Query 023926
Match_columns 275
No_of_seqs 190 out of 1246
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 07:39:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023926.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023926hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10861 signal peptidase I; P 99.9 1.2E-21 2.6E-26 185.6 11.9 84 185-275 64-159 (324)
2 TIGR02227 sigpep_I_bact signal 99.8 1.5E-20 3.2E-25 160.9 11.5 84 185-275 2-85 (163)
3 KOG0171 Mitochondrial inner me 99.7 5.3E-17 1.2E-21 141.4 7.0 74 194-274 24-98 (176)
4 COG0681 LepB Signal peptidase 99.6 3.1E-15 6.8E-20 124.6 8.5 85 182-275 8-94 (166)
5 TIGR02228 sigpep_I_arch signal 99.5 4.7E-13 1E-17 115.5 10.6 53 208-270 36-88 (158)
6 TIGR02754 sod_Ni_protease nick 99.4 3.1E-12 6.8E-17 98.6 8.5 61 207-274 2-62 (90)
7 KOG1568 Mitochondrial inner me 99.3 1.4E-12 3.1E-17 113.7 4.6 73 194-273 22-100 (174)
8 PF00717 Peptidase_S24: Peptid 99.3 8E-12 1.7E-16 91.1 7.1 57 207-275 1-57 (70)
9 cd06530 S26_SPase_I The S26 Ty 99.2 7.2E-11 1.6E-15 89.6 7.6 55 205-266 2-56 (85)
10 cd06462 Peptidase_S24_S26 The 98.8 2.4E-08 5.1E-13 74.0 8.1 58 205-274 2-60 (84)
11 cd06529 S24_LexA-like Peptidas 98.8 2.9E-08 6.3E-13 73.7 7.5 56 205-274 2-57 (81)
12 PRK13838 conjugal transfer pil 98.8 4.8E-08 1E-12 85.8 9.8 57 219-275 35-103 (176)
13 TIGR02771 TraF_Ti conjugative 98.5 5.1E-07 1.1E-11 78.9 8.9 67 200-275 21-99 (171)
14 COG2932 Predicted transcriptio 98.4 5.3E-07 1.2E-11 79.9 7.1 58 204-274 124-181 (214)
15 PRK00215 LexA repressor; Valid 97.9 4.2E-05 9.1E-10 67.1 8.4 55 204-273 119-174 (205)
16 PRK12423 LexA repressor; Provi 97.8 6.7E-05 1.5E-09 66.5 8.1 55 205-274 116-171 (202)
17 PRK10276 DNA polymerase V subu 97.8 7.8E-05 1.7E-09 62.4 7.8 49 205-267 53-102 (139)
18 PRK13884 conjugal transfer pep 97.8 9.7E-05 2.1E-09 65.0 8.7 43 233-275 49-103 (178)
19 KOG3342 Signal peptidase I [In 97.8 5.1E-05 1.1E-09 66.4 6.7 41 205-247 50-90 (180)
20 TIGR00498 lexA SOS regulatory 97.8 0.00011 2.4E-09 64.1 8.5 56 204-274 112-168 (199)
21 PF10502 Peptidase_S26: Signal 97.4 3.2E-05 6.9E-10 65.2 0.0 42 234-275 21-67 (138)
22 COG1974 LexA SOS-response tran 95.2 0.098 2.1E-06 47.3 8.2 52 204-268 113-165 (201)
23 COG0681 LepB Signal peptidase 85.9 0.9 2E-05 37.6 3.5 18 257-274 137-154 (166)
24 COG4959 TraF Type IV secretory 84.7 0.36 7.9E-06 42.7 0.6 40 235-274 54-98 (173)
25 PF12518 DUF3721: Protein of u 81.6 0.61 1.3E-05 31.3 0.6 9 125-133 23-31 (34)
26 TIGR00008 infA translation ini 70.6 4 8.7E-05 31.2 2.5 22 217-241 45-66 (68)
27 COG0361 InfA Translation initi 70.2 4.4 9.5E-05 31.7 2.7 26 216-245 46-71 (75)
28 PF06890 Phage_Mu_Gp45: Bacter 60.8 23 0.00049 31.2 5.7 42 225-275 65-109 (162)
29 PRK12442 translation initiatio 55.2 12 0.00026 30.1 2.7 25 217-245 47-71 (87)
30 PF01176 eIF-1a: Translation i 54.3 8.9 0.00019 28.4 1.8 10 235-244 42-51 (65)
31 cd04456 S1_IF1A_like S1_IF1A_l 54.1 12 0.00025 29.1 2.4 26 217-244 39-64 (78)
32 PF05257 CHAP: CHAP domain; I 53.4 34 0.00075 27.4 5.2 35 233-274 61-96 (124)
33 smart00652 eIF1a eukaryotic tr 51.1 12 0.00027 29.2 2.2 24 217-243 44-67 (83)
34 cd05793 S1_IF1A S1_IF1A: Trans 50.7 13 0.00028 28.7 2.2 22 218-242 40-61 (77)
35 PRK04012 translation initiatio 50.0 13 0.00029 30.2 2.3 24 218-244 61-84 (100)
36 PF10000 ACT_3: ACT domain; I 45.1 13 0.00027 28.5 1.4 18 211-228 12-29 (72)
37 PF14085 DUF4265: Domain of un 43.2 97 0.0021 25.4 6.4 27 220-246 11-37 (117)
38 TIGR02594 conserved hypothetic 40.5 67 0.0014 26.9 5.2 13 233-245 72-84 (129)
39 COG3602 Uncharacterized protei 40.1 26 0.00056 29.9 2.6 18 211-228 12-29 (134)
40 PF14118 YfzA: YfzA-like prote 37.4 23 0.00049 28.9 1.8 16 207-222 29-44 (94)
41 PF04319 NifZ: NifZ domain; I 33.7 65 0.0014 25.2 3.7 32 213-244 1-35 (75)
42 KOG0369 Pyruvate carboxylase [ 31.9 16 0.00034 39.6 0.1 34 8-41 586-622 (1176)
43 PF09285 Elong-fact-P_C: Elong 30.0 98 0.0021 22.8 3.9 36 212-263 20-56 (56)
44 PF15057 DUF4537: Domain of un 29.6 38 0.00083 28.2 2.0 18 209-226 48-65 (124)
45 PLN00208 translation initiatio 26.9 47 0.001 29.0 2.1 27 217-246 71-97 (145)
46 TIGR00523 eIF-1A eukaryotic/ar 26.2 57 0.0012 26.5 2.4 25 217-243 58-82 (99)
47 PTZ00329 eukaryotic translatio 26.0 50 0.0011 29.2 2.1 27 217-246 71-97 (155)
48 PF00278 Orn_DAP_Arg_deC: Pyri 24.1 90 0.0019 24.3 3.1 30 215-246 65-94 (116)
49 KOG4146 Ubiquitin-like protein 23.7 86 0.0019 25.8 2.9 36 206-245 56-96 (101)
50 COG5131 URM1 Ubiquitin-like pr 23.4 83 0.0018 25.7 2.7 30 216-245 57-91 (96)
51 cd05792 S1_eIF1AD_like S1_eIF1 23.3 57 0.0012 25.5 1.8 11 219-229 41-51 (78)
52 PRK00276 infA translation init 22.5 82 0.0018 23.7 2.5 11 235-245 47-57 (72)
No 1
>PRK10861 signal peptidase I; Provisional
Probab=99.86 E-value=1.2e-21 Score=185.61 Aligned_cols=84 Identities=40% Similarity=0.634 Sum_probs=76.6
Q ss_pred HHHHHHHHHHHHHHHHceeEeEEEcCCCCcccCCCCCEEEEEecccCC------------CCCCCCcEEEEEcCCccccc
Q 023926 185 AKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFF------------KRPEVSDIVIFRAPPILQEI 252 (275)
Q Consensus 185 a~~l~iAviv~llIr~fv~~~~~V~G~SMePTL~~GDrVLV~K~~y~~------------~~pkrGDIVVFk~P~~l~~~ 252 (275)
+..++++++++++++.|+++++.|+|+||+|||++||+|+|+|+.|++ ++|+|||||||+.|.+
T Consensus 64 ~~~~~~~l~i~~~ir~fv~~~~~Ips~SM~PTL~~GD~IlVnK~~yg~~~p~~~~~~~~~~~p~RGDIVVF~~P~~---- 139 (324)
T PRK10861 64 GASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPITQTTLIETGHPKRGDIVVFKYPED---- 139 (324)
T ss_pred HHHHHHHHhHHHHHHhhEEEEEEECCCcCcCcccCCCEEEEEEeecCccCccccccccccCCCCCCCEEEEecCCC----
Confidence 566788888999999999999999999999999999999999999864 5799999999999873
Q ss_pred cCCCCceEEEEEEEeCCCEEEEC
Q 023926 253 GFSSGDVFIKRIVATAGDCVEVS 275 (275)
Q Consensus 253 g~~~~k~~IKRVIGlPGDtVeIk 275 (275)
+++.|||||||+|||+|+++
T Consensus 140 ---~~~~yIKRVIGlPGD~I~~~ 159 (324)
T PRK10861 140 ---PKLDYIKRVVGLPGDKVTYD 159 (324)
T ss_pred ---CCCcEEEEeeecCCcEEEEE
Confidence 67899999999999999983
No 2
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=99.84 E-value=1.5e-20 Score=160.87 Aligned_cols=84 Identities=36% Similarity=0.652 Sum_probs=76.8
Q ss_pred HHHHHHHHHHHHHHHHceeEeEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEE
Q 023926 185 AKAAFTALTVSFLFKSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRI 264 (275)
Q Consensus 185 a~~l~iAviv~llIr~fv~~~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRV 264 (275)
+..++++++++++++.|+++++.|+|+||+|||++||+|+++|..|...++++||||+|+.|.+ .++.+||||
T Consensus 2 ~~~~~~~~~~~~~i~~~~~~~~~v~g~SM~Ptl~~Gd~vlv~k~~~~~~~~~rGDiVvf~~~~~-------~~~~~iKRV 74 (163)
T TIGR02227 2 ILSLLIAILLALLIRTFVFFPYKIPGGSMEPTLKEGDRILVNKFAYGTSDPKRGDIVVFKDPDD-------NKNIYVKRV 74 (163)
T ss_pred HHHHHHHHHHHHHHHhhEEEEEEECCcccccchhCCCEEEEEEeEcCCCCCCCCcEEEEecCCC-------CCceeEEEE
Confidence 5667788888999999999999999999999999999999999988788999999999998752 578999999
Q ss_pred EEeCCCEEEEC
Q 023926 265 VATAGDCVEVS 275 (275)
Q Consensus 265 IGlPGDtVeIk 275 (275)
+|+|||+|+++
T Consensus 75 ig~pGd~v~i~ 85 (163)
T TIGR02227 75 IGLPGDKVEFR 85 (163)
T ss_pred EecCCCEEEEE
Confidence 99999999874
No 3
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.68 E-value=5.3e-17 Score=141.39 Aligned_cols=74 Identities=46% Similarity=0.687 Sum_probs=65.3
Q ss_pred HHHHHHHceeEeEEEcCCCCcccCCC-CCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEE
Q 023926 194 VSFLFKSFLAEPRSIPSASMNPTLDV-GDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCV 272 (275)
Q Consensus 194 v~llIr~fv~~~~~V~G~SMePTL~~-GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtV 272 (275)
++.+...|++++..++|.||+|||++ ||+|+++|++|.++++++||||+++.|.+ .++++||||||+|||.|
T Consensus 24 f~h~t~~yl~e~~~~~gpSM~PTl~~~gd~l~aEkls~~f~~~~~gDIVi~~sP~~-------~~~~~cKRIva~eGD~v 96 (176)
T KOG0171|consen 24 FTHVTHEYLGEFVMCSGPSMEPTLHDGGDVLLAEKLSYRFRKPQVGDIVIAKSPPD-------PKEHICKRIVAMEGDLV 96 (176)
T ss_pred HHHHHHHHhcceeeccCCCcCceecCCCcEEehhhhhHhhcCCCCCCEEEEeCCCC-------chhhhhheeeccCCceE
Confidence 34455669999999999999998887 67777799999999999999999999985 78899999999999987
Q ss_pred EE
Q 023926 273 EV 274 (275)
Q Consensus 273 eI 274 (275)
++
T Consensus 97 ~v 98 (176)
T KOG0171|consen 97 EV 98 (176)
T ss_pred EE
Confidence 75
No 4
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=99.60 E-value=3.1e-15 Score=124.63 Aligned_cols=85 Identities=35% Similarity=0.609 Sum_probs=74.2
Q ss_pred hhhHHHHHHHHHHHHHH--HHceeEeEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCce
Q 023926 182 SDDAKAAFTALTVSFLF--KSFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDV 259 (275)
Q Consensus 182 ~~~a~~l~iAviv~llI--r~fv~~~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~ 259 (275)
.+++..++.++++++++ +.|+++++.|+|+||+|||+.||+|+++|..|....+..+|++ ..|. ..+..
T Consensus 8 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~V~s~SM~Ptl~~GD~v~v~k~~~~~~~~~~~~~~--~~~~-------~~~~~ 78 (166)
T COG0681 8 LELISSLLIAIILALIIGVRTFVFEPVVVPSGSMEPTLNVGDRVLVKKFSYGFGKLKVPDII--VLPA-------VVEGD 78 (166)
T ss_pred HHHHHHHHHHHHHhheeeeEEEEEEEEEECCCccccccccCCEEEEEeccccccCCccceee--ecCC-------CCCcc
Confidence 45577777888888888 8999999999999999999999999999999998889999988 3332 36789
Q ss_pred EEEEEEEeCCCEEEEC
Q 023926 260 FIKRIVATAGDCVEVS 275 (275)
Q Consensus 260 ~IKRVIGlPGDtVeIk 275 (275)
++||+++++||.|.++
T Consensus 79 ~~kr~~~~~GD~i~~~ 94 (166)
T COG0681 79 LIKRVIGLRGDIVVFK 94 (166)
T ss_pred eEEEeccCCCCEEEEE
Confidence 9999999999999874
No 5
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=99.45 E-value=4.7e-13 Score=115.45 Aligned_cols=53 Identities=25% Similarity=0.463 Sum_probs=46.5
Q ss_pred EcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCC
Q 023926 208 IPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGD 270 (275)
Q Consensus 208 V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGD 270 (275)
|.|+||+|||++||++++++.. ..++++||||+|++|. .++.++|||+++.++
T Consensus 36 V~g~SM~Ptl~~GD~vlv~~~~--~~~~~~GDIVvf~~~~--------~~~~iihRVi~v~~~ 88 (158)
T TIGR02228 36 VLSGSMEPTFNTGDLILVTGAD--PNDIQVGDVITYKSPG--------FNTPVTHRVIEINNS 88 (158)
T ss_pred EcCCCCcCCccCCCEEEEEecc--cCCCCCCCEEEEEECC--------CCccEEEEEEEEECC
Confidence 9999999999999999999954 3589999999999874 338899999998754
No 6
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=99.36 E-value=3.1e-12 Score=98.60 Aligned_cols=61 Identities=30% Similarity=0.499 Sum_probs=51.4
Q ss_pred EEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEE
Q 023926 207 SIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274 (275)
Q Consensus 207 ~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeI 274 (275)
.|+|+||+|||++||+|+|++.......+++||+|+|+.|.. +++.+|||+++++++.+.+
T Consensus 2 ~V~g~SM~P~l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~~~-------~~~~~vkRv~~~~~~~~~l 62 (90)
T TIGR02754 2 KVTGVSMSPTLPPGDRIIVVPWLKIFRVPPIGNVVVVRHPLQ-------PYGLIIKRLAAVDDNGLFL 62 (90)
T ss_pred EeeCCCccCccCCCCEEEEEEccccCCCCCCCeEEEEecCCC-------CcceEEEEeeEEcCCeEEE
Confidence 689999999999999999998644345567899999998752 4689999999999888765
No 7
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.31 E-value=1.4e-12 Score=113.72 Aligned_cols=73 Identities=29% Similarity=0.417 Sum_probs=63.7
Q ss_pred HHHHHHHceeEeEEEcCCCCcccCCCC------CEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEe
Q 023926 194 VSFLFKSFLAEPRSIPSASMNPTLDVG------DRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT 267 (275)
Q Consensus 194 v~llIr~fv~~~~~V~G~SMePTL~~G------DrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGl 267 (275)
+.+.+...+.....|.|.||+|||+++ |+|+++|+...-+.+.|||||+|++|.+ +++++||||+|+
T Consensus 22 v~~t~~DrV~~va~v~G~smqPtlnP~~~~~~~d~Vll~k~~v~n~~~~rGDiVvl~sP~~-------p~~~~iKRv~al 94 (174)
T KOG1568|consen 22 VLLTFSDRVVHVAQVYGSSMQPTLNPTMNTNEKDTVLLRKWNVKNRKVSRGDIVVLKSPND-------PDKVIIKRVAAL 94 (174)
T ss_pred eeeeeeeeEEEEeEEecCcCCCccCCCcccccccEEEEEeeccccceeccCCEEEEeCCCC-------hhheeeeeeecc
Confidence 345566778889999999999999984 9999999975446789999999999984 899999999999
Q ss_pred CCCEEE
Q 023926 268 AGDCVE 273 (275)
Q Consensus 268 PGDtVe 273 (275)
|||++.
T Consensus 95 egd~~~ 100 (174)
T KOG1568|consen 95 EGDIMV 100 (174)
T ss_pred cccEec
Confidence 999974
No 8
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=99.29 E-value=8e-12 Score=91.12 Aligned_cols=57 Identities=32% Similarity=0.591 Sum_probs=46.8
Q ss_pred EEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEEC
Q 023926 207 SIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEVS 275 (275)
Q Consensus 207 ~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeIk 275 (275)
+|.|+||+|+|++||+|++++.. .++.||+|+|+.+. .+..+|||+++.+|+.+.+.
T Consensus 1 ~V~GdSM~P~i~~Gd~v~v~~~~----~~~~gdivv~~~~~--------~~~~~iKrv~~~~~~~~~~~ 57 (70)
T PF00717_consen 1 RVEGDSMEPTIKDGDIVLVDPSS----EPKDGDIVVVKIDG--------DEELYIKRVVGEPGGIILIS 57 (70)
T ss_dssp EEESSTTGGTSSTTEEEEEEETS-------TTSEEEEEETT--------EESEEEEEEEEETTEEEEE-
T ss_pred CeECcCcccCeeCCCEEEEEEcC----CCccCeEEEEEECC--------ceeeEEEEEEEeCCCEEEEe
Confidence 58999999999999999999874 89999999999853 11399999999999998763
No 9
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=99.19 E-value=7.2e-11 Score=89.63 Aligned_cols=55 Identities=42% Similarity=0.810 Sum_probs=47.5
Q ss_pred eEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEE
Q 023926 205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVA 266 (275)
Q Consensus 205 ~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIG 266 (275)
.+.|.|+||+|++++||+|++++....+..+++||||+|+.+.. .++.++|||++
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~~-------~~~~~vkRv~~ 56 (85)
T cd06530 2 PVVVPGGSMEPTLQPGDLVLVNKLSYGFREPKRGDVVVFKSPGD-------PGKPIIKRVIG 56 (85)
T ss_pred eeEEcCCCCcCcccCCCEEEEEEeecccCCCCCCCEEEEeCCCC-------CCCEEEEEEEE
Confidence 57899999999999999999999864445799999999998741 36899999987
No 10
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=98.81 E-value=2.4e-08 Score=74.02 Aligned_cols=58 Identities=34% Similarity=0.619 Sum_probs=49.3
Q ss_pred eEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCC-CEEEE
Q 023926 205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAG-DCVEV 274 (275)
Q Consensus 205 ~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPG-DtVeI 274 (275)
.+.|.|+||+|++.+||.|++++.. ..++.||+|+++.+ .+..+|||+...++ +.+.+
T Consensus 2 ~~~v~g~SM~P~i~~gd~v~i~~~~---~~~~~G~iv~~~~~---------~~~~~ikrl~~~~~~~~~~l 60 (84)
T cd06462 2 ALRVEGDSMEPTIPDGDLVLVDKSS---YEPKRGDIVVFRLP---------GGELTVKRVIGLPGEGHYFL 60 (84)
T ss_pred eeEEcCCCccCcccCCCEEEEEecC---CCCcCCEEEEEEcC---------CCcEEEEEEEEECCCCEEEE
Confidence 4689999999999999999999864 24899999999973 24899999999997 66654
No 11
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=98.77 E-value=2.9e-08 Score=73.72 Aligned_cols=56 Identities=29% Similarity=0.517 Sum_probs=49.1
Q ss_pred eEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEE
Q 023926 205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274 (275)
Q Consensus 205 ~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeI 274 (275)
.+.|.|+||+|++++||.|++++.. .++.||++++.. +++.+|||+...+++.+.+
T Consensus 2 ~~~v~g~sM~p~i~~gd~lii~~~~----~~~~g~i~~~~~----------~~~~~ikr~~~~~~~~~~L 57 (81)
T cd06529 2 ALRVKGDSMEPTIPDGDLVLVDPSD----TPRDGDIVVARL----------DGELTVKRLQRRGGGRLRL 57 (81)
T ss_pred EEEEECCCcCCccCCCCEEEEcCCC----CCCCCCEEEEEE----------CCEEEEEEEEECCCCcEEE
Confidence 4689999999999999999999863 599999999997 3488999999999777665
No 12
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=98.76 E-value=4.8e-08 Score=85.76 Aligned_cols=57 Identities=21% Similarity=0.261 Sum_probs=42.2
Q ss_pred CCCEEEEEecccCCCCCCCCcEEEEEcCCcccc-----ccC-C------CCceEEEEEEEeCCCEEEEC
Q 023926 219 VGDRILAEKVSYFFKRPEVSDIVIFRAPPILQE-----IGF-S------SGDVFIKRIVATAGDCVEVS 275 (275)
Q Consensus 219 ~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~-----~g~-~------~~k~~IKRVIGlPGDtVeIk 275 (275)
+.+.+.+.++.+..+.+++||+|+|+.|...+. .++ . ....+||||+|+|||+|+++
T Consensus 35 ~S~pig~y~~~~~~~~~~rGDiVvf~~P~~~~~~~a~~r~yl~~g~~p~~~~~~iKRViglpGD~V~i~ 103 (176)
T PRK13838 35 PSEPLGLWRIEALDRPVAVGDLVFICPPETAAFREARERGYLRRGLCPGGFAPLIKTVAALAGQRVEIG 103 (176)
T ss_pred CCCEEEEEEEeccCCCCCCCcEEEEECCchhhhhhhhhcccccccccccCCCceEEEEEEeCCcEEEEC
Confidence 467888999876668899999999998753210 011 0 12469999999999999975
No 13
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=98.51 E-value=5.1e-07 Score=78.88 Aligned_cols=67 Identities=25% Similarity=0.276 Sum_probs=41.7
Q ss_pred HceeEeEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCcccc-----ccC-CC------CceEEEEEEEe
Q 023926 200 SFLAEPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQE-----IGF-SS------GDVFIKRIVAT 267 (275)
Q Consensus 200 ~fv~~~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~-----~g~-~~------~k~~IKRVIGl 267 (275)
.|......=.++||-..+ +. +.+ .+.++|||||+|+.|.+.+. .++ .. ...+||||+|+
T Consensus 21 ~~~~~~~~N~T~S~P~g~----Y~-~~~----~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRVigl 91 (171)
T TIGR02771 21 LYCVGARINTTKSLPLGL----YW-TTS----SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGL 91 (171)
T ss_pred cceeeEEEECCCCCcceE----EE-eCC----CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEe
Confidence 334334445566665544 33 222 25899999999998753210 011 11 13799999999
Q ss_pred CCCEEEEC
Q 023926 268 AGDCVEVS 275 (275)
Q Consensus 268 PGDtVeIk 275 (275)
|||+|+++
T Consensus 92 pGD~V~i~ 99 (171)
T TIGR02771 92 PGDRVTVR 99 (171)
T ss_pred CCCEEEEE
Confidence 99999974
No 14
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=98.43 E-value=5.3e-07 Score=79.89 Aligned_cols=58 Identities=21% Similarity=0.403 Sum_probs=49.0
Q ss_pred EeEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEE
Q 023926 204 EPRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274 (275)
Q Consensus 204 ~~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeI 274 (275)
....|.|+||+|++++||.|+|+.- .+..+||.|++..- .++.||||+...||-.+++
T Consensus 124 ~~i~V~GDSMeP~~~~Gd~ilVd~~----~~~~~gd~v~v~~~---------g~~~~VK~l~~~~~~~~~l 181 (214)
T COG2932 124 FALRVTGDSMEPTYEDGDTLLVDPG----VNTRRGDRVYVETD---------GGELYVKKLQREPGGLLRL 181 (214)
T ss_pred EEEEEeCCcccccccCCCEEEECCC----CceeeCCEEEEEEe---------CCeEEEEEEEEecCCeEEE
Confidence 3579999999999999999999986 36788997777652 4699999999999988754
No 15
>PRK00215 LexA repressor; Validated
Probab=97.93 E-value=4.2e-05 Score=67.07 Aligned_cols=55 Identities=18% Similarity=0.216 Sum_probs=44.4
Q ss_pred EeEEEcCCCCc-ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEE
Q 023926 204 EPRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVE 273 (275)
Q Consensus 204 ~~~~V~G~SMe-PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVe 273 (275)
..+.|.|+||. |++.+||+|+|++. ..++.||||++.. +++.+|||+.-. ++.++
T Consensus 119 ~~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivv~~~----------~~~~~vKrl~~~-~~~~~ 174 (205)
T PRK00215 119 FLLRVRGDSMIDAGILDGDLVIVRKQ----QTARNGQIVVALI----------DDEATVKRFRRE-GGHIR 174 (205)
T ss_pred EEEEEccCCCCCCCcCCCCEEEEeCC----CCCCCCCEEEEEE----------CCEEEEEEEEEe-CCEEE
Confidence 45789999995 79999999999974 3678999999986 348899999876 44444
No 16
>PRK12423 LexA repressor; Provisional
Probab=97.84 E-value=6.7e-05 Score=66.47 Aligned_cols=55 Identities=25% Similarity=0.342 Sum_probs=44.4
Q ss_pred eEEEcCCCCc-ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEE
Q 023926 205 PRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274 (275)
Q Consensus 205 ~~~V~G~SMe-PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeI 274 (275)
.+.|.|+||. |+|.+||.|+|++- ..++.||||++.. +++.+|||+.-. ++.+++
T Consensus 116 ~l~V~GdSM~~~~i~~Gd~viv~~~----~~~~~Gdivv~~~----------~~~~~vKrl~~~-~~~~~L 171 (202)
T PRK12423 116 LLQVQGDSMIDDGILDGDLVGVHRS----PEARDGQIVVARL----------DGEVTIKRLERS-GDRIRL 171 (202)
T ss_pred EEEEecCcCCCCCcCCCCEEEEeCC----CcCCCCCEEEEEE----------CCEEEEEEEEEe-CCEEEE
Confidence 4799999997 79999999999975 3688999999986 357889998765 455543
No 17
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=97.82 E-value=7.8e-05 Score=62.41 Aligned_cols=49 Identities=20% Similarity=0.286 Sum_probs=41.1
Q ss_pred eEEEcCCCCc-ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEe
Q 023926 205 PRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT 267 (275)
Q Consensus 205 ~~~V~G~SMe-PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGl 267 (275)
.++|.|+||+ |++.+||+|+|++-. .++.||+|++.. +++..+||+.-.
T Consensus 53 ~l~V~GdSM~~~~I~~GD~liVd~~~----~~~~Gdivv~~~----------~g~~~vKrl~~~ 102 (139)
T PRK10276 53 FVKASGDSMIDAGISDGDLLIVDSAI----TASHGDIVIAAV----------DGEFTVKKLQLR 102 (139)
T ss_pred EEEEecCCCCCCCCCCCCEEEEECCC----CCCCCCEEEEEE----------CCEEEEEEEEEC
Confidence 4799999998 689999999999753 578999999875 457889998864
No 18
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=97.82 E-value=9.7e-05 Score=64.99 Aligned_cols=43 Identities=33% Similarity=0.479 Sum_probs=30.5
Q ss_pred CCCCCCcEEEEEcCCcc-----cccc-----CC--CCceEEEEEEEeCCCEEEEC
Q 023926 233 KRPEVSDIVIFRAPPIL-----QEIG-----FS--SGDVFIKRIVATAGDCVEVS 275 (275)
Q Consensus 233 ~~pkrGDIVVFk~P~~l-----~~~g-----~~--~~k~~IKRVIGlPGDtVeIk 275 (275)
..+++||+|+|..|... .+.+ +. ....+||||+|+|||+|+++
T Consensus 49 ~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD~V~~~ 103 (178)
T PRK13884 49 APVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGDAVSVT 103 (178)
T ss_pred CCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCcEEEEE
Confidence 46899999999876521 0111 11 12479999999999999874
No 19
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=97.81 E-value=5.1e-05 Score=66.45 Aligned_cols=41 Identities=27% Similarity=0.378 Sum_probs=33.9
Q ss_pred eEEEcCCCCcccCCCCCEEEEEecccCCCCCCCCcEEEEEcCC
Q 023926 205 PRSIPSASMNPTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPP 247 (275)
Q Consensus 205 ~~~V~G~SMePTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~ 247 (275)
.+.|-++||||.++.||.++..... -...+.||||||+-+.
T Consensus 50 iVVVLSgSMePaF~RGDlLfL~N~~--~~p~~vGdivVf~veg 90 (180)
T KOG3342|consen 50 IVVVLSGSMEPAFHRGDLLFLTNRN--EDPIRVGDIVVFKVEG 90 (180)
T ss_pred EEEEEcCCcCcccccccEEEEecCC--CCcceeccEEEEEECC
Confidence 4789999999999999999987542 1346889999999864
No 20
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=97.79 E-value=0.00011 Score=64.13 Aligned_cols=56 Identities=25% Similarity=0.281 Sum_probs=45.7
Q ss_pred EeEEEcCCCCc-ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeCCCEEEE
Q 023926 204 EPRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATAGDCVEV 274 (275)
Q Consensus 204 ~~~~V~G~SMe-PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlPGDtVeI 274 (275)
..+.|.|+||+ |++.+||+|++++. ..++.||||++.. +++.+|||+.-. |+.+++
T Consensus 112 f~~~V~GdSM~~~~i~~Gd~v~v~~~----~~~~~G~ivvv~~----------~~~~~vKrl~~~-~~~i~L 168 (199)
T TIGR00498 112 FLLKVMGDSMVDAGICDGDLLIVRSQ----KDARNGEIVAAMI----------DGEVTVKRFYKD-GTKVEL 168 (199)
T ss_pred EEEEecCCCCCCCCCCCCCEEEEecC----CCCCCCCEEEEEE----------CCEEEEEEEEEE-CCEEEE
Confidence 46799999996 68999999999975 4789999999986 467899998765 555544
No 21
>PF10502 Peptidase_S26: Signal peptidase, peptidase S26 ; InterPro: IPR019533 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents a conserved region found in the S26A family of serine endopeptidases, which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. ; PDB: 3S04_B 1KN9_C 1B12_D 3IIQ_B 1T7D_A.
Probab=97.43 E-value=3.2e-05 Score=65.18 Aligned_cols=42 Identities=40% Similarity=0.712 Sum_probs=0.0
Q ss_pred CCCCCcEEEEEcCCccc----cccC-CCCceEEEEEEEeCCCEEEEC
Q 023926 234 RPEVSDIVIFRAPPILQ----EIGF-SSGDVFIKRIVATAGDCVEVS 275 (275)
Q Consensus 234 ~pkrGDIVVFk~P~~l~----~~g~-~~~k~~IKRVIGlPGDtVeIk 275 (275)
.+++||+|+|..|.... +.++ ..+..+||||+|+|||+|+++
T Consensus 21 ~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD~V~v~ 67 (138)
T PF10502_consen 21 KIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGDTVEVT 67 (138)
T ss_dssp -----------------------------------------------
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 47999999999886321 1122 346699999999999999874
No 22
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=95.20 E-value=0.098 Score=47.31 Aligned_cols=52 Identities=19% Similarity=0.217 Sum_probs=41.4
Q ss_pred EeEEEcCCCCc-ccCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEEEEEeC
Q 023926 204 EPRSIPSASMN-PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVATA 268 (275)
Q Consensus 204 ~~~~V~G~SMe-PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGlP 268 (275)
...+|.|+||. +.+.+||.|+|++- ...+.||||+..-+ .++.-+||..-..
T Consensus 113 f~L~V~GdSM~~~gi~dGDlvvV~~~----~~a~~GdiVvA~i~---------g~e~TvKrl~~~g 165 (201)
T COG1974 113 FFLRVSGDSMIDAGILDGDLVVVDPT----EDAENGDIVVALID---------GEEATVKRLYRDG 165 (201)
T ss_pred EEEEecCCccccCcCCCCCEEEEcCC----CCCCCCCEEEEEcC---------CCcEEEEEEEEeC
Confidence 45799999996 56777999999986 58899999999873 3457788876544
No 23
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=85.91 E-value=0.9 Score=37.64 Aligned_cols=18 Identities=28% Similarity=0.517 Sum_probs=15.9
Q ss_pred CceEEEEEEEeCCCEEEE
Q 023926 257 GDVFIKRIVATAGDCVEV 274 (275)
Q Consensus 257 ~k~~IKRVIGlPGDtVeI 274 (275)
...++||++++|||.+.+
T Consensus 137 ~~~~~~~~~~~~gd~~~~ 154 (166)
T COG0681 137 KKDYIKRVIGLPGDNILY 154 (166)
T ss_pred ccccccceEEeeccceee
Confidence 477999999999999875
No 24
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=84.73 E-value=0.36 Score=42.73 Aligned_cols=40 Identities=25% Similarity=0.369 Sum_probs=29.9
Q ss_pred CCCCcEEEEEcCCcc----ccccC-CCCceEEEEEEEeCCCEEEE
Q 023926 235 PEVSDIVIFRAPPIL----QEIGF-SSGDVFIKRIVATAGDCVEV 274 (275)
Q Consensus 235 pkrGDIVVFk~P~~l----~~~g~-~~~k~~IKRVIGlPGDtVeI 274 (275)
+.+||+|++..|... ..-|| ...-..+|||.|+|||+|.+
T Consensus 54 vt~g~lV~v~pP~~~a~~aA~RGYLp~~~pllK~i~Alpgq~Vci 98 (173)
T COG4959 54 VTKGDLVLVCPPQRAAFLAAQRGYLPPYIPLLKRILALPGQHVCI 98 (173)
T ss_pred cccCCEEEECCCchHhHhHhhcCccccccHHHHHHhcCCCCcEEE
Confidence 489999999887631 11233 35667899999999999976
No 25
>PF12518 DUF3721: Protein of unknown function; InterPro: IPR022196 This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length. There is a conserved WMPC sequence motif. There are two completely conserved residues (A and C) that may be functionally important.
Probab=81.57 E-value=0.61 Score=31.33 Aligned_cols=9 Identities=56% Similarity=1.782 Sum_probs=7.9
Q ss_pred cCccccCCC
Q 023926 125 GSKWLPCNE 133 (275)
Q Consensus 125 ~~kwlpc~~ 133 (275)
+.||+||++
T Consensus 23 g~~WMPC~~ 31 (34)
T PF12518_consen 23 GDKWMPCSN 31 (34)
T ss_pred cCccccCcc
Confidence 689999985
No 26
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=70.62 E-value=4 Score=31.22 Aligned_cols=22 Identities=23% Similarity=0.308 Sum_probs=15.3
Q ss_pred CCCCCEEEEEecccCCCCCCCCcEE
Q 023926 217 LDVGDRILAEKVSYFFKRPEVSDIV 241 (275)
Q Consensus 217 L~~GDrVLV~K~~y~~~~pkrGDIV 241 (275)
+.+||+|.|+.+.| ++.+||||
T Consensus 45 I~~GD~V~Ve~spy---d~tkgrIi 66 (68)
T TIGR00008 45 ILPGDKVKVELSPY---DLTRGRIT 66 (68)
T ss_pred ECCCCEEEEEECcc---cCCcEeEE
Confidence 44678888877765 56777775
No 27
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=70.18 E-value=4.4 Score=31.66 Aligned_cols=26 Identities=31% Similarity=0.420 Sum_probs=19.5
Q ss_pred cCCCCCEEEEEecccCCCCCCCCcEEEEEc
Q 023926 216 TLDVGDRILAEKVSYFFKRPEVSDIVIFRA 245 (275)
Q Consensus 216 TL~~GDrVLV~K~~y~~~~pkrGDIVVFk~ 245 (275)
-+.+||+|+|+.+.| ++++|||+ |++
T Consensus 46 ~I~~GD~V~Ve~~~~---d~~kg~I~-~Ry 71 (75)
T COG0361 46 RILPGDVVLVELSPY---DLTKGRIV-YRY 71 (75)
T ss_pred EeCCCCEEEEEeccc---ccccccEE-EEe
Confidence 466899999998875 57888875 443
No 28
>PF06890 Phage_Mu_Gp45: Bacteriophage Mu Gp45 protein; InterPro: IPR014462 This entry is represented by the Bacteriophage Mu, Gp45. The characteristics of the protein distribution suggest prophage matches.
Probab=60.81 E-value=23 Score=31.24 Aligned_cols=42 Identities=19% Similarity=0.336 Sum_probs=30.8
Q ss_pred EEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEE---EEEeCCCEEEEC
Q 023926 225 AEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKR---IVATAGDCVEVS 275 (275)
Q Consensus 225 V~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKR---VIGlPGDtVeIk 275 (275)
++.-.|+...++.||+++|... ...+++|| +|...+++++|+
T Consensus 65 ~~d~~yR~~~L~~GEvalY~~~---------G~~I~L~~~G~ii~~~~~~~~v~ 109 (162)
T PF06890_consen 65 VEDRRYRPKGLKPGEVALYDDE---------GQKIHLKRDGRIIEVTCKTVTVN 109 (162)
T ss_pred eCCccccccCCCCCcEEEEcCC---------CCEEEEEecceEEeccCceEEEe
Confidence 3444567778999999999863 45677776 777888888763
No 29
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=55.16 E-value=12 Score=30.11 Aligned_cols=25 Identities=32% Similarity=0.436 Sum_probs=18.5
Q ss_pred CCCCCEEEEEecccCCCCCCCCcEEEEEc
Q 023926 217 LDVGDRILAEKVSYFFKRPEVSDIVIFRA 245 (275)
Q Consensus 217 L~~GDrVLV~K~~y~~~~pkrGDIVVFk~ 245 (275)
+.+||+|.|+-+.| ++.+|+|| |++
T Consensus 47 Il~GD~V~VE~spY---DltkGRIi-yR~ 71 (87)
T PRK12442 47 ILAGDRVTLELSPY---DLTKGRIN-FRH 71 (87)
T ss_pred ecCCCEEEEEECcc---cCCceeEE-EEe
Confidence 44699999998875 57888874 554
No 30
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=54.28 E-value=8.9 Score=28.36 Aligned_cols=10 Identities=20% Similarity=0.315 Sum_probs=4.0
Q ss_pred CCCCcEEEEE
Q 023926 235 PEVSDIVIFR 244 (275)
Q Consensus 235 pkrGDIVVFk 244 (275)
+++||.|+..
T Consensus 42 I~~GD~V~V~ 51 (65)
T PF01176_consen 42 IKRGDFVLVE 51 (65)
T ss_dssp --TTEEEEEE
T ss_pred cCCCCEEEEE
Confidence 4445555444
No 31
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=54.06 E-value=12 Score=29.12 Aligned_cols=26 Identities=15% Similarity=0.322 Sum_probs=15.7
Q ss_pred CCCCCEEEEEecccCCCCCCCCcEEEEE
Q 023926 217 LDVGDRILAEKVSYFFKRPEVSDIVIFR 244 (275)
Q Consensus 217 L~~GDrVLV~K~~y~~~~pkrGDIVVFk 244 (275)
+..||+|+|+...| .+..+||||--.
T Consensus 39 I~~GD~VlV~~~~~--~~~~kg~Iv~r~ 64 (78)
T cd04456 39 IKRGDFLIVDPIEE--GEDVKADIIFVY 64 (78)
T ss_pred EcCCCEEEEEeccc--CCCceEEEEEEe
Confidence 34577777776654 245677765443
No 32
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=53.36 E-value=34 Score=27.38 Aligned_cols=35 Identities=20% Similarity=0.404 Sum_probs=20.2
Q ss_pred CCCCCCcEEEEEcCCccccccCCCCceEEEEEEEe-CCCEEEE
Q 023926 233 KRPEVSDIVIFRAPPILQEIGFSSGDVFIKRIVAT-AGDCVEV 274 (275)
Q Consensus 233 ~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKRVIGl-PGDtVeI 274 (275)
..|+.||||+|.... ...-=.|-=|.+. .+++|.+
T Consensus 61 ~~P~~Gdivv~~~~~-------~~~~GHVaIV~~v~~~~~i~v 96 (124)
T PF05257_consen 61 STPQPGDIVVWDSGS-------GGGYGHVAIVESVNDGGTITV 96 (124)
T ss_dssp S---TTEEEEEEECT-------TTTT-EEEEEEEE-TTSEEEE
T ss_pred cccccceEEEeccCC-------CCCCCeEEEEEEECCCCEEEE
Confidence 579999999995221 1233356667777 7777765
No 33
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=51.15 E-value=12 Score=29.24 Aligned_cols=24 Identities=21% Similarity=0.387 Sum_probs=15.2
Q ss_pred CCCCCEEEEEecccCCCCCCCCcEEEE
Q 023926 217 LDVGDRILAEKVSYFFKRPEVSDIVIF 243 (275)
Q Consensus 217 L~~GDrVLV~K~~y~~~~pkrGDIVVF 243 (275)
+..||+|+|+...| +..+||||--
T Consensus 44 I~~GD~VlVe~~~~---~~~kg~Iv~r 67 (83)
T smart00652 44 IRRGDIVLVDPWDF---QDVKADIIYK 67 (83)
T ss_pred EcCCCEEEEEecCC---CCCEEEEEEE
Confidence 34578888877664 3567775433
No 34
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=50.74 E-value=13 Score=28.74 Aligned_cols=22 Identities=23% Similarity=0.498 Sum_probs=14.5
Q ss_pred CCCCEEEEEecccCCCCCCCCcEEE
Q 023926 218 DVGDRILAEKVSYFFKRPEVSDIVI 242 (275)
Q Consensus 218 ~~GDrVLV~K~~y~~~~pkrGDIVV 242 (275)
.+||+|+|+...| +..+|||+-
T Consensus 40 ~~GD~V~Ve~~~~---d~~kg~Iv~ 61 (77)
T cd05793 40 NEGDIVLVAPWDF---QDDKADIIY 61 (77)
T ss_pred cCCCEEEEEeccc---cCCEEEEEE
Confidence 4577777776654 466777643
No 35
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=50.01 E-value=13 Score=30.24 Aligned_cols=24 Identities=21% Similarity=0.339 Sum_probs=17.4
Q ss_pred CCCCEEEEEecccCCCCCCCCcEEEEE
Q 023926 218 DVGDRILAEKVSYFFKRPEVSDIVIFR 244 (275)
Q Consensus 218 ~~GDrVLV~K~~y~~~~pkrGDIVVFk 244 (275)
..||+|+|+.+.| ++.+||||--.
T Consensus 61 ~~GD~VlVe~~~~---~~~kg~Iv~r~ 84 (100)
T PRK04012 61 REGDVVIVAPWDF---QDEKADIIWRY 84 (100)
T ss_pred cCCCEEEEEeccc---CCCEEEEEEEc
Confidence 4689999988775 36788876443
No 36
>PF10000 ACT_3: ACT domain; InterPro: IPR018717 This domain has no known function.; PDB: 1ZVP_C.
Probab=45.11 E-value=13 Score=28.55 Aligned_cols=18 Identities=33% Similarity=0.578 Sum_probs=12.6
Q ss_pred CCCcccCCCCCEEEEEec
Q 023926 211 ASMNPTLDVGDRILAEKV 228 (275)
Q Consensus 211 ~SMePTL~~GDrVLV~K~ 228 (275)
.||+|.|++|++||+.--
T Consensus 12 ~~m~P~L~~~~yVF~t~~ 29 (72)
T PF10000_consen 12 ASMSPELNPGEYVFCTVP 29 (72)
T ss_dssp ST-EEEE-SS-EEEEEE-
T ss_pred hhCCcEeCCCCEEEEEec
Confidence 489999999999999764
No 37
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=43.22 E-value=97 Score=25.38 Aligned_cols=27 Identities=15% Similarity=0.256 Sum_probs=22.0
Q ss_pred CCEEEEEecccCCCCCCCCcEEEEEcC
Q 023926 220 GDRILAEKVSYFFKRPEVSDIVIFRAP 246 (275)
Q Consensus 220 GDrVLV~K~~y~~~~pkrGDIVVFk~P 246 (275)
+|..-+...++...++..||+|.++..
T Consensus 11 ~~~y~l~n~Pf~a~glA~gDvV~~~~~ 37 (117)
T PF14085_consen 11 DDTYRLDNIPFFAYGLALGDVVRAEPD 37 (117)
T ss_pred CCEEEEEecccccCCCCCCCEEEEEeC
Confidence 567777777776789999999999974
No 38
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=40.51 E-value=67 Score=26.94 Aligned_cols=13 Identities=23% Similarity=0.373 Sum_probs=10.0
Q ss_pred CCCCCCcEEEEEc
Q 023926 233 KRPEVSDIVIFRA 245 (275)
Q Consensus 233 ~~pkrGDIVVFk~ 245 (275)
.+|+.||||+|+.
T Consensus 72 ~~p~~GDiv~f~~ 84 (129)
T TIGR02594 72 SKPAYGCIAVKRR 84 (129)
T ss_pred CCCCccEEEEEEC
Confidence 3678888888864
No 39
>COG3602 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.10 E-value=26 Score=29.92 Aligned_cols=18 Identities=39% Similarity=0.508 Sum_probs=15.4
Q ss_pred CCCcccCCCCCEEEEEec
Q 023926 211 ASMNPTLDVGDRILAEKV 228 (275)
Q Consensus 211 ~SMePTL~~GDrVLV~K~ 228 (275)
.||.|.|.+||+|+..--
T Consensus 12 ~smtPeL~~G~yVfcT~~ 29 (134)
T COG3602 12 ASMTPELLDGDYVFCTVA 29 (134)
T ss_pred HhcCccccCCceEEEEec
Confidence 389999999999998653
No 40
>PF14118 YfzA: YfzA-like protein
Probab=37.37 E-value=23 Score=28.92 Aligned_cols=16 Identities=19% Similarity=0.372 Sum_probs=13.6
Q ss_pred EEcCCCCcccCCCCCE
Q 023926 207 SIPSASMNPTLDVGDR 222 (275)
Q Consensus 207 ~V~G~SMePTL~~GDr 222 (275)
.+++.++.|.+++||.
T Consensus 29 ~~d~t~w~pnf~~g~~ 44 (94)
T PF14118_consen 29 IFDGTGWGPNFNEGDF 44 (94)
T ss_pred HhhccccccccCCCch
Confidence 4579999999999874
No 41
>PF04319 NifZ: NifZ domain; InterPro: IPR007415 NifZ is a short protein is found in the nif (nitrogen fixation) operon. It is required for the maturation of the nitrogenase MoFe protein. In the absence of NifZ, only one of the two P-clusters of the MoFe protein is matured to the ultimate [8Fe-7S] structure. The other P-cluster site in the protein contains a [4Fe-4S] cluster pair, suggesting that NifZ is specifically required for the formation of the second P-cluster [, , ].; GO: 0009399 nitrogen fixation
Probab=33.72 E-value=65 Score=25.19 Aligned_cols=32 Identities=25% Similarity=0.480 Sum_probs=22.8
Q ss_pred CcccCCCCCEEEEEecccC---CCCCCCCcEEEEE
Q 023926 213 MNPTLDVGDRILAEKVSYF---FKRPEVSDIVIFR 244 (275)
Q Consensus 213 MePTL~~GDrVLV~K~~y~---~~~pkrGDIVVFk 244 (275)
|+|.++.||+|.+.+--+. +-.-..|++++-+
T Consensus 1 ~~p~f~~G~~V~a~~~irNDGt~Pg~~~g~lLv~~ 35 (75)
T PF04319_consen 1 MPPRFEWGDKVRARKDIRNDGTFPGKEIGELLVRK 35 (75)
T ss_pred CCCccCCCCEEEEEEEeEcCCCCCCCCCCCEEEcC
Confidence 8999999999999886432 2234566666644
No 42
>KOG0369 consensus Pyruvate carboxylase [Energy production and conversion]
Probab=31.95 E-value=16 Score=39.58 Aligned_cols=34 Identities=24% Similarity=0.334 Sum_probs=28.0
Q ss_pred EehhHHHHHhhhhhCcccccCC---CCcchhhhcccc
Q 023926 8 NFSGYVAQNLAHSAGIRFGFST---TSTRSFHECLFR 41 (275)
Q Consensus 8 ~~s~~~a~~l~~s~g~r~~~~~---~~~r~~~~~~~r 41 (275)
.-+-|||+++++.+.+-+--|. +.-||||||-|+
T Consensus 586 ~IaPyvah~f~~lfslE~WGGATFDVamRFLhEcPWe 622 (1176)
T KOG0369|consen 586 KIAPYVAHAFAGLFSLENWGGATFDVAMRFLHECPWE 622 (1176)
T ss_pred hcchHHHHHhhhhhhhhhcCCchhhHHHHHHhcChHH
Confidence 3467999999999999887763 447999999885
No 43
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=29.96 E-value=98 Score=22.82 Aligned_cols=36 Identities=25% Similarity=0.398 Sum_probs=21.9
Q ss_pred CCcc-cCCCCCEEEEEecccCCCCCCCCcEEEEEcCCccccccCCCCceEEEE
Q 023926 212 SMNP-TLDVGDRILAEKVSYFFKRPEVSDIVIFRAPPILQEIGFSSGDVFIKR 263 (275)
Q Consensus 212 SMeP-TL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P~~l~~~g~~~~k~~IKR 263 (275)
++.| +|..|-.|.|..+ ++.||.|..+. .+.-|+.|
T Consensus 20 ~~K~A~letG~~i~VP~F------I~~Gd~I~VdT----------~~g~Yv~R 56 (56)
T PF09285_consen 20 SYKPATLETGAEIQVPLF------IEEGDKIKVDT----------RDGSYVER 56 (56)
T ss_dssp TEEEEEETTS-EEEEETT--------TT-EEEEET----------TTTEEEEE
T ss_pred CccEEEEcCCCEEEccce------ecCCCEEEEEC----------CCCeEeCC
Confidence 3444 3555777777654 68999999987 45667777
No 44
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=29.58 E-value=38 Score=28.19 Aligned_cols=18 Identities=44% Similarity=0.685 Sum_probs=15.7
Q ss_pred cCCCCcccCCCCCEEEEE
Q 023926 209 PSASMNPTLDVGDRILAE 226 (275)
Q Consensus 209 ~G~SMePTL~~GDrVLV~ 226 (275)
-+++|.+.|+.||.||+.
T Consensus 48 ~~~~~~~~L~~GD~VLA~ 65 (124)
T PF15057_consen 48 LSDAMRHSLQVGDKVLAP 65 (124)
T ss_pred ccCcccCcCCCCCEEEEe
Confidence 357889999999999997
No 45
>PLN00208 translation initiation factor (eIF); Provisional
Probab=26.92 E-value=47 Score=28.98 Aligned_cols=27 Identities=26% Similarity=0.512 Sum_probs=19.5
Q ss_pred CCCCCEEEEEecccCCCCCCCCcEEEEEcC
Q 023926 217 LDVGDRILAEKVSYFFKRPEVSDIVIFRAP 246 (275)
Q Consensus 217 L~~GDrVLV~K~~y~~~~pkrGDIVVFk~P 246 (275)
+.+||+|+|..+.| +..+||||--..+
T Consensus 71 I~~GD~VlVel~~~---d~~KgdIv~ry~~ 97 (145)
T PLN00208 71 IAAGDIILVGLRDY---QDDKADVILKYMP 97 (145)
T ss_pred ecCCCEEEEEccCC---CCCEEEEEEEcCH
Confidence 45799999987764 5788888655443
No 46
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=26.24 E-value=57 Score=26.48 Aligned_cols=25 Identities=24% Similarity=0.389 Sum_probs=13.4
Q ss_pred CCCCCEEEEEecccCCCCCCCCcEEEE
Q 023926 217 LDVGDRILAEKVSYFFKRPEVSDIVIF 243 (275)
Q Consensus 217 L~~GDrVLV~K~~y~~~~pkrGDIVVF 243 (275)
+..||+|+|..+. +..-.+||||--
T Consensus 58 I~~GD~VlVsp~d--~~~~~kg~Iv~r 82 (99)
T TIGR00523 58 IREGDVVIVKPWE--FQGDDKCDIVWR 82 (99)
T ss_pred ecCCCEEEEEEcc--CCCCccEEEEEE
Confidence 3457777775432 232346776543
No 47
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=26.04 E-value=50 Score=29.16 Aligned_cols=27 Identities=22% Similarity=0.544 Sum_probs=19.3
Q ss_pred CCCCCEEEEEecccCCCCCCCCcEEEEEcC
Q 023926 217 LDVGDRILAEKVSYFFKRPEVSDIVIFRAP 246 (275)
Q Consensus 217 L~~GDrVLV~K~~y~~~~pkrGDIVVFk~P 246 (275)
+.+||+|+|..+.| +..+||||--..+
T Consensus 71 I~~GD~VlVel~~y---d~~KgdIi~Ry~~ 97 (155)
T PTZ00329 71 INIGDIILVSLRDF---QDSKADVILKYTP 97 (155)
T ss_pred ecCCCEEEEeccCC---CCCEEEEEEEcCH
Confidence 45699999988765 5778887654443
No 48
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=24.07 E-value=90 Score=24.32 Aligned_cols=30 Identities=37% Similarity=0.464 Sum_probs=20.5
Q ss_pred ccCCCCCEEEEEecccCCCCCCCCcEEEEEcC
Q 023926 215 PTLDVGDRILAEKVSYFFKRPEVSDIVIFRAP 246 (275)
Q Consensus 215 PTL~~GDrVLV~K~~y~~~~pkrGDIVVFk~P 246 (275)
||-..+|++.-+..- ..+++.||+++|..-
T Consensus 65 ptC~~~D~i~~~~~l--P~~l~~GD~l~f~~~ 94 (116)
T PF00278_consen 65 PTCDSGDVIARDVML--PKELEVGDWLVFENM 94 (116)
T ss_dssp SSSSTTSEEEEEEEE--ESTTTTT-EEEESS-
T ss_pred CCcCCCceEeeeccC--CCCCCCCCEEEEecC
Confidence 677889998644332 138999999999763
No 49
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=23.66 E-value=86 Score=25.81 Aligned_cols=36 Identities=22% Similarity=0.302 Sum_probs=25.5
Q ss_pred EEEcCCCCcccCCCCCEEEEEecccCC-----CCCCCCcEEEEEc
Q 023926 206 RSIPSASMNPTLDVGDRILAEKVSYFF-----KRPEVSDIVIFRA 245 (275)
Q Consensus 206 ~~V~G~SMePTL~~GDrVLV~K~~y~~-----~~pkrGDIVVFk~ 245 (275)
+.|..+|..| |=++++|+..+.. ..++.||.|+|-+
T Consensus 56 lFi~~gsvrp----Gii~lINd~DWEllekedy~ledgD~ivfiS 96 (101)
T KOG4146|consen 56 LFIHHGSVRP----GIIVLINDMDWELLEKEDYPLEDGDHIVFIS 96 (101)
T ss_pred eEeeCCcCcC----cEEEEEeccchhhhcccccCcccCCEEEEEE
Confidence 5677777655 5677777754321 4689999999975
No 50
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=23.35 E-value=83 Score=25.73 Aligned_cols=30 Identities=23% Similarity=0.295 Sum_probs=22.6
Q ss_pred cCCCCCEEEEEecccCC-----CCCCCCcEEEEEc
Q 023926 216 TLDVGDRILAEKVSYFF-----KRPEVSDIVIFRA 245 (275)
Q Consensus 216 TL~~GDrVLV~K~~y~~-----~~pkrGDIVVFk~ 245 (275)
++++|=.+++|+..+.. +.++.||+|+|-+
T Consensus 57 ~lrpGiI~LINd~DWeLleke~y~ledgDiIvfis 91 (96)
T COG5131 57 ELRPGIICLINDMDWELLEKERYPLEDGDIIVFIS 91 (96)
T ss_pred CCcccEEEEEcCccHhhhhcccccCCCCCEEEEEe
Confidence 46778888888875432 4688999999975
No 51
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=23.29 E-value=57 Score=25.50 Aligned_cols=11 Identities=36% Similarity=0.594 Sum_probs=5.9
Q ss_pred CCCEEEEEecc
Q 023926 219 VGDRILAEKVS 229 (275)
Q Consensus 219 ~GDrVLV~K~~ 229 (275)
.||+|+|+.+.
T Consensus 41 rGd~VlV~p~~ 51 (78)
T cd05792 41 RGDFVLVEPIE 51 (78)
T ss_pred eCCEEEEEecc
Confidence 45555555544
No 52
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=22.54 E-value=82 Score=23.66 Aligned_cols=11 Identities=18% Similarity=-0.061 Sum_probs=8.5
Q ss_pred CCCCcEEEEEc
Q 023926 235 PEVSDIVIFRA 245 (275)
Q Consensus 235 pkrGDIVVFk~ 245 (275)
|..||+|.|..
T Consensus 47 i~vGD~V~ve~ 57 (72)
T PRK00276 47 ILPGDKVTVEL 57 (72)
T ss_pred cCCCCEEEEEE
Confidence 67788888873
Done!