RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18231
(540 letters)
>gnl|CDD|239200 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 = 130 bits (329), Expect = 8e-35
Identities = 33/97 (34%), Positives = 51/97 (52%), Gaps = 1/97 (1%)
Query: 27 SKLNFRQLVRSHNVDLCFTPMIIADSFIKSSKARNNEFSTSPEDTPLVVQFASNNHDDFV 86
+ L FR L R + DL +T MI A + ++ ++ R + +PE+ PL+VQ ++ +
Sbjct: 11 TDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQLGGSDPETLA 70
Query: 87 RATQYVAP-HCNGVDLNCGCPQRWAIKEGYGCALLSK 122
A + V +G+DLN GCP K G G ALL
Sbjct: 71 EAAKIVEELGADGIDLNMGCPSPKVTKGGAGAALLKD 107
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 130 bits (329), Expect = 4e-34
Identities = 81/323 (25%), Positives = 134/323 (41%), Gaps = 54/323 (16%)
Query: 171 RFPVDGSYCLTCGSDKKIKLWNPYRNLLLKTYGGHAHEVNDATAACDSSQIASGASDKSV 230
F DG T D IK+W+ LL+T GH V D A+ D + +ASG+SDK++
Sbjct: 16 AFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLASGSSDKTI 75
Query: 231 ILWEVTTGQPVRRWREHASKVTCVKFNEDSSVVISGSQDNTVMMWDVKSRSHHPIQVRCL 290
LW++ TG+ VR H S V+ V F+ D ++ S S+D T+ +WDV++ +CL
Sbjct: 76 RLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETG-------KCL 128
Query: 291 NEALKEARDSITSVHSLVKSTKNHLSNGLLTKLVFAFRCKYLNGLLSGVLMSTQHLMVLL 350
L+ D + SV +++ + + + T + L
Sbjct: 129 T-TLRGHTDWVNSV--AFSPDGTFVASSSQDGTIKLWD------------LRTGKCVATL 173
Query: 351 DFLGSTQIGDVTPISIHNSCFQALKEARDSITSVHVSD--HEILTASLDCRIRRYDIRTG 408
H + SV S ++L++S D I+ +D+ TG
Sbjct: 174 TG--------------HTG----------EVNSVAFSPDGEKLLSSSSDGTIKLWDLSTG 209
Query: 409 NLVTDYVG--EPIVDACFTRDCQCILTCSTDECLRLFDKATGELLEEYKGHKSGDFRIEC 466
+ G + F+ D + + S D +R++D TGE ++ GH + +
Sbjct: 210 KCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTN---SVTS 266
Query: 467 CLDSKDSQIFC-GSSDGKIYKWQ 488
S D + GS+DG I W
Sbjct: 267 LAWSPDGKRLASGSADGTIRIWD 289
Score = 112 bits (283), Expect = 8e-28
Identities = 76/340 (22%), Positives = 136/340 (40%), Gaps = 59/340 (17%)
Query: 198 LLKTYGGHAHEVNDATAACDSSQIASGASDKSVILWEVTTGQPVRRWREHASKVTCVKFN 257
L +T GH V + D +A+G+ D ++ +W++ TG+ +R + H V V +
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAAS 60
Query: 258 EDSSVVISGSQDNTVMMWDVKSRSHHPIQVRCLNEALKEARDSITSVHSLVKSTKNHLSN 317
D + + SGS D T+ +WD+++ C+ L ++SV
Sbjct: 61 ADGTYLASGSSDKTIRLWDLETG-------ECVRT-LTGHTSYVSSVA------------ 100
Query: 318 GLLTKLVFAFRCKYLNGLLSGVLMSTQHLMVLLDFLGSTQIGDVTPISIHNSCFQALKEA 377
++ + ++ DV C L+
Sbjct: 101 ----------------------FSPDGRILSSSSRDKTIKVWDVET----GKCLTTLRGH 134
Query: 378 RDSITSVHVSDHE--ILTASLDCRIRRYDIRTGNLVTDYVG--EPIVDACFTRDCQCILT 433
D + SV S + ++S D I+ +D+RTG V G + F+ D + +L+
Sbjct: 135 TDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLS 194
Query: 434 CSTDECLRLFDKATGELLEEYKGHKSGDFRIECCLDSKDSQIFCGSS-DGKIYKWQLVDS 492
S+D ++L+D +TG+ L +GH++G + S D + S DG I W L
Sbjct: 195 SSSDGTIKLWDLSTGKCLGTLRGHENG---VNSVAFSPDGYLLASGSEDGTIRVWDLRTG 251
Query: 493 SQISTLI-HSVGKAVVNSLCSHPTRKHIMSACGNN-VKLW 530
+ TL H+ V SL P K + S + +++W
Sbjct: 252 ECVQTLSGHTNS---VTSLAWSPDGKRLASGSADGTIRIW 288
Score = 94.7 bits (236), Expect = 1e-21
Identities = 66/272 (24%), Positives = 111/272 (40%), Gaps = 35/272 (12%)
Query: 148 SIRVYRPLTVNRELFVLSGLMHT------RFPVDGSYCLTCGSDKKIKLWNPYRNLLLKT 201
+I+V+ L L L G HT DG+Y + SDK I+LW+ ++T
Sbjct: 32 TIKVWD-LETGELLRTLKG--HTGPVRDVAASADGTYLASGSSDKTIRLWDLETGECVRT 88
Query: 202 YGGHAHEVNDATAACDSSQIASGASDKSVILWEVTTGQPVRRWREHASKVTCVKFNEDSS 261
GH V+ + D ++S + DK++ +W+V TG+ + R H V V F+ D +
Sbjct: 89 LTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGT 148
Query: 262 VVISGSQDNTVMMWDVKSRSHHPIQVRCLNEALKEARDSITSVHSLVKSTKNHLSNGLLT 321
V S SQD T+ +WD+ R+ + L + SV + + LS+
Sbjct: 149 FVASSSQDGTIKLWDL--RTGKCVAT------LTGHTGEVNSV-AFSPDGEKLLSSS-SD 198
Query: 322 KLVF-----AFRCKYL-----NGLLSGVLMSTQHLMVLLDFLGSTQIGDVTPISIHNSCF 371
+ +C NG+ S +L+ G+ ++ D+
Sbjct: 199 GTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECV---- 254
Query: 372 QALKEARDSITSVHVSDHE--ILTASLDCRIR 401
Q L +S+TS+ S + + S D IR
Sbjct: 255 QTLSGHTNSVTSLAWSPDGKRLASGSADGTIR 286
Score = 63.9 bits (156), Expect = 3e-11
Identities = 33/119 (27%), Positives = 51/119 (42%), Gaps = 9/119 (7%)
Query: 418 PIVDACFTRDCQCILTCSTDECLRLFDKATGELLEEYKGHKSGDFRIECCLDSKDSQIFC 477
+ F+ D + + T S D ++++D TGELL KGH + D +
Sbjct: 11 GVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGT--YLAS 68
Query: 478 GSSDGKIYKWQLVDSSQISTLI-HSVGKAVVNSLCSHPTRKHIMSACG--NNVKLWTAE 533
GSSD I W L + TL H + V+S+ P I+S+ +K+W E
Sbjct: 69 GSSDKTIRLWDLETGECVRTLTGH---TSYVSSVAFSPDG-RILSSSSRDKTIKVWDVE 123
Score = 46.2 bits (110), Expect = 2e-05
Identities = 17/70 (24%), Positives = 35/70 (50%)
Query: 165 SGLMHTRFPVDGSYCLTCGSDKKIKLWNPYRNLLLKTYGGHAHEVNDATAACDSSQIASG 224
+G+ F DG + D I++W+ ++T GH + V + D ++ASG
Sbjct: 220 NGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASG 279
Query: 225 ASDKSVILWE 234
++D ++ +W+
Sbjct: 280 SADGTIRIWD 289
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 89.7 bits (223), Expect = 1e-19
Identities = 31/116 (26%), Positives = 52/116 (44%), Gaps = 5/116 (4%)
Query: 31 FRQLVRSHNV-DLCFTPMIIADSFIKSSKARNNEFSTSPEDTPLVVQFASNNHDDFVRAT 89
FR+L R DL +T M+ A + + K E+ P+ VQ ++ + A
Sbjct: 26 FRRLARELGAYDLLYTEMVSAKALLHGRKKFLLLLDELEEERPVAVQLGGSDPELLAEAA 85
Query: 90 QYVAPHC-NGVDLNCGCPQRWAIKEGYGCALLSKQRTHPLLFSLPRTITRILYELP 144
+ + +DLNCGCP +K G G ALL + LL + + + + ++P
Sbjct: 86 KIAEELGADIIDLNCGCPSPKVVKGGAGAALL---KNPELLAEIVKAMVEAVGDIP 138
>gnl|CDD|216365 pfam01207, Dus, Dihydrouridine synthase (Dus). 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 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 = 82.4 bits (204), Expect = 3e-17
Identities = 37/127 (29%), Positives = 56/127 (44%), Gaps = 12/127 (9%)
Query: 27 SKLNFRQLVRSHNV-DLCFTPMIIADSFIKSSKARNNEFSTSPEDTPLVVQFASNNHDDF 85
+ L FR+LVR + DL T M+ A + ++ K R E TPL VQ ++
Sbjct: 9 TDLPFRRLVREYGAGDLVVTEMVTAKAQLRPEKQRELMLPELEEPTPLAVQLGGSDPALL 68
Query: 86 VRATQYVAPH-CNGVDLNCGCPQRWAIKEGYGCALLSKQRTHPLLFSLPRTITRILYELP 144
A + VA + +D+N GCP + + G G ALL P + +I+ +
Sbjct: 69 AEAAKLVADLGADIIDINMGCPAKKVTRGGAGAALLRD----------PDLVAQIVKAVV 118
Query: 145 KEWSIRV 151
K I V
Sbjct: 119 KAVDIPV 125
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 83.6 bits (205), Expect = 4e-17
Identities = 96/381 (25%), Positives = 160/381 (41%), Gaps = 36/381 (9%)
Query: 172 FPVDGSYCLTCGSDKKIKLWNPY--RNLLLKTYGGHAHEVND-ATAACDSSQIASGAS-- 226
F DG L+ SD IKLW+ L+ G H V+ A ++ D + I +S
Sbjct: 73 FSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLASSSL 132
Query: 227 DKSVILWEVTT-GQPVRRWREHASKVTCVKFNEDSSVVISGSQ-DNTVMMWDVKSR---- 280
D +V LW+++T G+ +R H+ VT + F+ D ++ SGS D T+ +WD+++
Sbjct: 133 DGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLS 192
Query: 281 --SHHPIQVRCLNEALKEARDSITSVHSLVKSTKNHLSNGLLTKLVFAFRCKYLNGLLSG 338
+ H V L + + + LS G L + L+G
Sbjct: 193 TLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWD-LSTGKLLRST-------LSGHSDS 244
Query: 339 VLMSTQHLMVLLDFLGSTQIGDVTPISIHNSCFQALKEARDSITSVHVSDHE--ILTASL 396
V+ S LL S + + +S + L S+ SV S + + S
Sbjct: 245 VVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSS 304
Query: 397 DCRIRRYDIRTGNLVT----DYVGEPIVDACFTRDCQCILT-CSTDECLRLFDKATGELL 451
D +R +D+ TG L++ P+ F+ D +++ S D +RL+D TG+ L
Sbjct: 305 DGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPL 364
Query: 452 EEYKGHKSGDFRIECCLDSKDSQIFC-GSSDGKIYKWQLVDSSQISTLIHSVGKAVVNSL 510
+ +GH + + S D ++ GS+DG + W L S + L + V SL
Sbjct: 365 KTLEGHSN----VLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSR--VTSL 418
Query: 511 CSHPTRKHIMSAC-GNNVKLW 530
P K + S N ++LW
Sbjct: 419 DFSPDGKSLASGSSDNTIRLW 439
Score = 74.4 bits (181), Expect = 4e-14
Identities = 65/310 (20%), Positives = 117/310 (37%), Gaps = 23/310 (7%)
Query: 243 RWREHASKVTCVKFNEDSSVVISGSQDNTVMMWDVKS--------RSHHPIQVRCLNEAL 294
R H +T + F+ D +++SGS D T+ +WD+ + H V L +
Sbjct: 60 LLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSS 119
Query: 295 KEARDSITSVHSLVKSTKNHLSNGLLTKLVFAFRCKYLNGLLSGVLMSTQHLMVLLDFLG 354
+ + + SL T KL+ + + L G
Sbjct: 120 PDGNSILLASSSLDG-TVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDG 178
Query: 355 STQIGDVTPISIHNSCFQALKEARDSITSVHVSDHE---ILTASLDCRIRRYDIRTGNLV 411
+ ++ D+ L D ++S+ S I + S D IR +D+ TG L+
Sbjct: 179 TIKLWDLRT----GKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLL 234
Query: 412 TDYVGEPI--VDACFTRDCQCILTCSTDECLRLFD-KATGELLEEYKGHKSGDFRIECCL 468
+ V + F+ D + + S+D +RL+D +++ LL GH S +
Sbjct: 235 RSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSV--AF 292
Query: 469 DSKDSQIFCGSSDGKIYKWQLVDSSQISTLIHSVGKAVVNSLCSHPTRKHIMSACGNN-- 526
+ GSSDG + W L +S+L + V+SL P ++S ++
Sbjct: 293 SPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGT 352
Query: 527 VKLWTAEEDY 536
++LW
Sbjct: 353 IRLWDLRTGK 362
Score = 72.4 bits (176), Expect = 2e-13
Identities = 86/348 (24%), Positives = 139/348 (39%), Gaps = 51/348 (14%)
Query: 148 SIRVYRPLTVNRELFVLSGLMHTRFPV----DGSYCLTCGS-DKKIKLWNPYRNLLLKTY 202
+++++ T + + L G + + DG + S D IKLW+ L T
Sbjct: 135 TVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTL 194
Query: 203 GGHAHEVNDATAACDSS-QIASGASDKSVILWEVTTGQPVRRWREHASKVTCVKFNEDSS 261
GH V+ + D IASG+SD ++ LW+++TG+ +R S F+ D S
Sbjct: 195 AGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGS 254
Query: 262 VVISGSQDNTVMMWDVKSRSHHPIQVRCLNEALKEARDSITSVHSLVKSTKNHLSNGLLT 321
++ SGS D T+ +WD++S S ++ + S+ SV
Sbjct: 255 LLASGSSDGTIRLWDLRS-SSSLLRTLSGHS------SSVLSVAFSPDGKL--------- 298
Query: 322 KLVFAFRCKYLNGLLSGVLMSTQHLMVLLDFLGSTQIGDVTPISIHNSCFQALKEARDSI 381
L SG S+ + L D + + H +L + D
Sbjct: 299 -------------LASG---SSDGTVRLWDLETGKLL-SSLTLKGHEGPVSSLSFSPD-- 339
Query: 382 TSVHVSDHEILTASLDCRIRRYDIRTGNLV-TDYVGEPIVDACFTRDCQCILTCSTDECL 440
+ S D IR +D+RTG + T ++ F+ D + + + STD +
Sbjct: 340 -----GSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTV 394
Query: 441 RLFDKATGELLEEYKGHKSGDFRIECCLDSKDSQIFC-GSSDGKIYKW 487
RL+D +TG LL GH S R+ S D + GSSD I W
Sbjct: 395 RLWDLSTGSLLRNLDGHTS---RVTSLDFSPDGKSLASGSSDNTIRLW 439
Score = 60.5 bits (145), Expect = 9e-10
Identities = 65/281 (23%), Positives = 113/281 (40%), Gaps = 51/281 (18%)
Query: 173 PVDGSYCLTCGSDKKIKLWN-PYRNLLLKTYGGHAHEVNDATAACDSSQIASGASDKSVI 231
P G + SD I+LW+ LL T GH+ V + + D S +ASG+SD ++
Sbjct: 208 PDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSP-DGSLLASGSSDGTIR 266
Query: 232 LWEV-TTGQPVRRWREHASKVTCVKFNEDSSVVISGSQDNTVMMWDVKSRSHHPIQVRCL 290
LW++ ++ +R H+S V V F+ D ++ SGS D TV +WD+++
Sbjct: 267 LWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLET----------- 315
Query: 291 NEALKEARDSITSVHSLVKSTKNHLSNGLLTKLVFAFRCKYLNGLLSGVLMSTQHLMVLL 350
L+ S G ++ L F+ L
Sbjct: 316 --------------GKLLSSLTLKGHEGPVSSLSFSPDGSLL------------------ 343
Query: 351 DFLGSTQIGDVTPISIHNSCFQALKEARDSITSVHVSDHEIL--TASLDCRIRRYDIRTG 408
G + G + + E ++ SV S + + S D +R +D+ TG
Sbjct: 344 -VSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTG 402
Query: 409 NLVTDYVG--EPIVDACFTRDCQCILTCSTDECLRLFDKAT 447
+L+ + G + F+ D + + + S+D +RL+D T
Sbjct: 403 SLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKT 443
Score = 57.4 bits (137), Expect = 9e-09
Identities = 43/140 (30%), Positives = 71/140 (50%), Gaps = 2/140 (1%)
Query: 145 KEWSIRVYRPLTVNRELFVLSGLMHTRFPVDGSYCLTCGS-DKKIKLWNPYRNLLLKTYG 203
+ W + + L+ + F DGS ++ GS D I+LW+ LKT
Sbjct: 309 RLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLE 368
Query: 204 GHAHEVNDATAACDSSQIASGASDKSVILWEVTTGQPVRRWREHASKVTCVKFNEDSSVV 263
GH V + + D ++SG++D +V LW+++TG +R H S+VT + F+ D +
Sbjct: 369 GH-SNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSL 427
Query: 264 ISGSQDNTVMMWDVKSRSHH 283
SGS DNT+ +WD+K+
Sbjct: 428 ASGSSDNTIRLWDLKTSLKS 447
Score = 42.8 bits (99), Expect = 4e-04
Identities = 34/145 (23%), Positives = 60/145 (41%), Gaps = 14/145 (9%)
Query: 130 FSLPRTITRILYELPKEWSIRVYRPLTVN--RELFVLSGLMHTRFPVDGSYCLTCGSDKK 187
S + ++ + +IR++ T + L S ++ F DG + +D
Sbjct: 334 LSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGT 393
Query: 188 IKLWNPYRNLLLKTYGGHAHEVNDATAACDSSQIASGASDKSVILWEVTTGQPVRRWREH 247
++LW+ LL+ GH V + D +ASG+SD ++ LW++ T
Sbjct: 394 VRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKS------ 447
Query: 248 ASKVTCVKFNEDSSVVISGSQDNTV 272
V F+ D V+ S S D +V
Sbjct: 448 ------VSFSPDGKVLASKSSDLSV 466
Score = 36.6 bits (83), Expect = 0.029
Identities = 36/164 (21%), Positives = 61/164 (37%), Gaps = 8/164 (4%)
Query: 373 ALKEARDSITSVHVSDHEILTASLDCRIRRYDIRTGNLVTDYVGEPIVDACFTRDCQCIL 432
S+ S+ S+ IL +L +L+ + I F+ D + +L
Sbjct: 22 GPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLSSLLLRGHEDSITSIAFSPDGELLL 81
Query: 433 TCSTDECLRLFDKATGE-LLEEYKGHKSGDFRIECCLDSKDSQIF---CGSSDGKIYKWQ 488
+ S+D ++L+D GE L++ +G + L S D S DG + W
Sbjct: 82 SGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVS-KLALSSPDGNSILLASSSLDGTVKLWD 140
Query: 489 LVDSSQISTLIHSVGKAVVNSLCSHPTRKHIMSACG--NNVKLW 530
L ++ + V SL P K + S +KLW
Sbjct: 141 LSTPGKLIRTL-EGHSESVTSLAFSPDGKLLASGSSLDGTIKLW 183
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats (blades)
of the beta propeller domain.
Length = 40
Score = 47.7 bits (114), Expect = 1e-07
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 237 TGQPVRRWREHASKVTCVKFNEDSSVVISGSQDNTVMMWD 276
+G+ ++ + H VT V F+ D + SGS D T+ +WD
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 34.2 bits (79), Expect = 0.008
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 198 LLKTYGGHAHEVNDATAACDSSQIASGASDKSVILWE 234
LLKT GH V + D +ASG+ D ++ LW+
Sbjct: 4 LLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 28.0 bits (63), Expect = 1.1
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 175 DGSYCLTCGSDKKIKLWN 192
DG Y + D IKLW+
Sbjct: 23 DGKYLASGSDDGTIKLWD 40
Score = 28.0 bits (63), Expect = 1.2
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 4/42 (9%)
Query: 447 TGELLEEYKGHKSGDFRIECCLDSKDSQIF-CGSSDGKIYKW 487
+GELL+ KGH + S D + GS DG I W
Sbjct: 1 SGELLKTLKGHTG---PVTSVAFSPDGKYLASGSDDGTIKLW 39
Score = 27.7 bits (62), Expect = 1.6
Identities = 10/40 (25%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 407 TGNLVTDYVG--EPIVDACFTRDCQCILTCSTDECLRLFD 444
+G L+ G P+ F+ D + + + S D ++L+D
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 45.4 bits (108), Expect = 8e-07
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 238 GQPVRRWREHASKVTCVKFNEDSSVVISGSQDNTVMMWD 276
G+ +R + H VT V F+ D +++ SGS D TV +WD
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 34.3 bits (79), Expect = 0.006
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 198 LLKTYGGHAHEVNDATAACDSSQIASGASDKSVILW 233
LL+T GH V + D + +ASG+ D +V +W
Sbjct: 3 LLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
Score = 28.9 bits (65), Expect = 0.65
Identities = 4/18 (22%), Positives = 10/18 (55%)
Query: 175 DGSYCLTCGSDKKIKLWN 192
DG+ + D +++W+
Sbjct: 22 DGNLLASGSDDGTVRVWD 39
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
This model represents one branch of COG0042 (Predicted
TIM-barrel enzymes, possibly dehydrogenases, nifR3
family). This branch includes NifR3 itself, from
Rhodobacter capsulatus. It excludes a broadly
distributed but more sparsely populated subfamily that
contains sll0926 from Synechocystis PCC6803, HI0634 from
Haemophilus influenzae, and BB0225 from Borrelia
burgdorferi. It also excludes a shorter and more distant
archaeal subfamily.The function of nifR3, a member of
this family, is unknown, but it is found in an operon
with nitrogen-sensing two component regulators in
Rhodobacter capsulatus.Members of this family show a
distant relationship to alpha/beta (TIM) barrel enzymes
such as dihydroorotate dehydrogenase and glycolate
oxidase [Unknown function, General].
Length = 319
Score = 40.8 bits (96), Expect = 0.001
Identities = 32/135 (23%), Positives = 55/135 (40%), Gaps = 21/135 (15%)
Query: 27 SKLNFRQLVRSHNVDLCFTPMIIADSFIKSSKARNNEFSTSPEDTPLVVQFASNNHDDFV 86
+ FR+LV + L M+ +++ + S+ + ++TP+ VQ ++ D
Sbjct: 19 TDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDETPISVQLFGSDPDTMA 78
Query: 87 RATQ----YVAPHCNGVDLNCGCPQRWAIKEGYGCALLSKQRTHPLLFSLPRTITRILYE 142
A + A +D+N GCP K+G G ALL P I +I+
Sbjct: 79 EAAKINEELGADI---IDINMGCPVPKITKKGAGSALLRD----------PDLIGKIVKA 125
Query: 143 LPKEWSIRVYRPLTV 157
+ V P+TV
Sbjct: 126 VVDA----VDIPVTV 136
>gnl|CDD|129825 TIGR00742, yjbN, tRNA dihydrouridine synthase A. This model
represents one branch of COG0042 (Predicted TIM-barrel
enzymes, possibly dehydrogenases, nifR3 family). It
represents a distinct subset by a set of shared unique
motifs, a conserved pattern of insertions/deletions
relative to other nifR3 homologs, and by subclustering
based on cross-genome bidirectional best hits. Members
are found in species as diverse as the proteobacteria, a
spirochete, a cyanobacterium, and Deinococcus
radiodurans. NifR3 itself, a protein of unknown function
associated with nitrogen regulation in Rhodobacter
capsulatus, is not a member of this branch. Members of
this family show a distant relationship to alpha/beta
(TIM) barrel enzymes such as dihydroorotate
dehydrogenase and glycolate oxidase [Protein synthesis,
tRNA and rRNA base modification].
Length = 318
Score = 40.6 bits (95), Expect = 0.001
Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 7/85 (8%)
Query: 25 WTSKLNFRQLVR--SHNVDLCFTPMIIADSFIKSSKARNNEFSTSPEDTPLVVQFASNNH 82
WT + +FR +R S + L +T MI A + I K +F SPE++P+ +Q ++
Sbjct: 11 WTDR-HFRYFLRLLSKHT-LLYTEMITAKAIIHGDKKDILKF--SPEESPVALQLGGSDP 66
Query: 83 DDFVRATQYV-APHCNGVDLNCGCP 106
+D + + + ++LN GCP
Sbjct: 67 NDLAKCAKIAEKRGYDEINLNVGCP 91
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 40.1 bits (93), Expect = 0.003
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 219 SQIASGASDKSVILWEVTTGQPVRRWREHASKVTCVKFNE-DSSVVISGSQDNTVMMWDV 277
SQ+AS + V +W+V Q V +EH +V + ++ D +++ SGS D +V +W +
Sbjct: 546 SQVASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSI 605
Score = 39.7 bits (92), Expect = 0.004
Identities = 25/97 (25%), Positives = 52/97 (53%), Gaps = 3/97 (3%)
Query: 185 DKKIKLWNPYRNLLLKTYGGHAHEV-NDATAACDSSQIASGASDKSVILWEVTTGQPVRR 243
+ +++W+ R+ L+ H V + ++ D + +ASG+ D SV LW + G +
Sbjct: 554 EGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGT 613
Query: 244 WREHASKVTCVKFNEDSSVVIS-GSQDNTVMMWDVKS 279
+ A+ + CV+F +S ++ GS D+ V +D+++
Sbjct: 614 IKTKAN-ICCVQFPSESGRSLAFGSADHKVYYYDLRN 649
Score = 35.1 bits (80), Expect = 0.11
Identities = 28/100 (28%), Positives = 51/100 (51%), Gaps = 3/100 (3%)
Query: 180 LTCGSDK-KIKLWNPYRNLLLKTYGGHAHEVNDATAACDSSQIASGASDKSVILWEVTTG 238
L GSD +KLW+ + + + T A+ + +A G++D V +++
Sbjct: 591 LASGSDDGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSLAFGSADHKVYYYDLRNP 650
Query: 239 Q-PVRRWREHASKVTCVKFNEDSSVVISGSQDNTVMMWDV 277
+ P+ H+ V+ V+F DSS ++S S DNT+ +WD+
Sbjct: 651 KLPLCTMIGHSKTVSYVRF-VDSSTLVSSSTDNTLKLWDL 689
Score = 30.4 bits (68), Expect = 2.6
Identities = 29/115 (25%), Positives = 50/115 (43%), Gaps = 13/115 (11%)
Query: 171 RFPVDGSYCLTCGS-DKKI---KLWNPYRNLLLKTYGGHAHEVNDATAACDSSQIASGAS 226
+FP + L GS D K+ L NP L L T GH + DSS + S ++
Sbjct: 624 QFPSESGRSLAFGSADHKVYYYDLRNP--KLPLCTMIGH-SKTVSYVRFVDSSTLVSSST 680
Query: 227 DKSVILWEVTTG------QPVRRWREHASKVTCVKFNEDSSVVISGSQDNTVMMW 275
D ++ LW+++ P+ + H + V + + +GS+ N V ++
Sbjct: 681 DNTLKLWDLSMSISGINETPLHSFMGHTNVKNFVGLSVSDGYIATGSETNEVFVY 735
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 37.4 bits (88), Expect = 0.014
Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 25 WTSKLNFRQLVR--SHNVDLCFTPMIIADSFIKSSKARNNEFSTSPEDTPLVVQFASNNH 82
WT + + R R S + L +T M+ + I + R F PE+ P+ +Q ++
Sbjct: 21 WTDR-HCRYFHRLLSRHA-LLYTEMVTTGAIIHGDRERLLAFD--PEEHPVALQLGGSDP 76
Query: 83 DDFVRATQYVAPHCNG---VDLNCGCP 106
D A + G ++LN GCP
Sbjct: 77 ADLAEAAKLAEDW--GYDEINLNVGCP 101
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 33.3 bits (76), Expect = 0.31
Identities = 16/59 (27%), Positives = 35/59 (59%)
Query: 221 IASGASDKSVILWEVTTGQPVRRWREHASKVTCVKFNEDSSVVISGSQDNTVMMWDVKS 279
+AS +D V +W+V G+ V + H+ ++T +++N D S++ + S+D + + D +
Sbjct: 141 LASAGADMVVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRD 199
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 32.9 bits (75), Expect = 0.35
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 98 GVDLNCGCPQRWAIKEGYGCALL 120
GVDLNCGCP + G G LL
Sbjct: 91 GVDLNCGCPSKTVNGSGGGATLL 113
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 31.8 bits (72), Expect = 1.1
Identities = 24/102 (23%), Positives = 46/102 (45%), Gaps = 10/102 (9%)
Query: 188 IKLWNPYRNLLLKTYGGHAHEVNDAT-AACDSSQIASGASDKSVILWEV--------TTG 238
I+L N R + GH + D C S +ASG+ D ++ +WE+
Sbjct: 56 IRLENQMRKPPVIKLKGHTSSILDLQFNPCFSEILASGSEDLTIRVWEIPHNDESVKEIK 115
Query: 239 QPVRRWREHASKVTCVKFNEDSSVVISGSQ-DNTVMMWDVKS 279
P + H K++ + +N + ++ S D+ V +WD+++
Sbjct: 116 DPQCILKGHKKKISIIDWNPMNYYIMCSSGFDSFVNIWDIEN 157
>gnl|CDD|133114 cd06904, M14_MpaA_like, Peptidase M14-like domain of Escherichia
coli Murein Peptide Amidase A and related proteins.
Peptidase M14-like domain of Escherichia coli Murein
Peptide Amidase A (MpaA) and related proteins. MpaA is a
member of the M14 family of metallocarboxypeptidases
(MCPs), however it has an exceptional type of activity,
it hydrolyzes the gamma-D-glutamyl-meso-diaminopimelic
acid (gamma-D-Glu-Dap) bond in murein peptides. MpaA is
specific for cleavage of the gamma-D-Glu-Dap bond of
free murein tripeptide; it may also cleave murein
tetrapeptide. MpaA has a different substrate specificity
and cellular role than endopeptidase I, ENP1 (ENP1 does
not belong to this group). MpaA works on free murein
peptide in the recycling pathway.
Length = 178
Score = 28.8 bits (65), Expect = 4.7
Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 9/68 (13%)
Query: 81 NHDDFVRATQYVAPHCNGVDLNCGCPQRWAIKEGYGCALLSKQRTHPLLFSLPRTITRIL 140
N D +RAT+ A NGVDLN P + S+ R +P +R L
Sbjct: 42 NPDGLLRATRCNA---NGVDLNRNFPTKDWPPGA------SRYRRYPGPKPGSEPESRAL 92
Query: 141 YELPKEWS 148
+L + +
Sbjct: 93 MDLIERFK 100
>gnl|CDD|220425 pfam09822, ABC_transp_aux, ABC-type uncharacterized transport
system. This domain is found in various eukaryotic and
prokaryotic intra-flagellar transport proteins involved
in gliding motility, as well as in several hypothetical
proteins.
Length = 268
Score = 28.8 bits (65), Expect = 5.8
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 440 LRLFDKATGELLEEYKGHKSGDFRIE 465
L+ ELLEEY G ++E
Sbjct: 41 LKPLRPRVRELLEEYAALSPGKIKVE 66
>gnl|CDD|215970 pfam00523, Fusion_gly, Fusion glycoprotein F0.
Length = 468
Score = 28.8 bits (65), Expect = 7.2
Identities = 26/117 (22%), Positives = 54/117 (46%), Gaps = 17/117 (14%)
Query: 291 NEALKEARDSITSVHSLVKSTKNHLSNGLLTKLVFAFRCKYLNGLLSGVLMSTQHLMVLL 350
N+A++E ++ + + + V++ +++++N L+ + C+ + L L Q+L L
Sbjct: 131 NKAVEEVQNGVQELATAVQALQDYINNELVPAIN-ELSCEIADIKLGIEL--NQYLTELT 187
Query: 351 DFLGSTQIGD--VTPISIHNSCFQALKEARDSITSVHVSDHEILTASLDCRIRRYDI 405
G QIG+ ++PISI QAL+ + IL + + +I
Sbjct: 188 TIFGP-QIGNPALSPISI-----QALRSLL------GSNIPPILEKQKNTNLNIAEI 232
>gnl|CDD|202159 pfam02212, GED, Dynamin GTPase effector domain.
Length = 90
Score = 27.1 bits (61), Expect = 7.5
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 2/35 (5%)
Query: 291 NEALKEARDSI--TSVHSLVKSTKNHLSNGLLTKL 323
N K D I ++ LV +K L LL L
Sbjct: 16 NIVRKRIADQIPKAIMYFLVNESKESLQKELLQLL 50
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 0.134 0.419
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,900,679
Number of extensions: 2383181
Number of successful extensions: 1996
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1943
Number of HSP's successfully gapped: 54
Length of query: 540
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 438
Effective length of database: 6,413,494
Effective search space: 2809110372
Effective search space used: 2809110372
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: 61 (27.3 bits)