RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032363
(142 letters)
>gnl|CDD|235464 PRK05435, rpmA, 50S ribosomal protein L27; Validated.
Length = 82
Score = 160 bits (407), Expect = 2e-52
Identities = 56/78 (71%), Positives = 64/78 (82%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
AHKKG GST+NGRDS +RLGVK FG Q K G IIVRQRGTKFHPG NVG GKDHT+F+
Sbjct: 2 AHKKGGGSTRNGRDSESKRLGVKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGKDHTLFA 61
Query: 116 LIDGLVKFEKFGPDRKQV 133
L+DG+VKFE+ G +RK V
Sbjct: 62 LVDGVVKFERKGRNRKYV 79
>gnl|CDD|201553 pfam01016, Ribosomal_L27, Ribosomal L27 protein.
Length = 80
Score = 145 bits (368), Expect = 1e-46
Identities = 58/78 (74%), Positives = 65/78 (83%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
AHKKG GSTKNGRDS G+RLGVK FG Q K G IIVRQRGTKFHPG+NVG+GKDHT+F+
Sbjct: 1 AHKKGGGSTKNGRDSNGKRLGVKKFGGQFVKAGNIIVRQRGTKFHPGENVGMGKDHTLFA 60
Query: 116 LIDGLVKFEKFGPDRKQV 133
L+DG VKFEK +RK V
Sbjct: 61 LVDGYVKFEKKPKNRKYV 78
>gnl|CDD|223289 COG0211, RpmA, Ribosomal protein L27 [Translation, ribosomal
structure and biogenesis].
Length = 87
Score = 144 bits (365), Expect = 4e-46
Identities = 56/78 (71%), Positives = 64/78 (82%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
AHKKG GST+NGRDS +RLGVK FG Q K G+IIVRQRGTKFHPG NVG GKDHT+F+
Sbjct: 2 AHKKGGGSTRNGRDSESKRLGVKKFGGQFVKAGSIIVRQRGTKFHPGVNVGRGKDHTLFA 61
Query: 116 LIDGLVKFEKFGPDRKQV 133
L+DG+VKFE G +RK V
Sbjct: 62 LVDGVVKFETKGKNRKYV 79
>gnl|CDD|214370 CHL00121, rpl27, ribosomal protein L27; Reviewed.
Length = 86
Score = 127 bits (322), Expect = 2e-39
Identities = 51/87 (58%), Positives = 62/87 (71%), Gaps = 3/87 (3%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
AHKKGAGSTKNGRDS +RLGVK FG + G I++RQRGTKF PG NVG GKD T+++
Sbjct: 2 AHKKGAGSTKNGRDSNAKRLGVKRFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDFTLYA 61
Query: 116 LIDGLVKFEKFGPDRKQVKYFAITNCL 142
LIDG VKF+K K+ K + N +
Sbjct: 62 LIDGFVKFKKK---NKKQKSINVINIV 85
>gnl|CDD|232803 TIGR00062, L27, ribosomal protein L27. Eubacterial, chloroplast,
and mitochondrial. Mitochondrial members have an
additional C-terminal domain [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 83
Score = 120 bits (303), Expect = 1e-36
Identities = 55/79 (69%), Positives = 62/79 (78%), Gaps = 1/79 (1%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
A KKG GSTKNGRDS +RLGVK G Q + G+IIVRQRGTKFHPG NVG+GKDHT+F+
Sbjct: 2 ATKKGVGSTKNGRDSEAKRLGVKRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGKDHTLFA 61
Query: 116 LIDGLVKFEKFG-PDRKQV 133
L DG+VKFEK G RK V
Sbjct: 62 LSDGVVKFEKKGKRSRKFV 80
>gnl|CDD|217966 pfam04209, HgmA, homogentisate 1,2-dioxygenase. Homogentisate
dioxygenase cleaves the aromatic ring during the
metabolic degradation of Phe and Tyr. Homogentisate
dioxygenase deficiency causes alkaptonuria. The
structure of homogentisate dioxygenase shows that the
enzyme forms a hexamer arrangement comprised of a dimer
of trimers. The active site iron ion is coordinated near
the interface between the trimers.
Length = 422
Score = 31.2 bits (71), Expect = 0.14
Identities = 23/94 (24%), Positives = 36/94 (38%), Gaps = 14/94 (14%)
Query: 15 KGLSLSSSSSSSFLKGDFTVCPKSVTVSLPPTSPLPLTIESAHKKGAGSTKNGRDSRGQR 74
K + S + F++G T+ + P S L I + K ++ G
Sbjct: 92 KPFPIPSKEPTDFVEGLHTIAG-----AGDPLSNHGLAIHVYSANKSMENKLFYNADGDF 146
Query: 75 LGV----KI-----FGDQVAKPGAIIVRQRGTKF 99
L V ++ FG + PG I V RGT+F
Sbjct: 147 LIVPQQGELDLYTEFGRLLVSPGEIAVIPRGTRF 180
>gnl|CDD|197753 smart00481, POLIIIAc, DNA polymerase alpha chain like domain. DNA
polymerase alpha chain like domain, incl. family of
hypothetical proteins.
Length = 67
Score = 28.8 bits (65), Expect = 0.27
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 111 HTIFSLIDGLVKFEKFG--PDRKQVKYFAIT 139
H+ +SL+DG + E+ +K AIT
Sbjct: 5 HSDYSLLDGALSPEELVKRAKELGLKAIAIT 35
>gnl|CDD|215565 PLN03083, PLN03083, E3 UFM1-protein ligase 1 homolog; Provisional.
Length = 803
Score = 28.6 bits (64), Expect = 1.1
Identities = 18/70 (25%), Positives = 27/70 (38%)
Query: 20 SSSSSSSFLKGDFTVCPKSVTVSLPPTSPLPLTIESAHKKGAGSTKNGRDSRGQRLGVKI 79
SS ++S+ KG KS + +P E A KKG + K GRD +
Sbjct: 409 SSPAASNSDKGSKKKKGKSTSTKGGTAESIPDDEEDAPKKGKKNQKKGRDKSSKVPSDSK 468
Query: 80 FGDQVAKPGA 89
G + +
Sbjct: 469 AGGKKESVKS 478
>gnl|CDD|220733 pfam10403, BHD_1, Rad4 beta-hairpin domain 1. This short domain is
found in the Rad4 protein. This domain binds to DNA.
Length = 57
Score = 26.4 bits (59), Expect = 1.6
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 109 KDHTIFSLIDGLVKFEKFGPDRKQVKYFAITN 140
K+H ++ L L + E PD K V F N
Sbjct: 14 KNHPLYVLERHLRRNEVIYPDAKPVGTFKGGN 45
>gnl|CDD|223033 PHA03291, PHA03291, envelope glycoprotein I; Provisional.
Length = 401
Score = 28.0 bits (62), Expect = 1.7
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 2/57 (3%)
Query: 36 PKSVTVSLPPTSPLPLTIESAHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIV 92
P++ T +P P T A +T SR + +I Q+A P +II
Sbjct: 245 PQAGTTPEAEGTPAPPTPGGGEAPPANATPAPEASRYELTVTQII--QIAIPASIIA 299
>gnl|CDD|216078 pfam00716, Peptidase_S21, Assemblin (Peptidase family S21).
Length = 326
Score = 27.4 bits (61), Expect = 2.6
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 36 PKSVTVSLPPTSPLPLTIESAHKKGA 61
++V +LPPT P+PL I+ H A
Sbjct: 6 RETVKSALPPTKPIPLNID--HLPEA 29
>gnl|CDD|216176 pfam00890, FAD_binding_2, FAD binding domain. This family includes
members that bind FAD. This family includes the
flavoprotein subunits from succinate and fumarate
dehydrogenase, aspartate oxidase and the alpha subunit
of adenylylsulphate reductase.
Length = 401
Score = 27.3 bits (61), Expect = 3.0
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 72 GQRLGVKIFGDQVAKPGAIIVRQRGTKF 99
G RLG + + + G I+V G +F
Sbjct: 256 GIRLGSGLLIEALRGEGGILVNDDGRRF 283
>gnl|CDD|214984 smart01030, BHD_1, Rad4 beta-hairpin domain 1. This short domain
is found in the Rad4 protein. This domain binds to DNA.
Length = 54
Score = 24.9 bits (55), Expect = 4.8
Identities = 10/38 (26%), Positives = 15/38 (39%)
Query: 103 KNVGLGKDHTIFSLIDGLVKFEKFGPDRKQVKYFAITN 140
++ K+H ++ L L K E P K V F
Sbjct: 7 TSIQDFKNHPLYVLERHLKKNEAIYPKAKPVGTFGYGK 44
>gnl|CDD|218404 pfam05056, DUF674, Protein of unknown function (DUF674). This
family is found in Arabidopsis thaliana and contains
several uncharacterized proteins.
Length = 462
Score = 26.3 bits (58), Expect = 6.4
Identities = 22/98 (22%), Positives = 39/98 (39%), Gaps = 8/98 (8%)
Query: 10 LIGSFKGLSLSSSSSSSFLK-GDFTVCPK---SVTVSLPPTSPL-PLTIESAHKKGAGST 64
L SFK LS ++ SS + C K +T PP + ++ + G T
Sbjct: 324 LFRSFKDLSGDEATESSKCALPHYYNCQKQLLGITTQQPPVYYRYVYSNCISYLRDYGLT 383
Query: 65 KNGRDSRGQRLGV---KIFGDQVAKPGAIIVRQRGTKF 99
++ + + + + K G + + +RGTKF
Sbjct: 384 EDSEKDKLKPVILIDPKSEGSGTSASESGGFVKRGTKF 421
>gnl|CDD|213988 cd07433, PHP_PolIIIA_DnaE1, Polymerase and Histidinol Phosphatase
domain of alpha-subunit of bacterial polymerase III
DnaE1. PolIIIAs that contain an N-terminal PHP domain
have been classified into four basic groups based on
genome composition, phylogenetic, and domain structural
analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also
called histidinol phosphatase-2/HIS2) domain is
associated with several types of DNA polymerases, such
as PolIIIA and family X DNA polymerases, stand alone
histidinol phosphate phosphatases (HisPPases), and a
number of uncharacterized protein families. DNA
polymerase III holoenzyme is one of the five eubacterial
DNA polymerases that are responsible for the replication
of the DNA duplex. PolIIIA core enzyme catalyzes the
reaction for polymerizing both DNA strands. dnaE1 is the
longest compared to dnaE2 and dnaE3. A unique motif was
also identified in dnaE1 and dnaE3 genes.
Length = 277
Score = 25.9 bits (58), Expect = 8.8
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 111 HTIFSLIDGLVKFEK 125
H+ +SL+DG V+ +K
Sbjct: 8 HSEYSLLDGAVRIKK 22
>gnl|CDD|165099 PHA02732, PHA02732, hypothetical protein; Provisional.
Length = 1467
Score = 26.3 bits (57), Expect = 9.3
Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 9/45 (20%)
Query: 3 TASMSASLIGSFKGLSLSSSSSSSFLKGDFTVCPKSVTVSLPPTS 47
MS + +FK L S++SS P + T PP S
Sbjct: 1210 IIGMSGTNTFTFKAAQLQLSAASS---------PPAATTPTPPPS 1245
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
0.317 0.134 0.385
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,831,484
Number of extensions: 596027
Number of successful extensions: 456
Number of sequences better than 10.0: 1
Number of HSP's gapped: 456
Number of HSP's successfully gapped: 21
Length of query: 142
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 55
Effective length of database: 7,078,804
Effective search space: 389334220
Effective search space used: 389334220
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 (21.6 bits)
S2: 54 (24.5 bits)