RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 018851
(349 letters)
>gnl|CDD|215458 PLN02853, PLN02853, Probable phenylalanyl-tRNA synthetase alpha
chain.
Length = 492
Score = 669 bits (1727), Expect = 0.0
Identities = 273/344 (79%), Positives = 300/344 (87%), Gaps = 3/344 (0%)
Query: 1 MAEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTG 60
MAEEA+LG L NE+ISDSG FAA G DHN+VV VIKSLHGFRY+DAQDIKRETWVLT
Sbjct: 3 MAEEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDAQDIKRETWVLTE 62
Query: 61 EGKKYAAEGSPEVQLFLAVPAEGSISKDELQKKLDPAVFKIGCSQAGKNKWVEM--GKQV 118
EGKKYAAEGSPEVQLF AVPAEGSISKDELQKKLDPAVF IG QA KNKW+EM QV
Sbjct: 63 EGKKYAAEGSPEVQLFAAVPAEGSISKDELQKKLDPAVFDIGFKQAMKNKWLEMGGKPQV 122
Query: 119 SRKVQNVEDKVKDLLLQVQNGHALSKEEISSLKARK-LIVPQTWKGYSVRKGPNYAPKRK 177
SRKVQ+VED+VK+LLL +Q G + ++I +LK R+ LI +TWKGYS++KGPNYAP+RK
Sbjct: 123 SRKVQHVEDEVKELLLAIQEGKEVDDKDIDALKKRRKLITLETWKGYSIKKGPNYAPERK 182
Query: 178 KAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEM 237
KAATDLTRE LQ GDWK+LEFKEYNFNA G P EGGHLHPLLKVR+Q + IFLQMGFEEM
Sbjct: 183 KAATDLTREMLQSGDWKDLEFKEYNFNALGAPPEGGHLHPLLKVRQQFRKIFLQMGFEEM 242
Query: 238 PTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297
PTNNFVESSFWNFDALFQPQQHPARDSHDTFFL+ P+TTR+LPEDYVERVK VHESGGYG
Sbjct: 243 PTNNFVESSFWNFDALFQPQQHPARDSHDTFFLKAPATTRQLPEDYVERVKTVHESGGYG 302
Query: 298 SRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVF 341
S GYGY+WKREEANKNLLRTHTTAVSSRML LA+K F PK+ F
Sbjct: 303 SIGYGYDWKREEANKNLLRTHTTAVSSRMLYKLAQKGFKPKRYF 346
>gnl|CDD|240361 PTZ00326, PTZ00326, phenylalanyl-tRNA synthetase alpha chain;
Provisional.
Length = 494
Score = 437 bits (1127), Expect = e-152
Identities = 180/357 (50%), Positives = 223/357 (62%), Gaps = 17/357 (4%)
Query: 1 MAEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTG 60
+ E IL LE +I +S A DH VV IKSL YI + K TW LT
Sbjct: 6 LEENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESANYITTEMKKSNTWTLTE 65
Query: 61 EGKKYAAEGSPEVQLFLAVPAEGSISKDELQKKLDPAVFKIGCSQAGKNKWVEMGKQV-- 118
EG+ Y GSPE +L+ + G ISK + KKL V IG A K KW+++ K
Sbjct: 66 EGEDYLKNGSPEYRLWQKLKEGG-ISKADDAKKLGGKVADIGLGNAMKKKWIKLNKGDKK 124
Query: 119 ----SRKVQNVEDKVKDLLLQVQ---NGHALSKEEISSLKARKLIVPQTWKGYSVRKGPN 171
+ V +V D V+ LL V + +E+ LK RKL + K + V KGP
Sbjct: 125 VFLSRKLVDSVVDTVRLLLKIVAKGSQAEKIDSKELKELKKRKLATLEKIKYFVVTKGPK 184
Query: 172 YAPKRKKAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQ 231
+A + KK TDLT+E L G WK EFKEYNFNA G+ GG+LHPLLKVR++ ++I L+
Sbjct: 185 FAKEIKKQITDLTQEMLLNGSWKNAEFKEYNFNALGKKIGGGNLHPLLKVRREFREILLE 244
Query: 232 MGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTR--ELPEDYVERVKR 289
MGFEEMPTN +VESSFWNFDALFQPQQHPARD+ DTFFL +P T++ +L +DYVERVK+
Sbjct: 245 MGFEEMPTNRYVESSFWNFDALFQPQQHPARDAQDTFFLSKPETSKVNDLDDDYVERVKK 304
Query: 290 VHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAE-----KPFAPKKVF 341
VHE GGYGS G+ Y+WK EEA KN+LRTHTTAVS+RML LA+ PF PKK F
Sbjct: 305 VHEVGGYGSIGWRYDWKLEEARKNILRTHTTAVSARMLYKLAQEYKKTGPFKPKKYF 361
>gnl|CDD|235239 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Provisional.
Length = 489
Score = 262 bits (673), Expect = 3e-84
Identities = 132/353 (37%), Positives = 185/353 (52%), Gaps = 20/353 (5%)
Query: 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEG 62
E+ +L L++ ++ + A + G V+ + L + ++ E +VLT EG
Sbjct: 8 EKKVLKALKELKEAT-LEELAEKLGLPPEAVMRAAEWLEEKGLVKVEERVEEVYVLTEEG 66
Query: 63 KKYAAEGSPEVQLFLAVPAEGSISKDELQKK-LDPAVFKIGCSQAGKNKWVEMGKQ-VSR 120
KKYA EG PE +L A+ G +S DEL++ LD I + W ++ K V
Sbjct: 67 KKYAEEGLPERRLLNALKDGGEVSLDELKEALLDKKEVGIALGNLARKGWAKIEKGKVIL 126
Query: 121 KVQNVEDKVKDLLLQVQNGHALSKEE-----ISSLKARKLIVPQTWKGYSVR---KGPNY 172
K ED + L + G E + LK RKL+ + SV G
Sbjct: 127 KPDAYEDPEEKALKALAEGDKEELSEEDLKVLKELKKRKLVEEKERTERSVELTDAGLEL 186
Query: 173 APK---RKKAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDIF 229
+ K+ T LT E L+ G+WKE EF+ YN A G HP + +++DI
Sbjct: 187 LKEGIELKEEITQLTPELLKSGEWKEKEFRPYNVKAPPPKIYPGKKHPYREFIDEVRDIL 246
Query: 230 LQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKR 289
++MGFEEM VE+ FWNFDALFQPQ HPAR+ DTF+L+ P +LPE+ VERVK
Sbjct: 247 VEMGFEEM-KGPLVETEFWNFDALFQPQDHPAREMQDTFYLKYPG-IGDLPEELVERVKE 304
Query: 290 VHESGG-YGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVF 341
VHE GG GSRG+GY+W + A + +LRTHTTA+S+R LA +P P+K F
Sbjct: 305 VHEHGGDTGSRGWGYKWDEDIAKRLVLRTHTTALSAR---YLASRPEPPQKYF 354
>gnl|CDD|223095 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit
[Translation, ribosomal structure and biogenesis].
Length = 335
Score = 146 bits (370), Expect = 5e-41
Identities = 56/167 (33%), Positives = 79/167 (47%), Gaps = 40/167 (23%)
Query: 178 KAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEM 237
A T+LT E G W+ L F++ + G+ G LHPL + ++++DIFL MGF E+
Sbjct: 73 DAITELTPELEAAGLWERLAFEKIDVTLPGRRIYPGSLHPLTQTIEEIEDIFLGMGFTEV 132
Query: 238 PTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297
+E+ F+NFDAL PQ HPARD DTF+
Sbjct: 133 EGPE-IETDFYNFDALNIPQDHPARDMQDTFY---------------------------- 163
Query: 298 SRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKP---FAPKKVF 341
K + K LLRTHT+ V +R L A+ P F+P +V+
Sbjct: 164 -------LKDDR-EKLLLRTHTSPVQARTLAENAKIPIKIFSPGRVY 202
>gnl|CDD|216483 pfam01409, tRNA-synt_2d, tRNA synthetases class II core domain (F).
Other tRNA synthetase sub-families are too dissimilar
to be included. This family includes only
phenylalanyl-tRNA synthetases. This is the core
catalytic domain.
Length = 245
Score = 135 bits (343), Expect = 5e-38
Identities = 55/144 (38%), Positives = 73/144 (50%), Gaps = 36/144 (25%)
Query: 201 YNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHP 260
Y+ G+ E G LHPL +V ++++DIFL MGFEE+ VES F+NFDAL PQ HP
Sbjct: 2 YDVTLPGRRIEPGGLHPLTRVLEEIRDIFLSMGFEEVE-GPEVESDFYNFDALNIPQDHP 60
Query: 261 ARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYGSRGYGYEWKREEANKNLLRTHTT 320
ARD DTF+L++P +EE + LLRTHTT
Sbjct: 61 ARDMQDTFYLKKPL--------------------------------KEEDRRLLLRTHTT 88
Query: 321 AVSSRMLKALAEKP---FAPKKVF 341
V +R L + P F+ +VF
Sbjct: 89 PVQARTLAKKNKPPIKIFSIGRVF 112
>gnl|CDD|238277 cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS)
alpha chain catalytic core domain. PheRS belongs to
class II aminoacyl-tRNA synthetases (aaRS) based upon
its structure and the presence of three characteristic
sequence motifs. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. While class II aaRSs generally
aminoacylate the 3'-OH ribose of the appropriate tRNA,
PheRS is an exception in that it attaches the amino acid
at the 2'-OH group, like class I aaRSs. PheRS is an
alpha-2/ beta-2 tetramer.
Length = 218
Score = 118 bits (298), Expect = 8e-32
Identities = 45/129 (34%), Positives = 64/129 (49%), Gaps = 42/129 (32%)
Query: 216 HPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPST 275
HPL KV ++++DIF+ MGF E+ VE+ F+NFDAL PQ HPARD DTF++ +P+
Sbjct: 1 HPLNKVIEEIEDIFVSMGFTEV-EGPEVETDFYNFDALNIPQDHPARDMQDTFYINDPA- 58
Query: 276 TRELPEDYVERVKRVHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKP- 334
+ LLRTHT+AV +R L L + P
Sbjct: 59 ------------------------------------RLLLRTHTSAVQARALAKL-KPPI 81
Query: 335 --FAPKKVF 341
F+ +V+
Sbjct: 82 RIFSIGRVY 90
>gnl|CDD|232988 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit. Most
phenylalanyl-tRNA synthetases are heterodimeric, with 2
alpha (pheS) and 2 beta (pheT) subunits. This model
describes the alpha subunit, which shows some similarity
to class II aminoacyl-tRNA ligases. Mitochondrial
phenylalanyl-tRNA synthetase is a single polypeptide
chain, active as a monomer, and similar to this chain
rather than to the beta chain, but excluded from this
model. An interesting feature of the alignment of all
sequences captured by this model is a deep split between
non-spirochete bacterial examples and all other
examples; supporting this split is a relative deletion
of about 50 residues in the former set between two
motifs well conserved throughout the alignment [Protein
synthesis, tRNA aminoacylation].
Length = 293
Score = 120 bits (303), Expect = 1e-31
Identities = 56/167 (33%), Positives = 77/167 (46%), Gaps = 43/167 (25%)
Query: 178 KAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEM 237
T L E G W +L+F+ Y+ + G G LHPL +V +++DIFL +GF E
Sbjct: 34 DELTKLKPELESAGLWSKLKFETYDVSLPGTKIYPGSLHPLTRVIDEIRDIFLGLGFTEE 93
Query: 238 PTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297
VE+ FWNFDAL PQ HPARD DTF+++
Sbjct: 94 T-GPEVETDFWNFDALNIPQDHPARDMQDTFYIK-------------------------- 126
Query: 298 SRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKP---FAPKKVF 341
++ LLRTHTTAV R ++ + P F+P +VF
Sbjct: 127 -------------DRLLLRTHTTAVQLRTMEEQEKPPIRIFSPGRVF 160
>gnl|CDD|234780 PRK00488, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Validated.
Length = 339
Score = 89.4 bits (223), Expect = 4e-20
Identities = 40/139 (28%), Positives = 63/139 (45%), Gaps = 46/139 (33%)
Query: 207 GQPAEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHD 266
G+ E G LHP+ + ++++DIF+ MGFE +E+ ++NF+AL P+ HPARD D
Sbjct: 99 GRRIELGSLHPITQTIEEIEDIFVGMGFEVA-EGPEIETDYYNFEALNIPKDHPARDMQD 157
Query: 267 TFFLEEPSTTRELPEDYVERVKRVHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRM 326
TF++++ LLRTHT+ V R
Sbjct: 158 TFYIDD---------------------------------------GLLLRTHTSPVQIRT 178
Query: 327 LKALAEKP----FAPKKVF 341
+ +KP AP +V+
Sbjct: 179 M--EKQKPPIRIIAPGRVY 195
>gnl|CDD|215422 PLN02788, PLN02788, phenylalanine-tRNA synthetase.
Length = 402
Score = 31.7 bits (72), Expect = 0.51
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 13/70 (18%)
Query: 216 HPLLKVRKQLKDIFLQMGFEEMPTNNF--------VESSFWNFDALFQPQQHPARDSHDT 267
HPL ++ + D F +E +N F + S+ NFD + P H +R +DT
Sbjct: 68 HPLGILKNAIYDYF-----DENYSNKFKKFDDLSPIVSTKQNFDDVLVPPDHVSRSYNDT 122
Query: 268 FFLEEPSTTR 277
++++ + R
Sbjct: 123 YYVDAQTVLR 132
>gnl|CDD|224759 COG1846, MarR, Transcriptional regulators [Transcription].
Length = 126
Score = 30.3 bits (68), Expect = 0.64
Identities = 26/101 (25%), Positives = 44/101 (43%), Gaps = 6/101 (5%)
Query: 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSL--HGF--RYIDAQDIKRETWVLTG 60
+L L + I+ A G D + V ++K L G R D +D + LT
Sbjct: 26 QVLLALYEAGGIT-VKELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTE 84
Query: 61 EGKKYAAEGSPEVQLFLAVPAEGSISKDELQKKLDPAVFKI 101
+G++ + P Q LA +S++EL+K L + K+
Sbjct: 85 KGRELLEQLLPAAQELLAE-ILAGLSEEELRKLLRKLLEKL 124
>gnl|CDD|236592 PRK09616, pheT, phenylalanyl-tRNA synthetase subunit beta;
Reviewed.
Length = 552
Score = 30.6 bits (70), Expect = 1.5
Identities = 12/34 (35%), Positives = 23/34 (67%), Gaps = 2/34 (5%)
Query: 213 GHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESS 246
G LHP+ K+ + ++D+ + +GF+E+ NF +S
Sbjct: 356 GRLHPIEKLERAIRDLMVGLGFQEV--MNFTLTS 387
>gnl|CDD|240391 PTZ00377, PTZ00377, alanine aminotransferase; Provisional.
Length = 481
Score = 30.3 bits (69), Expect = 1.6
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 268 FFLEEPSTTRELPEDYVERVKRVHESGGYGSRGY----GYEWKREE 309
F LE+PS + P D V R K + G G+ Y GY + R+
Sbjct: 78 FLLEDPSVSSLFPADVVARAKEYLNAIGGGTGAYTDSAGYPFVRKA 123
>gnl|CDD|224935 COG2024, COG2024, Phenylalanyl-tRNA synthetase alpha subunit
(archaeal type) [Translation, ribosomal structure and
biogenesis].
Length = 536
Score = 30.2 bits (68), Expect = 1.8
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 211 EGGHLHPLLKVRKQLKDIFLQMGFEEM 237
E G HPL + ++L++ +L+MGF EM
Sbjct: 42 ETGKPHPLYETIQRLREAYLRMGFSEM 68
>gnl|CDD|178307 PLN02705, PLN02705, beta-amylase.
Length = 681
Score = 30.3 bits (68), Expect = 1.8
Identities = 23/89 (25%), Positives = 34/89 (38%), Gaps = 7/89 (7%)
Query: 249 NFDALFQPQQHPARDSHDT------FFLEEPSTTRELPEDYVERVKRVHESGGYGSRGYG 302
N D + QP P R+ + F + P + + GG G G G
Sbjct: 18 NLDPIPQPDPFPNRNRNQPQSRRPRGFAATAAAAAIAPTENDVNNGNISSGGGGGGGGKG 77
Query: 303 YEWKREEANKNLLRT-HTTAVSSRMLKAL 330
+ +E + LR H A++SRML L
Sbjct: 78 KREREKEKERTKLRERHRRAITSRMLAGL 106
>gnl|CDD|129561 TIGR00469, pheS_mito, phenylalanyl-tRNA synthetase, mitochondrial.
Unlike all other known phenylalanyl-tRNA synthetases,
the mitochondrial form demonstrated from yeast is
monomeric. It is similar to but longer than the alpha
subunit (PheS) of the alpha 2 beta 2 form found in
Bacteria, Archaea, and eukaryotes, and shares the
characteristic motifs of class II aminoacyl-tRNA
ligases. This model models the experimental example from
Saccharomyces cerevisiae (designated MSF1) and its
orthologs from other eukaryotic species [Protein
synthesis, tRNA aminoacylation].
Length = 460
Score = 30.0 bits (67), Expect = 1.9
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 240 NNF--VESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTR 277
+NF V ++ NFD L P HP R D +++ E R
Sbjct: 72 DNFKPVVTTMENFDNLGFPADHPGRQKSDCYYINEQHLLR 111
>gnl|CDD|235754 PRK06253, PRK06253, O-phosphoseryl-tRNA synthetase; Reviewed.
Length = 529
Score = 29.5 bits (67), Expect = 2.7
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 213 GHLHPLLKVRKQLKDIFLQMGFEEM 237
G HP+ ++L++ +L+MGFEEM
Sbjct: 44 GKPHPVYDTIERLREAYLRMGFEEM 68
>gnl|CDD|233730 TIGR02104, pulA_typeI, pullulanase, type I. Pullulan is an
unusual, industrially important polysaccharide in which
short alpha-1,4 chains (maltotriose) are connected in
alpha-1,6 linkages. Enzymes that cleave alpha-1,6
linkages in pullulan and release maltotriose are called
pullulanases although pullulan itself may not be the
natural substrate. This family consists of pullulanases
related to the subfamilies described in TIGR02102 and
TIGR02103 but having a different domain architecture
with shorter sequences. Members are called type I
pullulanases.
Length = 605
Score = 29.2 bits (66), Expect = 3.6
Identities = 15/45 (33%), Positives = 18/45 (40%), Gaps = 7/45 (15%)
Query: 30 HNDVVNVIKSL------HG-FRYIDAQDIKRETWVLTGEGKKYAA 67
D VN IK L H FR A+DI++ L E A
Sbjct: 512 FKDDVNYIKGLIALRKAHPAFRLSSAEDIRKHLEFLPAEPSGVIA 556
>gnl|CDD|240294 PTZ00150, PTZ00150, phosphoglucomutase-2-like protein; Provisional.
Length = 584
Score = 28.9 bits (65), Expect = 4.3
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 303 YEWKREEANKNLLRTHTTAVSSRMLKALAEK 333
Y + + +K T VSSRMLK +AEK
Sbjct: 339 YRRQGIDKSKCFFIC--TVVSSRMLKKMAEK 367
>gnl|CDD|239586 cd03509, DesA_FADS-like, Fatty acid desaturase protein family
subgroup, a delta-12 acyl-lipid desaturase-like,
DesA-like, yet uncharacterized subgroup of membrane
fatty acid desaturase proteins found in alpha-, beta-,
and gamma-proteobacteria. Sequences of this domain
family appear to be structurally related to membrane
fatty acid desaturases and alkane hydroxylases. They all
share in common extensive hydrophobic regions that would
be capable of spanning the membrane bilayer at least
twice. Comparison of these sequences also reveals three
regions of conserved histidine cluster motifs that
contain eight histidine residues: HXXXH, HXXHH, and
HXXHH. These histidine residues are reported to be
catalytically essential and proposed to be the ligands
for the iron atoms contained within homologs, stearoyl
CoA desaturase and alkane hydroxylase.
Length = 288
Score = 28.5 bits (64), Expect = 4.7
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 278 ELPEDYVE-RVKRVHESGGYGSRGYGYEWKR 307
+LP Y R + +GG+ RGYG ++R
Sbjct: 245 DLPRLYRARRDAYLRRNGGFVYRGYGELFRR 275
>gnl|CDD|222672 pfam14314, Methyltrans_Mon, Virus-capping methyltransferase. This
is the methyltransferase region of the Mononegavirales
single-stranded RNA viral RNA polymerase enzymes. This
region is involved in the mRNA-capping of the virion
particles.
Length = 674
Score = 28.8 bits (65), Expect = 5.2
Identities = 12/41 (29%), Positives = 19/41 (46%)
Query: 119 SRKVQNVEDKVKDLLLQVQNGHALSKEEISSLKARKLIVPQ 159
S++ +N K+ +L V++G S I L L PQ
Sbjct: 196 SKRDKNRLRKLSELSRNVRSGEGWSDLHIKRLTKDILFCPQ 236
>gnl|CDD|223201 COG0123, AcuC, Deacetylases, including yeast histone deacetylase
and acetoin utilization protein [Chromatin structure and
dynamics / Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 340
Score = 28.5 bits (64), Expect = 6.2
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 280 PEDYVERVKRVHESGGYGSRGYGYEW 305
DYVE ++ + E GYG+
Sbjct: 62 SPDYVEFLESLSEEEGYGNLDGDTPV 87
>gnl|CDD|129562 TIGR00470, sepS, O-phosphoserine--tRNA ligase. This family of
archaeal proteins resembles known phenylalanyl-tRNA
synthetase alpha chains. Recently, it was shown to act
in a proposed pathway of tRNA(Cys) indirect
aminoacylation, resulting in Cys biosynthesis from
O-phosphoserine, in certain archaea. It charges
tRNA(Cys) with O-phosphoserine. The pscS gene product
converts the phosphoserine to Cys [Amino acid
biosynthesis, Serine family, Protein synthesis, tRNA
aminoacylation].
Length = 533
Score = 27.9 bits (62), Expect = 9.2
Identities = 11/25 (44%), Positives = 19/25 (76%)
Query: 213 GHLHPLLKVRKQLKDIFLQMGFEEM 237
G HPL++ ++L++ +L+MGF EM
Sbjct: 44 GKPHPLMETIERLREAYLRMGFSEM 68
>gnl|CDD|152344 pfam11909, NdhN, NADH-quinone oxidoreductase cyanobacterial subunit
N. The proton-pumping NADH:ubiquinone oxidoreductase
catalyzes the electron transfer from NADH to ubiquinone
linked with proton translocation across the membrane. It
is the largest, most complex and least understood of the
respiratory chain enzymes and is referred to as Complex
I. The subunit composition of the enzyme varies between
groups of organisms. Complex I originating from
mammalian mitochondria contains 45 different proteins,
whereas in bacteria, the corresponding complex NDH-1
consists of 14 different polypeptides. Homologues of
these 14 proteins are found among subunits of the
mitochondrial complex I, and therefore bacterial NDH-1
might be considered a model proton-pumping NADH
dehydrogenase with a minimal set of subunits.
Escherichia coli NDH-1 readily disintegrates into 3
subcomplexes: a water-soluble NADH dehydrogenase
fragment (NuoE, -F, and -G),the connecting fragment
(NuoB, -C, -D, and -I), and the membrane fragment (NuoA,
-H, -J, -K, -L, -M, -N). In cyanobacteria and their
descendants, the chloroplasts of green plants, the
subunit composition of NDH-1 remains obscure. The genes
for eleven subunits NdhA-NdhK, homologous to the
NuoA-NuoD and NuoH-NuoN of the E. coli complex, have
been found in the genome of Synechocystis sp. PCC 6803
which has a family of 6 ndhD genes and a family of 3
ndhF genes. Two reported multisubunit complexes, NDH-1L
and NDH-1M, represent distinct NDH-1 complexes in the
thylakoid membrane of Synechocystis 6803
-cyanobacterium. NDH-1L was shown to be essential for
photoheterotrophic cell growth, whereas expression of
NDH-1M was a prerequisite for CO2 uptake and played an
important role in growth of cells at low CO2. Here we
report the subunit composition of these two complexes.
Fifteen proteins were discovered in NDH-1L including
NdhL, a new component of the membrane fragment, and
Ssl1690 (designated as NdhO), a novel peripheral
subunit. The cyanobacterial NDH-1 complex contains
additional subunits, NdhM and NdhN, compared with the
minimal set of the bacterial enzyme and these seem to be
specific for thylakoid-located NDH-1 of photosynthetic
organisms.
Length = 154
Score = 27.3 bits (61), Expect = 9.5
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 117 QVSRKVQNVEDKVKDLLLQVQNGHALSKEEISSL 150
Q+ ++ + K K L+L + G LSK E+ L
Sbjct: 91 QLGYYLEELPPKAKGLVLWLLEGQVLSKSELEYL 124
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
0.315 0.132 0.388
Gapped
Lambda K H
0.267 0.0716 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,987,980
Number of extensions: 1730456
Number of successful extensions: 1301
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1282
Number of HSP's successfully gapped: 37
Length of query: 349
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 251
Effective length of database: 6,590,910
Effective search space: 1654318410
Effective search space used: 1654318410
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: 42 (22.0 bits)
S2: 59 (26.5 bits)