Query 017477
Match_columns 371
No_of_seqs 148 out of 241
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 08:54:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017477.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017477hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01566 ZF_HD_prot_N ZF-HD h 100.0 4.6E-34 1E-38 213.5 3.3 50 75-126 3-53 (53)
2 PF04770 ZF-HD_dimer: ZF-HD pr 100.0 5.5E-33 1.2E-37 213.4 3.8 55 72-128 4-59 (60)
3 TIGR01565 homeo_ZF_HD homeobox 99.9 1.5E-23 3.3E-28 160.3 5.4 50 233-282 1-58 (58)
4 PF00046 Homeobox: Homeobox do 96.5 0.00061 1.3E-08 49.8 -0.3 46 234-283 1-54 (57)
5 KOG0843 Transcription factor E 96.0 0.0028 6E-08 59.4 1.2 60 232-291 101-164 (197)
6 cd00086 homeodomain Homeodomai 92.0 0.099 2.1E-06 37.7 1.8 49 234-286 1-57 (59)
7 KOG0494 Transcription factor C 91.2 0.12 2.6E-06 51.3 2.0 55 232-288 140-200 (332)
8 KOG0493 Transcription factor E 91.1 0.14 3.1E-06 50.9 2.4 51 233-288 246-305 (342)
9 smart00389 HOX Homeodomain. DN 89.5 0.33 7.1E-06 34.8 2.6 45 234-282 1-53 (56)
10 PRK11470 hypothetical protein; 87.2 0.28 6.2E-06 46.3 1.3 41 233-276 78-123 (200)
11 PF12651 RHH_3: Ribbon-helix-h 83.0 0.91 2E-05 33.1 2.0 41 232-272 1-41 (44)
12 PF05572 Peptidase_M43: Pregna 81.4 0.95 2.1E-05 40.5 2.0 18 236-253 137-154 (154)
13 KOG0485 Transcription factor N 81.4 0.54 1.2E-05 45.8 0.4 54 229-288 100-163 (268)
14 KOG0484 Transcription factor P 79.1 0.32 6.9E-06 42.7 -1.7 58 232-289 16-77 (125)
15 KOG0844 Transcription factor E 78.8 0.66 1.4E-05 47.2 0.1 55 233-288 181-240 (408)
16 PF00356 LacI: Bacterial regul 74.7 3.4 7.3E-05 30.5 2.8 22 238-259 24-45 (46)
17 PRK10030 hypothetical protein; 73.4 1.4 3E-05 41.0 0.7 42 233-277 88-134 (197)
18 COG3040 Blc Bacterial lipocali 67.1 5.1 0.00011 37.6 2.9 25 237-261 140-165 (174)
19 PF01527 HTH_Tnp_1: Transposas 65.9 3.9 8.4E-05 31.0 1.6 32 235-274 2-33 (76)
20 cd04275 ZnMc_pappalysin_like Z 65.5 3.9 8.5E-05 38.9 1.9 18 235-252 207-224 (225)
21 PF13698 DUF4156: Domain of un 64.5 3.5 7.6E-05 34.3 1.2 22 71-92 47-68 (93)
22 KOG1168 Transcription factor A 64.4 3.5 7.6E-05 41.9 1.4 46 230-287 306-367 (385)
23 KOG2251 Homeobox transcription 62.0 8.2 0.00018 37.6 3.3 53 229-285 33-93 (228)
24 KOG3802 Transcription factor O 61.8 13 0.00029 38.8 5.0 55 231-289 292-354 (398)
25 PF04218 CENP-B_N: CENP-B N-te 60.6 9.1 0.0002 28.6 2.7 23 234-256 1-23 (53)
26 KOG0490 Transcription factor, 60.4 4.6 9.9E-05 36.4 1.3 55 230-288 57-119 (235)
27 PHA02893 hypothetical protein; 59.6 3.6 7.8E-05 34.7 0.5 8 109-116 69-76 (88)
28 COG1134 TagH ABC-type polysacc 57.8 7.7 0.00017 38.2 2.4 41 242-282 184-225 (249)
29 PF05708 DUF830: Orthopoxvirus 56.6 2.4 5.2E-05 36.5 -1.1 40 234-276 71-115 (158)
30 PHA03072 putative viral membra 52.1 3.9 8.4E-05 38.7 -0.6 23 255-277 130-154 (190)
31 COG0289 DapB Dihydrodipicolina 50.6 12 0.00026 37.2 2.4 20 238-257 101-120 (266)
32 PF03356 Pox_LP_H2: Viral late 48.6 4.7 0.0001 38.2 -0.6 24 255-278 130-155 (189)
33 PF05009 EBV-NA3: Epstein-Barr 48.0 4.3 9.3E-05 40.0 -1.0 42 243-285 130-181 (255)
34 PF00765 Autoind_synth: Autoin 47.1 1.9 4.2E-05 39.6 -3.3 42 241-282 6-56 (182)
35 cd03221 ABCF_EF-3 ABCF_EF-3 E 39.6 50 0.0011 28.4 4.4 41 241-281 102-144 (144)
36 COG3916 LasI N-acyl-L-homoseri 38.2 11 0.00024 36.3 0.1 41 234-274 11-51 (209)
37 KOG2767 Translation initiation 38.0 10 0.00022 39.4 -0.2 15 109-123 118-132 (400)
38 PF11761 CbiG_mid: Cobalamin b 38.0 24 0.00051 27.6 2.0 23 250-274 6-28 (93)
39 cd00029 C1 Protein kinase C co 37.4 14 0.00031 25.8 0.5 30 89-125 13-42 (50)
40 PF01113 DapB_N: Dihydrodipico 37.2 11 0.00023 32.1 -0.2 21 238-258 99-119 (124)
41 PHA03378 EBNA-3B; Provisional 35.3 12 0.00027 41.9 -0.0 32 244-277 275-314 (991)
42 smart00857 Resolvase Resolvase 35.2 29 0.00062 29.2 2.1 20 242-261 18-37 (148)
43 PF05077 DUF678: Protein of un 34.3 15 0.00033 30.3 0.3 8 109-116 57-64 (74)
44 COG4802 FtrB Ferredoxin-thiore 34.3 32 0.00069 30.2 2.3 30 241-271 2-35 (110)
45 PF13387 DUF4105: Domain of un 33.4 34 0.00074 30.8 2.5 27 234-260 99-125 (176)
46 PRK11041 DNA-binding transcrip 32.4 41 0.00089 30.9 2.9 22 239-260 3-24 (309)
47 KOG0847 Transcription factor, 32.3 31 0.00068 34.1 2.1 81 231-311 165-250 (288)
48 PF13565 HTH_32: Homeodomain-l 32.1 46 0.001 25.3 2.7 34 235-270 28-62 (77)
49 PF05419 GUN4: GUN4-like ; In 31.8 26 0.00056 31.2 1.4 16 246-261 82-97 (132)
50 smart00109 C1 Protein kinase C 31.7 19 0.00042 24.7 0.5 28 89-124 13-40 (49)
51 KOG0842 Transcription factor t 31.2 49 0.0011 33.6 3.4 57 230-291 150-215 (307)
52 PF01870 Hjc: Archaeal hollida 31.0 32 0.0007 28.6 1.7 20 237-256 48-67 (88)
53 PF05291 Bystin: Bystin; Inte 30.7 26 0.00056 35.5 1.3 23 234-256 253-275 (301)
54 COG2102 Predicted ATPases of P 29.8 57 0.0012 31.8 3.4 35 239-273 95-134 (223)
55 cd03215 ABC_Carb_Monos_II This 29.6 84 0.0018 27.7 4.3 41 241-281 136-181 (182)
56 cd03279 ABC_sbcCD SbcCD and ot 28.9 72 0.0016 29.0 3.8 42 240-281 164-210 (213)
57 KOG2252 CCAAT displacement pro 28.6 30 0.00064 37.7 1.4 46 233-283 420-474 (558)
58 smart00496 IENR2 Intron-encode 27.3 49 0.0011 22.4 1.8 15 239-253 4-18 (26)
59 TIGR00290 MJ0570_dom MJ0570-re 27.2 63 0.0014 31.0 3.2 34 240-273 95-133 (223)
60 PF06252 DUF1018: Protein of u 27.2 97 0.0021 26.3 4.1 37 238-274 53-91 (119)
61 PF01873 eIF-5_eIF-2B: Domain 27.2 23 0.00051 31.2 0.3 13 107-119 112-124 (125)
62 PRK09492 treR trehalose repres 26.9 62 0.0013 30.0 3.1 21 239-259 30-50 (315)
63 PF13551 HTH_29: Winged helix- 26.6 60 0.0013 25.7 2.5 23 233-255 51-73 (112)
64 PF13592 HTH_33: Winged helix- 26.4 74 0.0016 24.0 2.9 37 234-273 16-59 (60)
65 PF09932 DUF2164: Uncharacteri 26.3 72 0.0016 26.1 3.0 35 239-273 2-41 (76)
66 KOG1146 Homeobox protein [Gene 26.1 42 0.0009 40.1 2.1 60 230-291 900-965 (1406)
67 PRK14258 phosphate ABC transpo 26.1 86 0.0019 29.4 3.9 41 242-282 183-229 (261)
68 PHA03379 EBNA-3A; Provisional 26.0 16 0.00034 40.9 -1.1 39 244-283 268-314 (935)
69 PF00249 Myb_DNA-binding: Myb- 25.7 72 0.0016 22.7 2.6 22 237-258 1-22 (48)
70 PRK10061 DNA damage-inducible 25.7 8.5 0.00018 33.1 -2.6 52 233-284 16-68 (96)
71 cd03770 SR_TndX_transposase Se 25.5 52 0.0011 28.4 2.1 19 242-260 21-39 (140)
72 PRK10703 DNA-binding transcrip 24.4 73 0.0016 30.0 3.1 21 239-259 27-47 (341)
73 cd01994 Alpha_ANH_like_IV This 24.1 92 0.002 28.8 3.6 36 238-273 96-136 (194)
74 PF00130 C1_1: Phorbol esters/ 24.0 46 0.001 23.9 1.3 28 90-124 14-41 (53)
75 PRK13834 putative autoinducer 23.9 19 0.00041 33.7 -0.9 48 234-281 12-63 (207)
76 COG2963 Transposase and inacti 23.6 83 0.0018 26.0 2.9 30 237-274 5-34 (116)
77 PRK10727 DNA-binding transcrip 23.6 76 0.0017 30.1 3.1 22 239-260 27-48 (343)
78 cd00338 Ser_Recombinase Serine 23.5 61 0.0013 26.6 2.1 19 242-260 17-35 (137)
79 KOG4577 Transcription factor L 23.4 59 0.0013 33.4 2.4 48 230-282 164-220 (383)
80 PRK13636 cbiO cobalt transport 23.4 86 0.0019 29.9 3.4 43 240-282 172-220 (283)
81 PF07813 LTXXQ: LTXXQ motif fa 23.2 72 0.0016 25.0 2.4 25 238-262 13-37 (100)
82 TIGR01481 ccpA catabolite cont 22.9 81 0.0018 29.5 3.1 21 239-259 27-47 (329)
83 PF07130 YebG: YebG protein; 22.9 5.8 0.00013 32.7 -3.9 52 233-284 16-68 (75)
84 PF01902 ATP_bind_4: ATP-bindi 22.2 78 0.0017 30.2 2.8 34 240-273 95-133 (218)
85 PRK13877 conjugal transfer rel 21.4 75 0.0016 27.8 2.3 50 233-282 10-84 (114)
86 PF12323 HTH_OrfB_IS605: Helix 21.3 69 0.0015 22.8 1.8 21 234-254 5-25 (46)
87 smart00845 GatB_Yqey GatB doma 21.3 76 0.0016 27.9 2.4 26 248-274 75-100 (147)
88 cd03298 ABC_ThiQ_thiamine_tran 21.0 1.6E+02 0.0034 26.4 4.4 41 241-281 160-206 (211)
89 cd03257 ABC_NikE_OppD_transpor 20.9 1.1E+02 0.0024 27.5 3.4 41 241-281 177-223 (228)
90 COG3139 Uncharacterized protei 20.8 51 0.0011 28.1 1.1 21 238-260 31-51 (90)
91 PF07796 DUF1638: Protein of u 20.6 68 0.0015 28.6 2.0 26 237-262 125-152 (166)
92 PF06252 DUF1018: Protein of u 20.0 78 0.0017 26.9 2.1 28 234-261 16-43 (119)
No 1
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=100.00 E-value=4.6e-34 Score=213.51 Aligned_cols=50 Identities=84% Similarity=1.519 Sum_probs=45.5
Q ss_pred HHHhhhhhhccCCccccCcccccc-CCCCCCCCCCcccccccCccccccccCC
Q 017477 75 KECLKNHAASIGGHALDGCGEFMP-SPTATPSDPTSLKCAACGCHRNFHRREP 126 (371)
Q Consensus 75 RECLKNHAAsIGGHAvDGCGEFMP-SGeeGt~dp~ALKCAACGCHRNFHRKE~ 126 (371)
..-||||||+|||||||||||||| +|++++ +++||||||||||||||||+
T Consensus 3 ~EC~kNHAa~~Gg~a~DGCgEFmps~g~~~~--~~al~CaACgCHRnFHRre~ 53 (53)
T TIGR01566 3 KECLKNHAASIGGHALDGCGEFMPSSGEEGD--PESLTCAACGCHRNFHRKEP 53 (53)
T ss_pred HHHHHhhHHHhCCcccccccccccCCCCCCC--CcceeeeecCcccccccCCC
Confidence 467999999999999999999999 677665 67999999999999999995
No 2
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=99.97 E-value=5.5e-33 Score=213.39 Aligned_cols=55 Identities=76% Similarity=1.414 Sum_probs=50.0
Q ss_pred eehHHHhhhhhhccCCccccCccccccC-CCCCCCCCCcccccccCccccccccCCCC
Q 017477 72 VTYKECLKNHAASIGGHALDGCGEFMPS-PTATPSDPTSLKCAACGCHRNFHRREPDQ 128 (371)
Q Consensus 72 VrYRECLKNHAAsIGGHAvDGCGEFMPS-GeeGt~dp~ALKCAACGCHRNFHRKE~eg 128 (371)
.....-||||||+||||||||||||||+ |+||+ +++|+||||||||||||||+++
T Consensus 4 v~Y~EC~kNHAa~~Gg~a~DGCgEFm~~~g~eg~--~~al~CaACgCHRnFHRre~~~ 59 (60)
T PF04770_consen 4 VRYRECLKNHAASIGGHAVDGCGEFMPSPGEEGT--PEALKCAACGCHRNFHRREVEG 59 (60)
T ss_pred eeHHHHHhhHhHhhCCcccccccccccCCCCCCC--cccceecccCcchhcccCCcCC
Confidence 4567889999999999999999999999 88865 6799999999999999999865
No 3
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.88 E-value=1.5e-23 Score=160.31 Aligned_cols=50 Identities=58% Similarity=1.090 Sum_probs=48.9
Q ss_pred CCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCc
Q 017477 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKS 282 (371)
Q Consensus 233 KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKh 282 (371)
|||+||+||+|||++|.+|+|++||||||.|+.+|++||.+| |||||||+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k~ 58 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNKK 58 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCCC
Confidence 699999999999999999999999999999999999999999 99999995
No 4
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=96.49 E-value=0.00061 Score=49.82 Aligned_cols=46 Identities=24% Similarity=0.435 Sum_probs=38.5
Q ss_pred CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcC
Q 017477 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKST 283 (371)
Q Consensus 234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKht 283 (371)
||.||+||.+|.+.|.++-++ -+.-+.+++++.+.++ +|+.|.+..
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~----~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k 54 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE----NPYPSKEEREELAKELGLTERQVKNWFQNRRRK 54 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH----SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH----hccccccccccccccccccccccccCHHHhHHH
Confidence 789999999999999999885 4567777888888877 999987643
No 5
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=95.99 E-value=0.0028 Score=59.43 Aligned_cols=60 Identities=22% Similarity=0.359 Sum_probs=44.7
Q ss_pred CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHh---ccc-eeeecCCcCCCCCCCCC
Q 017477 232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFC---NEV-VWMHNNKSTFAKRDLNG 291 (371)
Q Consensus 232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC---~EI-VWMHNNKhtl~Kk~~~~ 291 (371)
.-||.||-||.||-.|+-..-|+-+|-.-...+.+-+..- .+| ||+-|..-..+|+....
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 4599999999999999988888887776655555444432 223 99999988777766543
No 6
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=92.00 E-value=0.099 Score=37.66 Aligned_cols=49 Identities=22% Similarity=0.449 Sum_probs=40.8
Q ss_pred CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCC
Q 017477 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAK 286 (371)
Q Consensus 234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~K 286 (371)
|+.|+.||.+|.+.|.++=++ -..-+.+++++.+.++ +|+-|.+...++
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~----~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEK----NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHh----CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 567899999999999998888 5577888999999987 899887765443
No 7
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=91.25 E-value=0.12 Score=51.34 Aligned_cols=55 Identities=24% Similarity=0.508 Sum_probs=31.8
Q ss_pred CCCccccCCCHHHHHHHHH-HHHHhCCcccCCCHHHHHHHh----ccc-eeeecCCcCCCCCC
Q 017477 232 GRKRFRTKFSQSQKEKMFE-FAERVGWKMQKRDDDLVHEFC----NEV-VWMHNNKSTFAKRD 288 (371)
Q Consensus 232 ~KKRFRTKFTqEQKEKMl~-FAEKLGWRIQK~DE~~VqqFC----~EI-VWMHNNKhtl~Kk~ 288 (371)
+|+||||.||+-|-|++.. |-|. -+-=.+-. +++..|- .+| ||+-|.+-...|+.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkea-HYPDv~Ar-e~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEA-HYPDVYAR-EMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhc-cCccHHHH-HHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 4567899999999887643 4332 11111111 1111111 123 99999998888875
No 8
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=91.11 E-value=0.14 Score=50.86 Aligned_cols=51 Identities=27% Similarity=0.506 Sum_probs=36.2
Q ss_pred CCccccCCCHHHHHHHH-HHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477 233 RKRFRTKFSQSQKEKMF-EFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD 288 (371)
Q Consensus 233 KKRFRTKFTqEQKEKMl-~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~ 288 (371)
.||-||-||.||-+|+. ||-|-- -.-|.--|+..+|+ +|+-|-+-.++|--
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enR-----YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENR-----YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhh-----hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 38999999999999986 565532 23455566777776 99998766555543
No 9
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=89.52 E-value=0.33 Score=34.84 Aligned_cols=45 Identities=22% Similarity=0.389 Sum_probs=34.3
Q ss_pred CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCc
Q 017477 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKS 282 (371)
Q Consensus 234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKh 282 (371)
||-||.||++|.+.|.++=++-- .-+.+++++-..++ .|+.|.+.
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~----~P~~~~~~~la~~~~l~~~qV~~WF~nrR~ 53 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNP----YPSREEREELAAKLGLSERQVKVWFQNRRA 53 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCC----CCCHHHHHHHHHHHCcCHHHHHHhHHHHhh
Confidence 56788999999999988776554 45666777776666 89988764
No 10
>PRK11470 hypothetical protein; Provisional
Probab=87.18 E-value=0.28 Score=46.30 Aligned_cols=41 Identities=20% Similarity=0.406 Sum_probs=33.7
Q ss_pred CCccccCCCHHHHHHHHHHHHHh-----CCcccCCCHHHHHHHhcccee
Q 017477 233 RKRFRTKFSQSQKEKMFEFAERV-----GWKMQKRDDDLVHEFCNEVVW 276 (371)
Q Consensus 233 KKRFRTKFTqEQKEKMl~FAEKL-----GWRIQK~DE~~VqqFC~EIVW 276 (371)
-+|.++.+|.+|+++|.++|++. .|+..-.|+ ..||+|.||
T Consensus 78 v~Rl~~~l~~~~~~~~~~~A~~~lGkpYD~~F~~~d~---~~YCSElV~ 123 (200)
T PRK11470 78 IKRLDAGLTEQQKQRIVEQVPSRLRKLYHTGFKYESS---RQFCSKFVF 123 (200)
T ss_pred EEEecCCCCHHHHHHHHHHHHHHcCCCCCCccCCCCC---ceehHHHHH
Confidence 48999999999999999999984 566555454 579999977
No 11
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=83.03 E-value=0.91 Score=33.08 Aligned_cols=41 Identities=24% Similarity=0.374 Sum_probs=36.0
Q ss_pred CCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhc
Q 017477 232 GRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCN 272 (371)
Q Consensus 232 ~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~ 272 (371)
.||||-+.+..|+-+|+.++|++.|-.+-+-=+.+|+.|=.
T Consensus 1 ~r~r~t~~l~~el~~~L~~ls~~t~i~~S~Ll~eAle~~l~ 41 (44)
T PF12651_consen 1 NRKRFTFSLDKELYEKLKELSEETGIPKSKLLREALEDYLE 41 (44)
T ss_pred CceEEEEecCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 37999999999999999999999998888877778887743
No 12
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=81.44 E-value=0.95 Score=40.53 Aligned_cols=18 Identities=22% Similarity=0.235 Sum_probs=13.5
Q ss_pred cccCCCHHHHHHHHHHHH
Q 017477 236 FRTKFSQSQKEKMFEFAE 253 (371)
Q Consensus 236 FRTKFTqEQKEKMl~FAE 253 (371)
-++.||+.||+||+++-|
T Consensus 137 c~~~FT~gQ~~RM~~~l~ 154 (154)
T PF05572_consen 137 CMNMFTPGQVARMRAVLE 154 (154)
T ss_dssp G--B-BHHHHHHHHHHHH
T ss_pred cccccCHHHHHHHHHHhC
Confidence 689999999999998865
No 13
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=81.37 E-value=0.54 Score=45.84 Aligned_cols=54 Identities=26% Similarity=0.460 Sum_probs=36.8
Q ss_pred CCCCCCccccCCCHHHH---H------HHHHHHHHhCCcccCCCHHHHHHHhccc-eeeecCCcCCCCCC
Q 017477 229 SSGGRKRFRTKFSQSQK---E------KMFEFAERVGWKMQKRDDDLVHEFCNEV-VWMHNNKSTFAKRD 288 (371)
Q Consensus 229 ~s~~KKRFRTKFTqEQK---E------KMl~FAEKLGWRIQK~DE~~VqqFC~EI-VWMHNNKhtl~Kk~ 288 (371)
+...|||-||-|+.-|- | |-|.-|||.|---+-|= -=-+| +|+-|.+++++++-
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqL------TETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQL------TETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhh------hhhhhhhhhhhhhHHHHHHH
Confidence 45679999999999874 3 33455777775433221 11345 99999999888874
No 14
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=79.11 E-value=0.32 Score=42.72 Aligned_cols=58 Identities=29% Similarity=0.413 Sum_probs=38.1
Q ss_pred CCCccccCCCHHH-HHHHHHHHHHhCCcccCCCHHHHHHHh--ccc-eeeecCCcCCCCCCC
Q 017477 232 GRKRFRTKFSQSQ-KEKMFEFAERVGWKMQKRDDDLVHEFC--NEV-VWMHNNKSTFAKRDL 289 (371)
Q Consensus 232 ~KKRFRTKFTqEQ-KEKMl~FAEKLGWRIQK~DE~~VqqFC--~EI-VWMHNNKhtl~Kk~~ 289 (371)
..+|.||.||.-| ||--.-|||--==-|--++|-++.==- ..| ||+-|..-.|.|..-
T Consensus 16 KQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 16 KQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 3489999999988 677778998654444444332211111 112 999999998888754
No 15
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=78.77 E-value=0.66 Score=47.16 Aligned_cols=55 Identities=24% Similarity=0.482 Sum_probs=30.4
Q ss_pred CCccccCCCHHHHHHHH-HHHHHhCCcccCCCHHHHHHHh---ccc-eeeecCCcCCCCCC
Q 017477 233 RKRFRTKFSQSQKEKMF-EFAERVGWKMQKRDDDLVHEFC---NEV-VWMHNNKSTFAKRD 288 (371)
Q Consensus 233 KKRFRTKFTqEQKEKMl-~FAEKLGWRIQK~DE~~VqqFC---~EI-VWMHNNKhtl~Kk~ 288 (371)
-+|+||-||-||-.|+. ||. |--|--.++.=++-.+.= .-| ||+-|.+-+-+++.
T Consensus 181 mRRYRTAFTReQIaRLEKEFy-rENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQR 240 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFY-RENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQR 240 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHH-HhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhh
Confidence 48999999999988874 343 222222222211111110 012 99999987555443
No 16
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=74.73 E-value=3.4 Score=30.49 Aligned_cols=22 Identities=27% Similarity=0.622 Sum_probs=19.1
Q ss_pred cCCCHHHHHHHHHHHHHhCCcc
Q 017477 238 TKFSQSQKEKMFEFAERVGWKM 259 (371)
Q Consensus 238 TKFTqEQKEKMl~FAEKLGWRI 259 (371)
-++++|-++|.++.||++||+.
T Consensus 24 ~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 24 PRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp SSSTHHHHHHHHHHHHHHTB-S
T ss_pred CCCCHHHHHHHHHHHHHHCCCC
Confidence 3688999999999999999974
No 17
>PRK10030 hypothetical protein; Provisional
Probab=73.38 E-value=1.4 Score=41.01 Aligned_cols=42 Identities=31% Similarity=0.650 Sum_probs=30.4
Q ss_pred CCccccCCCHHHHHHHHHHHHH-hC----CcccCCCHHHHHHHhccceee
Q 017477 233 RKRFRTKFSQSQKEKMFEFAER-VG----WKMQKRDDDLVHEFCNEVVWM 277 (371)
Q Consensus 233 KKRFRTKFTqEQKEKMl~FAEK-LG----WRIQK~DE~~VqqFC~EIVWM 277 (371)
-+|.+.++|.||++++.+||.+ || |.....| + .-||+|.||-
T Consensus 88 V~Rl~~~lt~~~~~~li~~A~~~lGkpYD~~f~~~d-~--~~YCSELV~~ 134 (197)
T PRK10030 88 VRRLENGLSVEQQQKLAQTAKRYLGKPYDFYFSWSD-D--RIYCSELVWK 134 (197)
T ss_pred EEEeCCCCCHHHHHHHHHHHHHHcCCCCCcccccCC-C--cEEeHHHHHH
Confidence 3688888999999999999976 44 2222223 2 5899999773
No 18
>COG3040 Blc Bacterial lipocalin [Cell envelope biogenesis, outer membrane]
Probab=67.13 E-value=5.1 Score=37.61 Aligned_cols=25 Identities=40% Similarity=0.646 Sum_probs=22.7
Q ss_pred ccC-CCHHHHHHHHHHHHHhCCcccC
Q 017477 237 RTK-FSQSQKEKMFEFAERVGWKMQK 261 (371)
Q Consensus 237 RTK-FTqEQKEKMl~FAEKLGWRIQK 261 (371)
||- .++|++++|++-|+++||-+-+
T Consensus 140 RtP~~s~~~~~~ml~~ak~~Gfdv~~ 165 (174)
T COG3040 140 RTPTLSQETLKRMLEIAKRRGFDVSK 165 (174)
T ss_pred cCCCCCHHHHHHHHHHHHHcCCCcce
Confidence 787 8999999999999999997754
No 19
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=65.94 E-value=3.9 Score=31.05 Aligned_cols=32 Identities=25% Similarity=0.240 Sum_probs=21.5
Q ss_pred ccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc
Q 017477 235 RFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV 274 (371)
Q Consensus 235 RFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI 274 (371)
|-|++||+|+|.+++..+..-| .-|.++|.+.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g--------~sv~~va~~~ 33 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG--------ESVSEVAREY 33 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH--------CHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC--------CceEeeeccc
Confidence 4578999999999999995545 4677888876
No 20
>cd04275 ZnMc_pappalysin_like Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor. This model includes pappalysins and related metalloprotease domains from all three kingdoms of life. The three-dimensional structure of an archaeal representative, ulilysin, has been solved.
Probab=65.47 E-value=3.9 Score=38.93 Aligned_cols=18 Identities=17% Similarity=0.307 Sum_probs=15.2
Q ss_pred ccccCCCHHHHHHHHHHH
Q 017477 235 RFRTKFSQSQKEKMFEFA 252 (371)
Q Consensus 235 RFRTKFTqEQKEKMl~FA 252 (371)
.-+..||+.||+||++.-
T Consensus 207 ~C~~~FT~~Q~~RM~~~~ 224 (225)
T cd04275 207 SCMNEFTPGQVTRMRSYL 224 (225)
T ss_pred chhcccCHHHHHHHHHHh
Confidence 457899999999999863
No 21
>PF13698 DUF4156: Domain of unknown function (DUF4156)
Probab=64.47 E-value=3.5 Score=34.31 Aligned_cols=22 Identities=27% Similarity=0.377 Sum_probs=18.4
Q ss_pred eeehHHHhhhhhhccCCccccC
Q 017477 71 VVTYKECLKNHAASIGGHALDG 92 (371)
Q Consensus 71 ~VrYRECLKNHAAsIGGHAvDG 92 (371)
.......|||.||.|||.+|-.
T Consensus 47 ~~ga~NdlrNeAa~lGgntV~~ 68 (93)
T PF13698_consen 47 MRGARNDLRNEAAKLGGNTVVL 68 (93)
T ss_pred HHHHHHHHHHHHHHhCCCEEEE
Confidence 4557889999999999998853
No 22
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=64.35 E-value=3.5 Score=41.88 Aligned_cols=46 Identities=35% Similarity=0.554 Sum_probs=31.9
Q ss_pred CCCCCccccCCCHHHH---------------HHHHHHHHHhCCcccCCCHHHHHHHhccc-eeeecCCcCCCCC
Q 017477 230 SGGRKRFRTKFSQSQK---------------EKMFEFAERVGWKMQKRDDDLVHEFCNEV-VWMHNNKSTFAKR 287 (371)
Q Consensus 230 s~~KKRFRTKFTqEQK---------------EKMl~FAEKLGWRIQK~DE~~VqqFC~EI-VWMHNNKhtl~Kk 287 (371)
..-|||.||-.-+-.| ||+-+.||||..|- +-| ||+=|-++.-++.
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKK------------NVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKK------------NVVRVWFCNQRQKQKRM 367 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhh------------ceEEEEeeccHHHHHHh
Confidence 4569999998766555 67777777776542 113 9999998865553
No 23
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=61.96 E-value=8.2 Score=37.60 Aligned_cols=53 Identities=23% Similarity=0.347 Sum_probs=35.6
Q ss_pred CCCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCC
Q 017477 229 SSGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFA 285 (371)
Q Consensus 229 ~s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~ 285 (371)
+..+.+|=||.||-+|-|-+.++=+| -|--|-..-++....| |||=|..-...
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~k----TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r 93 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAK----TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCR 93 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHh----hcCccHHHHHHHHHHhCCchhhhhhhhccccchhh
Confidence 34456899999999999987664443 2445555555555555 99999765443
No 24
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=61.81 E-value=13 Score=38.76 Aligned_cols=55 Identities=11% Similarity=0.211 Sum_probs=42.1
Q ss_pred CCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCCC
Q 017477 231 GGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRDL 289 (371)
Q Consensus 231 ~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~~ 289 (371)
.+|||.||-|+--.|+.+-.|=+| =+|-.-++|-+...+. ||+=|.+++.++-..
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~----npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLK----NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHh----CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 368889999999999887666554 4677777777766655 999999997666554
No 25
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=60.61 E-value=9.1 Score=28.64 Aligned_cols=23 Identities=22% Similarity=0.221 Sum_probs=18.4
Q ss_pred CccccCCCHHHHHHHHHHHHHhC
Q 017477 234 KRFRTKFSQSQKEKMFEFAERVG 256 (371)
Q Consensus 234 KRFRTKFTqEQKEKMl~FAEKLG 256 (371)
||.|+.+|-|||-+|+...|+-.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~ 23 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE 23 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT
T ss_pred CCCCccCCHHHHHHHHHHHHcCC
Confidence 78999999999999999988643
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=60.37 E-value=4.6 Score=36.42 Aligned_cols=55 Identities=20% Similarity=0.205 Sum_probs=36.0
Q ss_pred CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcCCCCCC
Q 017477 230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKSTFAKRD 288 (371)
Q Consensus 230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~ 288 (371)
..++||-||+||-+|-|-+..-=+++ +-.|-...+.-...+ ||+.|......|..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~----h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKV----HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCC----CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 35689999999998876654444444 444543333333333 99999988777665
No 27
>PHA02893 hypothetical protein; Provisional
Probab=59.62 E-value=3.6 Score=34.73 Aligned_cols=8 Identities=63% Similarity=1.585 Sum_probs=7.5
Q ss_pred cccccccC
Q 017477 109 SLKCAACG 116 (371)
Q Consensus 109 ALKCAACG 116 (371)
.|+|+|||
T Consensus 69 tL~CaACG 76 (88)
T PHA02893 69 NIKCIACG 76 (88)
T ss_pred ceeehhhc
Confidence 79999998
No 28
>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=57.84 E-value=7.7 Score=38.20 Aligned_cols=41 Identities=15% Similarity=0.435 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHhCCcc-cCCCHHHHHHHhccceeeecCCc
Q 017477 242 QSQKEKMFEFAERVGWKM-QKRDDDLVHEFCNEVVWMHNNKS 282 (371)
Q Consensus 242 qEQKEKMl~FAEKLGWRI-QK~DE~~VqqFC~EIVWMHNNKh 282 (371)
+-=++||.+|.|+-.==| --||.+.|+++|..++||++=+-
T Consensus 184 ~K~~~rl~e~~~~~~tiv~VSHd~~~I~~~Cd~~i~l~~G~i 225 (249)
T COG1134 184 EKCLERLNELVEKNKTIVLVSHDLGAIKQYCDRAIWLEHGQI 225 (249)
T ss_pred HHHHHHHHHHHHcCCEEEEEECCHHHHHHhcCeeEEEeCCEE
Confidence 446899999999883322 45999999999999999997543
No 29
>PF05708 DUF830: Orthopoxvirus protein of unknown function (DUF830); PDB: 2IF6_B 3KW0_C.
Probab=56.65 E-value=2.4 Score=36.46 Aligned_cols=40 Identities=30% Similarity=0.548 Sum_probs=26.2
Q ss_pred CccccCCCHHHHHHHHHHHHHh-----CCcccCCCHHHHHHHhcccee
Q 017477 234 KRFRTKFSQSQKEKMFEFAERV-----GWKMQKRDDDLVHEFCNEVVW 276 (371)
Q Consensus 234 KRFRTKFTqEQKEKMl~FAEKL-----GWRIQK~DE~~VqqFC~EIVW 276 (371)
.|.+..++++|++++.+||++. +++....++ .-||+|+||
T Consensus 71 ~r~~~~~~~~~~~~~~~~a~~~~g~~Y~~~~~~~~~---~~yCSelV~ 115 (158)
T PF05708_consen 71 YRLKDPLSEEQRQKAAEFAKSYIGKPYDFNFSLDDD---RFYCSELVA 115 (158)
T ss_dssp EEECCGTTCHHHHHHHHHHHCCTTS-B-CC-HCCSS---SB-HHHHHH
T ss_pred EEECCCCCHHHHHHHHHHHHHHcCCCccccccCCCC---CEEcHHHHH
Confidence 6777778999999999999653 333111122 269999954
No 30
>PHA03072 putative viral membrane protein; Provisional
Probab=52.06 E-value=3.9 Score=38.69 Aligned_cols=23 Identities=22% Similarity=0.572 Sum_probs=18.7
Q ss_pred hCCcccCCCH--HHHHHHhccceee
Q 017477 255 VGWKMQKRDD--DLVHEFCNEVVWM 277 (371)
Q Consensus 255 LGWRIQK~DE--~~VqqFC~EIVWM 277 (371)
=||.|+|-++ -.-||||+-|||=
T Consensus 130 DgWmvkKA~k~D~sAqQFCey~i~~ 154 (190)
T PHA03072 130 DGWMVKKAAKVDPSAQQFCEYLIKH 154 (190)
T ss_pred CceeEeeccccCccHHHHHHHHHHc
Confidence 3799999765 4679999999873
No 31
>COG0289 DapB Dihydrodipicolinate reductase [Amino acid transport and metabolism]
Probab=50.61 E-value=12 Score=37.23 Aligned_cols=20 Identities=45% Similarity=0.468 Sum_probs=18.2
Q ss_pred cCCCHHHHHHHHHHHHHhCC
Q 017477 238 TKFSQSQKEKMFEFAERVGW 257 (371)
Q Consensus 238 TKFTqEQKEKMl~FAEKLGW 257 (371)
|=||.|||++|.+|||+++-
T Consensus 101 TGf~~e~~~~l~~~a~~v~v 120 (266)
T COG0289 101 TGFTEEQLEKLREAAEKVPV 120 (266)
T ss_pred CCCCHHHHHHHHHHHhhCCE
Confidence 77999999999999999753
No 32
>PF03356 Pox_LP_H2: Viral late protein H2; InterPro: IPR005023 This entry represents the late protein H2 found in Vaccinia and other poxviruses. This protein is a highly conserved viral membrane protein found in all sequenced poxviruses, containing an N-terminal transmembrane domain and four conserved cysteines thought to be involved in the formation of intramolecular disulphide bonds []. H2 has been shown to be necessary for entry into the host cell and virus-induced cell-cell fusion, but is not required for virus morphogenesis or the attachment of virus particles to cells. It is part of an entry-fusion complex composed of eight viral membrane proteins [].
Probab=48.58 E-value=4.7 Score=38.16 Aligned_cols=24 Identities=21% Similarity=0.552 Sum_probs=19.1
Q ss_pred hCCcccCCCH--HHHHHHhccceeee
Q 017477 255 VGWKMQKRDD--DLVHEFCNEVVWMH 278 (371)
Q Consensus 255 LGWRIQK~DE--~~VqqFC~EIVWMH 278 (371)
=||.++|-++ -.-||||+-|||=+
T Consensus 130 DgWmvkKA~kvD~sAqQFCey~i~~~ 155 (189)
T PF03356_consen 130 DGWMVKKAAKVDPSAQQFCEYLIKNN 155 (189)
T ss_pred CceeEeeccccCccHHHHHHHHHHcc
Confidence 3799999765 46799999998744
No 33
>PF05009 EBV-NA3: Epstein-Barr virus nuclear antigen 3 (EBNA-3); InterPro: IPR007706 This family contains EBNA-3A, -3B, and -3C which are latent infection nuclear proteins important for Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4)-induced B-cell immortalisation and the immune response to EBVG infection. ; GO: 0016032 viral reproduction, 0042025 host cell nucleus; PDB: 3SJV_H 3DXA_M.
Probab=48.01 E-value=4.3 Score=40.00 Aligned_cols=42 Identities=26% Similarity=0.633 Sum_probs=1.9
Q ss_pred HHHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eee--ecCCcCCC
Q 017477 243 SQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWM--HNNKSTFA 285 (371)
Q Consensus 243 EQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWM--HNNKhtl~ 285 (371)
=|+|..++|.|=||| |||.|-..|..|-.+- =|| |=|-.-+-
T Consensus 130 l~~dqrv~Fv~F~G~-l~~~d~~~i~~wf~~~~Gt~k~~~PW~~~~P~~~py~ 181 (255)
T PF05009_consen 130 LQPDQRVSFVEFMGW-LQKCDNPAIKYWFHQAIGTTKPQTPWLSAHPNEVPYH 181 (255)
T ss_dssp -------SS--------------------------------------------
T ss_pred CChhhhhhHHHHHHH-HhcCCcHHHHHHHHHhcCCCCCCCCCCCCCCcccccc
Confidence 366778999999999 8999999999998887 799 44444443
No 34
>PF00765 Autoind_synth: Autoinducer synthetase; InterPro: IPR001690 Bacterial species have many methods of controlling gene expression and cell growth. Regulation of gene expression in response to changes in cell density is termed quorum sensing [, ]. Quorum-sensing bacteria produce, release and respond to hormone-like molecules (autoinducers) that accumulate in the external environment as the cell population grows. Once a threshold of these molecules is reached, a signal transduction cascade is triggered that ultimately leads to behavioural changes in the bacterium []. Autoinducers are thus clearly important mediators of molecular communication. Conjugal transfer of Agrobacterium octopine-type Ti plasmids is activated by octopine, a metabolite released from plant tumours []. Octopine causes conjugal donors to secrete a pheromone, Agrobacterium autoinducer (AAI), and exogenous AAI further stimulates conjugation. The putative AAI synthase and an AAI-responsive transcriptional regulator have been found to be encoded by the Ti plasmid traI and traR genes, respectively. TraR and TraI are similar to the LuxR and LuxI regulatory proteins of Vibrio fischeri, and AAI is similar in structure to the diffusable V. fischeri autoinducer, the inducing ligand of LuxR. TraR activates target genes in the presence of AAI and also activates traR and traI themselves, creating two positive-feedback loops. TraR-AAI-mediated activation in wild-type Agrobacterium strains is enhanced by culturing on solid media, suggesting a possible role in cell density sensing []. Production of light by the marine bacterium V. fischeri and by recombinant hosts containing cloned lux genes is controlled by the density of the culture []. Density-dependent regulation of lux gene expression has been shown to require a locus consisting of the luxR and luxI genes. In these and other Gram-negative bacteria, N-(3-oxohexanoyl)-L-homoserine lactone (OHHL) acts as the autoinducer by binding to transcriptional regulatory proteins and activating them []. OHHL and related molecules, such as N-butanoyl- (BHL), N-hexanoyl- (HHL) and N-oxododecanoyl- (PAI) homoserine lactones, are produced by a family of proteins that share a high level of sequence similarity. Proteins which currently members of this family include: luxI from V. fischeri. ahyI and asaI from Aeromonas species, which synthesize BHL and whose targets are ahyR and asaR respectively. carI from Erwinia carotovora. The target of OHHL is carR which activates genes involved in the biosynthesis of carbapenem antibiotics. eagI from Enterobacter agglomerans. The target of OHHL is not yet known. esaI from Erwinia stewartii. expI from Erwinia carotovora. lasI from Pseudomonas aeruginosa, which synthesizes PAI and whose target is lasR which activates the transcription of the elastase gene. rhlI (or vsmI) from P. aeruginosa, which synthesizes BHL and HHL and whose target is rhlR. swrI from Serratia liquefaciens, which synthesizes BHL. yenI from Yersinia enterocolitica. ; GO: 0007165 signal transduction; PDB: 3P2H_A 3P2F_A 1KZF_A 1K4J_A 1RO5_A.
Probab=47.09 E-value=1.9 Score=39.56 Aligned_cols=42 Identities=24% Similarity=0.499 Sum_probs=30.3
Q ss_pred CHHHHHHHH-----HHHHHhCCcccCCCHHHHHHHhccc----eeeecCCc
Q 017477 241 SQSQKEKMF-----EFAERVGWKMQKRDDDLVHEFCNEV----VWMHNNKS 282 (371)
Q Consensus 241 TqEQKEKMl-----~FAEKLGWRIQK~DE~~VqqFC~EI----VWMHNNKh 282 (371)
+++..++|. -|.|+|||.+...|.-+++||=.+= ||+.+.+.
T Consensus 6 ~~~~l~~~~rlR~~vFv~rlgW~v~~~dg~E~DqyD~~~~~ylv~~~~g~v 56 (182)
T PF00765_consen 6 SRRLLEEMFRLRHRVFVDRLGWDVPCEDGMEIDQYDDPDAVYLVALDDGRV 56 (182)
T ss_dssp HHHHHHHHHHHHHHHHTTCSCCCHHCCTSEE--TTGCTT-EEEEEEETTEE
T ss_pred CHHHHHHHHHHHHHHHHHhhCCCCcCCCCcEeeecCCCCCeEEEEEECCEE
Confidence 345556664 5899999999999999999997763 77777543
No 35
>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.
Probab=39.60 E-value=50 Score=28.38 Aligned_cols=41 Identities=10% Similarity=0.141 Sum_probs=30.2
Q ss_pred CHHHHHHHHHHHHHhCCc--ccCCCHHHHHHHhccceeeecCC
Q 017477 241 SQSQKEKMFEFAERVGWK--MQKRDDDLVHEFCNEVVWMHNNK 281 (371)
Q Consensus 241 TqEQKEKMl~FAEKLGWR--IQK~DE~~VqqFC~EIVWMHNNK 281 (371)
..+-+++++++-++++=. |--+|.+.+.+||.+|++|.|-|
T Consensus 102 D~~~~~~l~~~l~~~~~til~~th~~~~~~~~~d~v~~l~~g~ 144 (144)
T cd03221 102 DLESIEALEEALKEYPGTVILVSHDRYFLDQVATKIIELEDGK 144 (144)
T ss_pred CHHHHHHHHHHHHHcCCEEEEEECCHHHHHHhCCEEEEEeCCC
Confidence 456667777777766411 34588899999999999998755
No 36
>COG3916 LasI N-acyl-L-homoserine lactone synthetase [Signal transduction mechanisms / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=38.23 E-value=11 Score=36.33 Aligned_cols=41 Identities=20% Similarity=0.343 Sum_probs=30.5
Q ss_pred CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc
Q 017477 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV 274 (371)
Q Consensus 234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI 274 (371)
++|+-+.-+==|=|=+-|-|||||+..-.++-+++||=++=
T Consensus 11 ~~~~~~l~em~rlR~~vF~erL~W~v~~~~g~E~DqyD~~~ 51 (209)
T COG3916 11 ELFPKALEEMHRLRYQVFKERLGWDVVCIDGFEIDQYDNLD 51 (209)
T ss_pred hhcHHHHHHHHHHHHHHHHHhcCCceeccCCccccccCCCC
Confidence 44544444444555567999999999999999999996653
No 37
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=38.00 E-value=10 Score=39.40 Aligned_cols=15 Identities=47% Similarity=0.946 Sum_probs=11.9
Q ss_pred cccccccCccccccc
Q 017477 109 SLKCAACGCHRNFHR 123 (371)
Q Consensus 109 ALKCAACGCHRNFHR 123 (371)
+++|+||||+-+---
T Consensus 118 ~~~CkACG~r~~~d~ 132 (400)
T KOG2767|consen 118 SLKCKACGFRSDMDL 132 (400)
T ss_pred hhHHHHcCCcccccc
Confidence 699999999866533
No 38
>PF11761 CbiG_mid: Cobalamin biosynthesis central region; InterPro: IPR021745 Members of this family are involved in cobalamin synthesis. The gene encoded by P72862 from SWISSPROT has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process [].
Probab=38.00 E-value=24 Score=27.60 Aligned_cols=23 Identities=17% Similarity=0.582 Sum_probs=20.1
Q ss_pred HHHHHhCCcccCCCHHHHHHHhccc
Q 017477 250 EFAERVGWKMQKRDDDLVHEFCNEV 274 (371)
Q Consensus 250 ~FAEKLGWRIQK~DE~~VqqFC~EI 274 (371)
.||.++||+| .+-+.|.++.+-+
T Consensus 6 ~la~~~g~~i--~~~~~~k~vsaal 28 (93)
T PF11761_consen 6 LLARELGWRI--ENREAVKRVSAAL 28 (93)
T ss_pred hhhhhCCCEE--cCHHHHHHHHHHH
Confidence 4899999999 6678899999888
No 39
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=37.39 E-value=14 Score=25.76 Aligned_cols=30 Identities=20% Similarity=0.352 Sum_probs=21.5
Q ss_pred cccCccccccCCCCCCCCCCcccccccCccccccccC
Q 017477 89 ALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRRE 125 (371)
Q Consensus 89 AvDGCGEFMPSGeeGt~dp~ALKCAACGCHRNFHRKE 125 (371)
.=+-|+++|.+. ...+|+|..| ..+.|+|=
T Consensus 13 ~C~~C~~~i~~~-----~~~~~~C~~C--~~~~H~~C 42 (50)
T cd00029 13 FCDVCRKSIWGL-----FKQGLRCSWC--KVKCHKKC 42 (50)
T ss_pred Chhhcchhhhcc-----ccceeEcCCC--CCchhhhh
Confidence 457799999874 1358999987 56666653
No 40
>PF01113 DapB_N: Dihydrodipicolinate reductase, N-terminus; InterPro: IPR000846 Dihydrodipicolinate reductase catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate [, , ]. In Escherichia coli and Mycobacterium tuberculosis, dihydrodipicolinate reductase has equal specificity for NADH and NADPH, however in Thermotoga maritima there it has a greater affinity for NADPH []. In addition, the enzyme is inhibited by high concentrations of its substrate, which consequently acts as a feedback control on the lysine biosynthesis pathway. In T. maritima, the enzyme also lacks N-terminal and C-terminal loops which are present in enzyme of the former two organisms. This entry represents the N-terminal domain of dihydrodipicolinate reductase which binds the dinucleotide NAD(P)H.; GO: 0008839 dihydrodipicolinate reductase activity, 0009089 lysine biosynthetic process via diaminopimelate, 0055114 oxidation-reduction process; PDB: 3QY9_D 1VM6_C 1ARZ_A 1DIH_A 1DRW_A 1DRV_A 1DRU_A 2DAP_A 1DAP_B 3DAP_A ....
Probab=37.16 E-value=11 Score=32.11 Aligned_cols=21 Identities=29% Similarity=0.379 Sum_probs=17.9
Q ss_pred cCCCHHHHHHHHHHHHHhCCc
Q 017477 238 TKFSQSQKEKMFEFAERVGWK 258 (371)
Q Consensus 238 TKFTqEQKEKMl~FAEKLGWR 258 (371)
|=||+||++++.++|++++|=
T Consensus 99 TG~~~~~~~~l~~~a~~~~vl 119 (124)
T PF01113_consen 99 TGFSDEQIDELEELAKKIPVL 119 (124)
T ss_dssp SSSHHHHHHHHHHHTTTSEEE
T ss_pred CCCCHHHHHHHHHHhccCCEE
Confidence 558999999999999998763
No 41
>PHA03378 EBNA-3B; Provisional
Probab=35.31 E-value=12 Score=41.86 Aligned_cols=32 Identities=28% Similarity=0.734 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eee
Q 017477 244 QKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWM 277 (371)
Q Consensus 244 QKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWM 277 (371)
|++ .++|.|=||| |||.|-..|..|-.+- =||
T Consensus 275 t~n-RVaFveFmG~-L~k~d~~~Ik~Wf~q~iGt~kpt~PWl 314 (991)
T PHA03378 275 TRN-RVAFVEFVGW-LCKKDHTHIREWFRQCTGRPRPTKPWL 314 (991)
T ss_pred chh-hhHHHHHHHH-HhccccHHHHHHHHHhcCCCCCCCccc
Confidence 345 8999999999 8999999999998887 799
No 42
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=35.17 E-value=29 Score=29.16 Aligned_cols=20 Identities=25% Similarity=0.594 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHhCCcccC
Q 017477 242 QSQKEKMFEFAERVGWKMQK 261 (371)
Q Consensus 242 qEQKEKMl~FAEKLGWRIQK 261 (371)
+.|++.+.+||++.||.|-+
T Consensus 18 ~~Q~~~~~~~a~~~g~~i~~ 37 (148)
T smart00857 18 ERQLEALRAYAKANGWEVVR 37 (148)
T ss_pred HHHHHHHHHHHHHCCCEEEE
Confidence 68999999999999999743
No 43
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=34.32 E-value=15 Score=30.31 Aligned_cols=8 Identities=63% Similarity=1.609 Sum_probs=7.5
Q ss_pred cccccccC
Q 017477 109 SLKCAACG 116 (371)
Q Consensus 109 ALKCAACG 116 (371)
.|.|||||
T Consensus 57 tLsCsACG 64 (74)
T PF05077_consen 57 TLSCSACG 64 (74)
T ss_pred eEeehhcc
Confidence 69999998
No 44
>COG4802 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]
Probab=34.27 E-value=32 Score=30.25 Aligned_cols=30 Identities=27% Similarity=0.593 Sum_probs=20.7
Q ss_pred CHHHHHHHHHH----HHHhCCcccCCCHHHHHHHh
Q 017477 241 SQSQKEKMFEF----AERVGWKMQKRDDDLVHEFC 271 (371)
Q Consensus 241 TqEQKEKMl~F----AEKLGWRIQK~DE~~VqqFC 271 (371)
+.|-++||..| |||-|||+.-.-| ++..|-
T Consensus 2 ~~e~l~~my~~~eq~AeksG~~lnpD~e-~~~~v~ 35 (110)
T COG4802 2 SDEELNKMYRFTEQYAEKSGYRLNPDRE-FTAEVL 35 (110)
T ss_pred cHHHHHHHHHHHHHHHHhcCceeCCCHH-HHHHHH
Confidence 35778888876 6789999975444 444443
No 45
>PF13387 DUF4105: Domain of unknown function (DUF4105)
Probab=33.45 E-value=34 Score=30.81 Aligned_cols=27 Identities=11% Similarity=0.149 Sum_probs=24.3
Q ss_pred CccccCCCHHHHHHHHHHHHHhCCccc
Q 017477 234 KRFRTKFSQSQKEKMFEFAERVGWKMQ 260 (371)
Q Consensus 234 KRFRTKFTqEQKEKMl~FAEKLGWRIQ 260 (371)
..+|-.+|+|||++|+++.+++-|...
T Consensus 99 ~~y~LnLs~ee~~~l~~~l~e~~~~~~ 125 (176)
T PF13387_consen 99 WEYPLNLSPEEKQRLFRHLWENANPEN 125 (176)
T ss_pred EEEEeeCCHHHHHHHHHHHHHhccccc
Confidence 568889999999999999999988776
No 46
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=32.35 E-value=41 Score=30.93 Aligned_cols=22 Identities=27% Similarity=0.391 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHHHHHHhCCccc
Q 017477 239 KFSQSQKEKMFEFAERVGWKMQ 260 (371)
Q Consensus 239 KFTqEQKEKMl~FAEKLGWRIQ 260 (371)
+.++|-|||.++-|++|||+-.
T Consensus 3 ~Vs~~Tr~rV~~~a~elgY~pn 24 (309)
T PRK11041 3 KVSQATRQRVEQAVLEVGYSPQ 24 (309)
T ss_pred cCCHHHHHHHHHHHHHHCCCcC
Confidence 4789999999999999999875
No 47
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=32.27 E-value=31 Score=34.11 Aligned_cols=81 Identities=16% Similarity=0.214 Sum_probs=42.8
Q ss_pred CCCCccccCCCHHHHHHHHHHH--HHhCCcccCCCHHHHHHHhc-cc-eeeecCCcCCCCCCCCCC-CCCCCCCCCCCcc
Q 017477 231 GGRKRFRTKFSQSQKEKMFEFA--ERVGWKMQKRDDDLVHEFCN-EV-VWMHNNKSTFAKRDLNGA-GGSGSGSAGGGIG 305 (371)
Q Consensus 231 ~~KKRFRTKFTqEQKEKMl~FA--EKLGWRIQK~DE~~VqqFC~-EI-VWMHNNKhtl~Kk~~~~~-~~~~~~~~~~~~~ 305 (371)
++||--|-.|+-.|-...-.-- -|+=|---+-.++.---.|. +| ||+-|.+-...||....- ..+--.+++.+.|
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasakkkqds~ae~~ 244 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASAKKKQDSGAERG 244 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhccccCCCccccc
Confidence 5688889999987743322211 23334322222211111222 23 999999999999975443 2333344555555
Q ss_pred ccccCC
Q 017477 306 RINLDD 311 (371)
Q Consensus 306 ~~~~~~ 311 (371)
..++.+
T Consensus 245 ~gg~~~ 250 (288)
T KOG0847|consen 245 AGGAPS 250 (288)
T ss_pred ccCCCc
Confidence 544433
No 48
>PF13565 HTH_32: Homeodomain-like domain
Probab=32.12 E-value=46 Score=25.26 Aligned_cols=34 Identities=26% Similarity=0.476 Sum_probs=26.4
Q ss_pred ccccCCCHHHHHHHHHHHHHh-CCcccCCCHHHHHHH
Q 017477 235 RFRTKFSQSQKEKMFEFAERV-GWKMQKRDDDLVHEF 270 (371)
Q Consensus 235 RFRTKFTqEQKEKMl~FAEKL-GWRIQK~DE~~VqqF 270 (371)
|.|+ +.||++.++++.+.- .|.++.--+.+.++|
T Consensus 28 rp~~--~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~ 62 (77)
T PF13565_consen 28 RPRK--DPEQRERIIALIEEHPRWTPREIAEYLEEEF 62 (77)
T ss_pred CCCC--cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHh
Confidence 3355 999999999997765 898887777666666
No 49
>PF05419 GUN4: GUN4-like ; InterPro: IPR008629 In Arabidopsis, GUN4 is required for the functioning of the plastid mediated repression of nuclear transcription that is involved in controlling the levels of magnesium- protoporphyrin IX. GUN4 binds the product and substrate of Mg-chelatase, an enzyme that produces Mg-Proto, and activates Mg-chelatase. GUN4 is thought to participate in plastid-to-nucleus signalling by regulating magnesium-protoporphyrin IX synthesis or trafficking.; PDB: 1Y6I_A 1Z3X_A 1Z3Y_A.
Probab=31.82 E-value=26 Score=31.20 Aligned_cols=16 Identities=38% Similarity=0.752 Sum_probs=10.3
Q ss_pred HHHHHHHHHhCCcccC
Q 017477 246 EKMFEFAERVGWKMQK 261 (371)
Q Consensus 246 EKMl~FAEKLGWRIQK 261 (371)
+-...|++|||||.+.
T Consensus 82 ~~~~~F~~~VGW~~~~ 97 (132)
T PF05419_consen 82 EIWEKFGDRVGWRKGG 97 (132)
T ss_dssp --HHHHHHHCT--CTT
T ss_pred HHHHHHHHhcCCCCCC
Confidence 3488999999999663
No 50
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=31.67 E-value=19 Score=24.70 Aligned_cols=28 Identities=18% Similarity=0.408 Sum_probs=19.9
Q ss_pred cccCccccccCCCCCCCCCCcccccccCcccccccc
Q 017477 89 ALDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRR 124 (371)
Q Consensus 89 AvDGCGEFMPSGeeGt~dp~ALKCAACGCHRNFHRK 124 (371)
.=+-|+++|.... .+|+|..| ....|+|
T Consensus 13 ~C~~C~~~i~~~~------~~~~C~~C--~~~~H~~ 40 (49)
T smart00109 13 KCCVCRKSIWGSF------QGLRCSWC--KVKCHKK 40 (49)
T ss_pred CccccccccCcCC------CCcCCCCC--CchHHHH
Confidence 4588999998742 37999987 4555544
No 51
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=31.23 E-value=49 Score=33.58 Aligned_cols=57 Identities=18% Similarity=0.437 Sum_probs=41.5
Q ss_pred CCCCCccccCCCHHHHHHHHHHHHHhCCcccC-CCHHHHHHHhccc--------eeeecCCcCCCCCCCCC
Q 017477 230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQK-RDDDLVHEFCNEV--------VWMHNNKSTFAKRDLNG 291 (371)
Q Consensus 230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK-~DE~~VqqFC~EI--------VWMHNNKhtl~Kk~~~~ 291 (371)
..+|||-|-=||+-| .+|+=.| +|.|| .---+=++..+-| +|+-|...+.+|+....
T Consensus 150 ~~~kRKrRVLFSqAQ---V~ELERR--FrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk 215 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQ---VYELERR--FRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDK 215 (307)
T ss_pred cccccccccccchhH---HHHHHHH--HHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhh
Confidence 456788899999987 4555444 57887 4445666777777 99999999888776443
No 52
>PF01870 Hjc: Archaeal holliday junction resolvase (hjc); InterPro: IPR002732 This entry represents Holliday junction resolvases (hjc gene) and related proteins, primarily from archaeal species []. The Holliday junction is an essential intermediate of homologous recombination. Holliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. In the presence of divalent cations, these junctions exist predominantly as the stacked-X form in which the double-helical segments are coaxially stacked and twisted by 60 degrees in a right-handed direction across the junction cross-over. In this structure, the stacked arms resemble two adjacent double-helices, but are linked at the junction by two common strands that cross-over between the duplexes []. During homologous recombination, genetic information is physically exchanged between parental DNAs via crossing single strands of the same polarity within the four-way Holliday structure. This process is terminated by the endonucleolytic activity of resolvases, which convert the four-way DNA back to two double strands.; PDB: 2WJ0_A 2WIZ_B 2WIW_B 2WCW_C 2WCZ_A 1HH1_A 1GEF_D 1IPI_B 2EO0_B 1OB9_A ....
Probab=30.99 E-value=32 Score=28.64 Aligned_cols=20 Identities=35% Similarity=0.592 Sum_probs=18.3
Q ss_pred ccCCCHHHHHHHHHHHHHhC
Q 017477 237 RTKFSQSQKEKMFEFAERVG 256 (371)
Q Consensus 237 RTKFTqEQKEKMl~FAEKLG 256 (371)
+-++..||=|+|++||++.|
T Consensus 48 ~~~l~~eqve~L~~f~~~fg 67 (88)
T PF01870_consen 48 KIYLEKEQVEKLKEFSKRFG 67 (88)
T ss_dssp EEEEEHHHHHHHHHHHHHHT
T ss_pred ceeECHHHHHHHHHHHHHhC
Confidence 67789999999999999986
No 53
>PF05291 Bystin: Bystin; InterPro: IPR007955 Trophinin and tastin form a cell adhesion molecule complex that potentially mediates an initial attachment of the blastocyst to uterine epithelial cells at the time of implantation. Trophinin and tastin bind to an intermediary cytoplasmic protein called bystin. Bystin may be involved in implantation and trophoblast invasion because bystin is found with trophinin and tastin in the cells at human implantation sites and also in the intermediate trophoblasts at invasion front in the placenta from early pregnancy []. This family also includes the Saccharomyces cerevisiae protein ENP1. ENP1 is an essential protein in S. cerevisiae and is localised in the nucleus []. It is thought that ENP1 plays a direct role in the early steps of rRNA processing as enp1 defective S. cerevisiae cannot synthesise 20S pre-rRNA and hence 18S rRNA, which leads to reduced formation of 40S ribosomal subunits [].
Probab=30.67 E-value=26 Score=35.52 Aligned_cols=23 Identities=22% Similarity=0.554 Sum_probs=20.8
Q ss_pred CccccCCCHHHHHHHHHHHHHhC
Q 017477 234 KRFRTKFSQSQKEKMFEFAERVG 256 (371)
Q Consensus 234 KRFRTKFTqEQKEKMl~FAEKLG 256 (371)
+|+|+.+|+||||+++++-.+-+
T Consensus 253 qrYk~di~~eqk~~L~~ll~~~~ 275 (301)
T PF05291_consen 253 QRYKNDITEEQKEALLELLRKQK 275 (301)
T ss_pred HHHHHhCCHHHHHHHHHHHHhCC
Confidence 79999999999999999987654
No 54
>COG2102 Predicted ATPases of PP-loop superfamily [General function prediction only]
Probab=29.84 E-value=57 Score=31.81 Aligned_cols=35 Identities=26% Similarity=0.433 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHHHhCCcc-----cCCCHHHHHHHhcc
Q 017477 239 KFSQSQKEKMFEFAERVGWKM-----QKRDDDLVHEFCNE 273 (371)
Q Consensus 239 KFTqEQKEKMl~FAEKLGWRI-----QK~DE~~VqqFC~E 273 (371)
-++.+||++|...||+||-+. ++.-+..+.+++..
T Consensus 95 I~s~yqk~rve~lc~~lGl~~~~PLWg~d~~ell~e~~~~ 134 (223)
T COG2102 95 IASEYQKERVERLCEELGLKVYAPLWGRDPEELLEEMVEA 134 (223)
T ss_pred hhhHHHHHHHHHHHHHhCCEEeecccCCCHHHHHHHHHHc
Confidence 367999999999999999664 45556788888887
No 55
>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
Probab=29.62 E-value=84 Score=27.74 Aligned_cols=41 Identities=12% Similarity=0.352 Sum_probs=29.0
Q ss_pred CHHHHHHHHHHHHHh---CCc--ccCCCHHHHHHHhccceeeecCC
Q 017477 241 SQSQKEKMFEFAERV---GWK--MQKRDDDLVHEFCNEVVWMHNNK 281 (371)
Q Consensus 241 TqEQKEKMl~FAEKL---GWR--IQK~DE~~VqqFC~EIVWMHNNK 281 (371)
..+.+++++++-+++ |-. |--||.+.+.++|..|+||+|.|
T Consensus 136 D~~~~~~l~~~l~~~~~~~~tiii~sh~~~~~~~~~d~v~~l~~G~ 181 (182)
T cd03215 136 DVGAKAEIYRLIRELADAGKAVLLISSELDELLGLCDRILVMYEGR 181 (182)
T ss_pred CHHHHHHHHHHHHHHHHCCCEEEEEeCCHHHHHHhCCEEEEecCCc
Confidence 356666666666655 322 23488899999999999998753
No 56
>cd03279 ABC_sbcCD SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.
Probab=28.91 E-value=72 Score=29.00 Aligned_cols=42 Identities=7% Similarity=0.036 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHHHhCCc-----ccCCCHHHHHHHhccceeeecCC
Q 017477 240 FSQSQKEKMFEFAERVGWK-----MQKRDDDLVHEFCNEVVWMHNNK 281 (371)
Q Consensus 240 FTqEQKEKMl~FAEKLGWR-----IQK~DE~~VqqFC~EIVWMHNNK 281 (371)
+..+.++.+.++-+++-++ |--||.+.+.+||..|++|+|+-
T Consensus 164 lD~~~~~~~~~~l~~~~~~~~tii~itH~~~~~~~~~~~i~~~~~~~ 210 (213)
T cd03279 164 LDPEALEAVATALELIRTENRMVGVISHVEELKERIPQRLEVIKTPG 210 (213)
T ss_pred CCHHHHHHHHHHHHHHHhCCCEEEEEECchHHHHhhCcEEEEEecCC
Confidence 4577788888877777331 34578899999999999998863
No 57
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=28.61 E-value=30 Score=37.71 Aligned_cols=46 Identities=20% Similarity=0.295 Sum_probs=33.2
Q ss_pred CCccccCCCHHHHHHHHHHHHHhCCcccCCCHHH-HHHHhccc--------eeeecCCcC
Q 017477 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDL-VHEFCNEV--------VWMHNNKST 283 (371)
Q Consensus 233 KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~-VqqFC~EI--------VWMHNNKht 283 (371)
-||-|+-||++||+-++++ ++-+|+-..+ .+...++. =|+||-+-.
T Consensus 420 ~KKPRlVfTd~QkrTL~ai-----Fke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR 474 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAI-----FKENKRPSREMQETISQQLNLELSTVINFFMNARRR 474 (558)
T ss_pred CCCceeeecHHHHHHHHHH-----HhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence 4888999999999999987 4566665543 33444443 699998754
No 58
>smart00496 IENR2 Intron-encoded nuclease repeat 2. Short helical motif of unknown function (unpublished results).
Probab=27.31 E-value=49 Score=22.37 Aligned_cols=15 Identities=47% Similarity=0.457 Sum_probs=12.3
Q ss_pred CCCHHHHHHHHHHHH
Q 017477 239 KFSQSQKEKMFEFAE 253 (371)
Q Consensus 239 KFTqEQKEKMl~FAE 253 (371)
|.|.|.|+||-+-..
T Consensus 4 khSEETK~KMSea~~ 18 (26)
T smart00496 4 KHSEETKKKMSEAAX 18 (26)
T ss_pred CCCHHHHHHHHHhhc
Confidence 679999999988543
No 59
>TIGR00290 MJ0570_dom MJ0570-related uncharacterized domain. Proteins with this uncharacterized domain include two apparent ortholog families in the Archaea, one of which is universal among the first four completed archaeal genomes, and YLR143W, a much longer protein from Saccharomyces cerevisiae. The domain comprises the full length of the archaeal proteins and the first third of the yeast protein.
Probab=27.22 E-value=63 Score=31.01 Aligned_cols=34 Identities=26% Similarity=0.517 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHHHhCCcc-----cCCCHHHHHHHhcc
Q 017477 240 FSQSQKEKMFEFAERVGWKM-----QKRDDDLVHEFCNE 273 (371)
Q Consensus 240 FTqEQKEKMl~FAEKLGWRI-----QK~DE~~VqqFC~E 273 (371)
|+.+||.++...|+++|++. |+..++.+++|...
T Consensus 95 ~s~~qr~~~e~v~~~lgl~~~~PLW~~~~~~ll~e~i~~ 133 (223)
T TIGR00290 95 YSEYQKTRIERVCRELGLKSFAPLWHRDPEKLMEEFVEE 133 (223)
T ss_pred ccHHHHHHHHHHHHhcCCEEeccccCCCHHHHHHHHHHc
Confidence 77999999999999999876 56667899999855
No 60
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=27.20 E-value=97 Score=26.31 Aligned_cols=37 Identities=11% Similarity=0.181 Sum_probs=32.0
Q ss_pred cCCCHHHHHHHHHHHHHhC--CcccCCCHHHHHHHhccc
Q 017477 238 TKFSQSQKEKMFEFAERVG--WKMQKRDDDLVHEFCNEV 274 (371)
Q Consensus 238 TKFTqEQKEKMl~FAEKLG--WRIQK~DE~~VqqFC~EI 274 (371)
.+.+..|..||.++...+| |-|+...+..+..|+..+
T Consensus 53 ~~~~~~q~~KI~aLw~~~~~~~~v~~~s~~aL~~fvkr~ 91 (119)
T PF06252_consen 53 GMATSAQLRKIRALWKQLGKPGAVRDPSEAALDAFVKRQ 91 (119)
T ss_pred CCcchHHHHHHHHHHHHhhccCCccchHHHHHHHHHHHH
Confidence 3459999999999999999 456778889999999988
No 61
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=27.20 E-value=23 Score=31.17 Aligned_cols=13 Identities=54% Similarity=0.976 Sum_probs=10.7
Q ss_pred CCcccccccCccc
Q 017477 107 PTSLKCAACGCHR 119 (371)
Q Consensus 107 p~ALKCAACGCHR 119 (371)
.-.|+|.|||..|
T Consensus 112 ~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 112 LIFLKCKACGASR 124 (125)
T ss_dssp CCEEEETTTSCEE
T ss_pred EEEEEecccCCcC
Confidence 3479999999876
No 62
>PRK09492 treR trehalose repressor; Provisional
Probab=26.92 E-value=62 Score=30.02 Aligned_cols=21 Identities=14% Similarity=0.278 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHHHHHHhCCcc
Q 017477 239 KFSQSQKEKMFEFAERVGWKM 259 (371)
Q Consensus 239 KFTqEQKEKMl~FAEKLGWRI 259 (371)
++++|-|||.++.||+||++-
T Consensus 30 ~vs~~tr~rV~~~a~elgY~p 50 (315)
T PRK09492 30 GVSEETRERVEAVINQHGFSP 50 (315)
T ss_pred CCCHHHHHHHHHHHHHHCCCc
Confidence 589999999999999999965
No 63
>PF13551 HTH_29: Winged helix-turn helix
Probab=26.55 E-value=60 Score=25.73 Aligned_cols=23 Identities=22% Similarity=0.380 Sum_probs=19.5
Q ss_pred CCccccCCCHHHHHHHHHHHHHh
Q 017477 233 RKRFRTKFSQSQKEKMFEFAERV 255 (371)
Q Consensus 233 KKRFRTKFTqEQKEKMl~FAEKL 255 (371)
.+|.++++|+||++.++++.+.-
T Consensus 51 ~g~~~~~l~~~~~~~l~~~~~~~ 73 (112)
T PF13551_consen 51 GGRPRKRLSEEQRAQLIELLREN 73 (112)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHC
Confidence 35667779999999999999985
No 64
>PF13592 HTH_33: Winged helix-turn helix
Probab=26.43 E-value=74 Score=23.98 Aligned_cols=37 Identities=30% Similarity=0.599 Sum_probs=26.4
Q ss_pred CccccCCCHHHHHHHHHHHHHhCCccc-------CCCHHHHHHHhcc
Q 017477 234 KRFRTKFSQSQKEKMFEFAERVGWKMQ-------KRDDDLVHEFCNE 273 (371)
Q Consensus 234 KRFRTKFTqEQKEKMl~FAEKLGWRIQ-------K~DE~~VqqFC~E 273 (371)
++|.=++|.. -|..+-.|+||+.| |+|++++++|=.+
T Consensus 16 ~~fgv~ys~~---~v~~lL~r~G~s~~kp~~~~~k~d~~~q~~f~k~ 59 (60)
T PF13592_consen 16 EEFGVKYSPS---GVYRLLKRLGFSYQKPRPRPPKADEEAQEAFKKE 59 (60)
T ss_pred HHHCCEEcHH---HHHHHHHHcCCccccCCCCcccCCHHHHHHHHHh
Confidence 5555566544 46667779999876 4788999999544
No 65
>PF09932 DUF2164: Uncharacterized conserved protein (DUF2164); InterPro: IPR018680 This family of various hypothetical prokaryotic proteins has no known function.
Probab=26.34 E-value=72 Score=26.05 Aligned_cols=35 Identities=23% Similarity=0.471 Sum_probs=24.9
Q ss_pred CCCHHHHHHHHH-----HHHHhCCcccCCCHHHHHHHhcc
Q 017477 239 KFSQSQKEKMFE-----FAERVGWKMQKRDDDLVHEFCNE 273 (371)
Q Consensus 239 KFTqEQKEKMl~-----FAEKLGWRIQK~DE~~VqqFC~E 273 (371)
|||.|||+.|.+ |++.++=.|---+-+.+=.|+.+
T Consensus 2 ~l~ke~k~~li~~iq~yf~~E~d~eiG~~~Ae~LLDF~~~ 41 (76)
T PF09932_consen 2 KLSKEEKAELIDKIQRYFAEELDEEIGDFEAEFLLDFFIE 41 (76)
T ss_pred cCCHHHHHHHHHHHHHHHHHHhcCcHHHhHHHHHHHHHHH
Confidence 799999999987 67777777766555555555443
No 66
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=26.14 E-value=42 Score=40.09 Aligned_cols=60 Identities=27% Similarity=0.300 Sum_probs=44.2
Q ss_pred CCCCCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc------eeeecCCcCCCCCCCCC
Q 017477 230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV------VWMHNNKSTFAKRDLNG 291 (371)
Q Consensus 230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI------VWMHNNKhtl~Kk~~~~ 291 (371)
...+.|.||.|+-+|-.-|..|=|+ .++-+.++-+|++==.+. ||+-|+.....|-..++
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~--q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEA--QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhh--ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 3568999999999999999999877 466677776665432222 99999998765555433
No 67
>PRK14258 phosphate ABC transporter ATP-binding protein; Provisional
Probab=26.11 E-value=86 Score=29.39 Aligned_cols=41 Identities=10% Similarity=0.106 Sum_probs=28.2
Q ss_pred HHHHHHHHH----HHHHhCCc--ccCCCHHHHHHHhccceeeecCCc
Q 017477 242 QSQKEKMFE----FAERVGWK--MQKRDDDLVHEFCNEVVWMHNNKS 282 (371)
Q Consensus 242 qEQKEKMl~----FAEKLGWR--IQK~DE~~VqqFC~EIVWMHNNKh 282 (371)
.+-++++++ ++.+-|.. |--||..+|.++|.+|+||.++++
T Consensus 183 ~~~~~~l~~~l~~l~~~~~~tiiivsH~~~~i~~~~d~i~~l~~~~~ 229 (261)
T PRK14258 183 PIASMKVESLIQSLRLRSELTMVIVSHNLHQVSRLSDFTAFFKGNEN 229 (261)
T ss_pred HHHHHHHHHHHHHHHHhCCCEEEEEECCHHHHHHhcCEEEEEccCCC
Confidence 444444444 43333554 345999999999999999998663
No 68
>PHA03379 EBNA-3A; Provisional
Probab=26.01 E-value=16 Score=40.88 Aligned_cols=39 Identities=28% Similarity=0.556 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhCCcccCCCHHHHHHHhccc--------eeeecCCcC
Q 017477 244 QKEKMFEFAERVGWKMQKRDDDLVHEFCNEV--------VWMHNNKST 283 (371)
Q Consensus 244 QKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI--------VWMHNNKht 283 (371)
|+|..++|.|=||| |||.|--.|..|-.+- =||--|--.
T Consensus 268 tpeQRvsFmeFmG~-LqktDn~~Ik~Wf~qalGT~Kp~tPWl~EnP~~ 314 (935)
T PHA03379 268 TPDQRVPFMEFLGF-LQRTDLIYIKSFVSEALGTTSIQTPWLDENPST 314 (935)
T ss_pred ChhhhhhHHHHHHH-HhccCcHHHHHHHHHhcCCCCCCCCCccCCcch
Confidence 47778999999999 8999999999999887 688754433
No 69
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=25.71 E-value=72 Score=22.67 Aligned_cols=22 Identities=23% Similarity=0.480 Sum_probs=18.3
Q ss_pred ccCCCHHHHHHHHHHHHHhCCc
Q 017477 237 RTKFSQSQKEKMFEFAERVGWK 258 (371)
Q Consensus 237 RTKFTqEQKEKMl~FAEKLGWR 258 (371)
|-.||+|..+++++...+.|-+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~ 22 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD 22 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT
T ss_pred CCCCCHHHHHHHHHHHHHhCCc
Confidence 5689999999999999999965
No 70
>PRK10061 DNA damage-inducible protein YebG; Provisional
Probab=25.70 E-value=8.5 Score=33.10 Aligned_cols=52 Identities=15% Similarity=0.302 Sum_probs=37.6
Q ss_pred CCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc-eeeecCCcCC
Q 017477 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV-VWMHNNKSTF 284 (371)
Q Consensus 233 KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI-VWMHNNKhtl 284 (371)
|-.|=+|=-++.=+|||++||.|-==|++....+=++=+.++ +||=.||..+
T Consensus 16 kmtFtsKKEADAyDKMLD~Ad~L~~~L~~s~~~ldE~q~E~L~l~LA~nKd~l 68 (96)
T PRK10061 16 KMSFTSKKEADAYDKMLDTADLLDTWLTNSPVQMEDEQREALSLWLAEQKDVL 68 (96)
T ss_pred eeccCcHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 567777778999999999999987656655443333344455 8888888765
No 71
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=25.53 E-value=52 Score=28.36 Aligned_cols=19 Identities=26% Similarity=0.331 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHhCCccc
Q 017477 242 QSQKEKMFEFAERVGWKMQ 260 (371)
Q Consensus 242 qEQKEKMl~FAEKLGWRIQ 260 (371)
..|++.+.+||++.||.|-
T Consensus 21 e~Q~~~l~~~a~~~g~~i~ 39 (140)
T cd03770 21 ENQKAILEEYAKENGLENI 39 (140)
T ss_pred HHHHHHHHHHHHHCCCEEE
Confidence 6799999999999999764
No 72
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=24.40 E-value=73 Score=30.02 Aligned_cols=21 Identities=0% Similarity=0.143 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHHHHHHhCCcc
Q 017477 239 KFSQSQKEKMFEFAERVGWKM 259 (371)
Q Consensus 239 KFTqEQKEKMl~FAEKLGWRI 259 (371)
..++|-|+|.++.|++|||+-
T Consensus 27 ~vs~~tr~~V~~~a~elgY~p 47 (341)
T PRK10703 27 FVAEETRNAVWAAIKELHYSP 47 (341)
T ss_pred CCCHHHHHHHHHHHHHHCCCc
Confidence 579999999999999999975
No 73
>cd01994 Alpha_ANH_like_IV This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily of proteins is predicted to bind ATP. This domainhas a strongly conserved motif SGGKD at the N terminus.
Probab=24.06 E-value=92 Score=28.78 Aligned_cols=36 Identities=19% Similarity=0.400 Sum_probs=29.1
Q ss_pred cCCCHHHHHHHHHHHHHhCCcc-----cCCCHHHHHHHhcc
Q 017477 238 TKFSQSQKEKMFEFAERVGWKM-----QKRDDDLVHEFCNE 273 (371)
Q Consensus 238 TKFTqEQKEKMl~FAEKLGWRI-----QK~DE~~VqqFC~E 273 (371)
+-++..||+++...++++|.+. ++..++.+++|...
T Consensus 96 ~i~sd~~~~~~e~~~~~~gl~~~~PLW~~~~~~ll~e~~~~ 136 (194)
T cd01994 96 AILSEYQRTRVERVCERLGLEPLAPLWGRDQEELLREMIEA 136 (194)
T ss_pred ccccHHHHHHHHHHHHHcCCEEEecccCCCHHHHHHHHHHc
Confidence 3467899999999999999654 45566799999855
No 74
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=24.05 E-value=46 Score=23.90 Aligned_cols=28 Identities=29% Similarity=0.687 Sum_probs=18.3
Q ss_pred ccCccccccCCCCCCCCCCcccccccCcccccccc
Q 017477 90 LDGCGEFMPSPTATPSDPTSLKCAACGCHRNFHRR 124 (371)
Q Consensus 90 vDGCGEFMPSGeeGt~dp~ALKCAACGCHRNFHRK 124 (371)
=|=|+++|.+. -..+|+|..|+ ...|++
T Consensus 14 C~~C~~~i~g~-----~~~g~~C~~C~--~~~H~~ 41 (53)
T PF00130_consen 14 CDVCGKFIWGL-----GKQGYRCSWCG--LVCHKK 41 (53)
T ss_dssp -TTSSSBECSS-----SSCEEEETTTT---EEETT
T ss_pred CcccCcccCCC-----CCCeEEECCCC--ChHhhh
Confidence 36799999541 14589999765 555655
No 75
>PRK13834 putative autoinducer synthesis protein; Provisional
Probab=23.95 E-value=19 Score=33.67 Aligned_cols=48 Identities=17% Similarity=0.318 Sum_probs=32.7
Q ss_pred CccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhcc---c-eeeecCC
Q 017477 234 KRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNE---V-VWMHNNK 281 (371)
Q Consensus 234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~E---I-VWMHNNK 281 (371)
.++..-+.+=++-|=.-|.|++||.+...|.-+++||=.. . ||.+.+.
T Consensus 12 ~~~~~~l~~~~rLR~~VF~~elgW~~~~~~g~E~D~yD~~~~~yll~~~~~g 63 (207)
T PRK13834 12 EREASLLKQMHRLRARVFGGRLGWDVSITDGEERDQFDDLKPTYILAISDSG 63 (207)
T ss_pred hcCHHHHHHHHHHHHHHhccccCCCCCCCCCcCccCCCCCCCEEEEEEeCCC
Confidence 3444445566677778899999999987766677777543 2 6765553
No 76
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.58 E-value=83 Score=26.03 Aligned_cols=30 Identities=30% Similarity=0.264 Sum_probs=23.5
Q ss_pred ccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc
Q 017477 237 RTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV 274 (371)
Q Consensus 237 RTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI 274 (371)
|.|||.|-|.++.+++..-|- -|.+-|++.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~--------sv~~vAr~~ 34 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD--------TVSEVAREF 34 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc--------cHHHHHHHh
Confidence 999999999999999876554 455566663
No 77
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=23.56 E-value=76 Score=30.06 Aligned_cols=22 Identities=14% Similarity=0.197 Sum_probs=19.8
Q ss_pred CCCHHHHHHHHHHHHHhCCccc
Q 017477 239 KFSQSQKEKMFEFAERVGWKMQ 260 (371)
Q Consensus 239 KFTqEQKEKMl~FAEKLGWRIQ 260 (371)
+.++|-|+|.++-|++|||+..
T Consensus 27 ~Vs~~tr~rV~~~a~elgY~pn 48 (343)
T PRK10727 27 KASEASRLAVHSAMESLSYHPN 48 (343)
T ss_pred CCCHHHHHHHHHHHHHHCCCCC
Confidence 4889999999999999999754
No 78
>cd00338 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are protei
Probab=23.55 E-value=61 Score=26.64 Aligned_cols=19 Identities=32% Similarity=0.536 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHhCCccc
Q 017477 242 QSQKEKMFEFAERVGWKMQ 260 (371)
Q Consensus 242 qEQKEKMl~FAEKLGWRIQ 260 (371)
..|++.+.+||.+.||.|.
T Consensus 17 ~~Q~~~~~~~a~~~g~~i~ 35 (137)
T cd00338 17 ERQREALREYAARNGLEVV 35 (137)
T ss_pred HHHHHHHHHHHHHCCCEEE
Confidence 6899999999999999763
No 79
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=23.44 E-value=59 Score=33.38 Aligned_cols=48 Identities=23% Similarity=0.449 Sum_probs=32.9
Q ss_pred CCCCCccccCCCHHHHHHHHHHHHHhCCcc-cCCCHHHHHHHhccc--------eeeecCCc
Q 017477 230 SGGRKRFRTKFSQSQKEKMFEFAERVGWKM-QKRDDDLVHEFCNEV--------VWMHNNKS 282 (371)
Q Consensus 230 s~~KKRFRTKFTqEQKEKMl~FAEKLGWRI-QK~DE~~VqqFC~EI--------VWMHNNKh 282 (371)
-.+.||-||..|+.|-|-+.. -+.- -|----+-+|..+|. ||+-|.+-
T Consensus 164 d~~nKRPRTTItAKqLETLK~-----AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRA 220 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQ-----AYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRA 220 (383)
T ss_pred ccccCCCcceeeHHHHHHHHH-----HhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhH
Confidence 345699999999999987643 2222 222234566777776 99999864
No 80
>PRK13636 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=23.44 E-value=86 Score=29.93 Aligned_cols=43 Identities=16% Similarity=0.398 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHHHh----CCcc--cCCCHHHHHHHhccceeeecCCc
Q 017477 240 FSQSQKEKMFEFAERV----GWKM--QKRDDDLVHEFCNEVVWMHNNKS 282 (371)
Q Consensus 240 FTqEQKEKMl~FAEKL----GWRI--QK~DE~~VqqFC~EIVWMHNNKh 282 (371)
+..+.+++++++-+++ |..| --||-++|.++|.+|++|+|.+-
T Consensus 172 LD~~~~~~l~~~l~~l~~~~g~tillvsH~~~~~~~~~dri~~l~~G~i 220 (283)
T PRK13636 172 LDPMGVSEIMKLLVEMQKELGLTIIIATHDIDIVPLYCDNVFVMKEGRV 220 (283)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCEEEEEecCHHHHHHhCCEEEEEECCEE
Confidence 4467777777766655 5553 45999999999999999998765
No 81
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=23.24 E-value=72 Score=24.97 Aligned_cols=25 Identities=20% Similarity=0.183 Sum_probs=16.4
Q ss_pred cCCCHHHHHHHHHHHHHhCCcccCC
Q 017477 238 TKFSQSQKEKMFEFAERVGWKMQKR 262 (371)
Q Consensus 238 TKFTqEQKEKMl~FAEKLGWRIQK~ 262 (371)
=++|.|||+++.+|...+-=.+...
T Consensus 13 L~LT~eQ~~~~~~i~~~~~~~~~~~ 37 (100)
T PF07813_consen 13 LNLTDEQKAKWRAIRQAMKAKMKPL 37 (100)
T ss_dssp S--THHHHHHHHHHHHHHCTTS---
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 3689999999999988775444443
No 82
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=22.95 E-value=81 Score=29.45 Aligned_cols=21 Identities=14% Similarity=0.441 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHHHHHHhCCcc
Q 017477 239 KFSQSQKEKMFEFAERVGWKM 259 (371)
Q Consensus 239 KFTqEQKEKMl~FAEKLGWRI 259 (371)
+.++|-|+|.++-||+||++.
T Consensus 27 ~vs~~tr~rV~~~a~~lgY~p 47 (329)
T TIGR01481 27 NVKPATRKKVLEVIKRLDYRP 47 (329)
T ss_pred CCCHHHHHHHHHHHHHHCCCC
Confidence 588999999999999999975
No 83
>PF07130 YebG: YebG protein; InterPro: IPR009813 This family consists of several bacterial YebG proteins of around 75 residues in length. The exact function of this protein is unknown but it is thought to be involved in the SOS response. The induction of the yebG gene occurs as cell enter into the stationary growth phase and is dependent on is dependent on cyclic AMP and H-NS [].; PDB: 3ERM_E.
Probab=22.88 E-value=5.8 Score=32.70 Aligned_cols=52 Identities=17% Similarity=0.289 Sum_probs=30.4
Q ss_pred CCccccCCCHHHHHHHHHHHHHhCCcccCCCHHHHHHHhccc-eeeecCCcCC
Q 017477 233 RKRFRTKFSQSQKEKMFEFAERVGWKMQKRDDDLVHEFCNEV-VWMHNNKSTF 284 (371)
Q Consensus 233 KKRFRTKFTqEQKEKMl~FAEKLGWRIQK~DE~~VqqFC~EI-VWMHNNKhtl 284 (371)
|-+|=.|=-++.=+|||++||.|-==|++.....=++=+.++ .||=+||..+
T Consensus 16 kmtF~sKkEADAyDKmLd~Ad~L~~~L~~~~~~lde~~~E~l~l~LA~~kd~~ 68 (75)
T PF07130_consen 16 KMTFTSKKEADAYDKMLDLADNLTDFLEQSVLGLDEAQAEELALYLAENKDEL 68 (75)
T ss_dssp -----HHHHHHHHHHHHHHHHHHHHHHHHHSTT--HHHHHHHHHHHHTTHHHH
T ss_pred eeeeccHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCHHHH
Confidence 567777777899999999999987555543333333334444 6776666543
No 84
>PF01902 ATP_bind_4: ATP-binding region; InterPro: IPR002761 This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N-terminal. The structure of Q8U2K6 from SWISSPROT from Pyrococcus furiosus has been resolved to 2.7A and is suggested to be a putative N-type pytophosphatase. In some members of the family e.g. Q12429 from SWISSPROT, this domain is associated with IPR006175 from INTERPRO, another domain of unknown function. Proteins with this uncharacterised domain include two apparent ortholog families in the archaea, one of which is universal among the first four completed archaeal genomes. The domain comprises the full length of the archaeal proteins and the first third of fungal proteins.; PDB: 3RK0_A 3RK1_A 3RJZ_A 2D13_D.
Probab=22.22 E-value=78 Score=30.18 Aligned_cols=34 Identities=24% Similarity=0.384 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHHHHHhCCcc-----cCCCHHHHHHHhcc
Q 017477 240 FSQSQKEKMFEFAERVGWKM-----QKRDDDLVHEFCNE 273 (371)
Q Consensus 240 FTqEQKEKMl~FAEKLGWRI-----QK~DE~~VqqFC~E 273 (371)
|+.+||.++...++++|++. |+..++.+.+|...
T Consensus 95 ~~~~~r~~~e~vc~~lGl~~~~PLW~~d~~~ll~e~i~~ 133 (218)
T PF01902_consen 95 DSEYQRNWVERVCERLGLEAVFPLWGRDREELLREFIES 133 (218)
T ss_dssp S-HHHHHHHHHHHHHCT-EEE-TTTT--HHHHHHHHHHT
T ss_pred CcHHHHHHHHHHHHHcCCEEEecccCCCHHHHHHHHHHC
Confidence 78999999999999999886 34445788888875
No 85
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=21.41 E-value=75 Score=27.76 Aligned_cols=50 Identities=16% Similarity=0.405 Sum_probs=37.3
Q ss_pred CCccccCCCHHHHHHHHHHHHHhC-------------Cccc-CCCHHHHHHHh------ccc-----eeeecCCc
Q 017477 233 RKRFRTKFSQSQKEKMFEFAERVG-------------WKMQ-KRDDDLVHEFC------NEV-----VWMHNNKS 282 (371)
Q Consensus 233 KKRFRTKFTqEQKEKMl~FAEKLG-------------WRIQ-K~DE~~VqqFC------~EI-----VWMHNNKh 282 (371)
.+++++++|+|.|+++.+=|+..| .+|+ +-|.+.|.++- ..+ -||-+.+-
T Consensus 10 ~~~I~vrvt~eE~~~I~~kA~~AGlS~SeYLR~~aLg~~I~s~~D~e~v~eL~~in~dlgRlGgLlK~~l~~~~~ 84 (114)
T PRK13877 10 GRHLRVPVLPDEKAEIEANAAAAGLSVARYLRDVGQGYQIKGVIDYEYVRELARINGDLGRLGGLLKLWLTDDVR 84 (114)
T ss_pred CceeEEEeCHHHHHHHHHHHHHhCCCHHHHHHHHHcCCCccccCCHHHHHHHHHhcccHHHHHHHHHHHHhCCCC
Confidence 466899999999999999888766 4553 67778888776 233 77777654
No 86
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=21.28 E-value=69 Score=22.84 Aligned_cols=21 Identities=19% Similarity=0.260 Sum_probs=17.9
Q ss_pred CccccCCCHHHHHHHHHHHHH
Q 017477 234 KRFRTKFSQSQKEKMFEFAER 254 (371)
Q Consensus 234 KRFRTKFTqEQKEKMl~FAEK 254 (371)
.+||=+.|.||+++|...+.-
T Consensus 5 ~k~rl~Pt~~Q~~~L~~~~~~ 25 (46)
T PF12323_consen 5 YKYRLYPTKEQEEKLERWFGA 25 (46)
T ss_pred eEEEEecCHHHHHHHHHHHHH
Confidence 678889999999999887653
No 87
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=21.25 E-value=76 Score=27.89 Aligned_cols=26 Identities=31% Similarity=0.351 Sum_probs=22.5
Q ss_pred HHHHHHHhCCcccCCCHHHHHHHhccc
Q 017477 248 MFEFAERVGWKMQKRDDDLVHEFCNEV 274 (371)
Q Consensus 248 Ml~FAEKLGWRIQK~DE~~VqqFC~EI 274 (371)
-.++.++.||+ |-.||+++.++|.+|
T Consensus 75 ~~~ii~~~~l~-~isd~~el~~~v~~v 100 (147)
T smart00845 75 PEEIVEEKGLK-QISDEGELEAIVDEV 100 (147)
T ss_pred HHHHHHHcCCc-cCCCHHHHHHHHHHH
Confidence 45899999996 577888999999999
No 88
>cd03298 ABC_ThiQ_thiamine_transporter ABC-type thiamine tranport system; part of the binding-protein-dependent transport system tbpA-thiPQ for thiamine and TPP. Probably responsible for the translocation of thiamine across the membrane. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=20.97 E-value=1.6e+02 Score=26.36 Aligned_cols=41 Identities=12% Similarity=0.305 Sum_probs=28.7
Q ss_pred CHHHHHHHHHHHHH----hCCc--ccCCCHHHHHHHhccceeeecCC
Q 017477 241 SQSQKEKMFEFAER----VGWK--MQKRDDDLVHEFCNEVVWMHNNK 281 (371)
Q Consensus 241 TqEQKEKMl~FAEK----LGWR--IQK~DE~~VqqFC~EIVWMHNNK 281 (371)
..+-+++++++-.+ -|.. |--||-+.+.++|.+|+||++-|
T Consensus 160 D~~~~~~l~~~l~~~~~~~~~tii~~sH~~~~~~~~~d~i~~l~~G~ 206 (211)
T cd03298 160 DPALRAEMLDLVLDLHAETKMTVLMVTHQPEDAKRLAQRVVFLDNGR 206 (211)
T ss_pred CHHHHHHHHHHHHHHHHhcCCEEEEEecCHHHHHhhhCEEEEEECCE
Confidence 34555555554443 3655 35599999999999999998754
No 89
>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.
Probab=20.86 E-value=1.1e+02 Score=27.51 Aligned_cols=41 Identities=17% Similarity=0.323 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHHHHh----CCc--ccCCCHHHHHHHhccceeeecCC
Q 017477 241 SQSQKEKMFEFAERV----GWK--MQKRDDDLVHEFCNEVVWMHNNK 281 (371)
Q Consensus 241 TqEQKEKMl~FAEKL----GWR--IQK~DE~~VqqFC~EIVWMHNNK 281 (371)
..+-+++++++-.++ |-. |--||.+.+.++|.+|+||++-+
T Consensus 177 D~~~~~~l~~~l~~~~~~~~~tii~~sH~~~~~~~~~d~i~~l~~G~ 223 (228)
T cd03257 177 DVSVQAQILDLLKKLQEELGLTLLFITHDLGVVAKIADRVAVMYAGK 223 (228)
T ss_pred CHHHHHHHHHHHHHHHHHcCCEEEEEeCCHHHHHHhcCeEEEEeCCE
Confidence 456666666655444 543 35589999999999999998754
No 90
>COG3139 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.85 E-value=51 Score=28.07 Aligned_cols=21 Identities=24% Similarity=0.487 Sum_probs=13.8
Q ss_pred cCCCHHHHHHHHHHHHHhCCccc
Q 017477 238 TKFSQSQKEKMFEFAERVGWKMQ 260 (371)
Q Consensus 238 TKFTqEQKEKMl~FAEKLGWRIQ 260 (371)
+++|+||||--|... .=|..+
T Consensus 31 ~~LtqeQke~clQaV--mlwqar 51 (90)
T COG3139 31 VALTQEQKENCLQAV--MLWQAR 51 (90)
T ss_pred CcCCHHHHHHHHHHH--HHHHHh
Confidence 579999999755432 235554
No 91
>PF07796 DUF1638: Protein of unknown function (DUF1638); InterPro: IPR012437 This entry contains sequences covering an approximately 270 amino acid stretch of a group of hypothetical proteins and are confined to Bacteria and Archaea.
Probab=20.61 E-value=68 Score=28.60 Aligned_cols=26 Identities=31% Similarity=0.411 Sum_probs=21.8
Q ss_pred ccCCCHHH--HHHHHHHHHHhCCcccCC
Q 017477 237 RTKFSQSQ--KEKMFEFAERVGWKMQKR 262 (371)
Q Consensus 237 RTKFTqEQ--KEKMl~FAEKLGWRIQK~ 262 (371)
.|-..++. .++.++|||.+||.++-.
T Consensus 125 dtg~~~~~~~~~~~~~~a~~~~l~~~~~ 152 (166)
T PF07796_consen 125 DTGVYDEEDFEEKVREFAEFLGLPIEEI 152 (166)
T ss_pred ecccccchHHHHHHHHHHHHhCCCEEEE
Confidence 46666666 899999999999999865
No 92
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=20.02 E-value=78 Score=26.90 Aligned_cols=28 Identities=25% Similarity=0.432 Sum_probs=24.4
Q ss_pred CccccCCCHHHHHHHHHHHHHhCCcccC
Q 017477 234 KRFRTKFSQSQKEKMFEFAERVGWKMQK 261 (371)
Q Consensus 234 KRFRTKFTqEQKEKMl~FAEKLGWRIQK 261 (371)
|+-=+..|..|-++|++.-+++||+.++
T Consensus 16 k~S~k~lt~~el~~vl~~l~~~G~k~~~ 43 (119)
T PF06252_consen 16 KSSSKDLTEAELEKVLDELKRLGFKPPK 43 (119)
T ss_pred hhhHHHCCHHHHHHHHHHHHHccCcCcc
Confidence 5666789999999999999999998655
Done!