RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1114
(480 letters)
>gnl|CDD|185498 PTZ00173, PTZ00173, 60S ribosomal protein L10; Provisional.
Length = 213
Score = 362 bits (930), Expect = e-125
Identities = 136/192 (70%), Positives = 162/192 (84%)
Query: 76 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 135
YRYCKNKPYPKSRFCRGVPDPKIRI+D+G+KKA V++FP+CVH+VSDEYEQ+SSEALEA
Sbjct: 9 YRYCKNKPYPKSRFCRGVPDPKIRIYDIGRKKATVDEFPVCVHIVSDEYEQISSEALEAA 68
Query: 136 RICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVAR 195
RI NKY+VK GKD FH+R+R+HPFHV+RINKMLSCAGADRLQTGMRGA+GKP GT AR
Sbjct: 69 RISANKYMVKRAGKDGFHLRIRVHPFHVLRINKMLSCAGADRLQTGMRGAFGKPNGTCAR 128
Query: 196 VNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLRDQN 255
V IGQ ++S+R+ + + P IEALRRAK+KFPGRQKI VS KWGFT Y REEY+ LR +
Sbjct: 129 VRIGQILLSIRTKEAYVPQAIEALRRAKYKFPGRQKIVVSNKWGFTNYTREEYQKLRAEG 188
Query: 256 RILHDAHFDHWI 267
+++ D I
Sbjct: 189 KLIQDGVHVKLI 200
Score = 220 bits (562), Expect = 1e-69
Identities = 82/104 (78%), Positives = 96/104 (92%)
Query: 349 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 408
YRYCKNKPYPKSRFCRGVPDPKIRI+D+G+KKA V++FP+CVH+VSDEYEQ+SSEALEA
Sbjct: 9 YRYCKNKPYPKSRFCRGVPDPKIRIYDIGRKKATVDEFPVCVHIVSDEYEQISSEALEAA 68
Query: 409 RICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRFE 452
RI NKY+VK GKD FH+R+R+HPFHV+RINKMLSCAGADR +
Sbjct: 69 RISANKYMVKRAGKDGFHLRIRVHPFHVLRINKMLSCAGADRLQ 112
Score = 142 bits (359), Expect = 1e-39
Identities = 53/78 (67%), Positives = 63/78 (80%)
Query: 269 RLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSK 328
RLQTGMRGA+GKP GT ARV IGQ ++S+R+ + + P IEALRRAK+KFPGRQKI VS
Sbjct: 110 RLQTGMRGAFGKPNGTCARVRIGQILLSIRTKEAYVPQAIEALRRAKYKFPGRQKIVVSN 169
Query: 329 KWGFTKYDREEYETLRDQ 346
KWGFT Y REEY+ LR +
Sbjct: 170 KWGFTNYTREEYQKLRAE 187
Score = 130 bits (328), Expect = 4e-35
Identities = 48/73 (65%), Positives = 58/73 (79%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKP GT ARV IGQ ++S+R+ + + P IEALRRAK+KFPGRQKI VS KWGFT
Sbjct: 115 MRGAFGKPNGTCARVRIGQILLSIRTKEAYVPQAIEALRRAKYKFPGRQKIVVSNKWGFT 174
Query: 61 KYDREEYETLRDQ 73
Y REEY+ LR +
Sbjct: 175 NYTREEYQKLRAE 187
>gnl|CDD|129380 TIGR00279, L10e, ribosomal protein L10.e. This model finds the
archaeal and eukaryotic forms of ribosomal protein L10.
The protein is encoded by multiple loci in some
eukaryotes and has been assigned a number of
extra-ribosomal functions, some of which will require
re-evaluation in the context of identification as a
ribosomal protein. L10.e is distantly related to
eubacterial ribosomal protein L16 [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 172
Score = 222 bits (568), Expect = 5e-71
Identities = 87/174 (50%), Positives = 113/174 (64%), Gaps = 3/174 (1%)
Query: 69 TLRDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLS 128
R YRY KN+PY +S + +GVP KIRI+D+G K A +FP+CVHLV+ E EQ+
Sbjct: 2 ARRPARCYRYQKNRPYTRSEYIKGVPGSKIRIYDMGNKSA---EFPVCVHLVAKEPEQIR 58
Query: 129 SEALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGK 188
ALEA RI NKY+ + G+ +H+++R++P H++R NKM + AGADR+Q GMRGA+GK
Sbjct: 59 HNALEAARIAANKYMTRRAGRMGYHLKIRVYPHHILRENKMATGAGADRIQQGMRGAFGK 118
Query: 189 PQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTK 242
P GT ARV IGQ I SV + EALRRA KFP KI + K W K
Sbjct: 119 PVGTAARVKIGQKIFSVWTKPSNFDVAKEALRRAAMKFPVPCKIVIEKGWELLK 172
Score = 145 bits (366), Expect = 3e-41
Identities = 58/133 (43%), Positives = 82/133 (61%), Gaps = 4/133 (3%)
Query: 342 TLRDQNSYRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLS 401
R YRY KN+PY +S + +GVP KIRI+D+G K A +FP+CVHLV+ E EQ+
Sbjct: 2 ARRPARCYRYQKNRPYTRSEYIKGVPGSKIRIYDMGNKSA---EFPVCVHLVAKEPEQIR 58
Query: 402 SEALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRFELDGCNVKYR 461
ALEA RI NKY+ + G+ +H+++R++P H++R NKM + AGADR + G +
Sbjct: 59 HNALEAARIAANKYMTRRAGRMGYHLKIRVYPHHILRENKMATGAGADRIQ-QGMRGAFG 117
Query: 462 AEHGPLAAWKKVQ 474
G A K Q
Sbjct: 118 KPVGTAARVKIGQ 130
Score = 86.1 bits (213), Expect = 1e-19
Identities = 35/66 (53%), Positives = 39/66 (59%)
Query: 269 RLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSK 328
R+Q GMRGA+GKP GT ARV IGQ I SV + EALRRA KFP KI + K
Sbjct: 107 RIQQGMRGAFGKPVGTAARVKIGQKIFSVWTKPSNFDVAKEALRRAAMKFPVPCKIVIEK 166
Query: 329 KWGFTK 334
W K
Sbjct: 167 GWELLK 172
Score = 78.7 bits (194), Expect = 3e-17
Identities = 32/61 (52%), Positives = 35/61 (57%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKP GT ARV IGQ I SV + EALRRA KFP KI + K W
Sbjct: 112 MRGAFGKPVGTAARVKIGQKIFSVWTKPSNFDVAKEALRRAAMKFPVPCKIVIEKGWELL 171
Query: 61 K 61
K
Sbjct: 172 K 172
>gnl|CDD|235252 PRK04199, rpl10e, 50S ribosomal protein L10e; Reviewed.
Length = 172
Score = 171 bits (437), Expect = 1e-51
Identities = 76/167 (45%), Positives = 98/167 (58%), Gaps = 3/167 (1%)
Query: 76 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 135
YR+ Y + + GVP PKI FD+G DFP+ V LV +E Q+ ALEA
Sbjct: 9 YRHISKPAYTRREYIGGVPGPKIVKFDMGNLS---GDFPVEVSLVVEEPCQIRHNALEAA 65
Query: 136 RICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVAR 195
RI NKYL K G+ +H+++R++P HV+R NKM + AGADR+ GMR A+GKP GT AR
Sbjct: 66 RIAANKYLTKTVGRSNYHLKIRVYPHHVLRENKMATGAGADRVSDGMRLAFGKPVGTAAR 125
Query: 196 VNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTK 242
V GQ I +VR + + A EALRRA K P +I V K K
Sbjct: 126 VEKGQKIFTVRVNPEHLEAAKEALRRAAMKLPTPCRIVVEKGKELLK 172
Score = 108 bits (272), Expect = 1e-27
Identities = 46/102 (45%), Positives = 62/102 (60%), Gaps = 3/102 (2%)
Query: 349 YRYCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAG 408
YR+ Y + + GVP PKI FD+G DFP+ V LV +E Q+ ALEA
Sbjct: 9 YRHISKPAYTRREYIGGVPGPKIVKFDMGNLS---GDFPVEVSLVVEEPCQIRHNALEAA 65
Query: 409 RICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADR 450
RI NKYL K G+ +H+++R++P HV+R NKM + AGADR
Sbjct: 66 RIAANKYLTKTVGRSNYHLKIRVYPHHVLRENKMATGAGADR 107
Score = 70.3 bits (173), Expect = 3e-14
Identities = 31/66 (46%), Positives = 37/66 (56%)
Query: 269 RLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSK 328
R+ GMR A+GKP GT ARV GQ I +VR + + A EALRRA K P +I V K
Sbjct: 107 RVSDGMRLAFGKPVGTAARVEKGQKIFTVRVNPEHLEAAKEALRRAAMKLPTPCRIVVEK 166
Query: 329 KWGFTK 334
K
Sbjct: 167 GKELLK 172
Score = 62.6 bits (153), Expect = 1e-11
Identities = 29/61 (47%), Positives = 34/61 (55%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MR A+GKP GT ARV GQ I +VR + + A EALRRA K P +I V K
Sbjct: 112 MRLAFGKPVGTAARVEKGQKIFTVRVNPEHLEAAKEALRRAAMKLPTPCRIVVEKGKELL 171
Query: 61 K 61
K
Sbjct: 172 K 172
>gnl|CDD|238714 cd01433, Ribosomal_L16_L10e, Ribosomal_L16_L10e: L16 is an
essential protein in the large ribosomal subunit of
bacteria, mitochondria, and chloroplasts. Large subunits
that lack L16 are defective in peptidyl transferase
activity, peptidyl-tRNA hydrolysis activity, association
with the 30S subunit, binding of aminoacyl-tRNA and
interaction with antibiotics. L16 is required for the
function of elongation factor P (EF-P), a protein
involved in peptide bond synthesis through the
stimulation of peptidyl transferase activity by the
ribosome. Mutations in L16 and the adjoining bases of
23S rRNA confer antibiotic resistance in bacteria,
suggesting a role for L16 in the formation of the
antibiotic binding site. The GTPase RbgA (YlqF) is
essential for the assembly of the large subunit, and it
is believed to regulate the incorporation of L16. L10e
is the archaeal and eukaryotic cytosolic homolog of
bacterial L16. L16 and L10e exhibit structural
differences at the N-terminus.
Length = 112
Score = 138 bits (350), Expect = 1e-39
Identities = 43/126 (34%), Positives = 60/126 (47%), Gaps = 14/126 (11%)
Query: 108 AKVEDFPLCVHLVSDEYEQLSSEALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRIN 167
+ F LV+ E ++++E LEA RI N+YL K + +R+ P H +
Sbjct: 1 KGNKLFFGEYGLVALEPGRITAEQLEAARIAINRYLKKK----GGKLWIRVFPDHPVTKK 56
Query: 168 KMLSCAGADRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFP 227
L+T M GKP+G VARV GQ + VR + + A EALRRA K P
Sbjct: 57 P---------LETRMGKGKGKPEGWVARVKPGQILFEVRGVPEEEVA-KEALRRAAKKLP 106
Query: 228 GRQKIY 233
+ KI
Sbjct: 107 IKTKIV 112
Score = 76.8 bits (190), Expect = 4e-17
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 381 AKVEDFPLCVHLVSDEYEQLSSEALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRIN 440
+ F LV+ E ++++E LEA RI N+YL K + +R+ P H +
Sbjct: 1 KGNKLFFGEYGLVALEPGRITAEQLEAARIAINRYLKKK----GGKLWIRVFPDHPVTKK 56
Query: 441 K 441
Sbjct: 57 P 57
Score = 72.9 bits (180), Expect = 8e-16
Identities = 26/64 (40%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 265 HWIIR---LQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGR 321
+ L+T M GKP+G VARV GQ + VR + + A EALRRA K P +
Sbjct: 50 DHPVTKKPLETRMGKGKGKPEGWVARVKPGQILFEVRGVPEEEVA-KEALRRAAKKLPIK 108
Query: 322 QKIY 325
KI
Sbjct: 109 TKIV 112
Score = 67.1 bits (165), Expect = 9e-14
Identities = 24/52 (46%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIY 52
M GKP+G VARV GQ + VR + + A EALRRA K P + KI
Sbjct: 62 MGKGKGKPEGWVARVKPGQILFEVRGVPEEEVA-KEALRRAAKKLPIKTKIV 112
>gnl|CDD|223275 COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal
structure and biogenesis].
Length = 146
Score = 129 bits (326), Expect = 1e-35
Identities = 44/162 (27%), Positives = 65/162 (40%), Gaps = 23/162 (14%)
Query: 78 YCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAGRI 137
+ K R P I I G K F LV+ E Q+++ +EA RI
Sbjct: 1 HMLQPKRTKYRKQHKGRGPGITIAKGGNK-----VFFGEYGLVALEPGQITARQIEAARI 55
Query: 138 CCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADRLQTGMRGAYGKPQGTVARVN 197
N+YL + G + +R+ P + G DR+ G GKP+G ARV
Sbjct: 56 AANRYLKRGGG-----LWIRVFPDKPLTEKP-----GEDRMGKGK----GKPEGWAARVK 101
Query: 198 IGQPIMSVRSSDKFKPAVIEALRRAKFKFPG--RQKIYVSKK 237
G+ + + + EALRRA K P + I + K+
Sbjct: 102 PGRVLFEIAGVPEEL--AREALRRAAAKLPVKTKFVIRIEKR 141
Score = 82.6 bits (205), Expect = 9e-19
Identities = 25/100 (25%), Positives = 37/100 (37%), Gaps = 15/100 (15%)
Query: 351 YCKNKPYPKSRFCRGVPDPKIRIFDLGKKKAKVEDFPLCVHLVSDEYEQLSSEALEAGRI 410
+ K R P I I G K F LV+ E Q+++ +EA RI
Sbjct: 1 HMLQPKRTKYRKQHKGRGPGITIAKGGNK-----VFFGEYGLVALEPGQITARQIEAARI 55
Query: 411 CCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGADR 450
N+YL + G + +R+ P + G DR
Sbjct: 56 AANRYLKRGGG-----LWIRVFPDKPLTEKP-----GEDR 85
Score = 53.4 bits (129), Expect = 1e-08
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 269 RLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPG--RQKIYV 326
R+ G GKP+G ARV G+ + + + EALRRA K P + I +
Sbjct: 85 RMGKGK----GKPEGWAARVKPGRVLFEIAGVPEEL--AREALRRAAAKLPVKTKFVIRI 138
Query: 327 SKK 329
K+
Sbjct: 139 EKR 141
Score = 48.7 bits (117), Expect = 6e-07
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 6 GKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPG--RQKIYVSKK 56
GKP+G ARV G+ + + + EALRRA K P + I + K+
Sbjct: 91 GKPEGWAARVKPGRVLFEIAGVPEEL--AREALRRAAAKLPVKTKFVIRIEKR 141
>gnl|CDD|215820 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.
Length = 129
Score = 99.1 bits (248), Expect = 7e-25
Identities = 34/116 (29%), Positives = 53/116 (45%), Gaps = 16/116 (13%)
Query: 117 VHLVSDEYEQLSSEALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGAD 176
L + E ++++ +EA RI N+YL + GK + +R+ P + + G
Sbjct: 30 YGLKALEPGRITARQIEAARIAINRYLKRG-GK----LWIRVFPDKPVTKKPAETRMGKG 84
Query: 177 RLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKI 232
+ GKP+G VARV GQ + + + EALRRA K P + KI
Sbjct: 85 K---------GKPEGWVARVKPGQILFEIGGVS--EEVAKEALRRAASKLPIKTKI 129
Score = 60.9 bits (149), Expect = 2e-11
Identities = 14/61 (22%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 390 VHLVSDEYEQLSSEALEAGRICCNKYLVKNCGKDQFHIRMRLHPFHVIRINKMLSCAGAD 449
L + E ++++ +EA RI N+YL + GK + +R+ P + + G
Sbjct: 30 YGLKALEPGRITARQIEAARIAINRYLKRG-GK----LWIRVFPDKPVTKKPAETRMGKG 84
Query: 450 R 450
+
Sbjct: 85 K 85
Score = 49.4 bits (119), Expect = 2e-07
Identities = 20/46 (43%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 6 GKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKI 51
GKP+G VARV GQ + + + EALRRA K P + KI
Sbjct: 86 GKPEGWVARVKPGQILFEIGGVS--EEVAKEALRRAASKLPIKTKI 129
Score = 49.4 bits (119), Expect = 2e-07
Identities = 20/46 (43%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 279 GKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKI 324
GKP+G VARV GQ + + + EALRRA K P + KI
Sbjct: 86 GKPEGWVARVKPGQILFEIGGVS--EEVAKEALRRAASKLPIKTKI 129
>gnl|CDD|200457 cd11318, AmyAc_bac_fung_AmyA, Alpha amylase catalytic domain found
in bacterial and fungal Alpha amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes bacterial and fungal proteins. The
Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 391
Score = 35.2 bits (82), Expect = 0.069
Identities = 31/123 (25%), Positives = 45/123 (36%), Gaps = 24/123 (19%)
Query: 230 QKIYVSKKWGFTKYDREEYETLRD---QNRI--LHDAHFDHWIIRLQTGMRGAYGKPQGT 284
QK V K+G +EE +N I DA +H GA
Sbjct: 67 QKGTVRTKYG----TKEELLEAIKALHENGIQVYADAVLNH--------KAGADETETVK 114
Query: 285 VARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLR 344
V+ P + R+ + +P IEA KF FPGR Y KW + + +Y+
Sbjct: 115 AVEVD---P--NDRNKEISEPYEIEAW--TKFTFPGRGGKYSDFKWNWQHFSGVDYDQKT 167
Query: 345 DQN 347
+
Sbjct: 168 KKK 170
Score = 32.1 bits (74), Expect = 0.61
Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 17/85 (20%)
Query: 173 AGADRLQTGMRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKI 232
AGAD +T V+ P + R+ + +P IEA KF FPGR
Sbjct: 105 AGADETETVK----------AVEVD---P--NDRNKEISEPYEIEAW--TKFTFPGRGGK 147
Query: 233 YVSKKWGFTKYDREEYETLRDQNRI 257
Y KW + + +Y+ + I
Sbjct: 148 YSDFKWNWQHFSGVDYDQKTKKKGI 172
Score = 28.3 bits (64), Expect = 9.9
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 25 RSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLRDQN 74
R+ + +P IEA KF FPGR Y KW + + +Y+ +
Sbjct: 123 RNKEISEPYEIEAW--TKFTFPGRGGKYSDFKWNWQHFSGVDYDQKTKKK 170
>gnl|CDD|233705 TIGR02068, cya_phycin_syn, cyanophycin synthetase. Cyanophycin is
an insoluble storage polymer for carbon, nitrogen, and
energy, found in most Cyanobacteria. The polymer has a
backbone of L-aspartic acid, with most Asp side chain
carboxyl groups attached to L-arginine. The polymer is
made by this enzyme, cyanophycin synthetase, and
degraded by cyanophycinase. Heterologously expressed
cyanophycin synthetase in E. coli produces a closely
related, water-soluble polymer with some Arg replaced by
Lys. It is unclear whether enzymes that produce soluble
cyanophycin-like polymers in vivo in non-Cyanobacterial
species should be designated as cyanophycin synthetase
itself or as a related enzyme. This model makes the
designation as cyanophycin synthetase. Cyanophycin
synthesis is analogous to polyhydroxyalkanoic acid (PHA)
biosynthesis, except that PHA polymers lack nitrogen and
may be made under nitrogen-limiting conditions [Cellular
processes, Biosynthesis of natural products].
Length = 864
Score = 32.1 bits (73), Expect = 0.80
Identities = 26/74 (35%), Positives = 38/74 (51%), Gaps = 9/74 (12%)
Query: 213 PAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLRDQNRILHDAHFDHWIIRLQT 272
PA IEA+ A +P R++I V G DR + E L +Q +L A FD I++
Sbjct: 741 PAAIEAVGAAIRNWPARRRIGVIGGPG----DRRD-EDLVEQGELLGGA-FDQIILKEDD 794
Query: 273 GMRGAYGKPQGTVA 286
+R G+P+G A
Sbjct: 795 DVR---GRPRGEAA 805
>gnl|CDD|227565 COG5240, SEC21, Vesicle coat complex COPI, gamma subunit
[Intracellular trafficking and secretion].
Length = 898
Score = 30.7 bits (69), Expect = 2.1
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 27 SDKFKPAVIEALRRAKFKFPGRQKIYVS 54
SD FK I+ALR FP ++ Y+
Sbjct: 388 SDGFKIIAIDALRSLSLLFPSKKLSYLD 415
Score = 30.7 bits (69), Expect = 2.1
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 208 SDKFKPAVIEALRRAKFKFPGRQKIYVS 235
SD FK I+ALR FP ++ Y+
Sbjct: 388 SDGFKIIAIDALRSLSLLFPSKKLSYLD 415
Score = 30.7 bits (69), Expect = 2.1
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 300 SDKFKPAVIEALRRAKFKFPGRQKIYVS 327
SD FK I+ALR FP ++ Y+
Sbjct: 388 SDGFKIIAIDALRSLSLLFPSKKLSYLD 415
>gnl|CDD|184752 PRK14573, PRK14573, bifunctional D-alanyl-alanine synthetase
A/UDP-N-acetylmuramate--L-alanine ligase; Provisional.
Length = 809
Score = 30.6 bits (69), Expect = 2.1
Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 11/87 (12%)
Query: 204 SVRSSDKFKPAVIEAL--RRAKFKFPGRQKIYVSKKW------GFTKYDREEYETLRDQN 255
SV SD + +E L + A+F F G Q+ +V + +K + E N
Sbjct: 30 SVSGSDLSEGKTVEKLKAKGARF-FLGHQEEHVPEDAVVVYSSSISKDNVEYLSAKSRGN 88
Query: 256 RILHDAHFDHWIIRLQTGM--RGAYGK 280
R++H A +++ Q + G++GK
Sbjct: 89 RLVHRAELLAELMQEQISILVSGSHGK 115
>gnl|CDD|216226 pfam00978, RdRP_2, RNA dependent RNA polymerase. This family may
represent an RNA dependent RNA polymerase. The family
also contains the following proteins: 2A protein from
bromoviruses, putative RNA dependent RNA polymerase from
tobamoviruses, non structural polyprotein from
togaviruses.
Length = 441
Score = 29.9 bits (68), Expect = 3.4
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 7/43 (16%)
Query: 78 YCKNKPYPKSRF-------CRGVPDPKIRIFDLGKKKAKVEDF 113
+ + PY S+F VPDP + LGKKK +D
Sbjct: 338 FDPSVPYFCSKFLLEVDGGAFFVPDPLKLLQKLGKKKIPDDDD 380
Score = 29.9 bits (68), Expect = 3.4
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 7/43 (16%)
Query: 351 YCKNKPYPKSRF-------CRGVPDPKIRIFDLGKKKAKVEDF 386
+ + PY S+F VPDP + LGKKK +D
Sbjct: 338 FDPSVPYFCSKFLLEVDGGAFFVPDPLKLLQKLGKKKIPDDDD 380
>gnl|CDD|236759 PRK10785, PRK10785, maltodextrin glucosidase; Provisional.
Length = 598
Score = 29.6 bits (67), Expect = 4.2
Identities = 15/65 (23%), Positives = 21/65 (32%), Gaps = 24/65 (36%)
Query: 242 KYDREEY-----------------ETLRDQN-RILHDAHFDH------WIIRLQTGMRGA 277
KYD E+Y + + R++ D F+H W R G GA
Sbjct: 209 KYDTEDYRHVDPQLGGDAALLRLRHATQQRGMRLVLDGVFNHTGDSHPWFDRHNRGTGGA 268
Query: 278 YGKPQ 282
P
Sbjct: 269 CHHPD 273
>gnl|CDD|213607 TIGR01352, tonB_Cterm, TonB family C-terminal domain. This model
represents the C-terminal of TonB and is homologs. TonB
is an energy-transducer for TonB-dependent receptors of
Gram-negative bacteria. Most members are designated as
TonB or TonB-related proteins, but a few represent the
paralogous TolA protein. Several bacteria have up to
four TonB paralogs. In nearly every case, a
proline-rich repetive region is found N-terminal to
this domain; these low-complexity regions are highly
divergent and cannot readily be aligned. The region is
suggested to help span the periplasm [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 74
Score = 26.9 bits (60), Expect = 6.1
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 8/41 (19%)
Query: 8 PQGTVARVNIGQPIMSVRSSDK--FKPAVIEALRRAKFKFP 46
P G V V++ ++SS A +EA+R+A+F+ P
Sbjct: 20 PSGRVTSVSV------LKSSGDEALDRAALEAVRKARFEPP 54
Score = 26.9 bits (60), Expect = 6.1
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 8/41 (19%)
Query: 189 PQGTVARVNIGQPIMSVRSSDK--FKPAVIEALRRAKFKFP 227
P G V V++ ++SS A +EA+R+A+F+ P
Sbjct: 20 PSGRVTSVSV------LKSSGDEALDRAALEAVRKARFEPP 54
Score = 26.9 bits (60), Expect = 6.1
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 8/41 (19%)
Query: 281 PQGTVARVNIGQPIMSVRSSDK--FKPAVIEALRRAKFKFP 319
P G V V++ ++SS A +EA+R+A+F+ P
Sbjct: 20 PSGRVTSVSV------LKSSGDEALDRAALEAVRKARFEPP 54
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
0.323 0.139 0.432
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,917,935
Number of extensions: 2444491
Number of successful extensions: 2160
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2133
Number of HSP's successfully gapped: 50
Length of query: 480
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 379
Effective length of database: 6,457,848
Effective search space: 2447524392
Effective search space used: 2447524392
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 61 (27.2 bits)