RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7269
(235 letters)
>gnl|CDD|215329 PLN02610, PLN02610, probable methionyl-tRNA synthetase.
Length = 801
Score = 197 bits (502), Expect = 2e-58
Identities = 74/130 (56%), Positives = 99/130 (76%), Gaps = 4/130 (3%)
Query: 1 IEDKLQSWVSETSDQ--WSSNARVICKAWLKDGLKPRCITRDLKWGIPVPLPGFENKVFY 58
++DKL +++ETS WS NA AWL+DGLKPRCITRDLKWG+PVPL +++KVFY
Sbjct: 212 LKDKLVEYINETSVAGGWSQNAIQTTNAWLRDGLKPRCITRDLKWGVPVPLEKYKDKVFY 271
Query: 59 VWFDAPIGYMSLTQSYCGQYEAWWKSAPQSKITLYQFMAKDNVPFHSIMFPATLVAAGDQ 118
VWFDAPIGY+S+T Y ++E WWK+ P++ + LYQFM KDNVPFH++MFP+TL+ G+
Sbjct: 272 VWFDAPIGYVSITACYTPEWEKWWKN-PEN-VELYQFMGKDNVPFHTVMFPSTLLGTGEN 329
Query: 119 YTKVNHIMAT 128
+T + I T
Sbjct: 330 WTMMKTISVT 339
Score = 44.8 bits (106), Expect = 2e-05
Identities = 14/39 (35%), Positives = 28/39 (71%)
Query: 125 IMATGHKIGTPAPLFRKIEQAQVDEWKLKYGGQQSKESS 163
++ GHKIGTP PLF++++ +V+ ++ K+ G Q+ ++
Sbjct: 555 LVPAGHKIGTPEPLFKELKDEEVEAYREKFAGSQADRAA 593
>gnl|CDD|237029 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 187 bits (477), Expect = 3e-56
Identities = 58/135 (42%), Positives = 86/135 (63%), Gaps = 10/135 (7%)
Query: 2 EDKLQSWVSETSDQWSSNARVICKAWLKDGLKPRCITRDLKWGIPVPLPGFENKVFYVWF 61
++L++W+ E+S W N WLK+GLKPR ITRDL WGIPVP PGFE KVFYVWF
Sbjct: 197 AERLRAWI-ESSGDWPPNVLNFTLNWLKEGLKPRAITRDLDWGIPVPWPGFEGKVFYVWF 255
Query: 62 DAPIGYMSLTQSYCGQ------YEAWWKSAPQSKITLYQFMAKDNVPFHSIMFPATLVAA 115
DA IGY+S ++ + + ++ +W + Y F+ KDN+PFHSI++PA L+ +
Sbjct: 256 DAVIGYISASKEWAERTGDPEAWKEFWLD---PETKSYYFIGKDNIPFHSIIWPAMLLGS 312
Query: 116 GDQYTKVNHIMATGH 130
G+ + I+++ +
Sbjct: 313 GEPLKLPDEIVSSEY 327
Score = 41.4 bits (98), Expect = 2e-04
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 129 GHKIGTPAPLFRKIEQAQVDEWKLKYGGQ 157
GH I P PLF+KI+ Q++E + GG
Sbjct: 527 GHPINKPEPLFKKIDDEQIEEELERLGGA 555
>gnl|CDD|220185 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family
includes methionyl tRNA synthetases.
Length = 388
Score = 167 bits (424), Expect = 6e-50
Identities = 57/132 (43%), Positives = 76/132 (57%), Gaps = 9/132 (6%)
Query: 2 EDKLQSWVSETSDQWSSNARVICKAWLKDGLKPRCITRDLKWGIPVPLPGFENKVFYVWF 61
+DKL W+ E D+ SN + +WLK+GLK ITRDL WGIPV PG KV YVWF
Sbjct: 192 QDKLLEWIKENPDEPPSNVNEVVLSWLKEGLKDLSITRDLDWGIPV--PGDPGKVIYVWF 249
Query: 62 DAPIGYMSLTQSYCGQ---YEAWWKSAPQSKITLYQFMAKDNVPFHSIMFPATLVAAGDQ 118
DA IGY+S T+ G ++ +W P ++I F+ KD + FH+I +PA L+AAG
Sbjct: 250 DALIGYISATKYLSGNPEKWKKFWADDPDTEI--VHFIGKDIIRFHAIYWPAMLMAAG-- 305
Query: 119 YTKVNHIMATGH 130
+ A G
Sbjct: 306 LPLPTQVFAHGW 317
>gnl|CDD|173907 cd00814, MetRS_core, catalytic core domain of methioninyl-tRNA
synthetases. Methionine tRNA synthetase (MetRS)
catalytic core domain. This class I enzyme aminoacylates
the 2'-OH of the nucleotide at the 3' of the appropriate
tRNA. MetRS, which consists of the core domain and an
anti-codon binding domain, functions as a monomer.
However, in some species the anti-codon binding domain
is followed by an EMAP domain. In this case, MetRS
functions as a homodimer. The core domain is based on
the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. As a result of a deletion event, MetRS has a
significantly shorter core domain insertion than IleRS,
ValRS, and LeuR. Consequently, the MetRS insertion
lacks the editing function.
Length = 319
Score = 165 bits (419), Expect = 7e-50
Identities = 56/132 (42%), Positives = 75/132 (56%), Gaps = 9/132 (6%)
Query: 2 EDKLQSWVSETSDQ-WSSNARVICKAWLKDGLKPRCITRDL-KWGIPVPLPGFENKVFYV 59
+D+L W+ + D W NAR +WLK+GLK ITRDL WGIPVPL KV YV
Sbjct: 148 QDRLLEWLEKNPDFIWPENARNEVLSWLKEGLKDLSITRDLFDWGIPVPL--DPGKVIYV 205
Query: 60 WFDAPIGYMSLTQSYCGQYE-AWWKSAPQSKITLYQFMAKDNVPFHSIMFPATLVAAGDQ 118
WFDA IGY+S T Y ++ +WW ++ F+ KD + FH+I +PA L+ AG
Sbjct: 206 WFDALIGYISATGYYNEEWGNSWWWKDGWPEL--VHFIGKDIIRFHAIYWPAMLLGAG-- 261
Query: 119 YTKVNHIMATGH 130
I+A G+
Sbjct: 262 LPLPTRIVAHGY 273
>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
Length = 673
Score = 163 bits (415), Expect = 1e-46
Identities = 47/136 (34%), Positives = 74/136 (54%), Gaps = 13/136 (9%)
Query: 1 IEDKLQSWVSETSDQWSSNARVICKAWLKDGLKPRCITRDLKW-GIPVPLPGFENKVFYV 59
E+ L+ W+ S + N K WL++GL+ I+RD + G +P G KVFYV
Sbjct: 194 FEEFLKEWI-TRSGELQPNVANKMKEWLEEGLQDWDISRDAPYFGFEIP--GAPGKVFYV 250
Query: 60 WFDAPIGYMSLTQSYCGQ-----YEAWWKSAPQSKITLYQFMAKDNVPFHSIMFPATLVA 114
W DAPIGY+S T++ C + ++ +WK +++ Y F+ KD + FH++ +PA L
Sbjct: 251 WLDAPIGYISSTKNLCDKRGGLDWDEYWKKDSDTEL--YHFIGKDIIYFHTLFWPAMLEG 308
Query: 115 AGDQYTKVNHIMATGH 130
AG Y ++ A G
Sbjct: 309 AG--YRLPTNVFAHGF 322
Score = 39.7 bits (94), Expect = 9e-04
Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 6/55 (10%)
Query: 128 TGHKIGTPAPLFRKIEQAQVDEWKLKY------GGQQSKESSNNKKETKQAEITF 176
GH I LF +IE Q++ + ++ +E I+F
Sbjct: 516 AGHPINKFKILFTRIEDKQIEALIEASKEAAAAKAAAAAAAAPLAEEPIAETISF 570
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 142 bits (359), Expect = 3e-39
Identities = 56/133 (42%), Positives = 68/133 (51%), Gaps = 8/133 (6%)
Query: 2 EDKLQSWVSETSDQ-WSSNARVICKAWLKDGLKPRCITR-DLKWGIPVPLPGFENKVFYV 59
+DKL W D W +N R +LK+GLK ITR DL WGIPVP G KV YV
Sbjct: 198 QDKLLEWYESNPDFIWPANRRNEVLNFLKEGLKDLSITRTDLDWGIPVP--GDPGKVIYV 255
Query: 60 WFDAPIGYMSLTQSYC--GQYEAWWKSAPQSKITLYQFMAKDNVPFHSIMFPATLVAAGD 117
WFDA IGY+S G E + K P L F+ KD + FH++ +PA L+AAG
Sbjct: 256 WFDALIGYISALGELAEIGDDEDFKKFWPADDTELVHFIGKDIIRFHAVYWPAMLMAAG- 314
Query: 118 QYTKVNHIMATGH 130
I A G
Sbjct: 315 -LPLPTRIFAHGF 326
Score = 34.2 bits (79), Expect = 0.047
Identities = 11/37 (29%), Positives = 17/37 (45%)
Query: 120 TKVNHIMATGHKIGTPAPLFRKIEQAQVDEWKLKYGG 156
+ GHK+G P PLF +IE+ ++E
Sbjct: 522 LGARQPLLPGHKLGPPEPLFPRIEEEAIEELIEALKE 558
>gnl|CDD|232957 TIGR00398, metG, methionyl-tRNA synthetase. The methionyl-tRNA
synthetase (metG) is a class I amino acyl-tRNA ligase.
This model appears to recognize the methionyl-tRNA
synthetase of every species, including eukaryotic
cytosolic and mitochondrial forms. The UPGMA difference
tree calculated after search and alignment according to
This model shows an unusual deep split between two
families of MetG. One family contains forms from the
Archaea, yeast cytosol, spirochetes, and E. coli, among
others. The other family includes forms from yeast
mitochondrion, Synechocystis sp., Bacillus subtilis, the
Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori.
The E. coli enzyme is homodimeric, although monomeric
forms can be prepared that are fully active. Activity of
this enzyme in bacteria includes aminoacylation of
fMet-tRNA with Met; subsequent formylation of the Met to
fMet is catalyzed by a separate enzyme. Note that the
protein from Aquifex aeolicus is split into an alpha
(large) and beta (small) subunit; this model does not
include the C-terminal region corresponding to the beta
chain [Protein synthesis, tRNA aminoacylation].
Length = 530
Score = 125 bits (315), Expect = 3e-33
Identities = 51/136 (37%), Positives = 72/136 (52%), Gaps = 12/136 (8%)
Query: 1 IEDKLQSWVSE--TSDQWSSNARVICKAWLKDGLKPRCITRDLK-WGIPVPLPGFENKVF 57
E +L+ W+ + S +SN + + WLK GLK ITRDL WGIPVP NKV
Sbjct: 191 FEKELEEWIRKNPESGSPASNVKNKAQNWLKGGLKDLAITRDLVYWGIPVP--NDPNKVV 248
Query: 58 YVWFDAPIGYMS---LTQSYCGQYEAWWKSAPQSKITLYQFMAKDNVPFHSIMFPATLVA 114
YVWFDA IGY+S + ++ WW + ++ L F+ KD V FH+I +PA L+
Sbjct: 249 YVWFDALIGYISSLGILSGDTEDWKKWWNNDEDAE--LIHFIGKDIVRFHTIYWPAMLMG 306
Query: 115 AGDQYTKVNHIMATGH 130
G + + G+
Sbjct: 307 LG--LPLPTQVFSHGY 320
>gnl|CDD|237028 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed.
Length = 648
Score = 69.4 bits (171), Expect = 9e-14
Identities = 32/97 (32%), Positives = 46/97 (47%), Gaps = 21/97 (21%)
Query: 28 LKDGLKPRCITRD-LKWGIPVPLPGFENK-VFYVWFDA------PIGYMSLTQSYCGQYE 79
+K GL+ I+R WGIPVP F+ K V YVW DA +GY S ++
Sbjct: 197 IKPGLEDLSISRTSFDWGIPVP---FDPKHVVYVWIDALLNYITALGYGSDDDEL---FK 250
Query: 80 AWWKSAPQSKITLYQFMAKDNVPFHSIMFPATLVAAG 116
+W + + KD + FH+I +P L+A G
Sbjct: 251 KFWPAD-------VHLVGKDILRFHAIYWPIMLMALG 280
Score = 31.3 bits (72), Expect = 0.42
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 127 ATGHKIGTPAPLFRKIE-QAQVDEWKLKYGGQQSKESSNNKKETKQAEITFSSVEELEAA 185
G K+ PLF +I+ + ++ K + G KE +K+ ++ EIT +++E
Sbjct: 495 PAGTKVAKGEPLFPRIDVEEEIAYIKEQMEGSAPKEPEEKEKKPEKPEITIDDFDKVELR 554
Query: 186 VAT 188
VA
Sbjct: 555 VAE 557
>gnl|CDD|237012 PRK11893, PRK11893, methionyl-tRNA synthetase; Reviewed.
Length = 511
Score = 63.4 bits (155), Expect = 1e-11
Identities = 32/97 (32%), Positives = 48/97 (49%), Gaps = 16/97 (16%)
Query: 27 WLKDGLKPRCITR-DLKWGIPVPLPGFENKVFYVWFDAPIGYMS------LTQSYCGQYE 79
++K GLK I+R + WGIPVP G V YVWFDA Y++ + +
Sbjct: 193 FVKSGLKDLSISRTNFDWGIPVP--GDPKHVIYVWFDALTNYLTALGYPDDEELLAELFN 250
Query: 80 AWWKSAPQSKITLYQFMAKDNVPFHSIMFPATLVAAG 116
+W + + KD + FH++ +PA L+AAG
Sbjct: 251 KYWPADV-------HLIGKDILRFHAVYWPAFLMAAG 280
>gnl|CDD|185674 cd00668, Ile_Leu_Val_MetRS_core, catalytic core domain of
isoleucyl, leucyl, valyl and methioninyl tRNA
synthetases. Catalytic core domain of isoleucyl,
leucyl, valyl and methioninyl tRNA synthetases. These
class I enzymes are all monomers. However, in some
species, MetRS functions as a homodimer, as a result of
an additional C-terminal domain. These enzymes
aminoacylate the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. Enzymes in
this subfamily share an insertion in the core domain,
which is subject to both deletions and rearrangements.
This editing region hydrolyzes mischarged cognate tRNAs
and thus prevents the incorporation of chemically
similar amino acids. MetRS has a significantly shorter
insertion, which lacks the editing function.
Length = 312
Score = 61.3 bits (149), Expect = 4e-11
Identities = 23/93 (24%), Positives = 37/93 (39%), Gaps = 15/93 (16%)
Query: 26 AWLKDGLKPRCITRDLKWGIPVPLPGFENKVFYVWFDAPIGYMSLTQSYCGQ--YEAWWK 83
AWL+ L I+R WG P+P VF VWFD+ IG + + ++ +
Sbjct: 173 AWLESLLD-WAISRQRYWGTPLP-----EDVFDVWFDSGIGPLGSLGYPEEKEWFKDSYP 226
Query: 84 SAPQSKITLYQFMAKDNVPFHSIMFPATLVAAG 116
+ + KD + + + LVA
Sbjct: 227 -------ADWHLIGKDILRGWANFWITMLVALF 252
>gnl|CDD|177869 PLN02224, PLN02224, methionine-tRNA ligase.
Length = 616
Score = 55.5 bits (133), Expect = 5e-09
Identities = 39/113 (34%), Positives = 59/113 (52%), Gaps = 20/113 (17%)
Query: 25 KAWLKDGLKPRCITRDL-KWGIPVPLPGFENKVFYVWFDAPIGYMS-LTQSYCGQ----- 77
++W+K GL+ I+R L WGIPVP + + YVWFDA +GY+S LT+ Q
Sbjct: 258 QSWIKSGLRDFSISRALVDWGIPVP--DDDKQTIYVWFDALLGYISALTEDNKQQNLETA 315
Query: 78 YEAWWKSAPQSKITLYQFMAKDNVPFHSIMFPATLVAAGDQYTKVNHIMATGH 130
W ++ + KD + FH++ +PA L++AG + K M GH
Sbjct: 316 VSFGWPAS-------LHLIGKDILRFHAVYWPAMLMSAGLELPK----MVFGH 357
>gnl|CDD|222326 pfam13701, DDE_Tnp_1_4, Transposase DDE domain group 1.
Transposase proteins are necessary for efficient DNA
transposition. This domain is a member of the DDE
superfamily, which contain three carboxylate residues
that are believed to be responsible for coordinating
metal ions needed for catalysis.
Length = 443
Score = 33.1 bits (76), Expect = 0.11
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 1 IEDKLQSWVSETSDQWSSNARVICKA-WLKDGLKPRCITRDL 41
E +L S V T+ WS + RV+ KA W GL PR + L
Sbjct: 278 RELRLYSDVYYTAKSWSRSRRVVTKAEWGSKGLNPRFVVTPL 319
>gnl|CDD|187809 cd09678, Csb1_I-U, CRISPR/Cas system-associated protein Csb1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein; Contains several motifs
similar to Cas7 family; also known as GSU0053 family.
Length = 174
Score = 29.5 bits (66), Expect = 0.96
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 95 FMAKDNVPFHSIMFPATLVAAGDQYTKVNHIMATGHKIGTP----APLFRKIEQA 145
FM N + + P +V AG++ GH+ G + L +++QA
Sbjct: 62 FMDTGNNNAPAKLLPQIVVNAGNKKVNSLEA---GHRAGDAIIRCSELQGELKQA 113
>gnl|CDD|225096 COG2185, Sbm, Methylmalonyl-CoA mutase, C-terminal domain/subunit
(cobalamin-binding) [Lipid metabolism].
Length = 143
Score = 28.8 bits (65), Expect = 1.2
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 7/34 (20%)
Query: 176 FSSVEE-LEAAVATQGALLGTVDVIVMSSRTGAY 208
F + EE + AAV VDVI +SS G +
Sbjct: 49 FQTPEEAVRAAVEE------DVDVIGVSSLDGGH 76
>gnl|CDD|240805 cd12359, RRM2_VICKZ, RNA recognition motif 2 in the VICKZ family
proteins. This subfamily corresponds to the RRM2 of
IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the
VICKZ family that have been implicated in the
post-transcriptional regulation of several different
RNAs and in subcytoplasmic localization of mRNAs during
embryogenesis. IGF2BPs are composed of two RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), and four
hnRNP K homology (KH) domains. .
Length = 76
Score = 27.7 bits (62), Expect = 1.3
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 153 KYGGQQSKESSNNKKETKQAEITFSSVEELEAAVA 187
YG ++ E K ET +T+ S E+ + AV
Sbjct: 23 TYGTVKNCEQVPTKSETATVNVTYESPEQAQQAVN 57
>gnl|CDD|224624 COG1710, COG1710, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 139
Score = 28.7 bits (64), Expect = 1.5
Identities = 11/33 (33%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 15 QWSSNARVICKAWLKDGLKPRCITRDLKWGIPV 47
++ N + + L++G PR I++DL GIP+
Sbjct: 93 KYDRNTLLRIREMLRNGKTPREISKDL--GIPI 123
>gnl|CDD|173617 PTZ00427, PTZ00427, isoleucine-tRNA ligase, putative; Provisional.
Length = 1205
Score = 29.5 bits (66), Expect = 1.8
Identities = 11/23 (47%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 27 WLKDGLKPRCITRDLKWGIPVPL 49
W+KD K CI+R+ WG P+P+
Sbjct: 564 WIKDA-KDWCISRNRYWGTPIPI 585
>gnl|CDD|236157 PRK08126, PRK08126, hypothetical protein; Provisional.
Length = 432
Score = 28.9 bits (65), Expect = 2.6
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 99 DNVPFHSIMFPATLVAAGDQYTKVNHIMATGHKIGTPA 136
DN P S F + LV + + +V ++ + G PA
Sbjct: 363 DNQPIRSAQFASNLVLSEKRAAQVAQMLQSA---GVPA 397
>gnl|CDD|164918 PHA02456, PHA02456, zinc metallopeptidase motif-containing
protein.
Length = 141
Score = 28.0 bits (62), Expect = 2.6
Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 1/53 (1%)
Query: 38 TRDLKWGIPVPLPGFENKVFYVWFD-APIGYMSLTQSYCGQYEAWWKSAPQSK 89
D+ V + +D PI + +L Q CGQ+ W + P
Sbjct: 23 EWDVALQARVYWSLGAGGGLELAWDPVPIYFRALPQDLCGQFVGWIEIDPDYA 75
>gnl|CDD|232969 TIGR00422, valS, valyl-tRNA synthetase. The valyl-tRNA synthetase
(ValS) is a class I amino acyl-tRNA ligase and is
particularly closely related to the isoleucyl tRNA
synthetase [Protein synthesis, tRNA aminoacylation].
Length = 861
Score = 28.9 bits (65), Expect = 3.0
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 25 KAWLKDGLKPRCITRDLKWGIPVP 48
WL++ +K CI+R L WG +P
Sbjct: 390 LNWLRN-IKDWCISRQLIWGHRIP 412
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 28.4 bits (64), Expect = 3.5
Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 18/70 (25%)
Query: 27 WLKDGLKPRCITRDLKWGIPVPLPGFENKVFYVWFDAPIGYMSLTQSYCG--QYEAWWKS 84
W+++ ++ CI+R L WG +P VW+ G + + E +
Sbjct: 392 WMEN-IRDWCISRQLWWGHRIP----------VWYCKECGNV-----VVAEEEPEDPAAA 435
Query: 85 APQSKITLYQ 94
K L Q
Sbjct: 436 EKCPKEELEQ 445
>gnl|CDD|240878 cd12432, RRM_ACINU, RNA recognition motif in apoptotic chromatin
condensation inducer in the nucleus (acinus) and similar
proteins. This subfamily corresponds to the RRM of
Acinus, a caspase-3-activated nuclear factor that
induces apoptotic chromatin condensation after cleavage
by caspase-3 without inducing DNA fragmentation. It is
essential for apoptotic chromatin condensation and may
also participate in nuclear structural changes occurring
in normal cells. Acinus contains a P-loop motif and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), which
indicates Acinus might have ATPase and DNA/RNA-binding
activity. .
Length = 90
Score = 26.8 bits (60), Expect = 3.6
Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 3/23 (13%)
Query: 174 ITFSSVEELEAAVATQGALLGTV 196
+T+S+VEE AVAT+ AL G
Sbjct: 44 VTYSTVEE---AVATREALHGLQ 63
>gnl|CDD|215452 PLN02843, PLN02843, isoleucyl-tRNA synthetase.
Length = 974
Score = 28.6 bits (64), Expect = 3.7
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 7/23 (30%)
Query: 36 CITRDLKWGIPVPLPGFENKVFY 58
CI+R WG+P+P VFY
Sbjct: 470 CISRQRTWGVPIP-------VFY 485
>gnl|CDD|218988 pfam06321, P_gingi_FimA, Major fimbrial subunit protein (FimA).
This family consists of several Porphyromonas gingivalis
major fimbrial subunit protein (FimA) sequences.
Fimbriae of Porphyromonas gingivalis, a
periodontopathogen, play an important role in its
adhesion to and invasion of host cells. The fimA genes
encoding fimbrillin (FimA), a subunit protein of
fimbriae, have been classified into five types, types I
to V, based on nucleotide sequences. It has been found
that type II FimA can bind to epithelial cells most
efficiently through specific host receptors. Human
dental plaque is a multispecies microbial biofilm that
is associated with two common oral diseases, dental
caries and periodontal disease. There is an
inter-species contact-dependent communication system
between P. gingivalis and S. cristatus that involces the
Arc-A enzyme.
Length = 265
Score = 27.9 bits (62), Expect = 5.0
Identities = 12/80 (15%), Positives = 24/80 (30%), Gaps = 1/80 (1%)
Query: 96 MAKDNVPFHSIMFPATLVAAGDQYTKVNHIMATGHKIGTPAPLFRKIEQAQVDEWKLKYG 155
+ +P S + TL A + Y G P L R + + ++ K+ +
Sbjct: 122 APTNGLPMTSKVTTVTLAAGKNYYGYDGTTGGNKISTGVPVSLTRIVAKVELTGIKVDF- 180
Query: 156 GQQSKESSNNKKETKQAEIT 175
+ E+
Sbjct: 181 DPTNANIYTYFILFDLKEVY 200
>gnl|CDD|219178 pfam06792, UPF0261, Uncharacterized protein family (UPF0261).
Length = 403
Score = 27.5 bits (62), Expect = 6.4
Identities = 9/46 (19%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 168 ETKQAEITFSSVEELEAAVATQGALLGTVDVIVMSSRTGAYAVTSE 213
+TK E+ + L + G + +DV V+ + +++E
Sbjct: 11 DTKGEELAY-----LRDLIEAAGLEVLVIDVSVLGPPSFPPDISAE 51
>gnl|CDD|185677 cd00817, ValRS_core, catalytic core domain of valyl-tRNA
synthetases. Valine amino-acyl tRNA synthetase (ValRS)
catalytic core domain. This enzyme is a monomer which
aminoacylates the 2'-OH of the nucleotide at the 3' of
the appropriate tRNA. The core domain is based on the
Rossman fold and is responsible for the ATP-dependent
formation of the enzyme bound aminoacyl-adenylate. It
contains the characteristic class I HIGH and KMSKS
motifs, which are involved in ATP binding. ValRS has an
insertion in the core domain, which is subject to both
deletions and rearrangements. This editing region
hydrolyzes mischarged cognate tRNAs and thus prevents
the incorporation of chemically similar amino acids.
Length = 382
Score = 27.6 bits (62), Expect = 6.5
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 11/43 (25%)
Query: 25 KAWLKDGLKPRCITRDLKWGIPVPLPGFENKVFYVWFDAPIGY 67
+ WL++ ++ CI+R L WG +P W+ G+
Sbjct: 203 ENWLEN-IRDWCISRQLWWGHRIP----------AWYCKDGGH 234
>gnl|CDD|173909 cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA
synthetases. Isoleucine amino-acyl tRNA synthetases
(IleRS) catalytic core domain . This class I enzyme is a
monomer which aminoacylates the 2'-OH of the nucleotide
at the 3' of the appropriate tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. IleRS has an insertion in the core domain,
which is subject to both deletions and rearrangements.
This editing region hydrolyzes mischarged cognate tRNAs
and thus prevents the incorporation of chemically
similar amino acids.
Length = 338
Score = 27.2 bits (61), Expect = 7.6
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 10/37 (27%)
Query: 36 CITRDLKWGIPVPLPGFENK----------VFYVWFD 62
CI+R WG P+P+ E+ V VWFD
Sbjct: 193 CISRQRYWGTPIPVWYCEDCGEVLVRRVPDVLDVWFD 229
>gnl|CDD|226839 COG4408, COG4408, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 431
Score = 27.1 bits (60), Expect = 8.9
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 89 KITLYQFMAKDNVPFHSIMFP 109
+I L +F+ DN P + M
Sbjct: 275 EINLLRFLNDDNYPVRAEMLS 295
>gnl|CDD|240411 PTZ00419, PTZ00419, valyl-tRNA synthetase-like protein;
Provisional.
Length = 995
Score = 27.3 bits (61), Expect = 9.3
Identities = 9/22 (40%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 27 WLKDGLKPRCITRDLKWGIPVP 48
WL + ++ CI+R L WG +P
Sbjct: 438 WL-ENIQDWCISRQLWWGHRIP 458
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
0.320 0.132 0.409
Gapped
Lambda K H
0.267 0.0691 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,622,925
Number of extensions: 1039652
Number of successful extensions: 963
Number of sequences better than 10.0: 1
Number of HSP's gapped: 936
Number of HSP's successfully gapped: 39
Length of query: 235
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 141
Effective length of database: 6,768,326
Effective search space: 954333966
Effective search space used: 954333966
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 (21.8 bits)
S2: 57 (25.8 bits)