Query 013051
Match_columns 450
No_of_seqs 122 out of 168
Neff 5.1
Searched_HMMs 46136
Date Thu Mar 28 23:54:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013051.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013051hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2736 Presenilin [Signal tra 100.0 3E-134 7E-139 1009.5 28.0 396 1-450 6-406 (406)
2 PF01080 Presenilin: Presenili 100.0 1E-124 3E-129 961.6 6.3 393 4-441 4-403 (403)
3 smart00730 PSN Presenilin, sig 100.0 7.6E-47 1.6E-51 369.5 19.3 236 70-435 2-248 (249)
4 PF06550 DUF1119: Protein of u 98.5 3.9E-06 8.3E-11 83.9 16.2 140 72-223 32-174 (283)
5 PF04258 Peptidase_A22B: Signa 94.2 0.013 2.9E-07 59.3 0.0 52 367-418 214-272 (298)
6 KOG2442 Uncharacterized conser 80.2 1.6 3.4E-05 47.5 3.4 54 366-419 431-491 (541)
7 COG3389 Uncharacterized protei 78.1 8.9 0.00019 38.3 7.6 60 361-420 196-258 (277)
8 PRK10263 DNA translocase FtsK; 63.5 62 0.0014 39.7 11.5 17 22-38 29-45 (1355)
9 KOG2443 Uncharacterized conser 61.0 8.2 0.00018 40.5 3.4 53 366-418 252-313 (362)
10 PF10749 DUF2534: Protein of u 55.6 49 0.0011 28.1 6.4 38 115-172 29-66 (85)
11 PRK08343 secD preprotein trans 44.4 1.5E+02 0.0033 31.8 9.9 83 59-147 246-328 (417)
12 PF09125 COX2-transmemb: Cytoc 40.3 30 0.00066 25.1 2.5 15 102-116 14-28 (38)
13 PF02355 SecD_SecF: Protein ex 39.3 1.4E+02 0.003 28.5 7.8 77 62-145 19-95 (189)
14 PF14362 DUF4407: Domain of un 38.4 45 0.00098 33.6 4.5 19 394-412 46-64 (301)
15 PF13314 DUF4083: Domain of un 36.1 43 0.00094 26.6 3.1 25 369-407 3-27 (58)
16 KOG4694 Predicted membrane pro 35.6 44 0.00096 31.5 3.6 58 362-429 66-124 (174)
17 PF09971 DUF2206: Predicted me 31.1 84 0.0018 33.2 5.3 63 91-153 135-199 (367)
18 TIGR01129 secD protein-export 30.2 3.2E+02 0.007 29.1 9.5 79 61-147 235-313 (397)
19 COG5249 RER1 Golgi protein inv 30.1 1E+02 0.0022 28.9 5.0 61 159-222 19-94 (180)
20 TIGR02854 spore_II_GA sigma-E 28.8 1.6E+02 0.0034 30.0 6.6 45 102-154 62-107 (288)
21 PF08041 PetM: PetM family of 28.4 1.1E+02 0.0023 21.5 3.6 24 387-410 4-27 (31)
22 TIGR00916 2A0604s01 protein-ex 27.3 4.8E+02 0.01 24.7 9.3 29 125-153 91-119 (192)
23 KOG3807 Predicted membrane pro 27.0 49 0.0011 35.2 2.6 34 173-214 16-49 (556)
24 PF03176 MMPL: MMPL family; I 24.7 4.1E+02 0.0089 26.7 8.8 128 72-202 141-293 (333)
25 PF09858 DUF2085: Predicted me 24.6 1.6E+02 0.0034 25.3 4.9 32 395-426 24-55 (93)
26 PRK13023 bifunctional preprote 24.4 3.9E+02 0.0085 31.2 9.4 81 60-148 264-344 (758)
27 PRK11876 petM cytochrome b6-f 24.1 1E+02 0.0022 21.7 3.0 23 387-409 6-28 (32)
28 KOG2442 Uncharacterized conser 23.2 2.3E+02 0.0051 31.4 6.9 50 172-230 351-417 (541)
29 PF14329 DUF4386: Domain of un 23.1 2.4E+02 0.0052 26.7 6.4 34 168-201 144-180 (215)
30 PRK05812 secD preprotein trans 22.6 4.5E+02 0.0097 29.1 9.1 78 61-146 320-397 (498)
31 PF10066 DUF2304: Uncharacteri 21.2 5.5E+02 0.012 22.3 8.3 42 103-144 35-78 (115)
32 PRK13022 secF preprotein trans 21.1 5.5E+02 0.012 26.1 8.9 77 63-146 116-192 (289)
33 PF11674 DUF3270: Protein of u 20.5 1.5E+02 0.0032 25.6 3.8 23 386-408 63-85 (90)
34 COG0342 SecD Preprotein transl 20.4 3E+02 0.0066 30.5 7.3 86 61-154 330-417 (506)
35 TIGR00966 3a0501s07 protein-ex 20.1 7.4E+02 0.016 24.3 9.4 76 65-147 89-164 (246)
No 1
>KOG2736 consensus Presenilin [Signal transduction mechanisms]
Probab=100.00 E-value=3.2e-134 Score=1009.48 Aligned_cols=396 Identities=42% Similarity=0.707 Sum_probs=311.9
Q ss_pred CchhhHHHhhhhhhhhhhhhHHHHHHHHHHHhhccCccccCCCCCCccccceeEeecc--CCCCchhhHHHHHHHHHHHH
Q 013051 1 MESSILDSIGSEIIGVMTPVSLCMLLVVLLVYSLSPSEQSLSGASDPFRTAANLVYLE--RPDDSSTQKLEGAVLNALVF 78 (450)
Q Consensus 1 ~~~~~l~~~g~~vi~l~~PVslcM~~Vv~~v~~l~~~~~~~~~~~~~~~~~~~lvY~~--~~~ds~g~k~~~sl~Nali~ 78 (450)
||++.|+..|+|+|++|+||++||++||++++++++|++ .+.+ +++|++ +++|++|+|+++|++|++++
T Consensus 6 ~e~s~L~y~~~~vi~lf~PVslCM~~Vv~~i~~~~~~s~------~~~~---~~~y~pf~e~t~s~~~k~l~sl~N~li~ 76 (406)
T KOG2736|consen 6 MEESELKYGAKHVIGLFVPVSLCMLVVVATIKSVSFYSS------EQGR---QLIYTPFTEDTDSTGQKLLDSLLNALIM 76 (406)
T ss_pred chhhhhhccceEEEEEehhHHHHHHHHHHhheecceeec------ccch---heeecccccCCccHHHHHHHHHHHHHHH
Confidence 678999999999999999999999999999999999863 2222 566773 57899999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHHhhhhhhheeeeeeecCcc
Q 013051 79 VILIAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVLLFNFTIVGVLSLFSGGIP 158 (450)
Q Consensus 79 v~vI~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~l~NfgvvG~i~If~~k~P 158 (450)
|++|++|||+||+||||||||+||+||++||+++||+||++|+++++++||+|+||+|+++++||||++||+|||| |+|
T Consensus 77 i~viv~~Tfllv~ly~~rfyk~ik~wl~~Ss~llLf~~s~~~l~~v~~~~~ip~dy~T~~lll~nfgvvGm~~ihw-kgp 155 (406)
T KOG2736|consen 77 ISVIVVMTFLLVVLYKYRFYKFIKAWLILSSLLLLFLFSGIYLGEVFKTYNVPVDYITFLLLLWNFGVVGMYSIHW-KGP 155 (406)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcccceeeeeeeccccceEEEEEe-CCc
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999998 899
Q ss_pred hhhHHHHHHHHHHHHHHHHhc-CChhHHHHHHHHHHHHHHHhhcCCCChHHHHHHHHhhcCCCC-CeeeecccCcccccc
Q 013051 159 ILLRQAYMVCMGIIMAAWFTN-LPEWTTWALLLALALYDLFAVLAPGGPLKLLVELASSRDEEL-PALVYEARPTVSENE 236 (450)
Q Consensus 159 l~lqQ~YLI~iSalmA~~f~~-LPeWTtW~lL~~iaiyDL~AVL~P~GPLr~LVE~AqeRne~I-PALiYss~~~~~~~~ 236 (450)
++|||+|||++|+|||++|+| |||||||++|++|++|||+||||||||||+||||||||||++ |||||||++++...+
T Consensus 156 l~L~Q~YlI~~~aLmAl~fik~LPeWTtW~iL~ais~~DLvAVL~P~GPLr~LVEtA~~R~e~~fPAliYss~~v~~~~~ 235 (406)
T KOG2736|consen 156 LRLQQAYLIMISALMALFFIKYLPEWTTWFILVAISVYDLVAVLAPKGPLRMLVETAQERNEPIFPALIYSSRMVVLVSE 235 (406)
T ss_pred eeehhHHHHHHHHHHHHHHHHHCccHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHhcCcccchhheeecceEEeccc
Confidence 999999999999999999997 999999999999999999999999999999999999999988 999999999886332
Q ss_pred ccccccccccccccCCCCcchhhhccccCCCCCCCCCCCCCCcccccccCCcccccCccccccccccccccCCCCCCCCC
Q 013051 237 RNRRSGLRFLLGGVSDSGSVELQVVSRDNADGRENHGNPEYSAVNVGTFGNEMHERSSDEVERLPLVGHLRDGFSSSGSS 316 (450)
Q Consensus 237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 316 (450)
...++..+.-+.+.+...+.+.++..+++...++ + +.+.......+++|.....+++ +.++.
T Consensus 236 s~~~~~~~~~~~~~~s~~N~~~~~~~~~~s~~~p---------d-------~~~~s~~~~~~~~P~~~~~~~s--~~~~~ 297 (406)
T KOG2736|consen 236 SVIRRTVRQTIEPRESQNNAEYNEIRVRDSAAEP---------D-------SVGHSPRVEAERSPLILKPKNS--TRASV 297 (406)
T ss_pred cccchhhhccCcCccccCchhhhhhhhcccccCC---------c-------cccccccccCCCCCcccCCCCC--ccccc
Confidence 2111111100000000000000000000000000 0 0000011122333332211100 00000
Q ss_pred CCCccccccchhhhhhhccchhhhccccCCCccccccccccccccCCceeeccchhhHHHHHhhhhhhc-ChhHHHHHHH
Q 013051 317 SDRSTSVNRENEIVMEEEMSPLVDMSLLGNNRQRASDSLENSLITDRGIRLGLGDFIFYSVLVGRAAMY-DLMTVYACYL 395 (450)
Q Consensus 317 ~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~e~~~~~~~~~gIKLGLGDFIFYSVLVGrAA~~-d~~t~~aCfv 395 (450)
+. ++.+++.+.- ..+ +++|+|||||||||||||||||||||+| |||||+||||
T Consensus 298 ---------~~-----~~~~~~~~~~---------~~~---~~~e~r~ikLGlGDFIFYSvLvGkAa~~~d~~TviAC~v 351 (406)
T KOG2736|consen 298 ---------QG-----LSSSTLEETV---------GTG---EDNEERGIKLGLGDFIFYSVLVGKAAAYGDLNTVIACFV 351 (406)
T ss_pred ---------cc-----CCccchhhhc---------ccc---ccccccceeeccCceEEEEeeccchhhcCChHHHHHHHH
Confidence 00 0000000000 000 2368999999999999999999999998 5999999999
Q ss_pred HHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHhhhhHhhhHHhhhhhcccC
Q 013051 396 AIISGLGCTLILLSVCRRALPALPISITLGVLFYFLTRLLMEPFVVGTTTNLLMF 450 (450)
Q Consensus 396 AIL~GL~~TLlLLav~~kALPALPISI~lGliFYF~T~~~v~PF~~~~s~~l~~f 450 (450)
|||+|||+||+||++||||||||||||+||++|||+||++++||+++|++|++||
T Consensus 352 aIL~GL~~TL~llsv~~kALPALPisI~~G~iFYF~t~~l~epF~~~~ss~~~~~ 406 (406)
T KOG2736|consen 352 AILIGLCLTLLLLSVFKKALPALPISITFGLIFYFSTRLLVEPFVDQLSSNLVMI 406 (406)
T ss_pred HHHHHHHHHHHHHHHHhhcCcCCchHHHHHHHHHHHHHHHHHHHHHHhhhceeeC
Confidence 9999999999999999999999999999999999999999999999999999997
No 2
>PF01080 Presenilin: Presenilin Alzheimer disease; InterPro: IPR001108 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to MEROPS peptidase family A22 (presenilin family, clan AD): subfamily A22A, the type example being presenilin 1 from Homo sapiens (Human). Presenilins are polytopic transmembrane (TM) proteins, mutations in which are associated with the occurrence of early-onset familial Alzheimer's disease, a rare form of the disease that results from a single-gene mutation [, ]. The physiological functions of presenilins are unknown, but they may be related to developmental signalling, apoptotic signal transduction, or processing of selected proteins, such as the beta-amyloid precursor protein(beta-APP). There are a number of subtypes which belong to this presenilin family. That presenilin homologues have been identified in species that do not have an Alzhemier's disease correlate suggests that they may have functions unrelated to the disease, homologues having been identified in mouse, Drosophila melanogaster, Caenorhabditis elegans [] and other members of the eukarya including plants. ; GO: 0004190 aspartic-type endopeptidase activity, 0016021 integral to membrane; PDB: 2KR6_A.
Probab=100.00 E-value=1.5e-124 Score=961.63 Aligned_cols=393 Identities=48% Similarity=0.755 Sum_probs=74.9
Q ss_pred hhHHHhhhhhhhhhhhhHHHHHHHHHHHhhccCccccCCCCCCccccceeEeec--cCCCCchhhHHHHHHHHHHHHHHH
Q 013051 4 SILDSIGSEIIGVMTPVSLCMLLVVLLVYSLSPSEQSLSGASDPFRTAANLVYL--ERPDDSSTQKLEGAVLNALVFVIL 81 (450)
Q Consensus 4 ~~l~~~g~~vi~l~~PVslcM~~Vv~~v~~l~~~~~~~~~~~~~~~~~~~lvY~--~~~~ds~g~k~~~sl~Nali~v~v 81 (450)
+-+.-.|+|++++++||++||++||+++++++++++ + +.+++|+ ++++||+|+|+++|++||+++|++
T Consensus 4 ~~~~y~~~~v~~l~~PVsicM~lvv~~v~~~~~~~~----~------~~~~~y~~~~~~~~stg~~~~~sl~Nali~v~~ 73 (403)
T PF01080_consen 4 EELKYGAEHVIALLVPVSICMLLVVALVRSLSPYSS----N------SSYLVYTPFHSSSDSTGTKLWGSLINALIFVGV 73 (403)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHeeEeccccc----C------CceeEEEecCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 345567999999999999999999999999999963 1 2367777 466799999999999999999999
Q ss_pred HHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHHhhhhhhheeeeeeecCcchhh
Q 013051 82 IAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVLLFNFTIVGVLSLFSGGIPILL 161 (450)
Q Consensus 82 I~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~l~NfgvvG~i~If~~k~Pl~l 161 (450)
|++|||+||+||||||||+|||||+|||+++||++||+++++++++||+|+||+|+++++||||+|||+|||| |+|+++
T Consensus 74 I~v~Tf~lvlLyky~c~k~i~~wl~~Ss~~lL~~~~~~~~~~~~~~~~ip~D~it~~~~l~NfgvvGv~~if~-~~Pl~l 152 (403)
T PF01080_consen 74 IAVMTFVLVLLYKYRCYKFIKGWLIFSSFLLLFVFGGQYFQELLSAYNIPMDYITFAFLLWNFGVVGVLSIFW-KGPLLL 152 (403)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHhhhheeeeec-CCcHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999998 899999
Q ss_pred HHHHHHHHHHHHHHHHhc-CChhHHHHHHHHHHHHHHHhhcCCCChHHHHHHHHhhcCCCC-CeeeecccCccccccccc
Q 013051 162 RQAYMVCMGIIMAAWFTN-LPEWTTWALLLALALYDLFAVLAPGGPLKLLVELASSRDEEL-PALVYEARPTVSENERNR 239 (450)
Q Consensus 162 qQ~YLI~iSalmA~~f~~-LPeWTtW~lL~~iaiyDL~AVL~P~GPLr~LVE~AqeRne~I-PALiYss~~~~~~~~~~~ 239 (450)
||+|||++|+|||++|++ |||||||++|+++|+||||||||||||||+|||+|||||||| |||+|||++.+...+.++
T Consensus 153 ~Q~YLI~is~l~A~~~l~~lPeWTtW~lL~~iaiyDl~AVL~P~GPLr~Lve~a~er~e~i~PaLiY~a~~~~~~~~~~~ 232 (403)
T PF01080_consen 153 QQAYLIMISVLMALFFLKYLPEWTTWFLLVAIAIYDLFAVLCPCGPLRMLVELAQERNEPIFPALIYEARPVWPVAGSDS 232 (403)
T ss_dssp -----------------------------------------------------------------------HHHHHH---
T ss_pred HHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHeeEeCCCCcHHHHHHHHHHcCCcccceeeeecccccccccccc
Confidence 999999999999998866 999999999999999999999999999999999999999998 999999999876544222
Q ss_pred cccccccccccCCCCcchhhhccc--cCCCCCCCCCCCCCCcccccccCCcccccCccccccccccccccCCCCCCCCCC
Q 013051 240 RSGLRFLLGGVSDSGSVELQVVSR--DNADGRENHGNPEYSAVNVGTFGNEMHERSSDEVERLPLVGHLRDGFSSSGSSS 317 (450)
Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~ 317 (450)
.+..+ +..+.+++.. .++..++++..+++++.+.++. +...+. +++++++...++
T Consensus 233 ~~~~~---------~~~~~~~~~~~~~~~~~~p~s~~~~~~~~~~~~~--------~~~~~~------~~~~~~~~~~~s 289 (403)
T PF01080_consen 233 SESNE---------GEEETQRRSSNSNRSAINPDSVSTSQSPSNRSNT--------SSPREE------SDDESSSSESSS 289 (403)
T ss_dssp ---HT-----------TT-----TT--S-S------------------------------------------------SS
T ss_pred ccccc---------cccccccccccccccccccccccccccccccccc--------cCCccc------cccccccccccc
Confidence 11111 0000000000 0000001000000000000000 000000 000000000000
Q ss_pred CCccccccchhhhhhhccchhhhccccCCCccccccccccccccCCceeeccchhhHHHHHhhhhhhc-ChhHHHHHHHH
Q 013051 318 DRSTSVNRENEIVMEEEMSPLVDMSLLGNNRQRASDSLENSLITDRGIRLGLGDFIFYSVLVGRAAMY-DLMTVYACYLA 396 (450)
Q Consensus 318 ~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~e~~~~~~~~~gIKLGLGDFIFYSVLVGrAA~~-d~~t~~aCfvA 396 (450)
+ ....+.+++..++..+..+.... +.++ + +.++++||||||||||||||||||||+| ||+|+++||+|
T Consensus 290 ~---~~~~~~~~~~~~~~~~~~~~~~~------~~~~-~-~~~~~~~~klGlGDFiFYs~Lvg~aa~~~~~~~~~~~~~a 358 (403)
T PF01080_consen 290 Q---SDSSTAEERSRREQREVQSNSQP------SNDE-R-EDEEERGIKLGLGDFIFYSVLVGRAAMYGDWNTVVACFVA 358 (403)
T ss_dssp S---SS-S---THHHHHHHHHHHHHT--------------S---SS--SS-TTTHHHHHHHHHHHHHH-TTTTHHHHHHH
T ss_pred c---hhhcccCcccccccccccccccc------cccc-c-cccccCceeecchhHHHHHHHHhHHHhcCCHHHHHHHHHH
Confidence 0 00001111111111111111000 1111 1 2268999999999999999999999996 99999999999
Q ss_pred HHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHhhhhHhhhHH
Q 013051 397 IISGLGCTLILLSVCRRALPALPISITLGVLFYFLTRLLMEPFVV 441 (450)
Q Consensus 397 IL~GL~~TLlLLav~~kALPALPISI~lGliFYF~T~~~v~PF~~ 441 (450)
||+|||+||++|++||||||||||||+||++|||+||++++||+|
T Consensus 359 il~Gl~~Tl~~l~~~~~alPALPisi~~g~~~yf~~~~~~~pf~d 403 (403)
T PF01080_consen 359 ILIGLCLTLLLLAIFRKALPALPISIALGLIFYFLTRLLVEPFMD 403 (403)
T ss_dssp HHHHHHHHHHHHHHHT-S-SSSSS----HHHHHHHHTTTT--GGG
T ss_pred HHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhhccC
Confidence 999999999999999999999999999999999999999999986
No 3
>smart00730 PSN Presenilin, signal peptide peptidase, family. Presenilin 1 and presenilin 2 are polytopic membrane proteins, whose genes are mutated in some individuals with Alzheimer's disease. Distant homologues, present in eukaryotes and archaea, also contain conserved aspartic acid residues which are predicted to contribute to catalysis. At least one member of this family has been shown to possess signal peptide peptidase activity.
Probab=100.00 E-value=7.6e-47 Score=369.54 Aligned_cols=236 Identities=39% Similarity=0.602 Sum_probs=210.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHHhhhhhhhee
Q 013051 70 GAVLNALVFVILIAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVLLFNFTIVGV 149 (450)
Q Consensus 70 ~sl~Nali~v~vI~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~l~NfgvvG~ 149 (450)
++..|+...+.+++++|++|++||||+|+|++.+|+++++..++++.++........ +|+.|+++.+||++++|+
T Consensus 2 ~~~~n~~~~i~fii~~s~~Ll~Ly~~~~~~~i~~~~~f~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~v~~~ 76 (249)
T smart00730 2 YSLLNSLVAIVFPIVATFVLVLLYKFFKYLVIVLVIYFSSLGVLFLYSLLYPLEVFR-----VDYPTLLILLLNFAVVGF 76 (249)
T ss_pred cccccHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HhHHHHHHHHHHHHHHHH
Confidence 456799999999999999999999999999999999999999999999988877666 999999999999999999
Q ss_pred eeeeecCcchhhHHHHHHHHHHHHHH-HHhcCC-hhHHHHHHHHHHHHHHHhhcCCCChHHHHHHHHhhcCCC---CCee
Q 013051 150 LSLFSGGIPILLRQAYMVCMGIIMAA-WFTNLP-EWTTWALLLALALYDLFAVLAPGGPLKLLVELASSRDEE---LPAL 224 (450)
Q Consensus 150 i~If~~k~Pl~lqQ~YLI~iSalmA~-~f~~LP-eWTtW~lL~~iaiyDL~AVL~P~GPLr~LVE~AqeRne~---IPAL 224 (450)
.++|| | | ...|.+++.+|..++. .+.++| +||+|.+|.++++||+++|++|+||+|.+||.|++|||| +|++
T Consensus 77 ~~~~~-~-~-~w~~~~~lgi~~~~~~~~~~~l~~~~~~~iLL~~l~iYDif~Vf~t~~~~~vMv~vA~~~~~~~~~~P~l 153 (249)
T smart00730 77 WCIHR-K-G-AWIQQDLIGISLCMAILFILRLPSEWTAWILLGALFIYDIFAVFGTPGPLRVMVEVATGRDEPIKVFPAL 153 (249)
T ss_pred HHHHh-h-h-HHHHHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHheeecCCCCchHHhhHhccCCCCcccCChh
Confidence 99997 6 4 5667777888776665 466799 999999999999999999999999999999999999999 5999
Q ss_pred eecccCccccccccccccccccccccCCCCcchhhhccccCCCCCCCCCCCCCCcccccccCCcccccCccccccccccc
Q 013051 225 VYEARPTVSENERNRRSGLRFLLGGVSDSGSVELQVVSRDNADGRENHGNPEYSAVNVGTFGNEMHERSSDEVERLPLVG 304 (450)
Q Consensus 225 iYss~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 304 (450)
+|+++...+ +
T Consensus 154 l~~p~~~~~-----------------------------------~----------------------------------- 163 (249)
T smart00730 154 LYVPRLVVS-----------------------------------F----------------------------------- 163 (249)
T ss_pred hcccccccc-----------------------------------c-----------------------------------
Confidence 998753100 0
Q ss_pred cccCCCCCCCCCCCCccccccchhhhhhhccchhhhccccCCCccccccccccccccCCceeeccchhhHHHHHhhhhhh
Q 013051 305 HLRDGFSSSGSSSDRSTSVNRENEIVMEEEMSPLVDMSLLGNNRQRASDSLENSLITDRGIRLGLGDFIFYSVLVGRAAM 384 (450)
Q Consensus 305 ~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~e~~~~~~~~~gIKLGLGDFIFYSVLVGrAA~ 384 (450)
.. + ++++..||||||+||||+||++|++
T Consensus 164 ----------------------------------------------~~---~---~~~~~~~LGLGDiv~Pgilv~~a~~ 191 (249)
T smart00730 164 ----------------------------------------------ED---D---EEGRFSMLGLGDIVFPGILVASAAR 191 (249)
T ss_pred ----------------------------------------------cc---C---CCCccceecCCCeeeHHHHHHHHHH
Confidence 00 0 1356799999999999999999999
Q ss_pred cC------hhHHHHHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHhhhh
Q 013051 385 YD------LMTVYACYLAIISGLGCTLILLSVCRRALPALPISITLGVLFYFLTRLL 435 (450)
Q Consensus 385 ~d------~~t~~aCfvAIL~GL~~TLlLLav~~kALPALPISI~lGliFYF~T~~~ 435 (450)
+| +..+.+|++|.++||++|++++.++|||.||||.++.+++++||.++..
T Consensus 192 fd~~~~~~~~yf~~~~~ay~~GL~~t~~~l~~~~~aqPALlylvp~~l~~~~~~~~~ 248 (249)
T smart00730 192 FDVSVRSDSNYFLACFVAYGIGLILTLVLLALFKKAQPALPYLVPFTLVFYLLTALL 248 (249)
T ss_pred hhhcccCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHh
Confidence 98 7789999999999999999999999999999999999999999999864
No 4
>PF06550 DUF1119: Protein of unknown function (DUF1119); InterPro: IPR010545 This family consists of several hypothetical archaeal proteins of unknown function.
Probab=98.51 E-value=3.9e-06 Score=83.92 Aligned_cols=140 Identities=21% Similarity=0.282 Sum_probs=86.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHHhhhhhhheeee
Q 013051 72 VLNALVFVILIAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVLLFNFTIVGVLS 151 (450)
Q Consensus 72 l~Nali~v~vI~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~l~NfgvvG~i~ 151 (450)
..|++..++.|.+.|-+|+++.||+--++|++-+.+++++..+..-+.++..+. .........-++-- .++..
T Consensus 32 ~~Nsl~YI~~iL~fT~~mL~~ik~~~~~~I~~ii~~~i~~~~~YVf~~l~~~~~----~~~~~~~~~a~~~a---i~~~~ 104 (283)
T PF06550_consen 32 PSNSLYYIIAILVFTAFMLLAIKYGKKWIIRLIIYLAIFLTIFYVFSALLPLLL----TNAGLVNIIALILA---IALTA 104 (283)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh----hhhhhHHHHHHHHH---HHHHH
Confidence 468899999999999999999999999999999888888765554444333322 11111111111111 12222
Q ss_pred eeecCcch-hhHHHHHHHHHHHHHHHHhc-CChhHHHHHHHHHHHHHHHhhcCCCChHHHHHHHHhhc-CCCCCe
Q 013051 152 LFSGGIPI-LLRQAYMVCMGIIMAAWFTN-LPEWTTWALLLALALYDLFAVLAPGGPLKLLVELASSR-DEELPA 223 (450)
Q Consensus 152 If~~k~Pl-~lqQ~YLI~iSalmA~~f~~-LPeWTtW~lL~~iaiyDL~AVL~P~GPLr~LVE~AqeR-ne~IPA 223 (450)
..+ |.|- ++-..-=+++++=.|-.|-- |.-|++=++|+++|+||.++|---| -.+.+|+-- |-.+|-
T Consensus 105 ~L~-~ypEWYviD~~Gil~~aG~aaiFGISl~~lpaiiLL~iLAVYDaISVYkTk----HMltLAegv~d~klPi 174 (283)
T PF06550_consen 105 LLY-KYPEWYVIDIAGILMGAGAAAIFGISLGILPAIILLAILAVYDAISVYKTK----HMLTLAEGVMDLKLPI 174 (283)
T ss_pred HHH-hcchHHHHHHHHHHHHhHHHHHHhhhccHHHHHHHHHHHHHhhhhheecch----HHHHHHHHHhccCCce
Confidence 222 3343 23333334555555566754 9999999999999999999995433 344555544 234444
No 5
>PF04258 Peptidase_A22B: Signal peptide peptidase; InterPro: IPR007369 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of sequences contain aspartic endopeptidases belong to MEROPS peptidase family A22 (presenilin family, clan AD): subfamily A22B. The peptidases were originally classified by hierarchical homology to the most conserved member - IMPAS 1. They are also known as signal peptide peptidase (SPP) []. They belong to the I-CliP family of peptidases. SPP cleaves cleaves remnant signal peptides left behind in the membrane by the action of signal peptidase and also plays key roles in immune surveillance and the maturation of certain viral proteins []. SPPs do not require cofactors as demonstrated by expression in bacteria and purification of a proteolytically active form. The C-terminal region defines the functional domain, which is in itself sufficient for proteolytic activity []. ; GO: 0004190 aspartic-type endopeptidase activity, 0016021 integral to membrane; PDB: 1JUF_C 1INQ_C.
Probab=94.17 E-value=0.013 Score=59.35 Aligned_cols=52 Identities=27% Similarity=0.449 Sum_probs=0.0
Q ss_pred eccchhhHHHHHhhhhhhcChhH-------HHHHHHHHHHHHHHHHHHHHhhcccCCCC
Q 013051 367 LGLGDFIFYSVLVGRAAMYDLMT-------VYACYLAIISGLGCTLILLSVCRRALPAL 418 (450)
Q Consensus 367 LGLGDFIFYSVLVGrAA~~d~~t-------~~aCfvAIL~GL~~TLlLLav~~kALPAL 418 (450)
|||||=|.=+++++-+.++|... ..+|++|=.+||.+|.+.+.++|++-|||
T Consensus 214 LGlGDIviPGl~i~~~~rfD~~~~~~~~~Yf~~~~~~Y~~Gl~~t~~~~~~~~~~QPAL 272 (298)
T PF04258_consen 214 LGLGDIVIPGLFIAFCLRFDKSRNKSRKPYFIASLIGYALGLLLTFVALHLFKHGQPAL 272 (298)
T ss_dssp -----------------------------------------------------------
T ss_pred eccchHHHHHHHHHHHHHhhHhhccccchHHHHHHHHHHHHHHHHHHHHHHhCCCCCee
Confidence 99999999999999999987554 67889999999999999999999999998
No 6
>KOG2442 consensus Uncharacterized conserved protein, contains PA domain [General function prediction only]
Probab=80.22 E-value=1.6 Score=47.46 Aligned_cols=54 Identities=28% Similarity=0.353 Sum_probs=49.8
Q ss_pred eeccchhhHHHHHhhhhhhcChhH-------HHHHHHHHHHHHHHHHHHHHhhcccCCCCc
Q 013051 366 RLGLGDFIFYSVLVGRAAMYDLMT-------VYACYLAIISGLGCTLILLSVCRRALPALP 419 (450)
Q Consensus 366 KLGLGDFIFYSVLVGrAA~~d~~t-------~~aCfvAIL~GL~~TLlLLav~~kALPALP 419 (450)
=||+||-++=+.||.-+-+|||-+ .++|.+|==+||.+|-+-|+.-|+.=|||=
T Consensus 431 ilGFGDIl~PGlLVa~c~RfD~~~~~~~~iYfv~~tvaYgiGLlvTfvaL~LM~~GQPALL 491 (541)
T KOG2442|consen 431 ILGFGDILVPGLLVAFCLRFDVQVNSVSNIYFVWSTVAYGIGLLVTFVALVLMKGGQPALL 491 (541)
T ss_pred EeeecccccchHHHHHHHHhhhhccccceeEEehhHHHHHHHHHHHHHHHHHhcCCCceEE
Confidence 489999999999999999998865 478999999999999999999999999983
No 7
>COG3389 Uncharacterized protein conserved in archaea [Function unknown]
Probab=78.14 E-value=8.9 Score=38.30 Aligned_cols=60 Identities=30% Similarity=0.378 Sum_probs=38.5
Q ss_pred cCCceeeccchhhHHHHHhhhhhhc-ChhHHHHHHHHHHH-HHHHHHHHHHh-hcccCCCCch
Q 013051 361 TDRGIRLGLGDFIFYSVLVGRAAMY-DLMTVYACYLAIIS-GLGCTLILLSV-CRRALPALPI 420 (450)
Q Consensus 361 ~~~gIKLGLGDFIFYSVLVGrAA~~-d~~t~~aCfvAIL~-GL~~TLlLLav-~~kALPALPI 420 (450)
|++..-.|+||=+-=|+||-.|+-+ +-+.+...-++-+. ||..-+.|.-+ -+|+=|-||.
T Consensus 196 dgna~miG~GDavmPsIlVvSaa~f~~s~~l~f~~Lpal~GglvGl~vL~~v~r~Rp~pGLP~ 258 (277)
T COG3389 196 DGNAYMIGLGDAVMPSILVVSAAFFLISPILAFIVLPALAGGLVGLAVLYFVNRGRPHPGLPF 258 (277)
T ss_pred CCceEEEeechhhcccceeeehHHhccCCchhhhhHHHHhccHHHHHHHHHHhcCCCCCCCce
Confidence 4567889999999999999999997 43333333333222 22222333333 3489999996
No 8
>PRK10263 DNA translocase FtsK; Provisional
Probab=63.52 E-value=62 Score=39.68 Aligned_cols=17 Identities=29% Similarity=0.358 Sum_probs=9.7
Q ss_pred HHHHHHHHHHhhccCcc
Q 013051 22 LCMLLVVLLVYSLSPSE 38 (450)
Q Consensus 22 lcM~~Vv~~v~~l~~~~ 38 (450)
+|+++.+++.-++-+|+
T Consensus 29 lLlllAlfL~lALiSYs 45 (1355)
T PRK10263 29 LIVLFAVWLMAALLSFN 45 (1355)
T ss_pred HHHHHHHHHHHHHHhCC
Confidence 45666666665555554
No 9
>KOG2443 consensus Uncharacterized conserved protein [Function unknown]
Probab=60.95 E-value=8.2 Score=40.46 Aligned_cols=53 Identities=28% Similarity=0.523 Sum_probs=44.5
Q ss_pred eeccchhhHHHHHhhhhhhcChhHHH---------HHHHHHHHHHHHHHHHHHhhcccCCCC
Q 013051 366 RLGLGDFIFYSVLVGRAAMYDLMTVY---------ACYLAIISGLGCTLILLSVCRRALPAL 418 (450)
Q Consensus 366 KLGLGDFIFYSVLVGrAA~~d~~t~~---------aCfvAIL~GL~~TLlLLav~~kALPAL 418 (450)
=|||||=+==++++.=.-.||.--.- ..|+|=..||..|...+-+||.|=|||
T Consensus 252 MLGLGDIviPGiflAl~lRfD~~k~~~s~~~~YF~~t~i~Y~~gL~~ti~~~~~FkaAQPAL 313 (362)
T KOG2443|consen 252 MLGLGDIVIPGIFLALVLRFDIRKKRNSKVRTYFHNTFIAYFLGLLTTIVVLHIFKAAQPAL 313 (362)
T ss_pred eccccchhhHHHHHHHHHHhhHHHHhcccCceEEEEeHHHHHhhhHHHhhhhhhhhccchhh
Confidence 59999999999998877777643322 357888899999999999999999998
No 10
>PF10749 DUF2534: Protein of unknown function (DUF2534); InterPro: IPR019685 This entry represents proteins with unknown function, and appear to be restricted to Enterobacteriaceae.
Probab=55.62 E-value=49 Score=28.07 Aligned_cols=38 Identities=21% Similarity=0.366 Sum_probs=27.0
Q ss_pred HhHHHHHHHHHHHcCCCcchhhHHHHhhhhhhheeeeeeecCcchhhHHHHHHHHHHH
Q 013051 115 TMGGSIFLSIIQQFSIPVDAFTCFVLLFNFTIVGVLSLFSGGIPILLRQAYMVCMGII 172 (450)
Q Consensus 115 ~~g~~~~~~vl~~~nip~D~iT~~~~l~NfgvvG~i~If~~k~Pl~lqQ~YLI~iSal 172 (450)
++|-..+.-+.++||+|++- | ...+++.|+.+|.+=.+
T Consensus 29 Vv~rAt~gGVi~qYniP~s~-------------------W-ttsMf~~Q~ami~vYS~ 66 (85)
T PF10749_consen 29 VVGRATIGGVIEQYNIPFSE-------------------W-TTSMFILQGAMILVYSI 66 (85)
T ss_pred HHHHHHHHhHHHHhCCChhh-------------------h-hHHHHHHHHHHHHHHHH
Confidence 33444455599999999974 3 56778888888887443
No 11
>PRK08343 secD preprotein translocase subunit SecD; Reviewed
Probab=44.44 E-value=1.5e+02 Score=31.84 Aligned_cols=83 Identities=12% Similarity=0.073 Sum_probs=43.9
Q ss_pred CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHH
Q 013051 59 RPDDSSTQKLEGAVLNALVFVILIAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCF 138 (450)
Q Consensus 59 ~~~ds~g~k~~~sl~Nali~v~vI~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~ 138 (450)
..+...+..+.....+..+..+++.+.-++++.+.+||-.+++- .+.++ ..+...++.-++..++.++|.++.+
T Consensus 246 ~~~~~v~~slg~~~~~~~l~a~ii~~ilVl~~m~~~yr~~~~i~-~iaL~-----~~~~v~~~lg~l~l~g~tLtl~~Ia 319 (417)
T PRK08343 246 EGSGSVSPSLGEQFKKGSLIAGLLALLAVALVVFLRYREPRIAL-PMVIT-----SLSEVIIILGFAALIGWQLDLASIA 319 (417)
T ss_pred EEccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH-----HHHHHHHHHHHHHHHCCCccHHHHH
Confidence 33455666677776666666565555444444444554433222 11111 1111122222345688999999998
Q ss_pred HHhhhhhhh
Q 013051 139 VLLFNFTIV 147 (450)
Q Consensus 139 ~~l~Nfgvv 147 (450)
-++.-.|+.
T Consensus 320 GlIl~iGma 328 (417)
T PRK08343 320 GIIAVIGTG 328 (417)
T ss_pred HHHHHHHHe
Confidence 877765543
No 12
>PF09125 COX2-transmemb: Cytochrome C oxidase subunit II, transmembrane; InterPro: IPR015209 This N-terminal domain forms the transmembrane region in subunit II of cytochrome c oxidase from Thermus thermophilus. This domain adopts a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold []. ; PDB: 1EHK_B 2QPE_B 3S8F_B 4EV3_B 3BVD_B 3S8G_B 3EH3_B 3S3C_B 3S39_B 3QJQ_B ....
Probab=40.26 E-value=30 Score=25.08 Aligned_cols=15 Identities=13% Similarity=0.445 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHh
Q 013051 102 KNYVRFSAFFVLGTM 116 (450)
Q Consensus 102 ~gwL~~Ss~~lL~~~ 116 (450)
+||+.|+..|++.+.
T Consensus 14 r~Wi~F~l~mi~vFi 28 (38)
T PF09125_consen 14 RGWIAFALAMILVFI 28 (38)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HhHHHHHHHHHHHHH
Confidence 799999999987654
No 13
>PF02355 SecD_SecF: Protein export membrane protein; InterPro: IPR022813 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. The chaperone protein SecB [] is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion []. Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA. The structure of the Escherichia coli SecYEG assembly revealed a sandwich of two membranes interacting through the extensive cytoplasmic domains []. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. The SecD and SecF equivalents of the Gram-positive bacterium Bacillus subtilis are jointly present in one polypeptide, denoted SecDF, that is required to maintain a high capacity for protein secretion. Unlike the SecD subunit of the pre-protein translocase of E. coli, SecDF of B. subtilis was not required for the release of a mature secretory protein from the membrane, indicating that SecDF is involved in earlier translocation steps []. Comparison with SecD and SecF proteins from other organisms revealed the presence of 10 conserved regions in SecDF, some of which appear to be important for SecDF function. Interestingly, the SecDF protein of B. subtilis has 12 putative transmembrane domains. Thus, SecDF does not only show sequence similarity but also structural similarity to secondary solute transporters []. This entry represents bacterial SecD and SecF protein export membrane proteins and their archaeal homologues []. It is found in association with PF07549 from PFAM SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC []. SecD and SecF are required to maintain a proton motive force []. ; PDB: 3AQP_A 2RRN_A 3AQO_B.
Probab=39.26 E-value=1.4e+02 Score=28.49 Aligned_cols=77 Identities=17% Similarity=0.226 Sum_probs=37.9
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHHh
Q 013051 62 DSSTQKLEGAVLNALVFVILIAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVLL 141 (450)
Q Consensus 62 ds~g~k~~~sl~Nali~v~vI~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~l 141 (450)
+..|..+.+-+.+..+....+++.-..++++.+||. -+..+..+.....-....-++..+++++|-++++-++
T Consensus 19 ~~Vgp~~g~~~~~~~~~a~~~al~~i~iyi~~rf~~-------~~~~~aii~l~~dv~i~l~~~~~~~~~l~l~~iaall 91 (189)
T PF02355_consen 19 NTVGPTLGSDLLKSALIALIIALIAILIYIFLRFRW-------RFALAAIIALIHDVLITLGIFSLFGIELTLPSIAALL 91 (189)
T ss_dssp EEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTH-------HHHHHHHHHHHHHHHHHHHHHHHHT-EE-HHHHHHHH
T ss_pred EEEChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-------chHHHHHHHHHHHHHHHHHHHHHHCCcccHHHHHHHH
Confidence 334555555555555555545554455555666662 1111111112222222333556688999998888777
Q ss_pred hhhh
Q 013051 142 FNFT 145 (450)
Q Consensus 142 ~Nfg 145 (450)
.-.|
T Consensus 92 ~~iG 95 (189)
T PF02355_consen 92 TIIG 95 (189)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 6654
No 14
>PF14362 DUF4407: Domain of unknown function (DUF4407)
Probab=38.38 E-value=45 Score=33.58 Aligned_cols=19 Identities=32% Similarity=0.443 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHHHhhc
Q 013051 394 YLAIISGLGCTLILLSVCR 412 (450)
Q Consensus 394 fvAIL~GL~~TLlLLav~~ 412 (450)
+.+|++|++.-++.+.+.|
T Consensus 46 ~~ai~~glvwgl~I~~lDR 64 (301)
T PF14362_consen 46 WAAIPFGLVWGLVIFNLDR 64 (301)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4444444444444444433
No 15
>PF13314 DUF4083: Domain of unknown function (DUF4083)
Probab=36.06 E-value=43 Score=26.58 Aligned_cols=25 Identities=32% Similarity=0.733 Sum_probs=16.2
Q ss_pred cchhhHHHHHhhhhhhcChhHHHHHHHHHHHHHHHHHHH
Q 013051 369 LGDFIFYSVLVGRAAMYDLMTVYACYLAIISGLGCTLIL 407 (450)
Q Consensus 369 LGDFIFYSVLVGrAA~~d~~t~~aCfvAIL~GL~~TLlL 407 (450)
+||+|||.+.+| +.+|+|+..|++.
T Consensus 3 i~~~Iy~~~Vi~--------------l~vl~~~~Ftl~I 27 (58)
T PF13314_consen 3 IGDLIYYILVII--------------LIVLFGASFTLFI 27 (58)
T ss_pred HHHHHHHHHHHH--------------HHHHHHHHHHHHH
Confidence 577777765443 5667777777653
No 16
>KOG4694 consensus Predicted membrane protein [Function unknown]
Probab=35.61 E-value=44 Score=31.48 Aligned_cols=58 Identities=26% Similarity=0.320 Sum_probs=41.5
Q ss_pred CCceeeccchhhHHHHHhhhhhh-cChhHHHHHHHHHHHHHHHHHHHHHhhcccCCCCchHHHHHHHHH
Q 013051 362 DRGIRLGLGDFIFYSVLVGRAAM-YDLMTVYACYLAIISGLGCTLILLSVCRRALPALPISITLGVLFY 429 (450)
Q Consensus 362 ~~gIKLGLGDFIFYSVLVGrAA~-~d~~t~~aCfvAIL~GL~~TLlLLav~~kALPALPISI~lGliFY 429 (450)
.++|||||| ||.=|--+|.. .++-++- +++-|=++++| .+..++--||.=+++-++|=
T Consensus 66 ~E~vRLylG---y~gNL~e~~~al~gfl~~t-----~~iqlPl~vFL--~~n~~~~nLpLe~~~~~vft 124 (174)
T KOG4694|consen 66 AESVRLYLG---YSGNLCEGATALWGFLTVT-----PCIQLPLMVFL--RLNAAGRNLPLEIITNAVFT 124 (174)
T ss_pred HHHHHhhcc---hhhhHhhchHHHHHHHHHH-----HHHHHHHHHHH--HHccccccCcHHHHHHHHHH
Confidence 568999999 99888888866 4655543 33444444444 46779999999998877764
No 17
>PF09971 DUF2206: Predicted membrane protein (DUF2206); InterPro: IPR018701 This family of predicted membrane proteins from archaea has no known function.
Probab=31.07 E-value=84 Score=33.24 Aligned_cols=63 Identities=16% Similarity=0.234 Sum_probs=35.4
Q ss_pred HHHHhchHhHH--HHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHHhhhhhhheeeeee
Q 013051 91 LLYYYNFTNFL--KNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVLLFNFTIVGVLSLF 153 (450)
Q Consensus 91 lLYkyrc~k~i--~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~l~NfgvvG~i~If 153 (450)
++||.+-.|.- .-|+.+|..++..+..+..+--.-..+|..==|-...+++=.|.+.|.+.++
T Consensus 135 ~~~~~~~~k~~~~~~Yl~fs~~~~iiLia~i~lP~fa~~mn~~RLy~itli~LAPf~iiG~~~~~ 199 (367)
T PF09971_consen 135 LILKRIYKKIKFNIEYLAFSLVSLIILIASIVLPFFASVMNPTRLYQITLIFLAPFFIIGGITLF 199 (367)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhccchhhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455554544 7889999988877777753332222344433344444555555555555544
No 18
>TIGR01129 secD protein-export membrane protein SecD. SecD from Mycobacterium tuberculosis has a long Pro-rich insert.
Probab=30.21 E-value=3.2e+02 Score=29.14 Aligned_cols=79 Identities=18% Similarity=0.282 Sum_probs=42.4
Q ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHH
Q 013051 61 DDSSTQKLEGAVLNALVFVILIAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVL 140 (450)
Q Consensus 61 ~ds~g~k~~~sl~Nali~v~vI~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~ 140 (450)
+++.|..+....++..+.-.+++++-++++++.+|| ..|....-++.+ ...+..-++..+|+++|.++++-+
T Consensus 235 ~~~vgp~lg~~~i~~~~~a~~ig~ilV~l~~~~~yr----~~gl~a~ial~~----~v~~~l~~~~l~g~~l~l~siagl 306 (397)
T TIGR01129 235 ERTIGPSLGADSIEAGIKAGLIGLVLVLVFMILYYR----LFGLIAAIALVI----NIVLILAILSAFGATLTLPGIAGL 306 (397)
T ss_pred ccCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HhHHHHHHHHHH----HHHHHHHHHHHHCCCccHHHHHHH
Confidence 444555565555555555555555555555666666 233332222211 111122344567999999999877
Q ss_pred hhhhhhh
Q 013051 141 LFNFTIV 147 (450)
Q Consensus 141 l~Nfgvv 147 (450)
+.-.|..
T Consensus 307 il~iG~~ 313 (397)
T TIGR01129 307 ILTIGMA 313 (397)
T ss_pred HHHhhee
Confidence 7655543
No 19
>COG5249 RER1 Golgi protein involved in Golgi-to-ER retrieval [Intracellular trafficking and secretion]
Probab=30.12 E-value=1e+02 Score=28.95 Aligned_cols=61 Identities=23% Similarity=0.341 Sum_probs=38.0
Q ss_pred hhhHHHHH-----------HHHHHHHHHHHhcCChhHHH-HHHHHHHHHHH---HhhcCCCChHHHHHHHHhhcCCCCC
Q 013051 159 ILLRQAYM-----------VCMGIIMAAWFTNLPEWTTW-ALLLALALYDL---FAVLAPGGPLKLLVELASSRDEELP 222 (450)
Q Consensus 159 l~lqQ~YL-----------I~iSalmA~~f~~LPeWTtW-~lL~~iaiyDL---~AVL~P~GPLr~LVE~AqeRne~IP 222 (450)
..|+|-|| -..+.|.++++++.=-=-.| ++.-++++|=| .|-|+|||-.- +|-+. .||+||
T Consensus 19 k~LyqhylDr~~P~~~~RW~i~ggL~~lf~iRI~~~~gwY~icY~LgiyLLn~flaFLTPKfdms--~eq~e-~d~eie 94 (180)
T COG5249 19 KTLYQHYLDRLAPRPDVRWGITGGLFLLFCIRIWSTGGWYLICYCLGIYLLNAFLAFLTPKFDMS--FEQIE-DDDEIE 94 (180)
T ss_pred HHHHHHHHhhcCCCCcchhhHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHhCCCCccc--Hhhhc-cccccc
Confidence 46777776 35678888888762111123 45566777755 88999999543 55543 344554
No 20
>TIGR02854 spore_II_GA sigma-E processing peptidase SpoIIGA. Members of this protein family are the stage II sporulation protein SpoIIGA. This protein acts as an activating protease for Sigma-E, one of several specialized sigma factors of the sporulation process in Bacillus subtilis and related endospore-forming bacteria.
Probab=28.78 E-value=1.6e+02 Score=29.97 Aligned_cols=45 Identities=11% Similarity=0.242 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHHhhhhhhhe-eeeeee
Q 013051 102 KNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVLLFNFTIVG-VLSLFS 154 (450)
Q Consensus 102 ~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~l~NfgvvG-~i~If~ 154 (450)
-.-+.+|.+|+...||..-+...+|.. +.|.+.||.+.| ++|+|+
T Consensus 62 ~~k~~~s~lmv~iafg~~~~~~f~k~~--------~~fy~~sf~~gG~~~~~~~ 107 (288)
T TIGR02854 62 IAKLLYSFLIIFIAFGPKSLRFFLKLL--------FLFYFVSFATGGGLFALHF 107 (288)
T ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHH--------HHHHHHHHHHhhHHHhhhh
Confidence 344567777777777776666666542 455666766666 345554
No 21
>PF08041 PetM: PetM family of cytochrome b6f complex subunit 7; InterPro: IPR012595 This family consists of the PetM family of cytochrome b6f complex subunit IV. The cytochrome b6f complex consists of 7 subunits and contains 2 beta haem's and 1 chlorophyll alpha per cytochrome f. It is highly active in transferring electrons from decylplastoquinol to oxidised plastocyanin [].; GO: 0009512 cytochrome b6f complex; PDB: 2ZT9_F 1Q90_M 2E76_F 2E75_F 2E74_F 2D2C_S 1VF5_S.
Probab=28.39 E-value=1.1e+02 Score=21.53 Aligned_cols=24 Identities=21% Similarity=0.530 Sum_probs=20.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHh
Q 013051 387 LMTVYACYLAIISGLGCTLILLSV 410 (450)
Q Consensus 387 ~~t~~aCfvAIL~GL~~TLlLLav 410 (450)
+++...||+-+|+||.+--+||=+
T Consensus 4 f~~a~i~~~lvlvGla~Gf~LLki 27 (31)
T PF08041_consen 4 FNIAVICFGLVLVGLALGFVLLKI 27 (31)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHhhee
Confidence 456788999999999999888865
No 22
>TIGR00916 2A0604s01 protein-export membrane protein, SecD/SecF family. The SecA,SecB,SecD,SecE,SecF,SecG and SecY proteins form the protein translocation appartus in prokaryotes. This family is specific for the SecD and SecF proteins.
Probab=27.29 E-value=4.8e+02 Score=24.75 Aligned_cols=29 Identities=10% Similarity=-0.095 Sum_probs=20.7
Q ss_pred HHHcCCCcchhhHHHHhhhhhhheeeeee
Q 013051 125 IQQFSIPVDAFTCFVLLFNFTIVGVLSLF 153 (450)
Q Consensus 125 l~~~nip~D~iT~~~~l~NfgvvG~i~If 153 (450)
+..+++|+|-.|..-++.=+|+.=-=+||
T Consensus 91 m~l~G~~ln~~s~~glil~iGi~Vd~aIv 119 (192)
T TIGR00916 91 LSLFGATLTLPGIAGLLTIIGYSVDDTVV 119 (192)
T ss_pred HHHHCCcccHHHHHHHHHHHHHhhcCeEE
Confidence 44588999999998877766665444554
No 23
>KOG3807 consensus Predicted membrane protein ST7 (tumor suppressor in humans) [General function prediction only]
Probab=26.99 E-value=49 Score=35.23 Aligned_cols=34 Identities=35% Similarity=0.558 Sum_probs=24.9
Q ss_pred HHHHHhcCChhHHHHHHHHHHHHHHHhhcCCCChHHHHHHHH
Q 013051 173 MAAWFTNLPEWTTWALLLALALYDLFAVLAPGGPLKLLVELA 214 (450)
Q Consensus 173 mA~~f~~LPeWTtW~lL~~iaiyDL~AVL~P~GPLr~LVE~A 214 (450)
|+|..+.| |+.|+.+++..+|-| +||||+=-+++
T Consensus 16 ~~~swt~l--w~lw~~~v~~ll~~l------r~plki~e~l~ 49 (556)
T KOG3807|consen 16 LGWSWTLL--WSLWFVAVLGLLYAL------RIPLKICENLA 49 (556)
T ss_pred hhhhHHHH--HHHHHHHHHHHHHHH------hcchhhhccHH
Confidence 34444443 999999999998876 89999855444
No 24
>PF03176 MMPL: MMPL family; InterPro: IPR004869 Proteins of this entry are putative integral membrane proteins from bacteria. Several of the members are mycobacterial proteins. Many of the proteins contain two copies of this aligned region. The function of these proteins is not known, although it has been suggested that they may be involved in lipid transport [].; GO: 0016020 membrane
Probab=24.74 E-value=4.1e+02 Score=26.67 Aligned_cols=128 Identities=17% Similarity=0.194 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHHh-hhhhhhee-
Q 013051 72 VLNALVFVILIAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVLL-FNFTIVGV- 149 (450)
Q Consensus 72 l~Nali~v~vI~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~l-~NfgvvG~- 149 (450)
+...+.....+++.-.++++++-||-.+..-.-++...+-++..+|. ..-+....++++|.++..++. .=+|+ |+
T Consensus 141 ~~~~~~~~~~~~l~~i~lvl~~~fRs~~~~l~~l~~~~~~~~~~~g~--~~~~~~~~~~~~~~~~~~l~~~l~lgv-gid 217 (333)
T PF03176_consen 141 IQHDLLRSGLLALLLIFLVLLLVFRSVRAALLPLLPVLLSIVWTLGL--VALLMGLLGIPLSWITPALVFVLLLGV-GID 217 (333)
T ss_pred HHHHHHHhHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHhhccccceeehHhhhhhHHHh-hhh
Confidence 33344455555566666677777776554444444444444555555 122233467788776654422 22222 22
Q ss_pred eeeee---cC-----cchh---hH-----------HHHHHHHHHHHHHHHhcCChhHHHHHHHHHHH-HHHHhhcC
Q 013051 150 LSLFS---GG-----IPIL---LR-----------QAYMVCMGIIMAAWFTNLPEWTTWALLLALAL-YDLFAVLA 202 (450)
Q Consensus 150 i~If~---~k-----~Pl~---lq-----------Q~YLI~iSalmA~~f~~LPeWTtW~lL~~iai-yDL~AVL~ 202 (450)
-+||. ++ +.-. ++ -+=++.+..+.++.|..+|---..-++.++++ .++++.++
T Consensus 218 y~i~l~~r~ree~~~g~~~~~ai~~a~~~~g~~i~~s~ltt~~gf~~L~~s~~~~~~~~G~~~~~gi~~~~l~~l~ 293 (333)
T PF03176_consen 218 YSIHLINRYREELRRGMSRKEAIRRAVRSTGRAILLSALTTAIGFGSLLFSPFPPLRQFGLLAAIGILIALLLSLT 293 (333)
T ss_pred hHHHHHHHHHHHHHhccchHHHHHHHHhccCchhHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 23442 11 1110 11 12234555577778888998777765544443 35554443
No 25
>PF09858 DUF2085: Predicted membrane protein (DUF2085); InterPro: IPR019206 This entry, found in various hypothetical prokaryotic proteins, has no known function.
Probab=24.63 E-value=1.6e+02 Score=25.28 Aligned_cols=32 Identities=34% Similarity=0.403 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHhhcccCCCCchHHHHHH
Q 013051 395 LAIISGLGCTLILLSVCRRALPALPISITLGV 426 (450)
Q Consensus 395 vAIL~GL~~TLlLLav~~kALPALPISI~lGl 426 (450)
.+|.+|+.+.+++....|+.++.+|+.+++..
T Consensus 24 tGiy~G~~~~~~~~~~~r~~~~~~~~~~~~l~ 55 (93)
T PF09858_consen 24 TGIYLGLLIGLLLFYLGRIRLPPLSIWLALLL 55 (93)
T ss_pred HHHHHHHHHHHHHHHHhhcccccchHHHHHHH
Confidence 47888999989999888888887777776654
No 26
>PRK13023 bifunctional preprotein translocase subunit SecD/SecF; Reviewed
Probab=24.36 E-value=3.9e+02 Score=31.20 Aligned_cols=81 Identities=14% Similarity=0.196 Sum_probs=50.6
Q ss_pred CCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHH
Q 013051 60 PDDSSTQKLEGAVLNALVFVILIAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFV 139 (450)
Q Consensus 60 ~~ds~g~k~~~sl~Nali~v~vI~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~ 139 (450)
++.+.|..+.....+..+.-++++++-+++.+.++||- .|+...-++.+ ...+..-++..++++++-++.+-
T Consensus 264 ~~~~VgptLG~~~~~~~~~A~ii~~~lV~lfm~~~Y~~----~glia~iaL~~----~v~~tl~~l~l~g~~Lnl~siaG 335 (758)
T PRK13023 264 EERTIASALGEDYASAAVLAALLAALVVGLFMVLSYGI----LGVIALVALVV----NIIILTAVLSLIGASISLASIAG 335 (758)
T ss_pred eeeccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHH----HHHHHHHHHHHHCCCccHHHHHH
Confidence 34556777777777777777766666666666677763 34433222222 22222235556899999999999
Q ss_pred Hhhhhhhhe
Q 013051 140 LLFNFTIVG 148 (450)
Q Consensus 140 ~l~NfgvvG 148 (450)
++.-.|+.=
T Consensus 336 lIL~IGm~V 344 (758)
T PRK13023 336 LVLTIGLAV 344 (758)
T ss_pred HHHHHHHhc
Confidence 888766553
No 27
>PRK11876 petM cytochrome b6-f complex subunit PetM; Reviewed
Probab=24.09 E-value=1e+02 Score=21.74 Aligned_cols=23 Identities=22% Similarity=0.242 Sum_probs=19.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHH
Q 013051 387 LMTVYACYLAIISGLGCTLILLS 409 (450)
Q Consensus 387 ~~t~~aCfvAIL~GL~~TLlLLa 409 (450)
+++...||.-+|+||.+-.+||=
T Consensus 6 f~~A~i~~~LvlvGlalGf~LLk 28 (32)
T PRK11876 6 FGIAALFWVLIPVGLAGGALLLK 28 (32)
T ss_pred HHHHHHHHHHHHHHHHHHHHhee
Confidence 46678899999999999888774
No 28
>KOG2442 consensus Uncharacterized conserved protein, contains PA domain [General function prediction only]
Probab=23.23 E-value=2.3e+02 Score=31.41 Aligned_cols=50 Identities=42% Similarity=0.608 Sum_probs=32.9
Q ss_pred HHHHHHhcCCh--hHHHHHHHHHHHHHHHhhc---------------CCCChHHHHHHHHhhcCCCCCeeeecccC
Q 013051 172 IMAAWFTNLPE--WTTWALLLALALYDLFAVL---------------APGGPLKLLVELASSRDEELPALVYEARP 230 (450)
Q Consensus 172 lmA~~f~~LPe--WTtW~lL~~iaiyDL~AVL---------------~P~GPLr~LVE~AqeRne~IPALiYss~~ 230 (450)
+..+.-.+||. |-+ ++|.++-+||+|=|- --.|| +.-+|.||-|+==.+.
T Consensus 351 i~vLk~vRLPnlK~~t-iLL~c~f~YDiF~VFitp~~t~~geSVMieVA~G~--------~s~~EkiPMlLkVPrl 417 (541)
T KOG2442|consen 351 ITVLKTVRLPNLKVCT-ILLLCLFLYDIFFVFITPFITKNGESVMIEVARGP--------SSTEEKIPMLLKVPRL 417 (541)
T ss_pred HHHHHHhcCCchhHHH-HHHHHHHHHhhheeeeehhhccCCceEEEEEecCC--------CCCCCCcceEEEcchh
Confidence 45556677994 544 566777899998875 23577 4446777887655443
No 29
>PF14329 DUF4386: Domain of unknown function (DUF4386)
Probab=23.14 E-value=2.4e+02 Score=26.75 Aligned_cols=34 Identities=21% Similarity=0.181 Sum_probs=23.6
Q ss_pred HHHHHHHHHHh--c-CChhHHHHHHHHHHHHHHHhhc
Q 013051 168 CMGIIMAAWFT--N-LPEWTTWALLLALALYDLFAVL 201 (450)
Q Consensus 168 ~iSalmA~~f~--~-LPeWTtW~lL~~iaiyDL~AVL 201 (450)
.-+.++++.+. + +|.|-.|..+++=..|=+-.+.
T Consensus 144 ~~~lllg~l~~rs~~~Pr~l~~lg~v~g~~~l~~~~~ 180 (215)
T PF14329_consen 144 LWLLLLGYLLLRSRLLPRWLGALGLVAGIGYLADSLL 180 (215)
T ss_pred HHHHHHHHHHHHcCchhHHHHHHHHHHHHHHHHHHHH
Confidence 33446665543 3 8999999999988888664443
No 30
>PRK05812 secD preprotein translocase subunit SecD; Reviewed
Probab=22.62 E-value=4.5e+02 Score=29.08 Aligned_cols=78 Identities=14% Similarity=0.231 Sum_probs=44.2
Q ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHH
Q 013051 61 DDSSTQKLEGAVLNALVFVILIAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVL 140 (450)
Q Consensus 61 ~ds~g~k~~~sl~Nali~v~vI~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~ 140 (450)
+++.|..+.+..++..+.-++++++-++++++++|| ..|....-++. +......-++..++++++.++++-+
T Consensus 320 ~~~VgpslG~~~i~~~~~A~lig~ilV~i~m~~~yr----~~glia~iaL~----~~v~~~l~~~~l~g~~l~l~siaGl 391 (498)
T PRK05812 320 ERTIGPSLGADSIRAGLIAGLIGLALVLLFMILYYR----LFGLIANIALV----ANLVLILAVLSLLGATLTLPGIAGI 391 (498)
T ss_pred ccccCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHh----hhHHHHHHHHH----HHHHHHHHHHHHHCCCchHHHHHHH
Confidence 455666666666666666666666666666666666 13333322221 1111222244557899999999877
Q ss_pred hhhhhh
Q 013051 141 LFNFTI 146 (450)
Q Consensus 141 l~Nfgv 146 (450)
+.-.|+
T Consensus 392 il~iG~ 397 (498)
T PRK05812 392 VLTIGM 397 (498)
T ss_pred HHhhee
Confidence 765443
No 31
>PF10066 DUF2304: Uncharacterized conserved protein (DUF2304); InterPro: IPR019277 This entry represents hypothetical archaeal and bacterial proteins that have no known function.
Probab=21.17 E-value=5.5e+02 Score=22.30 Aligned_cols=42 Identities=17% Similarity=0.283 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHcCC--CcchhhHHHHhhhh
Q 013051 103 NYVRFSAFFVLGTMGGSIFLSIIQQFSI--PVDAFTCFVLLFNF 144 (450)
Q Consensus 103 gwL~~Ss~~lL~~~g~~~~~~vl~~~ni--p~D~iT~~~~l~Nf 144 (450)
.|+.++.+++++..-=.....+-+..|+ |.|.+-+..++.-+
T Consensus 35 ~Wl~~~i~~l~~~ifP~~~~~vA~~lGi~~~~n~lf~~~i~~ll 78 (115)
T PF10066_consen 35 LWLVFSIILLILSIFPNILDWVAKLLGIGRPPNLLFYLGILFLL 78 (115)
T ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHCCCchhHHHHHHHHHHHH
Confidence 5888888888777777777777777666 66666655554443
No 32
>PRK13022 secF preprotein translocase subunit SecF; Reviewed
Probab=21.05 E-value=5.5e+02 Score=26.08 Aligned_cols=77 Identities=16% Similarity=0.197 Sum_probs=37.1
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHHhh
Q 013051 63 SSTQKLEGAVLNALVFVILIAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVLLF 142 (450)
Q Consensus 63 s~g~k~~~sl~Nali~v~vI~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~l~ 142 (450)
..|.++.+.+.+.++....+++.-.++.+.+.|+. -.+=..+.++ ++.+++. .-++.-+++|+|..+.+-++.
T Consensus 116 ~Vg~~vg~~~~~~~~~a~~~al~~i~i~l~~~F~~---~~~l~~ilal-~~~v~~~---lg~~~l~g~~l~~~siaall~ 188 (289)
T PRK13022 116 FVGPQVGKELAQKGLLALLVALVGILIYIAFRFEW---RFALGAIIAL-LHDVIIT---LGIFSLFQIEFDLTVIAALLT 188 (289)
T ss_pred EEChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHH-HHHHHHH---HHHHHHHCCcccHHHHHHHHH
Confidence 34555656666655555544444444444444441 1111111111 1111111 113445689999888876666
Q ss_pred hhhh
Q 013051 143 NFTI 146 (450)
Q Consensus 143 Nfgv 146 (450)
=.|.
T Consensus 189 liG~ 192 (289)
T PRK13022 189 IIGY 192 (289)
T ss_pred HHHH
Confidence 4443
No 33
>PF11674 DUF3270: Protein of unknown function (DUF3270); InterPro: IPR021688 This family of proteins with unknown function appears to be restricted to Streptococcus.
Probab=20.50 E-value=1.5e+02 Score=25.60 Aligned_cols=23 Identities=35% Similarity=0.378 Sum_probs=15.9
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHH
Q 013051 386 DLMTVYACYLAIISGLGCTLILL 408 (450)
Q Consensus 386 d~~t~~aCfvAIL~GL~~TLlLL 408 (450)
.++|+.|-.+||++||++|.+.=
T Consensus 63 kl~t~~Af~~Ai~~Sl~~~~~~~ 85 (90)
T PF11674_consen 63 KLNTFWAFPLAILISLAITQLVR 85 (90)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHH
Confidence 56777777777777777665543
No 34
>COG0342 SecD Preprotein translocase subunit SecD [Intracellular trafficking and secretion]
Probab=20.44 E-value=3e+02 Score=30.49 Aligned_cols=86 Identities=13% Similarity=0.236 Sum_probs=47.8
Q ss_pred CCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHH
Q 013051 61 DDSSTQKLEGAVLNALVFVILIAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVL 140 (450)
Q Consensus 61 ~ds~g~k~~~sl~Nali~v~vI~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~ 140 (450)
+.+.|-.++.--+..-++-+++.+.-+++..+.+||. .|. ++++.++. ...++..++..+|..+|.+..+=+
T Consensus 330 ~rtVgpsLG~~~i~~gi~Agl~g~~~V~vfm~~~Yr~----~Gv--ia~ial~~--n~~lil~vls~lgatLtLpgIAGi 401 (506)
T COG0342 330 ERTVGPTLGADSIKAGLIAGLIGLALVAVFMLLYYRL----AGV--IAAIALGL--NGVLILAVLSLLGATLTLPGIAGI 401 (506)
T ss_pred eeeECcccChHHHHHHHHHHHHHHHHHHHHHHHHHHH----hHH--HHHHHHHH--HHHHHHHHHHHhcccccchhhhHH
Confidence 3445555554444444445544444444455556652 222 22222222 333444566667999999999999
Q ss_pred hhhhhh--heeeeeee
Q 013051 141 LFNFTI--VGVLSLFS 154 (450)
Q Consensus 141 l~Nfgv--vG~i~If~ 154 (450)
+...|+ =+-+-||-
T Consensus 402 ILtIGmaVDaNVlI~E 417 (506)
T COG0342 402 ILTIGMAVDANVLIFE 417 (506)
T ss_pred HHhhhhcccccEEeeH
Confidence 988553 35566764
No 35
>TIGR00966 3a0501s07 protein-export membrane protein SecF. This bacterial protein is always found with the homologous protein-export membrane protein SecD. In numerous lineages, this protein occurs as a SecDF fusion protein.
Probab=20.06 E-value=7.4e+02 Score=24.32 Aligned_cols=76 Identities=18% Similarity=0.189 Sum_probs=37.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchHhHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCCcchhhHHHHhhhh
Q 013051 65 TQKLEGAVLNALVFVILIAIVTFLLVLLYYYNFTNFLKNYVRFSAFFVLGTMGGSIFLSIIQQFSIPVDAFTCFVLLFNF 144 (450)
Q Consensus 65 g~k~~~sl~Nali~v~vI~vmTf~lVlLYkyrc~k~i~gwL~~Ss~~lL~~~g~~~~~~vl~~~nip~D~iT~~~~l~Nf 144 (450)
+..+.+.+.+.++....+++.-.++.+...|| .-.+...+.+ +.+.+++... ++.-+|++++-.+++-++.=.
T Consensus 89 ~~~v~~~~~~~~~~~~~la~i~i~l~l~~~f~---~r~~l~v~~~-ip~~l~~~~~---~l~~~g~~ln~~sl~gli~~i 161 (246)
T TIGR00966 89 GPSVGGELARKAVLALLAALVLILIYITVRFE---WRFALGAIVA-LVHDVIITVG---VYSLFGIEVNLTTVAALLTII 161 (246)
T ss_pred CHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHH-HHHHHHHHHH---HHHHHCCcccHHHHHHHHHHH
Confidence 44555555555554444433333333333333 2233333322 2233333322 223468999999888777655
Q ss_pred hhh
Q 013051 145 TIV 147 (450)
Q Consensus 145 gvv 147 (450)
|..
T Consensus 162 Gi~ 164 (246)
T TIGR00966 162 GYS 164 (246)
T ss_pred HHh
Confidence 544
Done!