RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1221
(690 letters)
>gnl|CDD|233047 TIGR00604, rad3, DNA repair helicase (rad3). All proteins in this
family for which funcitons are known are DNA-DNA
helicases that funciton in the initiation of
transcription and nucleotide excision repair as part of
the TFIIH complex. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 705
Score = 170 bits (432), Expect = 1e-44
Identities = 76/275 (27%), Positives = 129/275 (46%), Gaps = 22/275 (8%)
Query: 415 QSFLKGVQENNPNLSKPSEGGIEEAPSQVQEDQV--------RNPMLSVVTFLESLVNKN 466
+FL+ ++E + +P E + ++E ++ + + T + + N
Sbjct: 348 DAFLEHLKEK-TFIDRPLRFCSERLSNLLRELEITHPEDFSALVLLFTFATLVLTYTNGF 406
Query: 467 EDGRILVTKNPELSKSHIKYILLNPANHFTDIVQDARSIIVAGGTMEPVSEFKDQLFGSL 526
+G +N + +K++ L+P+ + + RS+I+A GT+ P+ F L
Sbjct: 407 LEGIEPY-ENKTVPNPILKFMCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLG--- 462
Query: 527 GVPESRIHHFSCGHVIPKENILPLILCSGPTNRKFDLTFENRTKGDTLKEIAMTITNLCT 586
H++ +EN+L LI+ G TFE R ++ + +
Sbjct: 463 --FNPVSQDSPT-HILKRENLLTLIVTRGSDQVPLSSTFEIRNDPSLVRNLGELLVEFSK 519
Query: 587 IVPKGMVCFFPSYDY-EAIVYNYMRDNHFIERIARIAKKKVVFREPKKTSEVDKVLSDYG 645
I+P G+V FFPSY Y E IV + + I KKK++F E K E L Y
Sbjct: 520 IIPDGIVVFFPSYSYLENIV----STWKEMGILENIEKKKLIFVETKDAQETSDALERYK 575
Query: 646 TSVEKG-GALMLSVIGGKLSEGLNFSDDLGRCVVV 679
+V +G GA++LSV GGK+SEG++F DDLGR V++
Sbjct: 576 QAVSEGRGAVLLSVAGGKVSEGIDFCDDLGRAVIM 610
Score = 114 bits (288), Expect = 2e-26
Identities = 48/217 (22%), Positives = 90/217 (41%), Gaps = 18/217 (8%)
Query: 205 QSFLKGVQENNPNLSKPPEGGIEEAPSQVQEDQV--------RNPMLSVVTFLESLVNKN 256
+FL+ ++E + +P E + ++E ++ + + T + + N
Sbjct: 348 DAFLEHLKEK-TFIDRPLRFCSERLSNLLRELEITHPEDFSALVLLFTFATLVLTYTNGF 406
Query: 257 EDGRILVTKNPELSKSHIKYILLNPANHFTDIVQDARSIIVAGGTMEPVSEFKDQLFGSL 316
+G +N + +K++ L+P+ + + RS+I+A GT+ P+ F L
Sbjct: 407 LEGIEPY-ENKTVPNPILKFMCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLG--- 462
Query: 317 GVPESRIHHFSCGHVIPKENILPLILCSGPTNRKFDLTFENRTKGDTLKEIAMTITNLCT 376
H++ +EN+L LI+ G TFE R ++ + +
Sbjct: 463 --FNPVSQDSPT-HILKRENLLTLIVTRGSDQVPLSSTFEIRNDPSLVRNLGELLVEFSK 519
Query: 377 IVPKGMVCFFPSYDY--EAIVYNYMPDIEKTQEKPKL 411
I+P G+V FFPSY Y + I + EK KL
Sbjct: 520 IIPDGIVVFFPSYSYLENIVSTWKEMGILENIEKKKL 556
>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
Length = 763
Score = 159 bits (403), Expect = 7e-41
Identities = 78/194 (40%), Positives = 107/194 (55%), Gaps = 25/194 (12%)
Query: 1 MVGEKNLSPEVADKIGEYVLKHGH-VDLVENLLAD--EFLAKSKQAKEGLEAIKLLFHYC 57
MV EK LS E ADKIG +V + G ++L+ L + EFL + ++ L+ ++++F
Sbjct: 522 MVEEKGLSNETADKIGNFVKERGPPLELLSKLRQEGSEFL-GNASSRAALDELEIMFKAL 580
Query: 58 QIYGLKDTIVFDLSLARGLDYYTGVIYEAVLKDQAVGSVAGGGRYDNLVGMFDPKNKTTP 117
+ IVFDLSLARGLDYYTGVIYEAV K VGS+A GGRYDNLVGMF K P
Sbjct: 581 EKSKAIGKIVFDLSLARGLDYYTGVIYEAVFKGAQVGSIAAGGRYDNLVGMFS--GKQVP 638
Query: 118 CVAAKLLHEVQGLLETSCRSCREDIGVERLFSIIENRNAEQGVKVKTTSTQVYVASAQKN 177
V L G+ER+F+I+E + E+ ++ T T+V V+ +
Sbjct: 639 AVGVSL-------------------GIERVFAIMEQQEEEKSQVIRPTETEVLVSIIGDD 679
Query: 178 LVEPRMQLCHELWG 191
+ +L ELW
Sbjct: 680 KLALAAELVSELWN 693
>gnl|CDD|238396 cd00773, HisRS-like_core, Class II Histidinyl-tRNA synthetase
(HisRS)-like catalytic core domain. HisRS is a
homodimer. It is responsible for the attachment of
histidine to the 3' OH group of ribose of the
appropriate tRNA. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. Class II assignment is based upon
its structure and the presence of three characteristic
sequence motifs. This domain is also found at the
C-terminus of eukaryotic GCN2 protein kinase and at the
N-terminus of the ATP phosphoribosyltransferase
accessory subunit, HisZ. HisZ along with HisG catalyze
the first reaction in histidine biosynthesis. HisZ is
found only in a subset of bacteria and differs from
HisRS in lacking a C-terminal anti-codon binding domain.
Length = 261
Score = 109 bits (274), Expect = 1e-26
Identities = 45/149 (30%), Positives = 66/149 (44%), Gaps = 29/149 (19%)
Query: 12 ADKIGEYVLKHGHVDLVENLLADEFLAKSKQA-------KEGLEAIKLLFHYCQIYGLKD 64
A + ++ +K H +++ + + KE L ++ L Y + G+
Sbjct: 134 ALGLKDFQIKINHRGILDGIAGLLEDREEYIERLIDKLDKEALAHLEKLLDYLEALGVDI 193
Query: 65 TIVFDLSLARGLDYYTGVIYEAVLKDQ-AVGSVAGGGRYDNLVGMFDPKNKTTPCVAAKL 123
DLSL RGLDYYTG+++EAV A GS+AGGGRYD L+ F + P V
Sbjct: 194 KYSIDLSLVRGLDYYTGIVFEAVADGLGAQGSIAGGGRYDGLLEEFG--GEDVPAV---- 247
Query: 124 LHEVQGLLETSCRSCREDIGVERLFSIIE 152
G IG+ERL +E
Sbjct: 248 -----GF----------AIGLERLLLALE 261
>gnl|CDD|223202 COG0124, HisS, Histidyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 106 bits (267), Expect = 2e-24
Identities = 56/189 (29%), Positives = 72/189 (38%), Gaps = 30/189 (15%)
Query: 3 GEKNLSPEVADKIGEYVLKHGHVDLVENLLADEFLAKSKQAKEGLEAIKLLFHYCQIYGL 62
E + + + K + A E L +E LE ++ L G+
Sbjct: 200 DEDSKRRLKTNPLRVLDSKKDSDQEL-LKNAPELLDYL--DEESLEHLEELLALLDALGI 256
Query: 63 KDTIVFDLSLARGLDYYTGVIYEAVL-KDQAVGSVAGGGRYDNLVGMFDPKNKTTPCVAA 121
D SL RGLDYYTG ++EAV A GSV GGGRYD LV F K TP V
Sbjct: 257 S--YEIDPSLVRGLDYYTGTVFEAVTDGLGAQGSVCGGGRYDGLVEEFG--GKPTPAV-- 310
Query: 122 KLLHEVQGLLETSCRSCREDIGVERLFSIIENRNAEQGVKVKTTSTQVYVASAQKNLVEP 181
G IGVERL +E E T VYV ++
Sbjct: 311 -------GFA----------IGVERLILALEEEGKE---DPVETRVDVYVVPLGEDAEPE 350
Query: 182 RMQLCHELW 190
++L +L
Sbjct: 351 ALKLAQKLR 359
>gnl|CDD|234586 PRK00037, hisS, histidyl-tRNA synthetase; Reviewed.
Length = 412
Score = 91.7 bits (229), Expect = 9e-20
Identities = 51/158 (32%), Positives = 67/158 (42%), Gaps = 41/158 (25%)
Query: 35 EFLAKSKQAKEGLEAIKLLFHYCQIYGLKDTIVFDLSLARGLDYYTGVIYEAVLKDQ-AV 93
++L +++KE E +K L L V D L RGLDYYTG ++E V D A
Sbjct: 222 DYL--DEESKEHFEELKELLD-----ALGIPYVIDPRLVRGLDYYTGTVFEFVTDDLGAQ 274
Query: 94 GSVAGGGRYDNLVGMFDPKNKTTPCV--AAKLLHEVQGLLETSCRSCREDIGVERLFSII 151
G+V GGGRYD LV F TP V A IGVERL ++
Sbjct: 275 GTVCGGGRYDGLVEQFG--GPPTPAVGFA---------------------IGVERLLLLL 311
Query: 152 ENRNAEQGVKVKTTSTQVYVASAQKNLVEPRMQLCHEL 189
E E G VYV ++ ++L +L
Sbjct: 312 E----ELGE----EPVDVYVVPLGEDAELAALKLAEKL 341
>gnl|CDD|213530 TIGR00442, hisS, histidyl-tRNA synthetase. This model finds a
histidyl-tRNA synthetase in every completed genome.
Apparent second copies from Bacillus subtilis,
Synechocystis sp., and Aquifex aeolicus are slightly
shorter, more closely related to each other than to
other hisS proteins, and actually serve as regulatory
subunits for an enzyme of histidine biosynthesis. They
were excluded from the seed alignment and score much
lower than do single copy histidyl-tRNA synthetases of
other genomes not included in the seed alignment. These
putative second copies of HisS score below the trusted
cutoff. The regulatory protein kinase GCN2 of
Saccharomyces cerevisiae (YDR283c), and related proteins
from other species designated eIF-2 alpha kinase, have a
domain closely related to histidyl-tRNA synthetase that
may serve to detect and respond to uncharged tRNA(his),
an indicator of amino acid starvation; these regulatory
proteins are not orthologous and so score below the
noise cutoff [Protein synthesis, tRNA aminoacylation].
Length = 397
Score = 91.4 bits (228), Expect = 1e-19
Identities = 44/148 (29%), Positives = 59/148 (39%), Gaps = 29/148 (19%)
Query: 44 KEGLEAIKLLFHYCQIYGLKDTIVFDLSLARGLDYYTGVIYEAVLKD-QAVGSVAGGGRY 102
+E + L G+ V D SL RGLDYYTG ++E V A GS+ GGGRY
Sbjct: 225 EESRAHFEELKELLDALGIP--YVIDPSLVRGLDYYTGTVFEFVTDGLGAQGSICGGGRY 282
Query: 103 DNLVGMFDPKNKTTPCV-AAKLLHEVQGLLETSCRSCREDIGVERLFSIIENRNAEQGVK 161
D LV TP V A IG+ERL ++E +
Sbjct: 283 DGLVEELG--GPPTPAVGFA--------------------IGIERLLLLLEELGLLPPEE 320
Query: 162 VKTTSTQVYVASAQKNLVEPRMQLCHEL 189
+S VYV + ++L +L
Sbjct: 321 ---SSPDVYVVPLGEEAELEALKLAQKL 345
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 84.5 bits (209), Expect = 7e-17
Identities = 49/245 (20%), Positives = 93/245 (37%), Gaps = 32/245 (13%)
Query: 441 SQVQEDQVRNPMLSVVTFLESLVNKNE------DGRILVTKNPELSKSHIKYILLNPANH 494
SQ + D+ + + + L+ L+++ D + + LL P+
Sbjct: 336 SQNELDRPTSILERLKEELDRLLSRELLLSDDPDYSYWLEIEEREGVLLLVLPLLVPSKL 395
Query: 495 FTDIVQDARSIIVAGGTMEPVSEFKDQLFGSLGVPESRIHHFSCGHVIPKENILPLILCS 554
++ S+++ T+ P+ F L G LG+ E ++ S E L +
Sbjct: 396 LEELFSKVASVVLTSATLSPLDSF-SSLLGLLGLEE-KLRFLSLPSPFNYEEQGQLYV-- 451
Query: 555 GPTNRKFDLTFENRTKGDTLKEIAMTITNLCTIVPKGMVCFFPSYDYEAIVYNYMRDNHF 614
PT + + L ++A + + P G++ FPSY+Y V ++D
Sbjct: 452 -PT------DLPEPREPELLAKLAAYLREILKASPGGVLVLFPSYEYLKRVAERLKDERS 504
Query: 615 IERIARIAKKKVVFREPKKTSEVDKVLSDYGTSVEKGGALMLSVIGGKLSEGLNFSDDLG 674
V + + E +++L + S E + V GG EG++F D
Sbjct: 505 ---------TLPVLTQGE--DEREELLEKFKASGEGL----ILVGGGSFWEGVDFPGDAL 549
Query: 675 RCVVV 679
R VV+
Sbjct: 550 RLVVI 554
Score = 62.1 bits (151), Expect = 6e-10
Identities = 35/184 (19%), Positives = 68/184 (36%), Gaps = 17/184 (9%)
Query: 231 SQVQEDQVRNPMLSVVTFLESLVNKNE------DGRILVTKNPELSKSHIKYILLNPANH 284
SQ + D+ + + + L+ L+++ D + + LL P+
Sbjct: 336 SQNELDRPTSILERLKEELDRLLSRELLLSDDPDYSYWLEIEEREGVLLLVLPLLVPSKL 395
Query: 285 FTDIVQDARSIIVAGGTMEPVSEFKDQLFGSLGVPESRIHHFSCGHVIPKENILPLILCS 344
++ S+++ T+ P+ F L G LG+ E ++ S E L +
Sbjct: 396 LEELFSKVASVVLTSATLSPLDSF-SSLLGLLGLEE-KLRFLSLPSPFNYEEQGQLYV-- 451
Query: 345 GPTNRKFDLTFENRTKGDTLKEIAMTITNLCTIVPKGMVCFFPSYDYEAIVYNYMPDIEK 404
PT + + L ++A + + P G++ FPSY+Y V + D
Sbjct: 452 -PT------DLPEPREPELLAKLAAYLREILKASPGGVLVLFPSYEYLKRVAERLKDERS 504
Query: 405 TQEK 408
T
Sbjct: 505 TLPV 508
>gnl|CDD|214694 smart00491, HELICc2, helicase superfamily c-terminal domain.
Length = 142
Score = 75.8 bits (187), Expect = 3e-16
Identities = 28/75 (37%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 606 YNYMRDNH-FIERIARIAKKKVVFREPKKTSEVDKVLSDYGTSVEKGGALMLSVIGGKLS 664
Y Y+ + + + K VF E K + E +++L Y + E GAL+L+V GK+S
Sbjct: 1 YRYLEQVVEYWKENGILEINKPVFIEGKDSGETEELLEKYSAACEARGALLLAVARGKVS 60
Query: 665 EGLNFSDDLGRCVVV 679
EG++F DDLGR V++
Sbjct: 61 EGIDFPDDLGRAVII 75
>gnl|CDD|237097 PRK12420, PRK12420, histidyl-tRNA synthetase; Provisional.
Length = 423
Score = 80.5 bits (199), Expect = 5e-16
Identities = 39/117 (33%), Positives = 61/117 (52%), Gaps = 5/117 (4%)
Query: 4 EKNLSPEVADKIGEYVLKHGHVDLVENLLADEFLAKSKQAKEGLEAIKLLFHYCQIYGLK 63
E+ +S E+AD I VL + + + + F + EG+ ++ L Y G+
Sbjct: 204 ERGISEEMADTICNTVLSCLQLSIAD--FKEAF--NNPLVAEGVNELQQLQQYLIALGIN 259
Query: 64 DTIVFDLSLARGLDYYTGVIYEAVLKDQAV-GSVAGGGRYDNLVGMFDPKNKTTPCV 119
+ +F+ LARGL YTG +YE LKD ++ S+ GGRYDN++G F + P V
Sbjct: 260 ENCIFNPFLARGLTMYTGTVYEIFLKDGSITSSIGSGGRYDNIIGAFRGDDMNYPTV 316
>gnl|CDD|232978 TIGR00443, hisZ_biosyn_reg, ATP phosphoribosyltransferase,
regulatory subunit. Apparant second copies of
histidyl-tRNA synthetase, found in Bacillus subtilis,
Synechocystis sp., Aquifex aeolicus, and others, are in
fact a regulatory subunit of ATP
phosphoribosyltransferase, and usually encoded by a gene
adjacent to that encoding the catalytic subunit [Amino
acid biosynthesis, Histidine family].
Length = 313
Score = 76.5 bits (189), Expect = 4e-15
Identities = 37/108 (34%), Positives = 55/108 (50%), Gaps = 3/108 (2%)
Query: 2 VGEKNLSPEVADKIGEYVLKHGHVDLVENLLADEFLAKSKQAKEGLEAIKLLFHYCQIYG 61
V E LSPEV +++ G + V LA S+ A+ L+ ++ + + G
Sbjct: 188 VAELGLSPEVRERLLALPRLRGDGEEVLEEARA--LAGSETAEAALDELEAVLELLEARG 245
Query: 62 LKDTIVFDLSLARGLDYYTGVIYEAVLKDQAVGSVAGGGRYDNLVGMF 109
+++ I DL L RG YYTG+I+E +AGGGRYD L+G F
Sbjct: 246 VEEYISLDLGLVRGYHYYTGLIFEGYAPGLGA-PLAGGGRYDELLGRF 292
>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain. This domain
is the second of two tandem AAA domains found in a wide
variety of helicase enzymes.
Length = 165
Score = 73.0 bits (180), Expect = 4e-15
Identities = 22/99 (22%), Positives = 40/99 (40%), Gaps = 14/99 (14%)
Query: 581 ITNLCTIVPKGMVCFFPSYDYEAIVYNYMRDNHFIERIARIAKKKVVFREPKKTSEVDKV 640
I L +P G++ FPSY V + + K + + + +K+
Sbjct: 1 ILELLEAIPGGVLVLFPSYSLLEQVAELLASEL-------LEKGIELLVQGEG--SREKL 51
Query: 641 LSDYGTSVEKGGALMLSVIGGKLSEGLNFSDDLGRCVVV 679
L + + GA++ V G EG++F D R V++
Sbjct: 52 LERF---KKGKGAILFGV--GSFWEGIDFPGDALRLVII 85
Score = 36.4 bits (85), Expect = 0.020
Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 8/68 (11%)
Query: 371 ITNLCTIVPKGMVCFFPSYDYEAIVYNYMPDIEKTQEKPKLSGLQSFLKGVQENNPNLS- 429
I L +P G++ FPSY V + + G++ ++G L
Sbjct: 1 ILELLEAIPGGVLVLFPSYSLLEQVAELL------ASELLEKGIELLVQGEGSREKLLER 54
Query: 430 -KPSEGGI 436
K +G I
Sbjct: 55 FKKGKGAI 62
>gnl|CDD|237043 PRK12292, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 391
Score = 76.8 bits (190), Expect = 6e-15
Identities = 29/74 (39%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 37 LAKSKQAKEGLEAIKLLFHYCQIYGLKDTIVFDLSLARGLDYYTGVIYEAVLKDQAVG-S 95
L S K L+ ++ L + YG + DL L R LDYYTG+++E + VG
Sbjct: 229 LLPSLPIKRALDELEALAEALEKYGYGIPLSLDLGLLRHLDYYTGIVFEGYV--DGVGNP 286
Query: 96 VAGGGRYDNLVGMF 109
+A GGRYD+L+G F
Sbjct: 287 IASGGRYDDLLGRF 300
>gnl|CDD|178145 PLN02530, PLN02530, histidine-tRNA ligase.
Length = 487
Score = 74.4 bits (183), Expect = 7e-14
Identities = 45/133 (33%), Positives = 68/133 (51%), Gaps = 20/133 (15%)
Query: 7 LSPEVADKIGEYVLKHGHVDLVENLLADEFLAKSKQAKEGLEAIKLLFHYCQIYGLKDTI 66
+S E + I + VL +D +E LL E + +K LF + YG +D +
Sbjct: 275 VSEEAIEGILD-VLSLKSLDDLEALLG--------ADSEAVADLKQLFSLAEAYGYQDWL 325
Query: 67 VFDLSLARGLDYYTGVIYEAVLKDQAVGSVAGGGRYDNLVGMFDPKNKTTP--------C 118
VFD S+ RGL YYTG+++E + + ++ GGGRYD L+ F ++ TP
Sbjct: 326 VFDASVVRGLAYYTGIVFEGFDRAGKLRAICGGGRYDRLLSTFGGED--TPACGFGFGDA 383
Query: 119 VAAKLLHEVQGLL 131
V +LL E +GLL
Sbjct: 384 VIVELLKE-KGLL 395
>gnl|CDD|222097 pfam13393, tRNA-synt_His, Histidyl-tRNA synthetase. This is a
family of class II aminoacyl-tRNA synthetase-like and
ATP phosphoribosyltransferase regulatory subunits.
Length = 308
Score = 71.8 bits (177), Expect = 1e-13
Identities = 33/109 (30%), Positives = 55/109 (50%), Gaps = 4/109 (3%)
Query: 1 MVGEKNLSPEVADKIGEYVLKHGHVDLVENLLADEFLAKSKQAKEGLEAIKLLFHYCQIY 60
++ E L P +AD + +G ++++ L E L S A L+ ++ L +
Sbjct: 188 LLAELGLDPALADALLALPELYGDPEVLDEAL--ELLPGSPAAAA-LDELEALAALLEAL 244
Query: 61 GLKDTIVFDLSLARGLDYYTGVIYEAVLKDQAVGSVAGGGRYDNLVGMF 109
G + DL+ RG +YYTG+++ A A ++A GGRYDNL +F
Sbjct: 245 GPGVRLTLDLAELRGYEYYTGLVFAAYA-PGAGQALARGGRYDNLGEVF 292
>gnl|CDD|183413 PRK12295, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 373
Score = 54.6 bits (132), Expect = 8e-08
Identities = 18/42 (42%), Positives = 23/42 (54%)
Query: 64 DTIVFDLSLARGLDYYTGVIYEAVLKDQAVGSVAGGGRYDNL 105
+ + F S R LDYYTG ++E +AGGGRYD L
Sbjct: 304 ERLRFSASFGRPLDYYTGFVFEIRAAGNGDPPLAGGGRYDGL 345
>gnl|CDD|226228 COG3705, HisZ, ATP phosphoribosyltransferase involved in histidine
biosynthesis [Amino acid transport and metabolism].
Length = 390
Score = 51.2 bits (123), Expect = 1e-06
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 61 GLKDTIVFDLSLARGLDYYTGVIYEAVLKDQAVGSVAGGGRYDNLVGMFDP 111
L + I DL R DYYTG+++ A ++A GGRYD L+G+F
Sbjct: 251 RLIEKIALDLGRLRHFDYYTGLVFLAYADGLG-DALASGGRYDGLLGLFGR 300
Score = 34.7 bits (80), Expect = 0.14
Identities = 17/47 (36%), Positives = 22/47 (46%), Gaps = 4/47 (8%)
Query: 63 KDTIVFDLSLARGLDYYTGVIYEAVLKDQAVGSVAGGGRYDNLVGMF 109
+ + R LDYYTG +EA +AGGGRYD L+
Sbjct: 321 LEERRYAALFGRELDYYTGAAFEAAQA----LRLAGGGRYDRLLTGL 363
>gnl|CDD|164576 CHL00201, syh, histidine-tRNA synthetase; Provisional.
Length = 430
Score = 44.1 bits (104), Expect = 2e-04
Identities = 30/119 (25%), Positives = 45/119 (37%), Gaps = 33/119 (27%)
Query: 72 LARGLDYYTGVIYE-AVLKDQAVGSVAGGGRYDNLVGMFDPKNKTTPCVAAKLLHEVQGL 130
L RGLDYY +E L ++ GGGRYD+L+ TP V
Sbjct: 256 LVRGLDYYNDTAFEIKTLSSNGQDTICGGGRYDSLIHQLG--GPKTPAVGCA-------- 305
Query: 131 LETSCRSCREDIGVERLFSIIENR-----------NAEQGVKVKTTSTQVYVASAQKNL 178
IG+ERL I ++ A QG+K + ++ ++N+
Sbjct: 306 -----------IGLERLLLIAKDNIILPKQSIDVYIATQGLKAQKKGWEIIQFLEKQNI 353
>gnl|CDD|237098 PRK12421, PRK12421, ATP phosphoribosyltransferase regulatory
subunit; Provisional.
Length = 392
Score = 33.0 bits (76), Expect = 0.47
Identities = 14/36 (38%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 68 FDLSLARGLDYYTGVIYEAVLKDQAVGSVAGGGRYD 103
DL+ RG Y+TG+++ A + + ++A GGRYD
Sbjct: 267 IDLAELRGYHYHTGLVFAAYIPGRG-QALARGGRYD 301
>gnl|CDD|215216 PLN02385, PLN02385, hydrolase; alpha/beta fold family protein.
Length = 349
Score = 32.0 bits (73), Expect = 1.1
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 381 GMVCFFPSYDYEAIVYNYMPDIEKTQEKPKLSGLQSFLKG 420
G+ + PS+D +V + + K + P+ GL SFL G
Sbjct: 131 GLHGYIPSFD--DLVDDVIEHYSKIKGNPEFRGLPSFLFG 168
>gnl|CDD|148689 pfam07230, Phage_T4_Gp20, Bacteriophage T4-like capsid assembly
protein (Gp20). This family consists of several
bacteriophage T4-like capsid assembly (or portal)
proteins. The exact mechanism by which the
double-stranded (ds) DNA bacteriophages incorporate the
portal protein at a unique vertex of the icosahedral
capsid is unknown. In phage T4, there is evidence that
this vertex, constituted by 12 subunits of gp20, acts as
an initiator for the assembly of the major capsid
protein and the scaffolding proteins into a prolate
icosahedron of precise dimensions. The regulation of
portal protein gene expression is an important regulator
of prohead assembly in bacteriophage T4.
Length = 500
Score = 30.0 bits (68), Expect = 5.0
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 300 GTMEPVSEFKDQLFGSLGVPESRI 323
G M+ V F +L+ +L +P SR+
Sbjct: 350 GEMDDVRYFNKKLYEALRIPLSRL 373
Score = 30.0 bits (68), Expect = 5.0
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 510 GTMEPVSEFKDQLFGSLGVPESRI 533
G M+ V F +L+ +L +P SR+
Sbjct: 350 GEMDDVRYFNKKLYEALRIPLSRL 373
>gnl|CDD|198394 cd10447, GIY-YIG_unchar_2, GIY-YIG domain of uncharacterized
hypothetical protein found in bacteria and archaea. The
family includes a group of uncharacterized hypothetical
proteins, mainly found in bacteria and a few found in
archaea, with a GIY-YIG domain that shows statistically
significant similarity to the N-terminal catalytic
domains of GIY-YIG family of intron-encoded homing
endonuclease I-TevI and catalytic GIY-YIG domain of
nucleotide excision repair endonuclease UvrC.
Length = 80
Score = 27.6 bits (62), Expect = 5.0
Identities = 10/41 (24%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 261 ILVTKNPELSKSHIKYILLNPANHFTDIVQDARSIIVAGGT 301
+ V+K+ L+K+HIKY+ + + ++A + G
Sbjct: 44 VFVSKDNNLTKAHIKYL----ESRLIQLAKEAGRYKLDNGN 80
Score = 27.6 bits (62), Expect = 5.0
Identities = 10/41 (24%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 471 ILVTKNPELSKSHIKYILLNPANHFTDIVQDARSIIVAGGT 511
+ V+K+ L+K+HIKY+ + + ++A + G
Sbjct: 44 VFVSKDNNLTKAHIKYL----ESRLIQLAKEAGRYKLDNGN 80
>gnl|CDD|236156 PRK08125, PRK08125, bifunctional UDP-glucuronic acid
decarboxylase/UDP-4-amino-4-deoxy-L-arabinose
formyltransferase; Validated.
Length = 660
Score = 30.0 bits (68), Expect = 5.3
Identities = 11/20 (55%), Positives = 14/20 (70%), Gaps = 2/20 (10%)
Query: 138 CREDI--GVERLFSIIENRN 155
C DI G+E LF IIEN++
Sbjct: 536 CFTDIRDGIEALFRIIENKD 555
>gnl|CDD|238436 cd00859, HisRS_anticodon, HisRS Histidyl-anticodon binding domain.
HisRS belongs to class II aminoacyl-tRNA synthetases
(aaRS). This alignment contains the anticodon binding
domain, which is responsible for specificity in
tRNA-binding, so that the activated amino acid is
transferred to a ribose 3' OH group of the appropriate
tRNA only.
Length = 91
Score = 27.5 bits (62), Expect = 7.5
Identities = 5/25 (20%), Positives = 10/25 (40%)
Query: 166 STQVYVASAQKNLVEPRMQLCHELW 190
VYV + + ++L +L
Sbjct: 1 EVDVYVVPLGEGALSEALELAEQLR 25
>gnl|CDD|238825 cd01647, RT_LTR, RT_LTR: Reverse transcriptases (RTs) from
retrotransposons and retroviruses which have long
terminal repeats (LTRs) in their DNA copies but not in
their RNA template. RT catalyzes DNA replication from an
RNA template, and is responsible for the replication of
retroelements. An RT gene is usually indicative of a
mobile element such as a retrotransposon or retrovirus.
RTs are present in a variety of mobile elements,
including retrotransposons, retroviruses, group II
introns, bacterial msDNAs, hepadnaviruses, and
Caulimoviruses.
Length = 177
Score = 28.7 bits (65), Expect = 7.6
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 17 EYVLKHGHVDLVENLLADEFLAKSKQAKEGLEAIKLLFHYCQIYGLK 63
+L D VE L D+ L SK +E LE ++ + + GLK
Sbjct: 112 NKILGDLLGDFVEVYL-DDILVYSKTEEEHLEHLREVLERLREAGLK 157
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
0.317 0.136 0.394
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 35,003,985
Number of extensions: 3473086
Number of successful extensions: 2841
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2815
Number of HSP's successfully gapped: 36
Length of query: 690
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 586
Effective length of database: 6,324,786
Effective search space: 3706324596
Effective search space used: 3706324596
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: 62 (27.6 bits)