RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7414
(320 letters)
>gnl|CDD|129561 TIGR00469, pheS_mito, phenylalanyl-tRNA synthetase, mitochondrial.
Unlike all other known phenylalanyl-tRNA synthetases,
the mitochondrial form demonstrated from yeast is
monomeric. It is similar to but longer than the alpha
subunit (PheS) of the alpha 2 beta 2 form found in
Bacteria, Archaea, and eukaryotes, and shares the
characteristic motifs of class II aminoacyl-tRNA
ligases. This model models the experimental example from
Saccharomyces cerevisiae (designated MSF1) and its
orthologs from other eukaryotic species [Protein
synthesis, tRNA aminoacylation].
Length = 460
Score = 264 bits (676), Expect = 1e-85
Identities = 119/309 (38%), Positives = 166/309 (53%), Gaps = 37/309 (11%)
Query: 38 LTINGKTYHTDDYT-NVTPKILSYLNKNLHNKKYHPLCMLKQRIINFFYSEFVGKKGTPI 96
L ING Y TD T NVT KI+ + N H K+ HPL +++ I F ++G P+
Sbjct: 8 LEINGIKYATDGQTTNVTDKIIKLTDANKHLKEDHPLGIIRDLIEKKFNGADNNQRGNPL 67
Query: 97 FSIYDSISPVVTVEENFDSLLVAKDHVSRSKNDCYYVNREYLLRAHTTAHQSELIRMGLD 156
F I+D+ PVVT ENFD+L DH R K+DCYY+N ++LLRAHT+AH+ E + GLD
Sbjct: 68 FKIFDNFKPVVTTMENFDNLGFPADHPGRQKSDCYYINEQHLLRAHTSAHELECFQGGLD 127
Query: 157 N-------FVVFGDVYRRDQIDSTHFPVFHQADGVHLLNRDQVSRGDIGVGTSLKIMTIF 209
+ F++ DVYRRD+ID TH+PVFHQADG + + ++ D+ I
Sbjct: 128 DSDNIKSGFLISADVYRRDEIDKTHYPVFHQADGAAIR---KRTKADLFEKEPGYIEKFE 184
Query: 210 TPTSQEYFYIKKCNKISESIGQNIVIFEQGGVHTDE---KQARHTLDATKVMEQKLKNSL 266
+ K N +I + + E KQ + A + E +LK+S+
Sbjct: 185 EDIRGTEADLNKENV--------KIILDDDSIPLKENNPKQEYASDLAVDLCEHELKHSI 236
Query: 267 VKLAKILFGDDI---------------QMRWISEYFPFTHPSWELEILLNDKWVEILGCG 311
+ K LFG I ++RWI YFPFT PSWE+EI D+W+E+ GCG
Sbjct: 237 EGITKDLFGKKISSMIKNKANNTPKELKVRWIDAYFPFTAPSWEIEIWFKDEWLELCGCG 296
Query: 312 VIRHEILDR 320
+IRH+IL R
Sbjct: 297 IIRHDILLR 305
>gnl|CDD|215422 PLN02788, PLN02788, phenylalanine-tRNA synthetase.
Length = 402
Score = 238 bits (609), Expect = 4e-76
Identities = 106/277 (38%), Positives = 147/277 (53%), Gaps = 62/277 (22%)
Query: 45 YHTDDYT-NVTPKILSYLNKNLHNKKYHPLCMLKQRIINFFYSEFVGKKGTPIFSIYDSI 103
DD T NV I S + LH + HPL +LK I ++F + K F +D +
Sbjct: 41 VREDDPTNNVPDHIFSKIGMQLHRRPDHPLGILKNAIYDYFDENYSNK-----FKKFDDL 95
Query: 104 SPVVTVEENFDSLLVAKDHVSRSKNDCYYVNREYLLRAHTTAHQSELIRMGLDNFVVFGD 163
SP+V+ ++NFD +LV DHVSRS ND YYV+ + +LR HT+AHQ+EL+R G +F+V GD
Sbjct: 96 SPIVSTKQNFDDVLVPPDHVSRSYNDTYYVDAQTVLRCHTSAHQAELLRAGHTHFLVTGD 155
Query: 164 VYRRDQIDSTHFPVFHQADGVHLLNRDQVSRGDIGVGTSLKIMTIFTPTSQEYFYIKKCN 223
VYRRD ID+TH+PVFHQ +GV + + ++ + GT L +++ +KK
Sbjct: 156 VYRRDSIDATHYPVFHQMEGVRVFSPEEWEASGLD-GTDL--------AAED---LKKTL 203
Query: 224 KISESIGQNIVIFEQGGVHTDEKQARHTLDATKVMEQKLKNSLVKLAKILFGDDIQMRWI 283
E ARH LFG D++MRW+
Sbjct: 204 ---------------------EGLARH----------------------LFG-DVEMRWV 219
Query: 284 SEYFPFTHPSWELEILLNDKWVEILGCGVIRHEILDR 320
YFPFT+PS+ELEI +W+E+LGCGV EIL
Sbjct: 220 DAYFPFTNPSFELEIFFKGEWLEVLGCGVTEQEILKN 256
>gnl|CDD|238277 cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS)
alpha chain catalytic core domain. PheRS belongs to
class II aminoacyl-tRNA synthetases (aaRS) based upon
its structure and the presence of three characteristic
sequence motifs. This domain is primarily responsible
for ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. While class II aaRSs generally
aminoacylate the 3'-OH ribose of the appropriate tRNA,
PheRS is an exception in that it attaches the amino acid
at the 2'-OH group, like class I aaRSs. PheRS is an
alpha-2/ beta-2 tetramer.
Length = 218
Score = 130 bits (329), Expect = 2e-36
Identities = 41/120 (34%), Positives = 61/120 (50%), Gaps = 13/120 (10%)
Query: 71 HPLCMLKQRIINFFYSEFVGKKGTPIFSIYDSISPVVTVEENFDSLLVAKDHVSRSKNDC 130
HPL + + I + F S +G F+ + V T NFD+L + +DH +R D
Sbjct: 1 HPLNKVIEEIEDIFVS--MG------FTEVEG-PEVETDFYNFDALNIPQDHPARDMQDT 51
Query: 131 YYVNREY--LLRAHTTAHQSELIRM--GLDNFVVFGDVYRRDQIDSTHFPVFHQADGVHL 186
+Y+N LLR HT+A Q+ + G VYR D+ID+TH P FHQ +G+ +
Sbjct: 52 FYINDPARLLLRTHTSAVQARALAKLKPPIRIFSIGRVYRNDEIDATHLPEFHQIEGLVV 111
Score = 81.8 bits (203), Expect = 2e-18
Identities = 27/65 (41%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 256 KVMEQKLKNSLVKLAKILFGDDIQMRWISEYFPFTHPSWELEILLND--KWVEILGCGVI 313
+ LK +L + AK LFG ++R+ YFPFT PS+E+++ W+EILGCG++
Sbjct: 114 GLTFADLKGTLEEFAKELFGPITKVRFRPSYFPFTEPSFEVDVYCPGCLGWLEILGCGMV 173
Query: 314 RHEIL 318
R E+L
Sbjct: 174 RPEVL 178
>gnl|CDD|223095 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit
[Translation, ribosomal structure and biogenesis].
Length = 335
Score = 96.9 bits (242), Expect = 5e-23
Identities = 45/162 (27%), Positives = 69/162 (42%), Gaps = 36/162 (22%)
Query: 47 TDDYTNVTPKILSY-LNKNLHNKKY--------------HPLCMLKQRIINFFYSEFVGK 91
D T +TP++ + L + L +K HPL + I + F
Sbjct: 72 EDAITELTPELEAAGLWERLAFEKIDVTLPGRRIYPGSLHPLTQTIEEIEDIF-----LG 126
Query: 92 KGTPIFSIYDSISPVVTVEENFDSLLVAKDHVSRSKNDCYYVNRE---YLLRAHTTAHQS 148
G F+ + + T NFD+L + +DH +R D +Y+ + LLR HT+ Q
Sbjct: 127 MG---FTEVEG-PEIETDFYNFDALNIPQDHPARDMQDTFYLKDDREKLLLRTHTSPVQ- 181
Query: 149 ELIRMGLDN------FVVFGDVYRRDQIDSTHFPVFHQADGV 184
R +N G VYR D +D+TH P FHQ +G+
Sbjct: 182 --ARTLAENAKIPIKIFSPGRVYRNDTVDATHSPEFHQIEGL 221
Score = 70.7 bits (174), Expect = 7e-14
Identities = 25/63 (39%), Positives = 40/63 (63%), Gaps = 2/63 (3%)
Query: 260 QKLKNSLVKLAKILFGDDIQMRWISEYFPFTHPSWELEILL--NDKWVEILGCGVIRHEI 317
LK +L + AK FG+D+++R+ YFPFT PS E+++ W+EILGCG++ +
Sbjct: 230 ADLKGTLEEFAKKFFGEDVKVRFRPSYFPFTEPSAEVDVYCPGCGGWLEILGCGMVHPNV 289
Query: 318 LDR 320
L+
Sbjct: 290 LEA 292
>gnl|CDD|232988 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit. Most
phenylalanyl-tRNA synthetases are heterodimeric, with 2
alpha (pheS) and 2 beta (pheT) subunits. This model
describes the alpha subunit, which shows some similarity
to class II aminoacyl-tRNA ligases. Mitochondrial
phenylalanyl-tRNA synthetase is a single polypeptide
chain, active as a monomer, and similar to this chain
rather than to the beta chain, but excluded from this
model. An interesting feature of the alignment of all
sequences captured by this model is a deep split between
non-spirochete bacterial examples and all other
examples; supporting this split is a relative deletion
of about 50 residues in the former set between two
motifs well conserved throughout the alignment [Protein
synthesis, tRNA aminoacylation].
Length = 293
Score = 85.8 bits (213), Expect = 3e-19
Identities = 47/177 (26%), Positives = 70/177 (39%), Gaps = 45/177 (25%)
Query: 35 KATLTINGKTYHTDDYTNVTPKILSY-LNKNLHNKKY--------------HPLCMLKQR 79
L K D+ T + P++ S L L + Y HPL +
Sbjct: 21 LGALINEVKIELQDELTKLKPELESAGLWSKLKFETYDVSLPGTKIYPGSLHPLTRVIDE 80
Query: 80 IINFF----YSEFVGKKGTPIFSIYDSISPVVTVEENFDSLLVAKDHVSRSKNDCYYVNR 135
I + F ++E G + F NFD+L + +DH +R D +Y+
Sbjct: 81 IRDIFLGLGFTEETGPEVETDF-------------WNFDALNIPQDHPARDMQDTFYIKD 127
Query: 136 EYLLRAHTTA--------HQSELIRMGLDNFVVFGDVYRRDQIDSTHFPVFHQADGV 184
LLR HTTA + IR+ G V+R D +D+TH P FHQ +G+
Sbjct: 128 RLLLRTHTTAVQLRTMEEQEKPPIRI-----FSPGRVFRNDTVDATHLPEFHQVEGL 179
Score = 51.5 bits (124), Expect = 2e-07
Identities = 23/59 (38%), Positives = 37/59 (62%), Gaps = 3/59 (5%)
Query: 262 LKNSLVKLAKILFGDDIQMRWISEYFPFTHPSWELEILLNDK--WVEILGCGVIRHEIL 318
LK L + K +FG+ ++R+ YFPFT PS E+++ + W+E+LG G+ R E+L
Sbjct: 190 LKGFLEEFLKKMFGE-TEIRFRPSYFPFTEPSAEIDVYCPEGKGWLEVLGAGMFRPEVL 247
>gnl|CDD|234780 PRK00488, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Validated.
Length = 339
Score = 79.8 bits (198), Expect = 7e-17
Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 19/120 (15%)
Query: 71 HPLCMLKQRIINFFYSEFVGKKGTPIFSIYDSISP-VVTVEENFDSLLVAKDHVSRSKND 129
HP+ + I + F G F + + P + T NF++L + KDH +R D
Sbjct: 108 HPITQTIEEIEDIF-----VGMG---FEVAEG--PEIETDYYNFEALNIPKDHPARDMQD 157
Query: 130 CYYVNREYLLRAHTTAHQSELIRMGLDN-----FVVFGDVYRRDQIDSTHFPVFHQADGV 184
+Y++ LLR HT+ Q IR + G VYR D D+TH P+FHQ +G+
Sbjct: 158 TFYIDDGLLLRTHTSPVQ---IRTMEKQKPPIRIIAPGRVYRNDSDDATHSPMFHQVEGL 214
Score = 58.2 bits (142), Expect = 1e-09
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 12/64 (18%)
Query: 262 LKNSLVKLAKILFGDDIQMRWISEYFPFTHPSWELEI------------LLNDKWVEILG 309
LK +L K FG+D+++R+ YFPFT PS E+++ W+EILG
Sbjct: 225 LKGTLEDFLKAFFGEDVKIRFRPSYFPFTEPSAEVDVSCFKCGGKGCRVCKGTGWLEILG 284
Query: 310 CGVI 313
CG++
Sbjct: 285 CGMV 288
>gnl|CDD|216483 pfam01409, tRNA-synt_2d, tRNA synthetases class II core domain (F).
Other tRNA synthetase sub-families are too dissimilar
to be included. This family includes only
phenylalanyl-tRNA synthetases. This is the core
catalytic domain.
Length = 245
Score = 74.9 bits (185), Expect = 9e-16
Identities = 40/133 (30%), Positives = 58/133 (43%), Gaps = 33/133 (24%)
Query: 71 HPLCMLKQRIINFF----YSEFVGKKGTPIFSIYDSISPVVTVEENFDSLLVAKDHVSRS 126
HPL + + I + F + E G V + NFD+L + +DH +R
Sbjct: 17 HPLTRVLEEIRDIFLSMGFEEVEG-------------PEVESDFYNFDALNIPQDHPARD 63
Query: 127 KNDCYYV-------NREYLLRAHTTAHQSELIRMGLDN------FVVFGDVYRRDQIDST 173
D +Y+ +R LLR HTT Q R G V+RRDQ+D+T
Sbjct: 64 MQDTFYLKKPLKEEDRRLLLRTHTTPVQ---ARTLAKKNKPPIKIFSIGRVFRRDQVDAT 120
Query: 174 HFPVFHQADGVHL 186
H P FHQ +G+ +
Sbjct: 121 HLPEFHQVEGLVV 133
Score = 61.4 bits (150), Expect = 6e-11
Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 262 LKNSLVKLAKILFGDDIQMRWISEYFPFTHPSWELEILL--NDKWVEILGCGVIRHEILD 319
LK L + + FG ++++R+ YFPFT PS E+++ W+EI G G++ +L+
Sbjct: 142 LKGVLEEFLRKFFGFEVKVRFRPSYFPFTEPSAEVDVYCCKLGGWIEIGGAGMVHPNVLE 201
>gnl|CDD|235239 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Provisional.
Length = 489
Score = 46.4 bits (111), Expect = 1e-05
Identities = 17/35 (48%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 286 YFPFTHPSWELEILL-NDKWVEILGCGVIRHEILD 319
YFPFT PS E+E+ WVE+ G G+ R E+L+
Sbjct: 412 YFPFTEPSVEVEVYHEGLGWVELGGAGIFRPEVLE 446
Score = 45.6 bits (109), Expect = 2e-05
Identities = 29/115 (25%), Positives = 43/115 (37%), Gaps = 42/115 (36%)
Query: 112 NFDSLLVAKDHVSRSKNDCYYV--------NREYL------------------------- 138
NFD+L +DH +R D +Y+ E +
Sbjct: 265 NFDALFQPQDHPAREMQDTFYLKYPGIGDLPEELVERVKEVHEHGGDTGSRGWGYKWDED 324
Query: 139 ------LRAHTTAHQSELIRMGLDNFV-VF--GDVYRRDQIDSTHFPVFHQADGV 184
LR HTTA + + + F G V+R D ID+TH P F+Q +G+
Sbjct: 325 IAKRLVLRTHTTALSARYLASRPEPPQKYFSIGRVFRPDTIDATHLPEFYQLEGI 379
>gnl|CDD|215458 PLN02853, PLN02853, Probable phenylalanyl-tRNA synthetase alpha
chain.
Length = 492
Score = 36.2 bits (84), Expect = 0.017
Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 9/69 (13%)
Query: 138 LLRAHTTAHQSE-LIRMGLDNFV-----VFGDVYRRDQIDSTHFPVFHQADGVHLLNRDQ 191
LLR HTTA S L ++ F V+R + +D TH FHQ +G+ + +R
Sbjct: 319 LLRTHTTAVSSRMLYKLAQKGFKPKRYFSIDRVFRNEAVDRTHLAEFHQVEGL-VCDRG- 376
Query: 192 VSRGD-IGV 199
++ GD IGV
Sbjct: 377 LTLGDLIGV 385
Score = 30.4 bits (69), Expect = 1.5
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 6/44 (13%)
Query: 279 QMRWISEYFPFTHPSWEL----EILLNDKWVEILGCGVIRHEIL 318
++R+ Y P+T PS E+ E L KWVE+ G+ R E+L
Sbjct: 397 KLRFKPAYNPYTEPSMEIFSYHEGL--KKWVEVGNSGMFRPEML 438
>gnl|CDD|233051 TIGR00611, recf, recF protein. All proteins in this family for
which functions are known are DNA binding proteins that
assist the filamentation of RecA onto DNA for the
initiation of recombination or recombinational repair.
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 = 365
Score = 33.1 bits (76), Expect = 0.16
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 138 LLRAHTTAHQSELIRMGLDNFVVFGDVYRRDQ 169
L R+H T+ LIR G + FV+ G V + D+
Sbjct: 48 LGRSHRTSRDKPLIRFGAEAFVIEGRVSKGDR 79
>gnl|CDD|129629 TIGR00538, hemN, oxygen-independent coproporphyrinogen III oxidase.
This model represents HemN, the oxygen-independent
coproporphyrinogen III oxidase that replaces HemF
function under anaerobic conditions. Several species,
including E. coli, Helicobacter pylori, and Aquifex
aeolicus, have both a member of this family and a member
of another, closely related family for which there is no
evidence of coproporphyrinogen III oxidase activity.
Members of this family have a perfectly conserved motif
PYRT[SC]YP in a region N-terminal to the region of
homology with the related uncharacterized protein
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 455
Score = 32.8 bits (75), Expect = 0.24
Identities = 18/90 (20%), Positives = 38/90 (42%), Gaps = 17/90 (18%)
Query: 121 DHVSRSKNDCYYVNREYLLR----AHTTAHQSELIRMGLDNFVVFGDVYRRD-------- 168
DH ++ ++ R+ L +TT ++L+ G+ + + GD Y ++
Sbjct: 286 DHFAKPDDELAVAQRKGELHRNFQGYTTQKDTDLLGFGVTSISMLGDCYAQNQKTLKQYY 345
Query: 169 -QIDSTHFPVFHQADGVHLLNRDQVSRGDI 197
+D PV G+ L++D R ++
Sbjct: 346 KAVDEGGNPVER---GI-ALSQDDCIRREV 371
>gnl|CDD|224116 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway)
[DNA replication, recombination, and repair].
Length = 363
Score = 31.4 bits (72), Expect = 0.66
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 137 YLLRAHTTAHQSELIRMGLDNFVVFGDV 164
L R+H T+ ELIR G D + V
Sbjct: 47 ALGRSHRTSRDKELIRTGADEAEISARV 74
>gnl|CDD|133392 cd04764, HTH_MlrA-like_sg1, Helix-Turn-Helix DNA binding domain
of putative MlrA-like transcription regulators.
Putative helix-turn-helix (HTH) MlrA-like transcription
regulators (subgroup 1). The MlrA protein, also known
as YehV, has been shown to control cell-cell
aggregation by co-regulating the expression of curli
and extracellular matrix production in Escherichia coli
and Salmonella typhimurium. These proteins belong to
the MerR superfamily of transcription regulators that
promote expression of several stress regulon genes by
reconfiguring the spacer between the -35 and -10
promoter elements. Their conserved N-terminal domains
contain predicted HTH motifs that mediate DNA binding,
while the dissimilar C-terminal domains bind specific
coactivator molecules. Many MlrA-like proteins in this
group appear to lack the long dimerization helix seen
in the N-terminal domains of typical MerR-like
proteins.
Length = 67
Score = 28.1 bits (63), Expect = 1.0
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 20 NLLRFSTHAVKNDVEKATLTINGKTYHTDDYTNVTPKILSYLNKNLHNKK 69
+ LR+ + + NG+ Y+TD+ + KI + L K L K+
Sbjct: 15 HTLRYYEKEFNLYIPRTE---NGRRYYTDEDIELLKKIKTLLEKGLSIKE 61
>gnl|CDD|240361 PTZ00326, PTZ00326, phenylalanyl-tRNA synthetase alpha chain;
Provisional.
Length = 494
Score = 30.3 bits (69), Expect = 1.4
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 11/58 (18%)
Query: 138 LLRAHTTAHQSE-LIRMGLD-----NFV---VFG-D-VYRRDQIDSTHFPVFHQADGV 184
+LR HTTA + L ++ + F F D V+R + +D+TH FHQ +G
Sbjct: 329 ILRTHTTAVSARMLYKLAQEYKKTGPFKPKKYFSIDRVFRNETLDATHLAEFHQVEGF 386
Score = 28.4 bits (64), Expect = 5.7
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 6/37 (16%)
Query: 286 YFPFTHPSWEL----EILLNDKWVEILGCGVIRHEIL 318
+ P+T PS E+ L KWVE+ G+ R E+L
Sbjct: 419 FNPYTEPSMEIFGYHPGL--KKWVEVGNSGIFRPEML 453
>gnl|CDD|234608 PRK00064, recF, recombination protein F; Reviewed.
Length = 361
Score = 30.1 bits (69), Expect = 1.5
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 138 LLRAHTTAHQSELIRMGLDNFVVFGDV 164
R+H TA ELIR G + V+ G V
Sbjct: 48 PGRSHRTARDKELIRFGAEAAVIHGRV 74
>gnl|CDD|213209 cd03242, ABC_RecF, ATP-binding cassette domain of RecF. RecF is a
recombinational DNA repair ATPase that maintains
replication in the presence of DNA damage. When
replication is prematurely disrupted by DNA damage,
several recF pathway gene products play critical roles
processing the arrested replication fork, allowing it to
resume and complete its task. This CD represents the
nucleotide binding domain of RecF. RecF belongs to a
large superfamily of ABC transporters involved in the
transport of a wide variety of different compounds
including sugars, ions, peptides, and more complex
organic molecules. The nucleotide binding domain shows
the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases with a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 270
Score = 30.0 bits (68), Expect = 1.6
Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 6/76 (7%)
Query: 138 LLRAHTTAHQSELIRMGLDNFVVFGDVYRRDQIDSTHFPVFHQADGVHLLNRDQVSR--G 195
++H T+ ELIR G + + + R+ + + LN +V R
Sbjct: 46 TGKSHRTSRDKELIRWGAEEAKISAVLERQGGELALELTIRSGGGRKARLNGIKVRRLSD 105
Query: 196 DIGVGTSLKIMTIFTP 211
+GV ++ F P
Sbjct: 106 LLGVLNAV----WFAP 117
>gnl|CDD|222508 pfam14033, DUF4246, Protein of unknown function (DUF4246). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and fungi.
Proteins in this family are typically between 392 and
644 amino acids in length.
Length = 496
Score = 29.1 bits (66), Expect = 3.2
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 54 TPKILSYLNKNLHNKKYHPLCMLKQRIIN 82
+I SY+N NLH K+ L +++IN
Sbjct: 206 DVRITSYIN-NLHPVKHRDLYRAIEKLIN 233
>gnl|CDD|180326 PRK05954, PRK05954, precorrin-8X methylmutase; Provisional.
Length = 203
Score = 28.1 bits (63), Expect = 4.5
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 18 YLNLLRFSTHAVKNDVEKATLTINGKTYHTDDYTNVTPKILSYLNKNLHN 67
++NLLRFS +A + + KT D T V I + +NK N
Sbjct: 45 FINLLRFSPNA----IAAGLAALRQKTPIITDVTMVKQGIQTLVNKTFQN 90
>gnl|CDD|173607 PTZ00417, PTZ00417, lysine-tRNA ligase; Provisional.
Length = 585
Score = 28.8 bits (64), Expect = 4.9
Identities = 16/40 (40%), Positives = 20/40 (50%)
Query: 139 LRAHTTAHQSELIRMGLDNFVVFGDVYRRDQIDSTHFPVF 178
LR T LI G+D G V+R + ID+TH P F
Sbjct: 305 LRIATELPLKMLIVGGIDKVYEIGKVFRNEGIDNTHNPEF 344
>gnl|CDD|144368 pfam00738, Polyhedrin, Polyhedrin. These proteins are found in
occlusion bodies in various viruses. The polyhedrin
protein protects the virus.
Length = 235
Score = 28.2 bits (63), Expect = 5.6
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 105 PVVTVEENFDSLLVAKDHVSRSKNDCYYVNREYLLRAHTTAHQSELIRMGLDNFVVFGDV 164
P+V +E D LV +R N CY ++ LR E+IR+ ++V +
Sbjct: 99 PIVNDQEIMDVFLVINMRPTRP-NRCYKFLAQHALRCDPDYVPHEVIRIVEPSYVGPNNE 157
Query: 165 YR 166
YR
Sbjct: 158 YR 159
>gnl|CDD|232951 TIGR00389, glyS_dimeric, glycyl-tRNA synthetase, dimeric type.
This model describes a glycyl-tRNA synthetase distinct
from the two alpha and two beta chains of the tetrameric
E. coli glycyl-tRNA synthetase. This enzyme is a
homodimeric class II tRNA synthetase and is recognized
by pfam model tRNA-synt_2b, which recognizes His, Ser,
Pro, and this set of glycyl-tRNA synthetases [Protein
synthesis, tRNA aminoacylation].
Length = 551
Score = 28.3 bits (63), Expect = 6.5
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 6/38 (15%)
Query: 70 YHPL-CMLKQRIINFFYSEFVGKKG-----TPIFSIYD 101
Y PL +LK I N + F+ + TPI + +
Sbjct: 32 YGPLGAVLKNNIKNAWRKFFIKNERVLEIDTPIITPEE 69
>gnl|CDD|131352 TIGR02299, HpaE, 5-carboxymethyl-2-hydroxymuconate semialdehyde
dehydrogenase. This model represents the dehydrogenase
responsible for the conversion of
5-carboxymethyl-2-hydroxymuconate semialdehyde to
5-carboxymethyl-2-hydroxymuconate (a tricarboxylic
acid). This is the step in the degradation of
4-hydroxyphenylacetic acid via homoprotocatechuate
following the oxidative opening of the aromatic ring.
Length = 488
Score = 28.2 bits (63), Expect = 7.1
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 34 EKATLTINGKTYHTDDYTNVT 54
+K ++G+TY D + N T
Sbjct: 111 DKCEEAMDGRTYPVDTHLNYT 131
>gnl|CDD|215278 PLN02502, PLN02502, lysyl-tRNA synthetase.
Length = 553
Score = 28.0 bits (63), Expect = 7.5
Identities = 13/45 (28%), Positives = 19/45 (42%)
Query: 134 NREYLLRAHTTAHQSELIRMGLDNFVVFGDVYRRDQIDSTHFPVF 178
N + LR T H L+ G + G +R + I + H P F
Sbjct: 276 NMDLYLRIATELHLKRLVVGGFERVYEIGRQFRNEGISTRHNPEF 320
>gnl|CDD|227396 COG5064, SRP1, Karyopherin (importin) alpha [Intracellular
trafficking and secretion].
Length = 526
Score = 27.9 bits (62), Expect = 7.7
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 258 MEQKLKNSLVKLAKILFGDDIQ 279
MEQ+ + L +L + LF DDI+
Sbjct: 65 MEQQFYSELPQLTQQLFSDDIE 86
>gnl|CDD|177725 PLN00110, PLN00110, flavonoid 3',5'-hydroxylase (F3'5'H);
Provisional.
Length = 504
Score = 27.9 bits (62), Expect = 7.7
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 2 FLRCIVKPVFSRHTSCYLNLLRFSTHA 28
+L+ I K F +H S LNL R ST A
Sbjct: 350 YLQAICKESFRKHPSTPLNLPRVSTQA 376
>gnl|CDD|177879 PLN02235, PLN02235, ATP citrate (pro-S)-lyase.
Length = 423
Score = 27.8 bits (62), Expect = 8.9
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 205 IMTIFTPTSQEYFYIKKCNKISESIGQNIVIFEQGGVHTDE 245
I+ F P QE++ + +S+ +G +I E GG+ +E
Sbjct: 106 IVEPFVPHDQEFYL----SIVSDRLGCSISFSECGGIEIEE 142
>gnl|CDD|181699 PRK09206, PRK09206, pyruvate kinase; Provisional.
Length = 470
Score = 27.7 bits (62), Expect = 9.7
Identities = 26/94 (27%), Positives = 40/94 (42%), Gaps = 35/94 (37%)
Query: 139 LRAHTTAHQSELIRM--------GLDNFVVFGDVYRRDQIDSTHFPVFHQADGVHLLNRD 190
+R H AH E I++ GL+NF D+I +DG+
Sbjct: 203 IREHLKAHGGENIQIISKIENQEGLNNF---------DEI-------LEASDGI------ 240
Query: 191 QVSRGDIGVGTSLKIMTIFTPTSQEYFYIKKCNK 224
V+RGD+GV +I +Q+ I+KCN+
Sbjct: 241 MVARGDLGV----EIPVEEVIFAQK-MMIEKCNR 269
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
0.323 0.138 0.418
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,367,989
Number of extensions: 1563740
Number of successful extensions: 1290
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1264
Number of HSP's successfully gapped: 40
Length of query: 320
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 223
Effective length of database: 6,635,264
Effective search space: 1479663872
Effective search space used: 1479663872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.4 bits)