGASFANGGEEYRMLARSVPN----VRVARPIRMQP----MMGNINE--GKGIFAPVVVLTRN 71 (125)
Q Consensus 4 ~s~~~~g~~~~-~-~~~w~~s~~~~ge~~~~l~~~vp~----~~~~~p~r~~~----~m~n~~~--~~G~FaPlVv~~r~ 71 (125)
..|..+.+++| | .||++||++||-.+++.-+++.=+ .-.+.-.|... .-.||.+ +.|+- =+|=++|.
T Consensus 18 ~~IGtS~l~GGafNWgsLwS~is~glkn~Gs~l~n~g~k~wnS~tgq~lrq~LkDsg~~~kVv~g~~~gi~-g~vDIgrq 96 (238)
T PF02993_consen 18 SDIGTSELRGGAFNWGSLWSSISSGLKNFGSFLKNYGSKAWNSQTGQQLRQGLKDSGLQEKVVEGAGSGIN-GLVDIGRQ 96 (238)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccccccccCcccccccchhhhhhhhhhHhHHHHHhhhhhhhhhHHHHHHHHHhhhhHHHHHHHHHhhhhh-HHHHHHHH
Confidence 56777778876 5 788889999988888876655432 23333333322 1222221 22332 24555555
Q ss_pred hhccchhhhhhhhHHH
Q 033200 72 IIGKKRFNQFRGKAIA 87 (125)
Q Consensus 72 ilG~krfNklRGKaIa 87 (125)
-| ++.+||+|-|+..
T Consensus 97 ~v-q~~lekrlek~~~ 111 (238)
T PF02993_consen 97 KV-QKDLEKRLEKALP 111 (238)
T ss_dssp ----------------
T ss_pred HH-HHHHHHHhccCCC
Confidence 55 5667777777665
No 46
>cd06892 PX_SNX5_like The phosphoinositide binding Phox Homology domain of Sorting Nexins 5 and 6. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Members of this subfamily include SNX5, SNX6, and similar proteins. They contain a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to other sorting nexins including SNX1-2. The PX-BAR structural unit helps determine the specific membrane-targeting of som
Probab=23.69 E-value=1.6e+02 Score=22.65 Aligned_cols=46 Identities=13% Similarity=0.202 Sum_probs=29.8
Q ss_pred CccCCCCCCccchhhhhHHHhhhccchhhhhhhhHHHHhHHHHHHH
Q 033200 51 MMGNINEGKGIFAPVVVLTRNIIGKKRFNQFRGKAIALHSQVITEF 96 (125)
Q Consensus 51 ~m~n~~~~~G~FaPlVv~~r~ilG~krfNklRGKaIaLHSQvIt~F 96 (125)
.|...-+++|.|++-.+.-|..-=...++.+|.|..++|-..++..
T Consensus 77 k~~klg~~d~~~~~ef~~~r~~~Le~~y~~~~~k~v~~~e~FL~Ri 122 (141)
T cd06892 77 KLQKLGEGEGSMTKEEFEKMKQELEAEYLAIFKKTVAMHEVFLRRL 122 (141)
T ss_pred eeeecccCccccchHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHh
Confidence 3434446778888876664433333468889999999986655543
No 47
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=23.52 E-value=1.4e+02 Score=18.00 Aligned_cols=29 Identities=21% Similarity=0.494 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChhhhh---------hHHHHHHHcCccc
Q 033200 93 ITEFCKSIGADAKQRQ---------GLIRLAKKNGERL 121 (125)
Q Consensus 93 It~FC~~iG~d~k~RQ---------~LIRlAk~NG~kL 121 (125)
+..|.+.+-.|+.-|+ .++++|+++|-.+
T Consensus 6 l~~Fl~~~~~d~~l~~~l~~~~~~~e~~~lA~~~Gy~f 43 (49)
T PF07862_consen 6 LKAFLEKVKSDPELREQLKACQNPEEVVALAREAGYDF 43 (49)
T ss_pred HHHHHHHHhcCHHHHHHHHhcCCHHHHHHHHHHcCCCC
Confidence 4566666666655554 4678898888543
No 48
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=23.15 E-value=1.3e+02 Score=17.70 Aligned_cols=26 Identities=19% Similarity=0.277 Sum_probs=20.9
Q ss_pred HHHHHHHHHhCCChhhhhhHHHHHHH
Q 033200 91 QVITEFCKSIGADAKQRQGLIRLAKK 116 (125)
Q Consensus 91 QvIt~FC~~iG~d~k~RQ~LIRlAk~ 116 (125)
.-..|.++.+|++...-+..++.|++
T Consensus 27 ~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 27 MSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 45678999999999999999999886
No 49
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=23.02 E-value=1.1e+02 Score=18.67 Aligned_cols=20 Identities=25% Similarity=0.287 Sum_probs=15.1
Q ss_pred HHHHHHHhCCChhhhhhHHH
Q 033200 93 ITEFCKSIGADAKQRQGLIR 112 (125)
Q Consensus 93 It~FC~~iG~d~k~RQ~LIR 112 (125)
|+++|+.+|+++.+-..+.+
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 78899999998877655543
No 50
>PF13393 tRNA-synt_His: Histidyl-tRNA synthetase; PDB: 3HRI_E 3HRK_A 3LC0_A 1Z7N_A 1Z7M_D 3NET_A 1H4V_B 3OD1_A 4E51_B 3RAC_A ....
Probab=22.95 E-value=80 Score=24.73 Aligned_cols=27 Identities=15% Similarity=0.372 Sum_probs=23.2
Q ss_pred hHHHHHHHHHHhCCChhhhhhHHHHHH
Q 033200 89 HSQVITEFCKSIGADAKQRQGLIRLAK 115 (125)
Q Consensus 89 HSQvIt~FC~~iG~d~k~RQ~LIRlAk 115 (125)
|.+++..+++.+|++..++..+.+.-.
T Consensus 153 h~~i~~~il~~~gl~~~~~~~l~~~l~ 179 (311)
T PF13393_consen 153 HTGILDAILEHLGLPEDLRRELLEALD 179 (311)
T ss_dssp EHHHHHHHHHHTTHHHHHHHHHHHHHH
T ss_pred CchhhHHHHhhcCCChhhhhhhhhhee
Confidence 899999999999999888888776653
No 51
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=22.66 E-value=1.5e+02 Score=16.40 Aligned_cols=27 Identities=11% Similarity=0.241 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCChhhhhhHHHHHHHcC
Q 033200 92 VITEFCKSIGADAKQRQGLIRLAKKNG 118 (125)
Q Consensus 92 vIt~FC~~iG~d~k~RQ~LIRlAk~NG 118 (125)
-+.+.|+.+|++...-.+.++.-.++|
T Consensus 16 s~~~l~~~l~~s~~tv~~~l~~L~~~g 42 (53)
T smart00420 16 SVEELAELLGVSEMTIRRDLNKLEEQG 42 (53)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 577899999999888777777666654
No 52
>PRK05255 hypothetical protein; Provisional
Probab=22.59 E-value=1.3e+02 Score=23.75 Aligned_cols=55 Identities=29% Similarity=0.454 Sum_probs=43.4
Q ss_pred hhhhhHHHhhhccc--------hhhhhhhhHHHHhHHHHHHHHHHh-CCChhhhhhHHHHHHHc
Q 033200 63 APVVVLTRNIIGKK--------RFNQFRGKAIALHSQVITEFCKSI-GADAKQRQGLIRLAKKN 117 (125)
Q Consensus 63 aPlVv~~r~ilG~k--------rfNklRGKaIaLHSQvIt~FC~~i-G~d~k~RQ~LIRlAk~N 117 (125)
.||.-++-.+-+.. ++.++|-..|+==-.+|++|.+.. .+|..+=-.|||-|++.
T Consensus 86 e~I~~al~~~~~~~~~~~~~~h~lE~wRdrLi~~~d~al~e~~~~~P~~DrQ~LRqLiR~A~kE 149 (171)
T PRK05255 86 EPIRAALDKLKNKHNQETARFHKLERWRDRLLAEGDDALTEFLEEYPDADRQQLRQLIRNAKKE 149 (171)
T ss_pred HHHHHHHHHHhchhHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHCchhhHHHHHHHHHHHHHH
Confidence 57777766666654 556889888986678999999998 78988877899999864
No 53
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=21.99 E-value=98 Score=21.68 Aligned_cols=21 Identities=29% Similarity=0.610 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCChhhhhhHHH
Q 033200 92 VITEFCKSIGADAKQRQGLIR 112 (125)
Q Consensus 92 vIt~FC~~iG~d~k~RQ~LIR 112 (125)
.+.+||..+|++++.-..|+.
T Consensus 9 t~~Elc~~~gi~~~~l~eLve 29 (101)
T PRK10265 9 TITEFCLHTGVSEEELNEIVG 29 (101)
T ss_pred eHHHHHHHHCcCHHHHHHHHH
Confidence 368999999999988777765
No 54
>TIGR01220 Pmev_kin_Gr_pos phosphomevalonate kinase, ERG8-type, Gram-positive branch. This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the animal type and this ERG8 type. This model represents the low GC Gram-positive organism forms of the ERG8 type of phosphomevalonate kinase.
Probab=21.51 E-value=2e+02 Score=23.94 Aligned_cols=50 Identities=14% Similarity=0.221 Sum_probs=34.4
Q ss_pred HHhhhccchhhhhhhhHHHHhHHHHHHHHH--HhCCChhhhhhHHHHHHHcCc
Q 033200 69 TRNIIGKKRFNQFRGKAIALHSQVITEFCK--SIGADAKQRQGLIRLAKKNGE 119 (125)
Q Consensus 69 ~r~ilG~krfNklRGKaIaLHSQvIt~FC~--~iG~d~k~RQ~LIRlAk~NG~ 119 (125)
++..+-...|.+| |+.+..+-+...++-+ -+|+.++.=..||..|+++|-
T Consensus 261 ~~~al~~~d~~~l-g~~~~~~~~lL~~l~~~~~~~vs~~~l~~li~~a~~~ga 312 (358)
T TIGR01220 261 AITAFETGDITSL-QKEIRRNRQELARLDDEVGVGIETEKLKALCDAAEAYGG 312 (358)
T ss_pred HHHHHHhCCHHHH-HHHHHHHHHHHHHhhcccCCCcCCHHHHHHHHHHhhcCc
Confidence 4445555556665 6777777777666644 346667777899999999874
No 55
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=21.46 E-value=1.8e+02 Score=17.12 Aligned_cols=27 Identities=15% Similarity=0.368 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCChhhhhhHHHHHHHcC
Q 033200 92 VITEFCKSIGADAKQRQGLIRLAKKNG 118 (125)
Q Consensus 92 vIt~FC~~iG~d~k~RQ~LIRlAk~NG 118 (125)
.+++.|+.+|++...-..+|+.-.+.|
T Consensus 23 t~~~la~~l~~~~~~vs~~v~~L~~~G 49 (62)
T PF12802_consen 23 TQSELAERLGISKSTVSRIVKRLEKKG 49 (62)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 678999999999988888888776655
No 56
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=21.05 E-value=1.1e+02 Score=25.96 Aligned_cols=25 Identities=20% Similarity=0.412 Sum_probs=23.3
Q ss_pred HHHHHHhCCChhhhhhHHHHHHHcC
Q 033200 94 TEFCKSIGADAKQRQGLIRLAKKNG 118 (125)
Q Consensus 94 t~FC~~iG~d~k~RQ~LIRlAk~NG 118 (125)
.|..+.+|+.+-.-++|+..||++|
T Consensus 30 ~eIA~~LgiSR~~v~rlL~~Ar~~G 54 (321)
T COG2390 30 SEIAERLGISRATVSRLLAKAREEG 54 (321)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 4788999999999999999999998
No 57
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=20.65 E-value=1.2e+02 Score=25.14 Aligned_cols=26 Identities=15% Similarity=0.318 Sum_probs=23.8
Q ss_pred HHHHHHHhCCChhhhhhHHHHHHHcC
Q 033200 93 ITEFCKSIGADAKQRQGLIRLAKKNG 118 (125)
Q Consensus 93 It~FC~~iG~d~k~RQ~LIRlAk~NG 118 (125)
-.|.++.+|+.+....+|+..|++.|
T Consensus 32 Q~eIA~~lgiSR~~VsRlL~~Ar~~G 57 (318)
T PRK15418 32 QSEIGERLGLTRLKVSRLLEKGRQSG 57 (318)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHcC
Confidence 36789999999999999999999987
No 58
>PF13875 DUF4202: Domain of unknown function (DUF4202)
Probab=20.55 E-value=2.5e+02 Score=22.72 Aligned_cols=46 Identities=22% Similarity=0.393 Sum_probs=40.2
Q ss_pred hccchhhhhhhhHHHHhHHHHHHHHHHhCCChhhhhhHHHHHHHcC
Q 033200 73 IGKKRFNQFRGKAIALHSQVITEFCKSIGADAKQRQGLIRLAKKNG 118 (125)
Q Consensus 73 lG~krfNklRGKaIaLHSQvIt~FC~~iG~d~k~RQ~LIRlAk~NG 118 (125)
+|.+-.-+-|-.--..|.+...+.|..+|.|...-+.+-++-.|.|
T Consensus 72 ~~r~GYl~WR~~l~~~hA~~~~~im~~~Gy~~~~i~rV~~lv~K~~ 117 (185)
T PF13875_consen 72 EGRAGYLQWRRALKKRHAAIAAEIMREAGYDEEEIDRVAALVRKEG 117 (185)
T ss_pred CCchhHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHhcc
Confidence 5777788999999999999999999999999999888877776654
No 59
>PF08102 Antimicrobial_7: Scorpion antimicrobial peptide ; InterPro: IPR012526 This family consists of antimicrobial peptides secreted by scorpions. Novel antimicrobial peptides have been isolated from scorpions, namely the opistoporin [] and the pandinin []. These peptides form essentially helical structures and demonstrate high antimicrobial activity against Gram-negative and Gram-positive bacteria respectively.; GO: 0005576 extracellular region
Probab=20.46 E-value=2e+02 Score=18.85 Aligned_cols=38 Identities=18% Similarity=0.329 Sum_probs=26.6
Q ss_pred chhhhhHHHhhhccchhhhhhhhHHHHhHHHHHHHH-HHhCCC
Q 033200 62 FAPVVVLTRNIIGKKRFNQFRGKAIALHSQVITEFC-KSIGAD 103 (125)
Q Consensus 62 FaPlVv~~r~ilG~krfNklRGKaIaLHSQvIt~FC-~~iG~d 103 (125)
++-|--.++.+.-.+.-++||+||+- .+++|+ +.||+.
T Consensus 4 wd~IK~~Akk~wnS~~~~~Lk~kaln----AaknfVaeKiGat 42 (43)
T PF08102_consen 4 WDWIKSTAKKAWNSDPVQQLKNKALN----AAKNFVAEKIGAT 42 (43)
T ss_pred HHHHHHHHHHHhcchHHHHHHHHHHH----HHHHHHHHHhCCC
Confidence 44455567777778888999999874 566765 556764
No 60
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=20.03 E-value=1.1e+02 Score=20.12 Aligned_cols=24 Identities=13% Similarity=0.203 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhCCChhhhhhHHHH
Q 033200 90 SQVITEFCKSIGADAKQRQGLIRL 113 (125)
Q Consensus 90 SQvIt~FC~~iG~d~k~RQ~LIRl 113 (125)
..-+..++..+|+++..|++|...
T Consensus 70 ~~~~~~l~~~lGLtP~sR~kl~~~ 93 (100)
T PF05119_consen 70 MKQMRSLASELGLTPASRAKLAVP 93 (100)
T ss_pred HHHHHHHHHHcCCCHHHHhhccCC
Confidence 345778899999999999988653
Done!