RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8860
(374 letters)
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type. [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 230 bits (588), Expect = 4e-75
Identities = 81/155 (52%), Positives = 114/155 (73%)
Query: 122 GKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFTAINNSRIAKSM 181
GK PI IP VEVT++ N +T+KGP G L + + V +K + L + N+S+ A+++
Sbjct: 4 GKKPIAIPAGVEVTIDGNVVTVKGPKGELSRTLHPGVTVKVEDGQLTVSRPNDSKEARAL 63
Query: 182 SGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICE 241
GT R++INNM+IGV++GFEKKL+++GVG+RA+++ LNL LG+SHP+ Y+IP I E
Sbjct: 64 HGTTRALINNMVIGVSEGFEKKLEIVGVGYRAQLQGKKLNLSLGYSHPVEYEIPEGITVE 123
Query: 242 TPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276
P TEI++KGI+KQ VG VAAEIR + KPEPYKG
Sbjct: 124 VPKPTEIVVKGIDKQLVGQVAAEIRAFRKPEPYKG 158
>gnl|CDD|235495 PRK05498, rplF, 50S ribosomal protein L6; Validated.
Length = 178
Score = 228 bits (585), Expect = 1e-74
Identities = 83/155 (53%), Positives = 114/155 (73%)
Query: 122 GKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFTAINNSRIAKSM 181
GK PI IP VEVT+N N +T+KGP G L + N V +K + N + T ++S+ A+++
Sbjct: 5 GKKPIAIPAGVEVTINGNVVTVKGPKGELSRTLNPDVTVKVEDNEITVTRPDDSKKARAL 64
Query: 182 SGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICE 241
GT R++INNM++GVT+GFEKKL+++GVG+RA+++ LNL LG+SHP+ Y+IP I E
Sbjct: 65 HGTTRALINNMVVGVTEGFEKKLEIVGVGYRAQVKGKKLNLSLGYSHPVEYEIPEGITVE 124
Query: 242 TPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276
P TEI++KGI+KQ VG VAAEIR Y PEPYKG
Sbjct: 125 VPKPTEIVVKGIDKQLVGQVAAEIRSYRPPEPYKG 159
>gnl|CDD|234658 PRK00136, rpsH, 30S ribosomal protein S8; Validated.
Length = 130
Score = 188 bits (480), Expect = 1e-59
Identities = 68/121 (56%), Positives = 94/121 (77%), Gaps = 1/121 (0%)
Query: 2 SMSDPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFEL 61
SM+DPIADMLT IRN Q+ + + MP+SK+K+AIA++LK+EGYIKD+ + + K L
Sbjct: 1 SMTDPIADMLTRIRNAQMAKHETVSMPASKLKVAIAEILKEEGYIKDYEVEEDGKQGI-L 59
Query: 62 KILLKYYMNRPVIECLKRVSRPGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKARSM 121
+I LKY PVIE +KRVS+PGLR+YK KD +PK++NGLG+ I+ST+ G++TDR+AR
Sbjct: 60 RITLKYGEGEPVIEGIKRVSKPGLRVYKKKDELPKVLNGLGIAIVSTSKGVMTDREARKA 119
Query: 122 G 122
G
Sbjct: 120 G 120
>gnl|CDD|223175 COG0097, RplF, Ribosomal protein L6P/L9E [Translation, ribosomal
structure and biogenesis].
Length = 178
Score = 184 bits (470), Expect = 2e-57
Identities = 71/156 (45%), Positives = 107/156 (68%), Gaps = 2/156 (1%)
Query: 122 GKMPIFIPPNVEVTLNSNKITLKGPLGILKQN-KNNLVNIKNDSNVLYFTAINNSRIAKS 180
GK PI IP V V++ +T+KGP G L + +N+V ++ + N+L + + ++
Sbjct: 5 GKRPIVIPAGVTVSIEGQVVTVKGPKGELTREFHDNVVKVEVEDNILVVRP-VDGKRKRA 63
Query: 181 MSGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIIC 240
+ GT+R++INNM+ GVT+GFEKKL+++GVG+RA++ L L LG+SHP++ +IP I
Sbjct: 64 LHGTVRALINNMVKGVTEGFEKKLEIVGVGYRAQVVGGNLELFLGYSHPVVIEIPEGITV 123
Query: 241 ETPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276
E P TEI+++GI+K+ VG VAA IR KPEPYKG
Sbjct: 124 EVPGPTEIVVEGIDKELVGQVAANIRAARKPEPYKG 159
>gnl|CDD|177062 CHL00140, rpl6, ribosomal protein L6; Validated.
Length = 178
Score = 171 bits (436), Expect = 2e-52
Identities = 73/155 (47%), Positives = 105/155 (67%)
Query: 122 GKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFTAINNSRIAKSM 181
GK+PI IP NV V+++ I +KGP G L + +L+ I+ N L+ + + S+ A+++
Sbjct: 5 GKLPIKIPDNVNVSIDDQIIKVKGPKGTLSRKIPDLITIEIQDNSLFVSKKDESKKARAL 64
Query: 182 SGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICE 241
G R++INNM+IGV++GFEKKL+L GVG+RA+++ L L LG+SHP+ KIP I E
Sbjct: 65 HGLYRTLINNMVIGVSEGFEKKLELQGVGYRAQVQGKDLILNLGYSHPVKIKIPPGISVE 124
Query: 242 TPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276
+ T I IKGI+K+ VG AA+IR PEPYKG
Sbjct: 125 VENNTNITIKGIDKELVGQFAAKIRSVRPPEPYKG 159
>gnl|CDD|215906 pfam00410, Ribosomal_S8, Ribosomal protein S8.
Length = 129
Score = 155 bits (395), Expect = 7e-47
Identities = 61/119 (51%), Positives = 90/119 (75%), Gaps = 1/119 (0%)
Query: 5 DPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKIL 64
DPIADMLT IRN Q+ K+ +++P+SK+KI+I K+LK+EGYIK F +I+ +N +K+
Sbjct: 1 DPIADMLTRIRNAQMAKKETVLIPASKLKISILKILKEEGYIKGFEVIEDERNGKFIKVT 60
Query: 65 LKYYMNR-PVIECLKRVSRPGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKARSMG 122
LKY N PVI +KR+S+PGLR+Y + +PK++ GLG+ I+ST+ G++TDR+AR G
Sbjct: 61 LKYDKNGKPVITGIKRISKPGLRVYVSYKELPKVLGGLGIAILSTSKGVMTDREARKKG 119
>gnl|CDD|223174 COG0096, RpsH, Ribosomal protein S8 [Translation, ribosomal
structure and biogenesis].
Length = 132
Score = 153 bits (388), Expect = 8e-46
Identities = 64/123 (52%), Positives = 90/123 (73%), Gaps = 2/123 (1%)
Query: 1 MSMSDPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFE 60
M M+DP+ADMLT IRN + K+ + MP+SK+K AI KVLK EGYIKDF +I K +
Sbjct: 1 MMMTDPLADMLTRIRNAERAKKEVVSMPASKLKGAILKVLKKEGYIKDFEVIDD-GRKGK 59
Query: 61 LKILLKYYMNR-PVIECLKRVSRPGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKAR 119
L++ LKY +N VI +KRVS+PGLR+Y+ K +P ++NGLG+ I+ST+ G++TD++AR
Sbjct: 60 LRVQLKYRINGCGVISPIKRVSKPGLRVYEKKRELPAVLNGLGIAIVSTSKGVMTDKEAR 119
Query: 120 SMG 122
G
Sbjct: 120 KKG 122
>gnl|CDD|214344 CHL00042, rps8, ribosomal protein S8.
Length = 132
Score = 138 bits (351), Expect = 3e-40
Identities = 56/120 (46%), Positives = 80/120 (66%), Gaps = 3/120 (2%)
Query: 5 DPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKIL 64
D IADMLT IRN +V K + +P++ I I K+L EG+I++ + NK+ L +
Sbjct: 4 DTIADMLTRIRNANMVKKGTVRIPATNITENIVKILLREGFIENVREHR-ENNKYFLVLT 62
Query: 65 LKYYMNR--PVIECLKRVSRPGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKARSMG 122
LKY N+ P I LKR+S+PGLRIY N IP+++ G+G+VI+ST+ GI+TDR+AR G
Sbjct: 63 LKYRGNKKKPYITTLKRISKPGLRIYSNYKEIPRVLGGMGIVILSTSKGIMTDREARLKG 122
>gnl|CDD|235524 PRK05593, rplR, 50S ribosomal protein L18; Reviewed.
Length = 117
Score = 135 bits (342), Expect = 3e-39
Identities = 52/97 (53%), Positives = 64/97 (65%), Gaps = 6/97 (6%)
Query: 279 RLMVHRTNLHIYANIIS-SNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAK 337
RL V R+N HIYA +I K L SASTLEK+VR KGGN AA +G+ IA+
Sbjct: 26 RLSVFRSNRHIYAQVIDDVKGKTLASASTLEKDVR-----AGLKGGNKEAAKKVGKLIAE 80
Query: 338 KALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLNF 374
+A GI +V FDR G++YHGR+K LADAAR+ GL F
Sbjct: 81 RAKAKGIKQVVFDRGGYKYHGRVKALADAAREAGLKF 117
>gnl|CDD|223334 COG0256, RplR, Ribosomal protein L18 [Translation, ribosomal
structure and biogenesis].
Length = 125
Score = 111 bits (281), Expect = 3e-30
Identities = 52/97 (53%), Positives = 65/97 (67%), Gaps = 3/97 (3%)
Query: 279 RLMVHRTNLHIYANIISSNAKI-LISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAK 337
RL+V R+N HIYA II L SASTL KE+R K G GGNT AA ++G+ IA+
Sbjct: 31 RLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYG--KKGGGGNTEAAYLVGKLIAE 88
Query: 338 KALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLNF 374
+AL GI +V FDR G++YHGR+ LAD AR+ GL F
Sbjct: 89 RALAKGIEEVVFDRGGYKYHGRVAALADGAREAGLEF 125
>gnl|CDD|214373 CHL00139, rpl18, ribosomal protein L18; Validated.
Length = 109
Score = 108 bits (271), Expect = 5e-29
Identities = 51/97 (52%), Positives = 68/97 (70%), Gaps = 5/97 (5%)
Query: 279 RLMVHRTNLHIYANIIS-SNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAK 337
RL V R+N HIYA II +N K L++ STLE +V+ +L++ A+ ++GQ++AK
Sbjct: 17 RLSVFRSNKHIYAQIIDDTNGKTLVACSTLEPDVKSSLSS----TSTCDASKLVGQKLAK 72
Query: 338 KALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLNF 374
K+LK GITKV FDR G YHGRIK LA+AAR+ GL F
Sbjct: 73 KSLKKGITKVVFDRGGKLYHGRIKALAEAAREAGLQF 109
>gnl|CDD|216159 pfam00861, Ribosomal_L18p, Ribosomal L18p/L5e family. This family
includes ribosomal proteins from the large subunit. This
family includes L18 from bacteria and L5 from
eukaryotes. It has been shown that the amino terminal 93
amino acids of rat Rpl5 are necessary and sufficient to
bind 5S rRNA in vitro. Suggesting that the entire family
has a function in rRNA binding.
Length = 119
Score = 101 bits (253), Expect = 3e-26
Identities = 50/97 (51%), Positives = 62/97 (63%), Gaps = 3/97 (3%)
Query: 279 RLMVHRTNLHIYANIISSNAKI-LISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAK 337
RL+V R+N HIYA II L+SASTL KE++ G G NT AA ++G +AK
Sbjct: 25 RLVVRRSNKHIYAQIIDDTKGGTLVSASTLSKELKK--YGLKGGGNNTAAAYLVGLLLAK 82
Query: 338 KALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLNF 374
+ALK GI V FDR G+ YHGR+ LA AR+ GLNF
Sbjct: 83 RALKKGIAVVVFDRGGYTYHGRVFALAKGAREAGLNF 119
>gnl|CDD|213499 TIGR00060, L18_bact, ribosomal protein L18, bacterial type. The
archaeal and eukaryotic type rpL18 is not detectable
under this model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 114
Score = 99.5 bits (248), Expect = 1e-25
Identities = 47/97 (48%), Positives = 64/97 (65%), Gaps = 9/97 (9%)
Query: 279 RLMVHRTNLHIYANIIS-SNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAK 337
RL+V R+N HIYA +I S +++L SASTLEK KL GN AA +G+ +A+
Sbjct: 26 RLVVFRSNRHIYAQVIDDSKSEVLASASTLEK--------KLKYTGNKDAAKKVGKLVAE 77
Query: 338 KALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLNF 374
+ + GI V FDR G++YHGR+ LA+AAR+ GLNF
Sbjct: 78 RLKEKGIKDVVFDRGGYKYHGRVAALAEAAREAGLNF 114
>gnl|CDD|238246 cd00432, Ribosomal_L18_L5e, Ribosomal L18/L5e: L18 (L5e) is a
ribosomal protein found in the central protuberance (CP)
of the large subunit. L18 binds 5S rRNA and induces a
conformational change that stimulates the binding of L5
to 5S rRNA. Association of 5S rRNA with 23S rRNA depends
on the binding of L18 and L5 to 5S rRNA. L18/L5e is
generally described as L18 in prokaryotes and archaea,
and as L5e (or L5) in eukaryotes. In bacteria, the CP
proteins L5, L18, and L25 are required for the ribosome
to incorporate 5S rRNA into the large subunit, one of
the last steps in ribosome assembly. In archaea, both
L18 and L5 bind 5S rRNA; in eukaryotes, only the L18
homolog (L5e) binds 5S rRNA but a homolog to L5 is also
identified.
Length = 103
Score = 98.8 bits (247), Expect = 1e-25
Identities = 50/95 (52%), Positives = 65/95 (68%), Gaps = 5/95 (5%)
Query: 279 RLMVHRTNLHIYANII-SSNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAK 337
RL+V ++N HIYA II S K L+SASTLE ++ LG G N AA ++G+ +AK
Sbjct: 13 RLVVRKSNKHIYAQIIDDSGDKTLVSASTLELAIK----GVLGSGNNVEAAYLVGRLLAK 68
Query: 338 KALKIGITKVAFDRSGFRYHGRIKFLADAARKNGL 372
+AL+ GI KV FDR G+RYHGR+K LA AR+ GL
Sbjct: 69 RALEKGIKKVVFDRGGYRYHGRVKALAKGAREGGL 103
>gnl|CDD|235496 PRK05518, rpl6p, 50S ribosomal protein L6P; Reviewed.
Length = 180
Score = 85.3 bits (212), Expect = 1e-19
Identities = 50/149 (33%), Positives = 77/149 (51%), Gaps = 10/149 (6%)
Query: 126 IFIPPNVEVTLNSNKITLKGPLGILKQN-KNNLVNI-KNDSNVLYFTAINNSRIAKSMSG 183
I IP V V + +T+KGP G L ++ V I D V+ T + K+M G
Sbjct: 10 IEIPEGVTVEIEGLVVTVKGPKGELTRDFWYPGVTISVEDGKVVIETEFARKKT-KAMVG 68
Query: 184 TMRSIINNMIIGVTKGFEKKLQLIGVGF--RAKIEKNYL---NLILGFSHPILYKIPFDI 238
T S I NMI GVT+GFE KL+++ F + K++ N + N LG P KI +
Sbjct: 69 TFASHIKNMIKGVTEGFEYKLKIVYSHFPMQVKVQGNEVVIENF-LGEKSPRRAKILGGV 127
Query: 239 ICETPSQTEILIKGINKQAVGHVAAEIRR 267
+ + +++++GI+K+ VG AA I +
Sbjct: 128 KVKVKGE-DVIVEGIDKEDVGQTAANIEQ 155
>gnl|CDD|234296 TIGR03653, arch_L6P, archaeal ribosomal protein L6P. Members of
this protein family are the archaeal ribosomal protein
L6P. The top-scoring proteins not selected by this model
are eukaryotic cytosolic ribosomal protein L9. Bacterial
ribosomal protein L6 scores lower and is described by a
distinct model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 170
Score = 83.9 bits (208), Expect = 2e-19
Identities = 52/146 (35%), Positives = 77/146 (52%), Gaps = 8/146 (5%)
Query: 126 IFIPPNVEVTLNSNKITLKGPLGILKQN-KNNLVNIK-NDSNVLYFTAINNSRIAKSMSG 183
I IP V VT+ N +T+KGP G + + + I D V+ T + K+M G
Sbjct: 4 IEIPEGVSVTIEGNIVTVKGPKGEVTRELWYPGIEISVEDGKVVIETDFARKK-DKAMVG 62
Query: 184 TMRSIINNMIIGVTKGFEKKLQLIGVGF--RAKIEKNYLNL--ILGFSHPILYKIPFDII 239
T RS I NMI GVT+GFE K++++ F + K+E N + + LG P KIP +
Sbjct: 63 TYRSHIKNMIKGVTEGFEYKMKVVYSHFPMQVKVEGNKVVIENFLGEKAPRRAKIPGGVK 122
Query: 240 CETPSQTEILIKGINKQAVGHVAAEI 265
+ E+++ GI+K+ VG AA I
Sbjct: 123 VKV-KGEEVIVTGIDKEDVGQTAANI 147
>gnl|CDD|215872 pfam00347, Ribosomal_L6, Ribosomal protein L6.
Length = 76
Score = 69.5 bits (171), Expect = 4e-15
Identities = 25/71 (35%), Positives = 35/71 (49%)
Query: 207 IGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICETPSQTEILIKGINKQAVGHVAAEIR 266
I VG R I+ L L+LG + +IP + + T I++ GI+K+ VG AA I
Sbjct: 1 IPVGVRVSIDGVNLVLVLGPKGELTREIPPGVTVKVEKITVIIVSGIDKEKVGQFAALIG 60
Query: 267 RYYKPEPYKGI 277
Y P P G
Sbjct: 61 TYRAPIPNMGK 71
Score = 43.0 bits (102), Expect = 8e-06
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 4/76 (5%)
Query: 128 IPPNVEVTLN-SNKITLKGPLGILKQNKNNLVNIKNDS-NVLYFTAINNSRIAKSMS--G 183
IP V V+++ N + + GP G L + V +K + V+ + I+ ++ + + G
Sbjct: 1 IPVGVRVSIDGVNLVLVLGPKGELTREIPPGVTVKVEKITVIIVSGIDKEKVGQFAALIG 60
Query: 184 TMRSIINNMIIGVTKG 199
T R+ I NM GV+ G
Sbjct: 61 TYRAPIPNMGKGVSYG 76
>gnl|CDD|240235 PTZ00032, PTZ00032, 60S ribosomal protein L18; Provisional.
Length = 211
Score = 71.8 bits (176), Expect = 1e-14
Identities = 37/105 (35%), Positives = 54/105 (51%), Gaps = 9/105 (8%)
Query: 279 RLMVHRTNLHIYANIISSNAK-ILISASTLEK--------EVRLTLNTKLGKGGNTFAAS 329
RL + TN +YA I+ + +L + T K T N GG AA
Sbjct: 107 RLTLKNTNNQMYATIVDDYTRHVLCFSCTNFKYLSHIFGTYPTKTTNRVRNNGGTIKAAY 166
Query: 330 IIGQRIAKKALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLNF 374
+G+ I +KAL GI+KV FDR+ ++Y G+++ LA+ AR GL F
Sbjct: 167 ELGKLIGRKALSKGISKVRFDRAHYKYAGKVEALAEGARAVGLQF 211
>gnl|CDD|179721 PRK04034, rps8p, 30S ribosomal protein S8P; Reviewed.
Length = 130
Score = 56.0 bits (136), Expect = 8e-10
Identities = 22/50 (44%), Positives = 37/50 (74%), Gaps = 1/50 (2%)
Query: 1 MSMSDPIADMLTYIRNGQIVNKKK-IIMPSSKIKIAIAKVLKDEGYIKDF 49
M + DP+A+ L+ I+N ++V KK+ II P+SK+ + +V++DEGYI +F
Sbjct: 1 MVLLDPLANALSTIKNAEMVGKKEVIIKPASKLIGNVLRVMQDEGYIGEF 50
>gnl|CDD|140206 PTZ00179, PTZ00179, 60S ribosomal protein L9; Provisional.
Length = 189
Score = 44.5 bits (105), Expect = 2e-05
Identities = 29/83 (34%), Positives = 46/83 (55%), Gaps = 3/83 (3%)
Query: 126 IFIPPNVEVTLNSNKITLKGPLGILKQNKNNL-VNIKNDSNVLYFTAIN--NSRIAKSMS 182
I IP +V V++ +T+KG G L ++ +L ++ + + FTA+ S+I S
Sbjct: 9 ITIPEDVTVSVKDRIVTVKGKRGTLTKDLRHLQLDFRVNKKNRTFTAVRWFGSKIPNSTI 68
Query: 183 GTMRSIINNMIIGVTKGFEKKLQ 205
T S + NMI GVTKGF K++
Sbjct: 69 NTALSHVRNMITGVTKGFRFKVR 91
>gnl|CDD|185487 PTZ00158, PTZ00158, 40S ribosomal protein S15A; Provisional.
Length = 130
Score = 43.6 bits (103), Expect = 2e-05
Identities = 31/130 (23%), Positives = 57/130 (43%), Gaps = 22/130 (16%)
Query: 1 MSMSDPIADMLTYIRNGQIVNKKK-IIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKF 59
M +AD L I N + K++ +I PSSK+ + +V++ GYI +F I+
Sbjct: 1 MVRMSVLADCLRSIVNAEKQGKRQVLIRPSSKVVVKFLQVMQKHGYIGEFEIVD------ 54
Query: 60 ELKILLKYYMNRPVIECLKRVSRPGL---RIYKNKDNIPKIMNGL------GLVIISTAS 110
+ + V+ R+++ G+ R K N + G V+++T+
Sbjct: 55 ------DHRSGKIVVNLNGRLNKCGVISPRFDVTLGEFEKWANNILPSRQFGHVVLTTSY 108
Query: 111 GIITDRKARS 120
GI+ +AR
Sbjct: 109 GIMDHEEARR 118
>gnl|CDD|240234 PTZ00027, PTZ00027, 60S ribosomal protein L6; Provisional.
Length = 190
Score = 43.6 bits (103), Expect = 5e-05
Identities = 30/89 (33%), Positives = 46/89 (51%), Gaps = 3/89 (3%)
Query: 126 IFIPPNVEVTLNSNKITLKGPLGILKQNKNNL-VNIK--NDSNVLYFTAINNSRIAKSMS 182
I IP V VT+ S K+T+ G G L ++ +L V+IK D + + +
Sbjct: 10 IRIPEGVTVTVKSRKVTVTGKYGELTRSFRHLPVDIKLSKDGKYIKVEMWFGTPSHLACI 69
Query: 183 GTMRSIINNMIIGVTKGFEKKLQLIGVGF 211
T+ S I NM+ GVTK F+ K++L+ F
Sbjct: 70 RTVCSHIKNMMTGVTKKFQYKMRLVYAHF 98
>gnl|CDD|215075 PLN00146, PLN00146, 40S ribosomal protein S15a; Provisional.
Length = 130
Score = 33.0 bits (76), Expect = 0.075
Identities = 28/123 (22%), Positives = 56/123 (45%), Gaps = 22/123 (17%)
Query: 7 IADMLTYIRNGQIVNKKKI-IMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKILL 65
+ D L + N + K+++ I PSSK+ I KV++ GYI +F ++
Sbjct: 7 LNDALKTMYNAEKRGKRQVLIRPSSKVVIKFLKVMQKHGYIGEFEVVD------------ 54
Query: 66 KYYMNRPVIECLKRVSRPGLRIYK---NKDNIPKIMNGL------GLVIISTASGIITDR 116
+ + V+E R+++ G+ + I L G ++++T++GI+
Sbjct: 55 DHRSGKIVVELNGRLNKCGVISPRFDVKVKEIEAWTARLLPSRQFGYIVLTTSAGIMDHE 114
Query: 117 KAR 119
+AR
Sbjct: 115 EAR 117
>gnl|CDD|236294 PRK08569, rpl18p, 50S ribosomal protein L18P; Reviewed.
Length = 193
Score = 33.0 bits (76), Expect = 0.14
Identities = 29/73 (39%), Positives = 39/73 (53%), Gaps = 13/73 (17%)
Query: 279 RLMVHRTNLHIYANIISSNAK---ILISASTLEKEVRLTLNTKLG-KG--GNTFAASIIG 332
RL+V +TN H+ A I+ + K L SA + +E+ K G KG GNT AA + G
Sbjct: 34 RLVVRKTNKHVIAQIVKYDPKGDRTLASAHS--RELA-----KYGWKGDTGNTPAAYLTG 86
Query: 333 QRIAKKALKIGIT 345
KKALK G+
Sbjct: 87 LLAGKKALKAGVE 99
>gnl|CDD|133214 cd05083, PTKc_Chk, Catalytic domain of the Protein Tyrosine Kinase,
Csk homologous kinase. Protein Tyrosine Kinase (PTK)
family; Csk homologous kinase (Chk); catalytic (c)
domain. The PTKc family is part of a larger superfamily
that includes the catalytic domains of other kinases
such as protein serine/threonine kinases, RIO kinases,
and phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. Csk
subfamily kinases are cytoplasmic (or nonreceptor) tyr
kinases containing the Src homology domains, SH3 and
SH2, N-terminal to the catalytic tyr kinase domain. They
negatively regulate the activity of Src kinases that are
anchored to the plasma membrane. Chk is also referred to
as megakaryocyte-associated tyrosine kinase (Matk). To
inhibit Src kinases, Chk is translocated to the membrane
via binding to specific transmembrane proteins,
G-proteins, or adaptor proteins near the membrane. Chk
inhibit Src kinases using a noncatalytic mechanism by
simply binding to them. As a negative regulator of Src
kinases, Chk may play important roles in cell
proliferation, survival, and differentiation, and
consequently, in cancer development and progression. Chk
is expressed in brain and hematopoietic cells. Studies
in mice reveal that Chk is not functionally redundant
with Csk and that it plays an important role as a
regulator of immune responses. Chk also plays a role in
neural differentiation in a manner independent of Src by
enhancing Mapk activation via Ras-mediated signaling.
Length = 254
Score = 32.2 bits (73), Expect = 0.33
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 312 RLTLNTKLGKG--GNTFAASIIGQRIAKKALKIGITKVAF 349
+LTL +G+G G GQ++A K +K +T AF
Sbjct: 7 KLTLGEIIGEGEFGAVLQGEYTGQKVAVKNIKCDVTAQAF 46
>gnl|CDD|235402 PRK05312, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase;
Provisional.
Length = 336
Score = 30.6 bits (70), Expect = 1.4
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 19/75 (25%)
Query: 295 SSNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFDRSGF 354
+NA +I+A +E+ V L L+ G+ AA+++ IAKK L +GF
Sbjct: 93 PANAAGVIAA--IERAVGLVLS---GE-----AAAVVTAPIAKKVLY---------DAGF 133
Query: 355 RYHGRIKFLADAARK 369
+ G +FLA+ A
Sbjct: 134 AFPGHTEFLAELAGV 148
>gnl|CDD|240657 cd12180, 2-Hacid_dh_15, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 308
Score = 30.0 bits (68), Expect = 1.8
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 331 IGQRIAKKALKIGITKVAFDRSG 353
IGQ +A++AL +G+ +A RSG
Sbjct: 146 IGQALARRALALGMRVLALRRSG 168
>gnl|CDD|219071 pfam06525, SoxE, Sulfocyanin (SoxE). This family consists of
several archaeal sulfocyanin (or blue copper protein)
sequences from a number of Sulfolobus species.
Length = 195
Score = 27.9 bits (62), Expect = 6.2
Identities = 22/88 (25%), Positives = 41/88 (46%), Gaps = 7/88 (7%)
Query: 103 LVIISTASGIITDRKARSMGKMPIFIPP--NVEVTLNSNKITLKGPLGILKQNKN--NLV 158
+ ++ ++G + S G+M I+IP NV VT +N+ +L L +++ N N
Sbjct: 64 IYLVVLSTGPTFNFNGTSNGQMKIYIPAGWNVIVTF-TNQESLPHNLNLVQNNTPTPNSP 122
Query: 159 NIKNDSNVLYFTAINNSRIAKS--MSGT 184
+I +D +L + S + SG
Sbjct: 123 DISSDGKILLYVGATPSNYTTNGISSGQ 150
>gnl|CDD|173846 cd01157, MCAD, Medium chain acyl-CoA dehydrogenase. MCADs are
mitochondrial beta-oxidation enzymes, which catalyze the
alpha,beta dehydrogenation of the corresponding medium
chain acyl-CoA by FAD, which becomes reduced. The
reduced form of MCAD is reoxidized in the oxidative
half-reaction by electron-transferring flavoprotein
(ETF), from which the electrons are transferred to the
mitochondrial respiratory chain coupled with ATP
synthesis. MCAD is a homotetramer.
Length = 378
Score = 28.3 bits (63), Expect = 6.3
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 10/51 (19%)
Query: 93 NIPKIMNGLGLVIISTA----------SGIITDRKARSMGKMPIFIPPNVE 133
+IP+ GLGL T +G+ T +A S+G+MP+ I N E
Sbjct: 50 HIPEDCGGLGLGTFDTCLITEELAYGCTGVQTAIEANSLGQMPVIISGNDE 100
>gnl|CDD|238303 cd00542, Ntn_PVA, Penicillin V acylase (PVA), also known as
conjugated bile salt acid hydrolase (CBAH), catalyzes
the hydrolysis of penicillin V to yield 6-amino
penicillanic acid (6-APA), an important key intermediate
of semisynthetic penicillins. PVA has an N-terminal
nucleophilic cysteine, as do other members of the Ntn
hydrolase family to which PVA belongs. This
nucleophilic cysteine is exposed by post-translational
prossessing of the PVA precursor. PVA forms a
homotetramer.
Length = 303
Score = 28.0 bits (63), Expect = 8.6
Identities = 11/54 (20%), Positives = 16/54 (29%), Gaps = 6/54 (11%)
Query: 120 SMGKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFTAIN 173
+G I IP E T S + + + D L F +N
Sbjct: 24 DLGSQIIIIPRGYEWTSRSQGKSYTTKYAFIG------MGAVGDDYPLLFDGVN 71
>gnl|CDD|223456 COG0379, NadA, Quinolinate synthase [Coenzyme metabolism].
Length = 324
Score = 27.6 bits (62), Expect = 9.9
Identities = 16/60 (26%), Positives = 26/60 (43%)
Query: 104 VIISTASGIITDRKARSMGKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKND 163
I+ T GI+ + + K I +P V ITL+ L L++ NN V + +
Sbjct: 248 FIVGTERGIVHRLQKEAPDKEFIPLPTAGAVCPTMKMITLEKILEALEEGGNNEVTVDEE 307
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
0.322 0.139 0.391
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,104,125
Number of extensions: 1911827
Number of successful extensions: 1915
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1878
Number of HSP's successfully gapped: 61
Length of query: 374
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 276
Effective length of database: 6,590,910
Effective search space: 1819091160
Effective search space used: 1819091160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 60 (27.0 bits)