RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy92
(638 letters)
>gnl|CDD|217409 pfam03178, CPSF_A, CPSF A subunit region. This family includes a
region that lies towards the C-terminus of the cleavage
and polyadenylation specificity factor (CPSF) A (160
kDa) subunit. CPSF is involved in mRNA polyadenylation
and binds the AAUAAA conserved sequence in pre-mRNA.
CPSF has also been found to be necessary for splicing of
single-intron pre-mRNAs. The function of the aligned
region is unknown but may be involved in RNA/DNA
binding.
Length = 318
Score = 272 bits (699), Expect = 1e-86
Identities = 116/377 (30%), Positives = 175/377 (46%), Gaps = 64/377 (16%)
Query: 231 QFHVSLFSPFSWEEIPQTNFPLHEWEHVLCLKNVSMEYEGTLSGLRGYIALGTNYNYSED 290
+ L P +WE I L E E VL +K+V++E G + Y+ +GT ++ ED
Sbjct: 1 ASCIRLVDPITWEVI--DTLELEENEAVLSVKSVNLEDSE---GRKEYLVVGTAFDLGED 55
Query: 291 VTCR-GRILLFDIIEVVPEPGQPLTKNKIKMIYAKEQKGPVTAICHVAGFLVTAVGQKIY 349
R GRI +F+IIE T K+K+++ E KG VTA+C G L+ GQK+
Sbjct: 56 PAARSGRIYVFEIIEPE-------TNRKLKLVHKTEVKGAVTALCEFQGRLLAGQGQKLR 108
Query: 350 IWQLKDNDLTGIAFIDT-EVYIASMVSVKNLILVGDYARSIALLRYQPEYRTLSLVARDY 408
++ L + L AF+DT Y+ S+ N I+VGD +S+ L Y E L L ARD
Sbjct: 109 VYDLGKDKLLPKAFLDTPITYVVSLKVFGNRIIVGDLMKSVTFLGYDEEPYRLILFARDT 168
Query: 409 KPTQPNSKGYYAGNPSRGIIDGSLVWKFLQLSLGERLEICKKIGSKHNDILDEFSSMGFM 468
+P + + L ++ + +
Sbjct: 169 QPRWVTA----------------------------------------AEFLVDYDT--IL 186
Query: 469 ISDKDKNVVLFMYQPEARESNGGH-RLIKKTDFHLGQHVNTFFKIRCKPSSISDAPGARS 527
+DK N+ + Y PEA ES G RL+ + +FHLG V +F K P + + S
Sbjct: 187 GADKFGNLHVLRYDPEAPESLDGDPRLLHRAEFHLGDIVTSFQKGSLVPK--TGGAESTS 244
Query: 528 RFLTWYASLDGALGFFLP-LPEKNYRRLLMLQNVMVTHTSHTGGLNPRAFRTYKGKGYYA 586
Y +LDG++G +P + E+ YRRL LQ + H GL+PRAFR+Y +
Sbjct: 245 SPQILYGTLDGSIGLLVPFISEEEYRRLQHLQQQLRDELPHLCGLDPRAFRSYYSRSP-- 302
Query: 587 GNPSRGIIDGSLVWKFL 603
P + +IDG L+ +FL
Sbjct: 303 --PVKNVIDGDLLERFL 317
>gnl|CDD|227490 COG5161, SFT1, Pre-mRNA cleavage and polyadenylation specificity
factor [RNA processing and modification].
Length = 1319
Score = 230 bits (588), Expect = 2e-64
Identities = 136/552 (24%), Positives = 219/552 (39%), Gaps = 61/552 (11%)
Query: 89 MRYFSNIAGYQGVFLCGPHPAWLFLTSRGELRAHPMTI-DGPVSTLAPFHNVNCPRGFLY 147
F G+ +F+ G P SR + + P+ ++ P RG+L
Sbjct: 824 DMVFIKAVGHSFMFVTGKGP--FLCRSRYTSSSKAFHRGNIPLVSVIPLSK----RGYLM 877
Query: 148 FNAKSELRISVLPTHLSYDA-PWPVRKVPLKCTPHFLAYHLETKTYCIVTSTAEPSTDYY 206
+ +R S Y PV++ P T L YH Y +V S E +
Sbjct: 878 VDNVLGVRASQYVFDNGYVGNKNPVKRTPKHKTLQKLVYH-CAGRYMVVGSCEEAG---F 933
Query: 207 KFNGEDKELVTDPRDSRFIPPLVSQFHVSLFSPFSWEEIPQTNFPLHEWEHVLCLKNVSM 266
GED E P D+ +F+V L+SP SWE I F E E+V +K + +
Sbjct: 934 SPKGEDGESGI-PVDTNVPHAEGYRFYVDLYSPKSWEVIDTYEFD--ENEYVFHIKYLIL 990
Query: 267 EYEGTLSGLRGYIALGTNYNYSEDVTCRGRILLFDIIEVVPEPGQPLTKNKIKMIYAKEQ 326
+ G YI +GT + ED RGR+ + +II VVP PG P T K+K++ +E
Sbjct: 991 DDMQGTKGKSPYILVGTTFIEGEDRPARGRLHVLEIISVVPSPGSPFTDCKLKVLGIEET 1050
Query: 327 KGPVTAICHVAGFLVTAVGQKIYIWQLKDND-LTGIAFIDTEVYIASMVSVKNLILVGDY 385
KG V +C V G + GQK+ + ++ + + + F D ++ +S+ VKNL+L GD
Sbjct: 1051 KGTVVRVCEVRGKIALCQGQKVMVRKIDRSSGIIPVGFYDLHIFTSSIKVVKNLLLAGDI 1110
Query: 386 ARSIALLRYQPEYRTLSLVARDYKPTQPNSKGYYAGNPSRGIIDGSLVWKFLQLSLGERL 445
+ ++ +Q E P R + S S
Sbjct: 1111 YQGLSFFGFQSE-------------------------PYRMHLISSSEPLRNATST---- 1141
Query: 446 EICKKIGSKHNDILDEFSSMGFMISDKDKNVVLFMYQPEARESNGGHRLIKKTDFHLGQH 505
+ L + + F+ D N+ Y P S G RL+K++ F L
Sbjct: 1142 -----------EFLVTGNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKRSSFTLH-- 1188
Query: 506 VNTFFKIRCKPSSISDAPGARSRFLTWYASLDGALGFFLPLPEKNYRRLLMLQNVMVTHT 565
+ K+ P + G + F+ Y+ DG L +P+ + +YRRLL +Q ++
Sbjct: 1189 -SAEIKMNLLPRNSEFGAGFKKNFIMVYSRSDGMLIHVVPISDAHYRRLLGIQTAIMARL 1247
Query: 566 SHTGGLNPRAFRTYKGKGYYAGNPSRGIIDGSLVWKFLQLSLGERLEICKKIGSKHNDIL 625
GGLNPR +R + R +D ++ F + R + K G +
Sbjct: 1248 KSVGGLNPRDYR-LNSDIHLHSLSLRSPLDLHIINLFSYFDMSTRESVASKAGRIDRKEI 1306
Query: 626 DELYDIE-ALSS 636
++ L S
Sbjct: 1307 SDMIASLNLLRS 1318
>gnl|CDD|213781 TIGR03170, flgA_cterm, flagella basal body P-ring formation protein
FlgA. This model describes a conserved C-terminal
region of the flagellar basal body P-ring formation
protein FlgA. This sequence region contains a SAF
domain, now described by pfam08666 [Cellular processes,
Chemotaxis and motility].
Length = 122
Score = 32.9 bits (76), Expect = 0.15
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 309 PGQPLTKNKIKMIYAKEQKGPVTAICHVAGFLVTAVGQ 346
GQPLT N ++ + ++ VT I G +T G+
Sbjct: 51 AGQPLTANMLRPPWLVKRGDTVTVIARGGGLSITTEGK 88
>gnl|CDD|235646 PRK05925, PRK05925, aspartate kinase; Provisional.
Length = 440
Score = 30.9 bits (70), Expect = 2.2
Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 592 GIIDGSLVWKFLQLSLGERLEICKKIGSKHNDILDEL 628
G+ D L+ +F +LS G+R + +KI KH +I EL
Sbjct: 41 GVTD--LLEEFCRLSKGKREALTEKIREKHEEIAKEL 75
Score = 29.0 bits (65), Expect = 9.4
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 426 GIIDGSLVWKFLQLSLGERLEICKKIGSKHNDILDE 461
G+ D L+ +F +LS G+R + +KI KH +I E
Sbjct: 41 GVTD--LLEEFCRLSKGKREALTEKIREKHEEIAKE 74
>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 = 29.4 bits (67), Expect = 5.1
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 11/68 (16%)
Query: 48 FRHPKGALKLRF-KKLKVLFVSDRSKRANEQPGLPRGVRISQ------MRYFSNIAGYQG 100
FR LK R+ +L V+ V R P L RG R+ ++ + +
Sbjct: 153 FREELADLKARYPDRLTVIHVLSRE---QGDPDLLRG-RLDAAKLNALLKNLLDATEFDE 208
Query: 101 VFLCGPHP 108
FLCGP P
Sbjct: 209 AFLCGPEP 216
>gnl|CDD|177093 CHL00194, ycf39, Ycf39; Provisional.
Length = 317
Score = 29.2 bits (66), Expect = 6.8
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 9/79 (11%)
Query: 296 RILLFDIIEVVPEPGQPLTKNKIKMIYAKEQKGPVTAICHVAGFLVTAVGQ-------KI 348
R + F I+ P PL K K + ++ G I +AGF + Q K
Sbjct: 104 RFIFFSILNAEQYPYIPLMKLKSDIEQKLKKSGIPYTIFRLAGFFQGLISQYAIPILEKQ 163
Query: 349 YIWQLKDNDLTGIAFIDTE 367
IW ++ T I++IDT+
Sbjct: 164 PIWITNES--TPISYIDTQ 180
>gnl|CDD|224181 COG1261, FlgA, Flagellar basal body P-ring biosynthesis protein
[Cell motility and secretion / Posttranslational
modification, protein turnover, chaperones].
Length = 220
Score = 28.5 bits (64), Expect = 8.9
Identities = 11/52 (21%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 295 GRILLFDIIEVVPEPGQPLTKNKIKMIYAKEQKGPVTAICHVAGFLVTAVGQ 346
G++ ++ PGQP+ + ++ + ++ VT + G +TA G+
Sbjct: 138 GKVSKRTLL-----PGQPILASMLRQAWLVKRGQIVTVVAEGGGISITAEGK 184
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
0.322 0.139 0.428
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 33,093,224
Number of extensions: 3265112
Number of successful extensions: 2252
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2240
Number of HSP's successfully gapped: 17
Length of query: 638
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 535
Effective length of database: 6,369,140
Effective search space: 3407489900
Effective search space used: 3407489900
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: 62 (27.6 bits)