Query psy4196
Match_columns 168
No_of_seqs 36 out of 38
Neff 2.5
Searched_HMMs 46136
Date Fri Aug 16 19:17:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4196.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4196hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01471 PG_binding_1: Putativ 61.6 6.3 0.00014 25.1 1.7 14 26-39 31-44 (57)
2 PF01726 LexA_DNA_bind: LexA D 57.8 15 0.00032 25.5 3.2 23 24-47 10-32 (65)
3 COG1963 Uncharacterized protei 44.2 18 0.00039 30.1 2.2 46 85-137 85-131 (153)
4 PF10045 DUF2280: Uncharacteri 41.0 1.8E+02 0.0038 22.9 7.1 88 12-135 9-96 (104)
5 PRK05686 fliG flagellar motor 37.5 2.8E+02 0.0061 24.2 8.7 138 7-164 77-224 (339)
6 cd04767 HTH_HspR-like_MBC Heli 34.6 31 0.00067 26.9 2.1 40 25-64 45-84 (120)
7 TIGR01562 FdhE formate dehydro 30.9 1.3E+02 0.0028 26.9 5.6 71 82-153 84-162 (305)
8 COG4030 Uncharacterized protei 30.8 59 0.0013 29.6 3.4 121 9-134 25-171 (315)
9 PRK03564 formate dehydrogenase 25.9 2E+02 0.0044 25.8 5.9 71 82-153 87-165 (309)
10 PRK14607 bifunctional glutamin 25.2 1E+02 0.0022 28.8 4.1 90 9-107 310-402 (534)
11 PF03109 ABC1: ABC1 family; I 24.9 1.5E+02 0.0032 22.1 4.2 62 78-143 56-117 (119)
12 PF14575 EphA2_TM: Ephrin type 23.7 28 0.00061 24.8 0.1 16 20-35 57-72 (75)
13 PF09662 Phenyl_P_gamma: Pheny 22.9 18 0.0004 27.5 -1.0 19 145-163 66-84 (84)
14 PF10264 Stork_head: Winged he 22.0 2.4E+02 0.0052 21.0 4.8 43 105-147 12-54 (80)
15 PF01713 Smr: Smr domain; Int 21.5 91 0.002 21.3 2.3 30 87-116 1-30 (83)
16 PF04216 FdhE: Protein involve 20.0 94 0.002 26.4 2.6 73 79-152 68-149 (290)
No 1
>PF01471 PG_binding_1: Putative peptidoglycan binding domain; InterPro: IPR002477 This entry represents peptidoglycan binding domain (PGBD), as well as related domains that share the same structure. PGBD may have a general peptidoglycan binding function, has a core structure consisting of a closed, three-helical bundle with a left-handed twist. It is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation [, , ]. Examples are: Muramoyl-pentapeptide carboxypeptidase (3.4.17.8 from EC) N-acetylmuramoyl-L-alanine amidase cwlA precursor (cell wall hydrolase, autolysin, 3.5.1.28 from EC) Autolytic lysozyme (1,4-beta-N-acetylmuramidase, autolysin, 3.2.1.17 from EC) Membrane-bound lytic murein transglycosylase B Zinc-containing D-alanyl-D-alanine-cleaving carboxypeptidase, VanX []. Many of the proteins having this domain are as yet uncharacterised. However, some are known to belong to MEROPS peptidase family M15 (clan MD), subfamily M15A metallopeptidases. A number of the proteins belonging to subfamily M15A are non-peptidase homologues as they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. Eukaryotic enzymes can contain structurally similar PGBD-like domains. Matrix metalloproteinases (MMP), which catalyse extracellular matrix degradation, have N-terminal domains that resemble PGBD. Examples are gelatinase A (MMP-2), which degrades type IV collagen [], stromelysin-1 (MMP-3), which plays a role in arthritis and tumour invasion [, ], and gelatinase B (MMP-9) secreted by neutrophils as part of the innate immune defence mechanism []. Several MMPs are implicated in cancer progression, since degradation of the extracellular matrix is an essential step in the cascade of metastasis [].; GO: 0008152 metabolic process; PDB: 1L6J_A 3BKH_A 3BKV_A 1GXD_A 1EAK_D 1CK7_A 1SLM_A 1LBU_A 1SU3_B.
Probab=61.58 E-value=6.3 Score=25.08 Aligned_cols=14 Identities=36% Similarity=0.570 Sum_probs=11.8
Q ss_pred HHHHHHHHHhcCcc
Q psy4196 26 LKAIEEFQLDNGIL 39 (168)
Q Consensus 26 l~aIe~FQ~eNgIl 39 (168)
.+||+.||..+|+.
T Consensus 31 ~~Av~~fQ~~~gL~ 44 (57)
T PF01471_consen 31 REAVKAFQKANGLP 44 (57)
T ss_dssp HHHHHHHHHHTTS-
T ss_pred HHHHHHHHHHcCcC
Confidence 48999999999975
No 2
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=57.77 E-value=15 Score=25.46 Aligned_cols=23 Identities=30% Similarity=0.593 Sum_probs=16.9
Q ss_pred CHHHHHHHHHHhcCccccchhhhc
Q psy4196 24 DPLKAIEEFQLDNGILLPSLRQML 47 (168)
Q Consensus 24 dPl~aIe~FQ~eNgIlLpsl~~~L 47 (168)
+.+.+|.+|..+||.. ||++.+-
T Consensus 10 ~vL~~I~~~~~~~G~~-Pt~rEIa 32 (65)
T PF01726_consen 10 EVLEFIREYIEENGYP-PTVREIA 32 (65)
T ss_dssp HHHHHHHHHHHHHSS----HHHHH
T ss_pred HHHHHHHHHHHHcCCC-CCHHHHH
Confidence 4578999999999988 8888873
No 3
>COG1963 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.25 E-value=18 Score=30.10 Aligned_cols=46 Identities=30% Similarity=0.457 Sum_probs=34.9
Q ss_pred ccccccCCchhhh-HHHHHHHHHHHHHHHHHHhccccccchHHHHHHHHhhhcC
Q psy4196 85 PLLDLHGVRRLDF-HNSVLEELRDKLVSHIKEIGQKEGRDRDRKLNEMLKKSFP 137 (168)
Q Consensus 85 ~lld~hgVrRldf-h~svle~Lr~~Ll~~I~~l~~~~~~~~~~kL~~lL~kSFp 137 (168)
=.-|+-||||.-= +..++.+|-+++.+..++++++ +|+++|--++-
T Consensus 85 vm~DA~GVRr~aG~QA~iLN~l~~~~~~e~~~~~~~-------~lKellGH~p~ 131 (153)
T COG1963 85 VMYDATGVRRSAGVQARILNQLIEELVNEKKDFDKK-------RLKELLGHTPL 131 (153)
T ss_pred HhhhhhhHHHhccchHHHHHHHHHHHHHhhccCCHH-------HHHHHhCCChH
Confidence 3468888888654 4568999999999888888876 68888765543
No 4
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=41.05 E-value=1.8e+02 Score=22.92 Aligned_cols=88 Identities=23% Similarity=0.282 Sum_probs=64.3
Q ss_pred HHHHHHHhhcCCCHHHHHHHHHHhcCccccchhhhccccccccccccccccchhHHHHHHHhhhhhhhhhhhcccccccC
Q psy4196 12 QNFLREALTSCTDPLKAIEEFQLDNGILLPSLRQMLPLLDLHGVRRLDFHNSVLEVEVTETLNLLLPSLRQMLPLLDLHG 91 (168)
Q Consensus 12 ~~~lreaLs~~tdPl~aIe~FQ~eNgIlLpsl~~~LpLLDL~~vr~~~~~~s~~~~e~~~t~~~~~p~~~~~~~lld~hg 91 (168)
..||-.+|-...-|.+..+-.+.+.||.. |-|++ |. .-|+- .-|
T Consensus 9 K~FIVQ~LAcfdTPs~v~~aVk~eFgi~v-srQqv---------------------e~------yDPTK--------~aG 52 (104)
T PF10045_consen 9 KAFIVQSLACFDTPSEVAEAVKEEFGIDV-SRQQV---------------------ES------YDPTK--------RAG 52 (104)
T ss_pred HHHHHHHHHhhCCHHHHHHHHHHHhCCcc-CHHHH---------------------HH------cCchH--------HHH
Confidence 46888999988889999999999999987 33333 21 11111 123
Q ss_pred CchhhhHHHHHHHHHHHHHHHHHHhccccccchHHHHHHHHhhh
Q psy4196 92 VRRLDFHNSVLEELRDKLVSHIKEIGQKEGRDRDRKLNEMLKKS 135 (168)
Q Consensus 92 VrRldfh~svle~Lr~~Ll~~I~~l~~~~~~~~~~kL~~lL~kS 135 (168)
-.=+.=+..++++-|+..++.+.+|+-....-|-+.|.+|.++.
T Consensus 53 ~~Ls~k~~~lF~~TR~~F~~~~~~IpIAnka~RLR~L~r~~~k~ 96 (104)
T PF10045_consen 53 RDLSKKWVDLFEETRKRFLEETADIPIANKAYRLRALQRMAEKA 96 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHhccchHHHHHHHHHHHHHHHH
Confidence 23344567889999999999999999765667888999988874
No 5
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=37.47 E-value=2.8e+02 Score=24.24 Aligned_cols=138 Identities=20% Similarity=0.268 Sum_probs=80.8
Q ss_pred cCCCcHHHHHHHhhcCCCHHHHH---HHHHHhcCccccchhhhccccccccccccccccchhHHHHHHHhhhhhhhhhhh
Q psy4196 7 SGIPGQNFLREALTSCTDPLKAI---EEFQLDNGILLPSLRQMLPLLDLHGVRRLDFHNSVLEVEVTETLNLLLPSLRQM 83 (168)
Q Consensus 7 ~Gi~G~~~lreaLs~~tdPl~aI---e~FQ~eNgIlLpsl~~~LpLLDL~~vr~~~~~~s~~~~e~~~t~~~~~p~~~~~ 83 (168)
....|.+++++.|+.+.++-+|= +++....+ ......|.-+|-..+. ..+.-|-|.|+-+.+-.+..
T Consensus 77 ~~~gg~~~~~~iL~~~l~~~~a~~il~~i~~~~~---~~~fe~L~~ld~~~l~------~lL~~EhpqtiA~iLs~l~~- 146 (339)
T PRK05686 77 ILMGGIDYARSLLEKALGEEKADSILERILESLG---TSGFDFLRKMDPQQLA------NFIRNEHPQTIALILSYLKP- 146 (339)
T ss_pred ccCChHHHHHHHHHHHcCHHHHHHHHHHHhcccc---CchHHHHhcCCHHHHH------HHHHhcCHHHHHHHHhCCCH-
Confidence 34567888999999877776543 34433322 2233444444442222 24566778887766543221
Q ss_pred cccccccCCchhhhHHHHHHHHHHHHHHHHHHhccccccchHHHHHHHHhhhcCcc------ccCchhHHHHHHHhcCCC
Q psy4196 84 LPLLDLHGVRRLDFHNSVLEELRDKLVSHIKEIGQKEGRDRDRKLNEMLKKSFPLV------RVKQLRPVVMAILRNTTH 157 (168)
Q Consensus 84 ~~lld~hgVrRldfh~svle~Lr~~Ll~~I~~l~~~~~~~~~~kL~~lL~kSFp~i------~v~~LrpVvmavL~~~~~ 157 (168)
-.+..+...+=++.+.+++.||..+++= ..+--+.+++.|.+.|-.+ .+.-.++ +-+||.+++.
T Consensus 147 --------~~aa~vL~~l~~~~~~~v~~ria~l~~v-~~~~~~~i~~~L~~~l~~~~~~~~~~~~g~~~-~a~Iln~~~~ 216 (339)
T PRK05686 147 --------DQAAEILSLLPEELRADVMMRIATLEGV-SPEALKEVEEVLEKKLSSMANADRTKMGGVKT-VAEILNNLDR 216 (339)
T ss_pred --------HHHHHHHHhCCHHHHHHHHHHHHccCCC-CHHHHHHHHHHHHHHHhhcccccccccCcHHH-HHHHHhcCCc
Confidence 1345556666678899999999999853 2234567777777777542 2333343 4588888864
Q ss_pred CcH-HHHH
Q psy4196 158 IDD-KYLR 164 (168)
Q Consensus 158 ip~-kyL~ 164 (168)
=-+ +.|.
T Consensus 217 ~~~~~il~ 224 (339)
T PRK05686 217 QTEKTILE 224 (339)
T ss_pred hHHHHHHH
Confidence 333 3443
No 6
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=34.64 E-value=31 Score=26.87 Aligned_cols=40 Identities=18% Similarity=0.323 Sum_probs=35.8
Q ss_pred HHHHHHHHHHhcCccccchhhhccccccccccccccccch
Q psy4196 25 PLKAIEEFQLDNGILLPSLRQMLPLLDLHGVRRLDFHNSV 64 (168)
Q Consensus 25 Pl~aIe~FQ~eNgIlLpsl~~~LpLLDL~~vr~~~~~~s~ 64 (168)
-++.|...+.+.|+.+..++..|-+++...+|..||++-.
T Consensus 45 rL~~I~~L~~e~G~~l~eI~~~L~l~~~~~~~~~~~~~~~ 84 (120)
T cd04767 45 RLRFIKKLINEKGLNIAGVKQILSMYPCWSIRDCDEGGRK 84 (120)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHhCcccccccccCCCcc
Confidence 3678999999999999999999999999999999998754
No 7
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=30.94 E-value=1.3e+02 Score=26.89 Aligned_cols=71 Identities=20% Similarity=0.209 Sum_probs=51.3
Q ss_pred hhcccccccCCchhhhHHHHHHHHHHHH--------HHHHHHhccccccchHHHHHHHHhhhcCccccCchhHHHHHHHh
Q psy4196 82 QMLPLLDLHGVRRLDFHNSVLEELRDKL--------VSHIKEIGQKEGRDRDRKLNEMLKKSFPLVRVKQLRPVVMAILR 153 (168)
Q Consensus 82 ~~~~lld~hgVrRldfh~svle~Lr~~L--------l~~I~~l~~~~~~~~~~kL~~lL~kSFp~i~v~~LrpVvmavL~ 153 (168)
+-.|.||..+..|..-++.+|.+|=+++ ..-|+.+-+....+...--..+|...|+.+. ...-|.++|.|.
T Consensus 84 ~g~PpL~~~~~~~d~~w~~~l~~LL~~l~~~~~~~~~~~l~~l~~~~~~~le~~a~alL~~~~~~~~-~a~apfi~AALq 162 (305)
T TIGR01562 84 HGMPPLDYDLLVREGAWLPWLDALLAGYPAPANAAAGAALEQLREAEEGQLKAMAIALLAGDFDLLS-AALVPFLGAALQ 162 (305)
T ss_pred cCCCCCChhhcccCHHHHHHHHHHHHHhcccccHHHHHHHHHHHhCCHHHHHHHHHHHhcCCccccc-hhhhHHHHHHHH
Confidence 4568888899888777777777666554 3445555555555677777888899999888 667888888853
No 8
>COG4030 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.80 E-value=59 Score=29.58 Aligned_cols=121 Identities=28% Similarity=0.380 Sum_probs=71.3
Q ss_pred CCcHHHHHHHhhcCCCHHHHHHHHHHhcCccccchhhhccccccccccccccccchhHHHH--------HHHhhh----h
Q psy4196 9 IPGQNFLREALTSCTDPLKAIEEFQLDNGILLPSLRQMLPLLDLHGVRRLDFHNSVLEVEV--------TETLNL----L 76 (168)
Q Consensus 9 i~G~~~lreaLs~~tdPl~aIe~FQ~eNgIlLpsl~~~LpLLDL~~vr~~~~~~s~~~~e~--------~~t~~~----~ 76 (168)
+|++..+-+-+|.-.|.+. .+.|.+.==.=-+|....|+|--|||..=|... --|. .+|+.. +
T Consensus 25 ~pngrrfF~~~SeyDD~la--~E~rReGYeaG~TLkLivPFL~ahGVt~~dlrr---~sE~sa~lvPgA~etm~~l~~~~ 99 (315)
T COG4030 25 FPNGRRFFSNLSEYDDYLA--YEVRREGYEAGYTLKLIVPFLAAHGVTNRDLRR---ISELSAKLVPGAEETMATLQERW 99 (315)
T ss_pred cCCHHHHHHhhhhhhhHHH--HHHhccCCCCCcchhhHHHHHHHhcCcHHHHHH---HHHhhcccCCChHHHHHHHhccC
Confidence 5666666667777666653 244544322233557778888889986533211 0111 122211 1
Q ss_pred hh-----hhhhhc-ccccccCCchhhhHHHHH--------HHHHHHHHHHHHHhccccccchHHHHHHHHhh
Q psy4196 77 LP-----SLRQML-PLLDLHGVRRLDFHNSVL--------EELRDKLVSHIKEIGQKEGRDRDRKLNEMLKK 134 (168)
Q Consensus 77 ~p-----~~~~~~-~lld~hgVrRldfh~svl--------e~Lr~~Ll~~I~~l~~~~~~~~~~kL~~lL~k 134 (168)
+| |.+|-+ -+-.+.||+|.+.|..-+ ++.|++++.+|.-++.-++.+-.++|.++...
T Consensus 100 tp~v~STSY~qy~~r~a~~ig~Prg~~~~Te~~lD~~~~PeeeR~E~L~~~~~~~~~~geelfe~lDe~F~r 171 (315)
T COG4030 100 TPVVISTSYTQYLRRTASMIGVPRGELHGTEVDLDSIAVPEEEREELLSIIDVIASLSGEELFEKLDELFSR 171 (315)
T ss_pred CceEEeccHHHHHHHHHHhcCCCccccccccccCccccCChHHHHHHHHhcCccccccHHHHHHHHHHHHhh
Confidence 22 334432 355678999999997643 68999999999866655555555666666544
No 9
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=25.87 E-value=2e+02 Score=25.83 Aligned_cols=71 Identities=21% Similarity=0.295 Sum_probs=52.1
Q ss_pred hhcccccccCCchhhhHHHHHHHHHH--------HHHHHHHHhccccccchHHHHHHHHhhhcCccccCchhHHHHHHHh
Q psy4196 82 QMLPLLDLHGVRRLDFHNSVLEELRD--------KLVSHIKEIGQKEGRDRDRKLNEMLKKSFPLVRVKQLRPVVMAILR 153 (168)
Q Consensus 82 ~~~~lld~hgVrRldfh~svle~Lr~--------~Ll~~I~~l~~~~~~~~~~kL~~lL~kSFp~i~v~~LrpVvmavL~ 153 (168)
+..|-||..+..|...++.+|..|=+ .+...++.+.+....+...--..+|...|+-|....- |+++|.|.
T Consensus 87 ~~~ppL~~~~~~r~~~w~~~L~~Ll~~l~~~~~~~~~~~l~~L~~~~~~~l~~~A~~Ll~~~~~~v~~~~a-~Fi~AALq 165 (309)
T PRK03564 87 QGKPPLDIHVFPRDKHWQKLLMALIAELKPEASGPALAVIENLEKASTQELEDMASALLASDFSSVSSDKA-PFIWAALS 165 (309)
T ss_pred cCCCCCCccccccChHHHHHHHHHHHHhcccCCHHHHHHHHHHHhCCHHHHHHHHHHHhcCCccccchhHH-HHHHHHHH
Confidence 34577899999999888888877665 3455666666655556677777888999998876544 77777665
No 10
>PRK14607 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase; Provisional
Probab=25.22 E-value=1e+02 Score=28.81 Aligned_cols=90 Identities=20% Similarity=0.239 Sum_probs=59.2
Q ss_pred CCcHHHHHHHhh--cCCCHHHHHHHHHHhcCccccchhhhccccc-cccccccccccchhHHHHHHHhhhhhhhhhhhcc
Q psy4196 9 IPGQNFLREALT--SCTDPLKAIEEFQLDNGILLPSLRQMLPLLD-LHGVRRLDFHNSVLEVEVTETLNLLLPSLRQMLP 85 (168)
Q Consensus 9 i~G~~~lreaLs--~~tdPl~aIe~FQ~eNgIlLpsl~~~LpLLD-L~~vr~~~~~~s~~~~e~~~t~~~~~p~~~~~~~ 85 (168)
-.|++.+.|+|- -...|.++-+.++ ++||..-....+-|-+. +-.+|+ ++-+.|-.|++-|-+.-+-|
T Consensus 310 ~~Gsadvle~lGv~~~~~~~~~~~~l~-~~g~~fl~ap~~~p~l~~~~~~R~--------~Lg~rTifN~lgpL~NP~~~ 380 (534)
T PRK14607 310 KSGSADVLEALGVKLEMTPEEAASVLR-ETGFSFLFAPLFHPAMKHAAPARR--------ELGIRTAFNLLGPLTNPARV 380 (534)
T ss_pred CccHHHHHHHcCCCCCCCHHHHHHHHH-HhCcEEeeccccCHHHHHHHHHHH--------HhCCCcHHHhHHhccCCCCC
Confidence 467889999994 3455666666665 57777433333333332 333454 66677889999997766666
Q ss_pred cccccCCchhhhHHHHHHHHHH
Q psy4196 86 LLDLHGVRRLDFHNSVLEELRD 107 (168)
Q Consensus 86 lld~hgVrRldfh~svle~Lr~ 107 (168)
=.-+.||-.-++...+.+.++.
T Consensus 381 ~~~v~Gv~~~~~~~~~a~~l~~ 402 (534)
T PRK14607 381 KYQIVGVFDPSYAEPLAQALQR 402 (534)
T ss_pred CcEEEeeCCHHHHHHHHHHHHH
Confidence 6777888777777666666653
No 11
>PF03109 ABC1: ABC1 family; InterPro: IPR004147 This entry includes ABC1 from yeast [] and AarF from Escherichia coli []. These proteins have a nuclear or mitochondrial subcellular location in eukaryotes. The exact molecular functions of these proteins is not clear, however yeast ABC1 suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex [] and E. coli AarF is required for ubiquinone production []. It has been suggested that members of the ABC1 family are novel chaperonins []. These proteins are unrelated to the ABC transporter proteins.
Probab=24.86 E-value=1.5e+02 Score=22.07 Aligned_cols=62 Identities=21% Similarity=0.265 Sum_probs=41.4
Q ss_pred hhhhhhcccccccCCchhhhHHHHHHHHHHHHHHHHHHhccccccchHHHHHHHHhhhcCccccCc
Q psy4196 78 PSLRQMLPLLDLHGVRRLDFHNSVLEELRDKLVSHIKEIGQKEGRDRDRKLNEMLKKSFPLVRVKQ 143 (168)
Q Consensus 78 p~~~~~~~lld~hgVrRldfh~svle~Lr~~Ll~~I~~l~~~~~~~~~~kL~~lL~kSFp~i~v~~ 143 (168)
-.++.+..+++.++..+.--..++++++++.+...++ ...+...-+++.+.+.++ |.|.||.
T Consensus 56 ~~l~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~ElD---f~~Ea~n~~~~~~~~~~~-~~v~vP~ 117 (119)
T PF03109_consen 56 RILRRLARLLERLPPFRRLDLEEIVDEFRDSLLEELD---FRREAANLERFRKNFADS-PRVYVPK 117 (119)
T ss_pred HHHHHHHHHHHHcccccccCHHHHHHHHHHHHHHHhC---HHHHHHHHHHHHHHhCCC-CCEecCC
Confidence 3445556666666655544467888899998885543 333345566777888777 8888886
No 12
>PF14575 EphA2_TM: Ephrin type-A receptor 2 transmembrane domain; PDB: 3KUL_A 2XVD_A 2VX1_A 2VWV_A 2VX0_A 2VWY_A 2VWZ_A 2VWW_A 2VWU_A 2VWX_A ....
Probab=23.73 E-value=28 Score=24.82 Aligned_cols=16 Identities=31% Similarity=0.590 Sum_probs=13.6
Q ss_pred hcCCCHHHHHHHHHHh
Q psy4196 20 TSCTDPLKAIEEFQLD 35 (168)
Q Consensus 20 s~~tdPl~aIe~FQ~e 35 (168)
.++-||-+|+.||-+|
T Consensus 57 ~TYEDP~qAV~eFAkE 72 (75)
T PF14575_consen 57 HTYEDPNQAVREFAKE 72 (75)
T ss_dssp GGSSSHHHHHHHCSSB
T ss_pred ccccCHHHHHHHHHhh
Confidence 5688999999999765
No 13
>PF09662 Phenyl_P_gamma: Phenylphosphate carboxylase gamma subunit (Phenyl_P_gamma); InterPro: IPR014097 Members of this protein family are the gamma subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. The gamma subunit has no known homologues.
Probab=22.92 E-value=18 Score=27.50 Aligned_cols=19 Identities=32% Similarity=0.595 Sum_probs=17.1
Q ss_pred hHHHHHHHhcCCCCcHHHH
Q psy4196 145 RPVVMAILRNTTHIDDKYL 163 (168)
Q Consensus 145 rpVvmavL~~~~~ip~kyL 163 (168)
||.-|.|+.+...+|++||
T Consensus 66 q~~SI~I~~ei~~~p~kyl 84 (84)
T PF09662_consen 66 QPWSIKILEEINKMPAKYL 84 (84)
T ss_pred cceeehHHHHHhhCchhhC
Confidence 5777899999999999996
No 14
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=22.00 E-value=2.4e+02 Score=21.00 Aligned_cols=43 Identities=19% Similarity=0.304 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHhccccccchHHHHHHHHhhhcCccccCchhHH
Q psy4196 105 LRDKLVSHIKEIGQKEGRDRDRKLNEMLKKSFPLVRVKQLRPV 147 (168)
Q Consensus 105 Lr~~Ll~~I~~l~~~~~~~~~~kL~~lL~kSFp~i~v~~LrpV 147 (168)
|-|-|...|.++.+.+.--.-+.|-+-|.+.||-+..|+-.-|
T Consensus 12 L~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i~~Ps~e~l 54 (80)
T PF10264_consen 12 LPEVLCWVISDLNAAGQPATQETLREHLRKHYPGIAIPSQEVL 54 (80)
T ss_pred HHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCCCCCCCHHHH
Confidence 6677888888888877777788999999999999999986533
No 15
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=21.52 E-value=91 Score=21.27 Aligned_cols=30 Identities=27% Similarity=0.371 Sum_probs=19.0
Q ss_pred ccccCCchhhhHHHHHHHHHHHHHHHHHHh
Q psy4196 87 LDLHGVRRLDFHNSVLEELRDKLVSHIKEI 116 (168)
Q Consensus 87 ld~hgVrRldfh~svle~Lr~~Ll~~I~~l 116 (168)
||+||.+..+....+-+.+.+-.-..+..+
T Consensus 1 iDLHG~~~~eA~~~l~~~l~~~~~~~~~~~ 30 (83)
T PF01713_consen 1 IDLHGLTVEEALRALEEFLDEARQRGIREL 30 (83)
T ss_dssp EE-TTS-HHHHHHHHHHHHHHHHHTTHSEE
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHHcCCCEE
Confidence 578999988887777776666554444443
No 16
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=20.04 E-value=94 Score=26.38 Aligned_cols=73 Identities=22% Similarity=0.263 Sum_probs=35.4
Q ss_pred hhhhhcccccccCCchhhhHHHHHHHHHHHHH---------HHHHHhccccccchHHHHHHHHhhhcCccccCchhHHHH
Q psy4196 79 SLRQMLPLLDLHGVRRLDFHNSVLEELRDKLV---------SHIKEIGQKEGRDRDRKLNEMLKKSFPLVRVKQLRPVVM 149 (168)
Q Consensus 79 ~~~~~~~lld~hgVrRldfh~svle~Lr~~Ll---------~~I~~l~~~~~~~~~~kL~~lL~kSFp~i~v~~LrpVvm 149 (168)
.+++-.|+|+..+.++...+..++++|-..+- ..++.+.+....+...-+..+|..-++...- .+.+++.
T Consensus 68 ~~~~g~PlL~~~~~~~d~~~~~~l~~ll~~l~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~l~~~~~~~~~-~l~~~~~ 146 (290)
T PF04216_consen 68 RLEQGMPLLAREPLPRDPAWRAALRELLAALAESGLPEAAAAALEALRAADEEDLEALAEALLAGEMPVDPE-ALAFFLW 146 (290)
T ss_dssp HHHTT--TT-HHHHHHH-TTHHHHHHHHHT--S-S-SHHHHHHHHHHHH--HHHHHHHHHHHHTT-GGGS-G-GGHHHHH
T ss_pred HhhcCCCCCCccccCcCHHHHHHHHHHHHHHhhccCCHHHHHHHHHHHhCCHHHHHHHHHHHHhcccCCCcH-HHHHHHH
Confidence 45666777777777665555444444332222 2345555445556677777778755554432 4555555
Q ss_pred HHH
Q psy4196 150 AIL 152 (168)
Q Consensus 150 avL 152 (168)
+.|
T Consensus 147 aaL 149 (290)
T PF04216_consen 147 AAL 149 (290)
T ss_dssp HHH
T ss_pred HHH
Confidence 544
Done!