Query psy1002
Match_columns 136
No_of_seqs 114 out of 377
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 15:48:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1002.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1002hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07542 ATP12: ATP12 chaperon 100.0 6.8E-48 1.5E-52 287.1 6.9 101 30-131 1-101 (122)
2 COG5387 Chaperone required for 100.0 5.6E-39 1.2E-43 262.8 7.8 123 4-131 11-134 (264)
3 KOG3015|consensus 100.0 4.6E-34 1E-38 236.7 7.9 109 26-134 41-152 (283)
4 PF14277 DUF4364: Domain of un 66.1 6.2 0.00013 30.7 2.8 42 41-82 110-152 (163)
5 PF06236 MelC1: Tyrosinase co- 54.2 5.8 0.00013 30.2 0.8 36 43-78 69-115 (125)
6 KOG3831|consensus 42.5 9.8 0.00021 30.4 0.4 22 107-128 146-167 (196)
7 smart00067 GHA Glycoprotein ho 36.5 11 0.00025 26.9 -0.0 24 6-34 39-62 (87)
8 COG1638 DctP TRAP-type C4-dica 35.2 72 0.0016 27.3 4.6 57 42-103 146-210 (332)
9 PF14317 YcxB: YcxB-like prote 28.4 69 0.0015 19.1 2.6 35 29-70 15-50 (62)
10 PRK04439 S-adenosylmethionine 27.4 67 0.0015 28.9 3.2 75 45-121 84-183 (399)
11 TIGR03342 dsrC_tusE_dsvC sulfu 26.0 40 0.00086 24.8 1.3 29 48-76 2-33 (108)
12 COG2920 DsrC Dissimilatory sul 25.4 50 0.0011 24.7 1.8 30 47-76 4-36 (111)
13 PRK11508 sulfur transfer prote 25.3 54 0.0012 24.2 1.9 30 47-76 2-34 (109)
14 PF10262 Rdx: Rdx family; Int 24.0 73 0.0016 21.1 2.2 41 34-75 33-75 (76)
15 TIGR03193 4hydroxCoAred 4-hydr 22.3 2.1E+02 0.0046 22.1 4.8 68 44-115 45-128 (148)
16 PF12375 DUF3653: Phage protei 22.1 70 0.0015 22.0 1.9 35 44-81 1-39 (76)
17 cd08489 PBP2_NikA The substrat 21.7 99 0.0021 26.5 3.1 45 51-95 323-376 (488)
18 COG2080 CoxS Aerobic-type carb 21.1 48 0.001 26.1 1.0 14 43-56 46-59 (156)
19 PF03983 SHD1: SLA1 homology d 20.8 28 0.00061 23.9 -0.3 45 26-70 8-54 (70)
No 1
>PF07542 ATP12: ATP12 chaperone protein; InterPro: IPR011419 This entry represents a group of ATPase F1F0-assembly proteins, including ATP12 and ATPAF2 (ATP synthase mitochondrial F1 complex assembly factor 2). These proteins are essential for the assembly of the mitochondrial F1-F0 complex. Mitochondrial F1-ATPase is an oligomeric enzyme composed of five distinct subunit polypeptides. The alpha and beta subunits make up the bulk of protein mass of F1. In Saccharomyces cerevisiae both subunits are synthesised as precursors with N-terminal targeting signals that are removed upon translocation of the proteins to the matrix compartment []. These proteins include examples from eukaryotes and bacteria and may have chaperone activity, being involved in F1 ATPase complex assembly. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0043461 proton-transporting ATP synthase complex assembly; PDB: 2R6I_B 2ZD2_B 2P4X_B 2R31_A.
Probab=100.00 E-value=6.8e-48 Score=287.07 Aligned_cols=101 Identities=47% Similarity=0.680 Sum_probs=84.9
Q ss_pred CccceeeeeEEeCCcEEEEeCCCcCCCCCCCeeeeCcHHHHHHHHHHHhhcccCcCCCccchhhhhhhhhcCCCCCCHHH
Q psy1002 30 KRFYKKVGILESNGDYEISLDHRKLKTPNGVLFKVSSEPLALAIAAEWDAQHETIQRSTMHLTAICNTVIDNPNRLTKFD 109 (136)
Q Consensus 30 kRFyK~v~V~~~~gg~~V~LDgR~lkTP~g~~L~vPs~~LA~avA~EW~~Q~e~I~p~~MPLT~La~tAID~~~~~~r~~ 109 (136)
|||||+|+|.+.++||+|+||||+||||+|++|+|||++||++||+||++|++.|+|++||||+||+||||++.+ +|+.
T Consensus 1 KRFyk~v~v~~~~~g~~V~LDgR~lkTP~~~~l~vps~~LA~avA~EW~~Q~~~i~p~~MPLT~L~~taiD~~~~-~r~~ 79 (122)
T PF07542_consen 1 KRFYKEVSVEENDGGFQVLLDGRPLKTPAGNPLVVPSEALAEAVAAEWDAQGEYIKPHTMPLTSLANTAIDRVAE-DREA 79 (122)
T ss_dssp B---S-EEEEEETTSEEEEETTEE-BETTSEB--BSSHHHHHHHHHHHHT-SSB--GGG-HHHHHHHHHHHTTCC-CHHH
T ss_pred CCCcceeeEEecCCCEEEEeCCCCCCCCCCCeeEcCcHHHHHHHHHHHHhhhcccCcccccHHHHHHHHHhccch-hHHH
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999987 8999
Q ss_pred HHHHHHhhhCCCeEEEeecCcc
Q psy1002 110 LVQNIINFLDTDTILYHANFFL 131 (136)
Q Consensus 110 v~~~ll~Yl~TDtlcyra~~~~ 131 (136)
++++|++|++||+||||+++++
T Consensus 80 ~~~~il~yl~tDtlc~r~~~~~ 101 (122)
T PF07542_consen 80 VIDEILRYLDTDTLCYRAPEPE 101 (122)
T ss_dssp HHHHHHHHHHC-CCCEE--SSH
T ss_pred HHHHHHHHcCCCeEEEeCCCcH
Confidence 9999999999999999999875
No 2
>COG5387 Chaperone required for the assembly of the mitochondrial F1-ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.6e-39 Score=262.75 Aligned_cols=123 Identities=40% Similarity=0.568 Sum_probs=113.5
Q ss_pred ccccccccchhhhhhhhccccCCCCCCccceeeeeEEeC-CcEEEEeCCCcCCCCCCCeeeeCcHHHHHHHHHHHhhccc
Q psy1002 4 GKQTTMRYPRLINSIQSCKYSALEKPKRFYKKVGILESN-GDYEISLDHRKLKTPNGVLFKVSSEPLALAIAAEWDAQHE 82 (136)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~kRFyK~v~V~~~~-gg~~V~LDgR~lkTP~g~~L~vPs~~LA~avA~EW~~Q~e 82 (136)
|++-+-.-|.+-.|.+..+| .+|||||++++.+.+ |||.|+||||++|||+||+|+||+++||++||.||++|.+
T Consensus 11 ~~llSd~t~~~~~~~q~q~p----lpkrfyk~a~aa~ve~Gg~aiqLDGR~~KtPa~k~l~vpt~~LA~lla~EWdaqs~ 86 (264)
T COG5387 11 GPLLSDKTPILRAQTQMQKP----LPKRFYKKATAADVEKGGFAIQLDGRTLKTPAGKPLVVPTEALAYLLALEWDAQSE 86 (264)
T ss_pred CccCCCCcHHHhhhHhhcCc----chHHHHHHhhcCccccCceEEEeCCCCCCCCCCCceeCcHHHHHHHHHHHhhcchh
Confidence 55666667777778888777 489999999999876 9999999999999999999999999999999999999999
Q ss_pred CcCCCccchhhhhhhhhcCCCCCCHHHHHHHHHhhhCCCeEEEeecCcc
Q psy1002 83 TIQRSTMHLTAICNTVIDNPNRLTKFDLVQNIINFLDTDTILYHANFFL 131 (136)
Q Consensus 83 ~I~p~~MPLT~La~tAID~~~~~~r~~v~~~ll~Yl~TDtlcyra~~~~ 131 (136)
+|+||+||+|+|++||||+... +++.+.++|++|++||+||||++++.
T Consensus 87 ~I~~~~mP~TrlV~taID~ia~-~~~~v~~~ilrf~~tDlLcYra~sp~ 134 (264)
T COG5387 87 SIDPHSMPLTRLVNTAIDGIAE-DSQAVFEQILRFLDTDLLCYRAESPF 134 (264)
T ss_pred ccCcccCcHHHHHHHHHHhhcc-cHHHHHHHHHHHccCCeeEecCCCHH
Confidence 9999999999999999999976 89999999999999999999998863
No 3
>KOG3015|consensus
Probab=100.00 E-value=4.6e-34 Score=236.70 Aligned_cols=109 Identities=48% Similarity=0.698 Sum_probs=103.5
Q ss_pred CCCCCccceeeeeEEeC--CcEEEEeCCCcCCCCCCCeeeeCcHHHHHHHHHHHhhcc-cCcCCCccchhhhhhhhhcCC
Q psy1002 26 LEKPKRFYKKVGILESN--GDYEISLDHRKLKTPNGVLFKVSSEPLALAIAAEWDAQH-ETIQRSTMHLTAICNTVIDNP 102 (136)
Q Consensus 26 ~~~~kRFyK~v~V~~~~--gg~~V~LDgR~lkTP~g~~L~vPs~~LA~avA~EW~~Q~-e~I~p~~MPLT~La~tAID~~ 102 (136)
.+..|||||+|++...+ |||.|.||||.+|||.|+++.|||++||.+||.||+.|. +.|+|++||||+||+||||++
T Consensus 41 ~Pt~krF~kkvs~~~g~~~g~~~v~LD~R~lKTP~g~~f~v~s~~LA~~ia~Ewdsq~s~~i~~~~mplt~L~~taid~~ 120 (283)
T KOG3015|consen 41 SPTSKRFYKKVSTLTGDAFGGQEVQLDGRTLKTPKGNPFKVRSEKLAIAIALEWDSQKSTSIRPFTMPLTSLVFTAIDNP 120 (283)
T ss_pred CCcHHHHHhhhhheecccCCceEEecccccccCCCCCeeecccHHHHHHHHHHHhhcccccccccccHHHHHHHHHhhcc
Confidence 33469999999999877 999999999999999999999999999999999999999 899999999999999999998
Q ss_pred CCCCHHHHHHHHHhhhCCCeEEEeecCcccCC
Q psy1002 103 NRLTKFDLVQNIINFLDTDTILYHANFFLRKG 134 (136)
Q Consensus 103 ~~~~r~~v~~~ll~Yl~TDtlcyra~~~~~~~ 134 (136)
.+.+++.+++.|++|++|||||||++..++.|
T Consensus 121 ~~~~kd~i~~~llrfldtDTvlf~~pe~e~l~ 152 (283)
T KOG3015|consen 121 SELNKDTISNQLLRFLDTDTVLFFSPESEDLG 152 (283)
T ss_pred CcccHHHHHHHHHHHhccCeEEEecCChhhhh
Confidence 88899999999999999999999999999876
No 4
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=66.05 E-value=6.2 Score=30.71 Aligned_cols=42 Identities=29% Similarity=0.428 Sum_probs=31.7
Q ss_pred eCCcEEEEeCCCcCCCCC-CCeeeeCcHHHHHHHHHHHhhccc
Q psy1002 41 SNGDYEISLDHRKLKTPN-GVLFKVSSEPLALAIAAEWDAQHE 82 (136)
Q Consensus 41 ~~gg~~V~LDgR~lkTP~-g~~L~vPs~~LA~avA~EW~~Q~e 82 (136)
.+|+|.|.|-=+--.++. .=.|.||+++-|.+|..-|.....
T Consensus 110 ~~~~y~V~l~i~e~~~~Li~l~l~vp~~~qA~~ic~nwk~n~~ 152 (163)
T PF14277_consen 110 SNGEYIVRLQIIENDSDLIDLKLNVPSEEQAEAICNNWKKNSQ 152 (163)
T ss_pred CCCCEEEEEEEEeCCceEEEEEEeCCCHHHHHHHHHHHhhCHH
Confidence 478899987544444444 456899999999999999986543
No 5
>PF06236 MelC1: Tyrosinase co-factor MelC1; InterPro: IPR010928 This family consists of several tyrosinase co-factor MELC1 proteins from a number of Streptomyces species. The melanin operon (melC) of Streptomyces antibioticus contains two genes, melC1 and melC2 (apotyrosinase). It is thought that MelC1 forms a transient binary complex with the downstream apotyrosinase MelC2 to facilitate the incorporation of copper ion and the secretion of tyrosinase indicating that MelC1 is a chaperone for the apotyrosinase MelC2 [].; GO: 0005507 copper ion binding, 0042438 melanin biosynthetic process; PDB: 1WX4_B 2ZWD_B 2ZMZ_B 1WX2_B 1WX5_D 3AWX_B 3AWS_B 2ZMY_B 3AX0_B 2ZWG_B ....
Probab=54.20 E-value=5.8 Score=30.22 Aligned_cols=36 Identities=28% Similarity=0.402 Sum_probs=23.7
Q ss_pred CcEEEEeCCCcCCCCC---CCeee-------eCc-HHHHHHHHHHHh
Q psy1002 43 GDYEISLDHRKLKTPN---GVLFK-------VSS-EPLALAIAAEWD 78 (136)
Q Consensus 43 gg~~V~LDgR~lkTP~---g~~L~-------vPs-~~LA~avA~EW~ 78 (136)
++|.|++|||+|.-.. |.-|+ +|+ .++|.+.-.|-.
T Consensus 69 ~~~~V~IDGr~LhvMr~ADGswlS~V~HYe~~pTpl~aARAAVdeL~ 115 (125)
T PF06236_consen 69 GGYEVTIDGRPLHVMRRADGSWLSVVNHYESYPTPLEAARAAVDELG 115 (125)
T ss_dssp -SEEEEETTEEE-EEE-TTS-EEETTEEEEEESSHHHHHHHHHHHHT
T ss_pred CceEEEECCeEeeeEEcCCCCEEeeeecccCCCCHHHHHHHHHHHhC
Confidence 4699999999986554 55554 455 467777777765
No 6
>KOG3831|consensus
Probab=42.54 E-value=9.8 Score=30.45 Aligned_cols=22 Identities=27% Similarity=0.511 Sum_probs=20.1
Q ss_pred HHHHHHHHHhhhCCCeEEEeec
Q psy1002 107 KFDLVQNIINFLDTDTILYHAN 128 (136)
Q Consensus 107 r~~v~~~ll~Yl~TDtlcyra~ 128 (136)
++++++.++.-+++|-||||+=
T Consensus 146 k~qivqfl~dmfd~~kv~y~sl 167 (196)
T KOG3831|consen 146 KEQIVQFLLDMFDLDKVCYRSL 167 (196)
T ss_pred HHHHHHHHHHHhhhhhHHHhhH
Confidence 6889999999999999999973
No 7
>smart00067 GHA Glycoprotein hormone alpha chain homologues. Also called gonadotropins. Glycoprotein hormones consist of two glycosylated chains (alpha and beta) of similar topology.
Probab=36.48 E-value=11 Score=26.88 Aligned_cols=24 Identities=38% Similarity=0.649 Sum_probs=18.3
Q ss_pred ccccccchhhhhhhhccccCCCCCCccce
Q psy1002 6 QTTMRYPRLINSIQSCKYSALEKPKRFYK 34 (136)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~kRFyK 34 (136)
..||-+|++|+++-.+=- .|.||+
T Consensus 39 kktM~vpKNITSEAtCCV-----Ak~~~~ 62 (87)
T smart00067 39 KKTMLVPKNITSEATCCV-----AKEFYR 62 (87)
T ss_pred hhccccCccccCceeEEE-----ecccEE
Confidence 358999999999877654 466666
No 8
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=35.23 E-value=72 Score=27.30 Aligned_cols=57 Identities=26% Similarity=0.457 Sum_probs=44.8
Q ss_pred CCcEEEEeCCC-cCCCCC---CCeeeeCcHHHHHHHHHHHhhcccCcCCCccch----hhhhhhhhcCCC
Q psy1002 42 NGDYEISLDHR-KLKTPN---GVLFKVSSEPLALAIAAEWDAQHETIQRSTMHL----TAICNTVIDNPN 103 (136)
Q Consensus 42 ~gg~~V~LDgR-~lkTP~---g~~L~vPs~~LA~avA~EW~~Q~e~I~p~~MPL----T~La~tAID~~~ 103 (136)
++||.-..-++ ||++|. |..+.||.-++.......+-+. |..||. +.|-..+||...
T Consensus 146 ~~G~R~~t~~k~PI~~peDlkGlkiRv~~s~~~~~~~~a~GA~-----P~pm~f~Evy~aLqtGvVDGqE 210 (332)
T COG1638 146 ENGFRQFTSNKRPIKTPEDLKGLKIRVPQSPLLLAMFKALGAN-----PTPMPFAEVYTALQTGVVDGQE 210 (332)
T ss_pred cCceeeeecCCCCCCChHHhCCCeeecCCCHHHHHHHHHcCCC-----CCCCCHHHHHHHHHcCCccccc
Confidence 57898888866 999998 9999999988888887777665 566665 456677778653
No 9
>PF14317 YcxB: YcxB-like protein
Probab=28.42 E-value=69 Score=19.12 Aligned_cols=35 Identities=9% Similarity=0.283 Sum_probs=26.1
Q ss_pred CCccceeee-eEEeCCcEEEEeCCCcCCCCCCCeeeeCcHHHH
Q psy1002 29 PKRFYKKVG-ILESNGDYEISLDHRKLKTPNGVLFKVSSEPLA 70 (136)
Q Consensus 29 ~kRFyK~v~-V~~~~gg~~V~LDgR~lkTP~g~~L~vPs~~LA 70 (136)
.+-.|+++. |.+.+..|-+.++++ ..+.||.+++.
T Consensus 15 ~~~~w~~i~~v~e~~~~~~l~~~~~-------~~~~iPk~~f~ 50 (62)
T PF14317_consen 15 SRIPWSDIKKVVETKDYFYLYLGKN-------QAFIIPKRAFS 50 (62)
T ss_pred EEEEchheEEEEEeCCEEEEEECCC-------eEEEEEHHHCC
Confidence 456788877 667778888888653 67899988766
No 10
>PRK04439 S-adenosylmethionine synthetase; Provisional
Probab=27.44 E-value=67 Score=28.86 Aligned_cols=75 Identities=17% Similarity=0.168 Sum_probs=51.1
Q ss_pred EEEEeCCCcCCCCCCCeeeeCcHHHHHHHHHHHhhcc-------------cCcCCCccchhhhhhhhhcCCC--------
Q psy1002 45 YEISLDHRKLKTPNGVLFKVSSEPLALAIAAEWDAQH-------------ETIQRSTMHLTAICNTVIDNPN-------- 103 (136)
Q Consensus 45 ~~V~LDgR~lkTP~g~~L~vPs~~LA~avA~EW~~Q~-------------e~I~p~~MPLT~La~tAID~~~-------- 103 (136)
..|.+.||..+...|.. +|...+|..-|.||=... -.|.|.+=-|+.+-.+.=..+.
T Consensus 84 i~ii~~GRAt~~~~g~~--iPv~~Ia~~Aak~~L~~~l~~lD~e~hv~i~~~i~~GS~dL~~vF~r~~~vp~ANDTS~gV 161 (399)
T PRK04439 84 IYIILGGRATKEVGGEE--IPVGEIAIEAAKEYLRENLRNLDPERHVIIDVRLGPGSTDLVDVFERESIVPLANDTSFGV 161 (399)
T ss_pred EEEEEecceeeeECCeE--ecHHHHHHHHHHHHHHHhCccCCccccEEEEEeeCCCcHHHHHHhCCCCCcccccccccee
Confidence 78899999999998776 999999999999997432 1344555556655543111110
Q ss_pred ----CCCHHHHHHHHHhhhCCC
Q psy1002 104 ----RLTKFDLVQNIINFLDTD 121 (136)
Q Consensus 104 ----~~~r~~v~~~ll~Yl~TD 121 (136)
-..-+.++-++-+||.+.
T Consensus 162 GyAPlS~~E~~Vl~~E~~lns~ 183 (399)
T PRK04439 162 GYAPLSETERLVLETERYLNSE 183 (399)
T ss_pred ecCCCCHHHHHHHHHHHHhcCc
Confidence 123577888888888543
No 11
>TIGR03342 dsrC_tusE_dsvC sulfur relay protein, TusE/DsrC/DsvC family. Members of this protein family may be described as TusE, a partner to TusBCD in a sulfur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Other members are DsrC, a functionally similar protein in species where the sulfur relay system exists primarily for sulfur metabolism rather than tRNA base modification. Some members of this family are known explicitly as the gamma subunit of sulfite reductases.
Probab=26.02 E-value=40 Score=24.81 Aligned_cols=29 Identities=28% Similarity=0.494 Sum_probs=20.4
Q ss_pred EeCCCcCCCC-CCCeeeeC--cHHHHHHHHHH
Q psy1002 48 SLDHRKLKTP-NGVLFKVS--SEPLALAIAAE 76 (136)
Q Consensus 48 ~LDgR~lkTP-~g~~L~vP--s~~LA~avA~E 76 (136)
.++|+.+.|- .|..+-.. |+++|.+||++
T Consensus 2 ~~~g~~i~~D~~GfL~~~~dW~e~vA~~lA~~ 33 (108)
T TIGR03342 2 EVNGKEIELDEDGYLLDLDDWSEDVAEALAEE 33 (108)
T ss_pred cCCCeeeeeCCCCCcCChHHCCHHHHHHHHHH
Confidence 3567777773 46655543 58999999988
No 12
>COG2920 DsrC Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]
Probab=25.44 E-value=50 Score=24.68 Aligned_cols=30 Identities=27% Similarity=0.364 Sum_probs=22.8
Q ss_pred EEeCCCcCCCCCCCeeeeC---cHHHHHHHHHH
Q psy1002 47 ISLDHRKLKTPNGVLFKVS---SEPLALAIAAE 76 (136)
Q Consensus 47 V~LDgR~lkTP~g~~L~vP---s~~LA~avA~E 76 (136)
+.++||.|+|-.---|.=+ ++.+|.+||++
T Consensus 4 l~~~gk~i~~D~dGyL~~~~dW~E~vAe~lA~~ 36 (111)
T COG2920 4 LEVEGKEIETDEDGYLKDSEDWSEKVAEALAER 36 (111)
T ss_pred eeecCeEEeecccchhcChhhhCHHHHHHHHHH
Confidence 5788999999885555555 47899999875
No 13
>PRK11508 sulfur transfer protein TusE; Provisional
Probab=25.30 E-value=54 Score=24.16 Aligned_cols=30 Identities=37% Similarity=0.593 Sum_probs=20.7
Q ss_pred EEeCCCcCCC-CCCCeeeeC--cHHHHHHHHHH
Q psy1002 47 ISLDHRKLKT-PNGVLFKVS--SEPLALAIAAE 76 (136)
Q Consensus 47 V~LDgR~lkT-P~g~~L~vP--s~~LA~avA~E 76 (136)
+.++|+.+-| ..|..+-.. |+++|.+||++
T Consensus 2 ~~v~g~~ie~D~eGfL~~~~dW~e~vA~~lA~~ 34 (109)
T PRK11508 2 LIFEGKEIETDTEGYLKESSQWSEPLAVVIAEN 34 (109)
T ss_pred eeECCEEeeeCCCCCcCChHHCCHHHHHHHHHH
Confidence 3466777776 345555533 58999999998
No 14
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=23.99 E-value=73 Score=21.12 Aligned_cols=41 Identities=10% Similarity=0.192 Sum_probs=22.9
Q ss_pred eeeeeEEe-CCcEEEEeCCCcCCCCCCCeeeeCc-HHHHHHHHH
Q psy1002 34 KKVGILES-NGDYEISLDHRKLKTPNGVLFKVSS-EPLALAIAA 75 (136)
Q Consensus 34 K~v~V~~~-~gg~~V~LDgR~lkTP~g~~L~vPs-~~LA~avA~ 75 (136)
-+++.... .|-|.|.+||..|-+-.. .-..|+ ++|..+|..
T Consensus 33 ~~v~~~~~~~G~FEV~v~g~lI~SK~~-~g~fP~~~~i~~~I~~ 75 (76)
T PF10262_consen 33 AEVELSPGSTGAFEVTVNGELIFSKLE-SGRFPDPDEIVQLIRD 75 (76)
T ss_dssp SEEEEEEESTT-EEEEETTEEEEEHHH-HTSSS-HHHHHHHHHH
T ss_pred eEEEEEeccCCEEEEEEccEEEEEehh-cCCCCCHHHHHHHHhc
Confidence 45555554 556999999986643221 115564 456666653
No 15
>TIGR03193 4hydroxCoAred 4-hydroxybenzoyl-CoA reductase, gamma subunit. 4-hydroxybenzoyl-CoA reductase converts 4-hydroxybenzoyl-CoA to benzoyl-CoA, a common intermediate in the degradation of aromatic compounds. This protein family represents the gamma chain of this three-subunit enzyme.
Probab=22.26 E-value=2.1e+02 Score=22.09 Aligned_cols=68 Identities=15% Similarity=0.122 Sum_probs=42.3
Q ss_pred cEEEEeCCCcCCC---C-----CCCeeeeCc-------HHHHHHHHHHHhhcccCcCCCc-cchhhhhhhhhcCCCCCCH
Q psy1002 44 DYEISLDHRKLKT---P-----NGVLFKVSS-------EPLALAIAAEWDAQHETIQRST-MHLTAICNTVIDNPNRLTK 107 (136)
Q Consensus 44 g~~V~LDgR~lkT---P-----~g~~L~vPs-------~~LA~avA~EW~~Q~e~I~p~~-MPLT~La~tAID~~~~~~r 107 (136)
--+|++|||++++ | ++.+..|-. .++..+.++++..|=.+=.|.. |-++.|..+ ++. .++
T Consensus 45 ACtVlvdg~~v~SCl~~~~~~~G~~V~TiEgl~~~~~l~pvq~af~~~~a~QCGfCtPG~vms~~~ll~~---~p~-ps~ 120 (148)
T TIGR03193 45 ACTVLVDGRPRLACSTLAHRVAGRKVETVEGLATNGRLSRLQQAFHERLGTQCGFCTPGMIMAAEALLRR---NPS-PSR 120 (148)
T ss_pred CCEEEECCeEeeccHhhHhhcCCCcEEEeCCCCCCCCCCHHHHHHHHcCCCcCCCCCccHHHHHHHHHHc---CCC-CCH
Confidence 3889999988764 2 233444432 4588888888888888888765 333444322 343 366
Q ss_pred HHHHHHHH
Q psy1002 108 FDLVQNII 115 (136)
Q Consensus 108 ~~v~~~ll 115 (136)
+++.+.|-
T Consensus 121 ~ei~~al~ 128 (148)
T TIGR03193 121 DEIRAALA 128 (148)
T ss_pred HHHHHHHc
Confidence 66666553
No 16
>PF12375 DUF3653: Phage protein; InterPro: IPR021077 This entry represents a phage protein found in bacteria and viruses, they are typically between 112 and 194 amino acids in length. Note that many members are hypothetical proteins.
Probab=22.14 E-value=70 Score=22.00 Aligned_cols=35 Identities=31% Similarity=0.592 Sum_probs=25.1
Q ss_pred cEEEEeCCCcCCCCCCCeeeeCcH----HHHHHHHHHHhhcc
Q psy1002 44 DYEISLDHRKLKTPNGVLFKVSSE----PLALAIAAEWDAQH 81 (136)
Q Consensus 44 g~~V~LDgR~lkTP~g~~L~vPs~----~LA~avA~EW~~Q~ 81 (136)
||.+ +|-.|=||.|..+. |.+ .|-..+|+||+..-
T Consensus 1 Gfr~--~~~~LiTPeGr~~~-p~~l~~~~~~~~ia~e~~~m~ 39 (76)
T PF12375_consen 1 GFRF--QGGRLITPEGRRFS-PQDLEWWSLTCDIAREWDRMM 39 (76)
T ss_pred Ccee--eCCeEECCCCCccC-HHHHHHHHHHHHHHHHHHHHH
Confidence 5666 45558899998875 442 57778999999643
No 17
>cd08489 PBP2_NikA The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides,
Probab=21.65 E-value=99 Score=26.51 Aligned_cols=45 Identities=9% Similarity=0.066 Sum_probs=29.0
Q ss_pred CCcCCCCCCCeeee----C-----cHHHHHHHHHHHhhcccCcCCCccchhhhh
Q psy1002 51 HRKLKTPNGVLFKV----S-----SEPLALAIAAEWDAQHETIQRSTMHLTAIC 95 (136)
Q Consensus 51 gR~lkTP~g~~L~v----P-----s~~LA~avA~EW~~Q~e~I~p~~MPLT~La 95 (136)
|..+++|.|+++.+ + .+.+|.+|++.|+..|=.++...++-..+.
T Consensus 323 ~~g~~~~~g~~~~~~l~~~~~~~~~~~~a~~i~~~l~~~Gi~v~~~~~~~~~~~ 376 (488)
T cd08489 323 GDGIREKDGKPLSLELVYQTDNALQKSIAEYLQSELKKIGIDLNIIGEEEQAYY 376 (488)
T ss_pred CCceEccCCceEEEEEEecCCCchHHHHHHHHHHHHHHcCcEEEEeeccHHHHH
Confidence 44456677776543 2 157999999999987655555555554443
No 18
>COG2080 CoxS Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]
Probab=21.08 E-value=48 Score=26.07 Aligned_cols=14 Identities=14% Similarity=0.380 Sum_probs=12.3
Q ss_pred CcEEEEeCCCcCCC
Q psy1002 43 GDYEISLDHRKLKT 56 (136)
Q Consensus 43 gg~~V~LDgR~lkT 56 (136)
|..+|++||+++|+
T Consensus 46 GACtVlvDG~~v~S 59 (156)
T COG2080 46 GACTVLVDGEAVNS 59 (156)
T ss_pred CceEEEECCeEehH
Confidence 55999999999985
No 19
>PF03983 SHD1: SLA1 homology domain 1, SHD1 ; InterPro: IPR007131 The SLA1 homology domain is found in the cytoskeleton assembly control protein SLA1, which is responsible for the correct formation of the actin cytoskeleton.; GO: 0008092 cytoskeletal protein binding, 0030674 protein binding, bridging, 0042802 identical protein binding, 0043130 ubiquitin binding; PDB: 2HBP_A.
Probab=20.83 E-value=28 Score=23.91 Aligned_cols=45 Identities=20% Similarity=0.188 Sum_probs=26.8
Q ss_pred CCCCCccceeeeeE-EeCCcEEEEeCCC-cCCCCCCCeeeeCcHHHH
Q psy1002 26 LEKPKRFYKKVGIL-ESNGDYEISLDHR-KLKTPNGVLFKVSSEPLA 70 (136)
Q Consensus 26 ~~~~kRFyK~v~V~-~~~gg~~V~LDgR-~lkTP~g~~L~vPs~~LA 70 (136)
....-|.|.+.+=. ..+.-|.=.-||+ .|+..+|..+.||...|.
T Consensus 8 ~~~~~RtWtD~tG~f~VeA~fv~~~dgkV~L~k~nG~~i~VP~~kLS 54 (70)
T PF03983_consen 8 DPSKTRTWTDRTGKFKVEAEFVGVNDGKVHLHKTNGVKIAVPLEKLS 54 (70)
T ss_dssp ----SEEEEBSSS--EEEEEEEEEETTEEEEE-TTS-EEEEETTSB-
T ss_pred CCCcceEEEeCCCCEEEEEEEEEeeCCEEEEEecCCeEEEeEhHHcC
Confidence 34456999887643 2234466667888 788889999999975443
Done!