RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18006
(180 letters)
>gnl|CDD|215149 PLN02265, PLN02265, probable phenylalanyl-tRNA synthetase beta
chain.
Length = 597
Score = 204 bits (521), Expect = 3e-63
Identities = 79/152 (51%), Positives = 107/152 (70%), Gaps = 1/152 (0%)
Query: 1 MCLQTKILG-SGAEVSVSIPPTRHDIIHTCDIYEDIAIAYGYNNIPKTMPRFASIARQVP 59
M LQ + G + VS+PPTR DI+H CD+ ED+AIAYGYNNIPK P+ ++ +Q P
Sbjct: 339 MQLQAEQSSDDGCTIRVSVPPTRSDILHPCDVAEDVAIAYGYNNIPKRKPKSMTVGKQQP 398
Query: 60 LNKLSDQLRGDIAQAGFTEVLTFALCSRDDVSVKLRQKMEFIPAVHIGNPKTLEFQIART 119
LN+ SD LR ++A AGFTEVLT+ LCS + L ++ + AV IGNP++ +F++ RT
Sbjct: 399 LNQFSDLLRAEVAMAGFTEVLTWILCSHKENFAMLNREDDGNSAVIIGNPRSADFEVVRT 458
Query: 120 TLVPGLLKTLAANKKMPLPLKLFEISDIVYKD 151
+L+PGLLKTL NK P P+KLFE+SD+V D
Sbjct: 459 SLLPGLLKTLGHNKDAPKPIKLFEVSDVVLLD 490
>gnl|CDD|232989 TIGR00471, pheT_arch, phenylalanyl-tRNA synthetase, beta subunit.
Every known example of the phenylalanyl-tRNA synthetase,
except the monomeric form of mitochondrial, is an alpha
2 beta 2 heterotetramer. The beta subunits break into
two subfamilies that are considerably different in
sequence, length, and pattern of gaps. This model
represents the subfamily that includes the beta subunit
from eukaryotic cytosol, the Archaea, and spirochetes
[Protein synthesis, tRNA aminoacylation].
Length = 551
Score = 151 bits (384), Expect = 1e-43
Identities = 67/147 (45%), Positives = 90/147 (61%), Gaps = 2/147 (1%)
Query: 10 SGAEVSVSIPPTRHDIIHTCDIYEDIAIAYGYNNIPKTMPRFASIARQVPLNKLSDQLRG 69
S ++ V IP R DI+H DI ED+AI YGYNN P +P +I R PLNK+SD +R
Sbjct: 314 SDEKLKVVIPAYRVDILHEVDIIEDVAIGYGYNNFPPELPLINTIGRLKPLNKVSDIIRE 373
Query: 70 DIAQAGFTEVLTFALCSRDDVSVKLRQKMEFIPAVHIGNPKTLEFQIARTTLVPGLLKTL 129
+ GF EV+ L S + ++R + V + NPKTLE+ I RT+L+PGLL+TL
Sbjct: 374 IMVGLGFQEVIPLTLTSEEVNFKRMRIEDN--NDVKVANPKTLEYTIVRTSLLPGLLETL 431
Query: 130 AANKKMPLPLKLFEISDIVYKDATAGT 156
+ NK LP K+FEI D+V KD + T
Sbjct: 432 SENKHHELPQKIFEIGDVVVKDDKSET 458
>gnl|CDD|236592 PRK09616, pheT, phenylalanyl-tRNA synthetase subunit beta;
Reviewed.
Length = 552
Score = 141 bits (357), Expect = 1e-39
Identities = 56/144 (38%), Positives = 86/144 (59%), Gaps = 1/144 (0%)
Query: 13 EVSVSIPPTRHDIIHTCDIYEDIAIAYGYNNIPKTMPRFASIARQVPLNKLSDQLRGDIA 72
+V V++PP R DI+H D+ ED+AIAYGYNN+ +P+ +I R P+ KL +R +
Sbjct: 314 KVKVTVPPYRVDILHEVDVIEDVAIAYGYNNLEPELPKVFTIGRLHPIEKLERAIRDLMV 373
Query: 73 QAGFTEVLTFALCSRDDVSVKLRQKMEFIPAVHIGNPKTLEFQIARTTLVPGLLKTLAAN 132
GF EV+ F L S + + K+ + E V + NP + ++ + RT+L+P LL+ L+ N
Sbjct: 374 GLGFQEVMNFTLTSEEVLFEKMNLEPEEDY-VEVLNPISEDYTVVRTSLLPSLLEFLSNN 432
Query: 133 KKMPLPLKLFEISDIVYKDATAGT 156
K P K+FEI D+V D + T
Sbjct: 433 KHREYPQKIFEIGDVVLIDESTET 456
>gnl|CDD|223150 COG0072, PheT, Phenylalanyl-tRNA synthetase beta subunit
[Translation, ribosomal structure and biogenesis].
Length = 650
Score = 140 bits (355), Expect = 4e-39
Identities = 52/149 (34%), Positives = 85/149 (57%), Gaps = 6/149 (4%)
Query: 9 GSGAEVSVSIPPTRHDIIHTCDIYEDIAIAYGYNNIPKTMPRFASIARQV--PLNKLSDQ 66
G ++V++P R DI+ D+ E++A YGYNNIP +P +I R PL K +
Sbjct: 300 VKGDGLTVTVPSYRVDILIEADLIEEVARIYGYNNIPPELPSAFTIGRGGLTPLQKFRRK 359
Query: 67 LRGDIAQAGFTEVLTFALCSRDDVSVKLRQKMEFIPAVHIGNPKTLEFQIARTTLVPGLL 126
+R + GF EV+T++L S ++ + + E + + NP + E+ + RT+L+PGLL
Sbjct: 360 VRRALVGLGFQEVITYSLTSPEEAKLFGLENDEALE---LANPISEEYSVLRTSLLPGLL 416
Query: 127 KTLAANKKMPLP-LKLFEISDIVYKDATA 154
+ L+ NK P +++FEI D+ KD A
Sbjct: 417 EALSYNKNRKNPDVRIFEIGDVFVKDEEA 445
>gnl|CDD|238392 cd00769, PheRS_beta_core, Phenylalanyl-tRNA synthetase (PheRS) beta
chain core domain. PheRS belongs to class II
aminoacyl-tRNA synthetases (aaRS) based upon its
structure. 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. While the alpha chain contains a
catalytic core domain, the beta chain has a
non-catalytic core domain.
Length = 198
Score = 90.8 bits (226), Expect = 3e-23
Identities = 37/95 (38%), Positives = 54/95 (56%), Gaps = 4/95 (4%)
Query: 59 PLNKLSDQLRGDIAQAGFTEVLTFALCSRDDVSVKLRQKMEFIPAVHIGNPKTLEFQIAR 118
PL KL +LR +A GF EV+T++L S ++ ++ AV + NP + E+ + R
Sbjct: 1 PLQKLERKLRRLLAGLGFQEVITYSLTSPEEA-ELFDGGLD--EAVELSNPLSEEYSVLR 57
Query: 119 TTLVPGLLKTLAANKKMP-LPLKLFEISDIVYKDA 152
T+L+PGLL LA N PL+LFEI + KD
Sbjct: 58 TSLLPGLLDALARNLNRKNKPLRLFEIGRVFLKDE 92
>gnl|CDD|234804 PRK00629, pheT, phenylalanyl-tRNA synthetase subunit beta;
Reviewed.
Length = 791
Score = 91.4 bits (228), Expect = 7e-22
Identities = 45/150 (30%), Positives = 70/150 (46%), Gaps = 14/150 (9%)
Query: 10 SGAEVSVSIPPTRHDIIHTCDIYEDIAIAYGYNNIPKTMPRFASIA-----RQVPLNKLS 64
G ++V++P R DI D+ E++A YGY+NIP T P A Q L +L
Sbjct: 438 DGDGLTVTVPSWRFDIEIEEDLVEEVARIYGYDNIPSTPPVAALTMGGLTEAQRLLRRLR 497
Query: 65 DQLRGDIAQAGFTEVLTFALCSRDDVSVKLRQKMEFIPAVHIGNPKTLEFQIARTTLVPG 124
L G+ EV+T++ S +D + + + NP + E + RT+L+PG
Sbjct: 498 RALAA----LGYQEVITYSFVSPED----AKLFGLNPEPLLLLNPISEELSVMRTSLLPG 549
Query: 125 LLKTLAANKKMPLP-LKLFEISDIVYKDAT 153
LL+ +A N + LFEI + D
Sbjct: 550 LLEAVAYNLNRGNKDVALFEIGRVFLPDGD 579
>gnl|CDD|232990 TIGR00472, pheT_bact, phenylalanyl-tRNA synthetase, beta subunit,
non-spirochete bacterial. Every known example of the
phenylalanyl-tRNA synthetase, except the monomeric form
of mitochondrial, is an alpha 2 beta 2 heterotetramer.
The beta subunits break into two subfamilies that are
considerably different in sequence, length, and pattern
of gaps. This model represents the subfamily that
includes the beta subunit from Bacteria other than
spirochetes, as well as a chloroplast-encoded form from
Porphyra purpurea. The chloroplast-derived sequence is
considerably shorter at the amino end, however, so This
model was built in fragment mode [Protein synthesis,
tRNA aminoacylation].
Length = 797
Score = 82.7 bits (205), Expect = 6e-19
Identities = 48/152 (31%), Positives = 70/152 (46%), Gaps = 14/152 (9%)
Query: 10 SGAEVSVSIPPTRHDIIHTCDIYEDIAIAYGYNNIPKTMPRFASIAR-----QVPLNKLS 64
V++P RHDI D+ E+IA YGY+NIP +S + L KL
Sbjct: 441 QKDGWEVTVPSYRHDIEIEEDLIEEIARIYGYDNIPAEPLSVSSKLNKNNENYLLLRKLR 500
Query: 65 DQLRGDIAQAGFTEVLTFALCSRDDVSVKLRQKMEFIPAVHIGNPKTLEFQIARTTLVPG 124
L G G EV+T++ + + + V I NP + E + RT+L+P
Sbjct: 501 TLLVG----LGLNEVITYSFVDPEK--AEKFNFPKLENLVEIKNPLSNERSVLRTSLLPS 554
Query: 125 LLKTLA--ANKKMPLPLKLFEISDIVYKDATA 154
LL+ LA N+K +K+FEI + KD A
Sbjct: 555 LLEVLAYNQNRKNKD-VKIFEIGKVFAKDGEA 585
>gnl|CDD|197942 smart00874, B5, tRNA synthetase B5 domain. This domain is found
in phenylalanine-tRNA synthetase beta subunits.
Length = 68
Score = 51.7 bits (125), Expect = 1e-09
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 10 SGAEVSVSIPPTRHDIIHTCDIYEDIAIAYGY 41
SG + V++P R DI+ D+ E++A YGY
Sbjct: 37 SGDTLEVTVPSYRFDILIEADLIEEVARIYGY 68
>gnl|CDD|202663 pfam03484, B5, tRNA synthetase B5 domain. This domain is found
in phenylalanine-tRNA synthetase beta subunits.
Length = 70
Score = 49.1 bits (118), Expect = 1e-08
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 13 EVSVSIPPTRHDIIHTCDIYEDIAIAYGY 41
+ V++P R DI+H D+ E+IA YGY
Sbjct: 42 TLKVTVPSYRPDILHEVDLIEEIARLYGY 70
>gnl|CDD|214391 CHL00192, syfB, phenylalanyl-tRNA synthetase beta chain;
Provisional.
Length = 704
Score = 47.8 bits (114), Expect = 9e-07
Identities = 37/131 (28%), Positives = 64/131 (48%), Gaps = 11/131 (8%)
Query: 16 VSIPPTRH-DIIHTCDIYEDIAIAYGYNNIPKTMPRFASIARQVPLNKLSDQLRGDIAQA 74
V IP R DI+ D+ E+IA YG+NN +P I R D++R +
Sbjct: 355 VLIPSYRKDDIVREIDVIEEIARIYGFNNFLSKLPNIKFIGRLDIDYNTRDKIRSYLRNL 414
Query: 75 GFTEVLTFALCSRDDVSVKLRQKMEFIPAVHIGNPKTLEFQIARTTLVPGLLKTLAAN-K 133
G TE++ ++L ++Q+ + + NP ++ R++L+PGL++ + N K
Sbjct: 415 GLTELIHYSL---------VKQESFSKNEIKLKNPLIKDYSTLRSSLLPGLIEAVQENLK 465
Query: 134 KMPLPLKLFEI 144
+ L+ FEI
Sbjct: 466 QGNSTLEGFEI 476
>gnl|CDD|181659 PRK09121, PRK09121,
5-methyltetrahydropteroyltriglutamate--homocysteine
methyltransferase; Provisional.
Length = 339
Score = 29.3 bits (66), Expect = 0.99
Identities = 12/46 (26%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 58 VPLNKLSDQLRGDIAQAGFTEVLTFALCSRDDVSVKLRQKMEFIPA 103
VP++ L + +RG G +V + + + ++V+ LR+ ++F+ A
Sbjct: 257 VPMD-LLELIRGKKVMVGAIDVASDTIETPEEVADTLRKALQFVDA 301
>gnl|CDD|176667 cd07243, 2_3_CTD_C, C-terminal domain of catechol 2,3-dioxygenase.
This subfamily contains the C-terminal, catalytic,
domain of catechol 2,3-dioxygenase. Catechol
2,3-dioxygenase (2,3-CTD, catechol:oxygen
2,3-oxidoreductase) catalyzes an extradiol cleavage of
catechol to form 2-hydroxymuconate semialdehyde with the
insertion of two atoms of oxygen. The enzyme is a
homotetramer and contains catalytically essential Fe(II)
. The reaction proceeds by an ordered bi-unit mechanism.
First, catechol binds to the enzyme, this is then
followed by the binding of dioxygen to form a tertiary
complex, and then the aromatic ring is cleaved to
produce 2-hydroxymuconate semialdehyde. Catechol
2,3-dioxygenase belongs to the type I extradiol
dioxygenase family. The subunit comprises the N- and
C-terminal domains of similar structure fold, resulting
from an ancient gene duplication. The active site is
located in a funnel-shaped space of the C-terminal
domain. This subfamily represents the C-terminal domain.
Length = 143
Score = 28.5 bits (64), Expect = 1.1
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 13 EVSVSIPPTRHDIIHTCDIY 32
+VS+ I PTRH I IY
Sbjct: 92 DVSIDIGPTRHGITRGQTIY 111
>gnl|CDD|226850 COG4427, COG4427, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 350
Score = 28.7 bits (64), Expect = 1.9
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 89 DVSVKLRQKMEFIPAVHIGNPKTLEFQIART-TLVPGLLKTLAANKKMPLPLKLFEI 144
++ LRQ+ EF+ P+T E + R+ L+PGLL + PL L EI
Sbjct: 96 AIARALRQEPEFLLDALDSPPQTNE--VRRSAALLPGLL---IVALQFGKPLVLSEI 147
>gnl|CDD|227943 COG5656, SXM1, Importin, protein involved in nuclear import
[Posttranslational modification, protein turnover,
chaperones].
Length = 970
Score = 28.7 bits (64), Expect = 1.9
Identities = 9/32 (28%), Positives = 15/32 (46%)
Query: 24 DIIHTCDIYEDIAIAYGYNNIPKTMPRFASIA 55
D I C I E + + + + +P F S+A
Sbjct: 744 DFIGVCRIIESLILNIRDELLSQYLPLFISVA 775
>gnl|CDD|181187 PRK07984, PRK07984, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 262
Score = 27.6 bits (61), Expect = 3.9
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 24 DIIHTCDIYEDIAIAYGYNNIPKTMPRFASIARQVPLNKLSDQLRGDIAQA 74
DI+ CD+ ED +I + + K P+F + DQL GD A
Sbjct: 58 DIVLPCDVAEDASIDAMFAELGKVWPKFDGFVHSIGFAP-GDQLDGDYVNA 107
>gnl|CDD|188401 TIGR03886, lyase_spl_fam, spore photoproduct lyase family protein.
This uncharacterized radical SAM domain protein occurs
rarely and sporadically in species that include select
Alphaproteobacteria and Actinobacteria, and in
Deinococcus deserti VCD115. It is a distant but
full-length homolog to the Bacillus subtilis spore
photoproduct lyase (spl), which monomerizes thymine
dimers created as DNA damage by uv radiation.
Length = 346
Score = 27.0 bits (60), Expect = 6.1
Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 101 IPAVHIGNPKTLE--FQIARTTLVPGLLKTLAA 131
IP +H GN +E +I R TLV G+ KTL A
Sbjct: 37 IPELH-GNEGNVEDWVRIKRETLVLGVKKTLTA 68
>gnl|CDD|234146 TIGR03211, catechol_2_3, catechol 2,3 dioxygenase. Members of this
family all are enzymes active as catechol 2,3
dioxygenase (1.13.11.2), although some members have
highly significant activity on catechol derivatives such
as 3-methylcatechol, 3-chlorocatechol, and
4-chlorocatechol (see Mars, et al.). This enzyme is also
called metapyrocatechase, as it performs a meta-cleavage
(an extradiol ring cleavage), in contrast to the
ortho-cleavage (intradiol ring cleavage)performed by
catechol 1,2-dioxygenase (EC 1.13.11.1), also called
pyrocatechase [Energy metabolism, Other].
Length = 303
Score = 26.8 bits (60), Expect = 6.2
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 13 EVSVSIPPTRHDIIHTCDIY 32
+VS+ I PTRH I IY
Sbjct: 232 DVSIDIGPTRHGITRGQTIY 251
>gnl|CDD|218872 pfam06048, DUF927, Domain of unknown function (DUF927). Family of
bacterial proteins of unknown function. The C-terminal
half of this family contains a P-loop motif.
Length = 284
Score = 26.5 bits (59), Expect = 7.4
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 107 GNPKTLEFQIARTTLVPGLLKTLAANKKMPLPLKLFEISDIVYKDATAGTLMFTPGGNRT 166
GNP TL + R+T GL T +A+ PL L EIS+ ++ M G +
Sbjct: 216 GNPDTL-IRSWRSTAN-GLEGTASAHNDTPLILD--EISEADPREVGGAVYMLANGQGKG 271
Query: 167 R 167
R
Sbjct: 272 R 272
>gnl|CDD|235754 PRK06253, PRK06253, O-phosphoseryl-tRNA synthetase; Reviewed.
Length = 529
Score = 26.8 bits (60), Expect = 8.0
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 5/40 (12%)
Query: 110 KTLEFQIARTTL----VPGLLKTLAA-NKKMPLPLKLFEI 144
K L+ + +R TL G TL++ +K PLP+KLF I
Sbjct: 175 KELKPESSRLTLRSHMTSGWFITLSSLLEKRPLPIKLFSI 214
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 0.137 0.398
Gapped
Lambda K H
0.267 0.0838 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,161,812
Number of extensions: 840124
Number of successful extensions: 564
Number of sequences better than 10.0: 1
Number of HSP's gapped: 549
Number of HSP's successfully gapped: 22
Length of query: 180
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 89
Effective length of database: 6,901,388
Effective search space: 614223532
Effective search space used: 614223532
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: 56 (25.1 bits)