RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 037974
(233 letters)
>gnl|CDD|178532 PLN02946, PLN02946, cysteine-tRNA ligase.
Length = 557
Score = 175 bits (444), Expect = 1e-51
Identities = 86/182 (47%), Positives = 114/182 (62%), Gaps = 9/182 (4%)
Query: 41 TLQDCEVALSPFQEDARSGSITPAAEDCIKKLRDEFYTRMSDDLNTSHILTGAFLDALKF 100
TL DCE +L S+ P +CI K DEF T MSDDL+T + A + LK
Sbjct: 379 TLHDCEESLQQHDSTFEKDSVPPDTLNCINKFHDEFVTSMSDDLHTP-VALAALSEPLKT 437
Query: 101 INN---SKKQPKQQQLSLIESLLKIENEVKVVLDVLGLLPEGSTYSEVLQQLKDKALKRA 157
IN+ ++K KQ++ +ESL +E +++ VL VLGL+P ++YSE LQQL++KAL+RA
Sbjct: 438 INDLLHTRKGKKQEKR--LESLAALEKKIRDVLSVLGLMP--TSYSEALQQLREKALRRA 493
Query: 158 ELAENDVLHLIEERATAKKNKDFSKSDQIRADLTRKGIALMDVRKETIWRPCVPV-EQEQ 216
+L E VL IEER A+KNK++ KSD IR DL GIALMD T WRP +P+ QEQ
Sbjct: 494 KLTEEQVLQKIEERTVARKNKEYEKSDAIRKDLAAVGIALMDSPDGTTWRPAIPLALQEQ 553
Query: 217 EA 218
A
Sbjct: 554 VA 555
>gnl|CDD|234705 PRK00260, cysS, cysteinyl-tRNA synthetase; Validated.
Length = 463
Score = 94.0 bits (235), Expect = 2e-22
Identities = 42/154 (27%), Positives = 67/154 (43%), Gaps = 16/154 (10%)
Query: 54 EDARSGSITPAAEDCIKKLRDEFYTRMSDDLNTSHILTGAFLDALKFINNSKKQPKQQQL 113
+ G A +++ ++ F M DD NT L + + IN + + ++
Sbjct: 324 AETALGEDDEALLAELEEFKERFIEAMDDDFNTPEALA-VLFELAREINRALETKDKEAA 382
Query: 114 SLIESLLKIENEVKVVLDVLGLLPEGSTYSEVLQQLKDKALKRAELAENDVLHLIEERAT 173
+ + +LL+ + DVLGL + E EL + ++ LIEER
Sbjct: 383 AALAALLRA------LADVLGLEQDEEALFEA---------AADELLDAEIEALIEERQE 427
Query: 174 AKKNKDFSKSDQIRADLTRKGIALMDVRKETIWR 207
A+K KDF+ +D IR +L GI L D T WR
Sbjct: 428 ARKAKDFALADAIRDELAALGIVLEDTPDGTTWR 461
>gnl|CDD|223293 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 464
Score = 79.6 bits (197), Expect = 3e-17
Identities = 38/139 (27%), Positives = 62/139 (44%), Gaps = 16/139 (11%)
Query: 69 IKKLRDEFYTRMSDDLNTSHILTGAFLDALKFINNSKKQPKQQQLSLIESLLKIENEVKV 128
+K+ F + DD NT L + K IN ++ K +++ +L +
Sbjct: 340 LKEFEARFREALDDDFNTPKALA-VLFELAKEINRLLEEGKSDAKAVLSALKAL------ 392
Query: 129 VLDVLGLLPEGSTYSEVLQQLKDKALKRAELAENDVLHLIEERATAKKNKDFSKSDQIRA 188
L +LGL +VL + E + ++ LIEER A+K K+++ +D+IR
Sbjct: 393 -LAILGL--------KVLGLFPQSGAQEDESDDEEIEALIEERLEARKAKNWALADEIRD 443
Query: 189 DLTRKGIALMDVRKETIWR 207
+L GI L D T WR
Sbjct: 444 ELLALGIILEDTPDGTTWR 462
>gnl|CDD|232974 TIGR00435, cysS, cysteinyl-tRNA synthetase. This model finds the
cysteinyl-tRNA synthetase from most but not from all
species. The enzyme from one archaeal species,
Archaeoglobus fulgidus, is found but the equivalent
enzymes from some other Archaea, including Methanococcus
jannaschii, are not found, although biochemical evidence
suggests that tRNA(Cys) in these species are charged
directly with Cys rather than through a misacylation and
correction pathway as for tRNA(Gln) [Protein synthesis,
tRNA aminoacylation].
Length = 464
Score = 73.6 bits (181), Expect = 4e-15
Identities = 54/161 (33%), Positives = 75/161 (46%), Gaps = 19/161 (11%)
Query: 48 ALSPFQED-ARSGSITPAAEDCIKKLRDEFYTRMSDDLNTSHILTGAFLDALKFINNSKK 106
AL A SG+ + K+ F M DDLNT++ L F + K IN +
Sbjct: 321 ALRVLDTSLAYSGNQSLNKFPDEKEFEARFVEAMDDDLNTANALAVLF-ELAKSINLTFV 379
Query: 107 QPKQQQLSLIESLLKIENEVKVVLDVLGLLPEGSTYSEVLQQLKDKALKRAELAENDVLH 166
L LIE L+ +E+ L +L LP +Q + L E
Sbjct: 380 SKADAAL-LIEHLIFLES----RLGLLLGLPSKP-----VQAGSNDDLGEIE-------A 422
Query: 167 LIEERATAKKNKDFSKSDQIRADLTRKGIALMDVRKETIWR 207
LIEER+ A+K KDF+K+D+IR +L +KGI L D + T WR
Sbjct: 423 LIEERSIARKEKDFAKADEIRDELAKKGIVLEDTPQGTTWR 463
>gnl|CDD|153417 cd07963, Anticodon_Ia_Cys, Anticodon-binding domain of cysteinyl
tRNA synthetases. This domain is found in cysteinyl
tRNA synthetases (CysRS), which belong to the class Ia
aminoacyl tRNA synthetases. It lies C-terminal to the
catalytic core domain, and recognizes and specifically
binds to the tRNA anticodon. CysRS catalyzes the
transfer of cysteine to the 3'-end of its tRNA.
Length = 156
Score = 67.2 bits (165), Expect = 3e-14
Identities = 45/154 (29%), Positives = 66/154 (42%), Gaps = 30/154 (19%)
Query: 62 TPAAEDCIKKLRDEFYTRMSDDLNTSHILTGAFLDALKF-----INNSKKQPKQQQLSLI 116
T D + + F M DD NT A A+ F IN KK+ ++ +L
Sbjct: 24 TTVDIDWGEPFAERFIAAMDDDFNTP----EAL--AVLFELAREINRLKKEDIEKAAALA 77
Query: 117 ESLLKIENEVKVVLDVLGLL---PEGSTYSEVLQQLKDKALKRAELAENDVLHLIEERAT 173
L + VLGLL PE LQ L+ ++ LI +R
Sbjct: 78 ALLKALGG-------VLGLLQQDPE-----AFLQG----GTGEGGLSVAEIEALIAQRNQ 121
Query: 174 AKKNKDFSKSDQIRADLTRKGIALMDVRKETIWR 207
A+K KD++++D+IR +L +GI L D + T WR
Sbjct: 122 ARKAKDWAEADRIRDELAAQGIILEDSPEGTTWR 155
>gnl|CDD|184731 PRK14536, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 490
Score = 56.5 bits (136), Expect = 2e-09
Identities = 38/138 (27%), Positives = 59/138 (42%), Gaps = 21/138 (15%)
Query: 70 KKLRDEFYTRMSDDLNTSHILTGAFLDALKFINNSKKQPKQQQLSLIESLLKIENEVKVV 129
+ L +F + DD +T L+ L+ + P LS+ ++ +
Sbjct: 372 ELLLTDFRAALEDDFSTPKALS-----ELQKLVKDTSVPPSLCLSV----------LQAM 416
Query: 130 LDVLGLLPEGSTYSEVLQQLKDKALKRAELAENDVLHLIEERATAKKNKDFSKSDQIRAD 189
VLGL E L + A +E ++ LIE RA A++ KDF +D+IR
Sbjct: 417 DTVLGL----GLIQEATASLSAQV--PAGPSEEEIGQLIEARAHARQTKDFPLADEIRDK 470
Query: 190 LTRKGIALMDVRKETIWR 207
L +GI L D TIW+
Sbjct: 471 LKAEGIELEDTHLGTIWK 488
>gnl|CDD|173000 PRK14534, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 481
Score = 44.1 bits (104), Expect = 3e-05
Identities = 39/140 (27%), Positives = 61/140 (43%), Gaps = 33/140 (23%)
Query: 70 KKLRDEFYTRMSDDLNTSHILTGAFLDALKFINNSKKQPKQQQLSLIESLLKIENEVKVV 129
K+ D F +++ DLN Q L+L+ ++K +N
Sbjct: 365 KEYYDSFLEKIAFDLNIP-----------------------QGLALLWDIIKDDN----- 396
Query: 130 LDVLGLLPEGSTYSEVLQ-QLKDKALKRAE---LAENDVLH-LIEERATAKKNKDFSKSD 184
L L L + EVL L+++ L+ E + +D + LIEER AK KDF ++D
Sbjct: 397 LSFLSKLRLAFKFDEVLSLGLREEILREIENHRIVIDDNMKSLIEERRLAKCEKDFKRAD 456
Query: 185 QIRADLTRKGIALMDVRKET 204
+IR KG L+D + T
Sbjct: 457 EIREYFASKGFVLIDTEEGT 476
>gnl|CDD|211925 TIGR04202, capSnatchArena, RNA endonuclease, cap-snatching,
arenavirus family. This model describes a shared
signature region from an RNA endonuclease region
associated with cap-snatching for mRNA production by RNA
viruses. This domain usually is part of a
multifunctional protein, the L protein responsible for
RNA-dependent RNA polymerase activity. Cap-snatching is
a viral alternative to synthesizing a eukaryotic-like
mRNA cap itself.
Length = 61
Score = 32.6 bits (75), Expect = 0.017
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 7/46 (15%)
Query: 162 NDVLHLIE-------ERATAKKNKDFSKSDQIRADLTRKGIALMDV 200
+VL L+E E K + + K ++ DL GI L+ V
Sbjct: 10 GNVLILLEVFVRVDPESFEKKTKEKYEKLLSLKGDLLSPGITLVPV 55
>gnl|CDD|173001 PRK14535, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 699
Score = 35.5 bits (81), Expect = 0.023
Identities = 39/150 (26%), Positives = 62/150 (41%), Gaps = 24/150 (16%)
Query: 62 TPAAEDCIKKLRDE----FYTRMSDDLNTSHILTGAFLDALKFINNSKKQPKQQQLSLIE 117
TPAAE + + ++ FY M+DD T + F A + + Q
Sbjct: 568 TPAAEFMLSENVNDYTRRFYAAMNDDFGTVEAVAVLFELAGEVNKTNDAQ---------- 617
Query: 118 SLLKIENEVKVVLDVLGLLPEGSTYSEVLQQLKDKALKRAELAENDVLHLIEERATAKKN 177
+ +K + ++GLL T E LQ L+ ++ LI R A+ +
Sbjct: 618 ----LAGCLKALGGIIGLLQRDPT--EFLQ----GGAASDGLSNEEIEDLIARRKQARAD 667
Query: 178 KDFSKSDQIRADLTRKGIALMDVRKETIWR 207
K++++SD+IR L I L D T WR
Sbjct: 668 KNWAESDRIRDLLNEHKIILEDNAGGTTWR 697
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 33.8 bits (77), Expect = 0.081
Identities = 24/115 (20%), Positives = 39/115 (33%), Gaps = 2/115 (1%)
Query: 53 QEDARSGSITPAAEDCIKKLRDEFYTRMSDDLNTSHILTGAFLDALKFINNSKKQPKQQQ 112
E A D + L +E R + A L+A+ F+ KK ++
Sbjct: 2144 LEREVKSVFVEAPRDMLFLLEEEVRKRKGSVMKFKSSKKPAVLEAVLFVYKIKKASLREI 2203
Query: 113 LSLIESLLKIENEVKVVLDVLGLLPEGSTYSEVLQQLKDKALKRAELAENDVLHL 167
S I + E++ V D+LG E + Q L+ R D +
Sbjct: 2204 RSFIRPPGDLCIEMEDVCDLLGF--EAKIWFGEQQSLRRDDFIRIIGKYPDEIEF 2256
>gnl|CDD|176643 cd00865, PEBP_bact_arch, PhosphatidylEthanolamine-Binding Protein
(PEBP) domain present in bacteria and archaea.
PhosphatidylEthanolamine-Binding Proteins (PEBPs) are
represented in all three major phylogenetic divisions
(eukaryotes, bacteria, archaea). The members in this
subgroup are present in bacterial and archaea. Members
here include Escherichia coli YBHB and YBCL which are
thought to regulate protein phosphorylation as well as
Sulfolobus solfataricus SsCEI which inhibits serine
proteases alpha-chymotrypsin and elastase. Although
their overall structures are similar, the members of the
PEBP family have very different substrates and
oligomerization states (monomer/dimer/tetramer). In a
few of the bacterial members present here the
dimerization interface is proposed to form the ligand
binding site, unlike in other PEBP members.
Length = 150
Score = 31.4 bits (72), Expect = 0.21
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 130 LDVLGLLPEGSTYSEVLQQLKDKALKRAEL 159
LDV LLP G+T +E+L +K L +AEL
Sbjct: 117 LDVPLLLPPGATRAELLFAMKGHVLAKAEL 146
>gnl|CDD|214848 smart00840, DALR_2, This DALR domain is found in
cysteinyl-tRNA-synthetases.
Length = 56
Score = 29.1 bits (66), Expect = 0.32
Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 6/62 (9%)
Query: 75 EFYTRMSDDLNTSHILTGAFLDALKFINNSKKQPKQQQLSLIESLLKIENEVKVVLDVLG 134
F M DD NT L + + IN + E L + ++ + VLG
Sbjct: 1 RFEEAMDDDFNTPEALA-VLFELAREINRLALKATDA-----EELAALAALLRALGGVLG 54
Query: 135 LL 136
LL
Sbjct: 55 LL 56
>gnl|CDD|224475 COG1559, COG1559, Aminodeoxychorismate lyase [Coenzyme transport
and metabolism].
Length = 342
Score = 29.9 bits (68), Expect = 1.1
Identities = 31/161 (19%), Positives = 61/161 (37%), Gaps = 27/161 (16%)
Query: 93 AFLDALKFINNSKKQPK------QQQLSLIESLLKIENEVKVVLDVLGLLPEGSTYSEVL 146
F LK+ N + K + +S + +LK+ K + +PEG T ++
Sbjct: 74 VFRLYLKY-NPAAGSLKAGEYRLRPGMSAAD-ILKLLESGKSAQFKV-TIPEGYTLKQIA 130
Query: 147 QQLKDKALKRAELAENDVLHLIEERATAKKNK----------DFSKSDQIRADLTRKGIA 196
++L + + L + + K + +F++ D+ ++ I
Sbjct: 131 KKLAEAPVLDGVLDGLAIAEIAARLPKLDKERLEGYLFPDTYEFTRGTS-AEDIIKRMIK 189
Query: 197 LMDVRKETIW---RPCVPVEQEQE----APLVEKEQQLGEE 230
MD + + W +P + E A +VEKE + EE
Sbjct: 190 AMDKKLDEAWEKRADDLPGKTPYELLTLASIVEKEAAVDEE 230
>gnl|CDD|204161 pfam09190, DALR_2, DALR domain. This DALR domain is found in
cysteinyl-tRNA-synthetases.
Length = 62
Score = 26.8 bits (60), Expect = 2.1
Identities = 17/62 (27%), Positives = 21/62 (33%), Gaps = 8/62 (12%)
Query: 75 EFYTRMSDDLNTSHILTGAFLDALKFINNSKKQPKQQQLSLIESLLKIENEVKVVLDVLG 134
F M DD NT + + K IN K +L L + VLG
Sbjct: 1 RFIEAMDDDFNTPEAIA-VLFELAKEINRLKTTDGAAAAALAALLRA-------LGGVLG 52
Query: 135 LL 136
LL
Sbjct: 53 LL 54
>gnl|CDD|239947 cd04506, SGNH_hydrolase_YpmR_like, Members of the SGNH-hydrolase
superfamily, a diverse family of lipases and esterases.
The tertiary fold of the enzyme is substantially
different from that of the alpha/beta hydrolase family
and unique among all known hydrolases; its active site
closely resembles the Ser-His-Asp(Glu) triad from other
serine hydrolases, but may lack the carboxlic acid. This
subfamily contains sequences similar to Bacillus YpmR.
Length = 204
Score = 28.8 bits (65), Expect = 2.2
Identities = 17/79 (21%), Positives = 38/79 (48%), Gaps = 13/79 (16%)
Query: 115 LIESLLKIENEVKVVLDVLGLLPEGSTYSEVLQQLKDKALKRAELAE----------NDV 164
++ L++ + KV + G+ G ++L++LK K + EL + ND+
Sbjct: 25 RLDKLIETKTVKKVTVQNFGV--SGDRSDQLLKRLKTKK-VQKELKKADVITITIGGNDL 81
Query: 165 LHLIEERATAKKNKDFSKS 183
+ ++E+ + +DF K+
Sbjct: 82 MQVLEKNFLSLDVEDFKKA 100
>gnl|CDD|177492 PHA02827, PHA02827, hypothetical protein; Provisional.
Length = 150
Score = 27.5 bits (61), Expect = 4.0
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 8/49 (16%)
Query: 94 FLDALKFINNSKKQPKQQQLSLIESLLKIENEVKVVLDVLGLLPEGSTY 142
FLD+ + ++SK S+I ++LK EN ++ V+GLL + Y
Sbjct: 69 FLDSKEGFDHSK--------SMIRAMLKKENYIREACAVIGLLARAAEY 109
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 28.3 bits (63), Expect = 4.4
Identities = 14/52 (26%), Positives = 25/52 (48%)
Query: 119 LLKIENEVKVVLDVLGLLPEGSTYSEVLQQLKDKALKRAELAENDVLHLIEE 170
+LKIE E+K + + G+L E L+ + ++AE + L +E
Sbjct: 434 ILKIEEELKEGIPIEGVLDVFPEDVEFLRSILKDEEVIKKVAERPFVSLKKE 485
>gnl|CDD|172739 PRK14251, PRK14251, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 251
Score = 27.7 bits (61), Expect = 4.9
Identities = 34/128 (26%), Positives = 51/128 (39%), Gaps = 15/128 (11%)
Query: 52 FQEDARSGSITPAAEDCIKKLRDEFYTRMSDDLNTSHILTGAFLDALKFINNSKKQPKQQ 111
F+E + I P+ C K RM+DD+ I TG +KF + K
Sbjct: 27 FEEKELTALIGPSG--CGKSTFLRCLNRMNDDIENIKI-TGE----IKFEGQNIYGSKM- 78
Query: 112 QLSLIESLLKIENEVKVVLDVLGLLPEGSTYSEVLQQLKDKALKRAELAENDVLHLIEER 171
L+++ EV +V P S Y V LK +K EL + V +++
Sbjct: 79 ------DLVELRKEVGMVFQQPTPFP-FSVYDNVAYGLKIAGVKDKELIDQRVEESLKQA 131
Query: 172 ATAKKNKD 179
A K+ KD
Sbjct: 132 AIWKETKD 139
>gnl|CDD|165206 PHA02875, PHA02875, ankyrin repeat protein; Provisional.
Length = 413
Score = 27.6 bits (61), Expect = 6.1
Identities = 29/113 (25%), Positives = 46/113 (40%), Gaps = 23/113 (20%)
Query: 66 EDCIKKLRDEFYTRMSDDLNTSHILTGAFLDALKFINNSKKQPKQQQLSLIESLLKIENE 125
E CI +LR + + I LD NS E++L
Sbjct: 297 EKCIIELRR---------IKSEKIGKKNILDLCILEKNSHNLD--------ENIL----- 334
Query: 126 VKVVLDVLGLLPEGSTYSEVLQQLKDKALKRAELAENDVLHLIEERATAKKNK 178
+ +LGL E Y +L++ D ALKRAE E+ + +I++ T ++K
Sbjct: 335 ARHSKKILGLNDEAHFYKYLLKEAADIALKRAEAIES-AIRVIDDEITGDESK 386
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
0.316 0.133 0.368
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,842,056
Number of extensions: 1125989
Number of successful extensions: 1173
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1165
Number of HSP's successfully gapped: 50
Length of query: 233
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 139
Effective length of database: 6,768,326
Effective search space: 940797314
Effective search space used: 940797314
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: 57 (25.8 bits)