RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6338
(135 letters)
>gnl|CDD|215487 PLN02900, PLN02900, alanyl-tRNA synthetase.
Length = 936
Score = 162 bits (412), Expect = 2e-47
Identities = 67/127 (52%), Positives = 78/127 (61%), Gaps = 5/127 (3%)
Query: 1 MLGNWSFNDYYKRDACRMALEFLTKPPVSLPLDRLYFTYFGGSDQYGLPCDEETLDIWLE 60
MLGNWSF DY+K++A A E LTK LP DRLY TYFGG + D+E IWL+
Sbjct: 106 MLGNWSFGDYFKKEAIGWAWELLTKV-YGLPADRLYATYFGGDE--KQAPDDEARAIWLD 162
Query: 61 LGVPRDHIKKEGMKCNFWEMGSTGPCGYSSEIHYDMKGEPSSALARVNADRNDLIEIWNI 120
+P + + G K NFWEMG TGPCG SEIHYD GE +A VN D IEIWN+
Sbjct: 163 Y-LPEERVLPFGCKDNFWEMGDTGPCGPCSEIHYDRIGERDAADL-VNNDDPRFIEIWNL 220
Query: 121 VFISHKR 127
VFI R
Sbjct: 221 VFIQFNR 227
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 152 bits (387), Expect = 6e-44
Identities = 59/130 (45%), Positives = 72/130 (55%), Gaps = 21/130 (16%)
Query: 1 MLGNWSFNDYYKRDACRMALEFLTKPPV-SLPLDRLYFTYFGGSDQYGLPCDEETLDIWL 59
MLGN+SF DY+K +A A E LT V LP ++LY T + D+E DIW
Sbjct: 88 MLGNFSFGDYFKEEAIEWAWELLTS--VLGLPKEKLYVTVY--------EDDDEAYDIWK 137
Query: 60 -ELGVPRDHIKKEGMKCNFWEMGSTGPCGYSSEIHYD-----MKGEPSSALARVNADRND 113
E+GVP + I + G K NFW MG TGPCG SEI YD G P S + DR
Sbjct: 138 KEIGVPPERIIRIGKKDNFWSMGDTGPCGPCSEIFYDRGEEYWGGPPGSPEE--DGDR-- 193
Query: 114 LIEIWNIVFI 123
IEIWN+VF+
Sbjct: 194 YIEIWNLVFM 203
>gnl|CDD|238360 cd00673, AlaRS_core, Alanyl-tRNA synthetase (AlaRS) class II core
catalytic domain. AlaRS is a homodimer. It is
responsible for the attachment of alanine 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 predicted structure and the presence of
three characteristic sequence motifs.
Length = 232
Score = 142 bits (359), Expect = 2e-43
Identities = 60/135 (44%), Positives = 78/135 (57%), Gaps = 9/135 (6%)
Query: 1 MLGNWSFNDYYKRDACRMALEFLTKPPVSLPLDRLYFTYFGGSDQYGLPCDEETLDIWLE 60
MLGN+SF DY+K +A A E LT+ LP DRLY + F G D EE W +
Sbjct: 85 MLGNFSFGDYFKEEAIAFAWELLTEVL-GLPKDRLYVSVFEGDD-------EEEAIWWWK 136
Query: 61 LGVPRDHIKKEGMKCNFWEMGSTGPCGYSSEIHYDMKGEPSSALARVNADRNDLIEIWNI 120
+G+P I++ G K NFWEMG GPCG SEI YD +GE A + N D + +EIWN+
Sbjct: 137 IGLPGIRIERIGFKDNFWEMGGNGPCGPCSEIFYD-RGEERDAASLPNEDDDRYLEIWNL 195
Query: 121 VFISHKRVSADTIVP 135
VF+ + R + T P
Sbjct: 196 VFMQYNRDADGTYRP 210
>gnl|CDD|216484 pfam01411, tRNA-synt_2c, tRNA synthetases class II (A). Other tRNA
synthetase sub-families are too dissimilar to be
included. This family includes only alanyl-tRNA
synthetases.
Length = 551
Score = 136 bits (345), Expect = 7e-39
Identities = 55/127 (43%), Positives = 73/127 (57%), Gaps = 14/127 (11%)
Query: 1 MLGNWSFNDYYKRDACRMALEFLTKPPVSLPLDRLYFTYFGGSDQYGLPCDEETLDIWLE 60
MLGN+SF DY+K +A A E LTK + L +RLY T + D+E IW +
Sbjct: 88 MLGNFSFGDYFKEEAIEFAWELLTKV-LGLDPERLYVTVYEW--------DDEAGPIWEK 138
Query: 61 L-GVPRDHIKKEGMKCNFWEMGSTGPCGYSSEIHYDMKGE---PSSALARVNADRNDLIE 116
+ G+P + I + G K NFWEMG TGPCG SEI YD +GE + AD + +E
Sbjct: 139 IVGIPEERILRFGDKDNFWEMGDTGPCGPCSEIDYD-RGEEIGGWPSGGPPTADDDRFLE 197
Query: 117 IWNIVFI 123
IWN+VF+
Sbjct: 198 IWNLVFM 204
>gnl|CDD|223092 COG0013, AlaS, Alanyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 879
Score = 137 bits (346), Expect = 2e-38
Identities = 54/136 (39%), Positives = 76/136 (55%), Gaps = 18/136 (13%)
Query: 1 MLGNWSFNDYYKRDACRMALEFLTKPPVSLPLDRLYFTYFGGSDQYGLPCDEETLDIWLE 60
MLGN+SF DY+K +A A EFLTK + LP ++LY T + D+E + W +
Sbjct: 92 MLGNFSFGDYFKEEAIEFAWEFLTK-VLGLPKEKLYVTVY--------EDDDEAYNEWEK 142
Query: 61 -LGVPRDHIKKEGMKCNFWEMGSTGPCGYSSEIHYD----MKGEPSSALARVNADRNDLI 115
+G+P + I + G NFWEMG GPCG SEI YD + G P + + D + +
Sbjct: 143 IIGIPPERIIRIGASDNFWEMG-DGPCGPCSEIFYDRGEEIGGGPPGS---PDEDGDRYL 198
Query: 116 EIWNIVFISHKRVSAD 131
EIWN+VF+ + R D
Sbjct: 199 EIWNLVFMQYNRDPGD 214
>gnl|CDD|232931 TIGR00344, alaS, alanine--tRNA ligase. The model describes
alanine--tRNA ligase. This enzyme catalyzes the reaction
(tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
pyrophosphate + AMP) [Protein synthesis, tRNA
aminoacylation].
Length = 851
Score = 122 bits (307), Expect = 3e-33
Identities = 53/139 (38%), Positives = 72/139 (51%), Gaps = 16/139 (11%)
Query: 1 MLGNWSFNDYYKRDACRMALEFLTKPPVSLPLDRLYFTYFGGSDQYGLPCDEETLDIWLE 60
MLGN+SF DY+K +A A E LT + L +RLY T + DEE +IW +
Sbjct: 83 MLGNFSFGDYFKEEAIAFAWELLTS-VLGLDKERLYVTVY--------EDDEEAYEIWEK 133
Query: 61 LGVPRDHIKKEGMKCNFWEMGSTGPCGYSSEIHYDM----KGEPSSALARVNADRNDLIE 116
G+P + I + G K NFW+MG GPCG +EI+YD G+P DR +E
Sbjct: 134 HGIPAERIIRCGDKDNFWDMGD-GPCGPCTEIYYDRGEFVGGKPGEPEFFEENDR--YVE 190
Query: 117 IWNIVFISHKRVSADTIVP 135
+WN+VF+ R P
Sbjct: 191 VWNLVFMQFNRDPDGNYTP 209
>gnl|CDD|234962 PRK01584, PRK01584, alanyl-tRNA synthetase; Provisional.
Length = 594
Score = 117 bits (296), Expect = 6e-32
Identities = 50/129 (38%), Positives = 72/129 (55%), Gaps = 4/129 (3%)
Query: 1 MLGNWSFNDYYKRDACRMALEFLTKPP-VSLPLDRLYFTYFGGSDQYGLPCDEETLDIWL 59
MLGNWS Y+K ++ + + EFLT P +++P D+LY T F G ++ +P DEET +W
Sbjct: 86 MLGNWSLGAYFKEESIKYSFEFLTSPDYLNIPKDKLYVTVFEGDEE--IPRDEETASVWE 143
Query: 60 ELGVPRDHIKKEGMKCNFW-EMGSTGPCGYSSEIHYDMKGEPSSALARVNADRNDLIEIW 118
LG+P+D I + N+W +G TGPCG +EI D S R EIW
Sbjct: 144 SLGIPKDRIFYLSREHNWWGPVGETGPCGPDTEIFVDTGKPKCSVNCRPTCSCGKYFEIW 203
Query: 119 NIVFISHKR 127
N VF+ + +
Sbjct: 204 NNVFMQYNK 212
>gnl|CDD|99813 cd06217, FNR_iron_sulfur_binding_3, Iron-sulfur binding ferredoxin
reductase (FNR) proteins combine the FAD and NAD(P)
binding regions of FNR with an iron-sulfur binding
cluster domain. Ferredoxin-NADP+ (oxido)reductase is an
FAD-containing enzyme that catalyzes the reversible
electron transfer between NADP(H) and electron carrier
proteins such as ferredoxin and flavodoxin. Isoforms of
these flavoproteins (i.e. having a non-covalently bound
FAD as a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria in which they participate in
a wide variety of redox metabolic pathways. The
C-terminal domain contains most of the NADP(H) binding
residues and the N-terminal domain interacts
non-covalently with the isoalloxazine rings of the
flavin molecule which lies largely in a large gap
between the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2 which then
transfers two electrons and a proton to NADP+ to form
NADPH.
Length = 235
Score = 27.2 bits (61), Expect = 2.3
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 52 EETLDIWLELGVPRDHIKKE 71
E + LELGVPRD I+ E
Sbjct: 214 EAATRLLLELGVPRDRIRTE 233
>gnl|CDD|177607 PHA03370, PHA03370, virion protein US2; Provisional.
Length = 269
Score = 27.2 bits (60), Expect = 2.6
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 8/34 (23%)
Query: 49 PCDEETLDIWLELGVPRDHIKKEGMKCNFWEMGS 82
P + T D + H + GMKC + +GS
Sbjct: 185 PKFDTTED--------KAHFEDSGMKCVYKIIGS 210
>gnl|CDD|178209 PLN02599, PLN02599, dihydroorotase.
Length = 364
Score = 27.0 bits (60), Expect = 3.0
Identities = 13/25 (52%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 32 LDRL-YFTYFGGSDQYGLPCDEETL 55
LD+L FT F G D YGLP + T+
Sbjct: 305 LDKLEAFTSFNGPDFYGLPRNTSTI 329
>gnl|CDD|218632 pfam05549, Allexi_40kDa, Allexivirus 40kDa protein.
Length = 271
Score = 27.1 bits (60), Expect = 3.3
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 26 PPVSLPLDRLY 36
PP +LPLD LY
Sbjct: 30 PPTTLPLDELY 40
>gnl|CDD|100814 PRK01207, PRK01207, methionine synthase; Provisional.
Length = 343
Score = 26.8 bits (59), Expect = 3.5
Identities = 11/19 (57%), Positives = 15/19 (78%), Gaps = 1/19 (5%)
Query: 4 NWSFNDYYKRDACRMALEF 22
+WSFND+Y RD +A+EF
Sbjct: 133 DWSFNDFY-RDRYDLAMEF 150
>gnl|CDD|213183 cd03216, ABC_Carb_Monos_I, First domain of the ATP-binding cassette
component of monosaccharide transport system. This
family represents the domain I of the carbohydrate
uptake proteins that transport only monosaccharides
(Monos). The Carb_Monos family is involved in the uptake
of monosaccharides, such as pentoses (such as xylose,
arabinose, and ribose) and hexoses (such as xylose,
arabinose, and ribose), that cannot be broken down to
simple sugars by hydrolysis. Pentoses include xylose,
arabinose, and ribose. Important hexoses include
glucose, galactose, and fructose. In members of the
Carb_monos family, the single hydrophobic gene product
forms a homodimer while the ABC protein represents a
fusion of two nucleotide-binding domains. However, it is
assumed that two copies of the ABC domains are present
in the assembled transporter.
Length = 163
Score = 26.2 bits (59), Expect = 4.4
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 16/49 (32%)
Query: 99 EPSSALARVNADRNDLIEIWN--------IVFISHK-----RVSADTIV 134
EP++AL +R L ++ ++FISH+ + AD +
Sbjct: 108 EPTAALTPAEVER--LFKVIRRLRAQGVAVIFISHRLDEVFEI-ADRVT 153
>gnl|CDD|177814 PLN02153, PLN02153, epithiospecifier protein.
Length = 341
Score = 26.1 bits (57), Expect = 7.1
Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 20/89 (22%)
Query: 4 NWSFNDYYKRDACRMALEFLTKPPV----------SLPLDRLYFTYFGGSDQYGL---PC 50
F+D+Y D + FLTK S+ D + FGG + GL P
Sbjct: 97 KREFSDFYSYDTVKNEWTFLTKLDEEGGPEARTFHSMASDENHVYVFGGVSKGGLMKTPE 156
Query: 51 DEETLDI-------WLELGVPRDHIKKEG 72
T++ W++L P ++ +K G
Sbjct: 157 RFRTIEAYNIADGKWVQLPDPGENFEKRG 185
>gnl|CDD|206233 pfam14063, DUF4254, Protein of unknown function (DUF4254). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and eukaryotes.
Proteins in this family are typically between 195 and
207 amino acids in length.
Length = 145
Score = 25.3 bits (56), Expect = 8.4
Identities = 6/14 (42%), Positives = 11/14 (78%)
Query: 103 ALARVNADRNDLIE 116
+ ++N +RNDL+E
Sbjct: 38 RIDQLNQERNDLVE 51
>gnl|CDD|99810 cd06214, PA_degradation_oxidoreductase_like, NAD(P) binding domain
of ferredoxin reductase like phenylacetic acid (PA)
degradation oxidoreductase. PA oxidoreductases of E.
coli hydroxylate PA-CoA in the second step of PA
degradation. Members of this group typically fuse a
ferredoxin reductase-like domain with an iron-sulfur
binding cluster domain. Ferredoxins catalyze electron
transfer between an NAD(P)-binding domain of the
alpha/beta class and a discrete (usually N-terminal)
domain which vary in orientation with respect to the
NAD(P) binding domain. The N-terminal portion may
contain a flavin prosthetic group, as in flavoenzymes,
or use flavin as a substrate. Ferredoxin-NADP+
(oxido)reductase is an FAD-containing enzyme that
catalyzes the reversible electron transfer between
NADP(H) and electron carrier proteins such as ferredoxin
and flavodoxin. Isoforms of these flavoproteins (i.e.
having a non-covalently bound FAD as a prosthetic group)
are present in chloroplasts, mitochondria, and bacteria
and participate in a wide variety of redox metabolic
pathways. The C-terminal domain contains most of the
NADP(H) binding residues and the N-terminal domain
interacts non-covalently with the isoalloxazine rings of
the flavin molecule which lies largely in a large gap
betweed the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2 which then
transfers two electrons and a proton to NADP+ to form
NADPH.
Length = 241
Score = 25.6 bits (57), Expect = 8.6
Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 3/20 (15%)
Query: 52 EETLDIWLELGVPRDHIKKE 71
E L LELGVP + I +E
Sbjct: 222 EAAL---LELGVPAERIHRE 238
>gnl|CDD|132604 TIGR03565, alk_sulf_monoox, alkanesulfonate monooxygenase,
FMNH(2)-dependent. Members of this protein family are
monooxygenases that catalyze desulfonation of aliphatic
sulfonates such as methane sulfonate. This enzyme uses
reduced FMN, although various others members of the same
luciferase-like monooxygenase family (pfam00296) are
F420-dependent enzymes [Central intermediary metabolism,
Sulfur metabolism].
Length = 346
Score = 25.7 bits (57), Expect = 8.7
Identities = 19/63 (30%), Positives = 22/63 (34%), Gaps = 14/63 (22%)
Query: 26 PPVSLPLDRLYFTYFGGSDQYGLPCDEETLDIWLELGVP-----------RDHIKKEGMK 74
PPV P LYF GGS E +D++L G P R K G
Sbjct: 162 PPVQQPYPPLYF---GGSSDAAHELAAEHVDVYLTWGEPPAQVAEKIADVRKRAAKRGRT 218
Query: 75 CNF 77
F
Sbjct: 219 VRF 221
>gnl|CDD|224053 COG1129, MglA, ABC-type sugar transport system, ATPase component
[Carbohydrate transport and metabolism].
Length = 500
Score = 25.5 bits (57), Expect = 9.6
Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 10/36 (27%)
Query: 99 EPSSALARVNADRNDLIEIWN--------IVFISHK 126
EP++AL +R L ++ I++ISH+
Sbjct: 171 EPTAALTVKETER--LFDLIRRLKAQGVAIIYISHR 204
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
0.321 0.140 0.457
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,020,047
Number of extensions: 605842
Number of successful extensions: 448
Number of sequences better than 10.0: 1
Number of HSP's gapped: 423
Number of HSP's successfully gapped: 25
Length of query: 135
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 48
Effective length of database: 7,078,804
Effective search space: 339782592
Effective search space used: 339782592
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: 53 (24.2 bits)