RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15220
(289 letters)
>gnl|CDD|234661 PRK00140, rplK, 50S ribosomal protein L11; Validated.
Length = 141
Score = 236 bits (605), Expect = 2e-79
Identities = 92/139 (66%), Positives = 113/139 (81%), Gaps = 1/139 (0%)
Query: 1 MVKKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIIT 60
M KK+ G+IKLQIPAGKANP+PP+GPALGQRG+NIMEFCK FNA+TQ + G PIPV+IT
Sbjct: 1 MAKKVVGYIKLQIPAGKANPAPPVGPALGQRGVNIMEFCKAFNARTQDQK-GLPIPVVIT 59
Query: 61 VFSDKSFTFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAA 120
V+ D+SFTF K P + L+KKAAGI+KGS +P+ +KVGK+T Q++EIA K DL AA
Sbjct: 60 VYEDRSFTFITKTPPASVLLKKAAGIEKGSGEPNKEKVGKITRAQVREIAETKMPDLNAA 119
Query: 121 SISAAMRTIAGSARSMGII 139
I AAMR IAG+ARSMGI+
Sbjct: 120 DIEAAMRMIAGTARSMGIV 138
>gnl|CDD|233500 TIGR01632, L11_bact, 50S ribosomal protein L11. This model
represents bacterial, chloroplast, and most
mitochondrial forms of 50S ribosomal protein L11
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 140
Score = 202 bits (517), Expect = 4e-66
Identities = 87/136 (63%), Positives = 108/136 (79%)
Query: 3 KKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITVF 62
KKI G IKLQ+PAG+ANP+PP+GPALGQRG+NIMEFCK FNA+T E G P+PV+ITV+
Sbjct: 1 KKIVGIIKLQVPAGQANPAPPVGPALGQRGVNIMEFCKQFNARTADYEPGLPVPVVITVY 60
Query: 63 SDKSFTFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASI 122
DKSFTF K PV++L+KKAAG++KGS P +KVGK+T Q++EIA IK DL I
Sbjct: 61 EDKSFTFIVKTPPVSYLLKKAAGVEKGSKNPKKEKVGKITRKQVREIAEIKMSDLNTKDI 120
Query: 123 SAAMRTIAGSARSMGI 138
AAM+ IAG+A+SMGI
Sbjct: 121 EAAMKIIAGTAKSMGI 136
>gnl|CDD|223158 COG0080, RplK, Ribosomal protein L11 [Translation, ribosomal
structure and biogenesis].
Length = 141
Score = 199 bits (508), Expect = 7e-65
Identities = 84/136 (61%), Positives = 105/136 (77%), Gaps = 1/136 (0%)
Query: 3 KKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITVF 62
KK+ IKLQ+PAGKANPSPP+GPALGQ G+NIMEFCK FNA T+ E G P+PV+ITV+
Sbjct: 2 KKVVKIIKLQVPAGKANPSPPVGPALGQLGVNIMEFCKEFNAATKD-EKGLPVPVVITVY 60
Query: 63 SDKSFTFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASI 122
D+SFTF K P + L+KKAAGI+KGS KP+ +KVGKLT Q++EIA K DL A +
Sbjct: 61 EDRSFTFIVKTPPASALLKKAAGIEKGSGKPNKNKVGKLTLAQVREIAKTKMPDLNAKDL 120
Query: 123 SAAMRTIAGSARSMGI 138
AA++ I G+ARSMG+
Sbjct: 121 EAAVKEILGTARSMGV 136
>gnl|CDD|180071 PRK05424, rplA, 50S ribosomal protein L1; Validated.
Length = 230
Score = 201 bits (515), Expect = 1e-64
Identities = 77/148 (52%), Positives = 109/148 (73%)
Query: 140 FDKNKIYSFDSAITLIKEAATAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIY 199
D+ K+YS + AI L+KE ATAKFDE++D++++L V+ +++DQ VRG++VLP TGK +
Sbjct: 14 VDRTKLYSLEEAIALVKETATAKFDETVDVAVNLGVDPRKADQQVRGAVVLPHGTGKTVR 73
Query: 200 IAAFVPKEKYEQAKIAGADIVGMEDLAQKIKSNEVSCDLVIASPESMHIVSSLGKILGPK 259
+A F EK E+AK AGADIVG EDL +KIK + D+VIA+P+ M V LG+ILGP+
Sbjct: 74 VAVFAKGEKAEEAKAAGADIVGGEDLIEKIKGGWLDFDVVIATPDMMGKVGKLGRILGPR 133
Query: 260 GLMPNIKDGTLNSDILTAIKNAKSGQIR 287
GLMPN K GT+ D+ A+K AK+G++
Sbjct: 134 GLMPNPKTGTVTMDVAKAVKEAKAGKVE 161
>gnl|CDD|197819 smart00649, RL11, Ribosomal protein L11/L12.
Length = 132
Score = 186 bits (475), Expect = 5e-60
Identities = 83/130 (63%), Positives = 100/130 (76%), Gaps = 1/130 (0%)
Query: 9 IKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITVFSDKSFT 68
IKLQIPAGKANP+PP+GPALGQ G+NIMEFCK FNA+T+ + G PIPV ITV++DKSFT
Sbjct: 1 IKLQIPAGKANPAPPLGPALGQLGINIMEFCKEFNARTKDKK-GLPIPVKITVYNDKSFT 59
Query: 69 FKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASISAAMRT 128
F K P + L+KKAAGI+KGS KP KVG +T Q+ EIA IK DL A + AA++
Sbjct: 60 FILKTPPASALLKKAAGIEKGSKKPGKKKVGNITLDQVYEIAKIKRPDLNAKDLEAAVKE 119
Query: 129 IAGSARSMGI 138
I G+ARSMGI
Sbjct: 120 ILGTARSMGI 129
>gnl|CDD|211630 TIGR01169, rplA_bact, ribosomal protein L1, bacterial/chloroplast.
This model describes bacterial (and chloroplast)
ribosomal protein L1. The apparent mitochondrial L1 is
sufficiently diverged to be the subject of a separate
model [Protein synthesis, Ribosomal proteins: synthesis
and modification].
Length = 227
Score = 189 bits (481), Expect = 1e-59
Identities = 79/147 (53%), Positives = 110/147 (74%)
Query: 141 DKNKIYSFDSAITLIKEAATAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIYI 200
D+NK+YS D AI L+KE ATAKFDE+++++I L ++ ++SDQ VRGS+VLP TGK + +
Sbjct: 14 DRNKLYSLDEAIDLLKETATAKFDETVEVAIRLGIDPRKSDQQVRGSVVLPHGTGKTVRV 73
Query: 201 AAFVPKEKYEQAKIAGADIVGMEDLAQKIKSNEVSCDLVIASPESMHIVSSLGKILGPKG 260
A F EK ++AK AGAD VG +DL +KIK + D+VIA+P+ M +V LG+ILGP+G
Sbjct: 74 AVFAKGEKAKEAKAAGADYVGSDDLIEKIKKGWLDFDVVIATPDMMRVVGKLGRILGPRG 133
Query: 261 LMPNIKDGTLNSDILTAIKNAKSGQIR 287
LMPN K GT+ +D+ A+KNAK GQ+
Sbjct: 134 LMPNPKTGTVTTDVAKAVKNAKKGQVE 160
>gnl|CDD|100101 cd00349, Ribosomal_L11, Ribosomal protein L11. Ribosomal protein
L11, together with proteins L10 and L7/L12, and 23S
rRNA, form the L7/L12 stalk on the surface of the large
subunit of the ribosome. The homologous eukaryotic
cytoplasmic protein is also called 60S ribosomal protein
L12, which is distinct from the L12 involved in the
formation of the L7/L12 stalk. The C-terminal domain
(CTD) of L11 is essential for binding 23S rRNA, while
the N-terminal domain (NTD) contains the binding site
for the antibiotics thiostrepton and micrococcin. L11
and 23S rRNA form an essential part of the
GTPase-associated region (GAR). Based on differences in
the relative positions of the L11 NTD and CTD during the
translational cycle, L11 is proposed to play a
significant role in the binding of initiation factors,
elongation factors, and release factors to the ribosome.
Several factors, including the class I release factors
RF1 and RF2, are known to interact directly with L11. In
eukaryotes, L11 has been implicated in regulating the
levels of ubiquinated p53 and MDM2 in the MDM2-p53
feedback loop, which is responsible for apoptosis in
response to DNA damage. In bacteria, the "stringent
response" to harsh conditions allows bacteria to
survive, and ribosomes that lack L11 are deficient in
stringent factor stimulation.
Length = 131
Score = 181 bits (462), Expect = 7e-58
Identities = 77/130 (59%), Positives = 104/130 (80%), Gaps = 1/130 (0%)
Query: 9 IKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITVFSDKSFT 68
IKLQ+PAGKA+P+PP+GPALGQ G+NIM+FCK FNA+T+ + G P+PV ITV++D+SFT
Sbjct: 1 IKLQVPAGKASPAPPLGPALGQLGVNIMKFCKEFNARTKDYK-GLPVPVKITVYNDRSFT 59
Query: 69 FKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASISAAMRT 128
F+ K P + L+KKAAGI+KGS KP+ +KVG +T Q+ EIA IK DL A ++ +A++
Sbjct: 60 FEVKTPPASALLKKAAGIEKGSKKPNKEKVGNITLDQVYEIAKIKLPDLNAKTLKSAVKE 119
Query: 129 IAGSARSMGI 138
I G+ARSMGI
Sbjct: 120 ILGTARSMGI 129
>gnl|CDD|223159 COG0081, RplA, Ribosomal protein L1 [Translation, ribosomal
structure and biogenesis].
Length = 228
Score = 165 bits (419), Expect = 3e-50
Identities = 69/148 (46%), Positives = 102/148 (68%), Gaps = 1/148 (0%)
Query: 141 DKNKIYSFDSAITLIKEAATAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIYI 200
D+NK+YS + A+ L+KE + KFDE+++++++L V+ ++ DQ VRGS+VLP TGK + +
Sbjct: 16 DRNKLYSLEEAVKLLKETSKRKFDETVEVAVNLKVDPRKPDQRVRGSVVLPNGTGKTVRV 75
Query: 201 AAFVPKEKYEQAKIAGADIVGMEDLAQKIKS-NEVSCDLVIASPESMHIVSSLGKILGPK 259
A F EK E+AK AGAD VG EDL + IK+ D+ IA+P+ M +V LGK+LGP+
Sbjct: 76 AVFADGEKAEEAKAAGADYVGGEDLIELIKNGRAKDFDVFIATPDMMPLVGKLGKVLGPR 135
Query: 260 GLMPNIKDGTLNSDILTAIKNAKSGQIR 287
GLMPN K GT+ D+ A++ K G +
Sbjct: 136 GLMPNPKTGTVTDDVAKAVEELKKGTVE 163
>gnl|CDD|177049 CHL00127, rpl11, ribosomal protein L11; Validated.
Length = 140
Score = 149 bits (378), Expect = 3e-45
Identities = 73/138 (52%), Positives = 99/138 (71%), Gaps = 1/138 (0%)
Query: 1 MVKKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIIT 60
M KK IKL +PAGKA P+PP+GPALGQ G+NI FCK +NA+T+ ++G IPV I+
Sbjct: 1 MAKKKLAIIKLALPAGKATPAPPVGPALGQHGVNINLFCKEYNARTKD-KIGLIIPVEIS 59
Query: 61 VFSDKSFTFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAA 120
V+ DKS+TF K P + L+ KAAGI+KGS +P+ KVG +T Q++EIA IK DL
Sbjct: 60 VYEDKSYTFILKTPPASVLLAKAAGIKKGSGEPNKKKVGSITIKQLEEIAQIKLPDLNTI 119
Query: 121 SISAAMRTIAGSARSMGI 138
S+S A++ I G+A++MGI
Sbjct: 120 SLSKAIKIIEGTAKNMGI 137
>gnl|CDD|177051 CHL00129, rpl1, ribosomal protein L1; Reviewed.
Length = 229
Score = 146 bits (371), Expect = 5e-43
Identities = 66/145 (45%), Positives = 99/145 (68%)
Query: 142 KNKIYSFDSAITLIKEAATAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIYIA 201
+ K+YS + AI L+KE ATAKF E+ + I LN++ K +DQ +R ++ LP TGK I IA
Sbjct: 16 EKKLYSPEEAINLLKETATAKFIETAEAHISLNIDPKYADQQLRTTVTLPKGTGKTIRIA 75
Query: 202 AFVPKEKYEQAKIAGADIVGMEDLAQKIKSNEVSCDLVIASPESMHIVSSLGKILGPKGL 261
+EK +AK AGADIVG +DL ++I + DL+IA+P+ M ++ LG++LGP+GL
Sbjct: 76 VLTNEEKITEAKNAGADIVGSDDLIEEITKGNLDFDLLIATPDMMPKLAKLGRVLGPRGL 135
Query: 262 MPNIKDGTLNSDILTAIKNAKSGQI 286
MP+ K GT+ +D+ +AI K G++
Sbjct: 136 MPSPKSGTVTTDLASAINEFKKGKL 160
>gnl|CDD|238235 cd00403, Ribosomal_L1, Ribosomal protein L1. The L1 protein,
located near the E-site of the ribosome, forms part of
the L1 stalk along with 23S rRNA. In bacteria and
archaea, L1 functions both as a ribosomal protein that
binds rRNA, and as a translation repressor that binds
its own mRNA. Like several other large ribosomal
subunit proteins, L1 displays RNA chaperone activity.
L1 is one of the largest ribosomal proteins. It is
composed of two domains that cycle between open and
closed conformations via a hinge motion. The RNA-binding
site of L1 is highly conserved, with both mRNA and rRNA
binding the same binding site.
Length = 208
Score = 124 bits (315), Expect = 5e-35
Identities = 58/141 (41%), Positives = 88/141 (62%), Gaps = 8/141 (5%)
Query: 151 AITLIKEAA--TAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIYIAAFVPKEK 208
AI +K+ + KFDE++++ I+L + ++ DQ +RG+++LP GK + + F E+
Sbjct: 4 AIKALKKTSVKKRKFDETVELQINLKKDDRKKDQRIRGTVILPHGLGKDVKVCVFAKDEQ 63
Query: 209 YEQAKIAGADIVGMEDLAQKIKSNEV-----SCDLVIASP-ESMHIVSSLGKILGPKGLM 262
++AK AGAD+VG EDL +KIK+ E DL +A P M + LGK+LGP+G M
Sbjct: 64 AKEAKAAGADVVGGEDLKKKIKNGEAKKLAKDFDLFLADPRIMMLLPKLLGKVLGPRGKM 123
Query: 263 PNIKDGTLNSDILTAIKNAKS 283
PN K GT+ D+ AI+ AKS
Sbjct: 124 PNPKTGTVTEDLAKAIEEAKS 144
>gnl|CDD|234908 PRK01143, rpl11p, 50S ribosomal protein L11P; Validated.
Length = 163
Score = 119 bits (300), Expect = 2e-33
Identities = 53/160 (33%), Positives = 88/160 (55%), Gaps = 8/160 (5%)
Query: 9 IKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITV-FSDKSF 67
+++ + GKA P PP+GPALG GLN+ + + N +T+ + G +PV + V K F
Sbjct: 5 VEVLVEGGKATPGPPLGPALGPLGLNVKQVVQEINEKTKDFK-GMQVPVKVIVDTDTKKF 63
Query: 68 TFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASISAAMR 127
+ + P T LIKK GI+KGS +P + VG L++ Q+ +IA +K DL + + AA++
Sbjct: 64 EIEVGIPPTTALIKKELGIEKGSGEPGHEVVGNLSFEQVVKIAIMKKDDLLSYDLKAAVK 123
Query: 128 TIAGSARSMGIIFDKNKIYSFDSAITLIKEAATAKFDESI 167
+ G+ SMG+ + + KE K+D+ +
Sbjct: 124 EVLGTCVSMGVTVEGKD------PKEVQKEVDEGKYDDLL 157
>gnl|CDD|216061 pfam00687, Ribosomal_L1, Ribosomal protein L1p/L10e family. This
family includes prokaryotic L1 and eukaryotic L10.
Length = 200
Score = 120 bits (303), Expect = 3e-33
Identities = 56/144 (38%), Positives = 86/144 (59%), Gaps = 9/144 (6%)
Query: 152 ITLIKEAATAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIYIAAFVPKE--KY 209
+ +K+ A KFDE++++ I+L + ++ DQ VRG++VLP GK + + K
Sbjct: 1 VKALKKTAKRKFDETVELQINLKKDPRKKDQNVRGTVVLPHGLGKDVKVCVIAKDPEAKA 60
Query: 210 EQAKIAGADIVGMEDLAQK--IKSNEVSC---DLVIASPESMHIVSS-LGKILGPKGLMP 263
++AK AGAD+VG EDL +K IK D+ +A P+ M ++ LGK+LGP+G MP
Sbjct: 61 KEAKDAGADVVGGEDLKEKYKIKKGRKLAKDFDVFLADPDIMPLLPKLLGKVLGPRGKMP 120
Query: 264 NIKDGTLNSDILTAIKNAKSGQIR 287
N K T+ D+ AI+ AKSG +
Sbjct: 121 NPKT-TVTPDVAKAIEEAKSGTVE 143
>gnl|CDD|184732 PRK14539, PRK14539, 50S ribosomal protein L11/unknown domain fusion
protein; Provisional.
Length = 196
Score = 109 bits (273), Expect = 5e-29
Identities = 65/166 (39%), Positives = 92/166 (55%), Gaps = 10/166 (6%)
Query: 1 MVKKITGFIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIIT 60
K++ KLQ AG+A P GP+L G+N+ EF K FN T+ G P+PV IT
Sbjct: 2 AKKEVVKVAKLQFNAGQAKP----GPSLAGVGINMPEFTKQFNDATRD-RGGEPVPVQIT 56
Query: 61 VFSDKSFTFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAA 120
V+ DKSF FK P +F IK+AA I+ GSA + VG +T Q++EIA K DL
Sbjct: 57 VYKDKSFDFKLFTAPASFKIKQAAKIKSGSANSKTTIVGTITLSQLEEIAKYKLPDLNTD 116
Query: 121 SISAAMRTIAGSARSMGIIFDKNKIYSFDSAITLIKEAATAKFDES 166
+ AM TIAG+A++MG++ + +D + +EA A +
Sbjct: 117 DVEEAMHTIAGTAKNMGVLVE-----GYDDVVKAKEEAKAAAKAAA 157
>gnl|CDD|217808 pfam03946, Ribosomal_L11_N, Ribosomal protein L11, N-terminal
domain. The N-terminal domain of Ribosomal protein L11
adopts an alpha/beta fold and is followed by the RNA
binding C-terminal domain.
Length = 59
Score = 101 bits (253), Expect = 1e-27
Identities = 41/60 (68%), Positives = 51/60 (85%), Gaps = 1/60 (1%)
Query: 8 FIKLQIPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQGIELGTPIPVIITVFSDKSF 67
IKLQ+PAGKANP+PP+GPALGQ G+NIMEFCK FNA T+ + G P+PV ITV++D+SF
Sbjct: 1 VIKLQVPAGKANPAPPLGPALGQLGVNIMEFCKEFNAATKDYK-GLPVPVKITVYNDRSF 59
>gnl|CDD|189492 pfam00298, Ribosomal_L11, Ribosomal protein L11, RNA binding
domain.
Length = 69
Score = 93.7 bits (234), Expect = 1e-24
Identities = 38/67 (56%), Positives = 49/67 (73%)
Query: 72 KVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIKEIATIKNVDLTAASISAAMRTIAG 131
K P ++L+KKAAGI+KGS KP +KVGK+T Q+ EIA IK DL A + AA++ I G
Sbjct: 1 KTPPASYLLKKAAGIEKGSGKPGKEKVGKITLKQVYEIAKIKMPDLNANDLEAAVKIIIG 60
Query: 132 SARSMGI 138
+ARSMGI
Sbjct: 61 TARSMGI 67
>gnl|CDD|233298 TIGR01170, rplA_mito, ribosomal protein L1, mitochondrial. This
model represents the mitochondrial homolog of bacterial
ribosomal protein L1. Unlike chloroplast L1, this form
was not sufficiently similar to bacterial forms to
include in a single bacterial/organellar L1 model
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 141
Score = 79.9 bits (197), Expect = 1e-18
Identities = 44/141 (31%), Positives = 78/141 (55%), Gaps = 2/141 (1%)
Query: 146 YSFDSAITLIKEAATAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIYIAAFVP 205
Y A +K + + + +++ + + ++ + V+G P GK+ IA F
Sbjct: 1 YKVIKAFVYLKTKSISMYVPKQSVNLDIGLLMELGKESVQGMFSFPHPFGKEPKIAVFTK 60
Query: 206 KE-KYEQAKIAGADIVGMEDLAQKIKSNEVS-CDLVIASPESMHIVSSLGKILGPKGLMP 263
+ E+A+ AGAD VG +DL +KI+ E+ D +IA P+ + ++ L ++LGPKGLMP
Sbjct: 61 GASEVEEAREAGADYVGGDDLIKKIEDGEIKPFDYLIAHPDIVPELAQLRRLLGPKGLMP 120
Query: 264 NIKDGTLNSDILTAIKNAKSG 284
+ K GT+ ++L+ I+ K G
Sbjct: 121 SPKRGTVGDNLLSMIETFKKG 141
>gnl|CDD|235254 PRK04203, rpl1P, 50S ribosomal protein L1P; Reviewed.
Length = 215
Score = 66.8 bits (164), Expect = 3e-13
Identities = 39/121 (32%), Positives = 65/121 (53%), Gaps = 15/121 (12%)
Query: 155 IKEAATAKFDESIDISIHL-NVNIKRSDQIVRGSIVLPFSTGKKIYIAAFVPKEKYEQAK 213
++EA F +S+D+ ++L ++++K+ + + +VLP GK++ IA E QAK
Sbjct: 15 LEEAPKRNFTQSVDLIVNLKDIDLKKPENRIDEEVVLPHGRGKEVKIAVIAKGELALQAK 74
Query: 214 IAGADIV-GMEDL---------AQKIKSNEVSCDLVIASPESMHIV-SSLGKILGPKGLM 262
AGAD V E+L A+K+ + D IA + M ++ LG +LGP+G M
Sbjct: 75 EAGADYVITREELEELGGDKRAAKKLAN---EYDFFIAEADLMPLIGRYLGPVLGPRGKM 131
Query: 263 P 263
P
Sbjct: 132 P 132
>gnl|CDD|240358 PTZ00321, PTZ00321, ribosomal protein L11; Provisional.
Length = 342
Score = 60.4 bits (146), Expect = 2e-10
Identities = 41/139 (29%), Positives = 63/139 (45%), Gaps = 15/139 (10%)
Query: 13 IPAGKANPSPPIGPALGQRGLNIMEFCKNFNAQTQ-----GIELGTPIPVIITVFSDKSF 67
I AGKA PP+G + GL M+F K+FN +T+ +EL V I V+ DKS+
Sbjct: 57 IKAGKAATGPPVGQEFSKLGLKAMDFAKSFNDRTKPHFKDDVEL----IVRIQVYFDKSY 112
Query: 68 TFKKKVTPVTFLIKKAAGIQKGSAKPHSDKVGKLTYLQIK---EIATIKNVDLTAAS--- 121
F + P + I +A ++ P + + ++ EIA +K
Sbjct: 113 LFTIEPPPTAWFILRALRKKRRETGPVPLRGHYCALMTLEMAYEIAKMKPRSWGRPEYPL 172
Query: 122 ISAAMRTIAGSARSMGIIF 140
I +R + G AR MG+ F
Sbjct: 173 IETRVRRVVGQARRMGVCF 191
>gnl|CDD|178004 PLN02376, PLN02376, 1-aminocyclopropane-1-carboxylate synthase.
Length = 496
Score = 32.4 bits (73), Expect = 0.28
Identities = 29/97 (29%), Positives = 43/97 (44%), Gaps = 10/97 (10%)
Query: 192 FSTGKKIYIAAFVPKEKYEQAKIAGADIVGMEDLAQKIKSNEVSCDLVIASPESMHIVSS 251
F T K I++ V E Y AG D V + ++ + +EV+ DL+ HIV S
Sbjct: 227 FVTRKNIHL---VVDEIYAATVFAGGDFVSVAEVVNDVDISEVNVDLI-------HIVYS 276
Query: 252 LGKILGPKGLMPNIKDGTLNSDILTAIKNAKSGQIRS 288
L K +G G I +S + A K + G + S
Sbjct: 277 LSKDMGLPGFRVGIVYSFNDSVVSCARKMSSFGLVSS 313
>gnl|CDD|235923 PRK07059, PRK07059, Long-chain-fatty-acid--CoA ligase; Validated.
Length = 557
Score = 32.3 bits (74), Expect = 0.33
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 9/64 (14%)
Query: 203 FVPKEKYEQAKIAGAD-IVGMEDLAQKIKSNEVSCDLVIASPESMHI-VSSLGKILGPKG 260
+ P+E Q K +GA+ IV +E+ A ++ V+A H+ V+S+G +LG KG
Sbjct: 107 YTPRELEHQLKDSGAEAIVVLENFATTVQQ-------VLAKTAVKHVVVASMGDLLGFKG 159
Query: 261 LMPN 264
+ N
Sbjct: 160 HIVN 163
>gnl|CDD|215327 PLN02607, PLN02607, 1-aminocyclopropane-1-carboxylate synthase.
Length = 447
Score = 30.6 bits (69), Expect = 0.92
Identities = 24/98 (24%), Positives = 43/98 (43%), Gaps = 18/98 (18%)
Query: 189 VLPFSTGKKIYIAAFVPKEKYEQAKIAGADIVGMEDLAQKIKSNEVSCDLVIASPESMHI 248
+L F K I++ V E Y + + ++ V + ++ + V+ E +HI
Sbjct: 225 ILDFVVRKNIHL---VSDEIYSGSVFSASEFVSVAEIVEARGYKGVA--------ERVHI 273
Query: 249 VSSLGKILGPKGLMPNIKDGTL---NSDILTAIKNAKS 283
V SL K LG +P + GT+ N ++T + S
Sbjct: 274 VYSLSKDLG----LPGFRVGTIYSYNDKVVTTARRMSS 307
>gnl|CDD|187547 cd05236, FAR-N_SDR_e, fatty acyl CoA reductases (FARs), extended
(e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding
proteins, many of which may function as fatty acyl CoA
reductases (FAR), acting on medium and long chain fatty
acids, and have been reported to be involved in diverse
processes such as biosynthesis of insect pheromones,
plant cuticular wax production, and mammalian wax
biosynthesis. In Arabidopsis thaliana, proteins with
this particular architecture have also been identified
as the MALE STERILITY 2 (MS2) gene product, which is
implicated in male gametogenesis. Mutations in MS2
inhibit the synthesis of exine (sporopollenin),
rendering plants unable to reduce pollen wall fatty
acids to corresponding alcohols. This N-terminal domain
shares the catalytic triad (but not the upstream Asn)
and characteristic NADP-binding motif of the extended
SDR family. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 320
Score = 30.3 bits (69), Expect = 1.0
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 158 AATAKFDESIDISIHLNV 175
AAT FDE +D ++ +NV
Sbjct: 102 AATVTFDERLDEALSINV 119
>gnl|CDD|185405 PTZ00029, PTZ00029, 60S ribosomal protein L10a; Provisional.
Length = 216
Score = 29.7 bits (67), Expect = 1.4
Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 4/86 (4%)
Query: 150 SAITLIKEAATAK---FDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIYIAAFVPK 206
AI I E + K F E++++ I L + D+ GS+ LP + +
Sbjct: 11 KAIAEILEGSEEKKRKFVETVELQIGLKDYDTQKDKRFSGSVKLPNVPKPNLKVCVLGDA 70
Query: 207 EKYEQAKIAGADIVGMEDLAQKIKSN 232
++AK G D + +E L +K N
Sbjct: 71 VHCDEAKKLGLDFMDIEGL-KKFNKN 95
>gnl|CDD|140252 PTZ00225, PTZ00225, 60S ribosomal protein L10a; Provisional.
Length = 214
Score = 28.9 bits (64), Expect = 2.9
Identities = 24/100 (24%), Positives = 47/100 (47%), Gaps = 3/100 (3%)
Query: 162 KFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIYIAAFVPKEKYEQAKIAGADIVG 221
KF ESID+ ++L + D+ GS+ LP ++ + + AK G +
Sbjct: 24 KFKESIDLQVNLKNYDPQKDKRFSGSLKLPNVCRPRMTVCLLCDLVHEDIAKKEGVPTMN 83
Query: 222 MEDLAQKIKSNEV---SCDLVIASPESMHIVSSLGKILGP 258
E+L + K+ ++ C+ A S I+ ++ +++GP
Sbjct: 84 QEELKKLNKNKKLVKKMCNQYDAFLCSESIIKTVPRLVGP 123
>gnl|CDD|100105 cd01335, Radical_SAM, Radical SAM superfamily. Enzymes of this
family generate radicals by combining a 4Fe-4S cluster
and S-adenosylmethionine (SAM) in close proximity. They
are characterized by a conserved CxxxCxxC motif, which
coordinates the conserved iron-sulfur cluster.
Mechanistically, they share the transfer of a single
electron from the iron-sulfur cluster to SAM, which
leads to its reductive cleavage to methionine and a
5'-deoxyadenosyl radical, which, in turn, abstracts a
hydrogen from the appropriately positioned carbon atom.
Depending on the enzyme, SAM is consumed during this
process or it is restored and reused. Radical SAM
enzymes catalyze steps in metabolism, DNA repair, the
biosynthesis of vitamins and coenzymes, and the
biosynthesis of many antibiotics. Examples are biotin
synthase (BioB), lipoyl synthase (LipA), pyruvate
formate-lyase (PFL), coproporphyrinogen oxidase (HemN),
lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide
reductase (ARR), and MoaA, an enzyme of the
biosynthesis of molybdopterin.
Length = 204
Score = 28.1 bits (62), Expect = 4.3
Identities = 12/70 (17%), Positives = 26/70 (37%), Gaps = 1/70 (1%)
Query: 146 YSFDSAITLIKEAATAKFDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIYIAAFVP 205
SF + +KE A S + + L + D + ++ F + ++ + +P
Sbjct: 122 ESFKERLEALKELREAGLGLSTTLLVGLGDEDEEDD-LEELELLAEFRSPDRVSLFRLLP 180
Query: 206 KEKYEQAKIA 215
+E A
Sbjct: 181 EEGTPLELAA 190
>gnl|CDD|216316 pfam01130, CD36, CD36 family. The CD36 family is thought to be a
novel class of scavenger receptors. There is also
evidence suggesting a possible role in signal
transduction. CD36 is involved in cell adhesion.
Length = 460
Score = 28.0 bits (63), Expect = 7.4
Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 8/56 (14%)
Query: 61 VFSDKSFTFKK-KVTPVTFLIK-------KAAGIQKGSAKPHSDKVGKLTYLQIKE 108
V S TF+ + PV K + G AKP ++VG Y + +E
Sbjct: 33 VLRPGSDTFESWENPPVPLYFKVYLFNVTNPEEVLNGGAKPIVEEVGPYVYREYRE 88
>gnl|CDD|171518 PRK12463, PRK12463, chorismate synthase; Reviewed.
Length = 390
Score = 27.8 bits (61), Expect = 7.6
Identities = 40/187 (21%), Positives = 82/187 (43%), Gaps = 18/187 (9%)
Query: 47 QGIELGTPIPVIITVFSDKSFTFKKKVTPVTFLIKKAAGIQKGSAKP---HSDKVGKLTY 103
G+ LG+PI +I+ K +T P++ K++ +++ KP H+D G + Y
Sbjct: 64 HGMTLGSPITLIVKNDDFKHWTKVMGAEPISE--KESKEMKRTITKPRPGHADLNGAIKY 121
Query: 104 -----LQIKEIATIKNVDLTAASISAAMRT-------IAGSARSMGIIFDKNKIYSFDSA 151
+ E ++ + + A+ + A + IAG +G + K+
Sbjct: 122 GHRDIRNVLERSSARETTVRVAAGAVAKQILKELGVEIAGHVLEIGGVKAKHISNLSIEE 181
Query: 152 ITLIKEAATAK-FDESIDISIHLNVNIKRSDQIVRGSIVLPFSTGKKIYIAAFVPKEKYE 210
I I E + + D++++ + ++ +S G IV + G I + ++V ++
Sbjct: 182 IQTITENSPVRCLDKTVEQEMMDAIDNAKSSGDSIGGIVEVIAEGMPIGVGSYVHYDRKL 241
Query: 211 QAKIAGA 217
AK+AGA
Sbjct: 242 DAKLAGA 248
>gnl|CDD|143458 cd07140, ALDH_F1L_FTFDH, 10-formyltetrahydrofolate dehydrogenase,
ALDH family 1L. 10-formyltetrahydrofolate dehydrogenase
(FTHFDH, EC=1.5.1.6), also known as aldehyde
dehydrogenase family 1 member L1 (ALDH1L1) in humans, is
a multi-domain homotetramer with an N-terminal formyl
transferase domain and a C-terminal ALDH domain. FTHFDH
catalyzes an NADP+-dependent dehydrogenase reaction
resulting in the conversion of 10-formyltetrahydrofolate
to tetrahydrofolate and CO2. The ALDH domain is also
capable of the oxidation of short chain aldehydes to
their corresponding acids.
Length = 486
Score = 27.8 bits (62), Expect = 7.7
Identities = 22/74 (29%), Positives = 30/74 (40%), Gaps = 20/74 (27%)
Query: 9 IKLQIPAGKANPSPPIGPALGQR------------------GLNIMEFCKNFNAQTQGIE 50
+K P G N P G +GQR G +IM+ C N + +E
Sbjct: 198 VKAGFPKGVINILPGSGSLVGQRLSDHPDVRKLGFTGSTPIGKHIMKSCAVSNLKKVSLE 257
Query: 51 LGTPIPVIITVFSD 64
LG P+II F+D
Sbjct: 258 LGGKSPLII--FAD 269
>gnl|CDD|236742 PRK10718, PRK10718, RpoE-regulated lipoprotein; Provisional.
Length = 191
Score = 27.3 bits (61), Expect = 9.1
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 9/54 (16%)
Query: 221 GMEDLAQKIKSNEVSCDLVIASPESMHIVSSL--GKILGPKGLMPNIKDGTLNS 272
G A + V C +P S HI S + G+ GP+GLMP+ D TL +
Sbjct: 135 GNCQKASGDDNRSVEC----KAPGSQHI-SYVFSGEWSGPEGLMPS--DDTLKN 181
>gnl|CDD|178621 PLN03072, PLN03072, 60S ribosomal protein L12; Provisional.
Length = 166
Score = 27.1 bits (60), Expect = 9.4
Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 8/94 (8%)
Query: 68 TFKKKVTPVTFLIKKAAGIQKGSAKPHSDK--------VGKLTYLQIKEIATIKNVDLTA 119
T + + V+ + AA + K +P D+ G ++ + EIA I A
Sbjct: 64 TVQNRQAKVSVVPSAAALVIKALKEPERDRKKVKNIKHNGNISLDDVIEIAKIMRPRSMA 123
Query: 120 ASISAAMRTIAGSARSMGIIFDKNKIYSFDSAIT 153
++ ++ I G+ S+G D I
Sbjct: 124 KELAGTVKEILGTCVSVGCTVDGKDPKDLQQEID 157
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.133 0.365
Gapped
Lambda K H
0.267 0.0820 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,489,610
Number of extensions: 1403231
Number of successful extensions: 1342
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1320
Number of HSP's successfully gapped: 41
Length of query: 289
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 193
Effective length of database: 6,679,618
Effective search space: 1289166274
Effective search space used: 1289166274
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (25.9 bits)