Query 030888
Match_columns 170
No_of_seqs 17 out of 19
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 06:06:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030888.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030888hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02978 SRP_SPB: Signal pepti 98.2 5.9E-06 1.3E-10 61.8 7.6 87 58-146 1-103 (104)
2 PRK10867 signal recognition pa 97.3 0.0015 3.3E-08 59.1 8.7 94 57-152 326-427 (433)
3 PRK00771 signal recognition pa 96.9 0.0038 8.2E-08 56.6 7.9 93 57-151 318-422 (437)
4 COG0541 Ffh Signal recognition 96.9 0.00079 1.7E-08 62.4 3.2 119 32-152 300-430 (451)
5 TIGR00959 ffh signal recogniti 95.9 0.034 7.3E-07 50.4 7.5 88 57-146 325-425 (428)
6 TIGR01425 SRP54_euk signal rec 95.8 0.016 3.4E-07 52.9 5.0 88 57-144 325-427 (429)
7 KOG0780 Signal recognition par 74.6 11 0.00023 36.2 6.7 117 32-154 301-430 (483)
8 PF04703 FaeA: FaeA-like prote 67.2 9 0.00019 26.8 3.5 44 97-159 2-45 (62)
9 PF00325 Crp: Bacterial regula 57.7 14 0.00031 23.1 2.8 23 119-141 5-27 (32)
10 PF11079 YqhG: Bacterial prote 55.4 29 0.00062 30.8 5.3 61 61-152 152-213 (260)
11 cd03572 ENTH_epsin_related ENT 54.2 21 0.00046 27.9 3.9 46 79-126 63-113 (122)
12 PF07120 DUF1376: Protein of u 52.7 22 0.00048 25.4 3.5 31 109-140 34-68 (88)
13 smart00027 EH Eps15 homology d 52.4 78 0.0017 22.1 7.2 65 100-165 12-87 (96)
14 PF04963 Sigma54_CBD: Sigma-54 52.2 8.7 0.00019 31.0 1.5 17 95-111 67-83 (194)
15 PF05920 Homeobox_KN: Homeobox 52.2 18 0.00039 23.1 2.7 22 116-137 13-34 (40)
16 KOG2065 Gamma-tubulin ring com 51.5 54 0.0012 32.4 6.9 103 33-143 62-182 (679)
17 PRK06842 fumarate hydratase; P 50.9 14 0.00031 31.0 2.6 22 144-165 34-55 (185)
18 PF12324 HTH_15: Helix-turn-he 50.2 30 0.00065 25.7 3.9 37 97-140 26-62 (77)
19 KOG0774 Transcription factor P 48.6 9.5 0.00021 34.8 1.3 22 116-137 218-239 (334)
20 PF05683 Fumerase_C: Fumarase 47.1 13 0.00028 31.7 1.9 27 140-166 56-82 (205)
21 PF11181 YflT: Heat induced st 43.4 9.5 0.00021 27.7 0.5 40 31-71 55-97 (103)
22 PRK06043 fumarate hydratase; P 43.4 22 0.00047 30.1 2.6 23 143-165 33-55 (192)
23 PRK14067 exodeoxyribonuclease 43.2 1.3E+02 0.0028 22.0 7.1 60 86-162 5-71 (80)
24 PRK09802 DNA-binding transcrip 42.5 60 0.0013 27.4 5.1 56 84-159 6-61 (269)
25 COG1838 FumA Tartrate dehydrat 41.7 23 0.0005 30.1 2.5 23 143-165 32-54 (184)
26 PF13412 HTH_24: Winged helix- 41.0 85 0.0019 19.3 4.9 36 95-137 3-38 (48)
27 PRK14069 exodeoxyribonuclease 39.3 1.7E+02 0.0038 22.3 7.1 56 86-157 6-66 (95)
28 TIGR02395 rpoN_sigma RNA polym 38.3 45 0.00098 30.5 4.0 26 86-111 115-144 (429)
29 PRK05932 RNA polymerase factor 37.7 67 0.0015 29.7 5.0 37 102-140 126-162 (455)
30 PRK14063 exodeoxyribonuclease 37.7 1.5E+02 0.0034 21.3 7.2 62 87-164 4-71 (76)
31 smart00352 POU Found in Pit-Oc 37.5 29 0.00063 25.6 2.2 29 57-85 5-33 (75)
32 PF10625 UspB: Universal stres 37.3 24 0.00052 27.9 1.9 27 2-28 24-53 (107)
33 smart00389 HOX Homeodomain. DN 37.3 90 0.0019 19.2 4.2 23 113-135 24-46 (56)
34 PF13960 DUF4218: Domain of un 36.5 43 0.00092 26.6 3.1 43 72-114 76-122 (128)
35 KOG3807 Predicted membrane pro 36.1 32 0.00069 33.0 2.7 52 70-141 284-338 (556)
36 PRK05807 hypothetical protein; 36.0 41 0.00088 26.1 2.9 25 131-157 99-123 (136)
37 PF14394 DUF4423: Domain of un 35.8 50 0.0011 26.5 3.5 36 99-139 27-64 (171)
38 TIGR02395 rpoN_sigma RNA polym 35.7 77 0.0017 29.0 5.1 37 102-140 101-137 (429)
39 PRK14066 exodeoxyribonuclease 34.6 1.8E+02 0.0038 21.0 7.0 54 87-156 3-61 (75)
40 PRK14532 adenylate kinase; Pro 33.9 40 0.00086 25.6 2.5 46 118-163 16-62 (188)
41 TIGR00432 arcsn_tRNA_tgt tRNA- 33.7 56 0.0012 31.2 4.0 51 61-111 206-257 (540)
42 PF04287 DUF446: tRNA pseudour 33.7 26 0.00056 26.8 1.5 67 90-165 4-71 (100)
43 PF08279 HTH_11: HTH domain; 33.4 1.2E+02 0.0027 18.9 4.6 43 96-157 1-43 (55)
44 PRK04960 universal stress prot 32.9 29 0.00062 27.7 1.6 27 2-28 24-53 (111)
45 PRK09183 transposase/IS protei 32.8 2.3E+02 0.005 23.7 7.1 49 121-169 30-79 (259)
46 TIGR03220 catechol_dmpE 2-oxop 32.2 1E+02 0.0023 25.8 5.0 46 61-106 2-47 (255)
47 PRK00768 nadE NAD synthetase; 32.0 61 0.0013 28.2 3.7 67 73-140 35-116 (268)
48 TIGR03218 catechol_dmpH 4-oxal 31.1 1.1E+02 0.0024 25.9 5.0 48 59-106 8-55 (263)
49 TIGR00987 himA integration hos 31.1 60 0.0013 23.2 3.0 23 121-143 10-32 (96)
50 PTZ00226 fumarate hydratase; P 30.9 41 0.00088 32.8 2.6 39 127-165 394-445 (570)
51 PF09720 Unstab_antitox: Putat 30.8 54 0.0012 21.3 2.5 26 141-167 28-53 (54)
52 PF12323 HTH_OrfB_IS605: Helix 30.5 99 0.0021 19.4 3.6 38 107-158 9-46 (46)
53 PRK14064 exodeoxyribonuclease 29.9 2.1E+02 0.0046 20.6 7.3 61 87-163 5-71 (75)
54 PF01417 ENTH: ENTH domain; I 29.4 78 0.0017 23.3 3.4 45 80-126 68-115 (125)
55 PF04539 Sigma70_r3: Sigma-70 29.1 53 0.0011 21.8 2.3 20 119-138 23-42 (78)
56 cd06445 ATase The DNA repair p 29.0 1.4E+02 0.003 20.8 4.4 39 97-139 2-42 (79)
57 TIGR02147 Fsuc_second hypothet 28.7 71 0.0015 27.7 3.5 36 99-139 125-162 (271)
58 PRK15391 fumarate hydratase Fu 28.4 48 0.001 32.2 2.6 25 141-165 391-415 (548)
59 PRK15390 fumarate hydratase Fu 28.3 48 0.001 32.2 2.6 25 141-165 391-415 (548)
60 PF08769 Spo0A_C: Sporulation 27.6 50 0.0011 24.9 2.1 34 120-153 44-80 (106)
61 PF13384 HTH_23: Homeodomain-l 27.6 56 0.0012 20.0 2.0 23 119-141 20-42 (50)
62 PF14818 DUF4482: Domain of un 27.3 44 0.00095 27.2 1.9 18 143-160 36-53 (141)
63 PRK00977 exodeoxyribonuclease 27.3 2.4E+02 0.0053 20.4 7.0 62 86-163 8-75 (80)
64 PF13518 HTH_28: Helix-turn-he 26.7 1.3E+02 0.0027 18.2 3.5 36 96-141 2-37 (52)
65 PF10183 ESSS: ESSS subunit of 26.7 56 0.0012 24.5 2.2 17 141-157 88-105 (105)
66 COG4303 EutB Ethanolamine ammo 26.4 32 0.0007 32.5 1.1 60 71-131 90-152 (453)
67 PF14198 TnpV: Transposon-enco 26.0 1.1E+02 0.0023 23.4 3.7 47 91-137 60-106 (111)
68 smart00411 BHL bacterial (prok 25.9 74 0.0016 21.8 2.6 21 120-140 8-28 (90)
69 PHA02547 55 RNA polymerase sig 25.8 57 0.0012 27.8 2.3 85 68-156 47-157 (179)
70 PRK04424 fatty acid biosynthes 25.8 1.8E+02 0.0038 23.4 5.1 65 94-167 6-80 (185)
71 cd00086 homeodomain Homeodomai 25.7 79 0.0017 19.4 2.5 24 113-136 24-47 (59)
72 smart00345 HTH_GNTR helix_turn 25.7 1.6E+02 0.0035 17.7 4.9 38 99-139 4-43 (60)
73 KOG4603 TBP-1 interacting prot 25.6 56 0.0012 28.3 2.3 54 103-159 80-134 (201)
74 PLN00133 class I-fumerate hydr 25.4 58 0.0013 31.9 2.6 39 127-165 400-451 (576)
75 PRK15389 fumarate hydratase; P 25.2 60 0.0013 31.4 2.6 26 140-165 389-414 (536)
76 TIGR02312 HpaH 2-oxo-hepta-3-e 24.5 1.5E+02 0.0034 25.1 4.7 44 60-103 6-49 (267)
77 PF07064 RIC1: RIC1; InterPro 24.1 45 0.00098 28.6 1.5 19 97-115 239-257 (258)
78 COG3877 Uncharacterized protei 24.1 1E+02 0.0023 24.9 3.4 28 94-122 75-102 (122)
79 TIGR02894 DNA_bind_RsfA transc 23.9 48 0.001 27.6 1.6 49 98-163 17-79 (161)
80 PF00046 Homeobox: Homeobox do 23.7 91 0.002 19.5 2.5 23 113-135 24-46 (57)
81 PF12345 DUF3641: Protein of u 23.6 20 0.00044 29.1 -0.7 25 101-131 101-126 (134)
82 PRK15392 putative fumarate hyd 23.5 67 0.0015 31.3 2.6 39 127-165 363-414 (550)
83 KOG2580 Mitochondrial import i 22.7 30 0.00064 33.1 0.1 55 36-91 286-354 (459)
84 PRK13533 7-cyano-7-deazaguanin 22.6 1.2E+02 0.0027 28.5 4.1 51 61-111 308-359 (487)
85 PF03938 OmpH: Outer membrane 22.1 1E+02 0.0022 23.1 2.9 30 126-155 17-46 (158)
86 TIGR02844 spore_III_D sporulat 22.1 2.1E+02 0.0046 20.9 4.4 55 93-155 4-60 (80)
87 cd04777 HTH_MerR-like_sg1 Heli 22.0 2.3E+02 0.005 20.4 4.6 23 118-140 46-68 (107)
88 PRK00118 putative DNA-binding 21.9 1.9E+02 0.004 22.1 4.3 40 99-138 3-55 (104)
89 PF03223 V-ATPase_C: V-ATPase 21.9 1.9E+02 0.0041 26.4 5.0 45 87-143 60-106 (371)
90 PRK10241 hydroxyacylglutathion 21.8 1.2E+02 0.0025 25.1 3.4 37 129-165 168-208 (251)
91 PRK12469 RNA polymerase factor 21.8 1.7E+02 0.0037 27.7 4.8 35 104-140 150-188 (481)
92 PRK08181 transposase; Validate 21.7 4E+02 0.0086 22.8 6.7 49 121-169 33-82 (269)
93 PF03007 WES_acyltransf: Wax e 21.6 56 0.0012 27.1 1.5 20 114-133 243-262 (263)
94 KOG4202 Phosphoribosylanthrani 21.5 42 0.00092 29.4 0.8 23 20-48 83-105 (227)
95 PF10058 DUF2296: Predicted in 21.3 37 0.00081 23.1 0.4 15 34-48 1-15 (54)
96 cd04781 HTH_MerR-like_sg6 Heli 20.7 2.5E+02 0.0053 20.8 4.6 37 119-155 48-88 (120)
97 TIGR02574 stabl_TIGR02574 puta 20.6 1E+02 0.0022 20.9 2.4 26 141-167 31-56 (63)
98 PF09702 Cas_Csa5: CRISPR-asso 20.4 78 0.0017 25.0 2.0 26 52-77 69-98 (105)
No 1
>PF02978 SRP_SPB: Signal peptide binding domain; InterPro: IPR004125 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the M domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 2FFH_B 3NDB_B 2V3C_C 1QZW_G 1QZX_B 3KL4_A 2JQE_A 1HQ1_A 1RY1_W 1MFQ_C ....
Probab=98.23 E-value=5.9e-06 Score=61.84 Aligned_cols=87 Identities=24% Similarity=0.430 Sum_probs=67.1
Q ss_pred cchHHHHHHHHHHhHHhccccchhc---cccch----------hhHHHHHHHHHHHHHHH---hccCCCCcccchhhHHH
Q 030888 58 SFTLLRFADELKKARKLGTLKQYIV---GRSSA----------TTFADTFEKQEAVLRCL---GAFDPNGENLQVSQKQE 121 (170)
Q Consensus 58 ~ftL~~FADelkkARr~Gsfk~fv~---Grsse----------at~~~afeK~EaiiR~L---~~~DptGE~l~asqk~~ 121 (170)
.|||+.|-+.+++-.++|+|++++. |-++. ..-...|.++++||-.. -.-|| +.|..|.+.+
T Consensus 1 ~F~l~Df~~Q~~~i~kmG~l~~i~~miPG~~~~~~~~~~~~~~~~~~~~lk~~~~Ii~SMT~~Er~~p--~ll~~sR~~R 78 (104)
T PF02978_consen 1 KFTLRDFLEQLQQIKKMGPLSKIMSMIPGMGNMMESLPSEQEEEEDEKKLKRMEAIIDSMTPEERDNP--KLLNESRRRR 78 (104)
T ss_dssp SSCHHHHHHHHHHHHHTSTTHHHHTTSSSSSSS-SSTTCSSSSHHHHHHHHHHHHHHTTSBHHHHHCG--GGHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHhcCCHHHHHHHCcCccccccccchhcchhhhHHHHHHHHHHHHCcCHHHHhCc--cccchHHHHH
Confidence 4999999999999999999998764 32221 22356689999999221 11443 3777899999
Q ss_pred HHhhcCccHHHHHHHHHHhHhHHHH
Q 030888 122 AAKQCNCTIAEVENTLAKFTWAKEA 146 (170)
Q Consensus 122 aAk~CnCTiadVE~~LAKftWaKeA 146 (170)
+|+-+|+|+.||...|..|.+.+.+
T Consensus 79 IA~GSG~~~~eV~~ll~~f~~~~~m 103 (104)
T PF02978_consen 79 IARGSGTTVQEVNELLKQFKQMKKM 103 (104)
T ss_dssp HHHHTTS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHhh
Confidence 9999999999999999999998764
No 2
>PRK10867 signal recognition particle protein; Provisional
Probab=97.26 E-value=0.0015 Score=59.14 Aligned_cols=94 Identities=27% Similarity=0.415 Sum_probs=72.3
Q ss_pred ccchHHHHHHHHHHhHHhccccchh---ccccc--hhhHHHHHHHHHHHHHHHhc---cCCCCcccchhhHHHHHhhcCc
Q 030888 57 ESFTLLRFADELKKARKLGTLKQYI---VGRSS--ATTFADTFEKQEAVLRCLGA---FDPNGENLQVSQKQEAAKQCNC 128 (170)
Q Consensus 57 ~~ftL~~FADelkkARr~Gsfk~fv---~Grss--eat~~~afeK~EaiiR~L~~---~DptGE~l~asqk~~aAk~CnC 128 (170)
+.|||+.|-+.|++-+++|++++.+ -|-+. ...-..-|.++++||...-. -+|. .|..|-|.+.|+-+|.
T Consensus 326 g~f~l~d~~~q~~~~~kmG~~~~~~~m~Pg~~~~~~~~~~~~~~~~~~ii~SMt~~Er~~p~--~~~~sR~~RIa~GsG~ 403 (433)
T PRK10867 326 GKFDLEDFLEQLQQMKKMGGLGSLLGMLPGMGNMKAQLDDKELKRIEAIINSMTPKERANPD--ILNGSRKRRIAKGSGT 403 (433)
T ss_pred CCCCHHHHHHHHHHHHhcCCHHHHHHhCCCcccccccccHHHHHHHHHHHHcCCHHHHhCcc--ccchHHHHHHHccCCC
Confidence 6799999999999999999998863 23221 11223788999999944321 2554 6778999999999999
Q ss_pred cHHHHHHHHHHhHhHHHHHHHHHH
Q 030888 129 TIAEVENTLAKFTWAKEAQKKIEK 152 (170)
Q Consensus 129 TiadVE~~LAKftWaKeA~kKi~K 152 (170)
++.||...|..|.=.+.+-+++.+
T Consensus 404 ~~~~v~~ll~~~~~~~~~~~~~~~ 427 (433)
T PRK10867 404 TVQEVNRLLKQFEQMKKMMKKMKG 427 (433)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhcC
Confidence 999999999999877766666654
No 3
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=96.91 E-value=0.0038 Score=56.59 Aligned_cols=93 Identities=23% Similarity=0.381 Sum_probs=72.3
Q ss_pred ccchHHHHHHHHHHhHHhccccchh---cccc---ch---hhHHHHHHHHHHHHHHHhc---cCCCCcccchhhHHHHHh
Q 030888 57 ESFTLLRFADELKKARKLGTLKQYI---VGRS---SA---TTFADTFEKQEAVLRCLGA---FDPNGENLQVSQKQEAAK 124 (170)
Q Consensus 57 ~~ftL~~FADelkkARr~Gsfk~fv---~Grs---se---at~~~afeK~EaiiR~L~~---~DptGE~l~asqk~~aAk 124 (170)
+.|||+.|-+.|++-+++|++.+.+ -|-+ ++ ..-..-|.++++||...-. -+|. -|..|-|.+.|+
T Consensus 318 ~~f~l~d~~~q~~~~~kmG~~~~~~~m~pg~~~~~~~~~~~~~~~~~~~~~~ii~SMt~~Er~~p~--~~~~sR~~Ria~ 395 (437)
T PRK00771 318 GKFTLKDMYKQLEAMNKMGPLKQILQMLPGLGGKLPDEALEVTEEKLKKYKAIMDSMTEEELENPE--IINASRIRRIAR 395 (437)
T ss_pred CCcCHHHHHHHHHHHHhcCCHHHHHHhCcCccccchhhhhcccHHHHHHHHHHHHcCCHHHHhCcc--cccHHHHHHHHc
Confidence 6799999999999999999998862 2322 11 1234678999999944321 2554 677899999999
Q ss_pred hcCccHHHHHHHHHHhHhHHHHHHHHH
Q 030888 125 QCNCTIAEVENTLAKFTWAKEAQKKIE 151 (170)
Q Consensus 125 ~CnCTiadVE~~LAKftWaKeA~kKi~ 151 (170)
-+|.|+.||...|.+|.=.+.+-+++.
T Consensus 396 GsG~~~~~v~~ll~~~~~~~~~~~~~~ 422 (437)
T PRK00771 396 GSGTTVEDVRELLKYYKMMKKAMKQLK 422 (437)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999987777776664
No 4
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=96.87 E-value=0.00079 Score=62.44 Aligned_cols=119 Identities=20% Similarity=0.351 Sum_probs=84.5
Q ss_pred chhhhhhhcccccCCCCCCCCCCCCccchHHHHHHHHHHhHHhccccchh---cccc---ch---hhHHHHHHHHHHHHH
Q 030888 32 GSWMDSIKGVFTGKKSSSEDGSVSSESFTLLRFADELKKARKLGTLKQYI---VGRS---SA---TTFADTFEKQEAVLR 102 (170)
Q Consensus 32 ~sW~dkiKgvftG~K~~~~~~~~~~~~ftL~~FADelkkARr~Gsfk~fv---~Grs---se---at~~~afeK~EaiiR 102 (170)
.|-++|+..++.-.+.......-..+.|||+.|.+-|..-+++|.+.+.+ -|-+ +. ..-..-|.++++||.
T Consensus 300 ~sLvEk~~~~~d~e~a~~~~~kl~~g~FtL~Df~~Ql~~m~kmGpl~~ll~miPG~~~~~~~~~~~~~e~~~kr~~aIi~ 379 (451)
T COG0541 300 LSLIEKAEEVVDEEEAEKLAEKLKKGKFTLEDFLEQLEQMKKMGPLSKLLSMIPGMGMKDSDKDIELDEKKLKRIEAIID 379 (451)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHccCCHHHHHHhCCCCCCCCchhhhhccHHHHHHHHHHHH
Confidence 45677777777554333211222336799999999999999999998765 3432 22 122566999999995
Q ss_pred HHh---ccCCCCcccchhhHHHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHH
Q 030888 103 CLG---AFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEK 152 (170)
Q Consensus 103 ~L~---~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~K 152 (170)
..- .-+|. .|.+|.|.+.|+-||+++.||...|-.|.=++.+-|++..
T Consensus 380 SMT~~Er~nP~--ii~~SR~rRIA~GSG~sv~dVn~Llkq~~~m~~mmk~m~~ 430 (451)
T COG0541 380 SMTPEERENPD--IINASRKRRIARGSGTSVQDVNKLLKQFKQMKKMMKKMSG 430 (451)
T ss_pred cCCHHHhhCcc--ccChHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhC
Confidence 542 23443 6779999999999999999999999999766655555543
No 5
>TIGR00959 ffh signal recognition particle protein. This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.
Probab=95.86 E-value=0.034 Score=50.43 Aligned_cols=88 Identities=22% Similarity=0.418 Sum_probs=67.6
Q ss_pred ccchHHHHHHHHHHhHHhccccchh---ccccc-----h--hhHHHHHHHHHHHHHHHhc---cCCCCcccchhhHHHHH
Q 030888 57 ESFTLLRFADELKKARKLGTLKQYI---VGRSS-----A--TTFADTFEKQEAVLRCLGA---FDPNGENLQVSQKQEAA 123 (170)
Q Consensus 57 ~~ftL~~FADelkkARr~Gsfk~fv---~Grss-----e--at~~~afeK~EaiiR~L~~---~DptGE~l~asqk~~aA 123 (170)
+.|||+.|-+.|++-+++|++++.+ -|-+. + .--.+-|.|+++||...-. -+|. -|..|-+.+.|
T Consensus 325 ~~f~l~d~~~q~~~~~kmG~~~~~~~~~Pg~~~~~~~~~~~~~~~~~~~~~~~ii~SMt~~Er~~p~--~~~~sR~~RIa 402 (428)
T TIGR00959 325 GQFDLEDFLEQLRQIKKMGPLSSLLKMIPGMGGVKPSLSDLELDEKQFKRIEAIISSMTPEERRNPK--ILNPSRRKRIA 402 (428)
T ss_pred CCCCHHHHHHHHHHHHhcCCHHHHHHhCcCccccccccccccccHHHHHHHHHHHHcCCHHHHhCcc--cccHHHHHHHH
Confidence 6799999999999999999998862 24221 1 1234689999999944321 2554 66689999999
Q ss_pred hhcCccHHHHHHHHHHhHhHHHH
Q 030888 124 KQCNCTIAEVENTLAKFTWAKEA 146 (170)
Q Consensus 124 k~CnCTiadVE~~LAKftWaKeA 146 (170)
+-+|.++.||...|.+|.=.+.+
T Consensus 403 ~GsG~~~~~v~~ll~~~~~~~~~ 425 (428)
T TIGR00959 403 AGSGTTVQDVNKLIKRFEQMKKM 425 (428)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHH
Confidence 99999999999999999765544
No 6
>TIGR01425 SRP54_euk signal recognition particle protein SRP54. This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.
Probab=95.77 E-value=0.016 Score=52.93 Aligned_cols=88 Identities=22% Similarity=0.300 Sum_probs=66.5
Q ss_pred ccchHHHHHHHHHHhHHhccccchh---cccc----ch---hhHHHHHHHHHHHHHHHhc---cCCCCccc--chhhHHH
Q 030888 57 ESFTLLRFADELKKARKLGTLKQYI---VGRS----SA---TTFADTFEKQEAVLRCLGA---FDPNGENL--QVSQKQE 121 (170)
Q Consensus 57 ~~ftL~~FADelkkARr~Gsfk~fv---~Grs----se---at~~~afeK~EaiiR~L~~---~DptGE~l--~asqk~~ 121 (170)
+.|||+.|-+.|+.-+++|++++.+ -|-+ .+ ..-..-|.++++||...-. -+|.-+.| ..|.|.+
T Consensus 325 ~~f~l~D~~~q~~~i~kmG~~~~i~~m~Pg~~~~~~~~~~~~~~~~~~~~~~aii~SMT~~Er~~~~p~i~~~~~sR~~R 404 (429)
T TIGR01425 325 GTFTLRDMYEQFQNLLKMGPLGQILSMIPGFSTDFMSKGNEEESMAKIKKLMTIMDSMTDQELDSTDGKVFSKQPSRIQR 404 (429)
T ss_pred CCCCHHHHHHHHHHHHhccCHHHHHHhCcCcchhhhhhhcccccHHHHHhHHHHHhcCCHHHHccCCCccccCCccHHHH
Confidence 6799999999999999999998762 2321 11 1233689999999965422 22222466 6799999
Q ss_pred HHhhcCccHHHHHHHHHHhHhHH
Q 030888 122 AAKQCNCTIAEVENTLAKFTWAK 144 (170)
Q Consensus 122 aAk~CnCTiadVE~~LAKftWaK 144 (170)
.|+-+|-++.||...|..|.=.+
T Consensus 405 Ia~GSG~~~~~V~~ll~~~~~~~ 427 (429)
T TIGR01425 405 VARGSGRSIRDVQELLEQYKKFA 427 (429)
T ss_pred HHccCCCCHHHHHHHHHHHHHHh
Confidence 99999999999999999997544
No 7
>KOG0780 consensus Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport]
Probab=74.58 E-value=11 Score=36.15 Aligned_cols=117 Identities=21% Similarity=0.281 Sum_probs=73.5
Q ss_pred chhhhhhhcccccCCCCCCCCCC-CCccchHHHHHHHHHHhHHhccccchh---ccccchhhHHHHHHHHHHHHHHHhcc
Q 030888 32 GSWMDSIKGVFTGKKSSSEDGSV-SSESFTLLRFADELKKARKLGTLKQYI---VGRSSATTFADTFEKQEAVLRCLGAF 107 (170)
Q Consensus 32 ~sW~dkiKgvftG~K~~~~~~~~-~~~~ftL~~FADelkkARr~Gsfk~fv---~Grsseat~~~afeK~EaiiR~L~~~ 107 (170)
.|.|||+-.|- +-..++--.. -.+.|||..|-|.+.+--++|.|++.. -|=| -++-.+-=|-+..+.|++.-+
T Consensus 301 ~glvek~~ev~--~~d~~el~~kl~~gkFtlrd~y~Qfq~imkmGp~s~v~~MiPG~s-~m~~~~e~Es~~~~krm~~mm 377 (483)
T KOG0780|consen 301 EGLVEKVQEVG--KDDAKELVEKLKQGKFTLRDFYDQFQNIMKMGPLSQVLGMIPGMS-MMSKGNEEESSAKLKRMMTMM 377 (483)
T ss_pred HHHHHHHHHHh--hhhHHHHHHHHHhCCccHHHHHHHHHHHHhhCCHHHHHhhCCCcc-cCCCcchhHHHHHHHHHHHHH
Confidence 57788888775 1111100001 236899999999999999999999863 2333 222222223333445555544
Q ss_pred CCCCc------cc---chhhHHHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHH
Q 030888 108 DPNGE------NL---QVSQKQEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLK 154 (170)
Q Consensus 108 DptGE------~l---~asqk~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLk 154 (170)
|.-.+ +| +.+...++|+.-|-++-||+..|+.|+=.. ..++|+.
T Consensus 378 DsMt~~Elds~~~f~~~p~R~~RvArgSG~~v~eV~ell~q~~~~~---~~~kk~~ 430 (483)
T KOG0780|consen 378 DSMTDEELDSPELFVEEPSRIMRVARGSGTSVQEVMELLAQYKKFA---AMMKKIG 430 (483)
T ss_pred HhcChhhccCccccccCchHhhhhhccCCccHHHHHHHHHHHHHHH---HHHHHhc
Confidence 43211 22 356788999999999999999999996544 4444554
No 8
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=67.18 E-value=9 Score=26.81 Aligned_cols=44 Identities=30% Similarity=0.443 Sum_probs=30.2
Q ss_pred HHHHHHHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHHhcCCC
Q 030888 97 QEAVLRCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLKEEGKP 159 (170)
Q Consensus 97 ~EaiiR~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLkeEGKP 159 (170)
-|.||.||...+ + .+.+ .|+|..|+-++-+|... +..|.+||+-
T Consensus 2 ke~Il~~i~~~~--~-p~~T---~eiA~~~gls~~~aR~y-------------L~~Le~eG~V 45 (62)
T PF04703_consen 2 KEKILEYIKEQN--G-PLKT---REIADALGLSIYQARYY-------------LEKLEKEGKV 45 (62)
T ss_dssp HHCHHHHHHHHT--S--EEH---HHHHHHHTS-HHHHHHH-------------HHHHHHCTSE
T ss_pred cHHHHHHHHHcC--C-CCCH---HHHHHHhCCCHHHHHHH-------------HHHHHHCCCE
Confidence 367888888853 2 2444 48888899888776554 5678999974
No 9
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=57.73 E-value=14 Score=23.10 Aligned_cols=23 Identities=26% Similarity=0.261 Sum_probs=19.2
Q ss_pred HHHHHhhcCccHHHHHHHHHHhH
Q 030888 119 KQEAAKQCNCTIAEVENTLAKFT 141 (170)
Q Consensus 119 k~~aAk~CnCTiadVE~~LAKft 141 (170)
+++.|...|||..-|-.+|.+|.
T Consensus 5 r~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 5 RQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHhCCcHHHHHHHHHHHH
Confidence 57899999999999999988763
No 10
>PF11079 YqhG: Bacterial protein YqhG of unknown function; InterPro: IPR024562 This family of putative proteins appears to be restricted to Firmicutes. Their function is not known.
Probab=55.36 E-value=29 Score=30.84 Aligned_cols=61 Identities=20% Similarity=0.333 Sum_probs=45.1
Q ss_pred HHHHHHHHHHhHHhccccchhccccchhhHHHHHHHHHHHH-HHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHH
Q 030888 61 LLRFADELKKARKLGTLKQYIVGRSSATTFADTFEKQEAVL-RCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAK 139 (170)
Q Consensus 61 L~~FADelkkARr~Gsfk~fv~Grsseat~~~afeK~Eaii-R~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAK 139 (170)
.++|-+.|..=.=-...-+|+.=.+---+...|+..-|..| ++|...|
T Consensus 152 ve~F~~~L~~~~LtpkiPdy~ftlsp~i~~~sa~~rlE~~l~~~l~~~d------------------------------- 200 (260)
T PF11079_consen 152 VENFHERLQGRQLTPKIPDYCFTLSPIIKPKSALKRLEQYLEQYLSQED------------------------------- 200 (260)
T ss_pred hhhHHHHHhcCCCCCCCCcceeecCCcCCHHHHHHHHHHHHHHHHHhCC-------------------------------
Confidence 46788888776666777777777776678888888877766 6666666
Q ss_pred hHhHHHHHHHHHH
Q 030888 140 FTWAKEAQKKIEK 152 (170)
Q Consensus 140 ftWaKeA~kKi~K 152 (170)
++||+||.+++++
T Consensus 201 ~~WA~eA~~R~~e 213 (260)
T PF11079_consen 201 HDWAEEARERWQE 213 (260)
T ss_pred cHHHHHHHHHHHH
Confidence 4699999888764
No 11
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=54.16 E-value=21 Score=27.90 Aligned_cols=46 Identities=20% Similarity=0.409 Sum_probs=32.6
Q ss_pred chhccccchhhHHHHHHHHHHHHHHHh----ccCC-CCcccchhhHHHHHhhc
Q 030888 79 QYIVGRSSATTFADTFEKQEAVLRCLG----AFDP-NGENLQVSQKQEAAKQC 126 (170)
Q Consensus 79 ~fv~Grsseat~~~afeK~EaiiR~L~----~~Dp-tGE~l~asqk~~aAk~C 126 (170)
.|+.+.++ ..|...+.++..+||-|. ..|| .|.-+.. ..-++|+.|
T Consensus 63 k~l~~~G~-~~f~~~~~~~~~~Ik~~~~f~g~~Dp~~Gd~~~~-~VR~~A~El 113 (122)
T cd03572 63 KHLCEKGN-SDFKRELQRNSAQIRECANYKGPPDPLKGDSLNE-KVREEAQEL 113 (122)
T ss_pred HHHHhhCC-HHHHHHHHHhHHHHHHHHHcCCCCCcccCcchhH-HHHHHHHHH
Confidence 34566654 789999999999998774 5788 7776665 344455554
No 12
>PF07120 DUF1376: Protein of unknown function (DUF1376); InterPro: IPR010781 This entry is represented by Bacteriophage PBC5 (Sinorhizobium phage PBC5), Orf49. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical bacterial proteins of around 95 residues in length. The function of this family is unknown.
Probab=52.69 E-value=22 Score=25.39 Aligned_cols=31 Identities=23% Similarity=0.460 Sum_probs=23.4
Q ss_pred CCCcccchhhHHHHHhhcCccHHH----HHHHHHHh
Q 030888 109 PNGENLQVSQKQEAAKQCNCTIAE----VENTLAKF 140 (170)
Q Consensus 109 ptGE~l~asqk~~aAk~CnCTiad----VE~~LAKf 140 (170)
-+|+.|.. +....|.-|+|++.+ |+.+|..|
T Consensus 34 ~~~~plp~-d~~~Lar~~~~s~~~~~~a~~~ll~~f 68 (88)
T PF07120_consen 34 DTEGPLPD-DDKRLARICGCSTKEWRKALDFLLREF 68 (88)
T ss_pred HhCCCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHhC
Confidence 35888885 888999999999886 44455555
No 13
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=52.40 E-value=78 Score=22.08 Aligned_cols=65 Identities=14% Similarity=0.120 Sum_probs=34.2
Q ss_pred HHHHHhccCCCCc-ccchhhHHHHHhhcCccHHHHHHHHHHhHh----------HHHHHHHHHHHHhcCCCCCCccc
Q 030888 100 VLRCLGAFDPNGE-NLQVSQKQEAAKQCNCTIAEVENTLAKFTW----------AKEAQKKIEKLKEEGKPMPKSMA 165 (170)
Q Consensus 100 iiR~L~~~DptGE-~l~asqk~~aAk~CnCTiadVE~~LAKftW----------aKeA~kKi~KLkeEGKPlPks~~ 165 (170)
+.+....+|..|. .|...+-.++-..-+++-.+|++++..+.= --.+-..+.++.. |+|+|-.|.
T Consensus 12 l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~~~d~~~~g~I~~~eF~~~~~~~~~~~~-g~~~~~~~~ 87 (96)
T smart00027 12 YEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWNLADIDNDGELDKDEFALAMHLIYRKLN-GYPIPASLP 87 (96)
T ss_pred HHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHHc-CCCCCccCC
Confidence 3344445555433 344444444444445666666666654321 0233444555554 999998775
No 14
>PF04963 Sigma54_CBD: Sigma-54 factor, core binding domain; InterPro: IPR007046 This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme []. The centre of this domain contains a very weak similarity to a helix-turn-helix motif, which may represent a DNA binding domain.; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent; PDB: 2K9L_A 2K9M_A.
Probab=52.22 E-value=8.7 Score=30.96 Aligned_cols=17 Identities=35% Similarity=0.632 Sum_probs=10.6
Q ss_pred HHHHHHHHHHhccCCCC
Q 030888 95 EKQEAVLRCLGAFDPNG 111 (170)
Q Consensus 95 eK~EaiiR~L~~~DptG 111 (170)
+..+.+|+.|-.|||.|
T Consensus 67 ~~v~~~l~~lQ~leP~G 83 (194)
T PF04963_consen 67 EEVEKALELLQSLEPAG 83 (194)
T ss_dssp HHHHHHHHHHHTTSS--
T ss_pred HHHHHHHHHHHcCCCCc
Confidence 44566777777888887
No 15
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=52.20 E-value=18 Score=23.14 Aligned_cols=22 Identities=27% Similarity=0.308 Sum_probs=18.7
Q ss_pred hhhHHHHHhhcCccHHHHHHHH
Q 030888 116 VSQKQEAAKQCNCTIAEVENTL 137 (170)
Q Consensus 116 asqk~~aAk~CnCTiadVE~~L 137 (170)
..+|++.|+.+|+|..||.+=+
T Consensus 13 ~~ek~~L~~~tgls~~Qi~~WF 34 (40)
T PF05920_consen 13 KEEKEELAKQTGLSRKQISNWF 34 (40)
T ss_dssp HHHHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHH
Confidence 6799999999999999999843
No 16
>KOG2065 consensus Gamma-tubulin ring complex protein [Cytoskeleton]
Probab=51.48 E-value=54 Score=32.43 Aligned_cols=103 Identities=22% Similarity=0.306 Sum_probs=77.5
Q ss_pred hhhhhhhcccccCCCCCCCCCCCC---ccchHHHHHHHHHHhH-----Hhccccchhcc--ccchhhHHHHHHHHH----
Q 030888 33 SWMDSIKGVFTGKKSSSEDGSVSS---ESFTLLRFADELKKAR-----KLGTLKQYIVG--RSSATTFADTFEKQE---- 98 (170)
Q Consensus 33 sW~dkiKgvftG~K~~~~~~~~~~---~~ftL~~FADelkkAR-----r~Gsfk~fv~G--rsseat~~~afeK~E---- 98 (170)
||+..+-|--.|+++++ +.+.| -.+-|.+||..++.|- .++.+-||..| |-|-+++..++.+.-
T Consensus 62 swIrsvTsH~~~r~~~~--s~q~~~~lhg~Ylra~a~Gi~~~L~~Yr~ail~lEq~~Lg~~~~sls~V~~~L~~ff~Lfp 139 (679)
T KOG2065|consen 62 SWIRSVTSHSSGRKSDT--SGQLPDSLHGYYLRALAKGIEMALEEYRAAILRLEQYCLGNERNSLSYVYNALYAFFPLFP 139 (679)
T ss_pred HHHHHhccCcccccccc--cccCCCccchHHHHHHHhhHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHhhhhhH
Confidence 99999999888888875 33444 3688999999999884 47889999999 778889988887753
Q ss_pred ---HHHHHHhccCCCCcccch-hhHHHHHhhcCccHHHHHHHHHHhHhH
Q 030888 99 ---AVLRCLGAFDPNGENLQV-SQKQEAAKQCNCTIAEVENTLAKFTWA 143 (170)
Q Consensus 99 ---aiiR~L~~~DptGE~l~a-sqk~~aAk~CnCTiadVE~~LAKftWa 143 (170)
.||--....|--|-+|-. -.|+ ||+ ..||.-+|++-.|-
T Consensus 140 ~~~~vi~eI~~~~irGcqlL~~l~k~----HCg--~p~ir~~l~~~l~~ 182 (679)
T KOG2065|consen 140 FMRNVITEIHVLNIRGCQLLHNLHKQ----HCG--HPDIRLELAIKLKP 182 (679)
T ss_pred HHHHHHHHHHhcccchhHHHHHHHHh----ccC--CCcHHHHHHHHHhh
Confidence 455556666666654433 2333 766 99999999998774
No 17
>PRK06842 fumarate hydratase; Provisional
Probab=50.86 E-value=14 Score=31.02 Aligned_cols=22 Identities=23% Similarity=0.536 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHhcCCCCCCccc
Q 030888 144 KEAQKKIEKLKEEGKPMPKSMA 165 (170)
Q Consensus 144 KeA~kKi~KLkeEGKPlPks~~ 165 (170)
-.||+||-++-++|+|+|-++.
T Consensus 34 DaAHkrl~e~l~~G~~lP~dl~ 55 (185)
T PRK06842 34 DAAHKRLIELLDKGEELPIDIK 55 (185)
T ss_pred HHHHHHHHHHHhcCCCCCcCcC
Confidence 4689999999999999997764
No 18
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=50.22 E-value=30 Score=25.71 Aligned_cols=37 Identities=24% Similarity=0.290 Sum_probs=26.1
Q ss_pred HHHHHHHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHHh
Q 030888 97 QEAVLRCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKF 140 (170)
Q Consensus 97 ~EaiiR~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKf 140 (170)
+-.++|.|+.=+|. . ....|..-|++..+|..+|+..
T Consensus 26 ~r~LLr~LA~G~PV----t---~~~LA~a~g~~~e~v~~~L~~~ 62 (77)
T PF12324_consen 26 LRPLLRLLAKGQPV----T---VEQLAAALGWPVEEVRAALAAM 62 (77)
T ss_dssp HHHHHHHHTTTS-B--------HHHHHHHHT--HHHHHHHHHH-
T ss_pred HHHHHHHHHcCCCc----C---HHHHHHHHCCCHHHHHHHHHhC
Confidence 45689999985555 3 4678888899999999999863
No 19
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=48.65 E-value=9.5 Score=34.82 Aligned_cols=22 Identities=45% Similarity=0.640 Sum_probs=19.3
Q ss_pred hhhHHHHHhhcCccHHHHHHHH
Q 030888 116 VSQKQEAAKQCNCTIAEVENTL 137 (170)
Q Consensus 116 asqk~~aAk~CnCTiadVE~~L 137 (170)
...|++.|++||-||.+|-|-+
T Consensus 218 ee~K~eLAkqCnItvsQvsnwf 239 (334)
T KOG0774|consen 218 EEAKEELAKQCNITVSQVSNWF 239 (334)
T ss_pred HHHHHHHHHHcCceehhhcccc
Confidence 4579999999999999998854
No 20
>PF05683 Fumerase_C: Fumarase C-terminus; InterPro: IPR004647 This entry represents various Fe-S type hydro-lyases, including the beta subunit from both L-tartrate dehydratase (TtdB; EC:4.2.1.32) and class 2 fumarate hydratase (FumC; (4.2.1.2 from EC) []. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of the archaeal proteins in this group is unknown.; GO: 0016836 hydro-lyase activity; PDB: 2ISB_A.
Probab=47.08 E-value=13 Score=31.70 Aligned_cols=27 Identities=33% Similarity=0.583 Sum_probs=16.5
Q ss_pred hHhHHHHHHHHHHHHhcCCCCCCcccc
Q 030888 140 FTWAKEAQKKIEKLKEEGKPMPKSMAE 166 (170)
Q Consensus 140 ftWaKeA~kKi~KLkeEGKPlPks~~E 166 (170)
||=--.||+||-++-++|+|+|-++..
T Consensus 56 ~taRDaaH~ri~e~l~~g~~lP~dl~g 82 (205)
T PF05683_consen 56 YTARDAAHKRIVELLERGEPLPFDLKG 82 (205)
T ss_dssp EE--HHHHHHHHHHHHHT---SS--TT
T ss_pred EEEhHHHHHHHHHHHHcCCCCCcccCC
Confidence 444456899999999999999988753
No 21
>PF11181 YflT: Heat induced stress protein YflT
Probab=43.43 E-value=9.5 Score=27.70 Aligned_cols=40 Identities=23% Similarity=0.322 Sum_probs=22.8
Q ss_pred cchhhhhhhcccccCCCCCCCCCC---CCccchHHHHHHHHHHh
Q 030888 31 QGSWMDSIKGVFTGKKSSSEDGSV---SSESFTLLRFADELKKA 71 (170)
Q Consensus 31 ~~sW~dkiKgvftG~K~~~~~~~~---~~~~ftL~~FADelkkA 71 (170)
..||+|+||+.|+...++ ..+.- .-+.-..++|..+|++-
T Consensus 55 ~~~~~d~~~~~f~~~~d~-~~~~l~~lGl~~~ea~~y~~~l~~G 97 (103)
T PF11181_consen 55 EESFWDKIKNFFTSGGDE-LRSKLESLGLSEDEAERYEEELDQG 97 (103)
T ss_pred cccHHHHHHHhccCCcHH-HHHHHHHcCCCHHHHHHHHHHHHCC
Confidence 389999999999922221 01111 11234556677776653
No 22
>PRK06043 fumarate hydratase; Provisional
Probab=43.37 E-value=22 Score=30.15 Aligned_cols=23 Identities=39% Similarity=0.638 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHhcCCCCCCccc
Q 030888 143 AKEAQKKIEKLKEEGKPMPKSMA 165 (170)
Q Consensus 143 aKeA~kKi~KLkeEGKPlPks~~ 165 (170)
--.||+||-++-++|+|+|-.|.
T Consensus 33 RDaaH~rl~e~~~~G~~lP~dl~ 55 (192)
T PRK06043 33 RDEAHARILEMKEKGKELPFSLE 55 (192)
T ss_pred eHHHHHHHHHHHhcCCCCCcCcC
Confidence 34689999999999999997764
No 23
>PRK14067 exodeoxyribonuclease VII small subunit; Provisional
Probab=43.21 E-value=1.3e+02 Score=22.02 Aligned_cols=60 Identities=20% Similarity=0.314 Sum_probs=38.0
Q ss_pred chhhHHHHHHHHHHHHHHHhccCCCCcccchhhH-----HHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHHhcC--C
Q 030888 86 SATTFADTFEKQEAVLRCLGAFDPNGENLQVSQK-----QEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLKEEG--K 158 (170)
Q Consensus 86 seat~~~afeK~EaiiR~L~~~DptGE~l~asqk-----~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLkeEG--K 158 (170)
-..||..+|++-|.|++-|-.=|-+ |..+-+ ....+.|+-. -.+|.+||+.|.+ | +
T Consensus 5 k~~sfEeal~~LEeIV~~LE~~~l~---Lees~~lyeeG~~L~k~C~~~-------------L~~ae~kI~~l~~-g~~~ 67 (80)
T PRK14067 5 KTADFEQQLARLQEIVDALEGGDLP---LEESVALYKEGLGLARACREQ-------------LAKARNEIRLFTE-GEVK 67 (80)
T ss_pred ccCCHHHHHHHHHHHHHHHHCCCCC---HHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHc-CCCC
Confidence 3579999999999999999765533 222211 2344555533 3456778887754 6 4
Q ss_pred CCCC
Q 030888 159 PMPK 162 (170)
Q Consensus 159 PlPk 162 (170)
|.|.
T Consensus 68 ~~~~ 71 (80)
T PRK14067 68 DFDP 71 (80)
T ss_pred CCCC
Confidence 5544
No 24
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=42.48 E-value=60 Score=27.40 Aligned_cols=56 Identities=14% Similarity=0.209 Sum_probs=42.6
Q ss_pred ccchhhHHHHHHHHHHHHHHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHHhcCCC
Q 030888 84 RSSATTFADTFEKQEAVLRCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLKEEGKP 159 (170)
Q Consensus 84 rsseat~~~afeK~EaiiR~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLkeEGKP 159 (170)
.|+|--.+...|++.+|+.+|...... .-.+.|++++++..= +.+-|..|.++|.+
T Consensus 6 ~~~~~~~~~~~eR~~~Il~~L~~~~~v-------tv~eLa~~l~VS~~T-------------IRRDL~~Le~~G~l 61 (269)
T PRK09802 6 ASGEKRVTGTSERREQIIQRLRQQGSV-------QVNDLSALYGVSTVT-------------IRNDLAFLEKQGIA 61 (269)
T ss_pred ccchhhhccHHHHHHHHHHHHHHcCCE-------eHHHHHHHHCCCHHH-------------HHHHHHHHHhCCCe
Confidence 456667777889999999999986632 346889999888743 46678888888875
No 25
>COG1838 FumA Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain [Energy production and conversion]
Probab=41.69 E-value=23 Score=30.11 Aligned_cols=23 Identities=17% Similarity=0.484 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHhcCCCCCCccc
Q 030888 143 AKEAQKKIEKLKEEGKPMPKSMA 165 (170)
Q Consensus 143 aKeA~kKi~KLkeEGKPlPks~~ 165 (170)
-..||+||.++.+.|+++|=++.
T Consensus 32 RD~AH~ri~e~~~~ge~lP~dl~ 54 (184)
T COG1838 32 RDAAHKRLLEMLDRGEELPVDLK 54 (184)
T ss_pred hhHHHHHHHHHHhcCCCCCccCC
Confidence 35799999999999999996654
No 26
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=41.00 E-value=85 Score=19.26 Aligned_cols=36 Identities=22% Similarity=0.243 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHH
Q 030888 95 EKQEAVLRCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTL 137 (170)
Q Consensus 95 eK~EaiiR~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~L 137 (170)
+.+..||.+|..-. . -...+.|+.||.+..-|-..|
T Consensus 3 ~~~~~Il~~l~~~~-~------~t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 3 ETQRKILNYLRENP-R------ITQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp HHHHHHHHHHHHCT-T------S-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHcC-C------CCHHHHHHHhCCCHHHHHHHH
Confidence 35678999998833 2 245689999999987665443
No 27
>PRK14069 exodeoxyribonuclease VII small subunit; Provisional
Probab=39.30 E-value=1.7e+02 Score=22.32 Aligned_cols=56 Identities=30% Similarity=0.375 Sum_probs=36.7
Q ss_pred chhhHHHHHHHHHHHHHHHhccCCCCcccchhhH-----HHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHHhcC
Q 030888 86 SATTFADTFEKQEAVLRCLGAFDPNGENLQVSQK-----QEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLKEEG 157 (170)
Q Consensus 86 seat~~~afeK~EaiiR~L~~~DptGE~l~asqk-----~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLkeEG 157 (170)
++.||..+|++-|.|++.|-.=|.+ |..+-+ .+..+.|+- .-.+|.+||+.|-+++
T Consensus 6 ~~~sFEeal~~LEeIV~~LEsgdl~---LEesl~lyeeGv~L~k~C~~-------------~L~~AE~kV~~L~~~~ 66 (95)
T PRK14069 6 SKISFEDALRELEQIAEKLERQDFS---LEESLKAYERGMELKKICSG-------------ILDDAEGKIEALTKDE 66 (95)
T ss_pred CCCCHHHHHHHHHHHHHHHHCCCCC---HHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHhcc
Confidence 4789999999999999999766643 222111 233444543 3456778888887544
No 28
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=38.27 E-value=45 Score=30.49 Aligned_cols=26 Identities=35% Similarity=0.561 Sum_probs=19.4
Q ss_pred chhhHHHHH----HHHHHHHHHHhccCCCC
Q 030888 86 SATTFADTF----EKQEAVLRCLGAFDPNG 111 (170)
Q Consensus 86 seat~~~af----eK~EaiiR~L~~~DptG 111 (170)
+...+++.+ +.-|++|..|-.+||.|
T Consensus 115 ~~~eia~~l~~~~~~ve~~l~~iq~leP~G 144 (429)
T TIGR02395 115 DLEEIADELEVSEEEVEKVLELIQRLDPAG 144 (429)
T ss_pred CHHHHHHHcCCCHHHHHHHHHHHhcCCCCc
Confidence 344455444 67788899999999999
No 29
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=37.74 E-value=67 Score=29.70 Aligned_cols=37 Identities=27% Similarity=0.385 Sum_probs=28.5
Q ss_pred HHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHHh
Q 030888 102 RCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKF 140 (170)
Q Consensus 102 R~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKf 140 (170)
.-++.+|+.| -|.. .-.+.|.+|+|+.++||.+|...
T Consensus 126 ~iI~~LD~~G-yL~~-~~~eia~~l~~~~~~v~~~l~~l 162 (455)
T PRK05932 126 YIIDALDDEG-YLTE-DLEEIAESLGVELDEVEAVLKRI 162 (455)
T ss_pred HHHHhCCCCC-CCCC-CHHHHHHHcCCCHHHHHHHHHHH
Confidence 3457889999 5654 56788899999999999988753
No 30
>PRK14063 exodeoxyribonuclease VII small subunit; Provisional
Probab=37.73 E-value=1.5e+02 Score=21.29 Aligned_cols=62 Identities=19% Similarity=0.317 Sum_probs=38.7
Q ss_pred hhhHHHHHHHHHHHHHHHhccCCCCcccchhhH-----HHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHH-HhcCCCC
Q 030888 87 ATTFADTFEKQEAVLRCLGAFDPNGENLQVSQK-----QEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKL-KEEGKPM 160 (170)
Q Consensus 87 eat~~~afeK~EaiiR~L~~~DptGE~l~asqk-----~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KL-keEGKPl 160 (170)
+.||..+|.+-|.|++-|-.=|-+ |..+-+ ...+++|+-.+. +|.+||..| .+.|.+.
T Consensus 4 ~~sfEeal~~LE~Iv~~LE~~~l~---Leesl~lyeeG~~L~k~C~~~L~-------------~aE~ki~~l~~~~~~~~ 67 (76)
T PRK14063 4 KLSFEEAISQLEHLVSKLEQGDVP---LEEAISYFKEGMELSKLCDEKLK-------------NVQEQMAVILGEDGELE 67 (76)
T ss_pred ccCHHHHHHHHHHHHHHHHCCCCC---HHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHhcCCCCC
Confidence 468999999999999988754422 222222 345667765544 456777765 4556554
Q ss_pred CCcc
Q 030888 161 PKSM 164 (170)
Q Consensus 161 Pks~ 164 (170)
|-+.
T Consensus 68 ~~~~ 71 (76)
T PRK14063 68 PFTA 71 (76)
T ss_pred CCCc
Confidence 5443
No 31
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=37.51 E-value=29 Score=25.60 Aligned_cols=29 Identities=28% Similarity=0.220 Sum_probs=24.0
Q ss_pred ccchHHHHHHHHHHhHHhccccchhcccc
Q 030888 57 ESFTLLRFADELKKARKLGTLKQYIVGRS 85 (170)
Q Consensus 57 ~~ftL~~FADelkkARr~Gsfk~fv~Grs 85 (170)
..=-|+.|++.++.+|+--.++|--+|..
T Consensus 5 ~~~ele~~~~~lk~~R~~lGLTQ~dvA~~ 33 (75)
T smart00352 5 DPRELEAFAKTFKQRRIKLGFTQADVGLA 33 (75)
T ss_pred CHHHHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 34458999999999999999988777744
No 32
>PF10625 UspB: Universal stress protein B (UspB); InterPro: IPR019598 Universal stress protein B (UspB) in Escherichia coli is a 14kDa protein which is predicted to be an integral membrane protein. Over expression of UspB results in cell death in stationary phase, and mutants of UspB are sensitive to ethanol exposure during stationary phase [].
Probab=37.30 E-value=24 Score=27.92 Aligned_cols=27 Identities=37% Similarity=0.364 Sum_probs=23.2
Q ss_pred chHHHHHHHHhhcchhhhhh---ccccccc
Q 030888 2 RSLRILTSIYHNHHLTLSQY---RSIFTTR 28 (170)
Q Consensus 2 ~s~r~l~~~~~~~~~~l~~~---r~I~sT~ 28 (170)
.|+|.|-.+++..+-+|+|+ ||.|+|-
T Consensus 24 SsLR~LL~imR~~dPLLYQ~VDG~GFFtth 53 (107)
T PF10625_consen 24 SSLRALLYIMREADPLLYQQVDGNGFFTTH 53 (107)
T ss_pred HHHHHHHHHHhcCCcHHHHhccCCCceecC
Confidence 47899999999999999998 8888774
No 33
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=37.27 E-value=90 Score=19.19 Aligned_cols=23 Identities=13% Similarity=0.095 Sum_probs=20.0
Q ss_pred ccchhhHHHHHhhcCccHHHHHH
Q 030888 113 NLQVSQKQEAAKQCNCTIAEVEN 135 (170)
Q Consensus 113 ~l~asqk~~aAk~CnCTiadVE~ 135 (170)
.....++.+.|+.||++..+|.+
T Consensus 24 ~P~~~~~~~la~~~~l~~~qV~~ 46 (56)
T smart00389 24 YPSREEREELAAKLGLSERQVKV 46 (56)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHH
Confidence 44588999999999999999976
No 34
>PF13960 DUF4218: Domain of unknown function (DUF4218)
Probab=36.48 E-value=43 Score=26.61 Aligned_cols=43 Identities=19% Similarity=0.397 Sum_probs=32.8
Q ss_pred HHhccccchhccccc-hhhHHHHHHHHHHH---HHHHhccCCCCccc
Q 030888 72 RKLGTLKQYIVGRSS-ATTFADTFEKQEAV---LRCLGAFDPNGENL 114 (170)
Q Consensus 72 Rr~Gsfk~fv~Grss-eat~~~afeK~Eai---iR~L~~~DptGE~l 114 (170)
|.+|.+|.||.-++. |+++..+.---|.+ .+||...++.|.+.
T Consensus 76 R~m~~Lk~~v~N~~~pEgsI~e~Y~~eE~~~fcs~y~~~~~~~~~~~ 122 (128)
T PF13960_consen 76 RYMGILKKYVRNKARPEGSIVEGYITEEVIEFCSRYFSDNVTIGNPV 122 (128)
T ss_pred HHHHHHhhhhhhccchhHHHHHHhhHHHHHHHHHHHHcCCccCCCCC
Confidence 678999999999776 99998887555554 38888888776543
No 35
>KOG3807 consensus Predicted membrane protein ST7 (tumor suppressor in humans) [General function prediction only]
Probab=36.06 E-value=32 Score=33.03 Aligned_cols=52 Identities=29% Similarity=0.360 Sum_probs=39.8
Q ss_pred HhHHhccccchhcc---ccchhhHHHHHHHHHHHHHHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHHhH
Q 030888 70 KARKLGTLKQYIVG---RSSATTFADTFEKQEAVLRCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKFT 141 (170)
Q Consensus 70 kARr~Gsfk~fv~G---rsseat~~~afeK~EaiiR~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKft 141 (170)
-|||+|.+++-|.| -+-|-.+...|.-||-.|..|--. |+ .+||.++|+||.
T Consensus 284 CARklGrlrEA~K~~RDL~ke~pl~t~lniheNLiEalLE~-------QA-------------YADvqavLakYD 338 (556)
T KOG3807|consen 284 CARKLGRLREAVKIMRDLMKEFPLLTMLNIHENLLEALLEL-------QA-------------YADVQAVLAKYD 338 (556)
T ss_pred HHHHhhhHHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHH-------HH-------------HHHHHHHHHhhc
Confidence 48999999998887 234777888888888888776432 22 578999999986
No 36
>PRK05807 hypothetical protein; Provisional
Probab=36.03 E-value=41 Score=26.05 Aligned_cols=25 Identities=24% Similarity=0.553 Sum_probs=21.8
Q ss_pred HHHHHHHHHhHhHHHHHHHHHHHHhcC
Q 030888 131 AEVENTLAKFTWAKEAQKKIEKLKEEG 157 (170)
Q Consensus 131 adVE~~LAKftWaKeA~kKi~KLkeEG 157 (170)
.+.|+.|++ |.|++..+|..||...
T Consensus 99 ~~~~~~l~~--~~~~s~~~~~~l~~~~ 123 (136)
T PRK05807 99 GNFEDRLSK--FLKDSEERFQDLKKHQ 123 (136)
T ss_pred cCHHHHHHH--HHHHHHHHHHHHHhhc
Confidence 688899986 7899999999999754
No 37
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=35.83 E-value=50 Score=26.47 Aligned_cols=36 Identities=22% Similarity=0.219 Sum_probs=28.6
Q ss_pred HHHHHHhccCCCCcccchhhHHHHHhhc--CccHHHHHHHHHH
Q 030888 99 AVLRCLGAFDPNGENLQVSQKQEAAKQC--NCTIAEVENTLAK 139 (170)
Q Consensus 99 aiiR~L~~~DptGE~l~asqk~~aAk~C--nCTiadVE~~LAK 139 (170)
-+||.|..+.|- +.+=.+.|+.| +-|.+||+++|..
T Consensus 27 ~~ir~l~~l~~~-----~~d~~~iak~l~p~is~~ev~~sL~~ 64 (171)
T PF14394_consen 27 PAIRELLPLMPF-----APDPEWIAKRLRPKISAEEVRDSLEF 64 (171)
T ss_pred HHHHHHhhcCCC-----CCCHHHHHHHhcCCCCHHHHHHHHHH
Confidence 467888877654 33667899999 9999999999864
No 38
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=35.67 E-value=77 Score=29.04 Aligned_cols=37 Identities=24% Similarity=0.384 Sum_probs=30.1
Q ss_pred HHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHHh
Q 030888 102 RCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKF 140 (170)
Q Consensus 102 R~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKf 140 (170)
.-++.+|+.| -|.. .-.+.|.+++|+..+||.+|+..
T Consensus 101 ~iI~~LD~~G-yL~~-~~~eia~~l~~~~~~ve~~l~~i 137 (429)
T TIGR02395 101 YIIDNLDEDG-YLEI-DLEEIADELEVSEEEVEKVLELI 137 (429)
T ss_pred HHHHhCCCCC-CCCC-CHHHHHHHcCCCHHHHHHHHHHH
Confidence 4457899999 5654 45678999999999999999765
No 39
>PRK14066 exodeoxyribonuclease VII small subunit; Provisional
Probab=34.59 E-value=1.8e+02 Score=21.04 Aligned_cols=54 Identities=26% Similarity=0.349 Sum_probs=36.3
Q ss_pred hhhHHHHHHHHHHHHHHHhccCCCCcccchhhH-----HHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHHhc
Q 030888 87 ATTFADTFEKQEAVLRCLGAFDPNGENLQVSQK-----QEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLKEE 156 (170)
Q Consensus 87 eat~~~afeK~EaiiR~L~~~DptGE~l~asqk-----~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLkeE 156 (170)
+.+|..+|.+-|.|++-|-.=|-+ |..+-+ ....++|+ .+-.+|.+||+.|-+.
T Consensus 3 ~~~fEeal~~LE~IV~~LE~g~l~---Leesl~lyeeG~~L~k~C~-------------~~L~~ae~kv~~l~~~ 61 (75)
T PRK14066 3 VEKFETALKKLEEVVKKLEGGELS---LDDSLKAFEEGVKHAAFCS-------------KKLDEAERRVEVLLKQ 61 (75)
T ss_pred cccHHHHHHHHHHHHHHHHCCCCC---HHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHhc
Confidence 568999999999999999765533 222211 23445554 3556778888888653
No 40
>PRK14532 adenylate kinase; Provisional
Probab=33.85 E-value=40 Score=25.57 Aligned_cols=46 Identities=9% Similarity=0.141 Sum_probs=32.9
Q ss_pred hHHHHHhhcCccHHHHHHHHHHhHhHH-HHHHHHHHHHhcCCCCCCc
Q 030888 118 QKQEAAKQCNCTIAEVENTLAKFTWAK-EAQKKIEKLKEEGKPMPKS 163 (170)
Q Consensus 118 qk~~aAk~CnCTiadVE~~LAKftWaK-eA~kKi~KLkeEGKPlPks 163 (170)
+=...|++.||+.-++.++|.+..|.. +..+++...-..|...|..
T Consensus 16 ~a~~la~~~g~~~is~~d~lr~~~~~~~~~~~~~~~~~~~g~~~~~~ 62 (188)
T PRK14532 16 QAKRLVEERGMVQLSTGDMLRAAIASGSELGQRVKGIMDRGELVSDE 62 (188)
T ss_pred HHHHHHHHcCCeEEeCcHHHHHHHHcCCHHHHHHHHHHHCCCccCHH
Confidence 334557788888888888888876543 3445677777789888854
No 41
>TIGR00432 arcsn_tRNA_tgt tRNA-guanine transglycosylase, archaeosine-15-forming. This tRNA-guanine transglycosylase (tgt) differs from the tgt of E. coli and other Bacteria in the site of action and the modification that results. It exchanges 7-cyano-7-deazaguanine (preQ0) with guanine at position 15 of archaeal tRNA; this nucleotide is subsequently converted to archaeosine, found exclusively in the Archaea. This enzyme from Haloferax volcanii has been purified, characterized, and partially sequenced and is the basis for identifying this family. In contrast, bacterial tgt catalyzes the exchange of preQ0 or preQ1 for the guanine base at position 34; this nucleotide is subsequently modified to queuosine. Archeoglobus fulgidus has both enzymes, while some other Archaea have just this one.
Probab=33.69 E-value=56 Score=31.24 Aligned_cols=51 Identities=18% Similarity=0.304 Sum_probs=42.5
Q ss_pred HHHHHHHHHHhHHhccccchhcccc-chhhHHHHHHHHHHHHHHHhccCCCC
Q 030888 61 LLRFADELKKARKLGTLKQYIVGRS-SATTFADTFEKQEAVLRCLGAFDPNG 111 (170)
Q Consensus 61 L~~FADelkkARr~Gsfk~fv~Grs-seat~~~afeK~EaiiR~L~~~DptG 111 (170)
|.++-++++.|-+-|+|.+|+-.|+ +...+.+++.....=-.||-.+||.-
T Consensus 206 ~~~~m~~iR~aI~~g~l~e~ve~r~R~hP~l~~~~r~l~~~~~~lE~~~P~~ 257 (540)
T TIGR00432 206 SFQEIETIKQAIKDGSLFELVEERVRAHPNLLEGYRQVKHYWDLIEKFDPRK 257 (540)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHhhCHHHHHHHHHHHHHHHHHHhhCCCc
Confidence 3466778888889999999999988 68888888888766678899999983
No 42
>PF04287 DUF446: tRNA pseudouridine synthase C; InterPro: IPR007384 This family includes an N-terminal region of unknown function from the Erwinia carotovora exoenzyme regulation regulon orf1 protein, which also contains a domain found in RNA pseudouridylate synthase IPR006145 from INTERPRO.; PDB: 2HGK_A.
Probab=33.68 E-value=26 Score=26.76 Aligned_cols=67 Identities=27% Similarity=0.439 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHHhHhHHH-HHHHHHHHHhcCCCCCCccc
Q 030888 90 FADTFEKQEAVLRCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKFTWAKE-AQKKIEKLKEEGKPMPKSMA 165 (170)
Q Consensus 90 ~~~afeK~EaiiR~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKftWaKe-A~kKi~KLkeEGKPlPks~~ 165 (170)
+...+..-|+-+|.++.-..+ .-....=....-=| =|+|+=-.|-.= ---||..|-+.|.|||.+|+
T Consensus 4 ~~~lL~~LE~~Lr~~~lWq~~--~P~~eAl~S~~PF~-------iDTl~f~qWLQwVFiPrm~~lie~~~pLP~~~~ 71 (100)
T PF04287_consen 4 LAELLDQLEAELRQLGLWQSE--PPSPEALASTEPFC-------IDTLSFEQWLQWVFIPRMRALIEQGQPLPTSFA 71 (100)
T ss_dssp HHHHHHHHHHHHHHTT----------GGGTTT--SS--------TTTS-THHHHTTTHHHHHHHHHHTT----TT--
T ss_pred HHHHHHHHHHHHHHhCccCCC--CCCHHHHcCCCCcc-------cccCCHHHHHHHHHHHHHHHHHHcCCCCCcccc
Confidence 445566667777777665411 11111111111112 133444444432 23588999999999999875
No 43
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=33.42 E-value=1.2e+02 Score=18.86 Aligned_cols=43 Identities=21% Similarity=0.337 Sum_probs=29.2
Q ss_pred HHHHHHHHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHHhcC
Q 030888 96 KQEAVLRCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLKEEG 157 (170)
Q Consensus 96 K~EaiiR~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLkeEG 157 (170)
++..||+.|..-++ .+.. .+.|..+||+-.-|.+ -|+.|++.|
T Consensus 1 R~~~il~~L~~~~~---~it~---~eLa~~l~vS~rTi~~-------------~i~~L~~~~ 43 (55)
T PF08279_consen 1 RQKQILKLLLESKE---PITA---KELAEELGVSRRTIRR-------------DIKELREWG 43 (55)
T ss_dssp HHHHHHHHHHHTTT---SBEH---HHHHHHCTS-HHHHHH-------------HHHHHHHTT
T ss_pred CHHHHHHHHHHcCC---CcCH---HHHHHHhCCCHHHHHH-------------HHHHHHHCC
Confidence 46789999966652 1334 6789999999776654 456677776
No 44
>PRK04960 universal stress protein UspB; Provisional
Probab=32.86 E-value=29 Score=27.68 Aligned_cols=27 Identities=33% Similarity=0.443 Sum_probs=23.3
Q ss_pred chHHHHHHHHhhcchhhhhh---ccccccc
Q 030888 2 RSLRILTSIYHNHHLTLSQY---RSIFTTR 28 (170)
Q Consensus 2 ~s~r~l~~~~~~~~~~l~~~---r~I~sT~ 28 (170)
.|+|.|-.+++-.+-+|+|+ ||.|+|-
T Consensus 24 SsLR~LL~imRe~dPLLYQ~VDG~GFFtth 53 (111)
T PRK04960 24 SSLRALLVVLRGCDPLLYQYVDGGGFFTSH 53 (111)
T ss_pred HHHHHHHHHHHccCchhheeecCCceeecC
Confidence 47899999999988899998 8888874
No 45
>PRK09183 transposase/IS protein; Provisional
Probab=32.76 E-value=2.3e+02 Score=23.66 Aligned_cols=49 Identities=16% Similarity=0.122 Sum_probs=39.1
Q ss_pred HHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHH-hcCCCCCCccccccc
Q 030888 121 EAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLK-EEGKPMPKSMAEVQF 169 (170)
Q Consensus 121 ~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLk-eEGKPlPks~~Evq~ 169 (170)
+.|..=+-+..|.=..|-...|...-+++++.+. .-+-|.+|++++..|
T Consensus 30 ~~~~~~~~~~~e~l~~ll~~E~~~R~~~~~~~~~k~a~~p~~~~l~~fd~ 79 (259)
T PRK09183 30 QQAVDQEWSYMDFLEHLLHEEKLARHQRKQAMYTRMAAFPAVKTFEEYDF 79 (259)
T ss_pred HHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhccc
Confidence 4455567777888888888999999999988875 555699999999876
No 46
>TIGR03220 catechol_dmpE 2-oxopent-4-enoate hydratase. Members of this protein family are 2-oxopent-4-enoate hydratase, which is also called 2-hydroxypent-2,4-dienoate hydratase. It is closely related to another gene found in the same operon, 4-oxalocrotonate decarboxylase, with which it interacts closely.
Probab=32.20 E-value=1e+02 Score=25.75 Aligned_cols=46 Identities=20% Similarity=0.211 Sum_probs=36.8
Q ss_pred HHHHHHHHHHhHHhccccchhccccchhhHHHHHHHHHHHHHHHhc
Q 030888 61 LLRFADELKKARKLGTLKQYIVGRSSATTFADTFEKQEAVLRCLGA 106 (170)
Q Consensus 61 L~~FADelkkARr~Gsfk~fv~Grsseat~~~afeK~EaiiR~L~~ 106 (170)
+..+|+.|-.||+-|.--..+..+....|..+|..=|+++++.+-.
T Consensus 2 ~~~~a~~L~~A~~~~~~~~~~~~~~~~~~~~dAyaiQ~~~~~~~~~ 47 (255)
T TIGR03220 2 ITQLGDELYQALVTRTPVAPLTSRGPDISIEDAYRIQQRMIARRLA 47 (255)
T ss_pred HHHHHHHHHHHHHHCCcCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 3688999999999998644455455688999999999999987643
No 47
>PRK00768 nadE NAD synthetase; Reviewed
Probab=32.04 E-value=61 Score=28.25 Aligned_cols=67 Identities=21% Similarity=0.255 Sum_probs=41.8
Q ss_pred Hhccccchhccccc--hhhHHHHHHHHHH-HHH---------HHhccCCCCcccchhhHHHHHhhcCc---cHHHHHHHH
Q 030888 73 KLGTLKQYIVGRSS--ATTFADTFEKQEA-VLR---------CLGAFDPNGENLQVSQKQEAAKQCNC---TIAEVENTL 137 (170)
Q Consensus 73 r~Gsfk~fv~Grss--eat~~~afeK~Ea-iiR---------~L~~~DptGE~l~asqk~~aAk~CnC---TiadVE~~L 137 (170)
+.| ++.+|+|=|| +++++.++-..-- .++ .++..-|....-...+-+.+|+++|| .+-+++.++
T Consensus 35 ~~g-~~g~VlGlSGGIDSav~a~L~~~A~~~~~~~~~~~~~~~~~l~mP~~~~~~~~da~~la~~lgi~~~~~i~I~~~~ 113 (268)
T PRK00768 35 KSG-LKSLVLGISGGQDSTLAGRLAQLAVEELRAETGDDDYQFIAVRLPYGVQADEDDAQDALAFIQPDRVLTVNIKPAV 113 (268)
T ss_pred HcC-CCeEEEECCCCHHHHHHHHHHHHHHHHhcccccCcceeEEEEECCCCCcCCHHHHHHHHHhcCCCeeEEEECHHHH
Confidence 344 8999999887 6677666433211 123 67778886433345677789999988 344444555
Q ss_pred HHh
Q 030888 138 AKF 140 (170)
Q Consensus 138 AKf 140 (170)
..|
T Consensus 114 ~~~ 116 (268)
T PRK00768 114 DAS 116 (268)
T ss_pred HHH
Confidence 444
No 48
>TIGR03218 catechol_dmpH 4-oxalocrotonate decarboxylase. Members of this protein family are 4-oxalocrotonate decarboxylase. Note that this protein, as characterized (indirectly) in Pseudomonas sp. strain CF600, was inactive except when coexpressed with DmpE, 2-oxopent-4-enoate hydratase, a homologous protein from the same operon. Both of these enzymes are active in the degradation of catechol, a common intermediate in the degradation of aromatic compounds such as benzoate, toluene, phenol, dimethylphenol (dmp), salicylate, etc.
Probab=31.10 E-value=1.1e+02 Score=25.88 Aligned_cols=48 Identities=19% Similarity=0.124 Sum_probs=37.3
Q ss_pred chHHHHHHHHHHhHHhccccchhccccchhhHHHHHHHHHHHHHHHhc
Q 030888 59 FTLLRFADELKKARKLGTLKQYIVGRSSATTFADTFEKQEAVLRCLGA 106 (170)
Q Consensus 59 ftL~~FADelkkARr~Gsfk~fv~Grsseat~~~afeK~EaiiR~L~~ 106 (170)
-+++++|+.|-.||+-+.--.-+.......|..+|..=|+++++.+-.
T Consensus 8 ~~~~~~A~~L~~Ar~~~~~i~~l~~~~p~~t~~dAYaiQ~~~~~~~~~ 55 (263)
T TIGR03218 8 EQIEALAEHLENAELQAHDIPKITDEYPDMDWADAYAIQWEIRRRKEA 55 (263)
T ss_pred HHHHHHHHHHHHHHHHCCcCCCCCccCCCCCHHHHHHHHHHHHHHHHh
Confidence 467899999999999988433333444468999999999999988733
No 49
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=31.09 E-value=60 Score=23.23 Aligned_cols=23 Identities=9% Similarity=-0.042 Sum_probs=19.7
Q ss_pred HHHhhcCccHHHHHHHHHHhHhH
Q 030888 121 EAAKQCNCTIAEVENTLAKFTWA 143 (170)
Q Consensus 121 ~aAk~CnCTiadVE~~LAKftWa 143 (170)
.+|.+|+++.+||+.+|.-|...
T Consensus 10 ~ia~~~~~s~~~v~~vv~~~~~~ 32 (96)
T TIGR00987 10 YLFDELGLSKREAKELVELFFEE 32 (96)
T ss_pred HHHHHhCcCHHHHHHHHHHHHHH
Confidence 46788999999999999988754
No 50
>PTZ00226 fumarate hydratase; Provisional
Probab=30.94 E-value=41 Score=32.83 Aligned_cols=39 Identities=31% Similarity=0.510 Sum_probs=29.0
Q ss_pred CccHHHHHHHHHHh-------------HhHHHHHHHHHHHHhcCCCCCCccc
Q 030888 127 NCTIAEVENTLAKF-------------TWAKEAQKKIEKLKEEGKPMPKSMA 165 (170)
Q Consensus 127 nCTiadVE~~LAKf-------------tWaKeA~kKi~KLkeEGKPlPks~~ 165 (170)
+-.+.+++.-|.++ |=--.||+||.++-++|+|||-.|.
T Consensus 394 ~~Pl~~~~e~l~~l~vGd~v~LsG~i~taRD~AH~rl~e~l~~Ge~lP~dlk 445 (570)
T PTZ00226 394 NQPMEEILKQLSKYPVKTRLSLTGTLIVARDIAHAKIVEMLENGEPLPEYMK 445 (570)
T ss_pred cCCCchhHHHHhcCCCCCEEEEEEEEEEEehHHHHHHHHHHhcCCCCCcCCC
Confidence 44455555666664 4456899999999999999997764
No 51
>PF09720 Unstab_antitox: Putative addiction module component; InterPro: IPR013406 This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins (IPR007712 from INTERPRO). It is likely that this protein and its partner comprise some form of addiction module - a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death [] - although these gene pairs are usually found on the bacterial main chromosome.
Probab=30.84 E-value=54 Score=21.30 Aligned_cols=26 Identities=23% Similarity=0.464 Sum_probs=20.8
Q ss_pred HhHHHHHHHHHHHHhcCCCCCCccccc
Q 030888 141 TWAKEAQKKIEKLKEEGKPMPKSMAEV 167 (170)
Q Consensus 141 tWaKeA~kKi~KLkeEGKPlPks~~Ev 167 (170)
-|..|+.+|++.++ .|+--+.+.+||
T Consensus 28 ~w~~el~rR~~~~~-~G~~~~i~~eev 53 (54)
T PF09720_consen 28 WWKEELERRLAEYE-SGKVQGIPWEEV 53 (54)
T ss_pred HHHHHHHHHHHHHH-cCCCCCCcHHHh
Confidence 49999999999986 577667777776
No 52
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=30.52 E-value=99 Score=19.35 Aligned_cols=38 Identities=18% Similarity=0.363 Sum_probs=27.6
Q ss_pred cCCCCcccchhhHHHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHHhcCC
Q 030888 107 FDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLKEEGK 158 (170)
Q Consensus 107 ~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLkeEGK 158 (170)
+.|| .+|+.....+++| ++|.|-.--..+.+-.++.||
T Consensus 9 l~Pt-----~~Q~~~L~~~~~~---------~R~vyN~~L~~~~~~y~~~~K 46 (46)
T PF12323_consen 9 LYPT-----KEQEEKLERWFGA---------CRFVYNWALAERKEAYKQNGK 46 (46)
T ss_pred EecC-----HHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHcCc
Confidence 5677 6788888888887 467777666666666777665
No 53
>PRK14064 exodeoxyribonuclease VII small subunit; Provisional
Probab=29.94 E-value=2.1e+02 Score=20.57 Aligned_cols=61 Identities=23% Similarity=0.348 Sum_probs=38.5
Q ss_pred hhhHHHHHHHHHHHHHHHhccCCCCcccchhh-----HHHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHHh-cCCCC
Q 030888 87 ATTFADTFEKQEAVLRCLGAFDPNGENLQVSQ-----KQEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLKE-EGKPM 160 (170)
Q Consensus 87 eat~~~afeK~EaiiR~L~~~DptGE~l~asq-----k~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLke-EGKPl 160 (170)
+.||..+|.+-|.|++-|-.=|-+ |..+= =...++.|+- .-.+|.+||++|-. +|...
T Consensus 5 ~~sfEe~l~~LE~IV~~LE~~~l~---Leesl~~ye~G~~L~k~c~~-------------~L~~ae~kv~~l~~~~~~~~ 68 (75)
T PRK14064 5 KKTFEEAIAELETIVEALENGSAS---LEDSLDMYQKGIELTKLCQD-------------KLQSAEKRMAKVVTDAGEEI 68 (75)
T ss_pred cCCHHHHHHHHHHHHHHHHCCCCC---HHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHcCCCCC
Confidence 358999999999999998765532 21111 1234455543 34567788888754 57665
Q ss_pred CCc
Q 030888 161 PKS 163 (170)
Q Consensus 161 Pks 163 (170)
|.+
T Consensus 69 ~~~ 71 (75)
T PRK14064 69 PFE 71 (75)
T ss_pred CCC
Confidence 554
No 54
>PF01417 ENTH: ENTH domain; InterPro: IPR001026 The ENTH (Epsin N-terminal homology) domain is approximately 150 amino acids in length and is always found located at the N-termini of proteins. The domain forms a compact globular structure, composed of 9 alpha-helices connected by loops of varying length. The general topology is determined by three helical hairpins that are stacked consecutively with a right hand twist []. An N-terminal helix folds back, forming a deep basic groove that forms the binding pocket for the Ins(1,4,5)P3 ligand []. The ligand is coordinated by residues from surrounding alpha-helices and all three phosphates are multiply coordinated. The coordination of Ins(1,4,5)P3 suggests that ENTH is specific for particular head groups. Proteins containing this domain have been found to bind PtdIns(4,5)P2 and PtdIns(1,4,5)P3 suggesting that the domain may be a membrane interacting module. The main function of proteins containing this domain appears to be to act as accessory clathrin adaptors in endocytosis, Epsin is able to recruit and promote clathrin polymerisation on a lipid monolayer, but may have additional roles in signalling and actin regulation []. Epsin causes a strong degree of membrane curvature and tubulation, even fragmentation of membranes with a high PtdIns(4,5)P2 content. Epsin binding to membranes facilitates their deformation by insertion of the N-terminal helix into the outer leaflet of the bilayer, pushing the head groups apart. This would reduce the energy needed to curve the membrane into a vesicle, making it easier for the clathrin cage to fix and stabilise the curved membrane. This points to a pioneering role for epsin in vesicle budding as it provides both a driving force and a link between membrane invagination and clathrin polymerisation. ; PDB: 1H0A_A 1EYH_A 1EDU_A 2QY7_B 1XGW_A 2V8S_E 1VDY_A 2DCP_A 1INZ_A 3ONL_B ....
Probab=29.42 E-value=78 Score=23.35 Aligned_cols=45 Identities=29% Similarity=0.543 Sum_probs=29.3
Q ss_pred hhccccchhhHHHHHHHHHHHHHHHhcc---CCCCcccchhhHHHHHhhc
Q 030888 80 YIVGRSSATTFADTFEKQEAVLRCLGAF---DPNGENLQVSQKQEAAKQC 126 (170)
Q Consensus 80 fv~Grsseat~~~afeK~EaiiR~L~~~---DptGE~l~asqk~~aAk~C 126 (170)
|+.-.+++ .|..-|..+-.+||.|..| ||.|...+.. -.+.|+++
T Consensus 68 yLl~nG~~-~~~~~~~~~~~~I~~l~~f~~~d~~g~d~~~~-VR~~A~~i 115 (125)
T PF01417_consen 68 YLLKNGSE-RFVDELRDHIDIIRELQDFQYVDPKGKDQGQN-VREKAKEI 115 (125)
T ss_dssp HHHHHS-H-HHHHHHHHTHHHHHGGGG---BBTTSTBHHHH-HHHHHHHH
T ss_pred HHHHHCCH-HHHHHHHHHHHHHhhcceeeccCCCCccHHHH-HHHHHHHH
Confidence 34444444 6777778888999999998 8878776663 44555543
No 55
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=29.08 E-value=53 Score=21.85 Aligned_cols=20 Identities=25% Similarity=0.393 Sum_probs=17.1
Q ss_pred HHHHHhhcCccHHHHHHHHH
Q 030888 119 KQEAAKQCNCTIAEVENTLA 138 (170)
Q Consensus 119 k~~aAk~CnCTiadVE~~LA 138 (170)
-.++|++||-+..+|.++|.
T Consensus 23 ~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 23 DEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHcccHHHHHHHHH
Confidence 46899999999999999986
No 56
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=28.98 E-value=1.4e+02 Score=20.79 Aligned_cols=39 Identities=28% Similarity=0.330 Sum_probs=29.2
Q ss_pred HHHHHHHHhccCCCCcccchhhHHHHHhhcCc--cHHHHHHHHHH
Q 030888 97 QEAVLRCLGAFDPNGENLQVSQKQEAAKQCNC--TIAEVENTLAK 139 (170)
Q Consensus 97 ~EaiiR~L~~~DptGE~l~asqk~~aAk~CnC--TiadVE~~LAK 139 (170)
|++|++.|..+ |-|+...= .+.|+.|++ ..-.|-.+|++
T Consensus 2 ~~~V~~~v~~I-P~G~v~TY---g~iA~~~g~p~~~R~Vg~al~~ 42 (79)
T cd06445 2 QRRVWEALRQI-PYGEVTTY---GQIAKLAGTPKAARAVGSALAR 42 (79)
T ss_pred HHHHHHHHhcC-CCCCcCcH---HHHHHHHCCCCcHHHHHHHHHh
Confidence 67899999988 88876655 467888888 66677766654
No 57
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=28.74 E-value=71 Score=27.74 Aligned_cols=36 Identities=28% Similarity=0.382 Sum_probs=27.9
Q ss_pred HHHHHHhccCCCCcccchhhHHHHHhhcC--ccHHHHHHHHHH
Q 030888 99 AVLRCLGAFDPNGENLQVSQKQEAAKQCN--CTIAEVENTLAK 139 (170)
Q Consensus 99 aiiR~L~~~DptGE~l~asqk~~aAk~Cn--CTiadVE~~LAK 139 (170)
-+||.|..+-|- +.+=.+.|+.|+ -|.+||.++|.-
T Consensus 125 ~virel~~~~~~-----~~~~~~ia~~l~p~is~~ev~~sL~~ 162 (271)
T TIGR02147 125 SVIRELLGVMPF-----ADDPEELAKRCFPKISAEQVKESLDL 162 (271)
T ss_pred HHHHHHhhcCCC-----CCCHHHHHHHhCCCCCHHHHHHHHHH
Confidence 477888887653 435567999999 799999999863
No 58
>PRK15391 fumarate hydratase FumB; Provisional
Probab=28.35 E-value=48 Score=32.22 Aligned_cols=25 Identities=24% Similarity=0.412 Sum_probs=21.0
Q ss_pred HhHHHHHHHHHHHHhcCCCCCCccc
Q 030888 141 TWAKEAQKKIEKLKEEGKPMPKSMA 165 (170)
Q Consensus 141 tWaKeA~kKi~KLkeEGKPlPks~~ 165 (170)
+=--.||+||.++-++|+|||-.|.
T Consensus 391 taRD~AH~rl~e~l~~Ge~lP~dlk 415 (548)
T PRK15391 391 VGRDIAHAKLKELIDAGKELPQYIK 415 (548)
T ss_pred EEhhHHHHHHHHHHhcCCCCCcCCC
Confidence 4456899999999999999997764
No 59
>PRK15390 fumarate hydratase FumA; Provisional
Probab=28.27 E-value=48 Score=32.20 Aligned_cols=25 Identities=16% Similarity=0.309 Sum_probs=20.9
Q ss_pred HhHHHHHHHHHHHHhcCCCCCCccc
Q 030888 141 TWAKEAQKKIEKLKEEGKPMPKSMA 165 (170)
Q Consensus 141 tWaKeA~kKi~KLkeEGKPlPks~~ 165 (170)
+=--.||+||.++-++|+|||-.|.
T Consensus 391 taRD~AH~rl~e~l~~Ge~lP~dl~ 415 (548)
T PRK15390 391 VGRDIAHAKLKERMDNGEGLPQYIK 415 (548)
T ss_pred EEehHHHHHHHHHHhcCCCCCcCCC
Confidence 3456899999999999999998764
No 60
>PF08769 Spo0A_C: Sporulation initiation factor Spo0A C terminal; InterPro: IPR014879 The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005509 calcium ion binding, 0006355 regulation of transcription, DNA-dependent, 0042173 regulation of sporulation resulting in formation of a cellular spore, 0005737 cytoplasm; PDB: 1FC3_C 1LQ1_D.
Probab=27.61 E-value=50 Score=24.90 Aligned_cols=34 Identities=24% Similarity=0.484 Sum_probs=24.0
Q ss_pred HHHHhhcCccHHHHHHHHH---HhHhHHHHHHHHHHH
Q 030888 120 QEAAKQCNCTIAEVENTLA---KFTWAKEAQKKIEKL 153 (170)
Q Consensus 120 ~~aAk~CnCTiadVE~~LA---KftWaKeA~kKi~KL 153 (170)
-++|+++++|..-||.+|. ...|.+.-..-++++
T Consensus 44 p~IA~k~~TT~s~VERaIR~aI~~~w~~g~~~~l~~i 80 (106)
T PF08769_consen 44 PDIAKKYGTTPSRVERAIRHAIEVAWTRGNPELLEKI 80 (106)
T ss_dssp HHHHHHTTS-HHHHHHHHHHHHHHHHHCS-CCCCHHC
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence 4799999999999999885 567775544444443
No 61
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.60 E-value=56 Score=20.04 Aligned_cols=23 Identities=17% Similarity=0.231 Sum_probs=16.7
Q ss_pred HHHHHhhcCccHHHHHHHHHHhH
Q 030888 119 KQEAAKQCNCTIAEVENTLAKFT 141 (170)
Q Consensus 119 k~~aAk~CnCTiadVE~~LAKft 141 (170)
..++|+++||+..-|-+.+.+|.
T Consensus 20 ~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 20 IREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHHHHHCcCHHHHHHHHHHcc
Confidence 45799999999999998888773
No 62
>PF14818 DUF4482: Domain of unknown function (DUF4482)
Probab=27.32 E-value=44 Score=27.24 Aligned_cols=18 Identities=56% Similarity=0.673 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHhcCCCC
Q 030888 143 AKEAQKKIEKLKEEGKPM 160 (170)
Q Consensus 143 aKeA~kKi~KLkeEGKPl 160 (170)
.|++|+||++|.+|-+|-
T Consensus 36 ~kemq~kieql~~e~~~~ 53 (141)
T PF14818_consen 36 WKEMQRKIEQLQKEVKPR 53 (141)
T ss_pred HHHHHHHHHHHHhhcchh
Confidence 489999999999998876
No 63
>PRK00977 exodeoxyribonuclease VII small subunit; Provisional
Probab=27.25 E-value=2.4e+02 Score=20.35 Aligned_cols=62 Identities=24% Similarity=0.403 Sum_probs=41.1
Q ss_pred chhhHHHHHHHHHHHHHHHhccCCCCcccchhhH-----HHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHHh-cCCC
Q 030888 86 SATTFADTFEKQEAVLRCLGAFDPNGENLQVSQK-----QEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLKE-EGKP 159 (170)
Q Consensus 86 seat~~~afeK~EaiiR~L~~~DptGE~l~asqk-----~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLke-EGKP 159 (170)
.+.||..+|++-|.|++-|-.=|-+ |..+-+ .+..++|+-.+. +|.+||+.|-+ .+++
T Consensus 8 ~~~sfEea~~~LEeIv~~LE~~~l~---Lees~~lyeeg~~L~k~C~~~L~-------------~ae~ki~~l~~~~~~~ 71 (80)
T PRK00977 8 KPLSFEEALAELEEIVTRLESGDLP---LEESLAAFERGVALARQCQKKLQ-------------QAEQRVEKLLDEDGKE 71 (80)
T ss_pred CcCCHHHHHHHHHHHHHHHHCCCCC---HHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHhccCCC
Confidence 4679999999999999999765532 323222 345667765544 45678888854 4666
Q ss_pred CCCc
Q 030888 160 MPKS 163 (170)
Q Consensus 160 lPks 163 (170)
.|..
T Consensus 72 ~~~~ 75 (80)
T PRK00977 72 ASLE 75 (80)
T ss_pred CCCC
Confidence 5543
No 64
>PF13518 HTH_28: Helix-turn-helix domain
Probab=26.68 E-value=1.3e+02 Score=18.23 Aligned_cols=36 Identities=19% Similarity=0.303 Sum_probs=24.1
Q ss_pred HHHHHHHHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHHhH
Q 030888 96 KQEAVLRCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKFT 141 (170)
Q Consensus 96 K~EaiiR~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKft 141 (170)
|.+.|..++ + |+ -..++|+++|.+...|.+.+.+|.
T Consensus 2 r~~iv~~~~---~--g~-----s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 2 RLQIVELYL---E--GE-----SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHHHH---c--CC-----CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 455565555 3 53 234599999999988877666663
No 65
>PF10183 ESSS: ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) ; InterPro: IPR019329 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry represents the ESSS subunit from mitochondrial NADH:ubiquinone oxidoreductase (complex I). It carries mitochondrial import sequences [].
Probab=26.66 E-value=56 Score=24.49 Aligned_cols=17 Identities=47% Similarity=0.976 Sum_probs=14.0
Q ss_pred HhH-HHHHHHHHHHHhcC
Q 030888 141 TWA-KEAQKKIEKLKEEG 157 (170)
Q Consensus 141 tWa-KeA~kKi~KLkeEG 157 (170)
+|| +||..+|+.+.++|
T Consensus 88 ~WA~rEA~~rl~~rEa~G 105 (105)
T PF10183_consen 88 TWARREAYRRLERREAEG 105 (105)
T ss_pred HHHHHHHHHHHhHHhhcC
Confidence 577 47999999888887
No 66
>COG4303 EutB Ethanolamine ammonia-lyase, large subunit [Amino acid transport and metabolism]
Probab=26.36 E-value=32 Score=32.53 Aligned_cols=60 Identities=15% Similarity=0.255 Sum_probs=37.2
Q ss_pred hHHhccccchhcccc-chhhHHHHHHH--HHHHHHHHhccCCCCcccchhhHHHHHhhcCccHH
Q 030888 71 ARKLGTLKQYIVGRS-SATTFADTFEK--QEAVLRCLGAFDPNGENLQVSQKQEAAKQCNCTIA 131 (170)
Q Consensus 71 ARr~Gsfk~fv~Grs-seat~~~afeK--~EaiiR~L~~~DptGE~l~asqk~~aAk~CnCTia 131 (170)
.--+|.|++|+.|-. +|+.+. ++.+ -..||-+.+.+=.+-.-+-..||+++-+|||-||+
T Consensus 90 ~~tV~e~RewlL~~~~~~~~i~-~~~~GLTsEmiAAV~Klmsn~DLi~~AkKi~v~~~~ntTiG 152 (453)
T COG4303 90 NWTVSELREWLLSDETSEDDIA-FTRKGLTSEMIAAVAKLMSNADLIYGAKKIRVIAKANTTIG 152 (453)
T ss_pred cccHHHHHHHHhcCCCCHHHHH-HHhccCCHHHHHHHHHHhhhhhHHHhhhhhhhhhhcccccc
Confidence 346788889988843 233332 2211 23344444444444446667899999999999986
No 67
>PF14198 TnpV: Transposon-encoded protein TnpV
Probab=25.97 E-value=1.1e+02 Score=23.45 Aligned_cols=47 Identities=17% Similarity=0.208 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHH
Q 030888 91 ADTFEKQEAVLRCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTL 137 (170)
Q Consensus 91 ~~afeK~EaiiR~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~L 137 (170)
..|-++.+.|+.-++.-+|.+|.|.+.+-.+-..++|.-=+.+|.++
T Consensus 60 ~~A~e~~e~l~~q~~~~~gvtE~LK~~dqm~wv~~mN~ir~~AeEiV 106 (111)
T PF14198_consen 60 EQAQERFERLVEQMAEKEGVTEELKAEDQMEWVRRMNNIRAQAEEIV 106 (111)
T ss_pred HHHHHHHHHHHHHHHHhcCCcHhhhhcCHHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999999999988888888887777776654
No 68
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=25.93 E-value=74 Score=21.79 Aligned_cols=21 Identities=10% Similarity=0.256 Sum_probs=17.8
Q ss_pred HHHHhhcCccHHHHHHHHHHh
Q 030888 120 QEAAKQCNCTIAEVENTLAKF 140 (170)
Q Consensus 120 ~~aAk~CnCTiadVE~~LAKf 140 (170)
.++|.+|+++.+||+.+|.-|
T Consensus 8 ~~ia~~~~~~~~~v~~vl~~l 28 (90)
T smart00411 8 DAIAEKAGLSKKDAKAAVDAF 28 (90)
T ss_pred HHHHHHhCCCHHHHHHHHHHH
Confidence 357889999999999999765
No 69
>PHA02547 55 RNA polymerase sigma factor; Provisional
Probab=25.81 E-value=57 Score=27.82 Aligned_cols=85 Identities=21% Similarity=0.239 Sum_probs=47.9
Q ss_pred HHHhHHhccccchhccc--cchhhHHHHHHHHHHHHHHHhccCCCCc-----------------ccchhhHHHHHhhcCc
Q 030888 68 LKKARKLGTLKQYIVGR--SSATTFADTFEKQEAVLRCLGAFDPNGE-----------------NLQVSQKQEAAKQCNC 128 (170)
Q Consensus 68 lkkARr~Gsfk~fv~Gr--sseat~~~afeK~EaiiR~L~~~DptGE-----------------~l~asqk~~aAk~CnC 128 (170)
|+-|-.+-..=+|..=. --|.-+++| .|++||||+.|||+-- +|+- .|.+.|..|.-
T Consensus 47 mkIa~glS~r~nF~~Yt~~wKedMI~Dg---Ie~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~k-Ekke~a~K~ky 122 (179)
T PHA02547 47 MKIAEGLSRRPNFSGYTQTWKEDMIADG---IEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKK-EKKEMAIKYKY 122 (179)
T ss_pred HHHHhccccCCccccchHHHHHHHHHHH---HHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 45555444444443222 114445555 5799999999999842 1222 45566665543
Q ss_pred cHHHHH-------HHHHHhHhHHHHHHHHHHHHhc
Q 030888 129 TIAEVE-------NTLAKFTWAKEAQKKIEKLKEE 156 (170)
Q Consensus 129 TiadVE-------~~LAKftWaKeA~kKi~KLkeE 156 (170)
=+..|= -.|+-++.-...+.|+-..++.
T Consensus 123 f~~~vyD~~d~dm~~~~D~~f~qd~~~k~~~ye~s 157 (179)
T PHA02547 123 FLHNVYDEVDDDMVAIADETFIQDIYDKMNQYEES 157 (179)
T ss_pred HHHhccccccchhHhhccHHHHHHHHHHHHHHHHH
Confidence 222221 1366777777787777666554
No 70
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=25.79 E-value=1.8e+02 Score=23.37 Aligned_cols=65 Identities=17% Similarity=0.174 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHH----------hHhHHHHHHHHHHHHhcCCCCCCc
Q 030888 94 FEKQEAVLRCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAK----------FTWAKEAQKKIEKLKEEGKPMPKS 163 (170)
Q Consensus 94 feK~EaiiR~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAK----------ftWaKeA~kKi~KLkeEGKPlPks 163 (170)
-+++++|+.+|...... .-.+.|.+.|++..-|..-|.. ..-|..+..|+.-||++ |+=..
T Consensus 6 ~~R~~~Il~~l~~~~~~-------~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r~~~~~~~~~~~~~~~~~~--~~vD~ 76 (185)
T PRK04424 6 KERQKALQELIEENPFI-------TDEELAEKFGVSIQTIRLDRMELGIPELRERIKHVAEKNYDKVKSLPEE--EVVGE 76 (185)
T ss_pred HHHHHHHHHHHHHCCCE-------EHHHHHHHHCcCHHHHHHHHHHHhcchHHHHHHHHHHHhHHhhhcCCcc--cceee
Confidence 37899999999985522 4578999999998766554432 23356677777777776 44333
Q ss_pred cccc
Q 030888 164 MAEV 167 (170)
Q Consensus 164 ~~Ev 167 (170)
+-|+
T Consensus 77 i~ei 80 (185)
T PRK04424 77 LIDL 80 (185)
T ss_pred EEEe
Confidence 3333
No 71
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=25.74 E-value=79 Score=19.42 Aligned_cols=24 Identities=21% Similarity=0.101 Sum_probs=20.5
Q ss_pred ccchhhHHHHHhhcCccHHHHHHH
Q 030888 113 NLQVSQKQEAAKQCNCTIAEVENT 136 (170)
Q Consensus 113 ~l~asqk~~aAk~CnCTiadVE~~ 136 (170)
.....++.+.|+.||.+..+|.+=
T Consensus 24 ~P~~~~~~~la~~~~l~~~qV~~W 47 (59)
T cd00086 24 YPSREEREELAKELGLTERQVKIW 47 (59)
T ss_pred CCCHHHHHHHHHHHCcCHHHHHHH
Confidence 344789999999999999999863
No 72
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=25.69 E-value=1.6e+02 Score=17.70 Aligned_cols=38 Identities=21% Similarity=0.366 Sum_probs=24.3
Q ss_pred HHHHHHhc--cCCCCcccchhhHHHHHhhcCccHHHHHHHHHH
Q 030888 99 AVLRCLGA--FDPNGENLQVSQKQEAAKQCNCTIAEVENTLAK 139 (170)
Q Consensus 99 aiiR~L~~--~DptGE~l~asqk~~aAk~CnCTiadVE~~LAK 139 (170)
.|.+.+.. +.| |+.+. .-.+.|.+++++-.-|..+|.+
T Consensus 4 ~l~~~i~~~~~~~-~~~l~--s~~~la~~~~vs~~tv~~~l~~ 43 (60)
T smart00345 4 RLREDIVSGELRP-GDKLP--SERELAAQLGVSRTTVREALSR 43 (60)
T ss_pred HHHHHHHcCCCCC-CCcCc--CHHHHHHHHCCCHHHHHHHHHH
Confidence 44444433 343 66775 2456899999998888766543
No 73
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=25.59 E-value=56 Score=28.27 Aligned_cols=54 Identities=26% Similarity=0.353 Sum_probs=35.8
Q ss_pred HHhccCCCCcccc-hhhHHHHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHHhcCCC
Q 030888 103 CLGAFDPNGENLQ-VSQKQEAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLKEEGKP 159 (170)
Q Consensus 103 ~L~~~DptGE~l~-asqk~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLkeEGKP 159 (170)
.|..+| |++.. +.++++.++.|.--=+++ ..|.+-.=+-|+|++|++|++|=+-
T Consensus 80 el~~ld--~~i~~l~ek~q~l~~t~s~veaEi-k~L~s~Lt~eemQe~i~~L~kev~~ 134 (201)
T KOG4603|consen 80 ELQVLD--GKIVALTEKVQSLQQTCSYVEAEI-KELSSALTTEEMQEEIQELKKEVAG 134 (201)
T ss_pred HHHHHh--HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhcChHHHHHHHHHHHHHHHH
Confidence 466667 55443 236677777765433333 3466777789999999999998543
No 74
>PLN00133 class I-fumerate hydratase; Provisional
Probab=25.37 E-value=58 Score=31.89 Aligned_cols=39 Identities=23% Similarity=0.309 Sum_probs=30.0
Q ss_pred CccHHHHHHHHHHh-------------HhHHHHHHHHHHHHhcCCCCCCccc
Q 030888 127 NCTIAEVENTLAKF-------------TWAKEAQKKIEKLKEEGKPMPKSMA 165 (170)
Q Consensus 127 nCTiadVE~~LAKf-------------tWaKeA~kKi~KLkeEGKPlPks~~ 165 (170)
|-...+|...|++| |=--.||+||.++-++|+|||-.|.
T Consensus 400 ~~p~~~~~~~l~~l~vGd~V~LsG~I~taRDaAH~rl~e~l~~Ge~LP~dlk 451 (576)
T PLN00133 400 NRPMSEIRETLSAHPVRTRLSLTGTLVVARDIAHAKLLERLEAGEGLPQYAK 451 (576)
T ss_pred CCCcchHHHHHhhCCCCCEEEEEEEEEEEeHHHHHHHHHHHhcCCCCCcCcC
Confidence 33456666777775 3456899999999999999998765
No 75
>PRK15389 fumarate hydratase; Provisional
Probab=25.17 E-value=60 Score=31.42 Aligned_cols=26 Identities=15% Similarity=0.299 Sum_probs=20.8
Q ss_pred hHhHHHHHHHHHHHHhcCCCCCCccc
Q 030888 140 FTWAKEAQKKIEKLKEEGKPMPKSMA 165 (170)
Q Consensus 140 ftWaKeA~kKi~KLkeEGKPlPks~~ 165 (170)
||=--.||+||.++-++|+|+|-.+.
T Consensus 389 ~taRDaaHkrl~e~~~~G~~lP~dl~ 414 (536)
T PRK15389 389 IVARDIAHAKLKERLDAGEGLPQYLK 414 (536)
T ss_pred EEEehHHHHHHHHHHhcCCCCCcCcC
Confidence 44456789999999999999997764
No 76
>TIGR02312 HpaH 2-oxo-hepta-3-ene-1,7-dioic acid hydratase. This model represents the enzyme which hydrates the double bond of 2-oxo-hepta-3-ene-1,7-dioic acid to form 4-hydroxy-2-oxo-heptane-1,7-dioic acid in the catabolism of 4-hydroxyphenylacetic acid. The gene for this enzyme is generally found adjacent to other genes of this pathway in an apparent operon.
Probab=24.55 E-value=1.5e+02 Score=25.11 Aligned_cols=44 Identities=23% Similarity=0.145 Sum_probs=35.3
Q ss_pred hHHHHHHHHHHhHHhccccchhccccchhhHHHHHHHHHHHHHH
Q 030888 60 TLLRFADELKKARKLGTLKQYIVGRSSATTFADTFEKQEAVLRC 103 (170)
Q Consensus 60 tL~~FADelkkARr~Gsfk~fv~Grsseat~~~afeK~EaiiR~ 103 (170)
+.+++|+.|-.||+-|.-=.-+..+.-..|..+|..=|.++++.
T Consensus 6 ~~~~~A~~L~~Ar~~~~~i~~l~~~~~~~~~~dAYaiQ~~~~~~ 49 (267)
T TIGR02312 6 LIQEAAAELYEAEKTRVQISQFSLRYPEITIEDAYRIQRAWVAM 49 (267)
T ss_pred HHHHHHHHHHHHHHHCCccCCCCcCCCCCCHHHHHHHHHHHHHH
Confidence 56899999999999998644333344468999999999999865
No 77
>PF07064 RIC1: RIC1; InterPro: IPR009771 This entry represents RIC1 (Ribosomal control protein1) and has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network. It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor [] which activates YPT6 by exchanging bound GDP for free GTP. RIC1 is thereby required for efficient fusion of endosome-derived vesicles with the Golgi. The RIC1-RGP1 complex participates in the recycling of SNC1, presumably by mediating fusion of endosomal vesicles with the Golgi compartment and may also be indirectly involved in the transcription of both ribosomal protein genes and ribosomal RNA [, , ].
Probab=24.09 E-value=45 Score=28.60 Aligned_cols=19 Identities=37% Similarity=0.588 Sum_probs=15.7
Q ss_pred HHHHHHHHhccCCCCcccc
Q 030888 97 QEAVLRCLGAFDPNGENLQ 115 (170)
Q Consensus 97 ~EaiiR~L~~~DptGE~l~ 115 (170)
-..++|+|..+||+|+-+.
T Consensus 239 c~eL~RFL~~ld~~~~~l~ 257 (258)
T PF07064_consen 239 CFELVRFLKALDPEGNTLP 257 (258)
T ss_pred HHHHHHHHHHhCcccCcCC
Confidence 3467899999999998765
No 78
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.07 E-value=1e+02 Score=24.87 Aligned_cols=28 Identities=32% Similarity=0.529 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHhccCCCCcccchhhHHHH
Q 030888 94 FEKQEAVLRCLGAFDPNGENLQVSQKQEA 122 (170)
Q Consensus 94 feK~EaiiR~L~~~DptGE~l~asqk~~a 122 (170)
=-|.++|||+++ +.|.||+-+.--|..+
T Consensus 75 R~kld~vlramg-y~p~~e~~~~i~~~~i 102 (122)
T COG3877 75 RTKLDEVLRAMG-YNPDSENSVNIGKKKI 102 (122)
T ss_pred HHHHHHHHHHcC-CCCCCCChhhhhHHHH
Confidence 347889999997 6888887766544443
No 79
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=23.95 E-value=48 Score=27.65 Aligned_cols=49 Identities=39% Similarity=0.584 Sum_probs=27.7
Q ss_pred HHHHHH-------HhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHHhHhHHHHHHHHH-------HHHhcCCCCCCc
Q 030888 98 EAVLRC-------LGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKFTWAKEAQKKIE-------KLKEEGKPMPKS 163 (170)
Q Consensus 98 EaiiR~-------L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKftWaKeA~kKi~-------KLkeEGKPlPks 163 (170)
|.|||+ |++||-.|+.|.- .|.-|| |.|.---.|+-+ +-++++++.|.+
T Consensus 17 EtVLrhIReG~TQL~AFeEvg~~L~R-----TsAACG------------FRWNs~VRkqY~~~i~~AKkqRk~~~~~~~~ 79 (161)
T TIGR02894 17 ETVLRHIREGSTQLSAFEEVGRALNR-----TAAACG------------FRWNAYVRKQYEEAIELAKKQRKELKREAGS 79 (161)
T ss_pred HHHHHHHhcchHHHHHHHHHHHHHcc-----cHHHhc------------chHHHHHHHHHHHHHHHHHHHHhccccCccc
Confidence 567765 6777777766643 355566 667544333322 235566765554
No 80
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=23.70 E-value=91 Score=19.53 Aligned_cols=23 Identities=26% Similarity=0.255 Sum_probs=20.3
Q ss_pred ccchhhHHHHHhhcCccHHHHHH
Q 030888 113 NLQVSQKQEAAKQCNCTIAEVEN 135 (170)
Q Consensus 113 ~l~asqk~~aAk~CnCTiadVE~ 135 (170)
.+...+..+.|+.||++..+|.+
T Consensus 24 ~p~~~~~~~la~~l~l~~~~V~~ 46 (57)
T PF00046_consen 24 YPSKEEREELAKELGLTERQVKN 46 (57)
T ss_dssp SCHHHHHHHHHHHHTSSHHHHHH
T ss_pred ccccccccccccccccccccccc
Confidence 46688999999999999999975
No 81
>PF12345 DUF3641: Protein of unknown function (DUF3641) ; InterPro: IPR024521 This domain is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. It is found in association with an N-terminal radical_SAM domain (Pfam:PF04055 from PFAM).
Probab=23.59 E-value=20 Score=29.08 Aligned_cols=25 Identities=28% Similarity=0.458 Sum_probs=15.2
Q ss_pred HHHHhccCCCCcccchhhHHHHHhhc-CccHH
Q 030888 101 LRCLGAFDPNGENLQVSQKQEAAKQC-NCTIA 131 (170)
Q Consensus 101 iR~L~~~DptGE~l~asqk~~aAk~C-nCTia 131 (170)
|+.|..-|..| +.+.+|.|| +||.+
T Consensus 101 i~dl~~~~l~~------~~I~~~~HCygCTAG 126 (134)
T PF12345_consen 101 ISDLLEEDLEG------RPIATADHCYGCTAG 126 (134)
T ss_pred HHHHhhcccCC------CceeecCcCccccCC
Confidence 34444444443 566678898 78764
No 82
>PRK15392 putative fumarate hydratase; Provisional
Probab=23.50 E-value=67 Score=31.32 Aligned_cols=39 Identities=28% Similarity=0.447 Sum_probs=30.2
Q ss_pred CccHHHHHHHHHHh-------------HhHHHHHHHHHHHHhcCCCCCCccc
Q 030888 127 NCTIAEVENTLAKF-------------TWAKEAQKKIEKLKEEGKPMPKSMA 165 (170)
Q Consensus 127 nCTiadVE~~LAKf-------------tWaKeA~kKi~KLkeEGKPlPks~~ 165 (170)
+-.+.||+.-|+++ +=--.||+||.++-++|+|||-.|.
T Consensus 363 ~~Pl~~~~~~l~~l~vGd~v~LsG~i~taRD~AH~rl~e~l~~Ge~lP~dlk 414 (550)
T PRK15392 363 NRPLRDVMQDLARLPVGTRVSLSGPIVVARDIAHAKIKARLDSGEPMPEYLK 414 (550)
T ss_pred cCCCChhHHHHhcCCCCCEEEEEEEEEEEhHHHHHHHHHHHhcCCCCCcCcC
Confidence 44466766777775 4456899999999999999997764
No 83
>KOG2580 consensus Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.69 E-value=30 Score=33.10 Aligned_cols=55 Identities=29% Similarity=0.330 Sum_probs=37.4
Q ss_pred hhhhcccccCCCCCCCCCC-------CCccchHHHHHHHHHHhHHhccccchhccc-------cchhhHH
Q 030888 36 DSIKGVFTGKKSSSEDGSV-------SSESFTLLRFADELKKARKLGTLKQYIVGR-------SSATTFA 91 (170)
Q Consensus 36 dkiKgvftG~K~~~~~~~~-------~~~~ftL~~FADelkkARr~Gsfk~fv~Gr-------sseat~~ 91 (170)
|||-+|+-|-=+.+|.+.. .| +|+++.|+.++...-.---+--||.|- |||++|+
T Consensus 286 dki~~~~~g~fsktE~Sev~tei~~iDP-sF~~~~Flr~~ee~IiPnVLeAyvkGD~evLK~wcsea~~~ 354 (459)
T KOG2580|consen 286 DKITDVDGGLFSKTEMSEVLTEIKKIDP-SFDKEDFLRECEEYIIPNVLEAYVKGDLEVLKKWCSEAPFS 354 (459)
T ss_pred HhhhhcccccchhhHHHHHHHHHHhcCC-CCCcHHHHHHHHHhhhHHHHHHHHhccHHHHHHHHhhhHHH
Confidence 4555555554444333322 23 599999999999998888888889883 6676653
No 84
>PRK13533 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional
Probab=22.59 E-value=1.2e+02 Score=28.52 Aligned_cols=51 Identities=22% Similarity=0.316 Sum_probs=39.1
Q ss_pred HHHHHHHHHHhHHhccccchhccccc-hhhHHHHHHHHHHHHHHHhccCCCC
Q 030888 61 LLRFADELKKARKLGTLKQYIVGRSS-ATTFADTFEKQEAVLRCLGAFDPNG 111 (170)
Q Consensus 61 L~~FADelkkARr~Gsfk~fv~Grss-eat~~~afeK~EaiiR~L~~~DptG 111 (170)
+.++-.+++.|-+-|+|.+||-+||- ...+.+++.....=-.||-.+||..
T Consensus 308 ~~~~m~~iR~aI~~g~l~e~ve~r~r~hP~l~~~~r~l~~~~~~le~~~P~~ 359 (487)
T PRK13533 308 TFEEIRRIKQAIKEGRLWELVEERARSHPSLLDAFRRLLKYSDYLEKYDPRS 359 (487)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHhhcCHHHHHHHHHHHHhHHHHHhcCCcc
Confidence 44677778888899999999999763 4466777777655557889999884
No 85
>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This entry includes outer membrane proteins such as OmpH (Skp) among others. OmpH (outer membrane protein H) is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin []. Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates []. The 17kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A [, ]. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins [].; GO: 0051082 unfolded protein binding; PDB: 1SG2_C 1U2M_C.
Probab=22.12 E-value=1e+02 Score=23.09 Aligned_cols=30 Identities=17% Similarity=0.252 Sum_probs=22.7
Q ss_pred cCccHHHHHHHHHHhHhHHHHHHHHHHHHh
Q 030888 126 CNCTIAEVENTLAKFTWAKEAQKKIEKLKE 155 (170)
Q Consensus 126 CnCTiadVE~~LAKftWaKeA~kKi~KLke 155 (170)
++--+-|++.++..|.+.++++++++++.+
T Consensus 17 ~kIa~Vd~~~v~~~~~~~k~~~~~l~~~~~ 46 (158)
T PF03938_consen 17 PKIAVVDVDKVFQESPAGKDAQAKLQEKFK 46 (158)
T ss_dssp -CEEEE-HHHHHHHHHHHHTHHHHHHHHHH
T ss_pred CcEEEeeHHHHHHhCHHHHHHHHHHHHHHH
Confidence 445566999999999999999988776644
No 86
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=22.09 E-value=2.1e+02 Score=20.88 Aligned_cols=55 Identities=11% Similarity=0.119 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHhccCCCCcccchhhHHHHHhhcCccHHHHHHHHHH--hHhHHHHHHHHHHHHh
Q 030888 93 TFEKQEAVLRCLGAFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAK--FTWAKEAQKKIEKLKE 155 (170)
Q Consensus 93 afeK~EaiiR~L~~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAK--ftWaKeA~kKi~KLke 155 (170)
..+++++|+.+|.. ... -=+++|+..|.+..-|-.+|.. -.=..+...+|.+.-+
T Consensus 4 ~~~R~~~I~e~l~~-~~~-------ti~dvA~~~gvS~~TVsr~L~~~~~~Vs~~Tr~rV~~aa~ 60 (80)
T TIGR02844 4 IEERVLEIGKYIVE-TKA-------TVRETAKVFGVSKSTVHKDVTERLPEINPELAEEVKEVLD 60 (80)
T ss_pred HHHHHHHHHHHHHH-CCC-------CHHHHHHHhCCCHHHHHHHhcCCCCCCCHHHHHHHHHHHc
Confidence 35789999999998 533 3567999999999999999975 2345566666766655
No 87
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=21.98 E-value=2.3e+02 Score=20.36 Aligned_cols=23 Identities=9% Similarity=0.040 Sum_probs=15.6
Q ss_pred hHHHHHhhcCccHHHHHHHHHHh
Q 030888 118 QKQEAAKQCNCTIAEVENTLAKF 140 (170)
Q Consensus 118 qk~~aAk~CnCTiadVE~~LAKf 140 (170)
+.+..++.+|.++.|+...|.-+
T Consensus 46 ~~I~~lr~~G~sL~eI~~~l~~~ 68 (107)
T cd04777 46 EFILELKGLGFSLIEIQKIFSYK 68 (107)
T ss_pred HHHHHHHHCCCCHHHHHHHHHhc
Confidence 34556677778888877777643
No 88
>PRK00118 putative DNA-binding protein; Validated
Probab=21.87 E-value=1.9e+02 Score=22.09 Aligned_cols=40 Identities=28% Similarity=0.264 Sum_probs=23.7
Q ss_pred HHHHHHhccCCCCcccchhhH-------------HHHHhhcCccHHHHHHHHH
Q 030888 99 AVLRCLGAFDPNGENLQVSQK-------------QEAAKQCNCTIAEVENTLA 138 (170)
Q Consensus 99 aiiR~L~~~DptGE~l~asqk-------------~~aAk~CnCTiadVE~~LA 138 (170)
.+.|++..||--|..|+..|+ .++|+..|++..-|...|.
T Consensus 3 ~~~~~~~l~d~~~~~L~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~ 55 (104)
T PRK00118 3 KTLRMNLLFDFYGSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIK 55 (104)
T ss_pred HHHHHHHHHHHHhccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344555555555555555444 4678888888777755544
No 89
>PF03223 V-ATPase_C: V-ATPase subunit C; InterPro: IPR004907 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents the C subunit that is part of the V1 complex, and is localised to the interface between the V1 and V0 complexes []. This subunit does not show any homology with F-ATPase subunits. The C subunit plays an essential role in controlling the assembly of V-ATPase, acting as a flexible stator that holds together the catalytic (V1) and membrane (V0) sectors of the enzyme []. The release of subunit C from the ATPase complex results in the dissociation of the V1 and V0 subcomplexes, which is an important mechanism in controlling V-ATPase activity in cells. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0033180 proton-transporting V-type ATPase, V1 domain; PDB: 1U7L_A.
Probab=21.85 E-value=1.9e+02 Score=26.41 Aligned_cols=45 Identities=31% Similarity=0.361 Sum_probs=21.6
Q ss_pred hhhHHHHHHHHHHHHHHHh--ccCCCCcccchhhHHHHHhhcCccHHHHHHHHHHhHhH
Q 030888 87 ATTFADTFEKQEAVLRCLG--AFDPNGENLQVSQKQEAAKQCNCTIAEVENTLAKFTWA 143 (170)
Q Consensus 87 eat~~~afeK~EaiiR~L~--~~DptGE~l~asqk~~aAk~CnCTiadVE~~LAKftWa 143 (170)
++.+...+.|.+.+++.|- .-+..++++...++ .+++-|.+|.|.
T Consensus 60 D~~~e~~~~Ki~~~~~~l~~~~~~~~~~~l~v~~~------------~~~~yl~~F~Wd 106 (371)
T PF03223_consen 60 DSFVESVVRKIERQLRDLLEGDKDKLQENLLVNGV------------SLEQYLTRFQWD 106 (371)
T ss_dssp HHHHHHHHHHHHHHHHHT-TSS-SSS--S--BTTB-------------HHHHHHT----
T ss_pred HHHHHHHHHHHHHHHHHHhhccccceeeEEEECCC------------cHHHHHHHheeh
Confidence 5666777888888888772 22333444444332 556666777773
No 90
>PRK10241 hydroxyacylglutathione hydrolase; Provisional
Probab=21.80 E-value=1.2e+02 Score=25.09 Aligned_cols=37 Identities=14% Similarity=0.280 Sum_probs=23.8
Q ss_pred cHHHHHHHHH---HhHhHHHHHHHHHHHHhcCCC-CCCccc
Q 030888 129 TIAEVENTLA---KFTWAKEAQKKIEKLKEEGKP-MPKSMA 165 (170)
Q Consensus 129 TiadVE~~LA---KftWaKeA~kKi~KLkeEGKP-lPks~~ 165 (170)
|...+.-+++ +-...++...++++|+++|+| +|.|++
T Consensus 168 ~~~n~~fa~~~~p~n~~l~~~~~~~~~~~~~~~~t~pstl~ 208 (251)
T PRK10241 168 TLSNMKFALSILPHDLSINDYYRKVKELRAKNQITLPVILK 208 (251)
T ss_pred hhhhHHHHHHhCCCCHHHHHHHHHHHHHHHCCCCcCCccHH
Confidence 4444444443 444566677788899999998 455654
No 91
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=21.80 E-value=1.7e+02 Score=27.67 Aligned_cols=35 Identities=26% Similarity=0.309 Sum_probs=26.5
Q ss_pred HhccCCCCcccchhhHHHHHhh----cCccHHHHHHHHHHh
Q 030888 104 LGAFDPNGENLQVSQKQEAAKQ----CNCTIAEVENTLAKF 140 (170)
Q Consensus 104 L~~~DptGE~l~asqk~~aAk~----CnCTiadVE~~LAKf 140 (170)
.+.+|+.| -|.. .-.+.|.. ++|+..+||.+|...
T Consensus 150 I~~LD~~G-yL~~-~~~eia~~~~~~l~~~~~~ve~vL~~i 188 (481)
T PRK12469 150 IDALDDDG-YLRQ-DLSELAEAADPELGLSEQELEVALRLV 188 (481)
T ss_pred HhhCCCCC-CCCC-CHHHHHhccccccCCCHHHHHHHHHHH
Confidence 46789999 5554 34567777 999999999988753
No 92
>PRK08181 transposase; Validated
Probab=21.70 E-value=4e+02 Score=22.85 Aligned_cols=49 Identities=24% Similarity=0.329 Sum_probs=38.6
Q ss_pred HHHhhcCccHHHHHHHHHHhHhHHHHHHHHHHHHhc-CCCCCCccccccc
Q 030888 121 EAAKQCNCTIAEVENTLAKFTWAKEAQKKIEKLKEE-GKPMPKSMAEVQF 169 (170)
Q Consensus 121 ~aAk~CnCTiadVE~~LAKftWaKeA~kKi~KLkeE-GKPlPks~~Evq~ 169 (170)
+-|..=+-+..|.=..|-...|+...+++++.+-+. |=|.+++|++..|
T Consensus 33 ~~a~~~~~~~~e~L~~ll~~E~~~R~~~~~~r~lk~A~~p~~~tle~fd~ 82 (269)
T PRK08181 33 EQADKEGWPAARFLAAIAEHELAERARRRIERHLAEAHLPPGKTLDSFDF 82 (269)
T ss_pred HHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHhhCCc
Confidence 445556677888888888999999999999876554 5599999998765
No 93
>PF03007 WES_acyltransf: Wax ester synthase-like Acyl-CoA acyltransferase domain; InterPro: IPR004255 This entry represents the N terminus (approximately 170 residues) of a number of hypothetical plant proteins. O-acyltransferase WSD1 is a bifunctional wax ester synthase/diacylglycerol acyltransferase, which is involved in cuticular wax biosynthesis [].; GO: 0004144 diacylglycerol O-acyltransferase activity
Probab=21.65 E-value=56 Score=27.07 Aligned_cols=20 Identities=25% Similarity=0.371 Sum_probs=16.4
Q ss_pred cchhhHHHHHhhcCccHHHH
Q 030888 114 LQVSQKQEAAKQCNCTIAEV 133 (170)
Q Consensus 114 l~asqk~~aAk~CnCTiadV 133 (170)
+.-.+-..+++.+||||-||
T Consensus 243 ~~l~~vk~i~~~~g~TvNDV 262 (263)
T PF03007_consen 243 LPLDDVKAIAKALGATVNDV 262 (263)
T ss_pred ecHHHHHHHHHHhCCChhhc
Confidence 34456788999999999998
No 94
>KOG4202 consensus Phosphoribosylanthranilate isomerase [Amino acid transport and metabolism]
Probab=21.55 E-value=42 Score=29.40 Aligned_cols=23 Identities=26% Similarity=0.472 Sum_probs=20.2
Q ss_pred hhccccccccccchhhhhhhcccccCCCC
Q 030888 20 QYRSIFTTRTLQGSWMDSIKGVFTGKKSS 48 (170)
Q Consensus 20 ~~r~I~sT~~l~~sW~dkiKgvftG~K~~ 48 (170)
+||+|++||+- ++-|||.-|+.+
T Consensus 83 ~y~n~s~sp~~------~lVGVF~nqp~e 105 (227)
T KOG4202|consen 83 SYRNISLSPAK------KLVGVFVNQPEE 105 (227)
T ss_pred hhccccCCcch------heEEEeecCCHH
Confidence 89999999997 679999988764
No 95
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=21.33 E-value=37 Score=23.12 Aligned_cols=15 Identities=33% Similarity=0.804 Sum_probs=13.7
Q ss_pred hhhhhhcccccCCCC
Q 030888 34 WMDSIKGVFTGKKSS 48 (170)
Q Consensus 34 W~dkiKgvftG~K~~ 48 (170)
|+|||=.++.|.-++
T Consensus 1 W~Dki~d~L~G~d~~ 15 (54)
T PF10058_consen 1 WFDKILDVLLGDDPT 15 (54)
T ss_pred ChHHHHHHHhCCCCc
Confidence 999999999998883
No 96
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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, an
Probab=20.73 E-value=2.5e+02 Score=20.75 Aligned_cols=37 Identities=11% Similarity=0.116 Sum_probs=19.9
Q ss_pred HHHHHhhcCccHHHHHHHHHHh----HhHHHHHHHHHHHHh
Q 030888 119 KQEAAKQCNCTIAEVENTLAKF----TWAKEAQKKIEKLKE 155 (170)
Q Consensus 119 k~~aAk~CnCTiadVE~~LAKf----tWaKeA~kKi~KLke 155 (170)
.+...+.+|.++.|+.+.+... .|..-...+++.|++
T Consensus 48 ~I~~lr~~G~~L~eI~~~l~~~~~~~~~~~~l~~~~~~l~~ 88 (120)
T cd04781 48 LIALGRAAGFSLDEIQAMLSHDGKPPIDRQLLKAKAAELDQ 88 (120)
T ss_pred HHHHHHHcCCCHHHHHHHHhccCCcHHHHHHHHHHHHHHHH
Confidence 4455666677777776666542 244444444444443
No 97
>TIGR02574 stabl_TIGR02574 putative addiction module component, TIGR02574 family. Members of this family are bacterial proteins, typically are about 75 amino acids long, always found as part of a pair (at least) of two small genes. The other in the pair always belongs to a subfamily of the larger family pfam05016 (although not necessarily scoring above the designated cutoff), which contains plasmid stabilization proteins. It is likely that this protein and its pfam05016 member partner comprise some form of addiction module, although these gene pairs usually are found on the bacterial main chromosome.
Probab=20.58 E-value=1e+02 Score=20.93 Aligned_cols=26 Identities=15% Similarity=0.227 Sum_probs=20.2
Q ss_pred HhHHHHHHHHHHHHhcCCCCCCccccc
Q 030888 141 TWAKEAQKKIEKLKEEGKPMPKSMAEV 167 (170)
Q Consensus 141 tWaKeA~kKi~KLkeEGKPlPks~~Ev 167 (170)
.|..|++++++.++ .|+.-+-+.+||
T Consensus 31 ~~~~el~~R~~~~~-~g~~~~i~~eev 56 (63)
T TIGR02574 31 AQKAELDRRLADYK-ADPSKASPWEEV 56 (63)
T ss_pred HHHHHHHHHHHHHH-cCCcCCCCHHHH
Confidence 58888999998885 577777777776
No 98
>PF09702 Cas_Csa5: CRISPR-associated protein (Cas_Csa5); InterPro: IPR010157 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a minor family of Cas protein found in various species of Sulfolobus and Pyrococcus (all archaeal). It is found with two different CRISPR loci in Sulfolobus solfataricus.
Probab=20.42 E-value=78 Score=25.01 Aligned_cols=26 Identities=27% Similarity=0.345 Sum_probs=21.9
Q ss_pred CCCCCccchHHHHHHHHH----HhHHhccc
Q 030888 52 GSVSSESFTLLRFADELK----KARKLGTL 77 (170)
Q Consensus 52 ~~~~~~~ftL~~FADelk----kARr~Gsf 77 (170)
-|..|++-..+.|-+..+ -|||+|+|
T Consensus 69 ~g~lPt~~eVe~Fl~~v~~di~~Arkvgal 98 (105)
T PF09702_consen 69 VGYLPTDEEVEDFLDDVERDIYYARKVGAL 98 (105)
T ss_pred cCCCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456889999999998765 59999987
Done!