Query 019483
Match_columns 340
No_of_seqs 158 out of 227
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 09:50:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019483.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019483hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2845 Activating signal coin 100.0 3.3E-59 7.1E-64 467.5 12.7 286 4-327 5-306 (505)
2 PF06221 zf-C2HC5: Putative zi 99.8 1.2E-21 2.6E-26 147.9 2.1 44 185-228 2-49 (57)
3 PF01480 PWI: PWI domain; Int 93.5 0.095 2.1E-06 41.3 3.8 60 4-72 4-72 (77)
4 PF13248 zf-ribbon_3: zinc-rib 90.6 0.11 2.3E-06 33.4 0.7 23 200-224 4-26 (26)
5 PF05361 PP1_inhibitor: PKC-ac 87.3 1.1 2.5E-05 40.1 5.1 62 4-74 51-120 (144)
6 smart00311 PWI PWI, domain in 86.9 2.1 4.5E-05 33.6 5.8 58 5-69 10-69 (74)
7 PF13240 zinc_ribbon_2: zinc-r 85.2 0.37 8E-06 30.4 0.7 22 201-224 2-23 (23)
8 COG1996 RPC10 DNA-directed RNA 82.5 0.66 1.4E-05 34.7 1.1 27 199-226 7-36 (49)
9 PRK00398 rpoP DNA-directed RNA 79.2 1.3 2.8E-05 31.6 1.7 27 200-226 5-33 (46)
10 PF14354 Lar_restr_allev: Rest 77.4 1.2 2.6E-05 33.0 1.2 15 212-226 1-15 (61)
11 COG2888 Predicted Zn-ribbon RN 76.3 1.6 3.5E-05 34.0 1.6 32 194-225 5-38 (61)
12 PF14447 Prok-RING_4: Prokaryo 75.8 1.7 3.6E-05 33.3 1.5 35 188-226 13-51 (55)
13 PF15135 UPF0515: Uncharacteri 75.1 1.5 3.3E-05 42.7 1.5 37 190-226 138-186 (278)
14 cd00729 rubredoxin_SM Rubredox 74.6 2.3 5E-05 29.0 1.8 24 200-223 4-27 (34)
15 PF10571 UPF0547: Uncharacteri 72.1 2 4.4E-05 28.0 1.0 23 200-224 2-24 (26)
16 PF15616 TerY-C: TerY-C metal 71.9 3 6.5E-05 36.9 2.4 40 184-225 76-116 (131)
17 PF01155 HypA: Hydrogenase exp 71.0 1.8 4E-05 36.5 0.8 31 194-224 66-96 (113)
18 PRK09710 lar restriction allev 68.6 2.4 5.1E-05 33.4 0.9 16 212-227 4-19 (64)
19 PF07295 DUF1451: Protein of u 67.7 3.6 7.8E-05 36.8 2.0 27 200-226 114-142 (146)
20 PRK12496 hypothetical protein; 61.8 4.1 8.8E-05 36.7 1.2 26 200-225 129-154 (164)
21 COG1439 Predicted nucleic acid 61.8 4.2 9.2E-05 37.7 1.3 25 199-225 140-164 (177)
22 cd00350 rubredoxin_like Rubred 60.3 6.4 0.00014 26.5 1.7 24 200-223 3-26 (33)
23 TIGR03655 anti_R_Lar restricti 58.2 4.7 0.0001 29.7 0.8 12 214-225 1-12 (53)
24 PRK14714 DNA polymerase II lar 57.9 6 0.00013 46.1 2.0 39 187-226 681-721 (1337)
25 PRK03824 hypA hydrogenase nick 56.3 7.5 0.00016 34.0 1.9 30 194-223 66-116 (135)
26 PF11023 DUF2614: Protein of u 55.8 4.1 9E-05 35.4 0.2 30 199-228 70-99 (114)
27 smart00834 CxxC_CXXC_SSSS Puta 54.5 9.4 0.0002 25.8 1.8 25 200-224 7-36 (41)
28 PRK11032 hypothetical protein; 54.1 8.6 0.00019 35.0 2.0 27 200-226 126-154 (160)
29 COG1592 Rubrerythrin [Energy p 52.2 7.6 0.00017 35.6 1.3 25 198-223 134-158 (166)
30 PRK03681 hypA hydrogenase nick 51.5 9.8 0.00021 32.3 1.8 30 194-223 66-96 (114)
31 smart00659 RPOLCX RNA polymera 51.1 10 0.00022 27.5 1.5 28 199-226 3-31 (44)
32 PF05191 ADK_lid: Adenylate ki 49.9 12 0.00025 26.1 1.7 26 200-225 3-32 (36)
33 smart00064 FYVE Protein presen 49.6 5.9 0.00013 29.8 0.2 12 199-210 27-38 (68)
34 TIGR00100 hypA hydrogenase nic 48.6 12 0.00026 31.8 1.9 31 194-224 66-96 (115)
35 PRK02935 hypothetical protein; 48.2 7.5 0.00016 33.6 0.6 30 199-228 71-100 (110)
36 cd00065 FYVE FYVE domain; Zinc 47.5 6.7 0.00014 28.3 0.2 12 199-210 19-30 (57)
37 PF06107 DUF951: Bacterial pro 46.4 10 0.00022 29.3 1.0 29 178-208 5-41 (57)
38 PF01363 FYVE: FYVE zinc finge 45.5 9.2 0.0002 28.8 0.7 12 199-210 26-37 (69)
39 COG2051 RPS27A Ribosomal prote 45.5 11 0.00024 30.0 1.1 17 198-214 38-54 (67)
40 PF07754 DUF1610: Domain of un 43.4 13 0.00027 24.1 1.0 21 201-221 1-23 (24)
41 PRK12380 hydrogenase nickel in 42.9 17 0.00037 30.8 2.0 29 195-223 67-95 (113)
42 PRK00564 hypA hydrogenase nick 41.8 14 0.00031 31.5 1.3 29 196-224 69-98 (117)
43 cd01407 SIR2-fam SIR2 family o 40.8 17 0.00037 33.4 1.8 39 186-226 99-145 (218)
44 PRK14890 putative Zn-ribbon RN 40.6 15 0.00032 28.6 1.1 26 199-224 8-35 (59)
45 PF12773 DZR: Double zinc ribb 40.5 13 0.00029 26.3 0.8 28 196-223 10-38 (50)
46 PF10977 DUF2797: Protein of u 39.1 14 0.00029 35.5 0.9 25 200-224 13-37 (235)
47 PF07765 KIP1: KIP1-like prote 39.0 1.1E+02 0.0023 24.9 5.8 24 4-37 12-35 (74)
48 KOG1729 FYVE finger containing 39.0 6.7 0.00015 38.7 -1.2 21 186-210 172-197 (288)
49 COG4855 Uncharacterized protei 38.8 4 8.7E-05 32.8 -2.3 31 195-227 1-36 (76)
50 KOG3362 Predicted BBOX Zn-fing 36.5 12 0.00027 33.9 0.2 58 164-227 83-142 (156)
51 PRK07218 replication factor A; 35.9 18 0.00039 37.5 1.3 24 196-223 295-318 (423)
52 COG2093 DNA-directed RNA polym 35.3 21 0.00046 28.2 1.2 26 200-227 6-31 (64)
53 PRK00481 NAD-dependent deacety 33.8 22 0.00047 33.4 1.3 39 186-226 112-154 (242)
54 TIGR00570 cdk7 CDK-activating 33.1 22 0.00048 35.6 1.3 25 203-227 25-56 (309)
55 PF03604 DNA_RNApol_7kD: DNA d 32.4 33 0.00071 23.4 1.7 26 200-225 2-28 (32)
56 PRK08351 DNA-directed RNA poly 32.3 29 0.00062 27.1 1.5 25 200-228 5-29 (61)
57 PF01667 Ribosomal_S27e: Ribos 32.1 21 0.00046 27.3 0.8 15 199-213 27-41 (55)
58 PF08271 TF_Zn_Ribbon: TFIIB z 31.0 26 0.00055 24.6 1.0 25 201-225 3-30 (43)
59 PF06689 zf-C4_ClpX: ClpX C4-t 29.8 21 0.00046 25.2 0.4 13 216-228 3-15 (41)
60 cd00240 TFIIFa Transcription i 29.7 20 0.00044 32.9 0.4 26 199-226 9-35 (162)
61 PRK09462 fur ferric uptake reg 29.6 30 0.00065 29.9 1.4 14 197-210 89-102 (148)
62 PF09082 DUF1922: Domain of un 29.6 23 0.00049 28.3 0.6 28 197-226 2-31 (68)
63 smart00504 Ubox Modified RING 29.4 37 0.0008 24.5 1.7 26 200-225 15-46 (63)
64 smart00531 TFIIE Transcription 29.3 19 0.00042 31.5 0.2 28 200-227 101-136 (147)
65 cd01413 SIR2_Af2 SIR2_Af2: Arc 28.9 36 0.00078 31.6 1.9 39 186-226 103-148 (222)
66 PRK05255 hypothetical protein; 28.5 99 0.0022 28.5 4.6 46 7-52 31-80 (171)
67 KOG2253 U1 snRNP complex, subu 28.2 1.2E+02 0.0025 33.6 5.7 64 4-68 589-656 (668)
68 PF06906 DUF1272: Protein of u 28.0 34 0.00073 26.6 1.2 10 197-206 4-13 (57)
69 PF09845 DUF2072: Zn-ribbon co 27.6 21 0.00046 31.7 0.1 26 200-225 3-30 (131)
70 PF01475 FUR: Ferric uptake re 27.4 32 0.00069 28.4 1.2 17 194-210 76-92 (120)
71 COG1867 TRM1 N2,N2-dimethylgua 27.3 44 0.00096 34.5 2.3 34 198-231 240-274 (380)
72 PRK14138 NAD-dependent deacety 27.0 37 0.0008 32.2 1.6 39 186-226 109-155 (244)
73 cd07153 Fur_like Ferric uptake 26.8 41 0.00089 27.3 1.7 15 197-211 72-86 (116)
74 PF04751 DUF615: Protein of un 26.2 1E+02 0.0022 27.9 4.2 57 8-64 21-84 (157)
75 KOG2146 Splicing coactivator S 26.2 50 0.0011 33.3 2.4 61 5-71 46-110 (354)
76 PRK06393 rpoE DNA-directed RNA 25.7 43 0.00094 26.4 1.5 25 199-227 6-30 (64)
77 PF09986 DUF2225: Uncharacteri 25.6 1.6E+02 0.0035 27.5 5.6 65 5-69 138-212 (214)
78 COG2075 RPL24A Ribosomal prote 25.5 30 0.00066 27.5 0.6 12 215-226 4-15 (66)
79 COG0801 FolK 7,8-dihydro-6-hyd 25.3 54 0.0012 30.0 2.3 57 270-326 49-110 (160)
80 TIGR02605 CxxC_CxxC_SSSS putat 25.3 49 0.0011 23.6 1.7 23 200-222 7-34 (52)
81 PF07631 PSD4: Protein of unkn 25.3 1.5E+02 0.0033 25.7 5.0 48 26-74 21-68 (128)
82 PTZ00083 40S ribosomal protein 24.9 37 0.0008 28.2 1.1 15 199-213 55-69 (85)
83 PRK11639 zinc uptake transcrip 24.9 35 0.00076 30.5 1.0 13 198-210 100-112 (169)
84 PRK11595 DNA utilization prote 24.6 25 0.00055 32.7 0.1 19 309-327 178-196 (227)
85 TIGR01384 TFS_arch transcripti 24.5 34 0.00074 27.9 0.8 25 200-224 2-26 (104)
86 TIGR02098 MJ0042_CXXC MJ0042 f 24.1 46 0.00099 22.4 1.2 27 199-225 3-36 (38)
87 PRK04023 DNA polymerase II lar 24.1 62 0.0014 37.5 2.9 42 183-226 624-675 (1121)
88 PRK14559 putative protein seri 24.0 47 0.001 36.3 1.9 25 199-225 28-52 (645)
89 PLN00209 ribosomal protein S27 23.8 39 0.00084 28.2 1.0 16 199-214 56-71 (86)
90 cd01412 SIRT5_Af1_CobB SIRT5_A 22.9 55 0.0012 30.1 1.9 39 186-226 99-142 (224)
91 PF02146 SIR2: Sir2 family; I 22.8 48 0.001 29.4 1.5 39 186-226 95-141 (178)
92 smart00290 ZnF_UBP Ubiquitin C 22.8 38 0.00083 23.8 0.7 12 198-209 11-22 (50)
93 PF00986 DNA_gyraseB_C: DNA gy 22.7 85 0.0018 24.8 2.6 25 38-62 39-65 (65)
94 PF09723 Zn-ribbon_8: Zinc rib 22.7 73 0.0016 22.4 2.1 24 199-222 6-34 (42)
95 PF09538 FYDLN_acid: Protein o 22.4 47 0.001 28.3 1.3 28 200-227 11-39 (108)
96 PF02591 DUF164: Putative zinc 22.3 33 0.00071 25.3 0.3 11 198-208 46-56 (56)
97 PF06524 NOA36: NOA36 protein; 22.2 39 0.00085 33.6 0.8 37 186-227 117-155 (314)
98 KOG3062 RNA polymerase II elon 22.1 1.8E+02 0.0038 28.9 5.2 62 247-312 17-78 (281)
99 smart00674 CENPB Putative DNA- 21.7 3E+02 0.0065 20.1 5.4 53 6-70 5-62 (66)
100 PF07778 CENP-I: Mis6 ; Inter 21.0 3.1E+02 0.0067 29.4 7.2 63 4-72 424-497 (511)
101 COG4481 Uncharacterized protei 20.4 43 0.00094 26.0 0.6 25 182-208 13-44 (60)
102 cd01410 SIRT7 SIRT7: Eukaryoti 20.3 72 0.0016 29.5 2.1 38 186-225 85-131 (206)
No 1
>KOG2845 consensus Activating signal cointegrator 1 [Transcription]
Probab=100.00 E-value=3.3e-59 Score=467.55 Aligned_cols=286 Identities=37% Similarity=0.566 Sum_probs=215.1
Q ss_pred hHhhHHHHHHHHHhhcccCCCcHHHHHHhhcccccCCchHHHHHHHHhh-CCcchH-HHHHHHHHHhccccCCCCCCCCC
Q 019483 4 AGEWLEKALVDLCKRIESLDLDGEVISGLVSYCEFAQPLDAKEYLDNII-GQEVGK-SVIEEYLRRRGLTDICSSTTNVP 81 (340)
Q Consensus 4 ~~~w~~~~L~~~~~~~~~L~~~~d~~~~ils~~el~~~~d~~eY~~nLL-G~e~~~-~Fi~e~~~r~~~~~~~~~~~~~~ 81 (340)
.|+||...++..|..-.++++.++||+||+++ +...|+.+||.+|| |++.-+ +| ++- .+ .--+
T Consensus 5 ~~e~l~~~~~~~l~k~~~~~~~d~~i~~~l~~---~~~~ef~~~f~~ll~~n~~k~~k~-~~~------h~-----~~li 69 (505)
T KOG2845|consen 5 SGEPLEHWCTQQLRKTSDEDISDEIIQYLLSI---ESDEEFREYFTELLSGNEGKEGKF-EEK------HD-----EFLI 69 (505)
T ss_pred cchhHHHHHHHHhccccchhhHHHHHHHhhhh---hhhHHHHHHHHHHhcccCCCCccc-hhh------cH-----HHhh
Confidence 57777655555533333366679999999994 79999999999999 777322 77 440 01 0112
Q ss_pred CCcccccccCCCcccc-cCCC--CCCCCCCCcccCCCcccchhhhcccccccCccccccccCCCCCccchhhhhcccCCC
Q 019483 82 TSKLQAYVKPRSDEGL-ASGT--KKPSKTPKEFTGTGHQAELKKVMVPSYQVEPKKDAVSSHNENLAESSESRTMNRGNQ 158 (340)
Q Consensus 82 s~~~~~~~k~~~~~~~-~~~~--kk~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~s~~~~~~~~~~ 158 (340)
++++|.+.|++....+ .+|. |+++++++ |.+++|+|. .|.. ..+..+|+. ++++.+
T Consensus 70 ~~~~q~~~k~~~~~~g~k~~d~~k~~~~~g~-----------~ss~~~~~~-~P~~---~ts~~~p~~--k~~~~s---- 128 (505)
T KOG2845|consen 70 SDPLQQCSKKDMILSGPKSGDHLKRKRKNGK-----------KSSTTPAFV-SPDT---TTSVKTPFK--KKQENS---- 128 (505)
T ss_pred cccccccchhhhhhccchhcccccccccccc-----------ccCCCCCCC-CCCc---cccccChhh--hhhccc----
Confidence 4456667776665332 3333 23333333 457788874 3321 233456664 344433
Q ss_pred cccccccccceehHHHh---hcCCcccCCCCccccccccCccccccccccceeeecccCcccCCCCcccccCCCcccc--
Q 019483 159 SNNRKKKAGKVISLAEA---AKGSIVFQQGKPCSCQARQHRLISNCLSCGKIVCEQEGEGPCQFCGALVLKEGSTYAG-- 233 (340)
Q Consensus 159 ~~~~~kkk~K~vsL~e~---~~~~~~~~~r~~C~C~A~~H~Li~NCL~CGKIiCeqEG~gPC~FCG~~v~~~~~~~~~-- 233 (340)
++.+++.-|+++||.. ..++|+++|||+|+|||++|||++|||+||||||+|||+|||+|||++|++.+..+..
T Consensus 129 -~~~k~k~~k~inl~i~~~e~s~~i~~~grk~C~CQg~kHpLi~NCL~CGkIVCeQEGsGPC~fCg~~V~t~eeq~~l~~ 207 (505)
T KOG2845|consen 129 -SSVKGKSLKNINLAIRQPEASLAILLKGRKPCNCQGRKHPLINNCLGCGKIVCEQEGSGPCGFCGTPVCTREEQGILNR 207 (505)
T ss_pred -ccccccccccHHHHhccHHHhhhhhhcCCccccccCCcCchhhcccccceeEEEecCcccccccCCeeechhHHHHHHH
Confidence 4444555599999874 2467888999999999999999999999999999999999999999999998754311
Q ss_pred ------cccCCCCCcHHHHHHHHHHHhHhhhhhcccccccccccccccccccCCccCCHHHHHHHHHHHHHHHHHHHhhc
Q 019483 234 ------LEEGFAPLSDAEAAAEAYTKRLVDYDRNAAARTTVIDDQSDYYEIEGNSWLSKEEKELIKKKQEEVAEAEQAKR 307 (340)
Q Consensus 234 ------~~~~~~p~~~a~~~A~~~rdkLLefdrtsA~RTkVIDDqsDyf~~~~n~WlS~~ER~~l~K~q~El~e~~~~~R 307 (340)
+. +-..++++..+|.+|++|||+||+||++||+||||++|||..+++.|||..||+.++++++|++|.+|++|
T Consensus 208 ~~n~~~l~-G~~~iss~~~~A~~~k~klLe~d~nS~rrt~viddqsDyf~~~s~~wlS~~erE~l~k~~eE~eelea~eR 286 (505)
T KOG2845|consen 208 ELNQKLLK-GKVSISSALEKAYVHKDKLLEYDRNSERRTKVIDDQSDYFSLESSSWLSALEREKLEKRQEELEELEAAER 286 (505)
T ss_pred Hhhhhhcc-CccccchhhhhHHHHHhhhccccccccccccccCCcchhhhccccccccHHHHHHHHhhHHHHHHHHHHHh
Confidence 11 11146778899999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCEEEEEEecCCEEeccccc
Q 019483 308 NKVVVTFDLVGRKVSTFCRI 327 (340)
Q Consensus 308 ~k~~vtiD~~grkVv~~e~~ 327 (340)
.+++||+||+||+|++++..
T Consensus 287 ~~~~~t~DfaGrk~~~e~~~ 306 (505)
T KOG2845|consen 287 QKVKLTFDFAGRKALEEETS 306 (505)
T ss_pred hheeeeeeccccccccchhh
Confidence 99999999999999887654
No 2
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=99.83 E-value=1.2e-21 Score=147.95 Aligned_cols=44 Identities=59% Similarity=1.309 Sum_probs=41.5
Q ss_pred CCccccccccCcc---ccccccccceeeeccc-CcccCCCCcccccCC
Q 019483 185 GKPCSCQARQHRL---ISNCLSCGKIVCEQEG-EGPCQFCGALVLKEG 228 (340)
Q Consensus 185 r~~C~C~A~~H~L---i~NCL~CGKIiCeqEG-~gPC~FCG~~v~~~~ 228 (340)
|+.|+|||++||| +||||+||||||++|| +|||+|||++|++..
T Consensus 2 r~~C~C~a~~H~L~~~~~NCl~CGkIiC~~Eg~~~pC~fCg~~l~~~~ 49 (57)
T PF06221_consen 2 RRKCNCQARRHPLFPYAPNCLNCGKIICEQEGPLGPCPFCGTPLLSSE 49 (57)
T ss_pred CcccccccccCCCccccccccccChhhcccccCcCcCCCCCCcccCHH
Confidence 6899999999999 8999999999999999 899999999998753
No 3
>PF01480 PWI: PWI domain; InterPro: IPR002483 The PWI domain, named after a highly conserved PWI tri-peptide located within its N-terminal region, is a ~80 amino acid module, which is found either at the N terminus or at the C terminus of eukaryotic proteins involved in pre-mRNA processing []. It is generally found in association with other domains such as RRM and RS. The PWI domain is a RNA/DNA-binding domain that has an equal preference for single- and double-stranded nucleic acids and is likely to have multiple important functions in pre-mRNA processing []. Proteins containing this domain include the SR-related nuclear matrix protein of 160kDa (SRm160) splicing and 3'-end cleavage-stimulatory factor, and the mammalian splicing factor PRP3. The PWI domain is a soluble, globular and independently folded domain which consists of a four-helix bundle, with structured N- and C-terminal elements [].; GO: 0006397 mRNA processing; PDB: 1MP1_A 1X4Q_A.
Probab=93.52 E-value=0.095 Score=41.34 Aligned_cols=60 Identities=18% Similarity=0.411 Sum_probs=46.3
Q ss_pred hHhhHHHHHHHHHhhcccCCCc-HHHHHHhhcccccC--------CchHHHHHHHHhhCCcchHHHHHHHHHHhcccc
Q 019483 4 AGEWLEKALVDLCKRIESLDLD-GEVISGLVSYCEFA--------QPLDAKEYLDNIIGQEVGKSVIEEYLRRRGLTD 72 (340)
Q Consensus 4 ~~~w~~~~L~~~~~~~~~L~~~-~d~~~~ils~~el~--------~~~d~~eY~~nLLG~e~~~~Fi~e~~~r~~~~~ 72 (340)
--.|+.+.|.++ ||++ +.++.||+.. |. ++.++.+=+..+|| +....|+.+|-++.-+..
T Consensus 4 lk~WI~~kl~e~------lG~edd~lvdyI~~~--l~~~~~~~~~~~~~l~~~L~~fL~-~~a~~Fv~~Lw~~l~~~q 72 (77)
T PF01480_consen 4 LKPWISKKLEEI------LGFEDDVLVDYIVAL--LKSHKSSNEPDPKELQEQLEDFLD-EEAEEFVDELWRLLISAQ 72 (77)
T ss_dssp HHHHHHHHHHHH------HSS--CHHHHHHHHH--CCTT--SSS--HHHHHHHHTTTTG-HHCHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHH------hCCCcHHHHHHHHHH--HHhccccccccHHHHHHHHHHHHH-hhHHHHHHHHHHHHHHHh
Confidence 356999999999 9986 5566899987 44 67777888888888 547799999988876644
No 4
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=90.60 E-value=0.11 Score=33.43 Aligned_cols=23 Identities=30% Similarity=0.628 Sum_probs=19.8
Q ss_pred ccccccceeeecccCcccCCCCccc
Q 019483 200 NCLSCGKIVCEQEGEGPCQFCGALV 224 (340)
Q Consensus 200 NCL~CGKIiCeqEG~gPC~FCG~~v 224 (340)
.|.+||.. ...+..-|..||+.|
T Consensus 4 ~Cp~Cg~~--~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 4 FCPNCGAE--IDPDAKFCPNCGAKL 26 (26)
T ss_pred CCcccCCc--CCcccccChhhCCCC
Confidence 69999997 478889999999875
No 5
>PF05361 PP1_inhibitor: PKC-activated protein phosphatase-1 inhibitor; InterPro: IPR008025 Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction [].; GO: 0042325 regulation of phosphorylation, 0005737 cytoplasm; PDB: 2RLT_A 1J2M_A 1K5O_A 1J2N_A.
Probab=87.33 E-value=1.1 Score=40.14 Aligned_cols=62 Identities=19% Similarity=0.363 Sum_probs=43.9
Q ss_pred hHhhHHHHHHHHHhhcccCCCc-HHH-----HHHhhcccccCCchHHHHHHHHhhC--CcchHHHHHHHHHHhccccCC
Q 019483 4 AGEWLEKALVDLCKRIESLDLD-GEV-----ISGLVSYCEFAQPLDAKEYLDNIIG--QEVGKSVIEEYLRRRGLTDIC 74 (340)
Q Consensus 4 ~~~w~~~~L~~~~~~~~~L~~~-~d~-----~~~ils~~el~~~~d~~eY~~nLLG--~e~~~~Fi~e~~~r~~~~~~~ 74 (340)
.++|+.+.|.+| .+.- ++| |..||+ |.+.++=..|+..||- ......||.|||.+...-...
T Consensus 51 vE~WId~qL~eL------y~~~e~~~p~EIDIDeLLD---l~sdeeR~~~LqelL~~C~~ptE~FI~ELL~kLkgL~k~ 120 (144)
T PF05361_consen 51 VEEWIDEQLQEL------YDCQEDEMPEEIDIDELLD---LESDEERRRKLQELLQDCPKPTEDFIQELLSKLKGLRKL 120 (144)
T ss_dssp HHHHHHHHHHHC------SSSSSTTS-SSSHHHHHHC---TSSTTHHHHHHHHHHTTCSSTTHHHHHHHHHHCTTT---
T ss_pred HHHHHHHHHHHH------hcCCCCCCCCcccHHHHhc---CCchHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC
Confidence 478999999999 3332 121 566777 6788888999999993 343569999999997764433
No 6
>smart00311 PWI PWI, domain in splicing factors.
Probab=86.90 E-value=2.1 Score=33.58 Aligned_cols=58 Identities=14% Similarity=0.279 Sum_probs=40.4
Q ss_pred HhhHHHHHHHHHhhcccCCCc-HHHHHHhhcccc-cCCchHHHHHHHHhhCCcchHHHHHHHHHHhc
Q 019483 5 GEWLEKALVDLCKRIESLDLD-GEVISGLVSYCE-FAQPLDAKEYLDNIIGQEVGKSVIEEYLRRRG 69 (340)
Q Consensus 5 ~~w~~~~L~~~~~~~~~L~~~-~d~~~~ils~~e-l~~~~d~~eY~~nLLG~e~~~~Fi~e~~~r~~ 69 (340)
-.|+.+.+.++ ||++ +.++.||++.+. =.+|.++...+... |-+....|+.+|-++.-
T Consensus 10 k~WI~~kv~e~------LG~~d~~vvd~i~~~l~~~~~~~~l~~~L~~~-~f~da~~Fv~~Lw~~l~ 69 (74)
T smart00311 10 KPWITKKVIEF------LGFEEDTLVEFILSQIRQHKGPQAKLLQINLT-GFEDAEEFVDKLWRLLI 69 (74)
T ss_pred HHHHHHHHHHH------HCCChHHHHHHHHHHHHhCCChHHHHHHHHhh-cchhHHHHHHHHHHHHH
Confidence 46899999998 9997 556789998753 12566665555333 44447899999977643
No 7
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=85.19 E-value=0.37 Score=30.43 Aligned_cols=22 Identities=27% Similarity=0.821 Sum_probs=18.3
Q ss_pred cccccceeeecccCcccCCCCccc
Q 019483 201 CLSCGKIVCEQEGEGPCQFCGALV 224 (340)
Q Consensus 201 CL~CGKIiCeqEG~gPC~FCG~~v 224 (340)
|.+||+-+ .++..-|..||++|
T Consensus 2 Cp~CG~~~--~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEI--EDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCC--CCcCcchhhhCCcC
Confidence 78899885 77888999999875
No 8
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=82.54 E-value=0.66 Score=34.69 Aligned_cols=27 Identities=41% Similarity=0.887 Sum_probs=20.8
Q ss_pred cccccccceeee--ccc-CcccCCCCccccc
Q 019483 199 SNCLSCGKIVCE--QEG-EGPCQFCGALVLK 226 (340)
Q Consensus 199 ~NCL~CGKIiCe--qEG-~gPC~FCG~~v~~ 226 (340)
--|+.||+++ + +++ .--|.+||.-++-
T Consensus 7 Y~C~~Cg~~~-~~~~~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 7 YKCARCGREV-ELDQETRGIRCPYCGSRILV 36 (49)
T ss_pred EEhhhcCCee-ehhhccCceeCCCCCcEEEE
Confidence 3699999999 4 233 3679999998864
No 9
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.19 E-value=1.3 Score=31.62 Aligned_cols=27 Identities=33% Similarity=0.691 Sum_probs=21.1
Q ss_pred ccccccceeeeccc--CcccCCCCccccc
Q 019483 200 NCLSCGKIVCEQEG--EGPCQFCGALVLK 226 (340)
Q Consensus 200 NCL~CGKIiCeqEG--~gPC~FCG~~v~~ 226 (340)
-|-+||..+=..+. ...|.|||+.+..
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred ECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 59999997744444 5899999998764
No 10
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=77.43 E-value=1.2 Score=32.97 Aligned_cols=15 Identities=40% Similarity=0.880 Sum_probs=11.7
Q ss_pred ccCcccCCCCccccc
Q 019483 212 EGEGPCQFCGALVLK 226 (340)
Q Consensus 212 EG~gPC~FCG~~v~~ 226 (340)
|-+-||+|||.....
T Consensus 1 ~~LkPCPFCG~~~~~ 15 (61)
T PF14354_consen 1 EELKPCPFCGSADVL 15 (61)
T ss_pred CCCcCCCCCCCcceE
Confidence 457899999987654
No 11
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=76.30 E-value=1.6 Score=34.00 Aligned_cols=32 Identities=28% Similarity=0.638 Sum_probs=26.6
Q ss_pred cCccccccccccceeeecccC--cccCCCCcccc
Q 019483 194 QHRLISNCLSCGKIVCEQEGE--GPCQFCGALVL 225 (340)
Q Consensus 194 ~H~Li~NCL~CGKIiCeqEG~--gPC~FCG~~v~ 225 (340)
.|..++-|.+||++|=-.|+. -||.-||+.++
T Consensus 5 ~~~~~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I 38 (61)
T COG2888 5 EMKDPPVCTSCGREIAPGETAVKFPCPNCGEVEI 38 (61)
T ss_pred cccCCceeccCCCEeccCCceeEeeCCCCCceee
Confidence 455578999999999888886 89999997665
No 12
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=75.77 E-value=1.7 Score=33.34 Aligned_cols=35 Identities=29% Similarity=0.773 Sum_probs=26.9
Q ss_pred cccccccCccccccccccceeee----cccCcccCCCCccccc
Q 019483 188 CSCQARQHRLISNCLSCGKIVCE----QEGEGPCQFCGALVLK 226 (340)
Q Consensus 188 C~C~A~~H~Li~NCL~CGKIiCe----qEG~gPC~FCG~~v~~ 226 (340)
|+=.++.|.+ |.||-+||. .|-..-|.|||.++-.
T Consensus 13 ~~~~~~~~~~----~pCgH~I~~~~f~~~rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 13 CGFVGTKGTV----LPCGHLICDNCFPGERYNGCPFCGTPFEF 51 (55)
T ss_pred cccccccccc----ccccceeeccccChhhccCCCCCCCcccC
Confidence 5555666666 469999998 5677999999998754
No 13
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=75.13 E-value=1.5 Score=42.74 Aligned_cols=37 Identities=24% Similarity=0.521 Sum_probs=28.8
Q ss_pred cccccCcc---------cccccccccee---eecccCcccCCCCccccc
Q 019483 190 CQARQHRL---------ISNCLSCGKIV---CEQEGEGPCQFCGALVLK 226 (340)
Q Consensus 190 C~A~~H~L---------i~NCL~CGKIi---CeqEG~gPC~FCG~~v~~ 226 (340)
|.-+--|+ .-+|++||+-. +.++...||+-||++|+.
T Consensus 138 C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~~qm~v~sPCy~C~~~v~P 186 (278)
T PF15135_consen 138 CRKRYDPVPCDKMWGIAEFHCPKCRHNFRGFAQMGVPSPCYGCGNPVYP 186 (278)
T ss_pred cccccCCCccccccceeeeecccccccchhhhhcCCCCCccCCCCccCc
Confidence 55555554 26999999976 566667999999999975
No 14
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=74.62 E-value=2.3 Score=29.03 Aligned_cols=24 Identities=38% Similarity=0.758 Sum_probs=18.6
Q ss_pred ccccccceeeecccCcccCCCCcc
Q 019483 200 NCLSCGKIVCEQEGEGPCQFCGAL 223 (340)
Q Consensus 200 NCL~CGKIiCeqEG~gPC~FCG~~ 223 (340)
-|..||-|+=..+-...|+.||++
T Consensus 4 ~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 4 VCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred ECCCCCCEeECCcCCCcCcCCCCc
Confidence 499999986434456899999984
No 15
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=72.08 E-value=2 Score=27.98 Aligned_cols=23 Identities=35% Similarity=0.730 Sum_probs=19.2
Q ss_pred ccccccceeeecccCcccCCCCccc
Q 019483 200 NCLSCGKIVCEQEGEGPCQFCGALV 224 (340)
Q Consensus 200 NCL~CGKIiCeqEG~gPC~FCG~~v 224 (340)
+|-.||++| .+...-|.+||...
T Consensus 2 ~CP~C~~~V--~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEV--PESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCc--hhhcCcCCCCCCCC
Confidence 689999996 77778999999753
No 16
>PF15616 TerY-C: TerY-C metal binding domain
Probab=71.88 E-value=3 Score=36.89 Aligned_cols=40 Identities=33% Similarity=0.702 Sum_probs=29.7
Q ss_pred CCCccccccccCccccccccccceeee-cccCcccCCCCcccc
Q 019483 184 QGKPCSCQARQHRLISNCLSCGKIVCE-QEGEGPCQFCGALVL 225 (340)
Q Consensus 184 ~r~~C~C~A~~H~Li~NCL~CGKIiCe-qEG~gPC~FCG~~v~ 225 (340)
|..-|-|-|..-.++ -| .||||.|. -++.--|+-||+.+.
T Consensus 76 g~PgCP~CGn~~~fa-~C-~CGkl~Ci~g~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 76 GAPGCPHCGNQYAFA-VC-GCGKLFCIDGEGEVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCCCcChhcEE-Ee-cCCCEEEeCCCCCEECCCCCCeee
Confidence 344587777654444 67 89999994 667799999999764
No 17
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=71.00 E-value=1.8 Score=36.50 Aligned_cols=31 Identities=23% Similarity=0.413 Sum_probs=22.9
Q ss_pred cCccccccccccceeeecccCcccCCCCccc
Q 019483 194 QHRLISNCLSCGKIVCEQEGEGPCQFCGALV 224 (340)
Q Consensus 194 ~H~Li~NCL~CGKIiCeqEG~gPC~FCG~~v 224 (340)
.-|+...|..||...=..+...+|+.||..-
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEPDEFDFSCPRCGSPD 96 (113)
T ss_dssp EE--EEEETTTS-EEECHHCCHH-SSSSSS-
T ss_pred ecCCcEECCCCCCEEecCCCCCCCcCCcCCC
Confidence 3466789999999998888889999999974
No 18
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=68.59 E-value=2.4 Score=33.43 Aligned_cols=16 Identities=31% Similarity=0.860 Sum_probs=13.0
Q ss_pred ccCcccCCCCcccccC
Q 019483 212 EGEGPCQFCGALVLKE 227 (340)
Q Consensus 212 EG~gPC~FCG~~v~~~ 227 (340)
.++-||+|||..+...
T Consensus 4 d~lKPCPFCG~~~~~v 19 (64)
T PRK09710 4 DNVKPCPFCGCPSVTV 19 (64)
T ss_pred ccccCCCCCCCceeEE
Confidence 4678999999988753
No 19
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=67.71 E-value=3.6 Score=36.76 Aligned_cols=27 Identities=30% Similarity=0.583 Sum_probs=20.9
Q ss_pred ccccccceeeeccc--CcccCCCCccccc
Q 019483 200 NCLSCGKIVCEQEG--EGPCQFCGALVLK 226 (340)
Q Consensus 200 NCL~CGKIiCeqEG--~gPC~FCG~~v~~ 226 (340)
-|.+||..++-... .-||+-||..-+.
T Consensus 114 ~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~ 142 (146)
T PF07295_consen 114 VCENCGHEVELTHPERLPPCPKCGHTEFT 142 (146)
T ss_pred ecccCCCEEEecCCCcCCCCCCCCCCeee
Confidence 57899999887554 4899999986543
No 20
>PRK12496 hypothetical protein; Provisional
Probab=61.83 E-value=4.1 Score=36.73 Aligned_cols=26 Identities=31% Similarity=0.622 Sum_probs=20.5
Q ss_pred ccccccceeeecccCcccCCCCcccc
Q 019483 200 NCLSCGKIVCEQEGEGPCQFCGALVL 225 (340)
Q Consensus 200 NCL~CGKIiCeqEG~gPC~FCG~~v~ 225 (340)
-|.+|||++=+....+-|.-||++|.
T Consensus 129 ~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 129 VCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred ECCCCCccccCCCCCCcCCCCCChhh
Confidence 49999999754444478999999885
No 21
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=61.79 E-value=4.2 Score=37.67 Aligned_cols=25 Identities=28% Similarity=0.676 Sum_probs=21.8
Q ss_pred cccccccceeeecccCcccCCCCcccc
Q 019483 199 SNCLSCGKIVCEQEGEGPCQFCGALVL 225 (340)
Q Consensus 199 ~NCL~CGKIiCeqEG~gPC~FCG~~v~ 225 (340)
--|.+|+||+= +-.+.|..||.++.
T Consensus 140 ~rC~GC~~~f~--~~~~~Cp~CG~~~~ 164 (177)
T COG1439 140 LRCHGCKRIFP--EPKDFCPICGSPLK 164 (177)
T ss_pred EEEecCceecC--CCCCcCCCCCCceE
Confidence 46999999986 77899999999975
No 22
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=60.28 E-value=6.4 Score=26.45 Aligned_cols=24 Identities=38% Similarity=0.694 Sum_probs=19.6
Q ss_pred ccccccceeeecccCcccCCCCcc
Q 019483 200 NCLSCGKIVCEQEGEGPCQFCGAL 223 (340)
Q Consensus 200 NCL~CGKIiCeqEG~gPC~FCG~~ 223 (340)
-|..||-|+=..+....|+-||+.
T Consensus 3 ~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCCcCCCcCcCCCCc
Confidence 489999998555667899999984
No 23
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=58.22 E-value=4.7 Score=29.66 Aligned_cols=12 Identities=42% Similarity=1.063 Sum_probs=9.4
Q ss_pred CcccCCCCcccc
Q 019483 214 EGPCQFCGALVL 225 (340)
Q Consensus 214 ~gPC~FCG~~v~ 225 (340)
+-||+|||..-.
T Consensus 1 LkPCPfCGg~~~ 12 (53)
T TIGR03655 1 LKPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCCcce
Confidence 469999998654
No 24
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=57.94 E-value=6 Score=46.06 Aligned_cols=39 Identities=23% Similarity=0.606 Sum_probs=23.4
Q ss_pred ccc-cccccCcccccccccccee-eecccCcccCCCCccccc
Q 019483 187 PCS-CQARQHRLISNCLSCGKIV-CEQEGEGPCQFCGALVLK 226 (340)
Q Consensus 187 ~C~-C~A~~H~Li~NCL~CGKIi-CeqEG~gPC~FCG~~v~~ 226 (340)
.|. |.+...+.+ -|.+||.-+ ....|..-|.+||.++..
T Consensus 681 fCP~CGs~te~vy-~CPsCGaev~~des~a~~CP~CGtplv~ 721 (1337)
T PRK14714 681 RCPDCGTHTEPVY-VCPDCGAEVPPDESGRVECPRCDVELTP 721 (1337)
T ss_pred cCcccCCcCCCce-eCccCCCccCCCccccccCCCCCCcccc
Confidence 344 555554444 666666632 223334589999999874
No 25
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.34 E-value=7.5 Score=33.97 Aligned_cols=30 Identities=20% Similarity=0.475 Sum_probs=22.7
Q ss_pred cCccccccccccceeeec---------------------ccCcccCCCCcc
Q 019483 194 QHRLISNCLSCGKIVCEQ---------------------EGEGPCQFCGAL 223 (340)
Q Consensus 194 ~H~Li~NCL~CGKIiCeq---------------------EG~gPC~FCG~~ 223 (340)
.-|...-|.+||.+.=.. +...+|+.||..
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 445667899999887554 345779999985
No 26
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=55.83 E-value=4.1 Score=35.35 Aligned_cols=30 Identities=20% Similarity=0.420 Sum_probs=21.6
Q ss_pred cccccccceeeecccCcccCCCCcccccCC
Q 019483 199 SNCLSCGKIVCEQEGEGPCQFCGALVLKEG 228 (340)
Q Consensus 199 ~NCL~CGKIiCeqEG~gPC~FCG~~v~~~~ 228 (340)
.-|.+|||..=..--..-|.||++++.-+.
T Consensus 70 V~CP~C~K~TKmLGr~D~CM~C~~pLTLd~ 99 (114)
T PF11023_consen 70 VECPNCGKQTKMLGRVDACMHCKEPLTLDP 99 (114)
T ss_pred eECCCCCChHhhhchhhccCcCCCcCccCc
Confidence 469999997422222379999999997543
No 27
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=54.45 E-value=9.4 Score=25.80 Aligned_cols=25 Identities=28% Similarity=0.607 Sum_probs=17.7
Q ss_pred ccccccceeeec-----ccCcccCCCCccc
Q 019483 200 NCLSCGKIVCEQ-----EGEGPCQFCGALV 224 (340)
Q Consensus 200 NCL~CGKIiCeq-----EG~gPC~FCG~~v 224 (340)
-|..||.++=.. ...-.|..||..+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 589999965222 3356899999854
No 28
>PRK11032 hypothetical protein; Provisional
Probab=54.10 E-value=8.6 Score=35.02 Aligned_cols=27 Identities=19% Similarity=0.331 Sum_probs=21.0
Q ss_pred ccccccceeeeccc--CcccCCCCccccc
Q 019483 200 NCLSCGKIVCEQEG--EGPCQFCGALVLK 226 (340)
Q Consensus 200 NCL~CGKIiCeqEG--~gPC~FCG~~v~~ 226 (340)
-|.+||.-++-.-. .-||+-||..-+.
T Consensus 126 vC~~Cg~~~~~~~p~~i~pCp~C~~~~F~ 154 (160)
T PRK11032 126 VCEKCHHHLAFYTPEVLPLCPKCGHDQFQ 154 (160)
T ss_pred EecCCCCEEEecCCCcCCCCCCCCCCeee
Confidence 58899998888654 4899999986543
No 29
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=52.24 E-value=7.6 Score=35.58 Aligned_cols=25 Identities=36% Similarity=0.720 Sum_probs=21.6
Q ss_pred ccccccccceeeecccCcccCCCCcc
Q 019483 198 ISNCLSCGKIVCEQEGEGPCQFCGAL 223 (340)
Q Consensus 198 i~NCL~CGKIiCeqEG~gPC~FCG~~ 223 (340)
+--|.-||=| |+-|-.++|+-||++
T Consensus 134 ~~vC~vCGy~-~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYT-HEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCc-ccCCCCCcCCCCCCh
Confidence 6789999987 555999999999985
No 30
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=51.49 E-value=9.8 Score=32.31 Aligned_cols=30 Identities=17% Similarity=0.319 Sum_probs=22.6
Q ss_pred cCccccccccccceeeecccC-cccCCCCcc
Q 019483 194 QHRLISNCLSCGKIVCEQEGE-GPCQFCGAL 223 (340)
Q Consensus 194 ~H~Li~NCL~CGKIiCeqEG~-gPC~FCG~~ 223 (340)
..|...-|..||..+=..+.. .+|+.||..
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 66 EQEAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eeCcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 345668899999877655554 789999975
No 31
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=51.14 E-value=10 Score=27.48 Aligned_cols=28 Identities=25% Similarity=0.433 Sum_probs=21.4
Q ss_pred cccccccceeeecc-cCcccCCCCccccc
Q 019483 199 SNCLSCGKIVCEQE-GEGPCQFCGALVLK 226 (340)
Q Consensus 199 ~NCL~CGKIiCeqE-G~gPC~FCG~~v~~ 226 (340)
-.|..||.-+=... +.-.|..||..|+-
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~rIly 31 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYRILY 31 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCceEEE
Confidence 36999999764443 45789999999874
No 32
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=49.92 E-value=12 Score=26.07 Aligned_cols=26 Identities=35% Similarity=0.788 Sum_probs=19.6
Q ss_pred ccccccceeeeccc----CcccCCCCcccc
Q 019483 200 NCLSCGKIVCEQEG----EGPCQFCGALVL 225 (340)
Q Consensus 200 NCL~CGKIiCeqEG----~gPC~FCG~~v~ 225 (340)
-|-.||+|+=..-. .|.|-.||..|.
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGELV 32 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEBEB
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCeeE
Confidence 48899999855333 489999999775
No 33
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=48.57 E-value=12 Score=31.76 Aligned_cols=31 Identities=16% Similarity=0.404 Sum_probs=23.6
Q ss_pred cCccccccccccceeeecccCcccCCCCccc
Q 019483 194 QHRLISNCLSCGKIVCEQEGEGPCQFCGALV 224 (340)
Q Consensus 194 ~H~Li~NCL~CGKIiCeqEG~gPC~FCG~~v 224 (340)
..|+..-|..||..+=..+-..+|+.||.+-
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred eeCcEEEcccCCCEEecCCcCccCcCCcCCC
Confidence 3456678999998776656678899999853
No 35
>PRK02935 hypothetical protein; Provisional
Probab=48.22 E-value=7.5 Score=33.56 Aligned_cols=30 Identities=20% Similarity=0.325 Sum_probs=22.1
Q ss_pred cccccccceeeecccCcccCCCCcccccCC
Q 019483 199 SNCLSCGKIVCEQEGEGPCQFCGALVLKEG 228 (340)
Q Consensus 199 ~NCL~CGKIiCeqEG~gPC~FCG~~v~~~~ 228 (340)
--|.+|+|..=..---.-|.||++||.-+.
T Consensus 71 V~CP~C~K~TKmLGrvD~CM~C~~PLTLd~ 100 (110)
T PRK02935 71 VICPSCEKPTKMLGRVDACMHCNQPLTLDR 100 (110)
T ss_pred eECCCCCchhhhccceeecCcCCCcCCcCc
Confidence 479999997433333489999999997543
No 36
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=47.55 E-value=6.7 Score=28.31 Aligned_cols=12 Identities=42% Similarity=1.326 Sum_probs=10.8
Q ss_pred cccccccceeee
Q 019483 199 SNCLSCGKIVCE 210 (340)
Q Consensus 199 ~NCL~CGKIiCe 210 (340)
.+|-.||+|+|.
T Consensus 19 ~~Cr~Cg~~~C~ 30 (57)
T cd00065 19 HHCRNCGRIFCS 30 (57)
T ss_pred cccCcCcCCcCh
Confidence 699999999986
No 37
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=46.36 E-value=10 Score=29.35 Aligned_cols=29 Identities=34% Similarity=0.958 Sum_probs=19.1
Q ss_pred CCcc-cCCCCccccccccCccc-------ccccccccee
Q 019483 178 GSIV-FQQGKPCSCQARQHRLI-------SNCLSCGKIV 208 (340)
Q Consensus 178 ~~~~-~~~r~~C~C~A~~H~Li-------~NCL~CGKIi 208 (340)
||+| ++-.|||+.. +-.++ --|++||++|
T Consensus 5 gDiV~mKK~HPCG~~--~Wei~R~GaDikikC~gCg~~i 41 (57)
T PF06107_consen 5 GDIVEMKKPHPCGSN--EWEIIRIGADIKIKCLGCGRQI 41 (57)
T ss_pred CCEEEEcCCCCCCCC--EEEEEEccCcEEEEECCCCCEE
Confidence 5554 4666898763 33332 4699999987
No 38
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=45.51 E-value=9.2 Score=28.78 Aligned_cols=12 Identities=42% Similarity=1.392 Sum_probs=7.7
Q ss_pred cccccccceeee
Q 019483 199 SNCLSCGKIVCE 210 (340)
Q Consensus 199 ~NCL~CGKIiCe 210 (340)
-+|-.||+|||.
T Consensus 26 hhCr~CG~~vC~ 37 (69)
T PF01363_consen 26 HHCRNCGRVVCS 37 (69)
T ss_dssp EE-TTT--EEEC
T ss_pred EccCCCCCEECC
Confidence 599999999993
No 39
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=45.49 E-value=11 Score=29.98 Aligned_cols=17 Identities=35% Similarity=0.888 Sum_probs=14.4
Q ss_pred ccccccccceeeecccC
Q 019483 198 ISNCLSCGKIVCEQEGE 214 (340)
Q Consensus 198 i~NCL~CGKIiCeqEG~ 214 (340)
.--|+.||+++|+--|.
T Consensus 38 ~V~C~~CG~~l~~PTGG 54 (67)
T COG2051 38 VVTCLICGTTLAEPTGG 54 (67)
T ss_pred EEEecccccEEEecCCC
Confidence 36899999999998774
No 40
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=43.37 E-value=13 Score=24.12 Aligned_cols=21 Identities=43% Similarity=1.070 Sum_probs=13.5
Q ss_pred cccccceeeecc-c-CcccCCCC
Q 019483 201 CLSCGKIVCEQE-G-EGPCQFCG 221 (340)
Q Consensus 201 CL~CGKIiCeqE-G-~gPC~FCG 221 (340)
|.+||++|=..| + .-+|.-||
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 667777766555 3 26777776
No 41
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=42.89 E-value=17 Score=30.82 Aligned_cols=29 Identities=17% Similarity=0.496 Sum_probs=20.9
Q ss_pred CccccccccccceeeecccCcccCCCCcc
Q 019483 195 HRLISNCLSCGKIVCEQEGEGPCQFCGAL 223 (340)
Q Consensus 195 H~Li~NCL~CGKIiCeqEG~gPC~FCG~~ 223 (340)
-|+..-|..||...=..+-..+|+.||..
T Consensus 67 vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred eCcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 35567899999665444556779999975
No 42
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.82 E-value=14 Score=31.48 Aligned_cols=29 Identities=17% Similarity=0.491 Sum_probs=20.1
Q ss_pred ccccccccccceeeecc-cCcccCCCCccc
Q 019483 196 RLISNCLSCGKIVCEQE-GEGPCQFCGALV 224 (340)
Q Consensus 196 ~Li~NCL~CGKIiCeqE-G~gPC~FCG~~v 224 (340)
|+..-|..||...=..+ ....|+.||.+-
T Consensus 69 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 69 KVELECKDCSHVFKPNALDYGVCEKCHSKN 98 (117)
T ss_pred CCEEEhhhCCCccccCCccCCcCcCCCCCc
Confidence 44578999997764443 334599999863
No 43
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=40.80 E-value=17 Score=33.44 Aligned_cols=39 Identities=28% Similarity=0.507 Sum_probs=29.5
Q ss_pred CccccccccCccccccccccceeeec-------ccC-cccCCCCccccc
Q 019483 186 KPCSCQARQHRLISNCLSCGKIVCEQ-------EGE-GPCQFCGALVLK 226 (340)
Q Consensus 186 ~~C~C~A~~H~Li~NCL~CGKIiCeq-------EG~-gPC~FCG~~v~~ 226 (340)
+..+|.|+.+.+. |+.||+++-.. +.. -.|..||..+..
T Consensus 99 ~v~elHG~~~~~~--C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~lrP 145 (218)
T cd01407 99 KVIELHGSLFRVR--CTKCGKEYPRDELQADIDREEVPRCPKCGGLLRP 145 (218)
T ss_pred CEEECcCCcCcce--eCCCcCCCcHHHHhHhhccCCCCcCCCCCCccCC
Confidence 6789999999876 99999986432 233 469999987654
No 44
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=40.55 E-value=15 Score=28.64 Aligned_cols=26 Identities=31% Similarity=0.740 Sum_probs=16.7
Q ss_pred cccccccceeeecccC--cccCCCCccc
Q 019483 199 SNCLSCGKIVCEQEGE--GPCQFCGALV 224 (340)
Q Consensus 199 ~NCL~CGKIiCeqEG~--gPC~FCG~~v 224 (340)
+.|.+||+.|=..|.. -+|.-||+.+
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~ 35 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGEVI 35 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCCee
Confidence 4677777777444422 6777777764
No 45
>PF12773 DZR: Double zinc ribbon
Probab=40.48 E-value=13 Score=26.34 Aligned_cols=28 Identities=25% Similarity=0.490 Sum_probs=12.1
Q ss_pred ccccccccccceeee-cccCcccCCCCcc
Q 019483 196 RLISNCLSCGKIVCE-QEGEGPCQFCGAL 223 (340)
Q Consensus 196 ~Li~NCL~CGKIiCe-qEG~gPC~FCG~~ 223 (340)
+=...|.+||.-+=. ......|.-||+.
T Consensus 10 ~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred ccccCChhhcCChhhccCCCCCCcCCcCC
Confidence 334455555554321 1112445555554
No 46
>PF10977 DUF2797: Protein of unknown function (DUF2797); InterPro: IPR021246 This family of proteins has no known function.
Probab=39.07 E-value=14 Score=35.55 Aligned_cols=25 Identities=28% Similarity=0.631 Sum_probs=20.0
Q ss_pred ccccccceeeecccCcccCCCCccc
Q 019483 200 NCLSCGKIVCEQEGEGPCQFCGALV 224 (340)
Q Consensus 200 NCL~CGKIiCeqEG~gPC~FCG~~v 224 (340)
+|++||+-.|.-=+.|.|.-|-..+
T Consensus 13 ~c~~cG~~~~~s~~qg~C~~C~~~~ 37 (235)
T PF10977_consen 13 QCLNCGRKTKKSFRQGYCYPCFQTL 37 (235)
T ss_pred EEecCCccccccCCCCceeCCCCcC
Confidence 8999999888877778887776654
No 47
>PF07765 KIP1: KIP1-like protein; InterPro: IPR011684 This is a group of sequences found exclusively in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase []. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions []. It has also been suggested that the coiled-coils of the protein allow it to dimerise in vivo [].
Probab=39.04 E-value=1.1e+02 Score=24.91 Aligned_cols=24 Identities=25% Similarity=0.634 Sum_probs=20.7
Q ss_pred hHhhHHHHHHHHHhhcccCCCcHHHHHHhhcccc
Q 019483 4 AGEWLEKALVDLCKRIESLDLDGEVISGLVSYCE 37 (340)
Q Consensus 4 ~~~w~~~~L~~~~~~~~~L~~~~d~~~~ils~~e 37 (340)
-.+||..+|.++ ++-+..||.+++
T Consensus 12 ~skWL~~~l~dm----------d~kvk~mlklie 35 (74)
T PF07765_consen 12 QSKWLQENLSDM----------DEKVKAMLKLIE 35 (74)
T ss_pred CCHHHHHHHHHH----------HHHHHHHHHHhc
Confidence 468999999999 888999999864
No 48
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=39.00 E-value=6.7 Score=38.74 Aligned_cols=21 Identities=48% Similarity=1.282 Sum_probs=16.6
Q ss_pred Ccccc-----ccccCccccccccccceeee
Q 019483 186 KPCSC-----QARQHRLISNCLSCGKIVCE 210 (340)
Q Consensus 186 ~~C~C-----~A~~H~Li~NCL~CGKIiCe 210 (340)
+.|.| ..++|= |-+||+|||.
T Consensus 172 ~~C~~~~Ftl~~RRHH----CR~CG~ivC~ 197 (288)
T KOG1729|consen 172 MVCGCTEFTLSERRHH----CRNCGDIVCA 197 (288)
T ss_pred ccCCCccccHHHHHHH----HHhcchHhhh
Confidence 46888 556664 9999999987
No 49
>COG4855 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.78 E-value=4 Score=32.77 Aligned_cols=31 Identities=35% Similarity=0.669 Sum_probs=25.8
Q ss_pred CccccccccccceeeecccC-----cccCCCCcccccC
Q 019483 195 HRLISNCLSCGKIVCEQEGE-----GPCQFCGALVLKE 227 (340)
Q Consensus 195 H~Li~NCL~CGKIiCeqEG~-----gPC~FCG~~v~~~ 227 (340)
|+...||+.| -+|..||- |.|.-||.-||.+
T Consensus 1 ~~~~~~~mKC--Y~C~eeGKDtdAV~iCIVCG~GlC~E 36 (76)
T COG4855 1 MLRWSNMMKC--YDCAEEGKDTDAVGICIVCGMGLCME 36 (76)
T ss_pred CcchhhhhHH--HHHHHhCCCcccEEEEEEeCchHHHH
Confidence 5667899988 47998884 8999999999875
No 50
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=36.48 E-value=12 Score=33.90 Aligned_cols=58 Identities=16% Similarity=0.231 Sum_probs=37.1
Q ss_pred ccccceehHHHhhcCCcccCCC--CccccccccCccccccccccceeeecccCcccCCCCcccccC
Q 019483 164 KKAGKVISLAEAAKGSIVFQQG--KPCSCQARQHRLISNCLSCGKIVCEQEGEGPCQFCGALVLKE 227 (340)
Q Consensus 164 kkk~K~vsL~e~~~~~~~~~~r--~~C~C~A~~H~Li~NCL~CGKIiCeqEG~gPC~FCG~~v~~~ 227 (340)
+++..|++|.+....+ ++++. |.|-=-...-||+.-|-.||-+ +.--|.-||+-.|+-
T Consensus 83 ~~RKnf~~~Ldea~~~-~~k~~~Y~~~~a~p~~KP~r~fCaVCG~~-----S~ysC~~CG~kyCsv 142 (156)
T KOG3362|consen 83 RFRKNFQALLDEALLN-LMKNPNYHTAYAKPSFKPLRKFCAVCGYD-----SKYSCVNCGTKYCSV 142 (156)
T ss_pred hHHHHHHHHHHccchh-hhhccchhhcccCCCCCCcchhhhhcCCC-----chhHHHhcCCceeec
Confidence 3444588888865443 22222 2333344555999999999933 566788899988864
No 51
>PRK07218 replication factor A; Provisional
Probab=35.94 E-value=18 Score=37.49 Aligned_cols=24 Identities=38% Similarity=0.974 Sum_probs=19.9
Q ss_pred ccccccccccceeeecccCcccCCCCcc
Q 019483 196 RLISNCLSCGKIVCEQEGEGPCQFCGAL 223 (340)
Q Consensus 196 ~Li~NCL~CGKIiCeqEG~gPC~FCG~~ 223 (340)
.|+.-|..|+|++ ..|.|.+||..
T Consensus 295 gli~rCP~C~r~v----~~~~C~~hG~v 318 (423)
T PRK07218 295 GLIERCPECGRVI----QKGQCRSHGAV 318 (423)
T ss_pred cceecCcCccccc----cCCcCCCCCCc
Confidence 4568899999998 44899999964
No 52
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=35.29 E-value=21 Score=28.22 Aligned_cols=26 Identities=31% Similarity=0.768 Sum_probs=21.3
Q ss_pred ccccccceeeecccCcccCCCCcccccC
Q 019483 200 NCLSCGKIVCEQEGEGPCQFCGALVLKE 227 (340)
Q Consensus 200 NCL~CGKIiCeqEG~gPC~FCG~~v~~~ 227 (340)
-|.+|++| ..+....|+.||..=+++
T Consensus 6 AC~~Ck~l--~~~d~e~CP~Cgs~~~te 31 (64)
T COG2093 6 ACKNCKRL--TPEDTEICPVCGSTDLTE 31 (64)
T ss_pred HHhhcccc--CCCCCccCCCCCCcccch
Confidence 59999999 577778899999975554
No 53
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=33.81 E-value=22 Score=33.38 Aligned_cols=39 Identities=21% Similarity=0.376 Sum_probs=27.0
Q ss_pred CccccccccCccccccccccceeeeccc----CcccCCCCccccc
Q 019483 186 KPCSCQARQHRLISNCLSCGKIVCEQEG----EGPCQFCGALVLK 226 (340)
Q Consensus 186 ~~C~C~A~~H~Li~NCL~CGKIiCeqEG----~gPC~FCG~~v~~ 226 (340)
+.-+++|..+.+. |+.||+++...+- .-+|..||.++..
T Consensus 112 ~v~elHG~~~~~~--C~~C~~~~~~~~~~~~~~p~C~~Cgg~lrP 154 (242)
T PRK00481 112 NVIELHGSLLRAR--CTKCGQTYDLDEYLKPEPPRCPKCGGILRP 154 (242)
T ss_pred ceeeccCCcCcee--eCCCCCCcChhhhccCCCCCCCCCCCccCC
Confidence 4567778877765 9999988753221 2349999987654
No 54
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.07 E-value=22 Score=35.59 Aligned_cols=25 Identities=36% Similarity=0.902 Sum_probs=20.0
Q ss_pred cccceeee-------cccCcccCCCCcccccC
Q 019483 203 SCGKIVCE-------QEGEGPCQFCGALVLKE 227 (340)
Q Consensus 203 ~CGKIiCe-------qEG~gPC~FCG~~v~~~ 227 (340)
.||=.+|. ..|.++|+-|+..+-..
T Consensus 25 ~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 25 VCGHTLCESCVDLLFVRGSGSCPECDTPLRKN 56 (309)
T ss_pred CCCCcccHHHHHHHhcCCCCCCCCCCCccchh
Confidence 78888876 56789999999988643
No 55
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=32.40 E-value=33 Score=23.41 Aligned_cols=26 Identities=35% Similarity=0.621 Sum_probs=17.3
Q ss_pred ccccccceeeeccc-CcccCCCCcccc
Q 019483 200 NCLSCGKIVCEQEG-EGPCQFCGALVL 225 (340)
Q Consensus 200 NCL~CGKIiCeqEG-~gPC~FCG~~v~ 225 (340)
.|..||..+=...+ .--|.+||.-++
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHRIL 28 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-SEE
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCeEE
Confidence 48889987643333 368999998775
No 56
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=32.33 E-value=29 Score=27.11 Aligned_cols=25 Identities=32% Similarity=0.733 Sum_probs=19.5
Q ss_pred ccccccceeeecccCcccCCCCcccccCC
Q 019483 200 NCLSCGKIVCEQEGEGPCQFCGALVLKEG 228 (340)
Q Consensus 200 NCL~CGKIiCeqEG~gPC~FCG~~v~~~~ 228 (340)
-|.+|.+|+ + ...|+-||..-+++.
T Consensus 5 AC~~C~~i~---~-~~~CP~Cgs~~~T~~ 29 (61)
T PRK08351 5 ACRHCHYIT---T-EDRCPVCGSRDLSDE 29 (61)
T ss_pred hhhhCCccc---C-CCcCCCCcCCccccc
Confidence 699999998 2 236999999776653
No 57
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=32.08 E-value=21 Score=27.29 Aligned_cols=15 Identities=27% Similarity=0.970 Sum_probs=8.3
Q ss_pred cccccccceeeeccc
Q 019483 199 SNCLSCGKIVCEQEG 213 (340)
Q Consensus 199 ~NCL~CGKIiCeqEG 213 (340)
-+|..||.++|+--|
T Consensus 27 V~C~~Cg~~L~~PtG 41 (55)
T PF01667_consen 27 VKCVVCGTVLAQPTG 41 (55)
T ss_dssp EE-SSSTSEEEEE-S
T ss_pred EEcccCCCEecCCCC
Confidence 466666666666555
No 58
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=31.01 E-value=26 Score=24.59 Aligned_cols=25 Identities=40% Similarity=0.853 Sum_probs=16.2
Q ss_pred cccccc--ee-eecccCcccCCCCcccc
Q 019483 201 CLSCGK--IV-CEQEGEGPCQFCGALVL 225 (340)
Q Consensus 201 CL~CGK--Ii-CeqEG~gPC~FCG~~v~ 225 (340)
|.+||. |+ =...|.-.|..||.-|-
T Consensus 3 Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 3 CPNCGSKEIVFDPERGELVCPNCGLVLE 30 (43)
T ss_dssp BTTTSSSEEEEETTTTEEEETTT-BBEE
T ss_pred CcCCcCCceEEcCCCCeEECCCCCCEee
Confidence 677776 33 33567778999988653
No 59
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=29.76 E-value=21 Score=25.19 Aligned_cols=13 Identities=38% Similarity=0.894 Sum_probs=6.6
Q ss_pred ccCCCCcccccCC
Q 019483 216 PCQFCGALVLKEG 228 (340)
Q Consensus 216 PC~FCG~~v~~~~ 228 (340)
-|+|||..--..+
T Consensus 3 ~CSFCgr~~~~v~ 15 (41)
T PF06689_consen 3 RCSFCGRPESEVG 15 (41)
T ss_dssp B-TTT--BTTTSS
T ss_pred CccCCCCCHHHHh
Confidence 5999999765433
No 60
>cd00240 TFIIFa Transcription initiation factor IIF, alpha subunit, N-terminal region of RAP74. Subunit of transcription initiation complex involved in initiation, elongation and promoter escape.Tetramer of 2 alpha and 2 beta TFIIF subunits interacts directly with RNA polymerase II. TFIIF inhibits non-specific transcription initiation by PolII and recruits the polymerase to the preinitiation complex on promoter DNA for site-specific transcription initiation. The PolII/TFIIF-complex attaches through direct interactions of TFIIF with promoter DNA, TFIIB and the TAF250 subunit of TFIID, and provides scaffolding for addition of TFIIE and TFIIH. Together with TFIIE, TFIIF participates in DNA strand separation (open complex formation). N-terminal domains of RAP30 and RAP74 co-fold to form a single core structure, a triple barrel heterodimer, and has pseudo-2-fold symmetry.
Probab=29.70 E-value=20 Score=32.86 Aligned_cols=26 Identities=19% Similarity=0.279 Sum_probs=22.7
Q ss_pred cccccccceeeecccCcccC-CCCccccc
Q 019483 199 SNCLSCGKIVCEQEGEGPCQ-FCGALVLK 226 (340)
Q Consensus 199 ~NCL~CGKIiCeqEG~gPC~-FCG~~v~~ 226 (340)
.||+.||+| -....++|. ||+.++..
T Consensus 9 ~~~~~~~~v--Mafn~~~~~d~~~~~~~~ 35 (162)
T cd00240 9 KLCLKKYRV--MAFNASDKVDFAGWVVVR 35 (162)
T ss_pred cccchhhhh--HhccCCCCccccccceeE
Confidence 589999999 788899999 99998753
No 61
>PRK09462 fur ferric uptake regulator; Provisional
Probab=29.63 E-value=30 Score=29.94 Aligned_cols=14 Identities=36% Similarity=0.607 Sum_probs=11.6
Q ss_pred cccccccccceeee
Q 019483 197 LISNCLSCGKIVCE 210 (340)
Q Consensus 197 Li~NCL~CGKIiCe 210 (340)
..-.|..||+|+|.
T Consensus 89 ~H~iC~~Cg~i~~i 102 (148)
T PRK09462 89 DHLICLDCGKVIEF 102 (148)
T ss_pred CceEECCCCCEEEe
Confidence 34579999999986
No 62
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=29.60 E-value=23 Score=28.34 Aligned_cols=28 Identities=36% Similarity=0.891 Sum_probs=20.5
Q ss_pred cccccccccceeeecccC--cccCCCCccccc
Q 019483 197 LISNCLSCGKIVCEQEGE--GPCQFCGALVLK 226 (340)
Q Consensus 197 Li~NCL~CGKIiCeqEG~--gPC~FCG~~v~~ 226 (340)
||--| .|||..=+.|+. --| .||..+--
T Consensus 2 lifrC-~Cgr~lya~e~~kTkkC-~CG~~l~v 31 (68)
T PF09082_consen 2 LIFRC-DCGRYLYAKEGAKTKKC-VCGKTLKV 31 (68)
T ss_dssp EEEEE-TTS--EEEETT-SEEEE-TTTEEEE-
T ss_pred EEEEe-cCCCEEEecCCcceeEe-cCCCeeee
Confidence 56679 899999999997 889 99997753
No 63
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=29.40 E-value=37 Score=24.54 Aligned_cols=26 Identities=15% Similarity=0.156 Sum_probs=19.5
Q ss_pred ccccccceeeec------ccCcccCCCCcccc
Q 019483 200 NCLSCGKIVCEQ------EGEGPCQFCGALVL 225 (340)
Q Consensus 200 NCL~CGKIiCeq------EG~gPC~FCG~~v~ 225 (340)
-.+.||.++|.. ...+.|++||.++.
T Consensus 15 v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 15 VILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 456899999863 23678999998763
No 64
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=29.32 E-value=19 Score=31.48 Aligned_cols=28 Identities=25% Similarity=0.520 Sum_probs=20.0
Q ss_pred ccccccceeeecc--------cCcccCCCCcccccC
Q 019483 200 NCLSCGKIVCEQE--------GEGPCQFCGALVLKE 227 (340)
Q Consensus 200 NCL~CGKIiCeqE--------G~gPC~FCG~~v~~~ 227 (340)
-|.+||+.+=..| |.--|++||+.|...
T Consensus 101 ~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 101 KCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred ECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 5778898775433 337899999988643
No 65
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=28.94 E-value=36 Score=31.64 Aligned_cols=39 Identities=18% Similarity=0.436 Sum_probs=27.6
Q ss_pred CccccccccCccccccccccceeee------cccC-cccCCCCccccc
Q 019483 186 KPCSCQARQHRLISNCLSCGKIVCE------QEGE-GPCQFCGALVLK 226 (340)
Q Consensus 186 ~~C~C~A~~H~Li~NCL~CGKIiCe------qEG~-gPC~FCG~~v~~ 226 (340)
+.++++|+.+.+. |+.||+.+=. ..+. -.|..||.++-.
T Consensus 103 ~v~elHG~l~~~~--C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~lrP 148 (222)
T cd01413 103 NVIELHGTLQTAY--CVNCGSKYDLEEVKYAKKHEVPRCPKCGGIIRP 148 (222)
T ss_pred cEEEccCCcCcce--ECCCCCCcchhHHHHhccCCCCcCCCCCCccCC
Confidence 5688999999876 9999986411 1223 459999987643
No 66
>PRK05255 hypothetical protein; Provisional
Probab=28.46 E-value=99 Score=28.52 Aligned_cols=46 Identities=20% Similarity=0.346 Sum_probs=33.5
Q ss_pred hHHHHHHHHHhh-cccCCCcHHHHHHhhcccccCCchHH---HHHHHHhh
Q 019483 7 WLEKALVDLCKR-IESLDLDGEVISGLVSYCEFAQPLDA---KEYLDNII 52 (340)
Q Consensus 7 w~~~~L~~~~~~-~~~L~~~~d~~~~ils~~el~~~~d~---~eY~~nLL 52 (340)
=|++.|+++-.. |..||+|+++...|+..--|++-+-. -.|++-|+
T Consensus 31 ~LG~~L~~Ls~~ql~~lpL~e~L~~Ai~ea~ri~~~eA~RRqlqyIGKLm 80 (171)
T PRK05255 31 DLGEELVELSKDQLAKLPLDEDLRDAILEAQRITSHEARRRQLQYIGKLM 80 (171)
T ss_pred HHHHHHHhCCHHHHhcCCCCHHHHHHHHHHhhhccchHHHHHHHHHHHHH
Confidence 356777777665 77799999999999986546543222 56888888
No 67
>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]
Probab=28.21 E-value=1.2e+02 Score=33.63 Aligned_cols=64 Identities=13% Similarity=0.191 Sum_probs=49.8
Q ss_pred hHhhHHHHHHHHHhh--cccCCCc-HHHHHHhhcccc-cCCchHHHHHHHHhhCCcchHHHHHHHHHHh
Q 019483 4 AGEWLEKALVDLCKR--IESLDLD-GEVISGLVSYCE-FAQPLDAKEYLDNIIGQEVGKSVIEEYLRRR 68 (340)
Q Consensus 4 ~~~w~~~~L~~~~~~--~~~L~~~-~d~~~~ils~~e-l~~~~d~~eY~~nLLG~e~~~~Fi~e~~~r~ 68 (340)
.+.||.+....|..+ ++.||.- +.+|.||++-+. =..|..|-+=|.-+|.+| +..|+-.+-+++
T Consensus 589 d~~lm~~rirpwV~KKIiEflGeeE~tLVdFI~s~i~~h~~~q~iL~dl~~ilDEd-AE~FV~KmWRlL 656 (668)
T KOG2253|consen 589 DSILMNERIRPWVNKKIIEFLGEEEDTLVDFICSNIRQHSSPQQILDDLAMILDED-AEVFVVKMWRLL 656 (668)
T ss_pred hhHHHHHHHHHHHHHHHHHHhCCcchhHHHHHHHHHHhcCCHHHHHHHHHHHHhcc-hHHHHHHHHHHH
Confidence 367999999999888 6669986 667788888654 367888888888888888 888987765554
No 68
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=28.01 E-value=34 Score=26.55 Aligned_cols=10 Identities=50% Similarity=0.979 Sum_probs=7.3
Q ss_pred cccccccccc
Q 019483 197 LISNCLSCGK 206 (340)
Q Consensus 197 Li~NCL~CGK 206 (340)
|-|||-.|++
T Consensus 4 lrpnCE~C~~ 13 (57)
T PF06906_consen 4 LRPNCECCDK 13 (57)
T ss_pred cCCCccccCC
Confidence 4578888876
No 69
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=27.65 E-value=21 Score=31.74 Aligned_cols=26 Identities=27% Similarity=0.700 Sum_probs=19.0
Q ss_pred ccccccceeee--cccCcccCCCCcccc
Q 019483 200 NCLSCGKIVCE--QEGEGPCQFCGALVL 225 (340)
Q Consensus 200 NCL~CGKIiCe--qEG~gPC~FCG~~v~ 225 (340)
-|++||+++=- .|=+.-|+-||...+
T Consensus 3 ~Ct~Cg~~f~dgs~eil~GCP~CGg~kF 30 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSGCPECGGNKF 30 (131)
T ss_pred ccCcCCCCcCCCcHHHHccCcccCCcce
Confidence 49999999732 233478999998764
No 70
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=27.41 E-value=32 Score=28.38 Aligned_cols=17 Identities=29% Similarity=0.589 Sum_probs=12.2
Q ss_pred cCccccccccccceeee
Q 019483 194 QHRLISNCLSCGKIVCE 210 (340)
Q Consensus 194 ~H~Li~NCL~CGKIiCe 210 (340)
.|-..-.|..||||++.
T Consensus 76 ~~h~h~iC~~Cg~v~~~ 92 (120)
T PF01475_consen 76 HHHHHFICTQCGKVIDL 92 (120)
T ss_dssp SSCEEEEETTTS-EEEE
T ss_pred CcceEEEECCCCCEEEe
Confidence 34445799999999976
No 71
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=27.26 E-value=44 Score=34.46 Aligned_cols=34 Identities=35% Similarity=0.719 Sum_probs=24.7
Q ss_pred ccccccccceee-ecccCcccCCCCcccccCCCcc
Q 019483 198 ISNCLSCGKIVC-EQEGEGPCQFCGALVLKEGSTY 231 (340)
Q Consensus 198 i~NCL~CGKIiC-eqEG~gPC~FCG~~v~~~~~~~ 231 (340)
+--|-.||.|+= ..++..+|++||..+..-|..+
T Consensus 240 ~~~c~~cg~~~~~~~~~~~~c~~Cg~~~~~~GPlW 274 (380)
T COG1867 240 IYHCSRCGEIVGSFREVDEKCPHCGGKVHLAGPLW 274 (380)
T ss_pred EEEcccccceecccccccccCCcccccceeccCcc
Confidence 367889997663 3566799999999766656544
No 72
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=27.00 E-value=37 Score=32.19 Aligned_cols=39 Identities=21% Similarity=0.452 Sum_probs=28.3
Q ss_pred CccccccccCccccccccccceeeecc--------cCcccCCCCccccc
Q 019483 186 KPCSCQARQHRLISNCLSCGKIVCEQE--------GEGPCQFCGALVLK 226 (340)
Q Consensus 186 ~~C~C~A~~H~Li~NCL~CGKIiCeqE--------G~gPC~FCG~~v~~ 226 (340)
+..+++|+.|.+. |+.||+++-..+ ..-.|.-||.++..
T Consensus 109 ~VielHG~~~~~~--C~~C~~~~~~~~~~~~~~~~~~p~Cp~Cgg~lrP 155 (244)
T PRK14138 109 KVIELHGNVEEYY--CVRCGKRYTVEDVIEKLEKSDVPRCDDCSGLIRP 155 (244)
T ss_pred eEEEccCCcCeeE--ECCCCCcccHHHHHHHHhcCCCCCCCCCCCeECC
Confidence 5688888888865 999999764321 23469999987654
No 73
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=26.83 E-value=41 Score=27.27 Aligned_cols=15 Identities=27% Similarity=0.521 Sum_probs=12.2
Q ss_pred cccccccccceeeec
Q 019483 197 LISNCLSCGKIVCEQ 211 (340)
Q Consensus 197 Li~NCL~CGKIiCeq 211 (340)
..-.|..||+|+|..
T Consensus 72 ~H~~C~~Cg~i~~~~ 86 (116)
T cd07153 72 HHLICTKCGKVIDFE 86 (116)
T ss_pred CceEeCCCCCEEEec
Confidence 357999999999853
No 74
>PF04751 DUF615: Protein of unknown function (DUF615); InterPro: IPR006839 The proteins in this entry are functionally uncharacterised. The entry contains the Escherichia coli (strain K12) protein YjgA (P0A8X0 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2P0T_A.
Probab=26.15 E-value=1e+02 Score=27.93 Aligned_cols=57 Identities=14% Similarity=0.321 Sum_probs=31.9
Q ss_pred HHHHHHHHHhh-cccCCCcHHHHHHhhcccccCCchHH---HHHHHHhh-CCcchH--HHHHHH
Q 019483 8 LEKALVDLCKR-IESLDLDGEVISGLVSYCEFAQPLDA---KEYLDNII-GQEVGK--SVIEEY 64 (340)
Q Consensus 8 ~~~~L~~~~~~-~~~L~~~~d~~~~ils~~el~~~~d~---~eY~~nLL-G~e~~~--~Fi~e~ 64 (340)
|++.|+++-.. |..||+++++...|+..--|++-+-. -.|++-|| +.+... .+|+.+
T Consensus 21 Lg~~L~~L~~~ql~~lpL~e~l~~Ai~~a~ri~~~~arrRQ~qyIGKLmR~~d~e~I~~al~~~ 84 (157)
T PF04751_consen 21 LGEELVELSPKQLAKLPLPEELRDAIMEARRITSHEARRRQLQYIGKLMREEDPEAIRAALDAL 84 (157)
T ss_dssp HHHHHTTS-HHHHTTS---HHHHHHHHHGGG--SHHHHHHHHHHHHHHGGGS-HHHHHHHHHHH
T ss_pred HHHHHHhCCHHHHhhCCCCHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 45566666554 66699999999999986556443333 67899988 443222 455444
No 75
>KOG2146 consensus Splicing coactivator SRm160/300, subunit SRm160 (contains PWI domain) [RNA processing and modification; General function prediction only]
Probab=26.15 E-value=50 Score=33.30 Aligned_cols=61 Identities=21% Similarity=0.255 Sum_probs=37.3
Q ss_pred HhhHHHHHHHHHhhcccCCCc-HHHHHHhhcccccCCchHHHHHHHHhhCC---cchHHHHHHHHHHhccc
Q 019483 5 GEWLEKALVDLCKRIESLDLD-GEVISGLVSYCEFAQPLDAKEYLDNIIGQ---EVGKSVIEEYLRRRGLT 71 (340)
Q Consensus 5 ~~w~~~~L~~~~~~~~~L~~~-~d~~~~ils~~el~~~~d~~eY~~nLLG~---e~~~~Fi~e~~~r~~~~ 71 (340)
--||.+.|.++ |+|. +-+|.||+..+|-+.-.+-.-.-.||-|- -+.-+|+.||-...-++
T Consensus 46 kPWItkrvnei------lgfEDdVViefvynqLee~k~ldpkkmQiNlTGFLngrnAreFmgeLW~LliS~ 110 (354)
T KOG2146|consen 46 KPWITKRVNEI------LGFEDDVVIEFVYNQLEEAKNLDPKKMQINLTGFLNGRNAREFMGELWSLLISE 110 (354)
T ss_pred hHHHHHHHHHh------hccccchhHHHHHHHHhhhcCCCchheeeeeehhcccccHHHHHHHHHHHHHhh
Confidence 45898889898 9996 55678888865411111112222333333 23559999998877753
No 76
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=25.73 E-value=43 Score=26.42 Aligned_cols=25 Identities=20% Similarity=0.502 Sum_probs=18.8
Q ss_pred cccccccceeeecccCcccCCCCcccccC
Q 019483 199 SNCLSCGKIVCEQEGEGPCQFCGALVLKE 227 (340)
Q Consensus 199 ~NCL~CGKIiCeqEG~gPC~FCG~~v~~~ 227 (340)
--|.+|.+|+ + ...|.-||..-+++
T Consensus 6 ~AC~~C~~i~---~-~~~Cp~Cgs~~~S~ 30 (64)
T PRK06393 6 RACKKCKRLT---P-EKTCPVHGDEKTTT 30 (64)
T ss_pred hhHhhCCccc---C-CCcCCCCCCCcCCc
Confidence 3599999998 2 34899999964443
No 77
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=25.62 E-value=1.6e+02 Score=27.46 Aligned_cols=65 Identities=18% Similarity=0.242 Sum_probs=46.8
Q ss_pred HhhHHHHHHHHHhhccc--C---CCcHHHHHHhhcccc--cCCchHHHHHHHHhhCC-cchH--HHHHHHHHHhc
Q 019483 5 GEWLEKALVDLCKRIES--L---DLDGEVISGLVSYCE--FAQPLDAKEYLDNIIGQ-EVGK--SVIEEYLRRRG 69 (340)
Q Consensus 5 ~~w~~~~L~~~~~~~~~--L---~~~~d~~~~ils~~e--l~~~~d~~eY~~nLLG~-e~~~--~Fi~e~~~r~~ 69 (340)
-.||..||-..-.-+++ . +.++.++.||+-... +-+.+++..||..+++. .+.. ..++--..+|+
T Consensus 138 ~~fl~~Al~~y~~a~~~e~~~~~~~~~~~l~YLigeL~rrlg~~~eA~~~fs~vi~~~~~s~~~~l~~~AR~~w~ 212 (214)
T PF09986_consen 138 KRFLRKALEFYEEAYENEDFPIEGMDEATLLYLIGELNRRLGNYDEAKRWFSRVIGSKKASKEPKLKDMARDQWQ 212 (214)
T ss_pred HHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHHHHHhCCHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHHH
Confidence 35777777777555555 3 567899999987655 78999999999999966 3333 66666666665
No 78
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=25.45 E-value=30 Score=27.50 Aligned_cols=12 Identities=33% Similarity=0.866 Sum_probs=10.3
Q ss_pred cccCCCCccccc
Q 019483 215 GPCQFCGALVLK 226 (340)
Q Consensus 215 gPC~FCG~~v~~ 226 (340)
..|+|||..+..
T Consensus 4 ~~CsFcG~~I~P 15 (66)
T COG2075 4 RVCSFCGKKIEP 15 (66)
T ss_pred eEecCcCCccCC
Confidence 579999999975
No 79
>COG0801 FolK 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase [Coenzyme metabolism]
Probab=25.34 E-value=54 Score=29.97 Aligned_cols=57 Identities=19% Similarity=0.284 Sum_probs=38.4
Q ss_pred ccccccccc--cCCccCCHHHHHH-HHHHHHHHHHHHHhhcCCEEEEEEe--cCCEEecccc
Q 019483 270 DDQSDYYEI--EGNSWLSKEEKEL-IKKKQEEVAEAEQAKRNKVVVTFDL--VGRKVSTFCR 326 (340)
Q Consensus 270 DDqsDyf~~--~~n~WlS~~ER~~-l~K~q~El~e~~~~~R~k~~vtiD~--~grkVv~~e~ 326 (340)
.||.|||.. .-..+|++.|=-. +++-|+++-+.|..+-+.++++||+ =|..+++.+.
T Consensus 49 ~~Q~~FlN~v~~v~T~L~p~eLL~~l~~iE~~~gR~R~~rwgPRtlDlDIllygd~~~~~~~ 110 (160)
T COG0801 49 EDQPDFLNAVVEVETTLSPRELLARLQAIERRLGRVRSERWGPRTLDLDILLYGDEVIETPR 110 (160)
T ss_pred CCCcchheEEEEEeccCCHHHHHHHHHHHHHHcCccccccCCCcceeeEEEEEcceeccCCC
Confidence 589999873 2346999987544 3555555555555566788899887 5777766644
No 80
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=25.32 E-value=49 Score=23.64 Aligned_cols=23 Identities=26% Similarity=0.673 Sum_probs=15.5
Q ss_pred ccccccceeeec-----ccCcccCCCCc
Q 019483 200 NCLSCGKIVCEQ-----EGEGPCQFCGA 222 (340)
Q Consensus 200 NCL~CGKIiCeq-----EG~gPC~FCG~ 222 (340)
-|..||.++=.. ++.-.|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 589999944222 23347999998
No 81
>PF07631 PSD4: Protein of unknown function (DUF1592); InterPro: IPR013042 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013043 from INTERPRO.
Probab=25.28 E-value=1.5e+02 Score=25.66 Aligned_cols=48 Identities=13% Similarity=0.241 Sum_probs=38.0
Q ss_pred HHHHHHhhcccccCCchHHHHHHHHhhCCcchHHHHHHHHHHhccccCC
Q 019483 26 GEVISGLVSYCEFAQPLDAKEYLDNIIGQEVGKSVIEEYLRRRGLTDIC 74 (340)
Q Consensus 26 ~d~~~~ils~~el~~~~d~~eY~~nLLG~e~~~~Fi~e~~~r~~~~~~~ 74 (340)
+++.+ ...=.+|.+++.+...+.-+|..+....|+..|...|...+.-
T Consensus 21 ~~L~~-aA~~g~L~~~~~l~~q~~RML~dpr~~~~~~~F~~qWL~l~~~ 68 (128)
T PF07631_consen 21 AELLD-AAAAGELRTPEQLRAQAERMLADPRARRFVERFFRQWLDLDRL 68 (128)
T ss_pred HHHHH-HHHhCCCCCHHHHHHHHHHHHcCccHHHHHHHHHHHHhCCCcc
Confidence 44433 4443568899999999999998877889999999999886644
No 82
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=24.94 E-value=37 Score=28.23 Aligned_cols=15 Identities=27% Similarity=0.776 Sum_probs=9.4
Q ss_pred cccccccceeeeccc
Q 019483 199 SNCLSCGKIVCEQEG 213 (340)
Q Consensus 199 ~NCL~CGKIiCeqEG 213 (340)
-.|..||.++|+--|
T Consensus 55 V~C~~Cg~~L~~PTG 69 (85)
T PTZ00083 55 VLCGGCSSQLCQPTG 69 (85)
T ss_pred EEccccCCEeeccCC
Confidence 466666666666555
No 83
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=24.85 E-value=35 Score=30.54 Aligned_cols=13 Identities=31% Similarity=0.613 Sum_probs=11.2
Q ss_pred ccccccccceeee
Q 019483 198 ISNCLSCGKIVCE 210 (340)
Q Consensus 198 i~NCL~CGKIiCe 210 (340)
.-.|..||||+|.
T Consensus 100 H~iC~~CGki~~i 112 (169)
T PRK11639 100 MFICDRCGAVKEE 112 (169)
T ss_pred eEEeCCCCCEEEe
Confidence 4579999999985
No 84
>PRK11595 DNA utilization protein GntX; Provisional
Probab=24.56 E-value=25 Score=32.66 Aligned_cols=19 Identities=5% Similarity=0.204 Sum_probs=13.5
Q ss_pred CEEEEEEecCCEEeccccc
Q 019483 309 KVVVTFDLVGRKVSTFCRI 327 (340)
Q Consensus 309 k~~vtiD~~grkVv~~e~~ 327 (340)
...++-|+.|+.|+...++
T Consensus 178 ~f~~~~~~~~~~vllvDDv 196 (227)
T PRK11595 178 AFRLELPVQGQHMAIVDDV 196 (227)
T ss_pred hhccCCCCCCCEEEEEeee
Confidence 3445556889989888776
No 85
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=24.53 E-value=34 Score=27.86 Aligned_cols=25 Identities=28% Similarity=0.654 Sum_probs=21.1
Q ss_pred ccccccceeeecccCcccCCCCccc
Q 019483 200 NCLSCGKIVCEQEGEGPCQFCGALV 224 (340)
Q Consensus 200 NCL~CGKIiCeqEG~gPC~FCG~~v 224 (340)
+|..||.+.=..++.-.|.-||...
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~~ 26 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYEK 26 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCcc
Confidence 6999999997777888999999753
No 86
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=24.13 E-value=46 Score=22.41 Aligned_cols=27 Identities=19% Similarity=0.445 Sum_probs=19.1
Q ss_pred cccccccceeeeccc-------CcccCCCCcccc
Q 019483 199 SNCLSCGKIVCEQEG-------EGPCQFCGALVL 225 (340)
Q Consensus 199 ~NCL~CGKIiCeqEG-------~gPC~FCG~~v~ 225 (340)
--|.+||..+-..+. .-.|.-||+.+.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 358899998776543 247999988653
No 87
>PRK04023 DNA polymerase II large subunit; Validated
Probab=24.06 E-value=62 Score=37.46 Aligned_cols=42 Identities=26% Similarity=0.620 Sum_probs=27.4
Q ss_pred CCCCcc-ccccccCccccccccccce-----eeec----ccCcccCCCCccccc
Q 019483 183 QQGKPC-SCQARQHRLISNCLSCGKI-----VCEQ----EGEGPCQFCGALVLK 226 (340)
Q Consensus 183 ~~r~~C-~C~A~~H~Li~NCL~CGKI-----iCeq----EG~gPC~FCG~~v~~ 226 (340)
.+.+.| .|.... ....|.+||.- .|.. .+..+|.-||..+..
T Consensus 624 Vg~RfCpsCG~~t--~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 624 IGRRKCPSCGKET--FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTP 675 (1121)
T ss_pred ccCccCCCCCCcC--CcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCCc
Confidence 355777 676653 44688888863 2333 334789999998864
No 88
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.03 E-value=47 Score=36.32 Aligned_cols=25 Identities=32% Similarity=0.597 Sum_probs=19.4
Q ss_pred cccccccceeeecccCcccCCCCcccc
Q 019483 199 SNCLSCGKIVCEQEGEGPCQFCGALVL 225 (340)
Q Consensus 199 ~NCL~CGKIiCeqEG~gPC~FCG~~v~ 225 (340)
.-|..||.. ..+|...|.-||+.+-
T Consensus 28 ~~Cp~CG~~--~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 28 KPCPQCGTE--VPVDEAHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCC--CCcccccccccCCccc
Confidence 458888877 5677788888888874
No 89
>PLN00209 ribosomal protein S27; Provisional
Probab=23.78 E-value=39 Score=28.17 Aligned_cols=16 Identities=31% Similarity=0.839 Sum_probs=10.2
Q ss_pred cccccccceeeecccC
Q 019483 199 SNCLSCGKIVCEQEGE 214 (340)
Q Consensus 199 ~NCL~CGKIiCeqEG~ 214 (340)
-.|..||.++|+--|.
T Consensus 56 V~C~~Cg~~L~~PTGG 71 (86)
T PLN00209 56 VVCGSCQTVLCQPTGG 71 (86)
T ss_pred EEccccCCEeeccCCC
Confidence 4677777776666553
No 90
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=22.86 E-value=55 Score=30.11 Aligned_cols=39 Identities=28% Similarity=0.514 Sum_probs=27.5
Q ss_pred CccccccccCccccccccccceeeec----ccC-cccCCCCccccc
Q 019483 186 KPCSCQARQHRLISNCLSCGKIVCEQ----EGE-GPCQFCGALVLK 226 (340)
Q Consensus 186 ~~C~C~A~~H~Li~NCL~CGKIiCeq----EG~-gPC~FCG~~v~~ 226 (340)
+..+++|+.|.+. |..||..+=.. ... -.|..||..+..
T Consensus 99 ~v~e~HG~~~~~~--C~~C~~~~~~~~~~~~~~~p~C~~Cgg~lrp 142 (224)
T cd01412 99 NVIELHGSLFRVR--CSSCGYVGENNEEIPEEELPRCPKCGGLLRP 142 (224)
T ss_pred ceEeeCCCcCccc--cCCCCCCCCcchhhhccCCCCCCCCCCccCC
Confidence 6688889988876 99999865211 122 459999987654
No 91
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=22.83 E-value=48 Score=29.36 Aligned_cols=39 Identities=31% Similarity=0.540 Sum_probs=28.0
Q ss_pred CccccccccCccccccccccceeee--------cccCcccCCCCccccc
Q 019483 186 KPCSCQARQHRLISNCLSCGKIVCE--------QEGEGPCQFCGALVLK 226 (340)
Q Consensus 186 ~~C~C~A~~H~Li~NCL~CGKIiCe--------qEG~gPC~FCG~~v~~ 226 (340)
+...+.|+.+.+ -|+.||+.+=. .+...+|.-||..+..
T Consensus 95 ~vielHG~l~~~--~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~lrp 141 (178)
T PF02146_consen 95 KVIELHGSLFRL--RCSKCGKEYDREDIVDSIDEEEPPRCPKCGGLLRP 141 (178)
T ss_dssp CEEETTEEEEEE--EETTTSBEEEGHHHHHHHHTTSSCBCTTTSCBEEE
T ss_pred hhHHHHhhhcee--eecCCCccccchhhcccccccccccccccCccCCC
Confidence 446677777665 69999998733 2334789999997654
No 92
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=22.78 E-value=38 Score=23.83 Aligned_cols=12 Identities=42% Similarity=1.231 Sum_probs=8.5
Q ss_pred ccccccccceee
Q 019483 198 ISNCLSCGKIVC 209 (340)
Q Consensus 198 i~NCL~CGKIiC 209 (340)
+.-||.||.|.|
T Consensus 11 l~~CL~C~~~~c 22 (50)
T smart00290 11 LWLCLTCGQVGC 22 (50)
T ss_pred eEEecCCCCccc
Confidence 446777877766
No 93
>PF00986 DNA_gyraseB_C: DNA gyrase B subunit, carboxyl terminus The Prosite motif does not match this Pfam entry.; InterPro: IPR002288 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions, domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA []. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication []. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB. This entry represents the C-terminal region (C-terminal part of domain 2) of subunit B found in topoisomerase II (gyrB) and topoisomerase IV (parE), which are primarily of bacterial origin. It does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. This region is involved in subunit interaction, which accounts for the difference between subunit B and single polypeptide topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome; PDB: 3LTN_D 3RAF_C 3FOF_C 3RAE_C 3KSA_D 3RAD_C 3FOE_D 3KSB_D 3K9F_D 2XCT_D ....
Probab=22.68 E-value=85 Score=24.76 Aligned_cols=25 Identities=24% Similarity=0.472 Sum_probs=20.3
Q ss_pred cCCchHHHHHHHHhhCCcchH--HHHH
Q 019483 38 FAQPLDAKEYLDNIIGQEVGK--SVIE 62 (340)
Q Consensus 38 l~~~~d~~eY~~nLLG~e~~~--~Fi~ 62 (340)
+.+..++++.|..|+|.++.. .||+
T Consensus 39 i~d~~~~~~~~~~LMG~~v~~Rr~fIe 65 (65)
T PF00986_consen 39 IEDAEEADELFEMLMGKNVEPRREFIE 65 (65)
T ss_dssp HCCHHHHHHHHHHHHSSTHHHHHHHHH
T ss_pred ECCHHHHHHHHHHHcCCCcHHHHHHhC
Confidence 568888999999999996555 8885
No 94
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=22.68 E-value=73 Score=22.39 Aligned_cols=24 Identities=29% Similarity=0.742 Sum_probs=17.2
Q ss_pred cccccccceeee-----cccCcccCCCCc
Q 019483 199 SNCLSCGKIVCE-----QEGEGPCQFCGA 222 (340)
Q Consensus 199 ~NCL~CGKIiCe-----qEG~gPC~FCG~ 222 (340)
--|..||...=. ....-+|.-||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 358899976543 234588999998
No 95
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=22.38 E-value=47 Score=28.35 Aligned_cols=28 Identities=29% Similarity=0.547 Sum_probs=17.6
Q ss_pred ccccccceeeeccc-CcccCCCCcccccC
Q 019483 200 NCLSCGKIVCEQEG-EGPCQFCGALVLKE 227 (340)
Q Consensus 200 NCL~CGKIiCeqEG-~gPC~FCG~~v~~~ 227 (340)
.|.+||+=+=-.-- .-.|++||+.+-..
T Consensus 11 ~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 68888874433222 34589999976543
No 96
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=22.29 E-value=33 Score=25.29 Aligned_cols=11 Identities=45% Similarity=1.108 Sum_probs=8.9
Q ss_pred cccccccccee
Q 019483 198 ISNCLSCGKIV 208 (340)
Q Consensus 198 i~NCL~CGKIi 208 (340)
+..|-+||||.
T Consensus 46 i~~Cp~CgRiL 56 (56)
T PF02591_consen 46 IVFCPNCGRIL 56 (56)
T ss_pred eEECcCCCccC
Confidence 35899999984
No 97
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=22.16 E-value=39 Score=33.60 Aligned_cols=37 Identities=27% Similarity=0.827 Sum_probs=29.8
Q ss_pred CccccccccCccc-cccccccceeeecccC-cccCCCCcccccC
Q 019483 186 KPCSCQARQHRLI-SNCLSCGKIVCEQEGE-GPCQFCGALVLKE 227 (340)
Q Consensus 186 ~~C~C~A~~H~Li-~NCL~CGKIiCeqEG~-gPC~FCG~~v~~~ 227 (340)
|.|.| ||. ..|+.|-|-|-..-|- -.|+||++.|+..
T Consensus 117 HaC~C-----pl~da~C~EC~R~vw~hGGrif~CsfC~~flCED 155 (314)
T PF06524_consen 117 HACTC-----PLQDAVCIECERGVWDHGGRIFKCSFCDNFLCED 155 (314)
T ss_pred ccccC-----cCCCcEeeeeecccccCCCeEEEeecCCCeeecc
Confidence 55555 554 7999999999888774 8899999999854
No 98
>KOG3062 consensus RNA polymerase II elongator associated protein [General function prediction only]
Probab=22.08 E-value=1.8e+02 Score=28.89 Aligned_cols=62 Identities=24% Similarity=0.219 Sum_probs=33.4
Q ss_pred HHHHHHHhHhhhhhcccccccccccccccccccCCccCCHHHHHHHHHHHHHHHHHHHhhcCCEEE
Q 019483 247 AAEAYTKRLVDYDRNAAARTTVIDDQSDYYEIEGNSWLSKEEKELIKKKQEEVAEAEQAKRNKVVV 312 (340)
Q Consensus 247 ~A~~~rdkLLefdrtsA~RTkVIDDqsDyf~~~~n~WlS~~ER~~l~K~q~El~e~~~~~R~k~~v 312 (340)
+|.++|+-|-+=-+ -.+-.||||+|=-+.-+++-==|+.|+++.=+..... .|+-++..+||
T Consensus 17 rA~~L~~~l~~~~~--K~~v~ii~deslg~~~ns~y~~s~~EK~lRg~L~S~v--~R~Lsk~~iVI 78 (281)
T KOG3062|consen 17 RAVELREALKERGT--KQSVRIIDDESLGIEKNSNYGDSQAEKALRGKLRSAV--DRSLSKGDIVI 78 (281)
T ss_pred HHHHHHHHHHhhcc--cceEEEechhhcCCCCcccccccHHHHHHHHHHHHHH--HhhcccCcEEE
Confidence 45666655544322 2277899999933333344445677776643222222 35556666655
No 99
>smart00674 CENPB Putative DNA-binding domain in centromere protein B, mouse jerky and transposases.
Probab=21.74 E-value=3e+02 Score=20.09 Aligned_cols=53 Identities=23% Similarity=0.359 Sum_probs=34.4
Q ss_pred hhHHHHHHHHHhhccc--CCCcHHHHHHhhcccccCCchHHHHHHHHhhC--C-cchHHHHHHHHHHhcc
Q 019483 6 EWLEKALVDLCKRIES--LDLDGEVISGLVSYCEFAQPLDAKEYLDNIIG--Q-EVGKSVIEEYLRRRGL 70 (340)
Q Consensus 6 ~w~~~~L~~~~~~~~~--L~~~~d~~~~ils~~el~~~~d~~eY~~nLLG--~-e~~~~Fi~e~~~r~~~ 70 (340)
..++++|.+|..++.. ++++..+|..... +|..-+| . .++...+..|++|.+.
T Consensus 5 ~~~E~~L~~wi~~~~~~g~~it~~~i~~~A~------------~i~~~~~~~~f~~s~~Wl~rF~~Rh~~ 62 (66)
T smart00674 5 ALLEKALYEWILRQEALGIPISGEQIREKAL------------EILQRLGLENFKASNGWLTRFKKRHNI 62 (66)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH------------HHHHHcCCCCCCCCHHHHHHHHHHcCC
Confidence 4688999999888444 7777777764333 1222223 2 4555888899888765
No 100
>PF07778 CENP-I: Mis6 ; InterPro: IPR012485 Centromere protein Cenp-I (also known as Mis6) is an essential centromere connector protein acting during G1-S phase of the cell cycle. Mis6 is thought to be required for recruiting Cenp-A, the centromere- specific histone H3 variant; an important event for centromere function and chromosome segregation during mitosis [, ].
Probab=20.96 E-value=3.1e+02 Score=29.39 Aligned_cols=63 Identities=17% Similarity=0.037 Sum_probs=45.3
Q ss_pred hHhhHHHHHHHHHhhcccCCCc-HHHHHHhhcccccCCchHHHHHHHHhh-----CCcc-hH----HHHHHHHHHhcccc
Q 019483 4 AGEWLEKALVDLCKRIESLDLD-GEVISGLVSYCEFAQPLDAKEYLDNII-----GQEV-GK----SVIEEYLRRRGLTD 72 (340)
Q Consensus 4 ~~~w~~~~L~~~~~~~~~L~~~-~d~~~~ils~~el~~~~d~~eY~~nLL-----G~e~-~~----~Fi~e~~~r~~~~~ 72 (340)
...+|.+.|.-| =|.+ .+.|=+||+|+.+.+-+|+.+++.+-| .... .+ +|..+|++.|-.--
T Consensus 424 ve~FL~kyL~~W------dG~~~R~~IL~LLs~iPl~~f~eL~~~ll~pLe~lf~~ss~~~kcslL~~y~~LL~nWl~~~ 497 (511)
T PF07778_consen 424 VEDFLYKYLPTW------DGSDCRSQILQLLSWIPLSSFSELYPLLLQPLEQLFLTSSPYFKCSLLQFYTNLLQNWLLWL 497 (511)
T ss_pred HHHHHHHHHhhc------CCCccHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 456677777777 6777 788899999998888888876555444 3321 23 89999999995433
No 101
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.39 E-value=43 Score=26.00 Aligned_cols=25 Identities=24% Similarity=0.729 Sum_probs=17.1
Q ss_pred cCCCCccccccccCccc-------ccccccccee
Q 019483 182 FQQGKPCSCQARQHRLI-------SNCLSCGKIV 208 (340)
Q Consensus 182 ~~~r~~C~C~A~~H~Li-------~NCL~CGKIi 208 (340)
++..|+|.= .+-+++ --|.+||++|
T Consensus 13 MKK~H~Cg~--NrwkIiRvGaDIkikC~nC~h~v 44 (60)
T COG4481 13 MKKPHACGT--NRWKIIRVGADIKIKCENCGHSV 44 (60)
T ss_pred ecCCCcccc--ceEEEEEecCcEEEEecCCCcEE
Confidence 355577764 455543 6899999987
No 102
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=20.27 E-value=72 Score=29.48 Aligned_cols=38 Identities=21% Similarity=0.483 Sum_probs=26.6
Q ss_pred CccccccccCccccccccccceeeec--------ccC-cccCCCCcccc
Q 019483 186 KPCSCQARQHRLISNCLSCGKIVCEQ--------EGE-GPCQFCGALVL 225 (340)
Q Consensus 186 ~~C~C~A~~H~Li~NCL~CGKIiCeq--------EG~-gPC~FCG~~v~ 225 (340)
+.-.+.|+.+.+. |+.||.++-.. +.. -.|..||.++-
T Consensus 85 ~vielHG~~~~~~--C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~lr 131 (206)
T cd01410 85 KLSELHGNMFIEV--CKSCGPEYVRDDVVETRGDKETGRRCHACGGILK 131 (206)
T ss_pred cEEEecCCcCccc--CCCCCCccchHHHHHHhhcCCCCCcCCCCcCccC
Confidence 5677888888775 99999876421 112 44999998754
Done!