RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5026
(293 letters)
>gnl|CDD|214598 smart00282, LamG, Laminin G domain.
Length = 132
Score = 96.3 bits (240), Expect = 7e-25
Identities = 45/125 (36%), Positives = 68/125 (54%), Gaps = 4/125 (3%)
Query: 169 DLTIVFKAIEPNGILLYNGHRADGVGDFIALYLNDRYVDFTFDLGTGAATLRSS-NPISL 227
++ F+ PNG+LLY G + G D++AL L D + +DLG+G A L S P++
Sbjct: 1 SISFSFRTTSPNGLLLYAGSKGGG--DYLALELRDGRLVLRYDLGSGPARLTSDPTPLND 58
Query: 228 GEWRKLRLTRTGRHAYLQVDRFPSSQILSPGPFTQLSLSLSLYLGGVPDYNIVSPKVKIK 287
G+W ++ + R GR L VD SPG T L+L LYLGG+P+ ++ P + +
Sbjct: 59 GQWHRVAVERNGRSVTLSVDGGNRVSGESPGGLTILNLDGPLYLGGLPE-DLKLPPLPVT 117
Query: 288 SSFIG 292
F G
Sbjct: 118 PGFRG 122
Score = 56.6 bits (137), Expect = 3e-10
Identities = 30/132 (22%), Positives = 52/132 (39%), Gaps = 26/132 (19%)
Query: 12 IQFKPESWDGILFLTGERDDLNGDFMTLLIFEGYVEF-----------STPYRPYAD--- 57
F+ S +G+L G + GD++ L + +G + ++ P D
Sbjct: 4 FSFRTTSPNGLLLYAGSKGG--GDYLALELRDGRLVLRYDLGSGPARLTSDPTPLNDGQW 61
Query: 58 --ITVHRTVRTLIL-------PYTVPSGLFSRITFREPVFVGGRGNTSGLSDKLPTEKGF 108
+ V R R++ L G + + P+++GG L LP GF
Sbjct: 62 HRVAVERNGRSVTLSVDGGNRVSGESPGGLTILNLDGPLYLGGLPEDLKLP-PLPVTPGF 120
Query: 109 KGCIRHLDINDH 120
+GCIR+L +N
Sbjct: 121 RGCIRNLKVNGK 132
>gnl|CDD|238058 cd00110, LamG, Laminin G domain; Laminin G-like domains are usually
Ca++ mediated receptors that can have binding sites for
steroids, beta1 integrins, heparin, sulfatides,
fibulin-1, and alpha-dystroglycans. Proteins that
contain LamG domains serve a variety of purposes
including signal transduction via cell-surface steroid
receptors, adhesion, migration and differentiation
through mediation of cell adhesion molecules.
Length = 151
Score = 97.1 bits (242), Expect = 7e-25
Identities = 46/125 (36%), Positives = 69/125 (55%), Gaps = 3/125 (2%)
Query: 168 LDLTIVFKAIEPNGILLYNGHRADGVGDFIALYLNDRYVDFTFDLGTGAATLRSSNPISL 227
L ++ F+ PNG+LLY G GDF+AL L D + +DLG+G+ L S P++
Sbjct: 22 LSISFSFRTTSPNGLLLYAGS--QNGGDFLALELEDGRLVLRYDLGSGSLVLSSKTPLND 79
Query: 228 GEWRKLRLTRTGRHAYLQVDRFPSSQILSPGPFTQLSLSLSLYLGGVPDYNIVSPKVKIK 287
G+W + + R GR L VD + SPG L+L LYLGG+P+ ++ SP + +
Sbjct: 80 GQWHSVSVERNGRSVTLSVDGERVVESGSPGGSALLNLDGPLYLGGLPE-DLKSPGLPVS 138
Query: 288 SSFIG 292
F+G
Sbjct: 139 PGFVG 143
Score = 52.4 bits (126), Expect = 2e-08
Identities = 31/133 (23%), Positives = 48/133 (36%), Gaps = 25/133 (18%)
Query: 8 WRFPIQFKPESWDGILFLTGERDDLNGDFMTLLIFEGYVEFS----------TPYRPYAD 57
F+ S +G+L G GDF+ L + +G + + P D
Sbjct: 22 LSISFSFRTTSPNGLLLYAG--SQNGGDFLALELEDGRLVLRYDLGSGSLVLSSKTPLND 79
Query: 58 -----ITVHRTVRTLIL------PYTVPSGLFSRITF-REPVFVGGRGNTSGLSDKLPTE 105
++V R R++ L S S + P+++GG LP
Sbjct: 80 GQWHSVSVERNGRSVTLSVDGERVVESGSPGGSALLNLDGPLYLGGLPEDLKSP-GLPVS 138
Query: 106 KGFKGCIRHLDIN 118
GF GCIR L +N
Sbjct: 139 PGFVGCIRDLKVN 151
>gnl|CDD|216930 pfam02210, Laminin_G_2, Laminin G domain. This family includes the
Thrombospondin N-terminal-like domain, a Laminin G
subfamily.
Length = 124
Score = 91.7 bits (228), Expect = 3e-23
Identities = 40/120 (33%), Positives = 63/120 (52%), Gaps = 4/120 (3%)
Query: 174 FKAIEPNGILLYNGHRADGVGDFIALYLNDRYVDFTFDLGTGA-ATLRSSNPISLGEWRK 232
F+ +PNG+LLY G DF+AL L D + +DLG+G L S ++ G+W +
Sbjct: 1 FRTTQPNGLLLYAGGEDGL--DFLALELEDGRLVLRYDLGSGGSVLLLSGKKLNDGQWHR 58
Query: 233 LRLTRTGRHAYLQVDRFPSSQILSPGPFTQLSLSLSLYLGGVPDYNIVSPKVKIKSSFIG 292
+ ++R GR L VD PG + L+L+ LYLGG+P+ + + + F+G
Sbjct: 59 VSVSRDGRSLTLSVDGGTVVSEALPGSSSILNLNGPLYLGGLPE-DSGLSLLPVTEGFVG 117
Score = 52.8 bits (127), Expect = 7e-09
Identities = 33/127 (25%), Positives = 52/127 (40%), Gaps = 26/127 (20%)
Query: 14 FKPESWDGILFLTGERDDLNGDFMTLLIFEGYVEFS-----------TPYRPYAD----- 57
F+ +G+L G D L DF+ L + +G + + D
Sbjct: 1 FRTTQPNGLLLYAGGEDGL--DFLALELEDGRLVLRYDLGSGGSVLLLSGKKLNDGQWHR 58
Query: 58 ITVHRTVRTLIL-------PYTVPSGLFSRITFREPVFVGGRGNTSGLSDKLPTEKGFKG 110
++V R R+L L G S + P+++GG SGLS LP +GF G
Sbjct: 59 VSVSRDGRSLTLSVDGGTVVSEALPGSSSILNLNGPLYLGGLPEDSGLS-LLPVTEGFVG 117
Query: 111 CIRHLDI 117
CIR++ +
Sbjct: 118 CIRNVRV 124
>gnl|CDD|215681 pfam00054, Laminin_G_1, Laminin G domain.
Length = 131
Score = 83.9 bits (208), Expect = 3e-20
Identities = 46/120 (38%), Positives = 69/120 (57%), Gaps = 3/120 (2%)
Query: 174 FKAIEPNGILLYNGHRADGVGDFIALYLNDRYVDFTFDLGTGAATLRSSNPISLGEWRKL 233
F+ EP+G+LLYNG + + DF+AL L D ++ ++DLG+GAA +RS + ++ G+W +
Sbjct: 1 FRTTEPSGLLLYNGTQTER--DFLALELRDGRLEVSYDLGSGAAVVRSGDKLNDGKWHSV 58
Query: 234 RLTRTGRHAYLQVDRFPSSQILSP-GPFTQLSLSLSLYLGGVPDYNIVSPKVKIKSSFIG 292
L R GR L VD SP G T L + LY+GG+P + ++ I SF G
Sbjct: 59 ELERNGRSGTLSVDGEARVTGESPLGATTDLDVDGPLYVGGLPSLAVKLRRLAISPSFDG 118
Score = 47.3 bits (113), Expect = 6e-07
Identities = 27/133 (20%), Positives = 48/133 (36%), Gaps = 25/133 (18%)
Query: 14 FKPESWDGILFLTGERDDLNGDFMTLLIFEGYVEFS----------TPYRPYAD-----I 58
F+ G+L G + + DF+ L + +G +E S D +
Sbjct: 1 FRTTEPSGLLLYNGTQTE--RDFLALELRDGRLEVSYDLGSGAAVVRSGDKLNDGKWHSV 58
Query: 59 TVHRTVRTLIL--------PYTVPSGLFSRITFREPVFVGGRGNTSGLSDKLPTEKGFKG 110
+ R R+ L P G + + P++VGG + + +L F G
Sbjct: 59 ELERNGRSGTLSVDGEARVTGESPLGATTDLDVDGPLYVGGLPSLAVKLRRLAISPSFDG 118
Query: 111 CIRHLDINDHLYN 123
CIR + +N +
Sbjct: 119 CIRDVIVNGKPLD 131
>gnl|CDD|232937 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5'
exoribonucleases. This model is defined to identify a
pair of paralogous 3-prime exoribonucleases in E. coli,
plus the set of proteins apparently orthologous to one
or the other in other eubacteria. VacB was characterized
originally as required for the expression of virulence
genes, but is now recognized as the exoribonuclease
RNase R (Rnr). Its paralog in E. coli and H. influenzae
is designated exoribonuclease II (Rnb). Both are
involved in the degradation of mRNA, and consequently
have strong pleiotropic effects that may be difficult to
disentangle. Both these proteins share domain-level
similarity (RNB, S1) with a considerable number of other
proteins, and full-length similarity scoring below the
trusted cutoff to proteins associated with various
phenotypes but uncertain biochemistry; it may be that
these latter proteins are also 3-prime exoribonucleases
[Transcription, Degradation of RNA].
Length = 654
Score = 35.8 bits (83), Expect = 0.026
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 43 EGYVEFSTPYRPYADITVHRTVRTLI 68
E Y F++P R Y D+T HR ++ ++
Sbjct: 497 EHYAHFTSPIRRYPDLTNHRLIKAVL 522
>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R. This family consists of an
exoribonuclease, ribonuclease R, also called VacB. It is
one of the eight exoribonucleases reported in E. coli
and is broadly distributed throughout the bacteria. In
E. coli, double mutants of this protein and
polynucleotide phosphorylase are not viable. Scoring
between trusted and noise cutoffs to the model are
shorter, divergent forms from the Chlamydiae, and
divergent forms from the Campylobacterales (including
Helicobacter pylori) and Leptospira interrogans
[Transcription, Degradation of RNA].
Length = 709
Score = 34.9 bits (81), Expect = 0.049
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 40 LIFEGYVEFSTPYRPYADITVHRTVR 65
L E Y F++P R Y D+ VHR ++
Sbjct: 546 LALEYYTHFTSPIRRYPDLIVHRLIK 571
>gnl|CDD|131117 TIGR02062, RNase_B, exoribonuclease II. This family consists of
exoribonuclease II, the product of the rnb gene, as
found in a number of gamma proteobacteria. In
Escherichia coli, it is one of eight different
exoribonucleases. It is involved in mRNA degradation and
tRNA precursor end processing [Transcription,
Degradation of RNA].
Length = 639
Score = 29.8 bits (67), Expect = 1.7
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 43 EGYVEFSTPYRPYADITVHRTVRTLIL--PYTVPS 75
E Y +++P R Y D+ HR ++ +I T P
Sbjct: 487 EAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQ 521
>gnl|CDD|110632 pfam01645, Glu_synthase, Conserved region in glutamate synthase.
This family represents a region of the glutamate
synthase protein. This region is expressed as a separate
subunit in the glutamate synthase alpha subunit from
archaebacteria, or part of a large multidomain enzyme in
other organisms. The aligned region of these proteins
contains a putative FMN binding site and Fe-S cluster.
Length = 367
Score = 29.2 bits (66), Expect = 2.3
Identities = 32/107 (29%), Positives = 41/107 (38%), Gaps = 25/107 (23%)
Query: 120 HLYNFNVSPGGDSLKGID--VALLRPATHYQVSSIPDQVYQGLGEQYLSLLDLTIVFKAI 177
HL VSP ++G V L+ P H+ + SI D L L K I
Sbjct: 152 HLPGEKVSPEIARIRGSPPGVGLISPPPHHDIYSIED------------LAQLIYDLKEI 199
Query: 178 EPN---GILLYNGHRADGVGDFIALYLNDRYVDFT----FDLGTGAA 217
P + L +GH GVG IA + D D GTGA+
Sbjct: 200 NPKAPISVKLVSGH---GVGT-IAAGVAKAGADIILIDGHDGGTGAS 242
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 29.3 bits (66), Expect = 3.2
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 40 LIFEGYVEFSTPYRPYADITVHRTVRTLI 68
L + Y F++P R Y D+++HR ++ L+
Sbjct: 558 LALQSYAHFTSPIRRYPDLSLHRAIKYLL 586
>gnl|CDD|226766 COG4316, COG4316, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 138
Score = 27.6 bits (61), Expect = 4.4
Identities = 14/52 (26%), Positives = 20/52 (38%)
Query: 196 FIALYLNDRYVDFTFDLGTGAATLRSSNPISLGEWRKLRLTRTGRHAYLQVD 247
IA + Y+ FD A R+ P ++GEW K+ L L
Sbjct: 85 TIAGLCVNGYIHAVFDFVEQAGYCRNGFPEAIGEWVKVELDDELLDKILSRK 136
>gnl|CDD|223631 COG0557, VacB, Exoribonuclease R [Transcription].
Length = 706
Score = 28.5 bits (64), Expect = 5.0
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 42 FEGYVEFSTPYRPYADITVHRTVRTLI 68
+ Y F++P R Y D+ VHR ++ L+
Sbjct: 547 LDYYTHFTSPIRRYPDLIVHRQLKALL 573
>gnl|CDD|216112 pfam00773, RNB, RNB domain. This domain is the catalytic domain of
ribonuclease II.
Length = 322
Score = 28.0 bits (63), Expect = 5.2
Identities = 12/27 (44%), Positives = 18/27 (66%)
Query: 42 FEGYVEFSTPYRPYADITVHRTVRTLI 68
E Y F++P R YAD+ VHR ++ L+
Sbjct: 296 LEIYTHFTSPIRRYADLVVHRQLKALL 322
>gnl|CDD|227117 COG4776, Rnb, Exoribonuclease II [Transcription].
Length = 645
Score = 28.2 bits (63), Expect = 5.5
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 40 LIFEGYVEFSTPYRPYADITVHRTVRTLIL 69
L E Y +++P R Y D+ HR ++ +I
Sbjct: 488 LGLEAYATWTSPIRKYGDMINHRLLKAVIK 517
>gnl|CDD|218731 pfam05752, Calici_MSP, Calicivirus minor structural protein. This
family consists of minor structural proteins largely
from human calicivirus isolates. Human calicivirus
causes gastroenteritis. The function of this family is
unknown.
Length = 167
Score = 27.0 bits (60), Expect = 8.0
Identities = 19/84 (22%), Positives = 28/84 (33%), Gaps = 10/84 (11%)
Query: 201 LNDRYVDFTFDLGTGAATLRSSNPISLG----EWRKLRLTRTGRHAYLQVDRFP-----S 251
L R D + DL LR + + G R+L + R Y +DR
Sbjct: 51 LQRRGQDLSRDLSVNGPALRVQSAVDAGFDPVSARRLAGSGE-RVIYGGLDRPIRQRGTL 109
Query: 252 SQILSPGPFTQLSLSLSLYLGGVP 275
I + +LS + G P
Sbjct: 110 PGIRETRHLQSMQGALSTFKNGTP 133
>gnl|CDD|226622 COG4138, BtuD, ABC-type cobalamin transport system, ATPase
component [Coenzyme metabolism].
Length = 248
Score = 27.5 bits (61), Expect = 8.1
Identities = 15/38 (39%), Positives = 23/38 (60%), Gaps = 6/38 (15%)
Query: 220 RSSNPISLGEWRKLRLTRTGRHAYLQV--DRFPSSQIL 255
RS+N +S GEW+++RL LQ+ D P+ Q+L
Sbjct: 121 RSTNQLSGGEWQRVRLAAV----VLQITPDANPAGQLL 154
>gnl|CDD|216965 pfam02298, Cu_bind_like, Plastocyanin-like domain. This family
represents a domain found in flowering plants related to
the copper binding protein plastocyanin. Some members of
this family may not bind copper due to the lack of key
residues.
Length = 84
Score = 26.1 bits (58), Expect = 8.2
Identities = 11/57 (19%), Positives = 20/57 (35%), Gaps = 11/57 (19%)
Query: 104 TEKGFKGCIRHLDINDHLYNFNVSPGGDSLKGIDVALLRPATHYQVSSIPDQVYQGL 160
T+ ++ C I + + G D + L +P HY + +P G
Sbjct: 39 TKADYESCNTSKPIRTY------TTGNDI-----IPLTKPGQHYFICGVPGHCKGGQ 84
>gnl|CDD|225333 COG2706, COG2706, 3-carboxymuconate cyclase [Carbohydrate transport
and metabolism].
Length = 346
Score = 27.3 bits (61), Expect = 9.0
Identities = 8/35 (22%), Positives = 13/35 (37%)
Query: 176 AIEPNGILLYNGHRADGVGDFIALYLNDRYVDFTF 210
A+ P+ LY + G A ++ TF
Sbjct: 46 AVNPDQRHLYVVNEPGEEGGVAAYRIDPDDGRLTF 80
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 0.142 0.434
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,631,435
Number of extensions: 1528796
Number of successful extensions: 1024
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1009
Number of HSP's successfully gapped: 27
Length of query: 293
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 197
Effective length of database: 6,679,618
Effective search space: 1315884746
Effective search space used: 1315884746
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 (21.8 bits)
S2: 59 (26.5 bits)