RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781167|ref|YP_003065580.1| tRNA-dihydrouridine synthase A
[Candidatus Liberibacter asiaticus str. psy62]
(322 letters)
>gnl|CDD|30391 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 233 bits (595), Expect = 6e-62
Identities = 96/304 (31%), Positives = 154/304 (50%), Gaps = 27/304 (8%)
Query: 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQ--EKPLALQIGGAD 58
M TD +R AR L LLYTEM+ A A+L G KK +L E+P+A+Q+GG+D
Sbjct: 18 MAGVTDLPFRRLARELGAYDLLYTEMVSAKALLHGRKKFLLLLDELEEERPVAVQLGGSD 77
Query: 59 ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKAL-SI 117
L EAAKI E+ G + I+LN GCPS +V +G GA L+ NP+++ + + AM +A+ I
Sbjct: 78 PELLAEAAKIAEELGADIIDLNCGCPSPKVVKGGAGAALLKNPELLAEIVKAMVEAVGDI 137
Query: 118 PVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYD 177
PVTVK R+G DD + + + ++ +G + + +H R L P D+D
Sbjct: 138 PVTVKIRLGWDD--DDILALEIARILEDAGADALTVHGRTRAQGYLGP--------ADWD 187
Query: 178 IVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYFSN 235
+ E+K+ P + + NG ++ + A ++L DGVMIGR A N + +D +
Sbjct: 188 YIKELKEAVPSIPVIANGDIKSLEDAKEMLEYTGADGVMIGRGALGNPWLFRQIDYLETG 247
Query: 236 PLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGK--LQQITRHMIGLFHGFPNSRRC 293
+ ++ + ++ L GK L+++ +H+ G P +R
Sbjct: 248 E----------LLPPTLAEVLDILREHLELLLEYYGKKGLRRLRKHLGYYLKGLPGAREL 297
Query: 294 RHIL 297
R L
Sbjct: 298 RRAL 301
>gnl|CDD|73368 cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like)
FMN-binding domain. Members of this family catalyze the
reduction of the 5,6-double bond of a uridine residue on
tRNA. Dihydrouridine modification of tRNA is widely
observed in prokaryotes and eukaryotes, and also in some
archaea. Most dihydrouridines are found in the D loop of
t-RNAs. The role of dihydrouridine in tRNA is currently
unknown, but may increase conformational flexibility of
the tRNA. It is likely that different family members
have different substrate specificities, which may
overlap. 1VHN, a putative flavin oxidoreductase, has
high sequence similarity to DUS. The enzymatic
mechanism of 1VHN is not known at the present..
Length = 231
Score = 218 bits (558), Expect = 1e-57
Identities = 89/237 (37%), Positives = 136/237 (57%), Gaps = 17/237 (7%)
Query: 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKK--NILGFSTQEKPLALQIGGAD 58
MV TD +R R L+YTEMI A A+LRG++K +L + +E+PL +Q+GG+D
Sbjct: 7 MVGVTDLPFRLLCRRYGA-DLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQLGGSD 65
Query: 59 ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
L EAAKIVE+ G + I+LN+GCPS +V +G GA L+ +P++V + + A+ +A+ IP
Sbjct: 66 PETLAEAAKIVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIP 125
Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
VTVK R+G DD+ + L K+++ +G + + +H R + R D+D
Sbjct: 126 VTVKIRLGWDDEEETL---ELAKALEDAGASALTVHGRTR--------EQRYSGPADWDY 174
Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKNSAMLTTVDEYF 233
+ EI KE + + NG + + AL+ L VDGVMIGR A N + + E
Sbjct: 175 IAEI-KEAVSIPVIANGDIFSLEDALRCLEQTGVDGVMIGRGALGNPWLFREIKELL 230
>gnl|CDD|144707 pfam01207, Dus, Dihydrouridine synthase (Dus). Members of this
family catalyse the reduction of the 5,6-double bond of
a uridine residue on tRNA. Dihydrouridine modification
of tRNA is widely observed in prokaryotes and
eukaryotes, and also in some archae. Most
dihydrouridines are found in the D loop of t-RNAs. The
role of dihydrouridine in tRNA is currently unknown, but
may increase conformational flexibility of the tRNA. It
is likely that different family members have different
substrate specificities, which may overlap. Dus 1 from
Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus
2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active
as a single subunit, requiring NADPH or NADH, and is
stimulated by the presence of FAD. Some family members
may be targeted to the mitochondria and even have a role
in mitochondria.
Length = 309
Score = 211 bits (539), Expect = 2e-55
Identities = 95/304 (31%), Positives = 142/304 (46%), Gaps = 33/304 (10%)
Query: 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQE--KPLALQIGGAD 58
M TD +R R L+ TEM+ A A LR +K+ L E PLA+Q+GG+D
Sbjct: 5 MAGVTDLPFRRLVREYGAGDLVVTEMVTAKAQLRPEKQRELMLPELEEPTPLAVQLGGSD 64
Query: 59 ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
+ L EAAK+V D G + I++N+GCP+ +V G GA L+ +PD+V + A+ KA+ IP
Sbjct: 65 PALLAEAAKLVADLGADIIDINMGCPAKKVTRGGAGAALLRDPDLVAQIVKAVVKAVDIP 124
Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKK---SGVNGIWIHARKAILKGLSPKDNRKIPNLD 175
VTVK RIG D+ + N V+ ++ +G + +H R + N + P D
Sbjct: 125 VTVKIRIGWDE-----SHENAVEIARRVEDAGAQALTVHGR-------TRAQNYEGP-AD 171
Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKIL--PSVDGVMIGRAAYKN---SAMLTTVD 230
+D + ++K+ I NG + D A + L DGVMIGR A N A TV
Sbjct: 172 WDAIKQVKQAVSIPVIA-NGDITDAEDAQRCLSYTGADGVMIGRGALGNPWLFAEQHTVK 230
Query: 231 EYFSNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNS 290
+P P+ + +S Y L+ +H+ GFP +
Sbjct: 231 TGEFDP---RPPLAEEAEI-VLEHLS-----YLEEFYGEDKGLRHARKHLAWYLKGFPGA 281
Query: 291 RRCR 294
R
Sbjct: 282 AELR 285
>gnl|CDD|37546 KOG2335, KOG2335, KOG2335, tRNA-dihydrouridine synthase
[Translation, ribosomal structure and biogenesis].
Length = 358
Score = 178 bits (454), Expect = 1e-45
Identities = 74/236 (31%), Positives = 122/236 (51%), Gaps = 16/236 (6%)
Query: 1 MVDWTDRHYRFFARLLTNNALLYTEMIVADAILRGDKKNILGFST--QEKPLALQIGGAD 58
MVD+++ +R RL LLYT MI A + +K ST +++PL +Q GG D
Sbjct: 26 MVDYSELAFRRLVRL-YGADLLYTPMIHAKTFVHSEKYRDSELSTSPEDRPLIVQFGGND 84
Query: 59 ISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIP 118
L++AA++V+ + + I+LN GCP G +GA LM NP++VG+ ++A+ L++P
Sbjct: 85 PENLLKAARLVQPYC-DGIDLNCGCPQKVAKRGGYGAFLMDNPELVGEMVSAVRANLNVP 143
Query: 119 VTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKDNRKIPNLDYDI 178
V+VK RI VD + + K ++ +GV+ + +H R KGL K D++
Sbjct: 144 VSVKIRIFVDLE----KTVDYAKMLEDAGVSLLTVHGRTREQKGL------KTGPADWEA 193
Query: 179 VYEIKKENPDLFIGLNGGLEDMSQALKILPS--VDGVMIGRAAYKNSAMLTTVDEY 232
+ +++ PD+ + NG + + + L DGVM R N A+ T
Sbjct: 194 IKAVRENVPDIPVIANGNILSLEDVERCLKYTGADGVMSARGLLYNPALFLTAGYG 249
>gnl|CDD|37544 KOG2333, KOG2333, KOG2333, Uncharacterized conserved protein
[General function prediction only].
Length = 614
Score = 86.9 bits (215), Expect = 7e-18
Identities = 77/285 (27%), Positives = 117/285 (41%), Gaps = 37/285 (12%)
Query: 23 YTEMIVADAILRGDKKN--ILGFSTQEKPLALQIGGADISKLVEAAK-IVEDFGYNEINL 79
EM +A +L+G +L E +Q+ G+ +AA+ I E + I+L
Sbjct: 293 CGEMAMATPLLQGTASEWALLKRHQSEDIFGVQLAGSKPDTAAKAAQVIAETCDVDFIDL 352
Query: 80 NVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALS--IPVTVKCRIGVDDQIPAVALR 137
N+GCP V+ G+ L+ P + + AM A+S IP+TVK R G + P
Sbjct: 353 NMGCPIDLVYRQGGGSALLNRPARLIRILRAM-NAVSGDIPITVKIRTGTKEGHPVA--H 409
Query: 138 NLVKSIKKS-GVNGIWIHARKAILKGLSPKDNRKIPNLDYDIVYEI-KKENPDL-FIGLN 194
L+ I G + + +H R + R + ++D + E K L IG N
Sbjct: 410 ELIPRIVNEWGASAVTLHGRS--------RQQRYTKSANWDYIEECADKAKSALPLIG-N 460
Query: 195 GGL---EDMSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKDF 251
G + ED + L P+VD VMI R A + T + E SS + + KDF
Sbjct: 461 GDILSWEDWYERLNQNPNVDSVMIARGALIKPWIFTEIKE--QQHWDISSTERLDILKDF 518
Query: 252 WRKISASMTDYAARHLHSGGKLQQITRHMIGLFHGFPNSRRCRHI 296
+Y H S K + TR + F F R+I
Sbjct: 519 --------CNYGLEHWGSDTKGVETTRRFLLEFLSF----FHRYI 551
>gnl|CDD|37545 KOG2334, KOG2334, KOG2334, tRNA-dihydrouridine synthase
[Translation, ribosomal structure and biogenesis].
Length = 477
Score = 72.3 bits (177), Expect = 2e-13
Identities = 55/180 (30%), Positives = 86/180 (47%), Gaps = 22/180 (12%)
Query: 50 LALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIA 109
L LQIG A +EAAK+V++ + I++N+GCP G GA L+ +PD + +
Sbjct: 84 LILQIGTASAELALEAAKLVDN-DVSGIDINMGCPKEFSIHGGMGAALLTDPDKLVAILY 142
Query: 110 AMCKALSIPVTVKCRI--GVDDQIPAVALRNLVKSIKKSGVNGIWIHARKAILKGLSPKD 167
++ K +PVT K R+ +D + LVK I +G+ I +H R +
Sbjct: 143 SLVKGNKVPVTCKIRLLDSKEDTL------KLVKRICATGIAAITVHCRT------RDER 190
Query: 168 NRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQ-----ALKILPSVDGVMIGRAAYKN 222
N++ DY + EI + + + +NGG D+ Q + D VMI RAA N
Sbjct: 191 NQEPATKDY--IREIAQACQMVPVIVNGGSMDIEQYSDIEDFQEKTGADSVMIARAAESN 248
>gnl|CDD|73402 cd04740, DHOD_1B_like, Dihydroorotate dehydrogenase (DHOD) class 1B
FMN-binding domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively..
Length = 296
Score = 57.4 bits (139), Expect = 5e-09
Identities = 53/205 (25%), Positives = 91/205 (44%), Gaps = 31/205 (15%)
Query: 44 STQEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDI 103
P+ I G+ + + VE A+ + D G + I LN+ CP+ + +FG +P+
Sbjct: 86 REFGTPVIASIAGSTVEEFVEVAEKLADAGADAIELNISCPNVKGGGMAFGT----DPEA 141
Query: 104 VGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNG-----------IW 152
V + + A+ KA +PV VK V D I +A ++ +++G +G I
Sbjct: 142 VAEIVKAVKKATDVPVIVKLTPNVTD-IVEIA-----RAAEEAGADGLTLINTLKGMAID 195
Query: 153 IHARKAILK----GLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMSQALK-IL 207
I RK IL GLS I + +VY++ K IG+ GG+ AL+ ++
Sbjct: 196 IETRKPILGNVTGGLS---GPAIKPIALRMVYQVYKAVEIPIIGV-GGIASGEDALEFLM 251
Query: 208 PSVDGVMIGRAAYKN-SAMLTTVDE 231
V +G A + + A ++
Sbjct: 252 AGASAVQVGTANFVDPEAFKEIIEG 276
>gnl|CDD|73372 cd02810, DHOD_DHPD_FMN, Dihydroorotate dehydrogenase (DHOD) and
Dihydropyrimidine dehydrogenase (DHPD) FMN-binding
domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
DHPD catalyzes the first step in pyrimidine degradation:
the NADPH-dependent reduction of uracil and thymine to
the corresponding 5,6-dihydropyrimidines. DHPD contains
two FAD, two FMN and eight [4Fe-4S] clusters, arranged
in two electron transfer chains that pass its
homodimeric interface twice. Two of the Fe-S clusters
show a hitherto unobserved coordination involving a
glutamine residue..
Length = 289
Score = 44.9 bits (106), Expect = 3e-05
Identities = 29/106 (27%), Positives = 51/106 (48%), Gaps = 9/106 (8%)
Query: 46 QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
+PL +GG+ VE A+ +E G + LN+ CP + G G L +P+ V
Sbjct: 97 PGQPLIASVGGSSKEDYVELARKIERAGAKALELNLSCP----NVGG-GRQLGQDPEAVA 151
Query: 106 DCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSGVNGI 151
+ + A+ A+ IP+ VK D + L K+ +++G +G+
Sbjct: 152 NLLKAVKAAVDIPLLVKLSPYFDLEDIV----ELAKAAERAGADGL 193
>gnl|CDD|73382 cd02940, DHPD_FMN, Dihydropyrimidine dehydrogenase (DHPD)
FMN-binding domain. DHPD catalyzes the first step in
pyrimidine degradation: the NADPH-dependent reduction of
uracil and thymine to the corresponding
5,6-dihydropyrimidines. DHPD contains two FAD, two FMN,
and eight [4Fe-4S] clusters, arranged in two electron
transfer chains that pass the dimer interface twice. Two
of the Fe-S clusters show a hitherto unobserved
coordination involving a glutamine residue..
Length = 299
Score = 40.2 bits (94), Expect = 7e-04
Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 64 EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKC 123
E AK+VE+ G + + LN CP G GA + +P++V + + +A+ IPV K
Sbjct: 117 ELAKLVEEAGADALELNFSCPHGMPERG-MGAAVGQDPELVEEICRWVREAVKIPVIAKL 175
Query: 124 RIGVDDQIPAVALRNLVKSIKKSGVNGI 151
+ D +R + ++ K+ G +G+
Sbjct: 176 TPNITD------IREIARAAKEGGADGV 197
>gnl|CDD|30516 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport
and metabolism].
Length = 310
Score = 35.6 bits (82), Expect = 0.020
Identities = 50/213 (23%), Positives = 83/213 (38%), Gaps = 33/213 (15%)
Query: 29 ADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVEDFGYNE-INLNVGCPSAR 87
ADA L K + GG + A+++E+ G + I LN+ CP+
Sbjct: 78 ADAFLEELKLAKYEGKPIGVNIGKNKGGPSEEAWADYARLLEEAGDADAIELNISCPNT- 136
Query: 88 VHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIPAVALRNLVKSIKKSG 147
G L +P+++ + A+ A +PV VK + D + + K+ +++G
Sbjct: 137 ----PGGRALGQDPELLEKLLEAVKAATKVPVFVKLAPNITD------IDEIAKAAEEAG 186
Query: 148 VNG------------IWIHARKAILK----GLSPKDNRKIPNLDYDIVYEIKKE-NPDLF 190
+G I + +K +L GLS + I +V E+ K D+
Sbjct: 187 ADGLIAINTTKSGMKIDLETKKPVLANETGGLSGPPLKPIAL---RVVAELYKRLGGDIP 243
Query: 191 IGLNGGLEDMSQAL-KILPSVDGVMIGRAAYKN 222
I GG+E AL IL V +G A
Sbjct: 244 IIGVGGIETGEDALEFILAGASAVQVGTALIYK 276
>gnl|CDD|73389 cd04727, pdxS, PdxS is a subunit of the pyridoxal 5'-phosphate
(PLP) synthase, an important enzyme in deoxyxylulose
5-phosphate (DXP)-independent pathway for de novo
biosynthesis of PLP, present in some eubacteria, in
archaea, fungi, plants, plasmodia, and some metazoa.
Together with PdxT, PdxS forms the PLP synthase, a
heteromeric glutamine amidotransferase (GATase), whereby
PdxT produces ammonia from glutamine and PdxS combines
ammonia with five- and three-carbon phosphosugars to
form PLP. PLP is the biologically active form of vitamin
B6, an essential cofactor in many biochemical processes.
PdxS subunits form two hexameric rings..
Length = 283
Score = 32.5 bits (74), Expect = 0.17
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 6/64 (9%)
Query: 63 VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
E A+I E+ G + P+ G G M +P ++ + + A +SIPV K
Sbjct: 18 AEQARIAEEAGAVAVMALERVPADIRAAG--GVARMADPKMIKEIMDA----VSIPVMAK 71
Query: 123 CRIG 126
RIG
Sbjct: 72 VRIG 75
>gnl|CDD|110664 pfam01680, SOR_SNZ, SOR/SNZ family. Members of this family are
enzymes involved in a new pathway of
pyridoxine/pyridoxal 5-phosphate biosynthesis. This
family was formerly known as UPF0019.
Length = 209
Score = 32.4 bits (74), Expect = 0.18
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 6/40 (15%)
Query: 94 GACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG--VDDQI 131
G M +P ++ + + A +SIPV K RIG V+ QI
Sbjct: 54 GVARMSDPKMIKEIMNA----VSIPVMAKVRIGHFVEAQI 89
>gnl|CDD|30563 COG0214, SNZ1, Pyridoxine biosynthesis enzyme [Coenzyme
metabolism].
Length = 296
Score = 31.4 bits (71), Expect = 0.31
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 6/64 (9%)
Query: 63 VEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVK 122
E A+I E+ G + P+ G G M +P ++ + + A +SIPV K
Sbjct: 30 AEQARIAEEAGAVAVMALERVPADIRAAG--GVARMADPKMIEEIMDA----VSIPVMAK 83
Query: 123 CRIG 126
RIG
Sbjct: 84 VRIG 87
>gnl|CDD|73395 cd04733, OYE_like_2_FMN, Old yellow enzyme (OYE)-related FMN
binding domain, group 2. Each monomer of OYE contains
FMN as a non-covalently bound cofactor, uses NADPH as a
reducing agent with oxygens, quinones, and
alpha,beta-unsaturated aldehydes and ketones, and can
act as electron acceptors in the catalytic reaction.
Other members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase..
Length = 338
Score = 31.3 bits (71), Expect = 0.35
Identities = 30/113 (26%), Positives = 47/113 (41%), Gaps = 25/113 (22%)
Query: 144 KKSGVNGIWIHARKAIL--KGLSPKDNRK-------IPN---LDYDIVYEIKKENPDLF- 190
+++G +G+ IHA L + LSP N++ + N L +I I+ F
Sbjct: 159 QEAGFDGVQIHAAHGYLLSQFLSPLTNKRTDEYGGSLENRARLLLEIYDAIRAAVGPGFP 218
Query: 191 --IGLN------GGL--EDMSQALKILP--SVDGVMIGRAAYKNSAMLTTVDE 231
I LN GG ED + ++ L VD V + Y++ AM E
Sbjct: 219 VGIKLNSADFQRGGFTEEDALEVVEALEEAGVDLVELSGGTYESPAMAGAKKE 271
>gnl|CDD|146268 pfam03537, DUF297, TM1410 hypothetical-related protein.
Length = 203
Score = 30.0 bits (68), Expect = 0.81
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 176 YDIVYEIKKENPDLFIGLNGGLEDMSQALKILPSVDGV 213
++ E+ P L I LN G E + + P VDGV
Sbjct: 131 VALIRELAARAPGLAIILNNGFELLPA---LAPLVDGV 165
>gnl|CDD|35341 KOG0119, KOG0119, KOG0119, Splicing factor 1/branch point binding
protein (RRM superfamily) [RNA processing and
modification].
Length = 554
Score = 30.0 bits (67), Expect = 0.94
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 152 WIHARKAILKGLSPKDNRKIPNLDYDIVYEIKKENPDL-FIGL 193
I + G P + K P +D VY KE PD+ F+GL
Sbjct: 115 IIEEILKLNPGFKPPADYKPPAKLHDKVYIPVKEFPDINFVGL 157
>gnl|CDD|37487 KOG2276, KOG2276, KOG2276, Metalloexopeptidases [Amino acid
transport and metabolism].
Length = 473
Score = 29.9 bits (67), Expect = 1.0
Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 10/65 (15%)
Query: 73 GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRI---GVDD 129
G + V PS +H G FG +V + + + +S V ++ RI G+ +
Sbjct: 212 GVIYFQIEVEGPSKDLHSGVFGG-------VVHEAMNDLVLVMSSLVDIQGRILIPGIYE 264
Query: 130 QIPAV 134
+ +
Sbjct: 265 DVAPL 269
>gnl|CDD|176521 cd08579, GDPD_memb_like, Glycerophosphodiester phosphodiesterase
domain of uncharacterized bacterial
glycerophosphodiester phosphodiesterases. This
subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in
uncharacterized bacterial glycerophosphodiester
phosphodiesterases. In addition to a C-terminal GDPD
domain, most members in this family have an N-terminus
that functions as a membrane anchor.
Length = 220
Score = 29.8 bits (68), Expect = 1.1
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 174 LDYDIVYEIKKENPDLFIGL 193
LDY ++ ++KK +P + G
Sbjct: 135 LDYRVIEKVKKLDPKIKTGY 154
>gnl|CDD|36635 KOG1421, KOG1421, KOG1421, Predicted signaling-associated protein
(contains a PDZ domain) [General function prediction
only].
Length = 955
Score = 29.6 bits (66), Expect = 1.3
Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 7/83 (8%)
Query: 12 FARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGGADISKLVEAAKIVED 71
A + AL + +LRGD+ GF+ + L + D+S ++ + ++
Sbjct: 601 VASFKYDPALEVQLKLTDTTVLRGDECTFEGFTEDLRALTAKTSVTDVSVVIIPSSVMPR 660
Query: 72 FGYN-------EINLNVGCPSAR 87
F NL+ C S R
Sbjct: 661 FRATNLEVISFMDNLSTSCLSGR 683
>gnl|CDD|73379 cd02931, ER_like_FMN, Enoate reductase (ER)-like FMN-binding
domain. Enoate reductase catalyzes the NADH-dependent
reduction of carbon-carbon double bonds of several
molecules, including nonactivated 2-enoates,
alpha,beta-unsaturated aldehydes, cyclic ketones, and
methylketones. ERs are similar to 2,4-dienoyl-CoA
reductase from E. coli and to the old yellow enzyme from
Saccharomyces cerevisiae..
Length = 382
Score = 29.2 bits (65), Expect = 1.5
Identities = 10/27 (37%), Positives = 21/27 (77%)
Query: 56 GADISKLVEAAKIVEDFGYNEINLNVG 82
G D+ + ++AAKI+E+ GY+ ++++ G
Sbjct: 248 GRDLEEGLKAAKILEEAGYDALDVDAG 274
>gnl|CDD|144801 pfam01338, Bac_thur_toxin, Bacillus thuringiensis toxin.
Length = 227
Score = 28.7 bits (64), Expect = 2.0
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 11/65 (16%)
Query: 200 MSQALKILPSVDGVMIGRAAYKNSAMLTTVDEYFSNPLTGSSPIKTRVDKD--FWRKISA 257
+ + ++IL SV GV++ + K S + + E F+N + T+ D+ FW +A
Sbjct: 94 IDKVIEILKSVLGVVLN-STVKQS-LTAAITETFTN-------LDTQKDEAWIFWGHETA 144
Query: 258 SMTDY 262
T+Y
Sbjct: 145 HQTNY 149
>gnl|CDD|32642 COG2813, RsmC, 16S RNA G1207 methylase RsmC [Translation, ribosomal
structure and biogenesis].
Length = 300
Score = 28.7 bits (64), Expect = 2.2
Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 7/41 (17%)
Query: 234 SNPLTGSSPIKTRVDKDFWRKISASMTDYAARHLHSGGKLQ 274
SNP P K ++ + AARHL GG+L
Sbjct: 230 SNP-----PF--HAGKAVVHSLAQEIIAAAARHLKPGGELW 263
>gnl|CDD|36819 KOG1606, KOG1606, KOG1606, Stationary phase-induced protein,
SOR/SNZ family [Coenzyme transport and metabolism].
Length = 296
Score = 28.4 bits (63), Expect = 2.6
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 10/86 (11%)
Query: 50 LALQIGGADISKLV--EAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDC 107
LA + G I +V E A+I E+ G + P+ +G G M +P ++ +
Sbjct: 16 LAQMLKGGVIMDVVNAEQARIAEEAGACAVMALERVPADIRAQG--GVARMSDPRMIKE- 72
Query: 108 IAAMCKALSIPVTVKCRIG--VDDQI 131
+ A+SIPV K RIG V+ QI
Sbjct: 73 ---IKNAVSIPVMAKVRIGHFVEAQI 95
>gnl|CDD|36605 KOG1391, KOG1391, KOG1391, Acetyl-CoA acetyltransferase [Lipid
transport and metabolism].
Length = 396
Score = 28.4 bits (63), Expect = 2.9
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 73 GYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIGVDDQIP 132
G + +L V A + + GA ++ I+G+ +A+ + + V R+GV + P
Sbjct: 25 GLSATDLGVVAAKAALKAANVGA-EAVDHVIMGNVLASSSDGIYLARHVGLRVGVPKETP 83
Query: 133 AVALRNLVKSIKKSGVNG 150
A+ + L S +S VNG
Sbjct: 84 ALTINRLCGSGFQSIVNG 101
>gnl|CDD|30455 COG0106, HisA, Phosphoribosylformimino-5-aminoimidazole carboxamide
ribonucleotide (ProFAR) isomerase [Amino acid transport
and metabolism].
Length = 241
Score = 27.8 bits (62), Expect = 4.5
Identities = 45/188 (23%), Positives = 75/188 (39%), Gaps = 43/188 (22%)
Query: 46 QEKPLALQIGGADISKLVEAAKIVEDFGYNEINLNVGCPSARVHEGSFGACLMLNPDIVG 105
+ + +Q+GG + E L+ G ARV G+ + NPD+V
Sbjct: 72 EATDVPVQVGGG-----------IRSLEDVEALLDAGV--ARVIIGTAA---VKNPDLVK 115
Query: 106 DCIAAMCKAL--SIPVTVKCRIGVD-----DQIPAVALRNLVKSIKKSGVNGIWIHA--R 156
+ +C+ I V + R G + V L L K +++ G+ I R
Sbjct: 116 E----LCEEYGDRIVVALDARDGKVAVSGWQEDSGVELEELAKRLEEVGLAHILYTDISR 171
Query: 157 KAILKGLSPKDNRKIPNLDYDIVYEIKKENPDLFIGLNGGLEDMS--QALKILPSVDGVM 214
L G + D+V E+ + I +GG+ + +ALK L V+GV+
Sbjct: 172 DGTLSGP-----------NVDLVKELAEAVDIPVIA-SGGVSSLDDIKALKELSGVEGVI 219
Query: 215 IGRAAYKN 222
+GRA Y+
Sbjct: 220 VGRALYEG 227
>gnl|CDD|33291 COG3488, COG3488, Predicted thiol oxidoreductase [Energy production
and conversion].
Length = 481
Score = 27.3 bits (60), Expect = 5.7
Identities = 17/55 (30%), Positives = 24/55 (43%)
Query: 72 FGYNEINLNVGCPSARVHEGSFGACLMLNPDIVGDCIAAMCKALSIPVTVKCRIG 126
FG+ ++ +A G G L P GDC AA L +P V+ R+G
Sbjct: 265 FGWKAQQPSIRQQNADAFAGDIGISTSLLPKHHGDCTAAQTLCLDLPNGVQPRLG 319
>gnl|CDD|34488 COG4879, COG4879, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 243
Score = 27.3 bits (60), Expect = 5.8
Identities = 12/48 (25%), Positives = 21/48 (43%)
Query: 9 YRFFARLLTNNALLYTEMIVADAILRGDKKNILGFSTQEKPLALQIGG 56
Y + L N A Y+ +A+ I G ++ L + AL++G
Sbjct: 158 YPELKQRLLNYARFYSAFKIAEEIALGKVRDRLTLKATKYAYALRLGF 205
>gnl|CDD|36673 KOG1460, KOG1460, KOG1460, GDP-mannose pyrophosphorylase
[Carbohydrate transport and metabolism, Cell
wall/membrane/envelope biogenesis, Posttranslational
modification, protein turnover, chaperones].
Length = 407
Score = 26.8 bits (59), Expect = 7.3
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 236 PLTGSSPIKTRVDKDFWRKI-SASMTDYAARH 266
PL GS + DFW +I +A YA+R
Sbjct: 231 PLAGSKQLYAYETTDFWSQIKTAGSALYASRL 262
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.322 0.137 0.408
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,902,565
Number of extensions: 205529
Number of successful extensions: 573
Number of sequences better than 10.0: 1
Number of HSP's gapped: 543
Number of HSP's successfully gapped: 33
Length of query: 322
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 228
Effective length of database: 4,232,491
Effective search space: 965007948
Effective search space used: 965007948
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 (21.9 bits)
S2: 57 (25.7 bits)