RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12853
(137 letters)
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 34.2 bits (79), Expect = 0.014
Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 25/58 (43%)
Query: 67 MLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE--KDEGCAQMLCKRCKH 122
+LC+ C ++ CP C P+ K G Q+ C C +
Sbjct: 436 LLCRDCGYIA---------------------ECPNCDSPLTLHKATG--QLRCHYCGY 470
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 30.6 bits (69), Expect = 0.22
Identities = 10/33 (30%), Positives = 12/33 (36%), Gaps = 6/33 (18%)
Query: 51 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS 83
C +C E C C H+FC CL
Sbjct: 218 CFLCLEEPEV------PSCTPCGHLFCLSCLLI 244
Score = 30.6 bits (69), Expect = 0.22
Identities = 10/33 (30%), Positives = 12/33 (36%), Gaps = 6/33 (18%)
Query: 99 CPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLAS 131
C +C E C C H+FC CL
Sbjct: 218 CFLCLEEPEV------PSCTPCGHLFCLSCLLI 244
>gnl|CDD|216524 pfam01485, IBR, IBR domain. The IBR (In Between Ring fingers)
domain is often found to occur between pairs of ring
fingers (pfam00097). This domain has also been called
the C6HC domain and DRIL (for double RING finger
linked) domain. Proteins that contain two Ring fingers
and an IBR domain (these proteins are also termed RBR
family proteins) are thought to exist in all eukaryotic
organisms. RBR family members play roles in protein
quality control and can indirectly regulate
transcription. Evidence suggests that RBR proteins are
often parts of cullin-containing ubiquitin ligase
complexes. The ubiquitin ligase Parkin is an RBR family
protein whose mutations are involved in forms of
familial Parkinson's disease.
Length = 63
Score = 28.7 bits (64), Expect = 0.25
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 45 SELIKCCP--MCSVPIEKDEGCAQ-MLCKRCKHVFCWYCLA 82
+ +K CP C IEK +G +Q + C +C FC+ C
Sbjct: 15 PKNLKWCPTPDCGNIIEKTDGGSQNVTCSKCGTEFCFSCKE 55
Score = 28.7 bits (64), Expect = 0.25
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 93 SELIKCCP--MCSVPIEKDEGCAQ-MLCKRCKHVFCWYCLA 130
+ +K CP C IEK +G +Q + C +C FC+ C
Sbjct: 15 PKNLKWCPTPDCGNIIEKTDGGSQNVTCSKCGTEFCFSCKE 55
>gnl|CDD|215494 PLN02915, PLN02915, cellulose synthase A [UDP-forming], catalytic
subunit.
Length = 1044
Score = 28.7 bits (64), Expect = 1.1
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 8/68 (11%)
Query: 49 KCCPMCSVPI-EKDEGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPIE 107
K C +C + K++G + C C C C SE +CCP C+ +
Sbjct: 16 KTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYER-------SEGNQCCPQCNTRYK 68
Query: 108 KDEGCAQM 115
+ +GC ++
Sbjct: 69 RHKGCPRV 76
>gnl|CDD|214763 smart00647, IBR, In Between Ring fingers. the domains occurs
between pairs og RING fingers.
Length = 64
Score = 26.6 bits (59), Expect = 1.5
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 49 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLA 82
C V ++EGC ++ C +C FC+ C
Sbjct: 25 DCSAAIIVT--EEEGCNRVTCPKCGFSFCFRCKV 56
Score = 26.6 bits (59), Expect = 1.5
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 97 KCCPMCSVPIEKDEGCAQMLCKRCKHVFCWYCLA 130
C V ++EGC ++ C +C FC+ C
Sbjct: 25 DCSAAIIVT--EEEGCNRVTCPKCGFSFCFRCKV 56
>gnl|CDD|215343 PLN02638, PLN02638, cellulose synthase A (UDP-forming), catalytic
subunit.
Length = 1079
Score = 28.0 bits (62), Expect = 2.1
Identities = 18/67 (26%), Positives = 25/67 (37%), Gaps = 9/67 (13%)
Query: 62 EGCAQMLCKRCKHVFCWYCLASRDYGGATFDSELIKCCPMCSVPI-------EKDEGCAQ 114
E + K KH C D G T D E C +C+ P+ E+ +G
Sbjct: 2 ESEGETGAKPMKHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYEYERKDG--N 59
Query: 115 MLCKRCK 121
C +CK
Sbjct: 60 QSCPQCK 66
>gnl|CDD|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
Gram-positive type. This model describes a polypeptide
chain of DNA polymerase III. Full-length homologs of
this protein are restricted to the Gram-positive
lineages, including the Mycoplasmas. This protein is
designated alpha chain and given the gene symbol polC,
but is not a full-length homolog of other polC genes.
The N-terminal region of about 200 amino acids is rich
in low-complexity sequence, poorly alignable, and not
included n this model [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1213
Score = 27.3 bits (61), Expect = 3.5
Identities = 16/43 (37%), Positives = 19/43 (44%), Gaps = 7/43 (16%)
Query: 68 LCKRCKHVFCWYCLASRDYG-GATFDSELIKCCPMCSVPIEKD 109
LC CK Y D G+ FD K CP C P++KD
Sbjct: 685 LCPNCK-----YSEFITDGSVGSGFDLP-DKDCPKCGAPLKKD 721
>gnl|CDD|236330 PRK08665, PRK08665, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 752
Score = 26.1 bits (58), Expect = 7.7
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 51 CPMCSVPIEKDEGCAQMLCKRC 72
CP C +E +EGC +C C
Sbjct: 727 CPECGSILEHEEGCV--VCHSC 746
Score = 26.1 bits (58), Expect = 7.7
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 99 CPMCSVPIEKDEGCAQMLCKRC 120
CP C +E +EGC +C C
Sbjct: 727 CPECGSILEHEEGCV--VCHSC 746
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
0.328 0.138 0.495
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,208,648
Number of extensions: 480229
Number of successful extensions: 670
Number of sequences better than 10.0: 1
Number of HSP's gapped: 664
Number of HSP's successfully gapped: 69
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 54 (24.6 bits)