RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy953
(164 letters)
>gnl|CDD|240411 PTZ00419, PTZ00419, valyl-tRNA synthetase-like protein;
Provisional.
Length = 995
Score = 193 bits (493), Expect = 8e-58
Identities = 72/127 (56%), Positives = 89/127 (70%)
Query: 1 AVKISPGHDHNDYEVAQRLNLPLITVFNEEGVIIGDYGEFTGMKRFDARTRVTEVLTEKG 60
AVKI+P HD NDYE+A+R NLP I +F +G I + GEF GM RFD R ++ E L E G
Sbjct: 315 AVKITPAHDPNDYEIAKRHNLPFINIFTLDGKINENGGEFAGMHRFDCRRKIEEELKEMG 374
Query: 61 LYRGTVSHAMVVPLCSRSKDVVEPLLKPQWYVRTGEMAEKAVQAVKTGELKIIPDHHTKT 120
L R V + M +P CSRS D+VEP+L PQWYV +MA++AV+AV+ GELKIIP H
Sbjct: 375 LLRDKVPNPMRLPRCSRSGDIVEPMLIPQWYVNCKDMAKRAVEAVRNGELKIIPSSHENV 434
Query: 121 WYQWLEN 127
WY WLEN
Sbjct: 435 WYHWLEN 441
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 171 bits (436), Expect = 3e-50
Identities = 54/127 (42%), Positives = 80/127 (62%)
Query: 1 AVKISPGHDHNDYEVAQRLNLPLITVFNEEGVIIGDYGEFTGMKRFDARTRVTEVLTEKG 60
AVKI+P HD ND+EV +R NLP+I + +E+G I + GE+ G+ RF+AR + L E G
Sbjct: 271 AVKITPAHDPNDFEVGKRHNLPMINIMDEDGTINENPGEYQGLDRFEARKAIVADLEELG 330
Query: 61 LYRGTVSHAMVVPLCSRSKDVVEPLLKPQWYVRTGEMAEKAVQAVKTGELKIIPDHHTKT 120
L H V RS V+EP L QW+V+ +A+ A++AV+ GE+K +P+ KT
Sbjct: 331 LLVKIEPHTHSVGHSDRSGVVIEPYLSDQWFVKMKPLAKPALEAVENGEIKFVPERWEKT 390
Query: 121 WYQWLEN 127
++ W+EN
Sbjct: 391 YFHWMEN 397
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 163 bits (416), Expect = 2e-47
Identities = 60/130 (46%), Positives = 84/130 (64%), Gaps = 1/130 (0%)
Query: 1 AVKISPGHDHNDYEVAQRLNLPLITVFNEEGVIIGDY-GEFTGMKRFDARTRVTEVLTEK 59
AVKI+P HD NDYEV +R NLPLI + +E+G I + GEF G+ RF+AR ++ E L E+
Sbjct: 268 AVKITPAHDFNDYEVGKRHNLPLINIIDEDGRINEEAAGEFAGLDRFEARKKIVEDLEEQ 327
Query: 60 GLYRGTVSHAMVVPLCSRSKDVVEPLLKPQWYVRTGEMAEKAVQAVKTGELKIIPDHHTK 119
GL H V C R +EPLL QW+V+ E+A+KA++AVK G++K +P+ K
Sbjct: 328 GLLVKIEPHKHSVGHCERCGTPIEPLLSKQWFVKVLELAKKALEAVKDGKIKFVPERMEK 387
Query: 120 TWYQWLENNR 129
+ W+EN R
Sbjct: 388 RYEDWMENIR 397
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 148 bits (375), Expect = 5e-42
Identities = 66/134 (49%), Positives = 88/134 (65%), Gaps = 4/134 (2%)
Query: 1 AVKISPGHDHNDYEVAQRLNLPLITVFNEEGVIIGDYG-EFTGMKRFDARTRVTEVLTEK 59
AVKI+P HD ND+EV +R NL I +F ++G I + G EF GM RF AR V E L +K
Sbjct: 381 AVKITPAHDPNDFEVGKRHNLEFINIFTDDGKINSNGGSEFAGMPRFAAREAVIEALQKK 440
Query: 60 GLYRGTVSHAMVVPLCSRSKDVVEPLLKPQWYVRTGEMAEKAVQAVKTGE---LKIIPDH 116
GLYRG ++ M + LCSR+ DVVEP++KPQW+V MA++A+ A GE L+ IP
Sbjct: 441 GLYRGAKNNEMRLGLCSRTNDVVEPMIKPQWFVNCSSMAKQALDAAIDGENKKLEFIPKQ 500
Query: 117 HTKTWYQWLENNRE 130
+ W +WLEN R+
Sbjct: 501 YLAEWKRWLENIRD 514
>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 = 137 bits (346), Expect = 5e-38
Identities = 53/127 (41%), Positives = 80/127 (62%)
Query: 1 AVKISPGHDHNDYEVAQRLNLPLITVFNEEGVIIGDYGEFTGMKRFDARTRVTEVLTEKG 60
AVK++P HD NDYE +R NL I + +E+G++ + G++ G+ RF+AR ++ E L E+G
Sbjct: 269 AVKVTPAHDFNDYEWGKRHNLEFINILDEDGLLNENAGKYQGLTRFEARKKIVEDLKEEG 328
Query: 61 LYRGTVSHAMVVPLCSRSKDVVEPLLKPQWYVRTGEMAEKAVQAVKTGELKIIPDHHTKT 120
L H V C RS VVEPLL QW+V+ ++A+KA++A + GE+K +P K
Sbjct: 329 LLVKIEPHTHNVGTCWRSGTVVEPLLSKQWFVKVEKLADKALEAAEEGEIKFVPKRMEKR 388
Query: 121 WYQWLEN 127
+ WL N
Sbjct: 389 YLNWLRN 395
>gnl|CDD|215739 pfam00133, tRNA-synt_1, tRNA synthetases class I (I, L, M and V).
Other tRNA synthetase sub-families are too dissimilar to
be included.
Length = 606
Score = 132 bits (335), Expect = 7e-37
Identities = 49/130 (37%), Positives = 73/130 (56%), Gaps = 2/130 (1%)
Query: 1 AVKISPGHDHNDYEVAQRLNLPLITVFNEEGVIIGDYGEFTGMKRFDARTRVTEVLTEKG 60
AV I+P H +DYEV +R NL I +++G + EF G+KRF AR ++ E+LTEKG
Sbjct: 295 AVHIAPAHGEDDYEVGKRHNLEFINPVDDDGTYNEEAPEFQGLKRFKARKKIVELLTEKG 354
Query: 61 LYRGTVSHAMVVPLCSRSKDVVEPLLKPQWYVRTGEMAEKAVQAVKTGELKIIPDHHTKT 120
L P C RS + PQW+VR +AE A++AV+ +++ +P K
Sbjct: 355 LLLKIEPIEHSYPHCWRSGTPIIYRATPQWFVRMKNLAEAALKAVE--KVQFVPKWGEKR 412
Query: 121 WYQWLENNRE 130
+ WLEN ++
Sbjct: 413 YGNWLENIQD 422
>gnl|CDD|237855 PRK14900, valS, valyl-tRNA synthetase; Provisional.
Length = 1052
Score = 125 bits (314), Expect = 8e-34
Identities = 53/127 (41%), Positives = 77/127 (60%)
Query: 1 AVKISPGHDHNDYEVAQRLNLPLITVFNEEGVIIGDYGEFTGMKRFDARTRVTEVLTEKG 60
AVK++P HD ND+EV +R L +ITV +G + + G G+ RF+AR V +L E+G
Sbjct: 286 AVKVTPAHDFNDFEVGKRHGLEMITVIGPDGRMTAEAGPLAGLDRFEARKEVKRLLAEQG 345
Query: 61 LYRGTVSHAMVVPLCSRSKDVVEPLLKPQWYVRTGEMAEKAVQAVKTGELKIIPDHHTKT 120
L RG H + + C RS ++EPLL QWYVR +A A++AV+ G + IP+ T T
Sbjct: 346 LDRGAKPHVLPLGRCQRSATILEPLLSDQWYVRIEPLARPAIEAVEQGRTRFIPEQWTNT 405
Query: 121 WYQWLEN 127
+ W+ N
Sbjct: 406 YMAWMRN 412
>gnl|CDD|215509 PLN02943, PLN02943, aminoacyl-tRNA ligase.
Length = 958
Score = 117 bits (294), Expect = 5e-31
Identities = 54/127 (42%), Positives = 78/127 (61%), Gaps = 4/127 (3%)
Query: 1 AVKISPGHDHNDYEVAQRLNLPLITVFNEEGVIIGDYGEFTGMKRFDARTRVTEVLTEKG 60
+KISPGHDHNDY +A++L LP++ V N++G + E G+ F+AR ++ L E G
Sbjct: 325 VLKISPGHDHNDYLLARKLGLPILNVMNKDGTL----NEVAGLYWFEAREKLWSDLEETG 380
Query: 61 LYRGTVSHAMVVPLCSRSKDVVEPLLKPQWYVRTGEMAEKAVQAVKTGELKIIPDHHTKT 120
L H + VP R +V+EPL+ QW+V +AEKA++AV+ GEL IIP+ K
Sbjct: 381 LAVKKEPHTLRVPRSQRGGEVIEPLVSKQWFVTMEPLAEKALKAVENGELTIIPERFEKI 440
Query: 121 WYQWLEN 127
+ WL N
Sbjct: 441 YNHWLSN 447
>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 = 90.8 bits (226), Expect = 3e-22
Identities = 39/87 (44%), Positives = 53/87 (60%), Gaps = 16/87 (18%)
Query: 56 LTEKGL-YRG------------TVSHAMVVPLCSRSKDVVEPLLKPQWYVRTGEMAEKAV 102
L EKGL YR +S V CSRS DV+EPLLKPQW+V+ ++A+KA+
Sbjct: 127 LYEKGLIYRDNRLVNWCPKLRTAISDIEV---CSRSGDVIEPLLKPQWFVKVKDLAKKAL 183
Query: 103 QAVKTGELKIIPDHHTKTWYQWLENNR 129
+AVK G++K +P+ K + WLEN R
Sbjct: 184 EAVKEGDIKFVPERMEKRYENWLENIR 210
>gnl|CDD|237306 PRK13208, valS, valyl-tRNA synthetase; Reviewed.
Length = 800
Score = 81.4 bits (202), Expect = 1e-18
Identities = 30/119 (25%), Positives = 53/119 (44%), Gaps = 2/119 (1%)
Query: 9 DHNDYEVAQRLNLPLITVFNEEGVIIGDYGEFTGMKRFDARTRVTEVLTEKGLYRGTVSH 68
D D + LNLP + +E+G + G+ G+ +AR ++ E L GL
Sbjct: 277 DKTDVTWWRELNLPTRIIIDEDGRMTEAAGKLAGLTIEEARKKIVEDLKSGGLLGKQEPI 336
Query: 69 AMVVPLCSRSKDVVEPLLKPQWYVRTGEMAEKAVQAVKTGELKIIPDHHTKTWYQWLEN 127
V C R +E L+ QW+++ ++ E+ ++ K E+ P+H W+E
Sbjct: 337 KHNVKFCERCDTPLEILVTRQWFIKVLDLKEELLERGK--EINWYPEHMRVRLENWIEG 393
>gnl|CDD|235681 PRK06039, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 975
Score = 70.5 bits (174), Expect = 8e-15
Identities = 33/135 (24%), Positives = 63/135 (46%), Gaps = 15/135 (11%)
Query: 2 VKISPGHDHNDYEVAQRLNLPLITVFNEEGVIIGDYGEFTGMKRFDARTRVTEVLTEKGL 61
V I+P +D+EV ++ LP++ +++G + ++ G DA + L E+GL
Sbjct: 318 VHIAPAFGEDDFEVGKKYGLPVVCPVDDDGRFTEEVPDYAGKFVKDADKEIIRDLKERGL 377
Query: 62 --YRGTVSHAMVVPLCSRSKDVVEPLL---KPQWYVRTGEMAEKAVQAVKTGELKIIPDH 116
T H+ P C R PL+ W++R ++ ++ ++ + + P+
Sbjct: 378 LFKAETYEHS--YPHCWRCD---TPLIYYATESWFIRVTKIKDRMLELNQK--INWYPE- 429
Query: 117 HTKT--WYQWLENNR 129
H K + +WLEN R
Sbjct: 430 HIKDGRFGKWLENAR 444
>gnl|CDD|223138 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 933
Score = 70.3 bits (173), Expect = 1e-14
Identities = 35/136 (25%), Positives = 65/136 (47%), Gaps = 13/136 (9%)
Query: 1 AVKISPGHDHNDYEVAQRLN-LPLITVFNEEGVIIGDYGEFTGMKRFDARTRVTEVLTEK 59
V +PGH DYEV ++ L ++ ++ G + ++ G+ DA ++ E L EK
Sbjct: 328 LVHTAPGHGEEDYEVGKKYGLLEVLNPVDDNGRYTEEAPKYEGLFVKDANKKIIEDLKEK 387
Query: 60 G--LYRGTVSHAMVVPLCSRSKDVVEPLL---KPQWYVRTGEMAEKAVQAVKTGELKIIP 114
G L + H+ P C R+K PL+ PQW+V ++ +K ++ + ++ +P
Sbjct: 388 GNLLKSEKIEHS--YPHCWRTKT---PLIYRATPQWFVSVDKLRDKMLKEIN--KVNWVP 440
Query: 115 DHHTKTWYQWLENNRE 130
D + +EN +
Sbjct: 441 DWGKNRFGNMVENRPD 456
>gnl|CDD|232953 TIGR00392, ileS, isoleucyl-tRNA synthetase. The isoleucyl tRNA
synthetase (IleS) is a class I amino acyl-tRNA ligase
and is particularly closely related to the valyl tRNA
synthetase. This model may recognize IleS from every
species, including eukaryotic cytosolic and
mitochondrial forms [Protein synthesis, tRNA
aminoacylation].
Length = 861
Score = 69.3 bits (170), Expect = 2e-14
Identities = 33/139 (23%), Positives = 66/139 (47%), Gaps = 13/139 (9%)
Query: 1 AVKISPGHDHNDYEVAQRLNLPLITVFNEEGVII-------GDYGEFTGMKRFDARTRVT 53
V +PGH DYE+ ++ L +++ +E+GV G + + A +
Sbjct: 328 IVHTAPGHGEEDYEIGKKYGLEVLSPVDEKGVYTEGVNDFQGRFVKDADKDIIKANKIII 387
Query: 54 EVLTEKG--LYRGTVSHAMVVPLCSRSKDVVEPLLKPQWYVRTGEMAEKAVQAVKTGELK 111
E L +KG L ++H+ P C R+K V QW+++T ++ ++ ++ +K ++
Sbjct: 388 EQLKDKGLLLKAEKITHSY--PHCWRTKTPVIYRATEQWFIKTKDIKDQMLEQIK--KVN 443
Query: 112 IIPDHHTKTWYQWLENNRE 130
+P+ + WLEN +
Sbjct: 444 WVPEWGEGRFGNWLENRPD 462
>gnl|CDD|235588 PRK05743, ileS, isoleucyl-tRNA synthetase; Reviewed.
Length = 912
Score = 56.3 bits (137), Expect = 7e-10
Identities = 36/116 (31%), Positives = 60/116 (51%), Gaps = 15/116 (12%)
Query: 1 AVKISPGHDHNDYEVAQRLNLPLITVFNEEGVIIGDYGEFTGMKRFDARTRVTEVLTEKG 60
V +PGH +DY V Q+ L ++ +++G + F G+ F A ++ E L EKG
Sbjct: 324 LVHTAPGHGEDDYVVGQKYGLEVLNPVDDDGRYTEEAPLFAGLFVFKANPKIIEKLEEKG 383
Query: 61 --LYRGTVSHAMVVPLCSRSKDVVEPLL---KPQWYV---RTG--EMAEKAVQAVK 106
L ++H+ P C R+K +P++ PQW++ + G E A KA++ VK
Sbjct: 384 ALLKEEKITHSY--PHCWRTK---KPVIFRATPQWFISMDKKGLREQALKAIEKVK 434
>gnl|CDD|234743 PRK00390, leuS, leucyl-tRNA synthetase; Validated.
Length = 805
Score = 50.5 bits (122), Expect = 7e-08
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 15/76 (19%)
Query: 6 PGHDHNDYEVAQRLNLPLITV--------------FNEEGVIIGDYGEFTGMKRFDARTR 51
P HD D+E A++ LP+ V + +GV+I + GE G+ +A+
Sbjct: 338 PAHDQRDFEFAKKYGLPIKPVIEPGDGDEDISEEAYTGDGVLI-NSGELDGLDSEEAKEA 396
Query: 52 VTEVLTEKGLYRGTVS 67
+ L EKGL + V+
Sbjct: 397 IIAWLEEKGLGKRKVN 412
>gnl|CDD|222257 pfam13603, tRNA-synt_1_2, Leucyl-tRNA synthetase, Domain 2. This
is a family of the conserved region of Leucine-tRNA
ligase or Leucyl-tRNA synthetase, EC:6.1.1.4.
Length = 178
Score = 44.8 bits (107), Expect = 3e-06
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 17/68 (25%)
Query: 6 PGHDHNDYEVAQRLNLPLITV----------------FNEEGVIIGDYGEFTGMKRFDAR 49
P HD D+E A++ NLP+ V + E+G++I + GEF G+ +A+
Sbjct: 112 PAHDQRDFEFAKKYNLPIKQVIKPEDGDEDDLIMEEAYTEKGILI-NSGEFDGLDSEEAK 170
Query: 50 TRVTEVLT 57
+ E L
Sbjct: 171 EAIAEKLE 178
>gnl|CDD|232956 TIGR00396, leuS_bact, leucyl-tRNA synthetase, eubacterial and
mitochondrial family. The leucyl-tRNA synthetases
belong to two families so broadly different that they
are represented by separate models. This model includes
both eubacterial and mitochondrial leucyl-tRNA
synthetases. It generates higher scores for some
valyl-tRNA synthetases than for any archaeal or
eukaryotic cytosolic leucyl-tRNA synthetase. Note that
the enzyme from Aquifex aeolicus is split into alpha and
beta chains; neither chain is long enough to score above
the trusted cutoff, but the alpha chain scores well
above the noise cutoff. The beta chain must be found by
a model and search designed for partial length matches
[Protein synthesis, tRNA aminoacylation].
Length = 842
Score = 44.4 bits (105), Expect = 1e-05
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 14/79 (17%)
Query: 1 AVKISPGHDHNDYEVAQRLNLPLITV-------------FNEEGVIIGDYGEFTGMKRFD 47
AV P HD D+E AQ+ LP+ V + E+GV++ + GEF G+ +
Sbjct: 331 AVMGVPAHDERDFEFAQKYGLPIKPVIDPAEKDLSLTAAYTEDGVLV-NSGEFNGLNSSE 389
Query: 48 ARTRVTEVLTEKGLYRGTV 66
AR + ++L ++G + V
Sbjct: 390 ARNAIIDMLEKEGKGKRKV 408
>gnl|CDD|178177 PLN02563, PLN02563, aminoacyl-tRNA ligase.
Length = 963
Score = 37.5 bits (87), Expect = 0.002
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 17/77 (22%)
Query: 1 AVKISPGHDHNDYEVAQRLNLPLITV--------------FNEEGVIIG---DYGEFTGM 43
A+ P HD D+E AQ+ +LP+ V + EGVI+ + G+
Sbjct: 418 AIMAVPAHDTRDFEFAQKFDLPIKWVVKPADGNEDDAEKAYTGEGVIVNSSSSGLDINGL 477
Query: 44 KRFDARTRVTEVLTEKG 60
+A +V E L E G
Sbjct: 478 SSKEAAKKVIEWLEETG 494
>gnl|CDD|237049 PRK12300, leuS, leucyl-tRNA synthetase; Reviewed.
Length = 897
Score = 35.6 bits (83), Expect = 0.007
Identities = 26/90 (28%), Positives = 48/90 (53%), Gaps = 8/90 (8%)
Query: 31 GVIIGDYGEFTGMKRFDARTRVTEVLTEKGLYRGTVSHAMVVPLCSR--SKDVVEPLLKP 88
GV+ + GE+ G +AR ++T+ L EKG+ + P+ R ++ VV+ ++K
Sbjct: 340 GVLKENTGEYAGKPVREAREKITKDLIEKGIA-DIMYEFSNRPVYCRCGTECVVK-VVKD 397
Query: 89 QWYVRTG--EMAEKAVQAVKTGELKIIPDH 116
QW++ E E A +A+ ++IIP+
Sbjct: 398 QWFIDYSDPEWKELAHKALD--NMEIIPEE 425
>gnl|CDD|237514 PRK13804, ileS, isoleucyl-tRNA synthetase; Provisional.
Length = 961
Score = 34.9 bits (81), Expect = 0.013
Identities = 33/126 (26%), Positives = 49/126 (38%), Gaps = 26/126 (20%)
Query: 2 VKISPGHDHNDYEV--AQRLNLPLITV-----FNEE--GVIIGDYGEFTGMKRFDARTRV 52
V +PGH D+ V +TV + E G + G K DA V
Sbjct: 347 VHTAPGHGREDFNVWMKYGRTEIPVTVDEDGFYTENAPGFGGARVIDDEGKKYGDANKAV 406
Query: 53 TEVLTEKG--LYRGTVSHAMVVPLCSRSKDVVEPLL---KPQWYVRT-------GEMAEK 100
E L E G L RG + H+ P RSK +P++ PQW++ + +
Sbjct: 407 IEKLIEAGLLLARGRLKHS--YPHSWRSK---KPVIFRNTPQWFISMDKDLGDGTTLRSR 461
Query: 101 AVQAVK 106
A+ A+
Sbjct: 462 ALDAID 467
>gnl|CDD|215452 PLN02843, PLN02843, isoleucyl-tRNA synthetase.
Length = 974
Score = 33.2 bits (76), Expect = 0.055
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 2 VKISPGHDHNDYEVAQRLNLPLITVFNEEGVIIGDYGEFTGMKRF-DARTRVTEVLTEKG 60
V +PGH DY + LPL++ ++ G + G+F+G+ + V E L E G
Sbjct: 341 VHTAPGHGQEDYITGLKYGLPLLSPVDDAGKFTEEAGQFSGLSVLGEGNAAVVEALDEAG 400
>gnl|CDD|223569 COG0495, LeuS, Leucyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 814
Score = 31.9 bits (73), Expect = 0.15
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 12/67 (17%)
Query: 6 PGHDHNDYEVAQRLNLPLITV-----------FNEEGVIIGDYGEFTGMKRFDARTRVTE 54
P HD D E A + LP+ V + EGV+I + G G+ +A+ ++
Sbjct: 345 PAHDERDLEFATKYKLPIKKVIMPEGTVGKKVYEGEGVLI-NSGGLDGLDYEEAKVKIRC 403
Query: 55 VLTEKGL 61
L ++GL
Sbjct: 404 GLVKRGL 410
>gnl|CDD|232955 TIGR00395, leuS_arch, leucyl-tRNA synthetase, archaeal and
cytosolic family. The leucyl-tRNA synthetases belong to
two families so broadly different that they are
represented by separate models. This model includes both
archaeal and cytosolic eukaryotic leucyl-tRNA
synthetases; the eubacterial and mitochondrial forms
differ so substantially that some other tRNA ligases
score higher by this model than does any eubacterial
LeuS [Protein synthesis, tRNA aminoacylation].
Length = 938
Score = 31.7 bits (72), Expect = 0.19
Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 2/86 (2%)
Query: 31 GVIIGDYGEFTGMKRFDARTRVTEVLTEKGLYRGTVSHAMVVPLCSRSKDVVEPLLKPQW 90
GV+I + + GMK +A+ +V L + GL + +C D + +++ QW
Sbjct: 387 GVMIYNIPPYKGMKVSEAKEKVKADLIDAGLADVMYEFSESPVICRCGTDCIVKVVEDQW 446
Query: 91 YVRTGEMAEKAVQAVKTGE-LKIIPD 115
+V+ + + K A + E ++IIP+
Sbjct: 447 FVKYSDESWKE-LAHECLEGMRIIPE 471
>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 = 30.3 bits (69), Expect = 0.39
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 19/79 (24%)
Query: 56 LTEKGL-YRGTVSHAMVVPLCSRSKDVVEPLL---KPQWYVRTGEMAEKAVQAVKTGELK 111
L EKGL YRG VVP PL+ PQW++R ++ ++ ++A ++
Sbjct: 128 LHEKGLLYRGY----KVVPW---------PLIYRATPQWFIRVTKIKDRLLEAND--KVN 172
Query: 112 IIPDHHTKTWYQWLENNRE 130
IP+ + WLEN R+
Sbjct: 173 WIPEWVKNRFGNWLENRRD 191
>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 = 30.5 bits (69), Expect = 0.40
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 88 PQWYVRTGEMAEKAVQAVKTGELKIIPDHHTKTWYQWLEN 127
QW+ + EK ++A++ KI+P+H WLE+
Sbjct: 140 EQWFFDMPKFKEKLLKALR--RGKIVPEHVKNRMEAWLES 177
>gnl|CDD|203437 pfam06405, RCC_reductase, Red chlorophyll catabolite reductase (RCC
reductase). This family consists of several red
chlorophyll catabolite reductase (RCC reductase)
proteins. Red chlorophyll catabolite (RCC) reductase
(RCCR) and pheophorbide (Pheide) a oxygenase (PaO)
catalyze the key reaction of chlorophyll catabolism,
porphyrin macrocycle cleavage of Pheide a to a primary
fluorescent catabolite (pFCC).
Length = 255
Score = 29.3 bits (66), Expect = 0.77
Identities = 13/46 (28%), Positives = 26/46 (56%), Gaps = 6/46 (13%)
Query: 114 PDHHTKTWYQ--WLENNREKKDRIGESQPFRERTLSVEDPRTLWSP 157
PD+ K +Y+ L+ R+ +++ E +P+ +L V R++ SP
Sbjct: 119 PDY-LKRYYEETQLDKQRQLLEKLPEVRPYFSSSLYV---RSVVSP 160
>gnl|CDD|234323 TIGR03710, OAFO_sf, 2-oxoacid:acceptor oxidoreductase, alpha
subunit. This family of proteins contains a C-terminal
thiamine diphosphate (TPP) binding domain typical of
flavodoxin/ferredoxin oxidoreductases (pfam01855) as
well as an N-terminal domain similar to the gamma
subunit of the same group of oxidoreductases
(pfam01558). The genes represented by this model are
always found in association with a neighboring gene for
a beta subunit (TIGR02177) which also occurs in a
4-subunit (alpha/beta/gamma/ferredoxin) version of the
system. This alpha/gamma plus beta structure was used to
define the set of sequences to include in this model.
This pair of genes is not consistantly observed in
proximity to any electron acceptor genes, but is found
next to putative ferredoxins or ferredoxin-domain
proteins in Azoarcus sp. EbN1, Bradyrhizobium japonicum
USDA 110, Frankia sp. CcI3, Rhodoferax ferrireducens DSM
15236, Rhodopseudomonas palustris BisB5, Os,
Sphingomonas wittichii RW1 and Streptomyces
clavuligerus. Other potential acceptors are also
sporadically observed in close proximity including
ferritin-like proteins, reberythrin, peroxiredoxin and a
variety of other flavin and iron-sulfur
cluster-containing proteins. The phylogenetic
distribution of this family encompasses archaea, a
number of deeply-branching bacterial clades and only a
small number of firmicutes and proteobacteria. The
enzyme from Sulfolobus has been characterized with
respect to its substrate specificity which is described
as wide, encompassing various 2-oxoacids such as
2-oxoglutarate, 2-oxobutyrate and pyruvate. The enzyme
from Hydrogenobacter thermophilus has been shown to have
a high specificity towards 2-oxoglutarate and is one of
the key enzymes in the reverse TCA cycle in this
organism. Furthermore, considering its binding of
coenzyme A, it can be reasonably inferred that the
product of the reaction is succinyl-CoA. The genes for
this enzyme in Prevotella intermedia 17, Persephonella
marina EX-H1 and Picrophilus torridus DSM 9790 are in
close proximity to a variety of TCA cycle genes.
Persephonella marina and P. torridus are believed to
encode complete TCA cycles, and none of these contains
the lipoate-based 2-oxoglutarate dehydrogenase
(E1/E2/E3) system. That system is presumed to be
replaced by this one. In fact, the lipoate system is
absent in most organisms possessing a member of this
family, providing additional circumstantial evidence
that many of these enzymes are capable of acting as
2-oxoglutarate dehydrogenases and.
Length = 562
Score = 29.4 bits (67), Expect = 0.78
Identities = 23/113 (20%), Positives = 45/113 (39%), Gaps = 9/113 (7%)
Query: 29 EEGVIIGDYGEFTGMKRFDAR------TRVTEVLTEKGLYRGTVSHAMVVPLCSRSKDVV 82
G+II D F AR T + + + + V+ + L + +
Sbjct: 85 PGGIIIYDSDLFDEEDLEKARVIPVPLTEIAKEAKGRKRMKNMVALGALAALLGLDLEPL 144
Query: 83 EPLLKPQWYVRTGEMAEKAVQAVKTGELKIIPDHHTKTWYQWLENNREKKDRI 135
E +++ + + + E+AE ++A++ G + KT Y L + DRI
Sbjct: 145 EEVIREK-FGKKPEIAEANLKALRAG-YDYAEETE-KTDYLVLPAPPKDGDRI 194
>gnl|CDD|215318 PLN02581, PLN02581, red chlorophyll catabolite reductase.
Length = 267
Score = 28.9 bits (65), Expect = 1.1
Identities = 15/46 (32%), Positives = 29/46 (63%), Gaps = 6/46 (13%)
Query: 114 PDHHTKTWYQ--WLENNREKKDRIGESQPFRERTLSVEDPRTLWSP 157
PD+ KT+Y+ L+ +R+K +++ + QP+ +L V R++ SP
Sbjct: 129 PDY-LKTYYEDTQLDAHRQKLEKLPQVQPYVSPSLYV---RSVVSP 170
>gnl|CDD|185281 PRK15383, PRK15383, type III secretion system protein; Provisional.
Length = 335
Score = 28.8 bits (64), Expect = 1.2
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 4/32 (12%)
Query: 109 ELKIIP-DHHTKTWYQWLENNREKKDRIGESQ 139
+ ++P DHHT +QW E N DR G+++
Sbjct: 36 DYPLLPLDHHTPLVFQWFERN---PDRFGQNE 64
>gnl|CDD|239198 cd02799, tRNA_bind_EMAP-II_like, tRNA-binding-domain-containing
EMAP2-like proteins. This family contains a diverse
fraction of tRNA binding proteins, including
Caenorhabditis elegans methionyl-tRNA synthetase
(CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS),
Saccharomyces cerevisiae Arc1p, human p43 and EMAP2.
CeMetRS and hTyrRS aminoacylate their cognate tRNAs.
Arc1p is a transactivator of yeast methionyl-tRNA and
glutamyl-tRNA synthetases. This domain has general
tRNA binding properties. In a subset of this family
this domain has the added capability of a cytokine. For
example the p43 component of the Human aminoacyl-tRNA
synthetase complex is cleaved to release EMAP-II
cytokine. EMAP-II has multiple activities during
apoptosis, angiogenesis and inflammation and
participates in malignant transformation. A
EMAP-II-like cytokine also is released from hTyrRS upon
cleavage. The active cytokine heptapeptide locates to
this domain.
Length = 105
Score = 26.8 bits (60), Expect = 2.6
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 63 RGTVSHAMVVPLCSRSKD--VVEPLLKP 88
RG S MV LC+ + D VE L P
Sbjct: 70 RGVKSQGMV--LCASNADHEKVELLEPP 95
>gnl|CDD|233435 TIGR01488, HAD-SF-IB, Haloacid Dehalogenase superfamily, subfamily
IB, phosphoserine phosphatase-like. This model
represents a subfamily of the Haloacid Dehalogenase
superfamily of aspartate-nucleophile hydrolases.
Subfamily IA, B, C and D are distinguished from the rest
of the superfamily by the presence of a variable domain
between the first and second conserved catalytic motifs.
In subfamilies IA and IB, this domain consists of an
alpha-helical bundle. It was necessary to model these
two subfamilies separately, breaking them at a an
apparent phylogenetic bifurcation, so that the resulting
model(s) are not so broadly defined that members of
subfamily III (which lack the variable domain) are
included. Subfamily IA includes the enzyme phosphoserine
phosphatase (TIGR00338) as well as three hypothetical
equivalogs. Many members of these hypothetical
equivalogs have been annotated as PSPase-like or
PSPase-family proteins. In particular, the hypothetical
equivalog which appears to be most closely related to
PSPase contains only Archaea (while TIGR00338 contains
only eukaryotes and bacteria) of which some are
annotated as PSPases. Although this is a reasonable
conjecture, none of these sequences has sufficient
evidence for this assignment. If such should be found,
this model should be retired while the PSPase model
should be broadened to include these sequences [Unknown
function, Enzymes of unknown specificity].
Length = 177
Score = 26.9 bits (60), Expect = 4.6
Identities = 11/76 (14%), Positives = 26/76 (34%), Gaps = 12/76 (15%)
Query: 13 YEVAQRLNLPLI----TVFNEEGVIIGDYGEFTGMKRFDARTRVTEVLTEKGLYRGTVSH 68
VA++L + + F++ G++ G + + E+L E +
Sbjct: 104 EPVAEKLGIDDVFANRLEFDDNGLLTGPIEGQVNPEGECKGKVLKELLEESKITLK--KI 161
Query: 69 AMV------VPLCSRS 78
V +P+ +
Sbjct: 162 IAVGDSVNDLPMLKLA 177
>gnl|CDD|198427 cd10029, UDG_F3_SMUG, SMUG: single-strand-selective monofunctional
uracil-DNA glycosylase. SMUG (single-strand-selective
monofunctional uracil-DNA glycosylase) is classified as
Family 3 of Uracil-DNA glycosylase (UDG) enzymes. SMUG
is a DNA repair enzyme that catalyzes the removal of
mismatched uracil and its derivatives from DNA to
initiate DNA base excision repair pathway. Uracil in DNA
can arise as a result of mis-incorporation of dUMP
residues by DNA polymerase or deamination of cytosine.
Uracil mispaired with guanine in DNA is one of the major
pro-mutagenic events, causing G:C->A:T mutations. Thus,
DNA repair enzymes are essential for maintaining the
integrity of genetic information. A Family 3 UDG from
human was first characterized to remove Uracil from
ssDNA, hence the name hSMUG (single-strand-selective
monofunctional uracil-DNA glycosylase). However,
subsequent research has shown that hSMUG1 and its rat
ortholog can remove Uracil and its oxidized pyrimidine
derivatives from both, ssDNA and dsDNA. The SMUG
targeted mismatched uracil derivatives include
5-hydroxyuracil (hoU), 5-hydroxymethyluracil (hmU) and
5-formyluracil (fU). SMUGs are found in Eubacteria and
Eukarya.
Length = 233
Score = 26.9 bits (60), Expect = 4.9
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 79 KDVVEPLLKPQWYVRTGEMAEKAVQAVKTGELKI 112
+ VE LL+P+W V G AE+ +A + +L +
Sbjct: 171 RRTVE-LLQPEWVVGVGAFAEQRAKAALSAKLDV 203
>gnl|CDD|115203 pfam06531, DUF1108, Protein of unknown function (DUF1108). This
family consists of several bacterial proteins from
Staphylococcus aureus as well as a number of phage
proteins. The function of this family is unknown.
Length = 86
Score = 25.2 bits (55), Expect = 8.0
Identities = 9/36 (25%), Positives = 21/36 (58%)
Query: 100 KAVQAVKTGELKIIPDHHTKTWYQWLENNREKKDRI 135
K + + +L D ++ Y+W+ENN +++D++
Sbjct: 44 KGIHVIDENDLYTALDILNQSIYEWIENNTDEQDKL 79
>gnl|CDD|223377 COG0300, DltE, Short-chain dehydrogenases of various substrate
specificities [General function prediction only].
Length = 265
Score = 26.4 bits (59), Expect = 8.2
Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 85 LLKPQWYV-RTGEMAEKAVQAVKTGELKIIP 114
LL P V ++AE A++A++ G+ +IIP
Sbjct: 203 LLSPGELVLSPEDVAEAALKALEKGKREIIP 233
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 0.134 0.404
Gapped
Lambda K H
0.267 0.0849 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,383,153
Number of extensions: 743155
Number of successful extensions: 814
Number of sequences better than 10.0: 1
Number of HSP's gapped: 798
Number of HSP's successfully gapped: 44
Length of query: 164
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 74
Effective length of database: 6,945,742
Effective search space: 513984908
Effective search space used: 513984908
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: 55 (24.7 bits)