RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9514
(611 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 = 260 bits (666), Expect = 3e-83
Identities = 99/336 (29%), Positives = 144/336 (42%), Gaps = 108/336 (32%)
Query: 260 KLYLSPLTTVGNLPFRRLCKKWGADITCSEMAVATELLKSSPQEWALIKRHESEDLFGVQ 319
KL L+P+ V +LPFR LC+++GAD+ +EM A LL+ + + L+ R+ E VQ
Sbjct: 1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQ 60
Query: 320 LCGNNPYVLTKCTQLLEEQMAVDFVDVNLGCPIEFIYKQGSGSGLLQRANLFGVQLCGNN 379
L G++P L + +++EE LG
Sbjct: 61 LGGSDPETLAEAAKIVEE----------LGA----------------------------- 81
Query: 380 PYVLTKCTQLLEEQMVVDFVDVNLGCPIEFIYKQGSGSGLLQRANILQSVITCMNEVSSL 439
D +D+N+GCP + K G+G+ LL+ ++ ++ + E +
Sbjct: 82 -----------------DGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPI 124
Query: 440 PITVKTRTGIHKDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYIEKCAQLCS 499
P+TVK R G WD
Sbjct: 125 PVTVKIRLG---------------------------------------WD---------- 135
Query: 500 RDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYIEKCAQLCSPAPLYGNGDIL 559
D D GAS +T+HGRTREQRY+ ADWDYI + + S P+ NGDI
Sbjct: 136 -DEEETLELAKALEDAGASALTVHGRTREQRYSGPADWDYIAEIKEAVSI-PVIANGDIF 193
Query: 560 SYEDYTESLKKSPSISGVMIGRGALIKPWIFQEIKE 595
S ED L+++ + GVMIGRGAL PW+F+EIKE
Sbjct: 194 SLEDALRCLEQT-GVDGVMIGRGALGNPWLFREIKE 228
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 168 bits (428), Expect = 2e-47
Identities = 91/358 (25%), Positives = 140/358 (39%), Gaps = 106/358 (29%)
Query: 251 EKKKIDWQGKLYLSPLTTVGNLPFRRLCKKWGADITCSEMAVATELLKSSPQEWALIKRH 310
+ I+ + ++ L+P+ V +LPFRRL ++ GA TE++ +
Sbjct: 3 KIGLIELRNRVILAPMAGVTDLPFRRLARELGAYDLL-----YTEMVSAKALLH------ 51
Query: 311 ESEDLFGVQLCGNNPYVLTKCTQLLEEQMAVDFVDVNLGCPIEFIYKQGSGSGLLQRANL 370
L +L EE+
Sbjct: 52 ------------GRKKFLLLLDELEEER-------------------------------P 68
Query: 371 FGVQLCGNNPYVLTKCTQLLEEQMVVDFVDVNLGCPIEFIYKQGSGSGLLQRANILQSVI 430
VQL G++P +L + ++ EE + D +D+N GCP + K G+G+ LL+ +L ++
Sbjct: 69 VAVQLGGSDPELLAEAAKIAEE-LGADIIDLNCGCPSPKVVKGGAGAALLKNPELLAEIV 127
Query: 431 TCMNE-VSSLPITVKTRTGIHKDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWD 489
M E V +P+TVK R G WD
Sbjct: 128 KAMVEAVGDIPVTVKIRLG---------------------------------------WD 148
Query: 490 YIEKCAQLCSRDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYIEKCAQLCSP 549
+ A +R D GA +T+HGRTR Q Y ADWDYI++ +
Sbjct: 149 DDDILALEIAR----------ILEDAGADALTVHGRTRAQGYLGPADWDYIKELKEAVPS 198
Query: 550 APLYGNGDILSYEDYTESLKKSPSISGVMIGRGALIKPWIFQEIKEKKLFDIYAIVWK 607
P+ NGDI S ED E L+ + GVMIGRGAL PW+F++I + ++
Sbjct: 199 IPVIANGDIKSLEDAKEMLEYT-GADGVMIGRGALGNPWLFRQIDYLETGELLPPTLA 255
>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 = 161 bits (410), Expect = 6e-45
Identities = 94/341 (27%), Positives = 143/341 (41%), Gaps = 107/341 (31%)
Query: 253 KKIDWQGKLYLSPLTTVGNLPFRRLCKKWGADITCSEMAVATELLKSSPQEWALIKRHES 312
I + ++ L+P+ V + PFRRL ++GA +T EM + ++ S + L+ E
Sbjct: 2 GNIQLKSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAED 61
Query: 313 EDLFGVQLCGNNPYVLTKCTQLLEEQMAVDFVDVNLGCPIEFIYKQGSGSGLLQRANLFG 372
E VQL G++P + + ++ EE A D +D+N+GCP+ I K+G+GS LL+ +L G
Sbjct: 62 ETPISVQLFGSDPDTMAEAAKINEELGA-DIIDINMGCPVPKITKKGAGSALLRDPDLIG 120
Query: 373 VQLCGNNPYVLTKCTQLLEEQMVVDFVDVNLGCPIEFIYKQGSGSGLLQRANILQSVITC 432
++++ VVD VD+
Sbjct: 121 ---------------KIVKA--VVDAVDI------------------------------- 132
Query: 433 MNEVSSLPITVKTRTGIHKDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYIE 492
P+TVK R G + N
Sbjct: 133 -------PVTVKIRIGWDDAH---IN--------------------------------AV 150
Query: 493 KCAQLCSRDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYIEKCAQLCSPAPL 552
+ A++ D GA +TLHGRTR Q Y+ +A+WD I + Q P+
Sbjct: 151 EAARIA--------------EDAGAQAVTLHGRTRAQGYSGEANWDIIARVKQ-AVRIPV 195
Query: 553 YGNGDILSYEDYTESLKKSPSISGVMIGRGALIKPWIFQEI 593
GNGDI S ED L+ + GVMIGRGAL PW+F++I
Sbjct: 196 IGNGDIFSPEDAKAMLETT-GCDGVMIGRGALGNPWLFRQI 235
>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 = 138 bits (349), Expect = 2e-36
Identities = 87/332 (26%), Positives = 132/332 (39%), Gaps = 108/332 (32%)
Query: 263 LSPLTTVGNLPFRRLCKKWGA-DITCSEMAVATELLKSSPQEWALIKRHESEDLFGVQLC 321
L+P+ V +LPFRRL +++GA D+ +EM A L+ Q ++ E VQL
Sbjct: 2 LAPMAGVTDLPFRRLVREYGAGDLVVTEMVTAKAQLRPEKQRELMLPELEEPTPLAVQLG 61
Query: 322 GNNPYVLTKCTQLLEEQMAVDFVDVNLGCPIEFIYKQGSGSGLLQRANLFGVQLCGNNPY 381
G++P +L + +L+ + A D +D+N+GCP + + + G+G+ LL+ +L
Sbjct: 62 GSDPALLAEAAKLVADLGA-DIIDINMGCPAKKVTRGGAGAALLRDPDL----------- 109
Query: 382 VLTKCTQLLEEQMVVDFVDVNLGCPIEFIYKQGSGSGLLQRANILQSVITCMNEVSSLPI 441
Q+++ VV VD+ P+
Sbjct: 110 ----VAQIVKA--VVKAVDI--------------------------------------PV 125
Query: 442 TVKTRTGIHKDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYIEKCAQLCSRD 501
TVK R G + + + D GA +T+HGRTR Q Y ADWD I Q+ +
Sbjct: 126 TVKIRIGWDESHENAVEIARRVEDAGAQALTVHGRTRAQNYEGPADWDAI---KQVK-QA 181
Query: 502 NNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYIEKCAQLCSPAPLYGNGDILSY 561
+I P+ NGDI
Sbjct: 182 VSI----------------------------------------------PVIANGDITDA 195
Query: 562 EDYTESLKKSPSISGVMIGRGALIKPWIFQEI 593
ED L + + GVMIGRGAL PW+F E
Sbjct: 196 EDAQRCLSYTGAD-GVMIGRGALGNPWLFAEQ 226
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 88.9 bits (220), Expect = 3e-19
Identities = 83/347 (23%), Positives = 133/347 (38%), Gaps = 131/347 (37%)
Query: 260 KLYLSPLTTVGNLPFRRLCKKWGADITCSEMAVATELLKSSPQEWALIKR-----HESE- 313
+L +P+ + + PFR LC + GA +T SEM + S+PQ W K H E
Sbjct: 11 RLIAAPMAGITDRPFRTLCYEMGAGLTVSEM------MSSNPQVWESDKSRLRMVHIDEP 64
Query: 314 DLFGVQLCGNNPYVLTKCTQLLEEQMAVDFVDVNLGCPIEFIYKQGSGSGLLQRANLFGV 373
+ VQ+ G++P +E ++V G I
Sbjct: 65 GIRTVQIAGSDP----------KEMADAARINVESGAQI--------------------- 93
Query: 374 QLCGNNPYVLTKCTQLLEEQMVVDFVDVNLGCPIEFIYKQGSGSGLLQRANILQSVITCM 433
+D+N+GCP + + ++ +GS LLQ ++++S++T +
Sbjct: 94 -------------------------IDINMGCPAKKVNRKLAGSALLQYPDLVKSILTEV 128
Query: 434 NEVSSLPITVKTRTGIHKDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYIEK 493
+P+T+K RTG + P+ R+ +
Sbjct: 129 VNAVDVPVTLKIRTG----------WAPEHRN-------------------------CVE 153
Query: 494 CAQLCSRDNNIIHNFMPKFRDWGASLITLHGRTREQRYTKQADWDYIEKCAQLCSPAPLY 553
AQL D G +T+HGRTR + +A++D I Q S P+
Sbjct: 154 IAQLA--------------EDCGIQALTIHGRTRACLFNGEAEYDSIRAVKQKVS-IPVI 198
Query: 554 GNGDILSYE------DYTESLKKSPSISGVMIGRGALIKPWIFQEIK 594
NGDI DYT + +MIGR A +PWIF+EI+
Sbjct: 199 ANGDITDPLKARAVLDYTGA-------DALMIGRAAQGRPWIFREIQ 238
>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 = 63.3 bits (154), Expect = 7e-11
Identities = 30/106 (28%), Positives = 57/106 (53%), Gaps = 3/106 (2%)
Query: 373 VQLCGNNPYVLTKCTQLLEEQMVVDFVDVNLGCPIEFIYKQGSGSGLLQRANILQSVITC 432
+QL G++P L KC ++ E++ D +++N+GCP + + G+ L+ A+++ +
Sbjct: 59 LQLGGSDPNDLAKCAKIAEKRGY-DEINLNVGCPSDRVQNGNFGACLMGNADLVADCVKA 117
Query: 433 MNEVSSLPITVKTRTGI-HKDN-NIIHNFMPKFRDWGASLITLHGR 476
M E ++P+TVK R GI D+ + +F+ G +H R
Sbjct: 118 MQEAVNIPVTVKHRIGIDPLDSYEFLCDFVEIVSGKGCQNFIVHAR 163
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 53.3 bits (128), Expect = 1e-07
Identities = 64/256 (25%), Positives = 93/256 (36%), Gaps = 78/256 (30%)
Query: 350 CPIEFIYKQGSGSGLLQRANLFGVQLCGNNPYVLTKCTQLLEEQMV--VDF----VDVNL 403
CP E + SG L R +QL G P Q L E V+ VD+N
Sbjct: 50 CP-ELHNASRTPSGTLVR-----IQLLGQYP-------QWLAENAARAVELGSWGVDLNC 96
Query: 404 GCPIEFIYKQGSGSGLLQRANILQSVITCMNEV--SSLPITVKTRTGIHKDNNIIHNF-- 459
GCP + + G G+ LL+ ++ M E + LP+TVK R G F
Sbjct: 97 GCPSKTVNGSGGGATLLKDPELIYQGAKAMREAVPAHLPVTVKVRLGWDSGE---RKFEI 153
Query: 460 MPKFRDWGASLITLHGRTREQRYTKQA-DWDYIEKCAQLCSRDNNIIHNFMPKFRDWGAS 518
+ GA+ + +HGRT+E Y + +W I
Sbjct: 154 ADAVQQAGATELVVHGRTKEDGYRAEHINWQAI--------------------------- 186
Query: 519 LITLHGRTREQRYTKQADWDYIEKCAQLCSPAPLYGNGDILSYEDYTESLKKSPSISGVM 578
G R QR T P+ NG+I ++ + + + VM
Sbjct: 187 -----GEIR-QRLT-----------------IPVIANGEIWDWQSAQQCMAIT-GCDAVM 222
Query: 579 IGRGALIKPWIFQEIK 594
IGRGAL P + + +K
Sbjct: 223 IGRGALNIPNLSRVVK 238
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 48.6 bits (117), Expect = 5e-06
Identities = 30/118 (25%), Positives = 54/118 (45%), Gaps = 27/118 (22%)
Query: 373 VQLCGNNPYVLTKCTQLLEEQMVVDF----VDVNLGCPIE------FIYKQGSGSGLLQR 422
+QL G++P L + +L E D+ +++N+GCP + F G+ L+
Sbjct: 69 LQLGGSDPADLAEAAKLAE-----DWGYDEINLNVGCPSDRVQNGRF------GACLMAE 117
Query: 423 ANILQSVITCMNEVSSLPITVKTRTGIHKDNNIIHNFMPKF----RDWGASLITLHGR 476
++ + M + S+P+TVK R GI D+ + F+ F + G +H R
Sbjct: 118 PELVADCVKAMKDAVSIPVTVKHRIGI--DDQDSYEFLCDFVDTVAEAGCDTFIVHAR 173
Score = 30.9 bits (71), Expect = 1.8
Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 318 VQLCGNNPYVLTKCTQLLEEQMAVDFVDVNLGCP 351
+QL G++P L + +L E D +++N+GCP
Sbjct: 69 LQLGGSDPADLAEAAKLA-EDWGYDEINLNVGCP 101
Score = 29.3 bits (67), Expect = 6.3
Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 555 NGDILSYEDYTESLKKSPSISGVMIGRGALIKPWIFQEI 593
NG I + E+ E L+ + GVMIGR A P++ E+
Sbjct: 211 NGGIKTLEEAKEHLQH---VDGVMIGRAAYHNPYLLAEV 246
>gnl|CDD|227395 COG5063, CTH1, CCCH-type Zn-finger protein [General function
prediction only].
Length = 351
Score = 38.1 bits (88), Expect = 0.011
Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 2/74 (2%)
Query: 64 RGPTFVTKPEDCYCPFLKDSTLEQTCKYGEKCKFVHDKNV--FMKSKPEDISEQCYVFLQ 121
RG L+ ST C+Y +K F H K + ++ P+ +E VF+
Sbjct: 102 RGSNANKPYGLYKTEMLRSSTEIPYCRYPDKNPFAHSKAISSLAQTHPKYKTESLEVFIN 161
Query: 122 HGYCPMGIACRFGS 135
GY P C F S
Sbjct: 162 PGYVPYSKRCCFIS 175
Score = 37.7 bits (87), Expect = 0.013
Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 4/50 (8%)
Query: 88 TCKYGEKCKFVH--DKNVFMKSKPED--ISEQCYVFLQHGYCPMGIACRF 133
C YG +C F H D ++ M + + C + G P G A
Sbjct: 285 YCPYGLRCCFKHGDDSDIEMYEEASLGYLDGPCRTRAKGGAFPSGGAVCK 334
Score = 29.6 bits (66), Expect = 5.0
Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 13/72 (18%)
Query: 70 TKPEDCYCPFLKDSTLEQTCKY---GEKCKFVHDKNVFMKSKPEDIS-----EQCYVFLQ 121
T PE C + T + TC Y G KC+F + + K + E C + +
Sbjct: 228 TNPELC-----ESFTRKGTCPYWISGVKCQFACRGHGLNELKSKKKKQNFRTEPCINWEK 282
Query: 122 HGYCPMGIACRF 133
GYCP G+ C F
Sbjct: 283 SGYCPYGLRCCF 294
>gnl|CDD|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and
similar).
Length = 27
Score = 30.6 bits (70), Expect = 0.13
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 88 TCKYGEKCKFVHDK 101
TCKYG++CKF H +
Sbjct: 14 TCKYGDRCKFAHGQ 27
Score = 28.3 bits (64), Expect = 0.66
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 114 EQCYVFLQHGYCPMGIACRF 133
E C F + G C G C+F
Sbjct: 4 ELCRFFSRTGTCKYGDRCKF 23
>gnl|CDD|214632 smart00356, ZnF_C3H1, zinc finger.
Length = 27
Score = 28.0 bits (63), Expect = 0.97
Identities = 6/14 (42%), Positives = 8/14 (57%)
Query: 88 TCKYGEKCKFVHDK 101
C G++CKF H
Sbjct: 14 YCPRGDRCKFAHPL 27
>gnl|CDD|218339 pfam04941, LEF-8, Late expression factor 8 (LEF-8). Late
expression factor 8 (LEF-8) is one of the primary
components of RNA polymerase produced by polyhedrosis
viruses. LEF-8 shows homology to the second largest
subunit of prokaryotic DNA-directed RNA polymerase.
Length = 748
Score = 30.9 bits (70), Expect = 2.1
Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 23/102 (22%)
Query: 87 QTCKYGEKCKFVHD-----KNVFMKSKPEDISEQCYVFLQHGYCPMGIACRFGSSHLDEN 141
Q+ Y ++ K + D K ++ SK S+Q F +N
Sbjct: 264 QSILYPKESKKIVDTIVNGKLIYSVSK--TFSKQKKNFPNQ----------------QDN 305
Query: 142 GGNIVKEDVLKEWKNTVGNKTVNMLANEVRQDLRKHTYNFEK 183
N E K +GN+ V + + +RQD+ K +F K
Sbjct: 306 SSNNNIEISPPVLKYRIGNEVVRITNDTMRQDMLKQKSDFVK 347
>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING
and CCCH-type Zn-fingers [General function prediction
only].
Length = 259
Score = 30.0 bits (67), Expect = 3.4
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 15/61 (24%)
Query: 51 KKNKQVLKGQNKARGPTFV-------TKPEDCYCPFLKDSTLEQTCKYGEKCKFVHDKNV 103
KNK++ K N PT T+P+ C KD C YG+ CKF+HD++
Sbjct: 116 GKNKRLTKQIN---QPTMFRDGEVIDTQPDVC-----KDYKETGYCGYGDSCKFLHDRSD 167
Query: 104 F 104
F
Sbjct: 168 F 168
>gnl|CDD|227416 COG5084, YTH1, Cleavage and polyadenylation specificity factor
(CPSF) Clipper subunit and related makorin family
Zn-finger proteins [General function prediction only].
Length = 285
Score = 29.5 bits (66), Expect = 4.7
Identities = 18/80 (22%), Positives = 27/80 (33%), Gaps = 5/80 (6%)
Query: 85 LEQTCKYGEKCKFVHDKNVFMKSKPEDISEQCYVFLQHGYCPMGIACRFGSSHLDENGGN 144
L CK G C+F+H+ ++ P C F G C G +C + D GN
Sbjct: 111 LRGLCKSGFSCEFLHEYDLRSSQGPP-----CRSFSLKGSCSSGPSCGYSHIDPDSFAGN 165
Query: 145 IVKEDVLKEWKNTVGNKTVN 164
+ +G
Sbjct: 166 CDQYSGATYGFCPLGASCKF 185
>gnl|CDD|240080 cd04729, NanE, N-acetylmannosamine-6-phosphate epimerase (NanE)
converts N-acetylmannosamine-6-phosphate to
N-acetylglucosamine-6-phosphate. This reaction is part
of the pathway that allows the usage of sialic acid as a
carbohydrate source. Sialic acids are a family of
related sugars that are found as a component of
glycoproteins, gangliosides, and other
sialoglycoconjugates.
Length = 219
Score = 29.1 bits (66), Expect = 6.1
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 516 GASLI--TLHGRTREQRYTKQADWDYIEKCAQLCSPAPLYGNGDI 558
G +I TL G T E T+ D++ +++ + P+ G I
Sbjct: 143 GFDIIGTTLSGYTEETAKTEDPDFELLKELRKALG-IPVIAEGRI 186
Score = 29.1 bits (66), Expect = 6.4
Identities = 9/33 (27%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 467 GASLI--TLHGRTREQRYTKQADWDYIEKCAQL 497
G +I TL G T E T+ D++ +++ +
Sbjct: 143 GFDIIGTTLSGYTEETAKTEDPDFELLKELRKA 175
>gnl|CDD|129819 TIGR00736, nifR3_rel_arch, TIM-barrel protein, putative. Members
of this family show a distant relationship by PSI-BLAST
to alpha/beta (TIM) barrel enzymes such as
dihydroorotate dehydrogenase and glycolate oxidase. At
least two closely related but well-separable families
among the bacteria, the nifR3/yhdG family and the yjbN
family, share a more distant relationship to this family
of shorter, exclusively archaeal proteins [Unknown
function, General].
Length = 231
Score = 28.3 bits (63), Expect = 9.2
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 396 VDFVDVNLGCPIEFIYKQGSGSGLLQRANILQSVITCMNEVSSLPITVKTRTGIHK 451
D +++N C I + G G LL+ +L+ +T M E++ PI VK R
Sbjct: 93 ADIIEINAHCRQPEITEIGIGQELLKNKELLKEFLTKMKELNK-PIFVKIRGNCIP 147
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
0.318 0.135 0.414
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,404,712
Number of extensions: 2912152
Number of successful extensions: 2244
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2208
Number of HSP's successfully gapped: 49
Length of query: 611
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 508
Effective length of database: 6,369,140
Effective search space: 3235523120
Effective search space used: 3235523120
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 (21.7 bits)
S2: 62 (27.6 bits)