Query psy5397
Match_columns 112
No_of_seqs 111 out of 183
Neff 4.1
Searched_HMMs 46136
Date Sat Aug 17 01:31:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5397.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5397hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02109 DAD: DAD family; Int 100.0 4.1E-63 9E-68 357.2 11.6 111 2-112 2-112 (112)
2 KOG1746|consensus 100.0 1.4E-59 3.1E-64 338.3 12.4 111 2-112 5-115 (115)
3 TIGR02838 spore_V_AC stage V s 89.9 1.2 2.7E-05 33.7 6.0 64 12-104 3-68 (141)
4 KOG1654|consensus 78.2 1.3 2.9E-05 32.7 1.5 30 61-91 55-87 (116)
5 PF04148 Erv26: Transmembrane 72.3 2.5 5.5E-05 33.8 1.8 49 8-56 30-93 (211)
6 PRK07668 hypothetical protein; 56.1 44 0.00096 27.3 6.2 88 3-94 55-143 (254)
7 PF14333 DUF4389: Domain of un 47.1 84 0.0018 20.9 6.2 36 34-71 27-62 (80)
8 PTZ00380 microtubule-associate 37.5 18 0.00039 26.7 1.1 19 61-79 51-69 (121)
9 PF06939 DUF1286: Protein of u 35.5 49 0.0011 24.4 3.1 38 32-69 7-44 (114)
10 PF09412 XendoU: Endoribonucle 32.3 54 0.0012 26.8 3.2 43 6-48 64-113 (265)
11 PRK14584 hmsS hemin storage sy 29.7 1.7E+02 0.0037 22.4 5.3 28 23-50 14-41 (153)
12 PF09877 DUF2104: Predicted me 28.3 1.3E+02 0.0028 21.7 4.2 29 13-41 22-51 (99)
13 PRK09400 secE preprotein trans 27.9 1.7E+02 0.0038 18.9 5.2 42 2-43 4-53 (61)
14 cd03495 SQR_TypeC_SdhD_like Su 27.3 1.3E+02 0.0027 20.7 4.0 29 8-36 63-91 (100)
15 PF03862 SpoVA: SpoVA protein; 26.6 1.2E+02 0.0026 22.3 3.9 42 56-104 9-50 (119)
16 PF03591 AzlC: AzlC protein; 26.5 2.5E+02 0.0055 20.3 7.5 77 29-106 30-127 (143)
17 PF07019 Rab5ip: Rab5-interact 26.4 1.9E+02 0.0041 18.8 4.7 17 88-104 57-73 (81)
18 TIGR00834 ae anion exchange pr 26.3 4.5E+02 0.0099 25.4 8.5 55 52-110 558-612 (900)
19 KOG1688|consensus 26.2 1.5E+02 0.0032 23.6 4.6 52 6-57 22-80 (188)
20 KOG0585|consensus 25.4 31 0.00068 31.5 0.8 14 41-54 308-321 (576)
21 PRK14094 psbM photosystem II r 22.7 1.3E+02 0.0028 19.3 3.0 17 68-84 21-37 (50)
22 COG0735 Fur Fe2+/Zn2+ uptake r 22.6 85 0.0018 22.9 2.5 61 5-67 6-66 (145)
23 PF05512 AWPM-19: AWPM-19-like 22.4 1.3E+02 0.0028 22.9 3.5 26 19-47 113-138 (142)
24 PF14012 DUF4229: Protein of u 22.4 2.3E+02 0.0051 18.5 5.0 50 29-78 9-60 (69)
25 PF06750 DiS_P_DiS: Bacterial 21.3 67 0.0015 22.0 1.7 20 60-79 3-22 (92)
26 COG4508 Dimeric dUTPase [Carbo 20.9 74 0.0016 24.6 1.9 58 41-100 50-116 (161)
27 TIGR00261 traB pheromone shutd 20.6 2.3E+02 0.005 24.4 5.1 72 24-95 266-344 (380)
28 PF11188 DUF2975: Protein of u 20.6 2.8E+02 0.0061 18.7 7.1 41 7-47 42-85 (136)
29 TIGR00994 3a0901s05TIC20 chlor 20.3 1.3E+02 0.0028 25.2 3.3 27 31-57 231-257 (267)
No 1
>PF02109 DAD: DAD family; InterPro: IPR003038 Members of this family are thought to be integral membrane proteins. Some members of this family have been shown to cause apoptosis if mutated [], these proteins are known as DAD for defender against death. The family also includes the epsilon subunit of the oligosaccharyltransferase that is involved in N-linked glycosylation [].; GO: 0016021 integral to membrane
Probab=100.00 E-value=4.1e-63 Score=357.21 Aligned_cols=111 Identities=59% Similarity=1.159 Sum_probs=109.6
Q ss_pred ccHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHHHHhhhhhhccCCCC
Q psy5397 2 AGFQAVLGKIHHEYVNNTPKKLKIIDAYLFYILLTGAFQFLYCCLVGTFPFNSFLSGFISCVSSFVLGVCLRLQVNPQNQ 81 (112)
Q Consensus 2 ~~~~~i~~~~~~~Y~~~Tp~rlKliD~fl~fl~~~giiQf~Yc~lvgtfPFNaFLsgf~s~VG~fVL~vsLR~Q~~~~nk 81 (112)
+++.++++++|++|.++||+|+|+||+|++|++++|++||+||+++||||||||||||++|||||||++|||+|+||+||
T Consensus 2 ~~~~~~~~~~~~~Y~~~Tp~rlkliD~fl~f~~~~gilQfvYc~lvgtFPFNaFLsGf~s~VG~fVL~vsLR~Q~~p~n~ 81 (112)
T PF02109_consen 2 SSFQEILSNFWQSYLKKTPQRLKLIDAFLAFLVLTGILQFVYCILVGTFPFNAFLSGFISCVGQFVLTVSLRIQLNPENK 81 (112)
T ss_pred chHHHHHHHHHHHHHHhCCchhhhHHHHHHHHHHHHHHHHhHheeecCCchHHHHHHHHHHHHHHHHHHHHHHhcccccc
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccCCCCCchHHHHHHHHHHHHHHhhhcccC
Q psy5397 82 KDFVGISPERGFADFIFAHVILHLVVMNFIG 112 (112)
Q Consensus 82 ~~F~~iS~eRAfaDfv~~slvLh~~v~nFiG 112 (112)
++|+++|||||||||++||+|||++|+||||
T Consensus 82 ~~f~~is~eRafaDfv~~slvLh~~v~nFig 112 (112)
T PF02109_consen 82 SEFPGISPERAFADFVFCSLVLHFVVFNFIG 112 (112)
T ss_pred cccCCCChhhhhHHHHHHHHHHHHheeeccC
Confidence 9999999999999999999999999999998
No 2
>KOG1746|consensus
Probab=100.00 E-value=1.4e-59 Score=338.32 Aligned_cols=111 Identities=68% Similarity=1.146 Sum_probs=109.0
Q ss_pred ccHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHHHHhhhhhhccCCCC
Q psy5397 2 AGFQAVLGKIHHEYVNNTPKKLKIIDAYLFYILLTGAFQFLYCCLVGTFPFNSFLSGFISCVSSFVLGVCLRLQVNPQNQ 81 (112)
Q Consensus 2 ~~~~~i~~~~~~~Y~~~Tp~rlKliD~fl~fl~~~giiQf~Yc~lvgtfPFNaFLsgf~s~VG~fVL~vsLR~Q~~~~nk 81 (112)
+++...+++++++|.++||+|+|+||+|+.|++++|++||.||+|+|||||||||||||||||||||++|||||+|||||
T Consensus 5 ~~~~~~ls~~l~~y~~~t~~kLKliD~yl~fiv~tg~iQf~y~lLVgtfPFNSFLSGfIscVg~fVLavclR~q~n~qn~ 84 (115)
T KOG1746|consen 5 SKVVSVLSKVLTDYQETTPTKLKLIDAYLGFIVLTGIIQFGYCLLVGTFPFNSFLSGFISCVGQFVLAVCLRIQVNQQNK 84 (115)
T ss_pred hhhHHHHHHHHHHHHHhCcchHHHHHHHHHHHHHHHHHHHhHHhheeccChHHHHHHHHHHHHHHHHHHHHHHHhccccc
Confidence 45788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccCCCCCchHHHHHHHHHHHHHHhhhcccC
Q psy5397 82 KDFVGISPERGFADFIFAHVILHLVVMNFIG 112 (112)
Q Consensus 82 ~~F~~iS~eRAfaDfv~~slvLh~~v~nFiG 112 (112)
++|++||||||||||++||+|||++|+||+|
T Consensus 85 ~~f~~iSpeRAFadFifasliLHlvv~nFlg 115 (115)
T KOG1746|consen 85 SEFKGISPERAFADFIFASLILHLVVVNFLG 115 (115)
T ss_pred ccccCCChhHHHHHHHHHHHHHHHHHhhccC
Confidence 9999999999999999999999999999998
No 3
>TIGR02838 spore_V_AC stage V sporulation protein AC. This model describes stage V sporulation protein AC, a paralog of stage V sporulation protein AE. Both are proteins found to present in a species if and only if that species is one of the Firmicutes capable of endospore formation, as of the time of the publication of the genome of Carboxydothermus hydrogenoformans. Mutants in spoVAC have a stage V sproulation defect.
Probab=89.95 E-value=1.2 Score=33.70 Aligned_cols=64 Identities=17% Similarity=0.332 Sum_probs=46.7
Q ss_pred HHHHhh-CCCchHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHHHHhhhhhh-ccCCCCCccCCCCC
Q psy5397 12 HHEYVN-NTPKKLKIIDAYLFYILLTGAFQFLYCCLVGTFPFNSFLSGFISCVSSFVLGVCLRLQ-VNPQNQKDFVGISP 89 (112)
Q Consensus 12 ~~~Y~~-~Tp~rlKliD~fl~fl~~~giiQf~Yc~lvgtfPFNaFLsgf~s~VG~fVL~vsLR~Q-~~~~nk~~F~~iS~ 89 (112)
|++|.| .+|++=.+.|...+|++ +|+||.+||..+-...|+- ++++. .|
T Consensus 3 Y~~~v~~~~Pk~~~~~n~l~AFlv----------------------GG~IC~iGQ~l~d~~~~~~~lt~~~-------a~ 53 (141)
T TIGR02838 3 YQNLVKKYEPKPPYLKNCVMAFLV----------------------GGLICLIGQLISDFYLRYFQFSEKT-------AG 53 (141)
T ss_pred HHHHHHhcCCCCcHHHHHHHHHHh----------------------CcHHHHHHHHHHHHHHHhccCChhh-------cc
Confidence 566644 48888888888777653 6899999999999887774 65332 46
Q ss_pred chHHHHHHHHHHHHH
Q psy5397 90 ERGFADFIFAHVILH 104 (112)
Q Consensus 90 eRAfaDfv~~slvLh 104 (112)
.+.-.-+++.+.+|-
T Consensus 54 ~~~~~~lV~lgaiLt 68 (141)
T TIGR02838 54 SPTSATLIFISALLT 68 (141)
T ss_pred cchhhHHHHHHHHHh
Confidence 666777777777663
No 4
>KOG1654|consensus
Probab=78.22 E-value=1.3 Score=32.69 Aligned_cols=30 Identities=27% Similarity=0.396 Sum_probs=22.5
Q ss_pred HHHHHHHHHhhhhhhccCCCCCcc---CCCCCch
Q psy5397 61 SCVSSFVLGVCLRLQVNPQNQKDF---VGISPER 91 (112)
Q Consensus 61 s~VG~fVL~vsLR~Q~~~~nk~~F---~~iS~eR 91 (112)
.+||||+-.+.=|+|++|+. ..| .+.+|..
T Consensus 55 ltvgqfi~iIRkRiqL~~~k-A~flfVn~~~p~t 87 (116)
T KOG1654|consen 55 LTVGQFIKIIRKRIQLSPEK-AFFLFVNNTSPPT 87 (116)
T ss_pred ccHHHHHHHHHHHhccChhH-eEEEEEcCcCCcc
Confidence 47999999999999999863 344 4555543
No 5
>PF04148 Erv26: Transmembrane adaptor Erv26; InterPro: IPR007277 Erv26 is an integral membrane protein that is packed into COPII vesicles and cycles between the ER and Golgi compartments. It directs pro-alkaline phosphatase into endoplasmic reticulum-derived COPII transport vesicles [].
Probab=72.29 E-value=2.5 Score=33.75 Aligned_cols=49 Identities=29% Similarity=0.509 Sum_probs=36.1
Q ss_pred HHHHHHHHhhCCCchHH--------------HHHHHHHHHHHHHHH-HHHHHHHhcCCchhhHH
Q psy5397 8 LGKIHHEYVNNTPKKLK--------------IIDAYLFYILLTGAF-QFLYCCLVGTFPFNSFL 56 (112)
Q Consensus 8 ~~~~~~~Y~~~Tp~rlK--------------liD~fl~fl~~~gii-Qf~Yc~lvgtfPFNaFL 56 (112)
++++-|+|.+.|.+.+| +.|.|=..+.+.|++ |.+|..+..+||+=.+-
T Consensus 30 lsElVEEht~~akril~~~I~~ii~~~vlL~~~D~~P~~~~l~si~s~~~Y~~~L~~fP~i~lt 93 (211)
T PF04148_consen 30 LSELVEEHTVLAKRILKRLIYFIIALHVLLLLFDGFPFWLTLFSIFSHLVYLRNLRTFPFISLT 93 (211)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhCCCCeeecC
Confidence 57888999887777666 236666666666665 99998888999986543
No 6
>PRK07668 hypothetical protein; Validated
Probab=56.11 E-value=44 Score=27.29 Aligned_cols=88 Identities=14% Similarity=0.083 Sum_probs=47.8
Q ss_pred cHHHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHHHHHHHHHHhc-CCchhhHHHHHHHHHHHHHHHhhhhhhccCCCC
Q psy5397 3 GFQAVLGKIHHEYVNNTPKKLKIIDAYLFYILLTGAFQFLYCCLVG-TFPFNSFLSGFISCVSSFVLGVCLRLQVNPQNQ 81 (112)
Q Consensus 3 ~~~~i~~~~~~~Y~~~Tp~rlKliD~fl~fl~~~giiQf~Yc~lvg-tfPFNaFLsgf~s~VG~fVL~vsLR~Q~~~~nk 81 (112)
+.++..+++-+.+.++..+..|.+|.++...+ |..=+...+... |-|++.-+..++-.. +++.++.+...---.+
T Consensus 55 sPk~yA~EL~~~~~~~~~~~~~~l~~~ii~~l--~~~~i~~~~f~~~~~~~~~s~~~iig~~--~~~~l~i~~~~~~~r~ 130 (254)
T PRK07668 55 SPKEYANELVKEMEVDRKENIKLILFIIIGIL--SFWIIANILFGNPNHPLTYSLIQLIGYP--ISLILTIIGLIFLLRM 130 (254)
T ss_pred CHHHHHHHHhcccCCCcchHHHHHHHHHHHHH--HHHHHHHHHhcCCCCceeeeehHHhhHH--HHHHHHHHHHHHHHHH
Confidence 45667777777777766688999999987766 333334444445 666665444443333 3333333333221122
Q ss_pred CccCCCCCchHHH
Q psy5397 82 KDFVGISPERGFA 94 (112)
Q Consensus 82 ~~F~~iS~eRAfa 94 (112)
..|+.-..+|-+.
T Consensus 131 ~~fk~~~~~~~~i 143 (254)
T PRK07668 131 ASFKSKLTEKWFL 143 (254)
T ss_pred HHHhccchhHHHH
Confidence 3444444554443
No 7
>PF14333 DUF4389: Domain of unknown function (DUF4389)
Probab=47.11 E-value=84 Score=20.95 Aligned_cols=36 Identities=19% Similarity=0.263 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHHHHhh
Q psy5397 34 LLTGAFQFLYCCLVGTFPFNSFLSGFISCVSSFVLGVC 71 (112)
Q Consensus 34 ~~~giiQf~Yc~lvgtfPFNaFLsgf~s~VG~fVL~vs 71 (112)
.+..++|++..+..|.+|-+ |.+|...+++...=+.
T Consensus 27 ~~~~~~q~~~~L~tg~~p~~--L~~f~~~l~~y~~rv~ 62 (80)
T PF14333_consen 27 GVLVLIQWFAILFTGRYPEP--LFDFGAGLSRYIYRVL 62 (80)
T ss_pred HHHHHHHHHHHHHcCCCCHh--HHHHHHHHHHHHHHHH
Confidence 45678899999999999765 6677777777665443
No 8
>PTZ00380 microtubule-associated protein (MAP); Provisional
Probab=37.46 E-value=18 Score=26.65 Aligned_cols=19 Identities=16% Similarity=0.167 Sum_probs=17.3
Q ss_pred HHHHHHHHHhhhhhhccCC
Q psy5397 61 SCVSSFVLGVCLRLQVNPQ 79 (112)
Q Consensus 61 s~VG~fVL~vsLR~Q~~~~ 79 (112)
.+||||+-.+--|+|++|+
T Consensus 51 ~tV~qF~~iIRkrl~l~~~ 69 (121)
T PTZ00380 51 ATVAELEAAVRQALGTSAK 69 (121)
T ss_pred CcHHHHHHHHHHHcCCChh
Confidence 4899999999999999986
No 9
>PF06939 DUF1286: Protein of unknown function (DUF1286); InterPro: IPR009705 This entry is represented by Sulfolobus virus STSV1, Orf8. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical archaeal proteins of around 120 residues in length. All members of this family seem to be Sulfolobus species specific. The function of this family is unknown.
Probab=35.53 E-value=49 Score=24.42 Aligned_cols=38 Identities=29% Similarity=0.513 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHHHH
Q psy5397 32 YILLTGAFQFLYCCLVGTFPFNSFLSGFISCVSSFVLG 69 (112)
Q Consensus 32 fl~~~giiQf~Yc~lvgtfPFNaFLsgf~s~VG~fVL~ 69 (112)
|..-+|.+-++=..+..+|+.--++||++|-.|+++.=
T Consensus 7 yVFs~GlLtLl~s~~~~~f~~al~~s~iiSvl~N~lID 44 (114)
T PF06939_consen 7 YVFSTGLLTLLSSFFLSNFYDALFLSGIISVLGNTLID 44 (114)
T ss_pred ehhhhhHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Confidence 34556777777766667888899999999999998864
No 10
>PF09412 XendoU: Endoribonuclease XendoU; InterPro: IPR018998 This is a entry represents endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis (African clawed frog). XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 2C1W_C.
Probab=32.33 E-value=54 Score=26.80 Aligned_cols=43 Identities=26% Similarity=0.301 Sum_probs=37.1
Q ss_pred HHHHHHHHHHhhC-------CCchHHHHHHHHHHHHHHHHHHHHHHHHhc
Q psy5397 6 AVLGKIHHEYVNN-------TPKKLKIIDAYLFYILLTGAFQFLYCCLVG 48 (112)
Q Consensus 6 ~i~~~~~~~Y~~~-------Tp~rlKliD~fl~fl~~~giiQf~Yc~lvg 48 (112)
..+..++++|..+ ||.+.+-+|+||=-++-|.++|.+|-.|+.
T Consensus 64 ~af~~LlDNY~~~tg~~E~~T~ee~~E~~~FLd~i~~T~vmk~~~~fL~~ 113 (265)
T PF09412_consen 64 AAFIALLDNYERDTGVAEVVTPEERQEQDAFLDAIMETKVMKLAHQFLVS 113 (265)
T ss_dssp HHHHHHHHHTTSSSSTTT---HHHHHHHHHHHHHHTTSHHHHHHHHHHHH
T ss_pred HHHHHHHhccccccCCcccCCHHHHHHHHHHHHHHHcCHHHHHHHHHHHH
Confidence 4577899999765 789999999999999999999999988873
No 11
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=29.66 E-value=1.7e+02 Score=22.45 Aligned_cols=28 Identities=21% Similarity=0.222 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q psy5397 23 LKIIDAYLFYILLTGAFQFLYCCLVGTF 50 (112)
Q Consensus 23 lKliD~fl~fl~~~giiQf~Yc~lvgtf 50 (112)
-+++|+++..+.-.|.+=++|-.+.+.+
T Consensus 14 p~liD~~lT~~aW~gfi~l~~~~~~~~~ 41 (153)
T PRK14584 14 PRLIDIILTALAWFGFLFLLVRGLLEMI 41 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3799999999999999999988887655
No 12
>PF09877 DUF2104: Predicted membrane protein (DUF2104); InterPro: IPR019211 This entry is found in various hypothetical archaeal proteins, has no known function.
Probab=28.30 E-value=1.3e+02 Score=21.72 Aligned_cols=29 Identities=21% Similarity=0.312 Sum_probs=21.5
Q ss_pred HHHhh-CCCchHHHHHHHHHHHHHHHHHHH
Q psy5397 13 HEYVN-NTPKKLKIIDAYLFYILLTGAFQF 41 (112)
Q Consensus 13 ~~Y~~-~Tp~rlKliD~fl~fl~~~giiQf 41 (112)
-+|+| ++|=..|-+|....-+-+.|.+-+
T Consensus 22 ySYkKy~~P~v~k~iD~~ALv~aiiG~~~~ 51 (99)
T PF09877_consen 22 YSYKKYREPFVEKKIDKLALVLAIIGGLIL 51 (99)
T ss_pred HHHHHhccchhhhcccHHHHHHHHHHHHHH
Confidence 34544 258899999999988888887743
No 13
>PRK09400 secE preprotein translocase subunit SecE; Reviewed
Probab=27.92 E-value=1.7e+02 Score=18.90 Aligned_cols=42 Identities=19% Similarity=0.326 Sum_probs=26.9
Q ss_pred ccHHHHHHHHHHHHhh-----CCCchHH---HHHHHHHHHHHHHHHHHHH
Q psy5397 2 AGFQAVLGKIHHEYVN-----NTPKKLK---IIDAYLFYILLTGAFQFLY 43 (112)
Q Consensus 2 ~~~~~i~~~~~~~Y~~-----~Tp~rlK---liD~fl~fl~~~giiQf~Y 43 (112)
++..+.+++++++|+. +.|.|=. +.=+-.+=.++.|.+.|+-
T Consensus 4 ~~~~e~~~~f~~d~~rvl~~~~KPd~~Ef~~ia~~~~iG~~i~G~iGf~I 53 (61)
T PRK09400 4 NKLQENVKNFLEDYKRVLKVARKPTREEFLLVAKVTGLGILLIGLIGFII 53 (61)
T ss_pred HHHHHhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4577888999999965 4676643 3334444555667666653
No 14
>cd03495 SQR_TypeC_SdhD_like Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory Complex II SdhD subunit of the only eukaryotic member, Reclinomonas americana. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. It is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. E. coli SQR is classified as Type C SQRs because it contains two transmembrane subunits and one heme group. The SdhD and SdhC subunits are membrane anchor subunits containing heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is
Probab=27.27 E-value=1.3e+02 Score=20.74 Aligned_cols=29 Identities=21% Similarity=0.375 Sum_probs=18.4
Q ss_pred HHHHHHHHhhCCCchHHHHHHHHHHHHHH
Q psy5397 8 LGKIHHEYVNNTPKKLKIIDAYLFYILLT 36 (112)
Q Consensus 8 ~~~~~~~Y~~~Tp~rlKliD~fl~fl~~~ 36 (112)
++...|+|-+.++.|.-++=....+...+
T Consensus 63 m~~IieDYV~~~~~R~~l~~~~~~~~~~~ 91 (100)
T cd03495 63 MQVVIEDYVHSEGLRLALIIAVKLFAIAT 91 (100)
T ss_pred HHHHHHHHhCchHHHHHHHHHHHHHHHHH
Confidence 57788999996666665554444444443
No 15
>PF03862 SpoVA: SpoVA protein; InterPro: IPR005562 Members of this family are all transcribed from the spoVA operon. These proteins are poorly characterised, but are thought to be involved in dipicolinic acid transport into the developing forespore during sporulation [].
Probab=26.56 E-value=1.2e+02 Score=22.30 Aligned_cols=42 Identities=14% Similarity=0.468 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHhhhhhhccCCCCCccCCCCCchHHHHHHHHHHHHH
Q psy5397 56 LSGFISCVSSFVLGVCLRLQVNPQNQKDFVGISPERGFADFIFAHVILH 104 (112)
Q Consensus 56 Lsgf~s~VG~fVL~vsLR~Q~~~~nk~~F~~iS~eRAfaDfv~~slvLh 104 (112)
.+|.+|.+||..+-.-.|...++ ...|.+.-.=+++++.+|-
T Consensus 9 vGG~IC~igQ~l~d~~~~~~~~~-------k~a~~~~~vtlv~~gaiLt 50 (119)
T PF03862_consen 9 VGGLICVIGQLLMDFYMMFGLSE-------KLAPAHTLVTLVFIGAILT 50 (119)
T ss_pred hchHHHHHHHHHHHHHHHcCCCh-------hhhhHHHHHHHHHHHHHHc
Confidence 46899999999999888855552 3467777777777777663
No 16
>PF03591 AzlC: AzlC protein; InterPro: IPR011606 Some proteins in this entry are encoded by a gene, which is a part of the azl operon. This operon is involved in branched-chain amino acid transport []. Overexpression of this gene results in resistance to a leucine analogue, 4-azaleucine. The protein has 5 potential transmembrane motifs.
Probab=26.46 E-value=2.5e+02 Score=20.27 Aligned_cols=77 Identities=19% Similarity=0.306 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHHHHHHHh--cCCchhhHHHHHHHHHHHHHHHhhhhhhccCCCC-------------------CccCCC
Q psy5397 29 YLFYILLTGAFQFLYCCLV--GTFPFNSFLSGFISCVSSFVLGVCLRLQVNPQNQ-------------------KDFVGI 87 (112)
Q Consensus 29 fl~fl~~~giiQf~Yc~lv--gtfPFNaFLsgf~s~VG~fVL~vsLR~Q~~~~nk-------------------~~F~~i 87 (112)
.+..++..|-.||+-.-+. |.=|..++++.+..-.=.+...++|+-+..+.++ +++++.
T Consensus 30 ~mS~lvfaGa~Qf~~~~l~~~ga~~~~i~~t~~lvN~R~~ly~~sl~~~~~~~~~~~~~~~~~~ltDe~fa~~~~~~~~~ 109 (143)
T PF03591_consen 30 LMSLLVFAGAAQFVAVGLLAAGASLLAIALTVLLVNLRHLLYGASLAPYLKKLSRWKRLLLAFFLTDESFAVAMSRFQPN 109 (143)
T ss_pred HHHHHHHhhHHHHHHHHHHHccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 4667788999999996554 6778999999999999999999999887763211 134444
Q ss_pred CCchHHHHHHHHHHHHHHh
Q psy5397 88 SPERGFADFIFAHVILHLV 106 (112)
Q Consensus 88 S~eRAfaDfv~~slvLh~~ 106 (112)
.+++ ...|.-+++..|+.
T Consensus 110 ~~~~-~~~~~g~~~~~~~~ 127 (143)
T PF03591_consen 110 PPDR-HAYYLGLGLLLYLS 127 (143)
T ss_pred Ccch-HHHHHHHHHHHHHH
Confidence 4444 56666666666653
No 17
>PF07019 Rab5ip: Rab5-interacting protein (Rab5ip)
Probab=26.43 E-value=1.9e+02 Score=18.83 Aligned_cols=17 Identities=18% Similarity=0.217 Sum_probs=7.4
Q ss_pred CCchHHHHHHHHHHHHH
Q psy5397 88 SPERGFADFIFAHVILH 104 (112)
Q Consensus 88 S~eRAfaDfv~~slvLh 104 (112)
++.+.+.|=+..++..+
T Consensus 57 ~~~~i~~~g~~~~l~~F 73 (81)
T PF07019_consen 57 GPWEIFTEGFFSGLSTF 73 (81)
T ss_pred CHHHHHHhhhhchHHHH
Confidence 44444444444444443
No 18
>TIGR00834 ae anion exchange protein. They preferentially catalyze anion exchange (antiport) reactions, typically acting as HCO3-:Cl- antiporters, but also transporting a range of other inorganic and organic anions. Additionally, renal Na+:HCO3- cotransporters have been found to be members of the AE family. They catalyze the reabsorption of HCO3- in the renal proximal tubule.
Probab=26.29 E-value=4.5e+02 Score=25.43 Aligned_cols=55 Identities=25% Similarity=0.319 Sum_probs=42.3
Q ss_pred hhhHHHHHHHHHHHHHHHhhhhhhccCCCCCccCCCCCchHHHHHHHHHHHHHHhhhcc
Q psy5397 52 FNSFLSGFISCVSSFVLGVCLRLQVNPQNQKDFVGISPERGFADFIFAHVILHLVVMNF 110 (112)
Q Consensus 52 FNaFLsgf~s~VG~fVL~vsLR~Q~~~~nk~~F~~iS~eRAfaDfv~~slvLh~~v~nF 110 (112)
.|.+|-+++-++|+|.++..||.=-+ ...| +-+--|..+||...--|+-++.+.+
T Consensus 558 ~~~~llsliL~lgTf~~a~~L~~fk~---s~yf-~~~vR~~isDfgv~iaI~~~t~v~~ 612 (900)
T TIGR00834 558 PNTALLSLVLMLGTFFLAMFLRKFKN---SRYF-PGKARRLIGDFGVPISILIMVLVDI 612 (900)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHhCC---CCcC-CchhhhhhhhhhHHHHHHHHHHHHH
Confidence 58889999999999999999997543 2244 4477899999998877777665544
No 19
>KOG1688|consensus
Probab=26.18 E-value=1.5e+02 Score=23.64 Aligned_cols=52 Identities=17% Similarity=0.337 Sum_probs=34.1
Q ss_pred HHHHHHHHHHhhCCCchHH-----HHHHHHHHHHHHHHHHHHH--HHHhcCCchhhHHH
Q psy5397 6 AVLGKIHHEYVNNTPKKLK-----IIDAYLFYILLTGAFQFLY--CCLVGTFPFNSFLS 57 (112)
Q Consensus 6 ~i~~~~~~~Y~~~Tp~rlK-----liD~fl~fl~~~giiQf~Y--c~lvgtfPFNaFLs 57 (112)
.-++++|++|.++|.++.+ ..=..++|++=+-.+|=-| |...|.|=-|.|++
T Consensus 22 ~~~~~~yQ~yLDr~tPh~~~RW~~tl~l~~iy~iRi~~~~G~YII~Y~LgIYlLNlfia 80 (188)
T KOG1688|consen 22 HELSQLYQHYLDRSTPHTAVRWVVTLVLLLIYCIRIYLVQGFYIITYALGIYLLNLFIA 80 (188)
T ss_pred HHHHHHHHHHHhccCCcchhhHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence 3456778888766444332 3445566666667777777 45558888888875
No 20
>KOG0585|consensus
Probab=25.39 E-value=31 Score=31.47 Aligned_cols=14 Identities=50% Similarity=1.053 Sum_probs=12.4
Q ss_pred HHHHHHhcCCchhh
Q psy5397 41 FLYCCLVGTFPFNS 54 (112)
Q Consensus 41 f~Yc~lvgtfPFNa 54 (112)
-+||++.|..||++
T Consensus 308 TLYCllfG~~PF~~ 321 (576)
T KOG0585|consen 308 TLYCLLFGQLPFFD 321 (576)
T ss_pred hHHHhhhccCCccc
Confidence 48999999999984
No 21
>PRK14094 psbM photosystem II reaction center protein M; Provisional
Probab=22.67 E-value=1.3e+02 Score=19.29 Aligned_cols=17 Identities=12% Similarity=0.227 Sum_probs=13.7
Q ss_pred HHhhhhhhccCCCCCcc
Q psy5397 68 LGVCLRLQVNPQNQKDF 84 (112)
Q Consensus 68 L~vsLR~Q~~~~nk~~F 84 (112)
+++-|-+|+++++|+.|
T Consensus 21 FLlilYVkT~s~~kssf 37 (50)
T PRK14094 21 FLIGLFISTQDGEKSSF 37 (50)
T ss_pred HhhheeEEecccCccce
Confidence 45678899999999877
No 22
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=22.64 E-value=85 Score=22.88 Aligned_cols=61 Identities=16% Similarity=0.092 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHhhCCCchHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHH
Q psy5397 5 QAVLGKIHHEYVNNTPKKLKIIDAYLFYILLTGAFQFLYCCLVGTFPFNSFLSGFISCVSSFV 67 (112)
Q Consensus 5 ~~i~~~~~~~Y~~~Tp~rlKliD~fl~fl~~~giiQf~Yc~lvgtfPFNaFLsgf~s~VG~fV 67 (112)
.++.+.+-++=.+-||||++++|...-=-== --.+-+|-.+...+|-=+ +|..=-++-+|+
T Consensus 6 ~~~~~~lk~~glr~T~qR~~vl~~L~~~~~~-~sAeei~~~l~~~~p~is-laTVYr~L~~l~ 66 (145)
T COG0735 6 EDAIERLKEAGLRLTPQRLAVLELLLEADGH-LSAEELYEELREEGPGIS-LATVYRTLKLLE 66 (145)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHHHHhcCCC-CCHHHHHHHHHHhCCCCC-HhHHHHHHHHHH
Confidence 3455555555455699999999976511000 124566766666666433 555444444444
No 23
>PF05512 AWPM-19: AWPM-19-like family; InterPro: IPR008390 Members of this family are 19 kDa membrane proteins. The levels of the plant protein AWPM-19 increase dramatically when there is an increase level of abscisic acid. The increase presence of this protein leads to greater tolerance of freezing [].
Probab=22.43 E-value=1.3e+02 Score=22.93 Aligned_cols=26 Identities=23% Similarity=0.448 Sum_probs=21.5
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy5397 19 TPKKLKIIDAYLFYILLTGAFQFLYCCLV 47 (112)
Q Consensus 19 Tp~rlKliD~fl~fl~~~giiQf~Yc~lv 47 (112)
.++|+|-+.+|. ++.++.|.+|..+.
T Consensus 113 r~~rLrtlEaf~---IIl~~tQLly~l~l 138 (142)
T PF05512_consen 113 RNWRLRTLEAFT---IILSATQLLYLLAL 138 (142)
T ss_pred ccchhhHHHHHH---HHHHHHHHHHHHHH
Confidence 689999999876 57788899997765
No 24
>PF14012 DUF4229: Protein of unknown function (DUF4229)
Probab=22.42 E-value=2.3e+02 Score=18.46 Aligned_cols=50 Identities=20% Similarity=0.186 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCc--hhhHHHHHHHHHHHHHHHhhhhhhccC
Q psy5397 29 YLFYILLTGAFQFLYCCLVGTFP--FNSFLSGFISCVSSFVLGVCLRLQVNP 78 (112)
Q Consensus 29 fl~fl~~~giiQf~Yc~lvgtfP--FNaFLsgf~s~VG~fVL~vsLR~Q~~~ 78 (112)
...|.+.++++..+-.......| .-+.+|-.+|..-++++.-.+|.+.+.
T Consensus 9 l~lfv~~~~vi~~v~~~~~~~~p~~~~~l~A~vis~~lS~~ll~~~R~~~~~ 60 (69)
T PF14012_consen 9 LGLFVVLFAVIWLVGLLIGVEVPLLVAALLALVISMPLSYVLLRRLRDRASA 60 (69)
T ss_pred HHHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677788887744333333332 234445555666667777888988874
No 25
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 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 domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=21.33 E-value=67 Score=22.03 Aligned_cols=20 Identities=25% Similarity=0.424 Sum_probs=17.2
Q ss_pred HHHHHHHHHHhhhhhhccCC
Q psy5397 60 ISCVSSFVLGVCLRLQVNPQ 79 (112)
Q Consensus 60 ~s~VG~fVL~vsLR~Q~~~~ 79 (112)
-+++|+|+-+++.|+....+
T Consensus 3 G~~lGSFl~~~~~R~p~~~~ 22 (92)
T PF06750_consen 3 GACLGSFLNVLAYRLPRGEE 22 (92)
T ss_pred HHHHHHHHHHHHHHhHhHhh
Confidence 47899999999999988753
No 26
>COG4508 Dimeric dUTPase [Carbohydrate transport and metabolism]
Probab=20.88 E-value=74 Score=24.64 Aligned_cols=58 Identities=22% Similarity=0.306 Sum_probs=38.5
Q ss_pred HHHHHHhcCCchhhHHHHHHHHHHHHHHHhhhhhhccCCCCCccCCCCCc---------hHHHHHHHHH
Q psy5397 41 FLYCCLVGTFPFNSFLSGFISCVSSFVLGVCLRLQVNPQNQKDFVGISPE---------RGFADFIFAH 100 (112)
Q Consensus 41 f~Yc~lvgtfPFNaFLsgf~s~VG~fVL~vsLR~Q~~~~nk~~F~~iS~e---------RAfaDfv~~s 100 (112)
|=|--+-+-=|-++-+---+-|+ .|+|+++|-.|.+.- .-.|+.+|+. |+.+||.-|+
T Consensus 50 FkYW~~~~p~~~~~ilEEY~dgl-HF~lsigl~~~~~d~-~ip~~~~stni~EQFl~vFi~I~ef~~~~ 116 (161)
T COG4508 50 FKYWKLSKPIDLAKILEEYSDGL-HFLLSIGLYYQLSDF-LIPFKVISTNINEQFLAVFISIAEFMKKP 116 (161)
T ss_pred HHhhhhcCCCcHHHHHHHHhhhH-HHHHHhHHHHHhhhh-hccccccCCcHHHHHHHHHHHHHHHHhCc
Confidence 44555556666666666655554 689999999999741 1236777775 5677776654
No 27
>TIGR00261 traB pheromone shutdown-related protein TraB. traB is a plasmid encoded gene that functions in the shutdown of the peptide sex pheromone cPD1 which is produced by the plasmid free recipient cell prior to conjugative transfer in Enterococcus faecalis. Once the recipient acquires the plasmid, production of cPD1 is shut down. The gene product may play another role in the other species in the family.
Probab=20.64 E-value=2.3e+02 Score=24.41 Aligned_cols=72 Identities=13% Similarity=0.171 Sum_probs=48.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHHHH-------hhhhhhccCCCCCccCCCCCchHHHH
Q psy5397 24 KIIDAYLFYILLTGAFQFLYCCLVGTFPFNSFLSGFISCVSSFVLG-------VCLRLQVNPQNQKDFVGISPERGFAD 95 (112)
Q Consensus 24 KliD~fl~fl~~~giiQf~Yc~lvgtfPFNaFLsgf~s~VG~fVL~-------vsLR~Q~~~~nk~~F~~iS~eRAfaD 95 (112)
..+|.+..+.+++|++=.+-++++|.-|.-+..|+..+-+.+.-=+ .-.-.+..+.+-++|+++.....+-+
T Consensus 266 ~~~~~~~~W~l~ng~laalg~~lA~~hplsil~a~~~ApltslnP~i~~G~~ag~vea~~r~p~v~D~~~l~~~~s~~~ 344 (380)
T TIGR00261 266 FLYKNLKLWILSNGILSAIGSILARGHPLTILTAFLGAPITSLIPLIATGMVAGLVEAYIRKPTVKDFENLQEAESIKE 344 (380)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHcCCHHHHHHHHHHhhHhhcCchHHHHHHHHHHHhhccCCCHHHHHHHhhcccHHH
Confidence 3788889999999999999999999999998888887766554221 11223334445556766554333333
No 28
>PF11188 DUF2975: Protein of unknown function (DUF2975); InterPro: IPR021354 This family of proteins have no known function. Some members are annotated as membrane proteins however this cannot be confirmed.
Probab=20.64 E-value=2.8e+02 Score=18.67 Aligned_cols=41 Identities=10% Similarity=0.331 Sum_probs=29.1
Q ss_pred HHHHHHHHHhhC---CCchHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy5397 7 VLGKIHHEYVNN---TPKKLKIIDAYLFYILLTGAFQFLYCCLV 47 (112)
Q Consensus 7 i~~~~~~~Y~~~---Tp~rlKliD~fl~fl~~~giiQf~Yc~lv 47 (112)
.+.++.++|.++ |++..|-+......+++.++++++.....
T Consensus 42 ~~~~ll~~i~~~~~Fs~~n~~~l~~ig~~~l~~~~~~~~~~~~~ 85 (136)
T PF11188_consen 42 QLRRLLRNIQKGKPFSPENIRRLRRIGWLLLIISILSFIANFIL 85 (136)
T ss_pred HHHHHHHHHHCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356677788777 45777777777777777777777765443
No 29
>TIGR00994 3a0901s05TIC20 chloroplast protein import component, Tic20 family. Two families of proteins are involved in the chloroplast envelope import appartus.They are the three proteins of the outer membrane (TOC) and four proteins in the inner membrane (TIC). This family is specific for the Tic20 protein.
Probab=20.34 E-value=1.3e+02 Score=25.19 Aligned_cols=27 Identities=19% Similarity=0.418 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHhcCCchhhHHH
Q psy5397 31 FYILLTGAFQFLYCCLVGTFPFNSFLS 57 (112)
Q Consensus 31 ~fl~~~giiQf~Yc~lvgtfPFNaFLs 57 (112)
++..+-+++|.+-|++.|.||.==++|
T Consensus 231 l~~~ifsviqcircAL~G~YaeIP~IS 257 (267)
T TIGR00994 231 GFTYLFTLLECIRCALAGMYADVPFMC 257 (267)
T ss_pred HHHHHHHHHHHHHHHhCCCcCCCchHH
Confidence 467778899999999999999765554
Done!