Query 035839
Match_columns 238
No_of_seqs 151 out of 324
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 06:54:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035839.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035839hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1816 Ubiquitin fusion-degra 100.0 4.4E-89 9.6E-94 615.9 21.1 219 12-238 13-238 (308)
2 PF03152 UFD1: Ubiquitin fusio 100.0 2.6E-75 5.7E-80 498.7 19.3 173 12-185 1-176 (176)
3 COG5140 UFD1 Ubiquitin fusion- 100.0 9.6E-68 2.1E-72 470.3 18.5 189 5-194 14-208 (331)
4 PLN03086 PRLI-interacting fact 100.0 3.6E-60 7.8E-65 462.3 22.5 159 31-190 89-263 (567)
5 PF02933 CDC48_2: Cell divisio 96.7 0.0091 2E-07 42.8 7.2 46 135-181 12-58 (64)
6 KOG0735 AAA+-type ATPase [Post 96.3 0.061 1.3E-06 55.9 12.8 147 35-185 16-167 (952)
7 TIGR01243 CDC48 AAA family ATP 95.9 0.21 4.5E-06 51.2 14.5 134 32-173 15-151 (733)
8 PF09262 PEX-1N: Peroxisome bi 93.6 0.079 1.7E-06 40.4 3.3 75 110-184 1-80 (80)
9 TIGR01439 lp_hng_hel_AbrB loop 86.4 3 6.4E-05 26.7 5.5 39 77-118 4-42 (43)
10 PF04014 Antitoxin-MazE: Antid 86.4 3.4 7.3E-05 27.7 5.9 39 78-119 5-43 (47)
11 PF02359 CDC48_N: Cell divisio 82.0 19 0.00041 27.0 9.3 68 32-105 14-84 (87)
12 PF07497 Rho_RNA_bind: Rho ter 80.6 1.1 2.5E-05 34.1 1.9 27 79-105 28-54 (78)
13 PF02359 CDC48_N: Cell divisio 78.5 1.7 3.6E-05 32.8 2.2 69 78-152 14-82 (87)
14 TIGR02609 doc_partner putative 78.5 5.6 0.00012 29.4 5.0 55 80-141 10-66 (74)
15 cd04459 Rho_CSD Rho_CSD: Rho p 77.5 2.5 5.4E-05 31.3 2.8 29 77-105 24-52 (68)
16 PRK09521 exosome complex RNA-b 75.9 8.8 0.00019 32.9 6.2 125 33-164 4-142 (189)
17 PRK14132 riboflavin kinase; Pr 74.9 3 6.6E-05 34.5 3.0 31 66-103 94-125 (126)
18 smart00553 SEP Domain present 74.1 1.4 2.9E-05 34.6 0.7 14 224-237 72-85 (93)
19 PRK09974 putative regulator Pr 72.6 12 0.00026 30.4 5.8 61 77-140 15-76 (111)
20 COG1935 Uncharacterized conser 70.8 7.5 0.00016 32.0 4.3 47 40-112 11-60 (122)
21 cd02787 MopB_CT_ydeP The MopB_ 68.7 8.5 0.00018 29.7 4.1 29 78-106 29-57 (112)
22 cd02786 MopB_CT_3 The MopB_CT_ 68.7 6.7 0.00015 30.2 3.5 29 78-106 29-57 (116)
23 PRK09798 antitoxin MazE; Provi 68.1 13 0.00027 28.4 4.8 50 81-141 14-63 (82)
24 PF01982 CTP-dep_RFKase: Domai 65.8 7.7 0.00017 31.9 3.4 18 86-103 103-120 (121)
25 PRK11347 antitoxin ChpS; Provi 64.7 18 0.0004 27.5 5.1 48 81-141 13-60 (83)
26 cd02776 MopB_CT_Nitrate-R-NarG 64.2 12 0.00026 30.8 4.3 33 73-105 24-56 (141)
27 COG2002 AbrB Regulators of sta 63.3 13 0.00028 28.3 4.0 42 77-120 11-52 (89)
28 PF13550 Phage-tail_3: Putativ 62.7 9.4 0.0002 30.7 3.4 27 140-166 137-163 (164)
29 cd02790 MopB_CT_Formate-Dh_H F 61.8 11 0.00024 28.7 3.5 29 77-105 32-60 (116)
30 cd02788 MopB_CT_NDH-1_NuoG2-N7 61.6 13 0.00028 28.2 3.8 33 73-105 22-54 (96)
31 cd02789 MopB_CT_FmdC-FwdD The 59.4 9.7 0.00021 29.6 2.8 29 77-105 28-56 (106)
32 cd00508 MopB_CT_Fdh-Nap-like T 59.3 14 0.0003 28.2 3.7 27 78-104 33-59 (120)
33 COG1339 Transcriptional regula 58.8 11 0.00023 33.8 3.3 19 86-104 194-212 (214)
34 cd02785 MopB_CT_4 The MopB_CT_ 57.8 15 0.00033 28.8 3.7 28 78-105 30-57 (124)
35 PRK08577 hypothetical protein; 57.5 15 0.00032 29.8 3.7 44 77-122 10-53 (136)
36 cd02792 MopB_CT_Formate-Dh-Na- 56.9 15 0.00032 28.4 3.5 28 77-104 32-59 (122)
37 cd02775 MopB_CT Molybdopterin- 56.3 16 0.00034 26.9 3.4 28 78-105 21-48 (101)
38 KOG2086 Protein tyrosine phosp 56.1 5 0.00011 38.9 0.8 16 222-237 252-267 (380)
39 TIGR02851 spore_V_T stage V sp 56.1 20 0.00043 31.0 4.5 46 71-119 4-49 (180)
40 cd02777 MopB_CT_DMSOR-like The 55.4 15 0.00033 28.8 3.4 26 79-104 33-58 (127)
41 cd02781 MopB_CT_Acetylene-hydr 55.4 15 0.00033 28.7 3.4 29 78-106 31-59 (130)
42 COG1188 Ribosome-associated he 54.9 19 0.00042 28.8 3.8 26 141-166 47-72 (100)
43 COG1153 FwdD Formylmethanofura 54.9 11 0.00023 31.3 2.5 28 77-104 28-55 (128)
44 cd02791 MopB_CT_Nitrate-R-NapA 54.8 17 0.00038 27.9 3.6 28 78-105 33-60 (122)
45 COG2336 MazE Growth regulator 54.0 15 0.00031 28.5 2.9 35 81-118 13-47 (82)
46 PF01568 Molydop_binding: Moly 53.9 17 0.00037 27.4 3.4 27 78-104 27-54 (110)
47 COG0243 BisC Anaerobic dehydro 53.6 21 0.00046 36.7 4.9 52 52-105 639-696 (765)
48 PF01191 RNA_pol_Rpb5_C: RNA p 52.0 30 0.00066 26.1 4.3 31 86-116 41-71 (74)
49 cd02779 MopB_CT_Arsenite-Ox Th 52.0 22 0.00047 27.6 3.8 29 77-105 30-58 (115)
50 PRK14165 winged helix-turn-hel 51.6 13 0.00029 33.2 2.8 39 66-104 158-215 (217)
51 cd02778 MopB_CT_Thiosulfate-R- 51.4 22 0.00048 27.5 3.7 29 77-105 27-55 (123)
52 cd02782 MopB_CT_1 The MopB_CT_ 51.2 20 0.00043 28.1 3.5 29 77-105 30-58 (129)
53 cd06166 Sortase_D_5 Sortase D 50.9 26 0.00057 27.9 4.2 30 137-166 59-88 (126)
54 cd02794 MopB_CT_DmsA-EC The Mo 50.0 22 0.00047 27.8 3.5 27 79-105 29-55 (121)
55 TIGR03243 arg_catab_AOST argin 49.8 22 0.00047 34.0 4.0 34 70-103 300-333 (335)
56 cd05829 Sortase_E Sortase E (S 48.7 26 0.00057 28.8 3.9 26 140-165 70-96 (144)
57 PF04322 DUF473: Protein of un 48.3 23 0.00049 29.1 3.4 47 39-111 10-59 (119)
58 PRK10737 FKBP-type peptidyl-pr 48.1 60 0.0013 28.7 6.2 16 172-187 111-126 (196)
59 PRK09570 rpoH DNA-directed RNA 47.6 26 0.00056 26.8 3.4 30 87-116 45-74 (79)
60 PRK15095 FKBP-type peptidyl-pr 47.6 77 0.0017 26.6 6.7 92 72-186 34-129 (156)
61 cd02793 MopB_CT_DMSOR-BSOR-TMA 47.5 25 0.00054 27.9 3.5 29 77-105 30-58 (129)
62 cd02783 MopB_CT_2 The MopB_CT_ 47.5 24 0.00052 29.2 3.6 32 77-111 29-60 (156)
63 PF03459 TOBE: TOBE domain; I 45.8 28 0.0006 23.9 3.1 23 82-104 35-57 (64)
64 cd02780 MopB_CT_Tetrathionate_ 43.7 34 0.00073 27.6 3.8 28 77-104 27-54 (143)
65 PF10636 hemP: Hemin uptake pr 43.3 55 0.0012 21.8 4.0 22 143-164 9-30 (38)
66 TIGR03244 arg_catab_AstA argin 41.9 35 0.00075 32.7 4.0 46 57-103 289-334 (336)
67 PRK10456 arginine succinyltran 41.8 35 0.00075 32.8 4.1 47 57-104 290-336 (344)
68 cd05828 Sortase_D_4 Sortase D 41.5 48 0.001 26.4 4.3 29 138-166 57-85 (127)
69 TIGR03245 arg_AOST_alph argini 40.3 37 0.0008 32.5 4.0 34 70-103 300-334 (336)
70 cd05830 Sortase_D_5 Sortase D 40.1 47 0.001 26.9 4.1 30 137-166 60-89 (137)
71 PRK08059 general stress protei 39.4 1.6E+02 0.0034 23.5 7.0 59 88-152 1-61 (123)
72 TIGR01076 sortase_fam LPXTG-si 38.1 49 0.0011 26.7 3.9 24 142-165 63-86 (136)
73 cd06165 Sortase_A_1 Sortase A 36.6 58 0.0013 25.8 4.1 24 143-166 64-87 (127)
74 cd00004 Sortase Sortases are c 36.1 62 0.0013 25.5 4.1 25 142-166 64-88 (128)
75 PF11717 Tudor-knot: RNA bindi 35.6 67 0.0014 22.2 3.7 28 143-170 1-29 (55)
76 PRK10183 hypothetical protein; 35.2 54 0.0012 23.7 3.2 22 143-164 27-48 (56)
77 cd02784 MopB_CT_PHLH The MopB_ 34.3 57 0.0012 26.9 3.7 27 79-105 37-63 (137)
78 PF04958 AstA: Arginine N-succ 33.4 54 0.0012 31.5 3.9 48 55-103 292-340 (342)
79 cd05705 S1_Rrp5_repeat_hs14 S1 33.0 44 0.00095 24.3 2.6 65 94-168 1-67 (74)
80 cd05706 S1_Rrp5_repeat_sc10 S1 32.5 97 0.0021 21.6 4.3 56 94-152 1-57 (73)
81 PF01272 GreA_GreB: Transcript 32.4 80 0.0017 23.0 3.9 24 143-166 53-76 (77)
82 PF09263 PEX-2N: Peroxisome bi 32.2 2.2E+02 0.0047 22.3 6.3 67 36-105 16-85 (87)
83 TIGR02620 cas_VVA1548 putative 31.7 30 0.00066 27.3 1.6 29 24-52 26-56 (93)
84 PF13473 Cupredoxin_1: Cupredo 29.3 80 0.0017 24.0 3.6 48 52-113 42-89 (104)
85 PRK07252 hypothetical protein; 29.2 1.5E+02 0.0031 23.9 5.2 54 95-152 2-57 (120)
86 PF04203 Sortase: Sortase fami 29.1 1E+02 0.0023 23.9 4.4 23 144-166 62-85 (128)
87 cd05704 S1_Rrp5_repeat_hs13 S1 29.0 92 0.002 22.2 3.7 56 94-153 1-59 (72)
88 PRK05807 hypothetical protein; 28.7 1.9E+02 0.0042 23.6 6.0 55 93-152 2-58 (136)
89 PLN03086 PRLI-interacting fact 27.8 5.2E+02 0.011 26.6 10.0 72 32-105 149-227 (567)
90 PF12148 DUF3590: Protein of u 27.6 40 0.00086 26.2 1.6 44 102-155 35-78 (85)
91 cd05827 Sortase_C_3 Sortase C 27.4 1.1E+02 0.0024 24.4 4.3 24 143-166 67-90 (131)
92 PF12945 YcgR_2: Flagellar pro 27.1 1.9E+02 0.0042 20.6 5.2 56 51-106 3-60 (87)
93 COG0836 {ManC} Mannose-1-phosp 27.0 1.6E+02 0.0034 28.3 5.8 57 98-155 245-302 (333)
94 PF11302 DUF3104: Protein of u 26.8 1.9E+02 0.0041 22.0 5.1 48 140-187 3-75 (75)
95 smart00675 DM11 Domains in hyp 26.3 1E+02 0.0023 26.4 4.1 78 75-152 37-128 (164)
96 PRK09376 rho transcription ter 26.1 1.1E+02 0.0024 30.2 4.7 39 66-104 48-101 (416)
97 PRK13532 nitrate reductase cat 25.9 66 0.0014 33.7 3.4 51 52-105 713-771 (830)
98 PRK10348 ribosome-associated h 25.4 1.1E+02 0.0024 25.5 4.0 25 142-166 48-72 (133)
99 TIGR00638 Mop molybdenum-pteri 25.3 1.2E+02 0.0025 20.9 3.6 23 82-104 37-59 (69)
100 PTZ00061 DNA-directed RNA poly 24.0 91 0.002 27.9 3.4 31 86-116 172-202 (205)
101 KOG0741 AAA+-type ATPase [Post 24.0 4E+02 0.0087 27.9 8.3 88 78-166 58-156 (744)
102 smart00333 TUDOR Tudor domain. 23.6 2.3E+02 0.0049 18.7 5.2 30 142-171 2-32 (57)
103 PF00667 FAD_binding_1: FAD bi 22.7 1.5E+02 0.0033 25.6 4.6 87 52-141 6-121 (219)
104 PRK06247 pyruvate kinase; Prov 22.1 2.4E+02 0.0053 28.2 6.3 38 140-179 115-152 (476)
105 PF08922 DUF1905: Domain of un 22.1 3.4E+02 0.0073 20.2 6.5 63 36-104 15-80 (80)
106 cd03701 IF2_IF5B_II IF2_IF5B_I 22.0 1.1E+02 0.0025 23.4 3.3 34 140-173 24-64 (95)
107 COG0187 GyrB Type IIA topoisom 21.9 1.1E+02 0.0023 31.9 3.8 46 108-154 165-210 (635)
108 cd05694 S1_Rrp5_repeat_hs2_sc2 21.7 3.2E+02 0.0069 19.8 8.0 63 94-166 2-72 (74)
109 TIGR03595 Obg_CgtA_exten Obg f 21.4 77 0.0017 23.1 2.1 17 89-105 49-65 (69)
110 PF01176 eIF-1a: Translation i 21.3 79 0.0017 22.6 2.1 24 81-104 29-52 (65)
111 cd04453 S1_RNase_E S1_RNase_E: 21.3 1.7E+02 0.0036 22.0 4.0 58 95-153 6-67 (88)
112 TIGR01553 formate-DH-alph form 20.6 62 0.0014 35.1 2.0 56 51-106 881-939 (1009)
113 TIGR01243 CDC48 AAA family ATP 20.4 1.1E+02 0.0023 31.6 3.6 71 78-153 15-85 (733)
114 PLN03111 DNA-directed RNA poly 20.3 1.2E+02 0.0026 27.2 3.4 31 86-116 173-203 (206)
115 TIGR02693 arsenite_ox_L arseni 20.2 1.5E+02 0.0032 31.3 4.6 29 77-105 722-750 (806)
No 1
>KOG1816 consensus Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.4e-89 Score=615.93 Aligned_cols=219 Identities=50% Similarity=0.886 Sum_probs=198.5
Q ss_pred cceeeEEEeeeecccCC---CCCCCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEeCCCcEeccHhH
Q 035839 12 CFEKHYHCYSLSHVAKP---QHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWM 88 (238)
Q Consensus 12 ~f~~~~~~y~~s~~~~~---~~~~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~i~lP~Wm 88 (238)
.|+++|||||++|+..+ ++++|||||||||||++|+++||.|||+|+|+|.+..|+||||||||+||||.||||+||
T Consensus 13 ~f~~~yrcy~~~~l~~~~~s~~~~GgKIilPPSaL~~Ls~lnI~yPMlFkLtn~~~~r~THcGVLEF~AeEG~vyLP~WM 92 (308)
T KOG1816|consen 13 QFETSYRCYPVSFLPGPDRSDVNKGGKIILPPSALDRLSSLNITYPMLFKLTNVDVDRVTHCGVLEFTAEEGRVYLPYWM 92 (308)
T ss_pred ceeeeeEecccccccCccccccccCCeEEeCHHHHHHHHHhcCCCceEEEEeccccceeeeeeEEEEEecCceEEeehHh
Confidence 39999999999999655 999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECCEEEEEEEEEecCC
Q 035839 89 MDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPS 168 (238)
Q Consensus 89 m~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~kP~ 168 (238)
|++|+|++||+|+|++++||+|||||||||+.+|+| |+|||||||++||||+|||+||+|.|+||++.|+|+|+|+||+
T Consensus 93 mq~L~le~gdlv~i~~v~lpkgtyvKLqP~s~dFLD-ItNpKAvLE~~LRn~acLT~gDvi~i~Yn~k~y~i~V~e~kPa 171 (308)
T KOG1816|consen 93 MQNLLLEEGDLVRIRSVTLPKGTYVKLQPHSVDFLD-ITNPKAVLENALRNYACLTTGDVILINYNEKTYELKVVETKPA 171 (308)
T ss_pred hhhccCCCCCeEEEEEeeccccceeeeccCCCCccc-cCChHHHHHHHHhhccccccCCEEEEecCCeEEEEEEEEecCC
Confidence 999999999999999999999999999999999999 9999999999999999999999999999999999999999999
Q ss_pred CceEEEeCceEEEecCCCCCCCCchhhhcccCCCCCcchhhcccCchhh----hhhcCCcccceeeeceecCCC
Q 035839 169 NAVSITETDCEVDFAPPLDYKEPDEKLVKRKVPFPSQVEEQSKQQPQAV----KEEANNKFKAFTGKGKLLGFK 238 (238)
Q Consensus 169 ~aVsIidTDl~VDf~ppl~y~e~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~f~~F~G~G~rldgk 238 (238)
+|||||||||+|||+||+||+||+++.+..... +..++..+. ...-+++|.+|+|+|+|||||
T Consensus 172 ~aVsIiEtD~~VDF~pP~gyke~~~~~~~~~~~-------k~~~~~v~~~ag~~~~~e~~~~~f~gsg~rLdgK 238 (308)
T KOG1816|consen 172 NAVSIIETDLNVDFDPPLGYKEPERQVAPAEKA-------KGEAEVVGSYAGYKNVIENKVEPFTGSGRRLDGK 238 (308)
T ss_pred ceeEEEEcceeecccCCcCccCcccccChhhcc-------cccceeeccccccccccccceeeeccccceeccc
Confidence 999999999999999999999999874321110 011111110 011178999999999999998
No 2
>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified []. This family includes UFD1, a 40kDa protein that is essential for vegetative cell viability []. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1ZC1_A 2YUJ_A.
Probab=100.00 E-value=2.6e-75 Score=498.70 Aligned_cols=173 Identities=57% Similarity=0.975 Sum_probs=149.8
Q ss_pred cceeeEEEeeeecc---cCCCCCCCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEeCCCcEeccHhH
Q 035839 12 CFEKHYHCYSLSHV---AKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWM 88 (238)
Q Consensus 12 ~f~~~~~~y~~s~~---~~~~~~~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~i~lP~Wm 88 (238)
+|+++|||||++|+ +++++++||||+||||||++|++++++|||+|+|+|..++++||||||||+|+||+|+||+||
T Consensus 1 ~f~~~~~~~~~~~~~~~~~~~~~~gdKiiLP~s~L~~L~~~~~~~P~~F~i~n~~~~~~th~GVlEFsA~eG~i~lP~wm 80 (176)
T PF03152_consen 1 KFDQTYRCYPVSFLPGADRPELEYGDKIILPPSALDELSRLNIPYPMLFEISNPDNGKRTHCGVLEFSAEEGTIYLPPWM 80 (176)
T ss_dssp -EEEEEEEEECCCSSTTS-CCCCCTTEEEE-HHHHHHHHHTT--SS-EEEEEETTTTEEEEEEEEEE--CTTEEEE-CHH
T ss_pred CccceEEEEeEEeecCCCCcccCCCCeEEcCHHHHHHHHhccCCCCEEEEEecCCCCcEEEEEEEEeEcCCCeEEeCccH
Confidence 48999999999999 899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECCEEEEEEEEEecCC
Q 035839 89 MDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPS 168 (238)
Q Consensus 89 m~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~kP~ 168 (238)
|++|++++||.|+|++++||||||||||||+.+|++ |+|||+|||++||||+|||+||+|.|+|+++.|+|+|+|+||+
T Consensus 81 m~~L~l~~g~~V~v~~~~LPkgt~vkLqP~~~~F~~-i~n~KavLE~~Lr~ystLT~Gd~I~i~~~~~~y~l~V~e~kP~ 159 (176)
T PF03152_consen 81 MQNLGLQEGDIVRVEYVSLPKGTFVKLQPQSSDFLD-ISNPKAVLERALRNYSTLTKGDTISIEYNNKTYELDVVEVKPE 159 (176)
T ss_dssp HHHHT--TTEEEEEEEEE----SEEEEEESCHHHHC-SS-HHHHHHHHHCC-SEEETTSEEEEECTTEEEEEEEEEECSS
T ss_pred HhhcCCCCCCEEEEEEeECCCCCEEEEeECCCcccc-ccchHHHHHhhcccCceeecCCEEEEEeCCEEEEEEEEEEcCC
Confidence 999999999999999999999999999999999999 9999999999999999999999999999999999999999999
Q ss_pred CceEEEeCceEEEecCC
Q 035839 169 NAVSITETDCEVDFAPP 185 (238)
Q Consensus 169 ~aVsIidTDl~VDf~pp 185 (238)
+|||||||||+|||+||
T Consensus 160 ~aV~IidTDl~vDf~~P 176 (176)
T PF03152_consen 160 NAVSIIDTDLEVDFEPP 176 (176)
T ss_dssp SCEE-SSS-SEEEE---
T ss_pred CEEEEEeCceEEEecCC
Confidence 99999999999999997
No 3
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.6e-68 Score=470.32 Aligned_cols=189 Identities=37% Similarity=0.657 Sum_probs=181.6
Q ss_pred CCCcccccceeeEEEeeeecc---cCCCCCCCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEeCCCc
Q 035839 5 KRDEYYTCFEKHYHCYSLSHV---AKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGF 81 (238)
Q Consensus 5 ~~~~~~~~f~~~~~~y~~s~~---~~~~~~~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~ 81 (238)
+++..++.|.+.|||||.+|+ .|++.++|+|||||||||..|++++|.|||+|+|++.+..+.||||||||+|+||.
T Consensus 14 f~n~~~q~F~e~~rcyp~am~~d~~r~n~NfGGKvilPpSaL~kLs~lni~yPmlF~~s~~~~~~~THgGVLEFiaEEGr 93 (331)
T COG5140 14 FLNDLFQLFGEKPRCYPRAMKFDGCRQNANFGGKVILPPSALVKLSSLNIQYPMLFEISHSDGIYRTHGGVLEFIAEEGR 93 (331)
T ss_pred hhhhhhhhhccCccceeeecccCccccCCCcCceEEcCHHHHHHHHhhccCCceEEEEecccceeEecccEEEEeecCCc
Confidence 456688999999999999997 35778999999999999999999999999999999999999999999999999999
Q ss_pred EeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECCEEEEEE
Q 035839 82 IYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYID 161 (238)
Q Consensus 82 i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~ 161 (238)
||||+|||+.|++++||.|+++|.++|.|+||||+|||.+|++ |+||||+||++||||+|||+||+|.|.||++.|.|+
T Consensus 94 VylP~WMm~tLs~epgdlv~~~~td~plG~fVKL~PqSVdFLd-I~dpkavLEn~LRNfstLt~~D~iei~ynd~v~~Ik 172 (331)
T COG5140 94 VYLPSWMMQTLSMEPGDLVVLRYTDFPLGKFVKLIPQSVDFLD-IEDPKAVLENCLRNFSTLTEGDEIEIQYNDEVGSIK 172 (331)
T ss_pred EeehHHHHHhccCCCCcEEEEEeccccccceEEecccccceEe-ccChHHHHHHHHhhccccccCCEEEEEECCeeeEEE
Confidence 9999999999999999999999999999999999999999999 999999999999999999999999999999999999
Q ss_pred EEEecCC---CceEEEeCceEEEecCCCCCCCCchh
Q 035839 162 VLETKPS---NAVSITETDCEVDFAPPLDYKEPDEK 194 (238)
Q Consensus 162 V~e~kP~---~aVsIidTDl~VDf~ppl~y~e~~~~ 194 (238)
+++++|+ +||||||||+.|||+||++|+|+..+
T Consensus 173 ~~~v~pe~S~~~i~vveTDLvvDF~pPiGy~e~~qq 208 (331)
T COG5140 173 FTVVHPEPSANAIYVVETDLVVDFLPPIGYKEKAQQ 208 (331)
T ss_pred EEEeccCCCcceEEEEecceeeeccCCccccchhhh
Confidence 9999996 89999999999999999999998543
No 4
>PLN03086 PRLI-interacting factor K; Provisional
Probab=100.00 E-value=3.6e-60 Score=462.29 Aligned_cols=159 Identities=42% Similarity=0.613 Sum_probs=152.5
Q ss_pred CCCCeeeecHHHHHHHHhCCC--CCceEEEEEeC-----------CCCCeEEEEEeeeEeCCCcEeccHhHHhhcCCCC-
Q 035839 31 EPGDKIIMPQSAFDRLAHTEV--GYPMMFELCNL-----------SSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQE- 96 (238)
Q Consensus 31 ~~gdKIiLP~SaL~~L~~~~i--~~Pm~F~i~n~-----------~~~~~th~GVlEF~A~EG~i~lP~Wmm~~L~l~~- 96 (238)
..||||+||||||++|+++++ .|||+|+|+|. ..+++||||||||+|+||+||||+|||++|++.+
T Consensus 89 ~~GdKI~LPpSaL~~L~~~~~~~~~Pm~F~l~~~~~~~~~~~~~~~~~~~th~GVlEF~A~EG~v~lP~wm~~~L~~~~~ 168 (567)
T PLN03086 89 GNGDKIKLPPSCFTELSDQGAFDKGPLYFRLSVVHQEGSGEMKDTDSQKTTHSGVLEFTAEEGSVGLPPHVWSNLFPSDP 168 (567)
T ss_pred CCCCeEEcCHHHHHHHHhcCCCCCCCeEEEEeccccccccccccccCCcEEEEEEEEEEcCCCeEEcCHHHHhhcCCCCC
Confidence 599999999999999999998 89999999984 3478999999999999999999999999999875
Q ss_pred --CCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECCEEEEEEEEEecCCCceEEE
Q 035839 97 --YELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSIT 174 (238)
Q Consensus 97 --gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsIi 174 (238)
|+.|+|++++|||||||||||++.+|++ |+|||||||++||||+|||+||+|.|+|+++.|+|+|+|++|++|||||
T Consensus 169 ~~~~~v~v~~~~Lpkgt~vklqP~~~~f~d-i~npKavLE~~Lr~~stLT~Gd~i~i~~~~~~y~~~V~ev~P~~aVsii 247 (567)
T PLN03086 169 PDVPLVEVRYIWLPKGTYAKLQPDGVGFSD-LPNHKAVLETALRQHATLSEDDVLVVNYGQLTYKLKVLELKPASSVSVL 247 (567)
T ss_pred CCCCeEEEEEeecCCCCEEEEeeccCCcCC-cccHHHHHHHHhhcCccccCCCEEEEecCCEEEEEEEEEEcCCCeeEEE
Confidence 8899999999999999999999999999 9999999999999999999999999999999999999999999999999
Q ss_pred eCceEEEecCCCCCCC
Q 035839 175 ETDCEVDFAPPLDYKE 190 (238)
Q Consensus 175 dTDl~VDf~ppl~y~e 190 (238)
||||+|||+||.++.+
T Consensus 248 eTDi~VDf~~p~~~~~ 263 (567)
T PLN03086 248 ETDIEVDIVGPDSVSN 263 (567)
T ss_pred eCceEEEeccCCcchh
Confidence 9999999999999743
No 5
>PF02933 CDC48_2: Cell division protein 48 (CDC48), domain 2; InterPro: IPR004201 This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C terminus. The VAT-N domain found in AAA ATPases (IPR003959 from INTERPRO) is a substrate 185-residue recognition domain [].; GO: 0005524 ATP binding; PDB: 1QDN_B 1QCS_A 1CR5_C 3QQ8_A 3HU2_A 3HU1_E 3HU3_A 3QWZ_A 3TIW_B 3QQ7_A ....
Probab=96.73 E-value=0.0091 Score=42.78 Aligned_cols=46 Identities=33% Similarity=0.405 Sum_probs=35.1
Q ss_pred HhhccCcccccCCEEEEEECCEEEEEEEEEecCCCceEEE-eCceEEE
Q 035839 135 AILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSIT-ETDCEVD 181 (238)
Q Consensus 135 ~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsIi-dTDl~VD 181 (238)
+.|.+ .-+++||+|.+.+.++.+.|.|.+++|.++|.|- +|.+++.
T Consensus 12 ~~l~~-~pv~~Gd~i~~~~~~~~~~~~V~~~~P~~~v~it~~T~i~i~ 58 (64)
T PF02933_consen 12 RQLEG-RPVTKGDTIVFPFFGQALPFKVVSTEPSGPVIITEDTEIEIK 58 (64)
T ss_dssp HHHTT-EEEETT-EEEEEETTEEEEEEEEEECSSSEEEEETTSEEEES
T ss_pred HHHcC-CCccCCCEEEEEeCCcEEEEEEEEEEcCCCEEECCCcEEEEc
Confidence 34444 4599999999999999999999999999977555 3445543
No 6
>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=96.34 E-value=0.061 Score=55.87 Aligned_cols=147 Identities=18% Similarity=0.182 Sum_probs=115.0
Q ss_pred eeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeE-eCCCcEeccHhHHhhcCCCCCCeEEEEEe-eeCCcee
Q 035839 35 KIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFT-ADEGFIYLPNWMMDNMKLQEYELVRVTNV-SLAKATY 112 (238)
Q Consensus 35 KIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~-A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~-~LPkgt~ 112 (238)
-|.||.+.+..|....-.+++.-.-+.....+.-..| -++ ..|..+-+=.-..+.|+|.+|+.|.++-. ..++++-
T Consensus 16 fv~lP~ql~~ai~~~~~~~av~~v~~~~~~~~s~~~g--~~s~~se~~ieIn~~~A~~l~L~e~~~V~l~~~~~v~~~~~ 93 (952)
T KOG0735|consen 16 FVNLPEQLLEAISEPVQNYAVQAVVSKNPIKKSWVFG--HGSGSSENVIEINRVYAHTLGLAENQEVKLSIIDHVHEATQ 93 (952)
T ss_pred hhccHHHHHHHHhccccCceeEEEEcCCChhheeecc--cCCCCccceEEeehhhHhhccCCCCCeEEEEEcCCccceeE
Confidence 3678999999988776566665444332333344455 444 35777888888999999999999999976 7999999
Q ss_pred EEEeecCccccccCCChHHH-HHHhhc-cCcccccCCEEEEEECC-EEEEEEEEEecCCCceEEEeCceEEEecCC
Q 035839 113 MKLQPHTKGFLDELSNPRAV-LEAILR-KFSCLTTGDTIMIMHNE-SKYYIDVLETKPSNAVSITETDCEVDFAPP 185 (238)
Q Consensus 113 vkLqP~s~~F~~~i~npKav-LE~~Lr-nys~LT~Gd~I~I~~~~-~~y~l~V~e~kP~~aVsIidTDl~VDf~pp 185 (238)
|.+.|.+++=|+ |-+--|. ||..|- ++.-+|. ....|+++. ..-.|.|..+.|+..+.=++++-+|=++|-
T Consensus 94 V~VeP~TsdDWE-IiElnA~~~e~~lL~Q~RIv~~-~~f~iwl~~~t~i~fqv~rl~Ps~~~gRl~~~Tev~VaPK 167 (952)
T KOG0735|consen 94 VEVEPVTSDDWE-IIELNAEWLEENLLVQTRIVTP-EIFIIWLPSGTVIQFQVDRLIPSMLYGRLLRGTEVLVAPK 167 (952)
T ss_pred EEEeeccCccHH-HHHhhHHHHhhhhhhheeeccc-ceeEEEEcCccEEEEEEeeeecccceeeecCCceEEEecC
Confidence 999999998888 8665555 677666 7888999 777888876 456799999999999999999999998774
No 7
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
Probab=95.93 E-value=0.21 Score=51.19 Aligned_cols=134 Identities=16% Similarity=0.160 Sum_probs=94.5
Q ss_pred CCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEee-eE--eCCCcEeccHhHHhhcCCCCCCeEEEEEeeeC
Q 035839 32 PGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVE-FT--ADEGFIYLPNWMMDNMKLQEYELVRVTNVSLA 108 (238)
Q Consensus 32 ~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlE-F~--A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LP 108 (238)
..+.+-|.++++.+|. +..==.-+|.. ..+.+.|-|.. .. .+.|.|.+..-+.+++++..||.|.|+-+.+|
T Consensus 15 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (733)
T TIGR01243 15 GRGIVRIDRQTAARLG---VEPGDFVEIEK--GDRSVVAIVWPLRPDDEGRGIIRMDGYLRANAGVTIGDTVTVERAEVK 89 (733)
T ss_pred CCCeEeeCHHHHHhcC---CCCCCEEEEec--CCCceeEEEEecCccccCCCEEeecHHHHhhcCCCCCCeEEEeecCCC
Confidence 5577889999998773 22111334442 34456666664 22 24689999999999999999999999998999
Q ss_pred CceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECCEEEEEEEEEecCCCceEE
Q 035839 109 KATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSI 173 (238)
Q Consensus 109 kgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsI 173 (238)
.++.|.+.|... ... -.+...++...+.+ ..+++||.|.+.+....+.+.|+++.|...+.+
T Consensus 90 ~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~-~~~~~g~~~~~~~~~~~~~~~v~~~~p~~~~~~ 151 (733)
T TIGR01243 90 EAKKVVLAPTQP-IRF-GRDFVDYVKEFLLG-KPISKGETVIVPVLEGALPFVVVSTQPAGFVYV 151 (733)
T ss_pred ccceEeeccccc-ccc-ccchHHHHHHHHcC-CCCCCCCEEEecccCcceeEEEEecCCCCcEEE
Confidence 999999999531 110 12233344444444 468999999999888788899999999655543
No 8
>PF09262 PEX-1N: Peroxisome biogenesis factor 1, N-terminal ; InterPro: IPR015342 This domain adopts a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation []. ; GO: 0005524 ATP binding, 0007031 peroxisome organization, 0005777 peroxisome; PDB: 1WLF_A.
Probab=93.59 E-value=0.079 Score=40.37 Aligned_cols=75 Identities=21% Similarity=0.260 Sum_probs=49.2
Q ss_pred ceeEEEeecCccccccCCChHHHHHHhhc-cCcccccCCEEEEEE-CCEEEEEEEEEecCCCc---eEEEeCceEEEecC
Q 035839 110 ATYMKLQPHTKGFLDELSNPRAVLEAILR-KFSCLTTGDTIMIMH-NESKYYIDVLETKPSNA---VSITETDCEVDFAP 184 (238)
Q Consensus 110 gt~vkLqP~s~~F~~~i~npKavLE~~Lr-nys~LT~Gd~I~I~~-~~~~y~l~V~e~kP~~a---VsIidTDl~VDf~p 184 (238)
++.|.+.|.+.|=++-|...-..||..|- +-.+++.|.++.++. ++..-.|+|..+.|... ...+..|-|+=++|
T Consensus 1 A~~V~veP~T~dDWEIlEl~A~~lE~~lL~QiRvv~~~~~~~v~v~~~~~i~~~V~~i~p~~~~~~~~~L~~~TEv~VaP 80 (80)
T PF09262_consen 1 AKSVEVEPLTSDDWEILELHAEFLEDQLLSQIRVVFPGQVFPVWVSQNTVIKFKVVSIEPSSSAEGCARLSPDTEVIVAP 80 (80)
T ss_dssp -SEEEEEESSHHHHHHHHHS-SSHHHHHHHH--EE-TT-EEEEESSSS-EEEEEEEEEES--S---SEE--TT-EEEE--
T ss_pred CcEEEEEcCCccHHHHHHHhHHHHHHHHHHhheeecCCCEEEEEEcCCeEEEEEEEEccCCCCceeEEEeCCCcEEEECC
Confidence 46788999998777733555556777666 688999999999998 56788999999999866 78888898887764
No 9
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=86.38 E-value=3 Score=26.75 Aligned_cols=39 Identities=23% Similarity=0.399 Sum_probs=31.2
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeec
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPH 118 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~ 118 (238)
.+.|.+.||.-+.+.|++.+||.+.+... +.| -+.|.|.
T Consensus 4 ~~kgri~iP~~~r~~l~~~~gd~~~i~~~--~~~-~l~l~p~ 42 (43)
T TIGR01439 4 DKKGQIVIPKEIREKLGLKEGDRLEVIRV--EDG-EIILRPA 42 (43)
T ss_pred CcCCeEEecHHHHHHcCcCCCCEEEEEEe--CCC-EEEEEEC
Confidence 36799999999999999999999888753 333 5666664
No 10
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=86.35 E-value=3.4 Score=27.71 Aligned_cols=39 Identities=13% Similarity=0.295 Sum_probs=30.6
Q ss_pred CCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecC
Q 035839 78 DEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHT 119 (238)
Q Consensus 78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s 119 (238)
..+.|.||.-+.+.|++++||.|.+... ..| -+.+.|..
T Consensus 5 ~s~~v~iPk~~~~~l~l~~Gd~v~i~~~--~~g-~i~i~p~~ 43 (47)
T PF04014_consen 5 NSGQVTIPKEIREKLGLKPGDEVEIEVE--GDG-KIVIRPVK 43 (47)
T ss_dssp TCSEEEE-HHHHHHTTSSTTTEEEEEEE--TTS-EEEEEEST
T ss_pred CCceEECCHHHHHHcCCCCCCEEEEEEe--CCC-EEEEEECC
Confidence 4688999999999999999999998865 333 67777753
No 11
>PF02359 CDC48_N: Cell division protein 48 (CDC48), N-terminal domain; InterPro: IPR003338 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc forms a novel six-stranded beta-clam fold []. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. ; GO: 0005524 ATP binding; PDB: 1CZ4_A 1CZ5_A 3CF3_C 3CF1_A 3CF2_A 1S3S_D 1E32_A 1R7R_A 2PJH_B 1CR5_B ....
Probab=82.03 E-value=19 Score=26.96 Aligned_cols=68 Identities=12% Similarity=0.001 Sum_probs=50.1
Q ss_pred CCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEe---CCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 32 PGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTA---DEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 32 ~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A---~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
..+-++|.|..+++ +++..--+-.|.. ++.|+|=|.--.. +.|.|-|..-+.+++++.-||.|.|+-+
T Consensus 14 ~~n~v~v~~~~m~~---l~l~~gd~v~i~g---~~~tv~~v~~~~~~~~~~g~I~l~~~~R~n~~v~igd~V~V~~~ 84 (87)
T PF02359_consen 14 GTNCVRVSPEDMEE---LGLFPGDVVLISG---KRKTVAFVFPDRPDDSPPGVIRLSGIQRKNAGVSIGDRVTVRPY 84 (87)
T ss_dssp CTTEEEEEHHHHHC---TTT-TTEEEEEET---TTEEEEEEEEECCSTTCTTEEEE-HHHHHHCT--TTSEEEEEEE
T ss_pred CCCEEEEcHHHHHH---cCCCCccEEEEeC---CceEEEEEEECCCCCCCCCEEEECHHHHhhCCcCCCCEEEEEEC
Confidence 56789999999974 4555555667765 4458888875543 4799999999999999999999999854
No 12
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=80.60 E-value=1.1 Score=34.06 Aligned_cols=27 Identities=15% Similarity=0.130 Sum_probs=19.8
Q ss_pred CCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 79 EGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 79 EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
+.-||+|.++.+..+|+.||.|.=...
T Consensus 28 ~~DvYVs~~qIrrf~LR~GD~V~G~vr 54 (78)
T PF07497_consen 28 PDDVYVSPSQIRRFGLRTGDLVEGQVR 54 (78)
T ss_dssp TTSEEE-CCCCCCTT--TTEEEEEEEE
T ss_pred CCCEEECHHHHHHcCCCCCCEEEEEEe
Confidence 456899999999999999999875443
No 13
>PF02359 CDC48_N: Cell division protein 48 (CDC48), N-terminal domain; InterPro: IPR003338 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc forms a novel six-stranded beta-clam fold []. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. ; GO: 0005524 ATP binding; PDB: 1CZ4_A 1CZ5_A 3CF3_C 3CF1_A 3CF2_A 1S3S_D 1E32_A 1R7R_A 2PJH_B 1CR5_B ....
Probab=78.53 E-value=1.7 Score=32.77 Aligned_cols=69 Identities=17% Similarity=0.200 Sum_probs=45.4
Q ss_pred CCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEE
Q 035839 78 DEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIM 152 (238)
Q Consensus 78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~ 152 (238)
..|.++|..-.|+.|++.+||.|.|... +-|.+.+.|.... + ...=.--|-...|...-+..||.|.|.
T Consensus 14 ~~n~v~v~~~~m~~l~l~~gd~v~i~g~---~~tv~~v~~~~~~--~-~~~g~I~l~~~~R~n~~v~igd~V~V~ 82 (87)
T PF02359_consen 14 GTNCVRVSPEDMEELGLFPGDVVLISGK---RKTVAFVFPDRPD--D-SPPGVIRLSGIQRKNAGVSIGDRVTVR 82 (87)
T ss_dssp CTTEEEEEHHHHHCTTT-TTEEEEEETT---TEEEEEEEEECCS--T-TCTTEEEE-HHHHHHCT--TTSEEEEE
T ss_pred CCCEEEEcHHHHHHcCCCCccEEEEeCC---ceEEEEEEECCCC--C-CCCCEEEECHHHHhhCCcCCCCEEEEE
Confidence 5689999999999999999999999872 2266666664322 1 100011144677778888999999985
No 14
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=78.51 E-value=5.6 Score=29.42 Aligned_cols=55 Identities=16% Similarity=0.267 Sum_probs=37.8
Q ss_pred CcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCc--cccccCCChHHHHHHhhccCc
Q 035839 80 GFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTK--GFLDELSNPRAVLEAILRKFS 141 (238)
Q Consensus 80 G~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~--~F~~~i~npKavLE~~Lrnys 141 (238)
-.|-||.=+++.|+|.+||.|.|... +.-+.+.|... +|-+ .....++..++.|-
T Consensus 10 ~~vtIPk~i~~~lgl~~Gd~v~v~~~----~~~iii~~~~~~~~~~~---~~~~~~~~~~~~y~ 66 (74)
T TIGR02609 10 LVVTLPKEVLESLGLKEGDTLYVDEE----EGGLKLKRFDEGKELEK---KMQMAVERAMSKYD 66 (74)
T ss_pred eEEEECHHHHHHcCcCCCCEEEEEEE----CCEEEEEECCCCccHHH---HHHHHHHHHHHHHH
Confidence 45889999999999999999976433 34477778765 4432 22235666666553
No 15
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=77.46 E-value=2.5 Score=31.31 Aligned_cols=29 Identities=14% Similarity=0.063 Sum_probs=23.9
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
+.+.-||+|.++.+..+|+.||.|.=.-.
T Consensus 24 ~~~~DvyVs~~~Irr~~LR~GD~V~G~vr 52 (68)
T cd04459 24 PGPDDIYVSPSQIRRFNLRTGDTVVGQIR 52 (68)
T ss_pred CCCCCEEECHHHHHHhCCCCCCEEEEEEe
Confidence 35566899999999999999999876433
No 16
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=75.90 E-value=8.8 Score=32.94 Aligned_cols=125 Identities=9% Similarity=0.066 Sum_probs=75.4
Q ss_pred CCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEeCCCcEeccHhHHhhcCCCCCCeEEEEEe-eeCCce
Q 035839 33 GDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNV-SLAKAT 111 (238)
Q Consensus 33 gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~-~LPkgt 111 (238)
..++.||-..|...... ...+=+|... ..-+.+++|.++...+...|.+=+|.-.....+.||.|.-+-+ ..++|=
T Consensus 4 ~~~~V~PGe~l~~~~e~-~~G~Gty~~~--~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g~ 80 (189)
T PRK09521 4 QGDLVLPGDYLAVIEEY-LPGEGTYEDN--GEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQRA 80 (189)
T ss_pred cCCEECCCCccccccce-EcCCCEEeeC--CEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCeE
Confidence 45567776655322211 2334455532 2346789999999777778888778754566688999987765 367788
Q ss_pred eEEEeec----------CccccccCCChHHHHHHhhcc-CcccccCCEEEEEECC--EEEEEEEEE
Q 035839 112 YMKLQPH----------TKGFLDELSNPRAVLEAILRK-FSCLTTGDTIMIMHNE--SKYYIDVLE 164 (238)
Q Consensus 112 ~vkLqP~----------s~~F~~~i~npKavLE~~Lrn-ys~LT~Gd~I~I~~~~--~~y~l~V~e 164 (238)
+|.|-.. -..|+. +++... ...++ ..++..||+|....-. ..+.|.+.+
T Consensus 81 ~V~I~~~~~~~~~l~~~~~G~l~-~s~i~~---~~~~~~~~~~~~GD~V~akV~~i~~~i~LS~k~ 142 (189)
T PRK09521 81 LVRIVSIEGSERELATSKLAYIH-ISQVSD---GYVESLTDAFKIGDIVRAKVISYTDPLQLSTKG 142 (189)
T ss_pred EEEEEEecccccccCCCceeeEE-hhHcCh---hhhhhHHhccCCCCEEEEEEEecCCcEEEEEec
Confidence 8887421 234554 443322 11222 5668999999876422 455555543
No 17
>PRK14132 riboflavin kinase; Provisional
Probab=74.95 E-value=3 Score=34.50 Aligned_cols=31 Identities=26% Similarity=0.393 Sum_probs=24.8
Q ss_pred CeEE-EEEeeeEeCCCcEeccHhHHhhcCCCCCCeEEEE
Q 035839 66 KTTH-CGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVT 103 (238)
Q Consensus 66 ~~th-~GVlEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~ 103 (238)
|+.| -.|+|++|+.. +-+.|+|++||.|.|+
T Consensus 94 rT~h~~~~lEiIAp~~-------LR~~L~LkDGD~V~I~ 125 (126)
T PRK14132 94 KTDHSKNVLEIIAPIK-------LRKFLNLKDGDVVKIV 125 (126)
T ss_pred cCCCCCCeEEEECCcc-------hHhhcCCCCCCEEEEE
Confidence 4455 45888888765 8999999999999986
No 18
>smart00553 SEP Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.
Probab=74.11 E-value=1.4 Score=34.64 Aligned_cols=14 Identities=50% Similarity=0.930 Sum_probs=12.4
Q ss_pred cccceeeeceecCC
Q 035839 224 KFKAFTGKGKLLGF 237 (238)
Q Consensus 224 ~f~~F~G~G~rldg 237 (238)
.+++|+|+|+||++
T Consensus 72 ~~~~F~G~G~~LGs 85 (93)
T smart00553 72 AFKPFSGSGQKLGS 85 (93)
T ss_pred CccCCccCCccCCC
Confidence 47899999999986
No 19
>PRK09974 putative regulator PrlF; Provisional
Probab=72.55 E-value=12 Score=30.37 Aligned_cols=61 Identities=15% Similarity=0.104 Sum_probs=39.5
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCcccccc-CCChHHHHHHhhccC
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDE-LSNPRAVLEAILRKF 140 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~-i~npKavLE~~Lrny 140 (238)
...|+|-+|.-+-+.|||.+||.|.+. +..+..|.+.+...+=-+- |...-.+||+-++++
T Consensus 15 TsKGQvTIPk~IR~~Lgl~~GdkI~f~---i~~dG~V~i~~~~~~~~Dp~ig~FL~fLa~Di~~~ 76 (111)
T PRK09974 15 TDRGQTTVPAPVRKALKLKKRDSIHYE---ILPGGQVFICRLGDEEEDPVLGAFLDFLAADIQNN 76 (111)
T ss_pred ecCCCEeccHHHHHHcCCCCCCEEEEE---EeCCCEEEEEECCCCCCCchHHHHHHHHHHHHHhC
Confidence 367999999999999999999998763 3334456666653211110 223355677666543
No 20
>COG1935 Uncharacterized conserved protein [Function unknown]
Probab=70.85 E-value=7.5 Score=32.01 Aligned_cols=47 Identities=21% Similarity=0.360 Sum_probs=35.4
Q ss_pred HHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEeCCCcEeccHhHHhhcCCCCCCeEEEEEe---eeCCcee
Q 035839 40 QSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNV---SLAKATY 112 (238)
Q Consensus 40 ~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~---~LPkgt~ 112 (238)
-+++++|.+.++. +|+|.|..+ ..--++|++||.|.++++ +|-+||.
T Consensus 11 ~~vie~l~~~~~r---TieiRsa~N-----------------------~~tv~rl~~GDlVFlT~~~~~Dl~~Gts 60 (122)
T COG1935 11 RRVIESLLRNPIR---TIEIRSARN-----------------------LLTVLRLHEGDLVFLTSTSLEDLTKGTS 60 (122)
T ss_pred HHHHHHHHhCCce---EEEEEcccc-----------------------hHHhhcCCCCCEEEEehhHhhHhhcCcc
Confidence 3577777776554 788887554 455678999999999988 6788875
No 21
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=68.74 E-value=8.5 Score=29.66 Aligned_cols=29 Identities=7% Similarity=0.123 Sum_probs=25.9
Q ss_pred CCCcEeccHhHHhhcCCCCCCeEEEEEee
Q 035839 78 DEGFIYLPNWMMDNMKLQEYELVRVTNVS 106 (238)
Q Consensus 78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~ 106 (238)
++..|+|-.--++.|||.+||.|+|.+..
T Consensus 29 ~~~~v~i~p~dA~~lgI~dGd~V~v~s~~ 57 (112)
T cd02787 29 RRDVVFMNPDDIARLGLKAGDRVDLESAF 57 (112)
T ss_pred CccEEEECHHHHHHhCCCCCCEEEEEecC
Confidence 46789999999999999999999999753
No 22
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=68.67 E-value=6.7 Score=30.16 Aligned_cols=29 Identities=17% Similarity=0.050 Sum_probs=25.9
Q ss_pred CCCcEeccHhHHhhcCCCCCCeEEEEEee
Q 035839 78 DEGFIYLPNWMMDNMKLQEYELVRVTNVS 106 (238)
Q Consensus 78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~ 106 (238)
++..|+|..--++.|||++||.|+|++..
T Consensus 29 ~~~~v~i~p~dA~~lgi~~Gd~V~v~s~~ 57 (116)
T cd02786 29 GEPTLLIHPADAAARGIADGDLVVVFNDR 57 (116)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEcCC
Confidence 56789999999999999999999988753
No 23
>PRK09798 antitoxin MazE; Provisional
Probab=68.13 E-value=13 Score=28.39 Aligned_cols=50 Identities=18% Similarity=0.348 Sum_probs=36.6
Q ss_pred cEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCc
Q 035839 81 FIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFS 141 (238)
Q Consensus 81 ~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys 141 (238)
-+-+|.=+++.|+|.+||.|.|+.. +.-+.++|... .|+.-||.-|.+|+
T Consensus 14 ~vRIPk~~l~~l~l~~g~~vei~v~----~~~iiI~p~~~-------~~r~~l~eLla~~~ 63 (82)
T PRK09798 14 AVRIPATLMQALNLNIDDEVKIDLV----DGKLIIEPVRK-------EPVFTLAELVNDIT 63 (82)
T ss_pred eEEcCHHHHHHcCCCCCCEEEEEEE----CCEEEEEECCC-------CCCCCHHHHHhcCC
Confidence 3779999999999999999988873 45577898632 33445666665554
No 24
>PF01982 CTP-dep_RFKase: Domain of unknown function DUF120; InterPro: IPR023602 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents a CTP-dependent riboflavin kinase domain, found primarily in archaea, that catalyses the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples []. The N-terminal is a winged helix-turn-helix DNA-binding domain, and the C-terminal half is most similar in sequence to a group of cradle-loop barrels.; GO: 0016773 phosphotransferase activity, alcohol group as acceptor; PDB: 2VBV_A 2VBU_A 2VBS_A 2VBT_A 2P3M_A 2OYN_A 3CTA_A.
Probab=65.78 E-value=7.7 Score=31.89 Aligned_cols=18 Identities=22% Similarity=0.252 Sum_probs=12.3
Q ss_pred HhHHhhcCCCCCCeEEEE
Q 035839 86 NWMMDNMKLQEYELVRVT 103 (238)
Q Consensus 86 ~Wmm~~L~l~~gd~V~v~ 103 (238)
.-+-+.|+|++||.|.|+
T Consensus 103 ~~LR~~L~L~DGD~V~v~ 120 (121)
T PF01982_consen 103 VKLRDTLGLKDGDEVEVE 120 (121)
T ss_dssp S-HHHHTT--TT-EEEEE
T ss_pred cchHhhcCCCCCCEEEEE
Confidence 348899999999999986
No 25
>PRK11347 antitoxin ChpS; Provisional
Probab=64.72 E-value=18 Score=27.54 Aligned_cols=48 Identities=21% Similarity=0.320 Sum_probs=35.1
Q ss_pred cEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCc
Q 035839 81 FIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFS 141 (238)
Q Consensus 81 ~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys 141 (238)
-+-||.=++++|++++||.|.|+... .-+.++|.... ..||.-|..|.
T Consensus 13 ~vriPk~il~~l~l~~G~~v~i~v~~----~~iii~p~~~~---------~tL~eLla~~~ 60 (83)
T PRK11347 13 GMVIPNIVMKELNLQPGQSVEAQVSN----NQLILTPISRR---------YSLDELLAQCD 60 (83)
T ss_pred eEEeCHHHHHHcCCCCCCEEEEEEEC----CEEEEEECCCC---------CCHHHHHhcCC
Confidence 37799999999999999999887643 34888997433 33566555443
No 26
>cd02776 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=64.20 E-value=12 Score=30.78 Aligned_cols=33 Identities=9% Similarity=0.186 Sum_probs=27.8
Q ss_pred eeeEeCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 73 VEFTADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 73 lEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
++...++..++|-.=-++.|+|++||.|+|.+.
T Consensus 24 l~~~~~~~~v~inp~dA~~lgI~dGd~V~v~~~ 56 (141)
T cd02776 24 LRLQRGGPVVWMNPKDAAELGIKDNDWVEVFND 56 (141)
T ss_pred HhcCCCCCEEEECHHHHHHcCCCCCCEEEEEeC
Confidence 344556788999999999999999999998763
No 27
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=63.26 E-value=13 Score=28.35 Aligned_cols=42 Identities=12% Similarity=0.230 Sum_probs=31.9
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCc
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTK 120 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~ 120 (238)
...|+|++|.-+-+.||+++||.|.+.... .+..+-|+|...
T Consensus 11 ~~~GqIvIPkeiR~~lgi~~Gd~lei~~~~--~~~~ivl~k~~~ 52 (89)
T COG2002 11 DRKGQIVIPKEIREALGIKEGDVLEIIVDG--DGGRIVLKKYKP 52 (89)
T ss_pred CcCceEEecHHHHHHhCCCCCCEEEEEEeC--CCCEEEEEECCc
Confidence 367999999999999999999998876542 222266777654
No 28
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=62.70 E-value=9.4 Score=30.68 Aligned_cols=27 Identities=19% Similarity=0.249 Sum_probs=23.4
Q ss_pred CcccccCCEEEEEECCEEEEEEEEEec
Q 035839 140 FSCLTTGDTIMIMHNESKYYIDVLETK 166 (238)
Q Consensus 140 ys~LT~Gd~I~I~~~~~~y~l~V~e~k 166 (238)
+..|..||+|.|.+.++.+.++|.+++
T Consensus 137 ~~~l~pGDvi~l~~~~~~~~~RI~~i~ 163 (164)
T PF13550_consen 137 GLALEPGDVIALSDDGRDMRFRITEIE 163 (164)
T ss_pred hccCCCCCEEEEEeCCCceEEEEEEEe
Confidence 446889999999999999999998875
No 29
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=61.77 E-value=11 Score=28.73 Aligned_cols=29 Identities=21% Similarity=0.256 Sum_probs=25.8
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
.++..|+|..=-++.|||++||.|+|.+-
T Consensus 32 ~~~~~v~in~~dA~~lgi~~Gd~V~v~~~ 60 (116)
T cd02790 32 APEEYVEINPEDAKRLGIEDGEKVRVSSR 60 (116)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 46778999999999999999999999873
No 30
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=61.59 E-value=13 Score=28.19 Aligned_cols=33 Identities=15% Similarity=0.081 Sum_probs=27.5
Q ss_pred eeeEeCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 73 VEFTADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 73 lEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
|.-.+++..|.|-.--++.|||.+||.|+|.+.
T Consensus 22 l~~~~~~~~v~inp~dA~~lGi~~Gd~V~v~s~ 54 (96)
T cd02788 22 IAERAPAPYARLSPADAARLGLADGDLVEFSLG 54 (96)
T ss_pred HHhcCCCCEEEECHHHHHHcCCCCCCEEEEEEC
Confidence 333457789999999999999999999998764
No 31
>cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=59.37 E-value=9.7 Score=29.59 Aligned_cols=29 Identities=14% Similarity=0.000 Sum_probs=25.7
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
.++..|+|-.=-++.|||.+||.|+|++.
T Consensus 28 ~~~~~v~i~p~dA~~lgi~~Gd~V~v~~~ 56 (106)
T cd02789 28 DACAYCEINPEDYKLLGKPEGDKVKVTSE 56 (106)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 46678999999999999999999998864
No 32
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=59.32 E-value=14 Score=28.20 Aligned_cols=27 Identities=22% Similarity=0.332 Sum_probs=24.8
Q ss_pred CCCcEeccHhHHhhcCCCCCCeEEEEE
Q 035839 78 DEGFIYLPNWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~ 104 (238)
++..|+|..--++.|||.+||.|+|.+
T Consensus 33 ~~~~v~inp~dA~~lgi~~Gd~V~v~~ 59 (120)
T cd00508 33 PEPFVEIHPEDAARLGIKDGDLVRVSS 59 (120)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEe
Confidence 567899999999999999999999987
No 33
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=58.85 E-value=11 Score=33.85 Aligned_cols=19 Identities=16% Similarity=0.225 Sum_probs=16.4
Q ss_pred HhHHhhcCCCCCCeEEEEE
Q 035839 86 NWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 86 ~Wmm~~L~l~~gd~V~v~~ 104 (238)
-.+-+.|+|.+||.|+|+-
T Consensus 194 v~LR~~LnLkDGD~V~ieV 212 (214)
T COG1339 194 VKLRDELNLKDGDEVTIEV 212 (214)
T ss_pred HhHHHHhCCCCCCEEEEEE
Confidence 4588899999999999874
No 34
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=57.81 E-value=15 Score=28.78 Aligned_cols=28 Identities=18% Similarity=0.039 Sum_probs=25.3
Q ss_pred CCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 78 DEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
++..|+|-.--++.|||.+||.|+|.+.
T Consensus 30 ~~~~v~i~p~dA~~~gi~~Gd~V~v~s~ 57 (124)
T cd02785 30 PEPRVKINPIDAAARGIAHGDLVEVYND 57 (124)
T ss_pred CCCeEEECHHHHHHcCCCCCCEEEEEeC
Confidence 5678999999999999999999998874
No 35
>PRK08577 hypothetical protein; Provisional
Probab=57.52 E-value=15 Score=29.79 Aligned_cols=44 Identities=16% Similarity=0.160 Sum_probs=32.3
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccc
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGF 122 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F 122 (238)
...|.|.+|.=+-+.||+.+||.|.+..-. .+.-+.+.|....+
T Consensus 10 ~~~g~i~ip~~~r~~l~~~~g~~~~~~~~~--~~~~~~~~~~~~~~ 53 (136)
T PRK08577 10 DSKGRITIPLEIREALGIREGMYVLLIADT--DKKEIHLEPIALPG 53 (136)
T ss_pred CcCCeEEecHHHHHHcCcCCCCEEEEEEEC--CCCEEEEEEcCCCC
Confidence 467999999999999999999998876431 12255666654333
No 36
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=56.86 E-value=15 Score=28.38 Aligned_cols=28 Identities=14% Similarity=0.226 Sum_probs=25.2
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEE
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~ 104 (238)
.++..|.|..=-++.|||.+||.|+|.+
T Consensus 32 ~~~~~v~i~p~dA~~lgi~~Gd~V~v~s 59 (122)
T cd02792 32 QPEMFVEISPELAAERGIKNGDMVWVSS 59 (122)
T ss_pred CCCcEEEECHHHHHHcCCCCCCEEEEEc
Confidence 4677899999999999999999999886
No 37
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=56.34 E-value=16 Score=26.94 Aligned_cols=28 Identities=18% Similarity=0.191 Sum_probs=24.6
Q ss_pred CCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 78 DEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
.+..|+|..--++.|+|++||.|.|++-
T Consensus 21 ~~~~v~~~~~da~~lgl~~Gd~v~v~~~ 48 (101)
T cd02775 21 PEPVVEINPEDAAALGIKDGDLVRVESR 48 (101)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 4578999999999999999999988753
No 38
>KOG2086 consensus Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure]
Probab=56.13 E-value=5 Score=38.87 Aligned_cols=16 Identities=44% Similarity=0.806 Sum_probs=14.2
Q ss_pred CCcccceeeeceecCC
Q 035839 222 NNKFKAFTGKGKLLGF 237 (238)
Q Consensus 222 ~~~f~~F~G~G~rldg 237 (238)
++.|++|+|.|+||++
T Consensus 252 ~~~~~pF~G~Gq~LGs 267 (380)
T KOG2086|consen 252 KPVFKPFSGEGQRLGS 267 (380)
T ss_pred CcccCCCCCcCeecCC
Confidence 4579999999999986
No 39
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=56.11 E-value=20 Score=31.01 Aligned_cols=46 Identities=15% Similarity=0.274 Sum_probs=35.4
Q ss_pred EEeeeEeCCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecC
Q 035839 71 GVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHT 119 (238)
Q Consensus 71 GVlEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s 119 (238)
|+.==..+-|.|.+|--|-+.|++++||.|.+.... .| .+.|++.+
T Consensus 4 g~v~~id~~Gri~iP~~iR~~l~i~~gd~~~~~~~~--~~-~iil~k~~ 49 (180)
T TIGR02851 4 GIVRRIDDLGRVVIPKEIRRTLRIREGDPLEIFTDR--EG-EVILKKYS 49 (180)
T ss_pred ceEEEECCCCcEEEeHHHHHHcCCCCCCeEEEEEeC--CC-EEEEEECC
Confidence 444445678999999999999999999999886532 23 37777765
No 40
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=55.37 E-value=15 Score=28.84 Aligned_cols=26 Identities=15% Similarity=0.230 Sum_probs=24.0
Q ss_pred CCcEeccHhHHhhcCCCCCCeEEEEE
Q 035839 79 EGFIYLPNWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 79 EG~i~lP~Wmm~~L~l~~gd~V~v~~ 104 (238)
+..|+|-.=.++.|||.+||.|+|++
T Consensus 33 ~~~v~i~p~dA~~lgi~~Gd~V~v~s 58 (127)
T cd02777 33 REPVWINPLDAAARGIKDGDIVRVFN 58 (127)
T ss_pred CCeEEECHHHHHHcCCCCCCEEEEEc
Confidence 56799999999999999999999886
No 41
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=55.35 E-value=15 Score=28.73 Aligned_cols=29 Identities=7% Similarity=0.020 Sum_probs=25.5
Q ss_pred CCCcEeccHhHHhhcCCCCCCeEEEEEee
Q 035839 78 DEGFIYLPNWMMDNMKLQEYELVRVTNVS 106 (238)
Q Consensus 78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~ 106 (238)
++..|+|-.=-++.|||.+||.|+|.+..
T Consensus 31 ~~~~v~inp~dA~~~gi~~Gd~V~v~s~~ 59 (130)
T cd02781 31 PDPVAEINPETAAKLGIADGDWVWVETPR 59 (130)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEECCC
Confidence 56789999999999999999999988753
No 42
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=54.92 E-value=19 Score=28.76 Aligned_cols=26 Identities=19% Similarity=0.367 Sum_probs=23.0
Q ss_pred cccccCCEEEEEECCEEEEEEEEEec
Q 035839 141 SCLTTGDTIMIMHNESKYYIDVLETK 166 (238)
Q Consensus 141 s~LT~Gd~I~I~~~~~~y~l~V~e~k 166 (238)
..+-.||+|.|.++++.+.+.|+.+.
T Consensus 47 ~~VK~GD~l~i~~~~~~~~v~Vl~~~ 72 (100)
T COG1188 47 KEVKVGDILTIRFGNKEFTVKVLALG 72 (100)
T ss_pred cccCCCCEEEEEeCCcEEEEEEEecc
Confidence 34678999999999999999999874
No 43
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=54.86 E-value=11 Score=31.34 Aligned_cols=28 Identities=14% Similarity=0.083 Sum_probs=23.9
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEE
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~ 104 (238)
-.-..|++-+-.|..|++++||.|.|++
T Consensus 28 ~a~a~~~inp~D~~~Lgv~EGD~VkVks 55 (128)
T COG1153 28 NACAVCEINPEDMKQLGVSEGDKVKVKS 55 (128)
T ss_pred hheeEEEECHHHHHHhCCCcCCeEEEEe
Confidence 3445688888899999999999999987
No 44
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=54.81 E-value=17 Score=27.95 Aligned_cols=28 Identities=29% Similarity=0.311 Sum_probs=24.9
Q ss_pred CCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 78 DEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
.+..|+|..-.++.||+.+||.|+|.+-
T Consensus 33 ~~~~v~in~~dA~~lgi~~Gd~V~v~~~ 60 (122)
T cd02791 33 PEPYVEIHPEDAARLGLKEGDLVRVTSR 60 (122)
T ss_pred CCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 4567999999999999999999998864
No 45
>COG2336 MazE Growth regulator [Signal transduction mechanisms]
Probab=54.00 E-value=15 Score=28.48 Aligned_cols=35 Identities=14% Similarity=0.226 Sum_probs=25.9
Q ss_pred cEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeec
Q 035839 81 FIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPH 118 (238)
Q Consensus 81 ~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~ 118 (238)
-+-+|.=||+.|++.+||-|.++.. .+..+.+.|.
T Consensus 13 avrIP~~l~kql~l~~g~~v~v~v~---n~~~i~~~p~ 47 (82)
T COG2336 13 AVRIPAALLKQLNLTIGDEVEVEVG---NDQSILIRPV 47 (82)
T ss_pred eeeccHHHHHHhCCCcCceEEEEEc---CCcEEEeccc
Confidence 3779999999999999999887643 2334445554
No 46
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=53.90 E-value=17 Score=27.44 Aligned_cols=27 Identities=19% Similarity=0.283 Sum_probs=22.1
Q ss_pred CCC-cEeccHhHHhhcCCCCCCeEEEEE
Q 035839 78 DEG-FIYLPNWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 78 ~EG-~i~lP~Wmm~~L~l~~gd~V~v~~ 104 (238)
.+. .|+|-.--++.|||++||.|+|++
T Consensus 27 ~~~~~v~inp~dA~~~Gi~~Gd~V~v~s 54 (110)
T PF01568_consen 27 PEPPFVEINPEDAAKLGIKDGDWVRVSS 54 (110)
T ss_dssp HSTEEEEEEHHHHHHCT--TTCEEEEEE
T ss_pred CCCCEEEEcHHHHHHhcCcCCCEEEEEe
Confidence 344 899999999999999999999987
No 47
>COG0243 BisC Anaerobic dehydrogenases, typically selenocysteine-containing [Energy production and conversion]
Probab=53.56 E-value=21 Score=36.72 Aligned_cols=52 Identities=21% Similarity=0.309 Sum_probs=36.6
Q ss_pred CCceEEEEEeCCCCCeEEEEEe------eeEeCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 52 GYPMMFELCNLSSGKTTHCGVV------EFTADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 52 ~~Pm~F~i~n~~~~~~th~GVl------EF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
.|| |.|+.......+|.+.- .-.++++.|+|-+-=++.|||++||.|+|.+.
T Consensus 639 ~yP--l~L~t~r~~~~~hs~~~~~~~~~~~~~~~~~v~inp~DA~~~GI~~GD~V~V~~~ 696 (765)
T COG0243 639 EYP--LQLTTGRLKNHLHSTTYNLRVPLRAIAPRPFVWINPEDAAKLGIKDGDLVRVENR 696 (765)
T ss_pred CCC--EEEecCCcCceecccccccchhHhhCCCCceEEECHHHHHHcCCCcCCEEEEEcC
Confidence 567 55554433334444332 22357789999999999999999999999875
No 48
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=52.04 E-value=30 Score=26.08 Aligned_cols=31 Identities=10% Similarity=0.180 Sum_probs=24.7
Q ss_pred HhHHhhcCCCCCCeEEEEEeeeCCceeEEEe
Q 035839 86 NWMMDNMKLQEYELVRVTNVSLAKATYMKLQ 116 (238)
Q Consensus 86 ~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLq 116 (238)
.-|.+.+|+++||.|+|.-.+---|.++..+
T Consensus 41 DPv~r~~g~k~GdVvkI~R~S~taG~~v~YR 71 (74)
T PF01191_consen 41 DPVARYLGAKPGDVVKIIRKSETAGEYVTYR 71 (74)
T ss_dssp SHHHHHTT--TTSEEEEEEEETTTSEEEEEE
T ss_pred ChhhhhcCCCCCCEEEEEecCCCCCCcEEEE
Confidence 4588999999999999999998888887653
No 49
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=51.99 E-value=22 Score=27.59 Aligned_cols=29 Identities=21% Similarity=0.076 Sum_probs=25.8
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
.++..|.|-.--++.|||.+||.|+|.+.
T Consensus 30 ~~~~~v~in~~dA~~lgi~~Gd~V~v~s~ 58 (115)
T cd02779 30 VPLPYIEVNPEDAKREGLKNGDLVEVYND 58 (115)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEeC
Confidence 46778999999999999999999998874
No 50
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=51.60 E-value=13 Score=33.17 Aligned_cols=39 Identities=21% Similarity=0.343 Sum_probs=27.2
Q ss_pred CeEEEEEeeeEeC----CCcEecc---------------HhHHhhcCCCCCCeEEEEE
Q 035839 66 KTTHCGVVEFTAD----EGFIYLP---------------NWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 66 ~~th~GVlEF~A~----EG~i~lP---------------~Wmm~~L~l~~gd~V~v~~ 104 (238)
..|+++|.=|-+- +|.|++| .-+-+.|+|.+||.|.|+.
T Consensus 158 ~r~~g~~~~~~~~i~~i~~aiv~P~rt~h~~~~~EiIap~~LR~~l~l~dgd~v~i~i 215 (217)
T PRK14165 158 ERTFGGVKCYPVKVEGIECAVIVPERTHYPSDLIEIISPVYLRKELNLKDGDRVEVLV 215 (217)
T ss_pred CceeEEEEEEEEEECceeEEEEeecCCCCCCCeEEEECChhhHHhcCCCCCCEEEEEE
Confidence 4567777666542 4444544 4588899999999999874
No 51
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=51.38 E-value=22 Score=27.45 Aligned_cols=29 Identities=10% Similarity=0.219 Sum_probs=25.5
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
.++..|+|..=-++.|||.+||.|+|.+.
T Consensus 27 ~~~~~v~i~p~dA~~~gi~~Gd~V~v~s~ 55 (123)
T cd02778 27 TPENTLWINPETAARLGIKDGDRVEVSSA 55 (123)
T ss_pred CCCCeEEECHHHHHHcCCCCCCEEEEEeC
Confidence 46678999999999999999999998763
No 52
>cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=51.24 E-value=20 Score=28.14 Aligned_cols=29 Identities=17% Similarity=0.116 Sum_probs=25.9
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
.++..|.|-.--++.|+|.+||.|+|++.
T Consensus 30 ~~~~~v~i~p~dA~~~gi~~Gd~V~v~s~ 58 (129)
T cd02782 30 RNRCTLRIHPDDAAALGLADGDKVRVTSA 58 (129)
T ss_pred CCCceEEECHHHHHHcCCCCCCEEEEEcC
Confidence 46778999999999999999999998874
No 53
>cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=50.91 E-value=26 Score=27.90 Aligned_cols=30 Identities=13% Similarity=0.314 Sum_probs=24.5
Q ss_pred hccCcccccCCEEEEEECCEEEEEEEEEec
Q 035839 137 LRKFSCLTTGDTIMIMHNESKYYIDVLETK 166 (238)
Q Consensus 137 Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~k 166 (238)
+++...|.+||.|.|...++.|...|.+++
T Consensus 59 F~~L~~l~~Gd~v~v~~~~~~~~Y~V~~~~ 88 (126)
T cd06166 59 FNRLDEVEKGDEIKVTTKNGTYKYKITSIF 88 (126)
T ss_pred cCChHHCCCCCEEEEEECCEEEEEEEEEEE
Confidence 445566779999999999999999987754
No 54
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=50.01 E-value=22 Score=27.75 Aligned_cols=27 Identities=11% Similarity=0.025 Sum_probs=23.8
Q ss_pred CCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 79 EGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 79 EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
+..|+|-.=-++.||+.+||.|+|++.
T Consensus 29 ~~~v~i~p~~A~~~gi~~Gd~V~v~s~ 55 (121)
T cd02794 29 PQEVWINPLDAAARGIKDGDRVLVFND 55 (121)
T ss_pred CCCEEECHHHHHHcCCCCCCEEEEEcC
Confidence 456899999999999999999998864
No 55
>TIGR03243 arg_catab_AOST arginine and ornithine succinyltransferase subunits. In many bacteria, the sole member of this protein family is arginine N-succinyltransferase (EC 2.3.1.109), the AstA protein of the arginine succinyltransferase (ast) pathway. However, in Pseudomonas aeruginosa and several other species, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST).
Probab=49.79 E-value=22 Score=34.00 Aligned_cols=34 Identities=26% Similarity=0.333 Sum_probs=28.6
Q ss_pred EEEeeeEeCCCcEeccHhHHhhcCCCCCCeEEEE
Q 035839 70 CGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVT 103 (238)
Q Consensus 70 ~GVlEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~ 103 (238)
|.+.....+.+.+.|+.-+++.|++++||.|++-
T Consensus 300 a~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~ 333 (335)
T TIGR03243 300 AVLAPLSADAGTLILSADAADALGVSEGDTVRVV 333 (335)
T ss_pred EEEecccCCCCeeecCHHHHHhcCCCCCCeEEEe
Confidence 4446666678889999999999999999999874
No 56
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=48.71 E-value=26 Score=28.77 Aligned_cols=26 Identities=15% Similarity=0.217 Sum_probs=20.9
Q ss_pred CcccccCCEEEEEE-CCEEEEEEEEEe
Q 035839 140 FSCLTTGDTIMIMH-NESKYYIDVLET 165 (238)
Q Consensus 140 ys~LT~Gd~I~I~~-~~~~y~l~V~e~ 165 (238)
...|.+||.|.|.. +++.|...|.++
T Consensus 70 L~~l~~GD~I~v~~~~g~~~~Y~V~~~ 96 (144)
T cd05829 70 LGDLRKGDKVEVTRADGQTATFRVDRV 96 (144)
T ss_pred hhcCCCCCEEEEEECCCCEEEEEEeEE
Confidence 34577999999999 777788888775
No 57
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=48.31 E-value=23 Score=29.13 Aligned_cols=47 Identities=19% Similarity=0.179 Sum_probs=31.7
Q ss_pred cHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEeCCCcEeccHhHHhhcCCCCCCeEEEEEe---eeCCce
Q 035839 39 PQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNV---SLAKAT 111 (238)
Q Consensus 39 P~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~---~LPkgt 111 (238)
-+.+|++|.+.+ +-+|+|.|..+- .--+.+++||.|.++++ +|-+||
T Consensus 10 s~~vi~eL~~~~---~RTiEirSa~N~-----------------------~~~~~~~~Gd~VFlT~~~~~Dl~~Gt 59 (119)
T PF04322_consen 10 SRRVIDELKKNH---IRTIEIRSAHNV-----------------------IALESLDPGDRVFLTSVSLEDLTPGT 59 (119)
T ss_pred CHHHHHHHHhCC---ceEEEEEcchhe-----------------------eeeecCCCCCEEEEecCCHHHCCCCC
Confidence 367888887654 459999986551 12245688888888887 455554
No 58
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=48.09 E-value=60 Score=28.66 Aligned_cols=16 Identities=19% Similarity=0.171 Sum_probs=11.8
Q ss_pred EEEeCceEEEecCCCC
Q 035839 172 SITETDCEVDFAPPLD 187 (238)
Q Consensus 172 sIidTDl~VDf~ppl~ 187 (238)
.|-+..+.|||--||-
T Consensus 111 ev~~d~V~vD~NHPLA 126 (196)
T PRK10737 111 AVEDDHVVVDGNHMLA 126 (196)
T ss_pred EEcCCEEEEECCCcCC
Confidence 3456678899988873
No 59
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=47.62 E-value=26 Score=26.84 Aligned_cols=30 Identities=3% Similarity=0.079 Sum_probs=25.3
Q ss_pred hHHhhcCCCCCCeEEEEEeeeCCceeEEEe
Q 035839 87 WMMDNMKLQEYELVRVTNVSLAKATYMKLQ 116 (238)
Q Consensus 87 Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLq 116 (238)
-+.+.+|+++||.|+|...+---|.++..+
T Consensus 45 Pv~r~~g~k~GdVvkI~R~S~taG~~v~YR 74 (79)
T PRK09570 45 PVVKAIGAKPGDVIKIVRKSPTAGEAVYYR 74 (79)
T ss_pred hhhhhcCCCCCCEEEEEECCCCCCccEEEE
Confidence 477889999999999998887788887654
No 60
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=47.62 E-value=77 Score=26.56 Aligned_cols=92 Identities=18% Similarity=0.198 Sum_probs=55.5
Q ss_pred EeeeEeCCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCc---ccccCCE
Q 035839 72 VVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFS---CLTTGDT 148 (238)
Q Consensus 72 VlEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys---~LT~Gd~ 148 (238)
=+.|+--.|.+ +|.|=-.=++++.|+.+.+. ||. +.+|- -.||..|.+-.+.+|. -+-.|..
T Consensus 34 P~~f~~G~g~v-i~gle~aL~gm~~Ge~~~v~---ipp---------~~ayG--~~d~~~v~~vp~~~f~~~~~~~~G~~ 98 (156)
T PRK15095 34 PALFRLGDGSL-SEGLEQQLLGLKVGDKKTFS---LEP---------EAAFG--VPSPDLIQYFSRRDFMDAGEPEIGAI 98 (156)
T ss_pred CEEEEeCCCCc-cHHHHHHHcCCCCCCEEEEE---ECh---------HHhcC--CCChHHEEEecHHHCCcccCCCCCCE
Confidence 34555445554 79999888899999987653 332 12332 2455555444444443 3677877
Q ss_pred EEEEE-CCEEEEEEEEEecCCCceEEEeCceEEEecCCC
Q 035839 149 IMIMH-NESKYYIDVLETKPSNAVSITETDCEVDFAPPL 186 (238)
Q Consensus 149 I~I~~-~~~~y~l~V~e~kP~~aVsIidTDl~VDf~ppl 186 (238)
+.+.. .+..+...|++ |-+..+.|||--||
T Consensus 99 ~~~~~~~G~~~~~~V~~--------i~~~~v~vD~NHPL 129 (156)
T PRK15095 99 MLFTAMDGSEMPGVIRE--------INGDSITVDFNHPL 129 (156)
T ss_pred EEEECCCCCEEEEEEEE--------EcCCEEEEECCCcC
Confidence 76653 23445555555 44567888888886
No 61
>cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=47.49 E-value=25 Score=27.88 Aligned_cols=29 Identities=17% Similarity=0.062 Sum_probs=25.6
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
.++..|+|=.--++.|||++||.|+|.+.
T Consensus 30 ~~~~~v~i~p~dA~~~gi~~Gd~V~v~s~ 58 (129)
T cd02793 30 QGREPIRINPADAAARGIADGDIVRVFND 58 (129)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 45678999999999999999999998874
No 62
>cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=47.48 E-value=24 Score=29.24 Aligned_cols=32 Identities=9% Similarity=0.283 Sum_probs=27.6
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCce
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKAT 111 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt 111 (238)
.++..|+|-.--++.|||.+||.|+|.+ +.|+
T Consensus 29 ~~~~~v~inp~dA~~~GI~dGd~V~v~s---~~G~ 60 (156)
T cd02783 29 HTRNYLYMHPKTAKELGIKDGDWVWVES---VNGR 60 (156)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEc---CCee
Confidence 4567899999999999999999999998 4464
No 63
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=45.82 E-value=28 Score=23.94 Aligned_cols=23 Identities=9% Similarity=-0.003 Sum_probs=18.5
Q ss_pred EeccHhHHhhcCCCCCCeEEEEE
Q 035839 82 IYLPNWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 82 i~lP~Wmm~~L~l~~gd~V~v~~ 104 (238)
+.++.|-...|+|++||.|.+..
T Consensus 35 a~it~~~~~~L~L~~G~~V~~~i 57 (64)
T PF03459_consen 35 ARITPESAEELGLKPGDEVYASI 57 (64)
T ss_dssp EEEEHHHHHHCT-STT-EEEEEE
T ss_pred EEEcHHHHHHcCCCCCCEEEEEE
Confidence 67999999999999999998754
No 64
>cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins.
Probab=43.67 E-value=34 Score=27.59 Aligned_cols=28 Identities=14% Similarity=0.171 Sum_probs=25.2
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEE
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~ 104 (238)
.++..+.|-.=-++.|+|++||.|+|++
T Consensus 27 ~~~~~v~inp~dA~~lgI~~Gd~V~v~s 54 (143)
T cd02780 27 KPENPVWINPEDAAKLGIKTGDRVRVVT 54 (143)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEe
Confidence 3567899999999999999999999887
No 65
>PF10636 hemP: Hemin uptake protein hemP; InterPro: IPR019600 This entry represents bacterial proteins that are involved in the uptake of the iron source hemin []. ; PDB: 2JRA_B 2LOJ_A.
Probab=43.28 E-value=55 Score=21.81 Aligned_cols=22 Identities=18% Similarity=0.362 Sum_probs=18.5
Q ss_pred cccCCEEEEEECCEEEEEEEEE
Q 035839 143 LTTGDTIMIMHNESKYYIDVLE 164 (238)
Q Consensus 143 LT~Gd~I~I~~~~~~y~l~V~e 164 (238)
+.-+..|.|.|++..|.|++..
T Consensus 9 ~~~~~ev~I~H~g~~Y~LR~Tr 30 (38)
T PF10636_consen 9 FGGGREVRIEHGGQIYRLRITR 30 (38)
T ss_dssp TTTTSEEEEEETTEEEEEEEET
T ss_pred hCCCCEEEEEeCCeEEEeeEcc
Confidence 3456899999999999999864
No 66
>TIGR03244 arg_catab_AstA arginine N-succinyltransferase. In many bacteria, the arginine succinyltransferase (ast) pathway operon consists of five genes, including this protein, arginine N-succinyltransferase (EC 2.3.1.109). In a few species, such as Pseudomonas aeruginosa, the member of this family is encoded adjacent to a paralog, and the two polypeptides form a heterodimeric enzyme, active on both arginine and ornithine. In such species, this polypeptide may be treated as the beta subunit of an enzyme that may be named either arginine N-succinyltransferase (AST) or arginine and orthithine N-succinyltransferase (AOST).
Probab=41.89 E-value=35 Score=32.68 Aligned_cols=46 Identities=20% Similarity=0.268 Sum_probs=32.9
Q ss_pred EEEEeCCCCCeEEEEEeeeEeCCCcEeccHhHHhhcCCCCCCeEEEE
Q 035839 57 FELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVT 103 (238)
Q Consensus 57 F~i~n~~~~~~th~GVlEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~ 103 (238)
+-|+|..... --|.+.....+.+.+.|+.-+++.|++++||.|++-
T Consensus 289 ~Lv~n~~~~~-FRa~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~ 334 (336)
T TIGR03244 289 YIVANTSLSD-FRATLAPSDLDAGELVLTAAQADALRVSAGDLVRIV 334 (336)
T ss_pred EEEECCCCCC-eEEEEecccCCCCeEecCHHHHHhcCCCCCCeEEEe
Confidence 4466643221 123345566677889999999999999999999874
No 67
>PRK10456 arginine succinyltransferase; Provisional
Probab=41.84 E-value=35 Score=32.78 Aligned_cols=47 Identities=15% Similarity=0.099 Sum_probs=33.2
Q ss_pred EEEEeCCCCCeEEEEEeeeEeCCCcEeccHhHHhhcCCCCCCeEEEEE
Q 035839 57 FELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 57 F~i~n~~~~~~th~GVlEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~ 104 (238)
+-|+|..... --|.+.....+.+.+.|+.-+++.|++++||.|++--
T Consensus 290 ~Lv~n~~~~~-FRa~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~~ 336 (344)
T PRK10456 290 CLVANENYHH-FRAVLVRTDPATERLILTAAQLDALKCHAGDRVRLVR 336 (344)
T ss_pred EEEECCCCCC-eEEEEecccCCCCeEecCHHHHHhcCCCCCCeEEEEe
Confidence 4455543211 1233456666778899999999999999999998753
No 68
>cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase.
Probab=41.46 E-value=48 Score=26.45 Aligned_cols=29 Identities=28% Similarity=0.340 Sum_probs=23.5
Q ss_pred ccCcccccCCEEEEEECCEEEEEEEEEec
Q 035839 138 RKFSCLTTGDTIMIMHNESKYYIDVLETK 166 (238)
Q Consensus 138 rnys~LT~Gd~I~I~~~~~~y~l~V~e~k 166 (238)
++...|.+||.|.+...++.|..+|.+++
T Consensus 57 ~~L~~l~~Gd~i~v~~~~~~~~Y~V~~~~ 85 (127)
T cd05828 57 RFLGELEPGDIITLQTLGGTYTYRVTSTR 85 (127)
T ss_pred hChhcCCCCCEEEEEECCEEEEEEEeeEE
Confidence 33445668999999999999999998764
No 69
>TIGR03245 arg_AOST_alph arginine/ornithine succinyltransferase, alpha subunit. In some bacteria, including Pseudomonas aeruginosa, the astB gene (arginine N-succinyltransferase) is replaced by tandem paralogs that form a heterodimer. This heterodimer from P. aeruginosa is characterized as arginine and ornithine N-2 succinyltransferase (AOST). Members of this protein family represent the less widespread paralog, designated AruI, or arginine/ornithine succinyltransferase, alpha subunit.
Probab=40.33 E-value=37 Score=32.50 Aligned_cols=34 Identities=18% Similarity=0.247 Sum_probs=27.5
Q ss_pred EEEeeeE-eCCCcEeccHhHHhhcCCCCCCeEEEE
Q 035839 70 CGVVEFT-ADEGFIYLPNWMMDNMKLQEYELVRVT 103 (238)
Q Consensus 70 ~GVlEF~-A~EG~i~lP~Wmm~~L~l~~gd~V~v~ 103 (238)
|.++... .+.+.+.|+.-+++.|++++||.|++-
T Consensus 300 a~~~~~~~~~~~~~~l~~~~a~aL~v~~Gd~Vr~~ 334 (336)
T TIGR03245 300 ATLADVTDVDGDLLRLKRDAAEALGVSEGDNVRFA 334 (336)
T ss_pred EEEeccccCCCCeeecCHHHHHhcCCCCCCeEEEe
Confidence 3345555 567788999999999999999999874
No 70
>cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell.
Probab=40.06 E-value=47 Score=26.89 Aligned_cols=30 Identities=20% Similarity=0.334 Sum_probs=24.1
Q ss_pred hccCcccccCCEEEEEECCEEEEEEEEEec
Q 035839 137 LRKFSCLTTGDTIMIMHNESKYYIDVLETK 166 (238)
Q Consensus 137 Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~k 166 (238)
+++...|.+||.|.|...+..|..+|.+++
T Consensus 60 F~~L~~l~~Gd~i~v~~~~~~~~Y~V~~~~ 89 (137)
T cd05830 60 FNDLDKLRPGDKIVVETADGWYTYVVRSSE 89 (137)
T ss_pred cccHhhCCCCCEEEEEECCeEEEEEEeEEE
Confidence 334455889999999999999999988764
No 71
>PRK08059 general stress protein 13; Validated
Probab=39.40 E-value=1.6e+02 Score=23.50 Aligned_cols=59 Identities=17% Similarity=0.316 Sum_probs=37.0
Q ss_pred HHhhcCCCCCCeEEEEEe-eeCCceeEEEeecCccccccCCChHHHHHHhhcc-CcccccCCEEEEE
Q 035839 88 MMDNMKLQEYELVRVTNV-SLAKATYMKLQPHTKGFLDELSNPRAVLEAILRK-FSCLTTGDTIMIM 152 (238)
Q Consensus 88 mm~~L~l~~gd~V~v~~~-~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrn-ys~LT~Gd~I~I~ 152 (238)
||+. ++.|+.|.-+-+ .-+.|-||.|.+.-..|+. +++-.. ...++ ...+..||+|.+.
T Consensus 1 ~~~~--~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~-~sel~~---~~~~~~~~~~~vGD~I~vk 61 (123)
T PRK08059 1 MMSQ--YEVGSVVTGKVTGIQPYGAFVALDEETQGLVH-ISEITH---GFVKDIHDFLSVGDEVKVK 61 (123)
T ss_pred Cccc--CCCCCEEEEEEEEEecceEEEEECCCCEEEEE-HHHCCc---ccccCHHHcCCCCCEEEEE
Confidence 4555 467888776654 4578999999887667765 432110 00112 3467899999875
No 72
>TIGR01076 sortase_fam LPXTG-site transpeptidase (sortase) family protein. of an LPXTG motif to the cell wall. It also includes a protein required for correct assembly of an LPXTG-containing fimbrial protein, a set of homologous proteins from Streptococcus pneumoniae, in which LPXTG proteins are common. However, related proteins are found in Bacillus subtilis and Methanobacterium thermoautotrophicum, in which LPXTG-mediated cell wall attachment is not known.
Probab=38.11 E-value=49 Score=26.74 Aligned_cols=24 Identities=21% Similarity=0.239 Sum_probs=20.5
Q ss_pred ccccCCEEEEEECCEEEEEEEEEe
Q 035839 142 CLTTGDTIMIMHNESKYYIDVLET 165 (238)
Q Consensus 142 ~LT~Gd~I~I~~~~~~y~l~V~e~ 165 (238)
.|.+||.|.+...+..|...|.++
T Consensus 63 ~l~~GD~i~v~~~~~~~~Y~V~~~ 86 (136)
T TIGR01076 63 KLKKGDMLYLHVGNEVLTYQVTST 86 (136)
T ss_pred HCCCCCEEEEEECCcEEEEEEEEE
Confidence 377999999999988888888765
No 73
>cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra
Probab=36.60 E-value=58 Score=25.81 Aligned_cols=24 Identities=25% Similarity=0.458 Sum_probs=20.6
Q ss_pred cccCCEEEEEECCEEEEEEEEEec
Q 035839 143 LTTGDTIMIMHNESKYYIDVLETK 166 (238)
Q Consensus 143 LT~Gd~I~I~~~~~~y~l~V~e~k 166 (238)
|.+||.|.+...++.|...|.+.+
T Consensus 64 l~~Gd~I~l~~~~~~~~Y~V~~~~ 87 (127)
T cd06165 64 VKVGDKIYLTDKDNVYEYKVTSKK 87 (127)
T ss_pred CcCCCEEEEEECCEEEEEEEeeEE
Confidence 448999999999999999988754
No 74
>cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s
Probab=36.07 E-value=62 Score=25.51 Aligned_cols=25 Identities=24% Similarity=0.349 Sum_probs=21.4
Q ss_pred ccccCCEEEEEECCEEEEEEEEEec
Q 035839 142 CLTTGDTIMIMHNESKYYIDVLETK 166 (238)
Q Consensus 142 ~LT~Gd~I~I~~~~~~y~l~V~e~k 166 (238)
.|.+||.|.|...++.|...|.+++
T Consensus 64 ~l~~Gd~v~v~~~~~~~~Y~V~~~~ 88 (128)
T cd00004 64 NLKKGDKIYLTDGGKTYVYKVTSIL 88 (128)
T ss_pred HCCCCCEEEEEECCEEEEEEEEEEE
Confidence 4566999999999999999998764
No 75
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=35.56 E-value=67 Score=22.17 Aligned_cols=28 Identities=14% Similarity=0.373 Sum_probs=23.1
Q ss_pred cccCCEEEEEE-CCEEEEEEEEEecCCCc
Q 035839 143 LTTGDTIMIMH-NESKYYIDVLETKPSNA 170 (238)
Q Consensus 143 LT~Gd~I~I~~-~~~~y~l~V~e~kP~~a 170 (238)
|.+|+.+.+.+ ++..|.=+|+++++.+.
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~~ 29 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKNG 29 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECTT
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecCC
Confidence 46899999999 89999999999987543
No 76
>PRK10183 hypothetical protein; Provisional
Probab=35.20 E-value=54 Score=23.66 Aligned_cols=22 Identities=18% Similarity=0.421 Sum_probs=19.3
Q ss_pred cccCCEEEEEECCEEEEEEEEE
Q 035839 143 LTTGDTIMIMHNESKYYIDVLE 164 (238)
Q Consensus 143 LT~Gd~I~I~~~~~~y~l~V~e 164 (238)
|.-+..|.|.|++..|.|++..
T Consensus 27 l~g~~~v~I~H~G~~Y~LR~Tr 48 (56)
T PRK10183 27 LGPDGKVIIDHDGQEYLLRKTQ 48 (56)
T ss_pred hCCCCEEEEEECCcEEEeEEcc
Confidence 5677899999999999999865
No 77
>cd02784 MopB_CT_PHLH The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=34.30 E-value=57 Score=26.87 Aligned_cols=27 Identities=11% Similarity=0.188 Sum_probs=24.4
Q ss_pred CCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 79 EGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 79 EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
+..|+|-.--.+.|+|.+||.|+|.+-
T Consensus 37 ~~~v~InP~dA~~lGI~dGD~V~V~s~ 63 (137)
T cd02784 37 DNAALVSPRTAEALGLLQGDVVRIRRG 63 (137)
T ss_pred CceEEECHHHHHHcCCCCCCEEEEEeC
Confidence 567999999999999999999999874
No 78
>PF04958 AstA: Arginine N-succinyltransferase beta subunit; InterPro: IPR007041 Arginine N-succinyltransferase catalyses the transfer of succinyl-CoA to arginine to produce succinylarginine. This is the first step in arginine catabolism via the arginine succinyltransferase pathway. Six major L-arginine-degrading pathways have been described for prokaryotes []. Many bacteria arginine succinyltransferase 2.3.1.109 from EC, which is the AstA protein of the succinyltransferase (ast) pathway operon consists of five genes. In a few species, such as Pseudomonas aeruginosa, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST). This entry represents the family of proteins that make up the beta subunit of the heterodimer of Ast and AOST.; GO: 0008791 arginine N-succinyltransferase activity, 0006527 arginine catabolic process; PDB: 1YLE_A.
Probab=33.37 E-value=54 Score=31.45 Aligned_cols=48 Identities=17% Similarity=0.151 Sum_probs=25.2
Q ss_pred eEEEEEeCCCCCeEEEEEeeeEeC-CCcEeccHhHHhhcCCCCCCeEEEE
Q 035839 55 MMFELCNLSSGKTTHCGVVEFTAD-EGFIYLPNWMMDNMKLQEYELVRVT 103 (238)
Q Consensus 55 m~F~i~n~~~~~~th~GVlEF~A~-EG~i~lP~Wmm~~L~l~~gd~V~v~ 103 (238)
..+-|+|..... --|-+-+-... .+.+.|+.-+++.|++++||.|++-
T Consensus 292 ~~~Lvan~~~~~-FRa~~~~~~~~~~~~~~l~~~~a~~L~v~~Gd~Vr~~ 340 (342)
T PF04958_consen 292 PPYLVANTRLED-FRATLAPAALDDGDQLVLSPEVADALQVSEGDPVRVV 340 (342)
T ss_dssp EEEEEE---STT---EEEEEE---TTS-EEE-HHHHHHHT--TT-EEEEE
T ss_pred CeEEEECCCccC-eEEEEEecccCCCCeEEcCHHHHhhcCCCCCCEEEEe
Confidence 445566643221 11344444444 8999999999999999999999873
No 79
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=32.97 E-value=44 Score=24.29 Aligned_cols=65 Identities=15% Similarity=0.209 Sum_probs=38.8
Q ss_pred CCCCCeEEEEEe-eeCCceeEEEeecCccccccCCChHHHHHHhhccC-cccccCCEEEEEECCEEEEEEEEEecCC
Q 035839 94 LQEYELVRVTNV-SLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKF-SCLTTGDTIMIMHNESKYYIDVLETKPS 168 (238)
Q Consensus 94 l~~gd~V~v~~~-~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrny-s~LT~Gd~I~I~~~~~~y~l~V~e~kP~ 168 (238)
+++|+.|.-.-. -.+.|-||.|-|.-..|+. ++|--.-.-..++++ ..+..||.+. .+|++++++
T Consensus 1 ~k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~-~~~ls~~~~~~~~~~~~~~~~G~~v~---------~kVl~id~~ 67 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVL-FQNVTKYFVSDPSLYNKYLPEGKLLT---------AKVLSVNSE 67 (74)
T ss_pred CCCCCEEEEEEEEEeCCcEEEEeCCCCEEEEE-HHHccCccccChhhHhcccCCCCEEE---------EEEEEEECC
Confidence 467888875533 3599999999998888887 543111000011111 3456777665 456666665
No 80
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=32.53 E-value=97 Score=21.62 Aligned_cols=56 Identities=7% Similarity=-0.033 Sum_probs=35.3
Q ss_pred CCCCCeEEEEEe-eeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEE
Q 035839 94 LQEYELVRVTNV-SLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIM 152 (238)
Q Consensus 94 l~~gd~V~v~~~-~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~ 152 (238)
|+.|+.|.-+-. --+.|=||.|.+.-..|+. +++... +..-+.-..+..||+|.+.
T Consensus 1 ~~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~-~s~l~~--~~~~~~~~~~~~Gd~v~~~ 57 (73)
T cd05706 1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSF-ITDALD--DYSEALPYKFKKNDIVRAC 57 (73)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEeCCCcEEEEE-hhhccC--ccccccccccCCCCEEEEE
Confidence 467888876554 3678999999888778887 654221 0000112447888888774
No 81
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=32.38 E-value=80 Score=23.03 Aligned_cols=24 Identities=17% Similarity=0.263 Sum_probs=19.2
Q ss_pred cccCCEEEEEECCEEEEEEEEEec
Q 035839 143 LTTGDTIMIMHNESKYYIDVLETK 166 (238)
Q Consensus 143 LT~Gd~I~I~~~~~~y~l~V~e~k 166 (238)
...||++.+...+..+.+.|++++
T Consensus 53 ~~~Gd~v~~~~~~g~~~~~I~~I~ 76 (77)
T PF01272_consen 53 KKVGDEVEVELPGGERKYEILEIE 76 (77)
T ss_dssp -BTT-EEEEEETTBEEEEEEEEEE
T ss_pred CCCCCEEEEEeCCceEEEEEEEEE
Confidence 468999999999888889988864
No 82
>PF09263 PEX-2N: Peroxisome biogenesis factor 1, N-terminal ; InterPro: IPR015343 This domain adopts a Cdc48 domain 2-like fold, with a beta-alpha-beta(3) arrangement. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation []. ; PDB: 1WLF_A.
Probab=32.21 E-value=2.2e+02 Score=22.33 Aligned_cols=67 Identities=12% Similarity=0.093 Sum_probs=34.5
Q ss_pred eeecHHHHHHHHhCCCCCceEEEEEeCCCCC--eEEEEEeeeE-eCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 36 IIMPQSAFDRLAHTEVGYPMMFELCNLSSGK--TTHCGVVEFT-ADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 36 IiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~--~th~GVlEF~-A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
+-||+....+|.-.+.. -+|++-..... -+-+.-+-|+ .+|..+-|-.-+-++|||.+|+.|.++-+
T Consensus 16 L~Lp~~l~~~L~L~q~q---AvEvsWg~~~pvfLSW~e~r~~~~~~en~~EinrqlgeKLGl~dGeQvfLrpC 85 (87)
T PF09263_consen 16 LHLPSRLASQLHLQQNQ---AVEVSWGHQSPVFLSWVEGRSFSDQGENVAEINRQLGEKLGLSDGEQVFLRPC 85 (87)
T ss_dssp EEE-HHHHHHTT--TT-----EEEESSS---EEE-EEE-SS-------EEEEEHHHHHHTT--TT-EEEEEE-
T ss_pred EECCHHHHHHHHHhhCc---eEEEEeCCCCcEEEEeecccccCCccccHHHHHHHHHHhhCCCcCCeEeeeeC
Confidence 56899988877544332 45555432211 2234455554 37899999999999999999999887654
No 83
>TIGR02620 cas_VVA1548 putative CRISPR-associated protein, VVA1548 family. This model represents a conserved domain of about 95 amino acids exclusively in species with CRISPR (Clustered Regularly Interspaced Short Palidromic Repeats). In all bacterial species with members so far (Vibrio vulnificus YJ016, Mannheimia succiniciproducens MBEL55E, and Nitrosomonas europaea ATCC 19718) and but not in the archaeon Methanothermobacter thermautotrophicus str. Delta H, the gene for this protein is in the midst of a cluster of Cas protein gene near CRISPR repeats.
Probab=31.67 E-value=30 Score=27.35 Aligned_cols=29 Identities=24% Similarity=0.391 Sum_probs=24.2
Q ss_pred cccCCCCCCCCeee--ecHHHHHHHHhCCCC
Q 035839 24 HVAKPQHEPGDKII--MPQSAFDRLAHTEVG 52 (238)
Q Consensus 24 ~~~~~~~~~gdKIi--LP~SaL~~L~~~~i~ 52 (238)
.++-..+..||+|| ||.+...++++....
T Consensus 26 HLd~~~i~~GD~ViGtLPv~Laa~vc~kGa~ 56 (93)
T TIGR02620 26 HLDPIDISQGDKVIGTLPVSLAADICKKGAR 56 (93)
T ss_pred ccCHHHhcCCCEEEEeCCHHHHHHHHhCCcE
Confidence 45667889999997 999999999986554
No 84
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=29.27 E-value=80 Score=23.99 Aligned_cols=48 Identities=25% Similarity=0.242 Sum_probs=28.5
Q ss_pred CCceEEEEEeCCCCCeEEEEEeeeEeCCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeE
Q 035839 52 GYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYM 113 (238)
Q Consensus 52 ~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~v 113 (238)
.-|..+.++|.+.. .-+|..++ +.....|.+|+..+++...+..|+|-
T Consensus 42 G~~v~l~~~N~~~~------~h~~~i~~--------~~~~~~l~~g~~~~~~f~~~~~G~y~ 89 (104)
T PF13473_consen 42 GQPVTLTFTNNDSR------PHEFVIPD--------LGISKVLPPGETATVTFTPLKPGEYE 89 (104)
T ss_dssp TCEEEEEEEE-SSS-------EEEEEGG--------GTEEEEE-TT-EEEEEEEE-S-EEEE
T ss_pred CCeEEEEEEECCCC------cEEEEECC--------CceEEEECCCCEEEEEEcCCCCEEEE
Confidence 44677777775443 25566554 33345578899999998899999874
No 85
>PRK07252 hypothetical protein; Provisional
Probab=29.16 E-value=1.5e+02 Score=23.92 Aligned_cols=54 Identities=13% Similarity=0.292 Sum_probs=33.2
Q ss_pred CCCCeEEEEEe-eeCCceeEEEeecCccccccCCChHHHHHHhhcc-CcccccCCEEEEE
Q 035839 95 QEYELVRVTNV-SLAKATYMKLQPHTKGFLDELSNPRAVLEAILRK-FSCLTTGDTIMIM 152 (238)
Q Consensus 95 ~~gd~V~v~~~-~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrn-ys~LT~Gd~I~I~ 152 (238)
+.|+.+.-.-+ -.+.|-||.|.+.-..|+. +++... ....+ ...+..||+|.+.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~Gllh-iseLs~---~~~~~~~~~~~vGD~V~Vk 57 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIH-ISEIKT---GFIDNIHQLLKVGEEVLVQ 57 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEE-HHHcCC---ccccChhhccCCCCEEEEE
Confidence 45776665444 3578999999877777876 543221 01111 2347889988875
No 86
>PF04203 Sortase: Sortase family; InterPro: IPR005754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to MEROPS peptidase family C60 (clan C-) and include the members of both subfamilies of sortases. The Staphylococcus aureus sortase is a transpeptidase that attaches surface proteins to the cell wall; it cleaves between the Gly and Thr of the LPXTG motif and catalyses the formation of an amide bond between the carboxyl-group of threonine and the amino-group of the cell-wall peptidoglycan []. Sortase homologues are found in almost all Gram-positives, a single Gram-negative (Shewanella putrefaciens) and an archaean (Methanobacterium thermoautotrophicum), where cell wall LPXTG-mediated decoration has not been reported [, ]. Surface proteins not only promote interaction between the invading pathogen and animal tissues, but also provide ingenious strategies for bacterial escape from the host's immune response. In the case of S. aureus protein A, immunoglobulins are captured on the microbial surface and camouflage bacteria during the invasion of host tissues. S. aureus mutants lacking the srtA gene fail to anchor and display some surface proteins and are impaired in the ability to cause animal infections. Sortase acts on surface proteins that are initiated into the secretion (Sec) pathway and have their signal peptide removed by signal peptidase. The S. aureus genome encodes two sets of sortase and secretion genes. It is conceivable that S. aureus has evolved more than one pathway for the transport of 20 surface proteins to the cell wall envelope. ; PDB: 2W1K_A 2OQZ_A 1RZ2_A 2OQW_A 1T2W_A 1IJA_A 1T2P_A 1T2O_C 2KID_A 3RCC_N ....
Probab=29.09 E-value=1e+02 Score=23.89 Aligned_cols=23 Identities=26% Similarity=0.411 Sum_probs=18.7
Q ss_pred ccCCEEEEEE-CCEEEEEEEEEec
Q 035839 144 TTGDTIMIMH-NESKYYIDVLETK 166 (238)
Q Consensus 144 T~Gd~I~I~~-~~~~y~l~V~e~k 166 (238)
.+||.|.|.. +++.|...|.+++
T Consensus 62 ~~gd~i~~~~~~g~~~~Y~V~~~~ 85 (128)
T PF04203_consen 62 KKGDEIYLTTPDGKTYEYRVTSVK 85 (128)
T ss_dssp HTT-EEEEEETSSEEEEEEEEEEE
T ss_pred CCCCEEEEEEecCEEEEEEEEEEE
Confidence 8999999999 7888888887755
No 87
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=28.99 E-value=92 Score=22.23 Aligned_cols=56 Identities=9% Similarity=0.097 Sum_probs=36.5
Q ss_pred CCCCCeEEEEEeee-C-CceeEEEeecCccccccCCChHHHHHHhhcc-CcccccCCEEEEEE
Q 035839 94 LQEYELVRVTNVSL-A-KATYMKLQPHTKGFLDELSNPRAVLEAILRK-FSCLTTGDTIMIMH 153 (238)
Q Consensus 94 l~~gd~V~v~~~~L-P-kgt~vkLqP~s~~F~~~i~npKavLE~~Lrn-ys~LT~Gd~I~I~~ 153 (238)
|++|+.|.=+-+.+ + .|-|+.|-|....++. +++... ...++ ...+..||.|.+..
T Consensus 1 l~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvh-is~~s~---~~~~~~~~~~~~Gd~v~~kV 59 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVS-IFHLSD---SYTENPLEGFKPGKIVRCCI 59 (72)
T ss_pred CCCCCEEEEEEEEeeCCcEEEEECCCCCEEEEE-HHHhcC---cccCCHHHhCCCCCEEEEEE
Confidence 46788877555553 3 6999999998888887 653211 12222 23467899998864
No 88
>PRK05807 hypothetical protein; Provisional
Probab=28.71 E-value=1.9e+02 Score=23.62 Aligned_cols=55 Identities=13% Similarity=0.216 Sum_probs=35.1
Q ss_pred CCCCCCeEEEEEe-eeCCceeEEEeecCccccccCCChHHHHHHhhcc-CcccccCCEEEEE
Q 035839 93 KLQEYELVRVTNV-SLAKATYMKLQPHTKGFLDELSNPRAVLEAILRK-FSCLTTGDTIMIM 152 (238)
Q Consensus 93 ~l~~gd~V~v~~~-~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrn-ys~LT~Gd~I~I~ 152 (238)
.++.|+.|.-.-. --+-|-||.| .....|+. +++... ...++ ...+..||.|.+.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L-~~~~Glvh-iseis~---~~v~~~~~~~kvGd~V~Vk 58 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEV-EGKTGLVH-ISEVAD---TYVKDIREHLKEQDKVKVK 58 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEE-CCEEEEEE-hhhccc---ccccCccccCCCCCEEEEE
Confidence 3567888776644 5789999999 54566776 553221 11222 3458899998874
No 89
>PLN03086 PRLI-interacting factor K; Provisional
Probab=27.78 E-value=5.2e+02 Score=26.58 Aligned_cols=72 Identities=18% Similarity=0.187 Sum_probs=42.9
Q ss_pred CCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEeCCCcEeccHh--HHhhcC-----CCCCCeEEEEE
Q 035839 32 PGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNW--MMDNMK-----LQEYELVRVTN 104 (238)
Q Consensus 32 ~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~i~lP~W--mm~~L~-----l~~gd~V~v~~ 104 (238)
.-|.|.||+-+++.|...+....-+-+|++..-.+-|++-..--++ |+.=++.| ++++-. |..||+|.|.|
T Consensus 149 ~EG~v~lP~wm~~~L~~~~~~~~~~v~v~~~~Lpkgt~vklqP~~~--~f~di~npKavLE~~Lr~~stLT~Gd~i~i~~ 226 (567)
T PLN03086 149 EEGSVGLPPHVWSNLFPSDPPDVPLVEVRYIWLPKGTYAKLQPDGV--GFSDLPNHKAVLETALRQHATLSEDDVLVVNY 226 (567)
T ss_pred CCCeEEcCHHHHhhcCCCCCCCCCeEEEEEeecCCCCEEEEeeccC--CcCCcccHHHHHHHHhhcCccccCCCEEEEec
Confidence 3578999999999875322222236677765555556666553332 22234444 444332 67899999987
Q ss_pred e
Q 035839 105 V 105 (238)
Q Consensus 105 ~ 105 (238)
-
T Consensus 227 ~ 227 (567)
T PLN03086 227 G 227 (567)
T ss_pred C
Confidence 4
No 90
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=27.63 E-value=40 Score=26.22 Aligned_cols=44 Identities=18% Similarity=0.349 Sum_probs=20.8
Q ss_pred EEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECC
Q 035839 102 VTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNE 155 (238)
Q Consensus 102 v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~ 155 (238)
|+|-.-|...-+.++.. +. =||| +++-.+.-|..|+.++|+||-
T Consensus 35 Ikyddype~gvv~~~~~--~i-----RpRA---Rt~l~w~~L~VG~~VMvNYN~ 78 (85)
T PF12148_consen 35 IKYDDYPENGVVEMRSK--DI-----RPRA---RTILKWDELKVGQVVMVNYNV 78 (85)
T ss_dssp EEETT-GGG-EEEEEGG--GE-----EE------SBE-GGG--TT-EEEEEE-T
T ss_pred EEeccCCCcCceecccc--cc-----ccee---eEeccHHhCCcccEEEEecCC
Confidence 55555555444444433 11 1444 455578899999999999983
No 91
>cd05827 Sortase_C_3 Sortase C (SrtC) or subfamily-3 sortases are membrane cysteine transpeptidases found in Gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Sortase C cleaves surface proteins at the LPXTG motif between Thr and Gly and catalyzes the formation of an amide bond between the carboxyl group of Thr and the amino group of cell-wall cross bridges. It is a narrow-range enzyme required for anchoring a few substrates. It plays a role in Streptococcus pneumoniae pathogenesis and is required in the assembly of pili on the surface of Corynebacterium diphtheriae. Sortase C is
Probab=27.44 E-value=1.1e+02 Score=24.39 Aligned_cols=24 Identities=21% Similarity=0.187 Sum_probs=20.8
Q ss_pred cccCCEEEEEECCEEEEEEEEEec
Q 035839 143 LTTGDTIMIMHNESKYYIDVLETK 166 (238)
Q Consensus 143 LT~Gd~I~I~~~~~~y~l~V~e~k 166 (238)
|.+||.|.|...+..|...|.+++
T Consensus 67 l~~gd~i~l~t~~~~~~Y~V~~~~ 90 (131)
T cd05827 67 LKKGDKFYIHVLGETLAYQVDQIE 90 (131)
T ss_pred CCCCCEEEEEECCeEEEEEEEEEE
Confidence 559999999999999999988764
No 92
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=27.11 E-value=1.9e+02 Score=20.61 Aligned_cols=56 Identities=25% Similarity=0.251 Sum_probs=33.6
Q ss_pred CCCceEEEEEeCCCCC-eEEEEEeeeEeCCCc-EeccHhHHhhcCCCCCCeEEEEEee
Q 035839 51 VGYPMMFELCNLSSGK-TTHCGVVEFTADEGF-IYLPNWMMDNMKLQEYELVRVTNVS 106 (238)
Q Consensus 51 i~~Pm~F~i~n~~~~~-~th~GVlEF~A~EG~-i~lP~Wmm~~L~l~~gd~V~v~~~~ 106 (238)
+..++.-+++++...+ ...+=|.++..+.-. |-+|.|=-+.+.+.+|+.|.|++..
T Consensus 3 iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~~P~~~g~~~~l~~g~~v~v~~~~ 60 (87)
T PF12945_consen 3 IGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIISMPMEKGRPIPLREGEEVIVRFIS 60 (87)
T ss_dssp TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE---CCHHHCCS-TT-EEEEEEEE
T ss_pred CCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEEcCccCCcEEeecCCCEEEEEEEE
Confidence 4556777787765333 466778888877333 5588666667889999999998863
No 93
>COG0836 {ManC} Mannose-1-phosphate guanylyltransferase [Cell envelope biogenesis, outer membrane]
Probab=26.97 E-value=1.6e+02 Score=28.31 Aligned_cols=57 Identities=18% Similarity=0.270 Sum_probs=47.0
Q ss_pred CeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhcc-CcccccCCEEEEEECC
Q 035839 98 ELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRK-FSCLTTGDTIMIMHNE 155 (238)
Q Consensus 98 d~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrn-ys~LT~Gd~I~I~~~~ 155 (238)
+.+.|.|.-+.|..-+..-|.+-.+-| |.+|.|+.|-.-+. --....||++.+.-+|
T Consensus 245 p~iSIDYAiMEkt~~~aVVp~~f~WsD-lGsW~Al~~~~~~d~~gNv~~gd~~~~dt~n 302 (333)
T COG0836 245 PAISIDYAIMEKTSKAAVVPADFGWSD-LGSWHALWEVLDKDENGNVCEGDVVTIDTEN 302 (333)
T ss_pred cccchhHHHHhhhcceEEEecCCCccc-ccCHHHHHHHhhcCCCCCEEecceEEeccCC
Confidence 356778888999999999999999988 99999999877774 3457899998887544
No 94
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=26.77 E-value=1.9e+02 Score=22.03 Aligned_cols=48 Identities=21% Similarity=0.565 Sum_probs=30.7
Q ss_pred CcccccCCEEEEEECC-------EEEEE-EEEEec-----C------------CCceEEEeCceEEEecCCCC
Q 035839 140 FSCLTTGDTIMIMHNE-------SKYYI-DVLETK-----P------------SNAVSITETDCEVDFAPPLD 187 (238)
Q Consensus 140 ys~LT~Gd~I~I~~~~-------~~y~l-~V~e~k-----P------------~~aVsIidTDl~VDf~ppl~ 187 (238)
|-.+..||++.|..++ +.|.+ .|+.++ | ..-|+.|++|....+.+++|
T Consensus 3 FL~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~~~tlFQVadVDtG~I~wVnaD~Vt~Iv~~~~ 75 (75)
T PF11302_consen 3 FLSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPKVPTLFQVADVDTGVIRWVNADEVTHIVPSLD 75 (75)
T ss_pred ccccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCCCCceEEEEEccCCeEEEEEchheeeeeeccC
Confidence 4456677777777665 23332 333332 2 25789999999998888764
No 95
>smart00675 DM11 Domains in hypothetical proteins in Drosophila including 2 in CG15241 and CG9329.
Probab=26.29 E-value=1e+02 Score=26.40 Aligned_cols=78 Identities=12% Similarity=0.170 Sum_probs=49.4
Q ss_pred eEeCCCcEeccHhHHhhcCCCCCCeEEEEE--eeeCCceeEE--EeecCccccccCCChHHHHH----Hhhcc-----Cc
Q 035839 75 FTADEGFIYLPNWMMDNMKLQEYELVRVTN--VSLAKATYMK--LQPHTKGFLDELSNPRAVLE----AILRK-----FS 141 (238)
Q Consensus 75 F~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~--~~LPkgt~vk--LqP~s~~F~~~i~npKavLE----~~Lrn-----ys 141 (238)
|.-+++.|++-.=+--...++++|.|.++. .++..|++.. |-=...+|-..+-||...-= ++..| -.
T Consensus 37 ~~~d~~~i~vsGn~t~~wdi~P~DrI~~~~~~~~~eRG~W~PTv~s~~~~dFC~~m~d~~q~WY~~wtk~i~N~~evk~k 116 (164)
T smart00675 37 VDMDPDGLHISGNITVIWDVQPTDRISARVSVMHFERGTWQPTVFNMATPDFCKSMFDKNQYWYKYWTKYISNKEEIKEK 116 (164)
T ss_pred EEEcCCeEEEeeeEEEEEecCCCCeEEEEEEEEEecCCeeeeeEEeeeccChhHHhcCCCcchHHHHHHhcccHHHHHhc
Confidence 334555566665555556799999988774 4899999863 44456677775666554433 33332 44
Q ss_pred cc-ccCCEEEEE
Q 035839 142 CL-TTGDTIMIM 152 (238)
Q Consensus 142 ~L-T~Gd~I~I~ 152 (238)
|+ ++|.++..+
T Consensus 117 C~~~~Gtv~~~e 128 (164)
T smart00675 117 CLTTKGTVLVYE 128 (164)
T ss_pred CCCCCCeEEEec
Confidence 87 778777663
No 96
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=26.14 E-value=1.1e+02 Score=30.21 Aligned_cols=39 Identities=18% Similarity=0.157 Sum_probs=30.3
Q ss_pred CeEEEEEeeeE---------------eCCCcEeccHhHHhhcCCCCCCeEEEEE
Q 035839 66 KTTHCGVVEFT---------------ADEGFIYLPNWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 66 ~~th~GVlEF~---------------A~EG~i~lP~Wmm~~L~l~~gd~V~v~~ 104 (238)
.....||||.. +.++-||+|..+.+..+|+.||.|.=..
T Consensus 48 ~~~~~g~le~~~~g~gflr~~~~~y~~~~~d~yvs~~~ir~~~lr~gd~v~g~~ 101 (416)
T PRK09376 48 DIFGEGVLEILPDGFGFLRSPDANYLPGPDDIYVSPSQIRRFNLRTGDTVEGKI 101 (416)
T ss_pred ceEEEEEEEEcCCCCeEEeCCCcCCCCCCCCeeeCHHHHHhcCCCCCCEEEEEe
Confidence 35678999933 2335599999999999999999887543
No 97
>PRK13532 nitrate reductase catalytic subunit; Provisional
Probab=25.91 E-value=66 Score=33.66 Aligned_cols=51 Identities=16% Similarity=0.066 Sum_probs=36.8
Q ss_pred CCceEEEEEeCCCCCeEEEEE--------eeeEeCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 52 GYPMMFELCNLSSGKTTHCGV--------VEFTADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 52 ~~Pm~F~i~n~~~~~~th~GV--------lEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
.|| |.|.+......+|.+- .+. .+|..|.|=.=-++.+||.+||.|+|.+.
T Consensus 713 ~yp--l~Lit~r~~~~~hs~~~~~~~~~l~~~-~~~~~v~inp~DA~~~GI~dGD~V~V~n~ 771 (830)
T PRK13532 713 EYD--LWLSTGRVLEHWHTGSMTRRVPELYRA-FPEAVCFMHPEDAKARGLRRGDEVKVVSR 771 (830)
T ss_pred CCC--eEEecccchhhccccCccCchHHHHhh-CCCCEEEECHHHHHHcCCCCCCEEEEEeC
Confidence 467 5555544444556542 222 36788999999999999999999999875
No 98
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional
Probab=25.42 E-value=1.1e+02 Score=25.47 Aligned_cols=25 Identities=8% Similarity=0.080 Sum_probs=22.1
Q ss_pred ccccCCEEEEEECCEEEEEEEEEec
Q 035839 142 CLTTGDTIMIMHNESKYYIDVLETK 166 (238)
Q Consensus 142 ~LT~Gd~I~I~~~~~~y~l~V~e~k 166 (238)
.+..||+|.|.+++..+.+.|+.+.
T Consensus 48 ~V~~gd~l~v~~~~~~~~v~Vl~l~ 72 (133)
T PRK10348 48 IVELNATLTLRQGNDERTVIVKAIT 72 (133)
T ss_pred ccCCCCEEEEEECCEEEEEEEeECc
Confidence 3568999999999999999999875
No 99
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=25.28 E-value=1.2e+02 Score=20.90 Aligned_cols=23 Identities=9% Similarity=-0.077 Sum_probs=20.0
Q ss_pred EeccHhHHhhcCCCCCCeEEEEE
Q 035839 82 IYLPNWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 82 i~lP~Wmm~~L~l~~gd~V~v~~ 104 (238)
+.+|.+-.+.|+|++|+.|.+..
T Consensus 37 a~i~~~~~~~l~l~~G~~v~~~i 59 (69)
T TIGR00638 37 AVITLESVAELGLKPGKEVYAVI 59 (69)
T ss_pred EEecHHHHhhCCCCCCCEEEEEE
Confidence 36999999999999999987654
No 100
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=24.02 E-value=91 Score=27.95 Aligned_cols=31 Identities=13% Similarity=0.215 Sum_probs=26.1
Q ss_pred HhHHhhcCCCCCCeEEEEEeeeCCceeEEEe
Q 035839 86 NWMMDNMKLQEYELVRVTNVSLAKATYMKLQ 116 (238)
Q Consensus 86 ~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLq 116 (238)
.-+.+.+|++.||.|.|...+--.|.||..+
T Consensus 172 DPvary~g~k~G~vvkI~R~S~taG~~v~YR 202 (205)
T PTZ00061 172 DPVARYFGLSKGQVVKIIRPSETAGRYVTYR 202 (205)
T ss_pred ChhhHhcCCCCCCEEEEEECCCCCCcceEEE
Confidence 3478899999999999999888888888654
No 101
>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=23.97 E-value=4e+02 Score=27.92 Aligned_cols=88 Identities=13% Similarity=0.148 Sum_probs=56.3
Q ss_pred CCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCc-eeEEEeecCccccccCC-------ChHHHHHHhhccCc--ccccCC
Q 035839 78 DEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKA-TYMKLQPHTKGFLDELS-------NPRAVLEAILRKFS--CLTTGD 147 (238)
Q Consensus 78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkg-t~vkLqP~s~~F~~~i~-------npKavLE~~Lrnys--~LT~Gd 147 (238)
+.|.|.+-.---+-.++.-|+.|.|+--..+.. .++..--.+.+|++ -. |-..+-+.--|.|. .+|+|.
T Consensus 58 ~~g~i~fs~~qR~wa~~Sl~qev~V~~~~~~~~~~~l~~m~le~dF~~-k~~~~sep~Dad~ma~qF~~~y~~q~fsvgQ 136 (744)
T KOG0741|consen 58 PPGNIGFSLPQRKWAGWSLGQEVEVKPFTFDGSCDYLGSMTLEIDFLN-KKNTTSEPFDADEMAKQFKRQYNSQAFSVGQ 136 (744)
T ss_pred CCceeccchhhhhhhhcccCceeEEEecccCcccccceeEEEEehhhh-cCCCCCCCCCHHHHHHHHHHHhcCcccCCcc
Confidence 445555443223333444467899984333333 67777777788876 43 34444455555676 599999
Q ss_pred EEEEEECC-EEEEEEEEEec
Q 035839 148 TIMIMHNE-SKYYIDVLETK 166 (238)
Q Consensus 148 ~I~I~~~~-~~y~l~V~e~k 166 (238)
.+.++|++ +.+.+.|..++
T Consensus 137 ~~~f~f~~~~~l~l~v~~ie 156 (744)
T KOG0741|consen 137 QLVFEFNGNKLLGLKVKDIE 156 (744)
T ss_pred EEEEEecCceEeeeEEEEEe
Confidence 99999996 77888887664
No 102
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=23.59 E-value=2.3e+02 Score=18.74 Aligned_cols=30 Identities=10% Similarity=0.221 Sum_probs=24.9
Q ss_pred ccccCCEEEEEE-CCEEEEEEEEEecCCCce
Q 035839 142 CLTTGDTIMIMH-NESKYYIDVLETKPSNAV 171 (238)
Q Consensus 142 ~LT~Gd~I~I~~-~~~~y~l~V~e~kP~~aV 171 (238)
.+..|+.+...+ ++.-|.=.|+++.+...+
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~~~~~ 32 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDGEQLY 32 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECCCCEE
Confidence 357899999999 888999999999886443
No 103
>PF00667 FAD_binding_1: FAD binding domain; InterPro: IPR003097 This domain is found in sulphite reductase, NADPH cytochrome P450 reductase, nitric oxide synthase and methionine synthase reductase. Flavoprotein pyridine nucleotide cytochrome reductases [] (FPNCR) catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin:NADP+reductases (FNR) [], plant and fungal NAD(P)H:nitrate reductases [, ], NADH:cytochrome b5 reductases [], NADPH:P450 reductases [], NADPH:sulphite reductases [], nitric oxide synthases [], phthalate dioxygenase reductase [], and various other flavoproteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3QFR_B 3FJO_A 3QFC_B 3QE2_B 3QFS_A 3QFT_A 2B5O_B 2QTZ_A 2QTL_A 2BPO_B ....
Probab=22.71 E-value=1.5e+02 Score=25.59 Aligned_cols=87 Identities=20% Similarity=0.344 Sum_probs=47.6
Q ss_pred CCceEEEEEe------CCCCCeEEEEEeeeE-eCCCcEecc---------------HhHHhhcCCCCCCeEEEEEee---
Q 035839 52 GYPMMFELCN------LSSGKTTHCGVVEFT-ADEGFIYLP---------------NWMMDNMKLQEYELVRVTNVS--- 106 (238)
Q Consensus 52 ~~Pm~F~i~n------~~~~~~th~GVlEF~-A~EG~i~lP---------------~Wmm~~L~l~~gd~V~v~~~~--- 106 (238)
..|+..+|.. ....|.|+. +||. .+.|.-|-| .++++.||+.....|.|+...
T Consensus 6 ~~p~~a~V~~~~~Lt~~~~~r~~~h--ieldl~~~~l~Y~pGD~l~V~P~N~~~~V~~~l~~lgl~~d~~v~~~~~~~~~ 83 (219)
T PF00667_consen 6 KNPFPATVLENRRLTSPGSDRSTRH--IELDLSDSGLSYQPGDHLGVYPPNDPEEVERLLKRLGLDPDEPVTLKPKEQNN 83 (219)
T ss_dssp TB-EEEEEEEEEE-SSTTSSSEEEE--EEEE-TTSTG---TT-EEEEE-SSEHHHHHHHHHHHTSGTTSEEEEEESSTTS
T ss_pred CCCEEEEEEeEEEcCCCCCCceEEE--EEEEeCCCCCcccCCCEEEEEccCCHHHHHHHHHHhCCCcceEEEEEeccccc
Confidence 3466666643 234454443 6663 344666644 579999999998889888765
Q ss_pred ---eCCceeEEEeecCccccccCCC-hHHHHHHhhccCc
Q 035839 107 ---LAKATYMKLQPHTKGFLDELSN-PRAVLEAILRKFS 141 (238)
Q Consensus 107 ---LPkgt~vkLqP~s~~F~~~i~n-pKavLE~~Lrnys 141 (238)
.|-..-+.|.=.=+.++| |.. |+.-+=..|-.|+
T Consensus 84 ~~~~~~~~~~tl~~~l~~~~D-i~~~p~~~~l~~la~~~ 121 (219)
T PF00667_consen 84 SVKPPFPSPITLRDLLTHYLD-ITSPPSRSFLRALAEFA 121 (219)
T ss_dssp SCCSSSSSSEEHHHHHHHTB--TSSB--HHHHHHHHCTB
T ss_pred ccccccccceeeeeeeeeeee-cccccccceeeeeeecC
Confidence 555555555443345566 665 4444434444444
No 104
>PRK06247 pyruvate kinase; Provisional
Probab=22.14 E-value=2.4e+02 Score=28.21 Aligned_cols=38 Identities=13% Similarity=0.158 Sum_probs=29.1
Q ss_pred CcccccCCEEEEEECCEEEEEEEEEecCCCceEEEeCceE
Q 035839 140 FSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCE 179 (238)
Q Consensus 140 ys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsIidTDl~ 179 (238)
+..+..||.|.|.++. ..|.|.++++...+|.+..+=.
T Consensus 115 ~~~v~~G~~I~idDG~--i~l~V~~~~~~~i~~~v~~~G~ 152 (476)
T PRK06247 115 AAALKPGDRLLVDDGK--VRLVVEACDGDDVVCRVVEGGP 152 (476)
T ss_pred HhhcCCCCEEEEeCCe--EEEEEEEEECCEEEEEEEeCcE
Confidence 4568999999997554 4678888888888887776543
No 105
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=22.14 E-value=3.4e+02 Score=20.16 Aligned_cols=63 Identities=16% Similarity=0.112 Sum_probs=32.3
Q ss_pred eeecHHHHHHHHhCCC-CCceEEEEEeCCCCCeEEEEEeeeEeCCCcEecc--HhHHhhcCCCCCCeEEEEE
Q 035839 36 IIMPQSAFDRLAHTEV-GYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLP--NWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 36 IiLP~SaL~~L~~~~i-~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~i~lP--~Wmm~~L~l~~gd~V~v~~ 104 (238)
|.+|..+.++|...+- ..|..=.| ++ .++-+-|-. --+|.-+|| .=|.++++++.||.|.|+.
T Consensus 15 v~vP~~v~~~l~~~~~g~v~V~~tI----~g-~~~~~sl~p-~g~G~~~Lpv~~~vRk~~g~~~Gd~V~v~l 80 (80)
T PF08922_consen 15 VEVPFDVAEELGEGGWGRVPVRGTI----DG-HPWRTSLFP-MGNGGYILPVKAAVRKAIGKEAGDTVEVTL 80 (80)
T ss_dssp EE--S-HHHHH--S--S-EEEEEEE----TT-EEEEEEEEE-SSTT-EEEEE-HHHHHHHT--TTSEEEEEE
T ss_pred EEeCHHHHHHhccccCCceEEEEEE----CC-EEEEEEEEE-CCCCCEEEEEcHHHHHHcCCCCCCEEEEEC
Confidence 6799999999875511 11222222 11 333333333 456776666 6699999999999999863
No 106
>cd03701 IF2_IF5B_II IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.
Probab=22.04 E-value=1.1e+02 Score=23.38 Aligned_cols=34 Identities=32% Similarity=0.459 Sum_probs=21.4
Q ss_pred CcccccCCEEEEE--ECCEEEEEE-----EEEecCCCceEE
Q 035839 140 FSCLTTGDTIMIM--HNESKYYID-----VLETKPSNAVSI 173 (238)
Q Consensus 140 ys~LT~Gd~I~I~--~~~~~y~l~-----V~e~kP~~aVsI 173 (238)
--||.+||+|.+- |....-.++ |.+..|+.+|.|
T Consensus 24 ~GtL~~Gd~iv~G~~~GkVr~~~d~~g~~v~~a~Ps~~v~i 64 (95)
T cd03701 24 NGTLKKGDVIVAGGTYGKIRTMVDENGKALLEAGPSTPVEI 64 (95)
T ss_pred cCeEecCCEEEECCccceEEEEECCCCCCccccCCCCCEEE
Confidence 3478899999984 333333333 566677777743
No 107
>COG0187 GyrB Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit [DNA replication, recombination, and repair]
Probab=21.86 E-value=1.1e+02 Score=31.92 Aligned_cols=46 Identities=20% Similarity=0.325 Sum_probs=40.9
Q ss_pred CCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEEC
Q 035839 108 AKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHN 154 (238)
Q Consensus 108 Pkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~ 154 (238)
..||.|+|.|-..-|-. ...--.+|.++||..+.|-.|=+|.++..
T Consensus 165 ~~GT~V~F~PD~~iF~~-~~f~~~~l~~RlrelA~L~~gl~I~l~d~ 210 (635)
T COG0187 165 KTGTKVRFKPDPEIFGE-TEFDYEILKRRLRELAFLNKGVKITLTDE 210 (635)
T ss_pred CCccEEEEEcChHhcCC-cccCHHHHHHHHHHHhccCCCCEEEEEec
Confidence 45999999999888876 88888999999999999999988888754
No 108
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.74 E-value=3.2e+02 Score=19.76 Aligned_cols=63 Identities=17% Similarity=0.210 Sum_probs=38.2
Q ss_pred CCCCCeEEEE--EeeeCCceeEEEeecC-ccccccCCChHHHHHHhhccCcccccCCEEEEEE-----CCEEEEEEEEEe
Q 035839 94 LQEYELVRVT--NVSLAKATYMKLQPHT-KGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMH-----NESKYYIDVLET 165 (238)
Q Consensus 94 l~~gd~V~v~--~~~LPkgt~vkLqP~s-~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~-----~~~~y~l~V~e~ 165 (238)
|.+|+.|.-. ++. +.|-||.|-... ..|+. .++ +.....|.+||.+.+.. +++.+.|.+...
T Consensus 2 l~~G~~v~g~V~si~-d~G~~v~~g~~gv~Gfl~-~~~--------~~~~~~~~~Gq~v~~~V~~vd~~~~~v~ls~k~~ 71 (74)
T cd05694 2 LVEGMVLSGCVSSVE-DHGYILDIGIPGTTGFLP-KKD--------AGNFSKLKVGQLLLCVVEKVKDDGRVVSLSADPS 71 (74)
T ss_pred CCCCCEEEEEEEEEe-CCEEEEEeCCCCcEEEEE-HHH--------CCcccccCCCCEEEEEEEEEECCCCEEEEEEeec
Confidence 6778877644 444 899999995433 67876 322 22116788898887653 234555554444
Q ss_pred c
Q 035839 166 K 166 (238)
Q Consensus 166 k 166 (238)
+
T Consensus 72 ~ 72 (74)
T cd05694 72 K 72 (74)
T ss_pred c
Confidence 3
No 109
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=21.37 E-value=77 Score=23.15 Aligned_cols=17 Identities=12% Similarity=0.282 Sum_probs=12.9
Q ss_pred HhhcCCCCCCeEEEEEe
Q 035839 89 MDNMKLQEYELVRVTNV 105 (238)
Q Consensus 89 m~~L~l~~gd~V~v~~~ 105 (238)
+...|+++||+|+|--.
T Consensus 49 L~~~G~~~GD~V~Ig~~ 65 (69)
T TIGR03595 49 LRKAGAKDGDTVRIGDF 65 (69)
T ss_pred HHHcCCCCCCEEEEccE
Confidence 35677889999998643
No 110
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=21.33 E-value=79 Score=22.61 Aligned_cols=24 Identities=13% Similarity=0.216 Sum_probs=17.0
Q ss_pred cEeccHhHHhhcCCCCCCeEEEEE
Q 035839 81 FIYLPNWMMDNMKLQEYELVRVTN 104 (238)
Q Consensus 81 ~i~lP~Wmm~~L~l~~gd~V~v~~ 104 (238)
.|.||.-+...+.+.+||.|.|+.
T Consensus 29 l~~i~gK~r~~iwI~~GD~V~V~~ 52 (65)
T PF01176_consen 29 LARIPGKFRKRIWIKRGDFVLVEP 52 (65)
T ss_dssp EEEE-HHHHTCC---TTEEEEEEE
T ss_pred EEEeccceeeeEecCCCCEEEEEe
Confidence 588999988899999999988875
No 111
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=21.28 E-value=1.7e+02 Score=22.04 Aligned_cols=58 Identities=17% Similarity=0.180 Sum_probs=38.1
Q ss_pred CCCCeEEEEEeeeCC---ceeEEEeecCccccccCCChHHHHHHhhcc-CcccccCCEEEEEE
Q 035839 95 QEYELVRVTNVSLAK---ATYMKLQPHTKGFLDELSNPRAVLEAILRK-FSCLTTGDTIMIMH 153 (238)
Q Consensus 95 ~~gd~V~v~~~~LPk---gt~vkLqP~s~~F~~~i~npKavLE~~Lrn-ys~LT~Gd~I~I~~ 153 (238)
+.|+.+.-+-+++-+ |-||.|-+.-..|+. +++.-...=...++ -..|.+||.|.+..
T Consensus 6 ~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh-~seis~~~~~~v~~~~~~~~~Gd~v~VqV 67 (88)
T cd04453 6 IVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLH-LSDILPAYFKKHKKIAKLLKEGQEILVQV 67 (88)
T ss_pred CCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEE-hHHcCchhccccCCHHHcCCCCCEEEEEE
Confidence 568888777666554 999999987788988 76431100011222 23588999998864
No 112
>TIGR01553 formate-DH-alph formate dehydrogenase, alpha subunit, proteobacterial-type. This model is well-defined, with a large, unpopulated trusted/noise gap.
Probab=20.65 E-value=62 Score=35.11 Aligned_cols=56 Identities=14% Similarity=0.084 Sum_probs=39.7
Q ss_pred CCCceEE---EEEeCCCCCeEEEEEeeeEeCCCcEeccHhHHhhcCCCCCCeEEEEEee
Q 035839 51 VGYPMMF---ELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVS 106 (238)
Q Consensus 51 i~~Pm~F---~i~n~~~~~~th~GVlEF~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~ 106 (238)
-.||++. ++...-...+-++-.|.=..+|.+|-|.+-.++.|||++||.|+|++.+
T Consensus 881 ~~yP~~ltTgR~~eh~~t~Tr~~~~l~~~~p~~fveI~p~~A~~~GI~~Gd~V~v~s~r 939 (1009)
T TIGR01553 881 KRYPFVATTYRLTEHWHTWTRNTPWLLEAEPQMFCEISEELATEKGIQNGDKVILESVR 939 (1009)
T ss_pred cCCCEEEEccccceecCcccccCHHHHHhCcccEEEECHHHHHHcCCcCCCEEEEEcCC
Confidence 4688764 3322111133344455556788999999999999999999999999876
No 113
>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.
Probab=20.42 E-value=1.1e+02 Score=31.62 Aligned_cols=71 Identities=14% Similarity=0.229 Sum_probs=46.2
Q ss_pred CCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEE
Q 035839 78 DEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMH 153 (238)
Q Consensus 78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~ 153 (238)
.-|.+.|..-.|+.|++.+||.|.|+.- -+.+-.+.-|...+ + ...-.--+...+|....+..||.+.|.-
T Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~--~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (733)
T TIGR01243 15 GRGIVRIDRQTAARLGVEPGDFVEIEKG--DRSVVAIVWPLRPD--D-EGRGIIRMDGYLRANAGVTIGDTVTVER 85 (733)
T ss_pred CCCeEeeCHHHHHhcCCCCCCEEEEecC--CCceeEEEEecCcc--c-cCCCEEeecHHHHhhcCCCCCCeEEEee
Confidence 4478999999999999999999999831 11234444443221 1 1111112455677667799999999964
No 114
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=20.28 E-value=1.2e+02 Score=27.18 Aligned_cols=31 Identities=13% Similarity=0.210 Sum_probs=25.8
Q ss_pred HhHHhhcCCCCCCeEEEEEeeeCCceeEEEe
Q 035839 86 NWMMDNMKLQEYELVRVTNVSLAKATYMKLQ 116 (238)
Q Consensus 86 ~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLq 116 (238)
.-+.+.+|++.||.|.|...+=--|.||..+
T Consensus 173 DPvary~g~k~G~vvkI~R~S~taG~~v~YR 203 (206)
T PLN03111 173 DPIARYYGLKRGQVVKIIRPSETAGRYVTYR 203 (206)
T ss_pred ChhhHhcCCCCCCEEEEEECCCCCCCceEEE
Confidence 4478899999999999998887888887654
No 115
>TIGR02693 arsenite_ox_L arsenite oxidase, large subunit. This model represents the large subunit of an arsenite oxidase complex. The small subunit is a Rieske protein. Homologs to both large and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7. This enzyme acts in energy metabolim by arsenite oxidation, rather than detoxification by reduction of arsenate to arsenite prior to export.
Probab=20.20 E-value=1.5e+02 Score=31.31 Aligned_cols=29 Identities=21% Similarity=0.108 Sum_probs=26.3
Q ss_pred eCCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839 77 ADEGFIYLPNWMMDNMKLQEYELVRVTNV 105 (238)
Q Consensus 77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~ 105 (238)
.++..|.|-+--++.|||.+||.|+|.+.
T Consensus 722 ~p~p~v~InP~DA~~lGI~dGD~V~V~n~ 750 (806)
T TIGR02693 722 LPLPYIEVNPEDAKRLGLKSGDLVEVYND 750 (806)
T ss_pred CCCCEEEECHHHHHHcCCCCCCEEEEEcC
Confidence 47788999999999999999999998874
Done!