RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9086
(115 letters)
>gnl|CDD|201631 pfam01158, Ribosomal_L36e, Ribosomal protein L36e.
Length = 95
Score = 122 bits (308), Expect = 9e-38
Identities = 66/107 (61%), Positives = 75/107 (70%), Gaps = 12/107 (11%)
Query: 6 ELAVGLKKGHRNTKIKWANSLAQKTSKIVKMRPSRLKGIQTKNTKFTRDLVREVCGHAPY 65
+AVGL KGH+ TK + K RPSR KG +K TKF RD++REV G APY
Sbjct: 1 GIAVGLNKGHKVTK------------RPRKPRPSRRKGKLSKRTKFVRDIIREVAGFAPY 48
Query: 66 EKRAMELLKVSKDKRALKFLKRRLGTHIRAKRKREELSNILTQMRKA 112
EKR +ELLKV KDKRALKF K+RLGTH RAKRKREELSN+L RKA
Sbjct: 49 EKRVIELLKVGKDKRALKFAKKRLGTHRRAKRKREELSNVLAAQRKA 95
>gnl|CDD|185509 PTZ00196, PTZ00196, 60S ribosomal protein L36; Provisional.
Length = 98
Score = 84.7 bits (210), Expect = 6e-23
Identities = 54/110 (49%), Positives = 70/110 (63%), Gaps = 12/110 (10%)
Query: 3 PRYELAVGLKKGHRNTKIKWANSLAQKTSKIVKMRPSRLKGIQTKNTKFTRDLVREVCGH 62
PR +AVGL KGH TK + K PS+ KG+ +K + +D++REVCG
Sbjct: 1 PRTGIAVGLNKGHIVTK------------RARKPSPSKRKGLLSKRKRLVKDVIREVCGF 48
Query: 63 APYEKRAMELLKVSKDKRALKFLKRRLGTHIRAKRKREELSNILTQMRKA 112
+PYE+R +ELLKV KDKRALK+ K+RLGTH RAK KR+E+ L RK
Sbjct: 49 SPYERRMIELLKVGKDKRALKYAKKRLGTHKRAKAKRDEIQEALRAQRKK 98
>gnl|CDD|227384 COG5051, RPL36A, Ribosomal protein L36E [Translation, ribosomal
structure and biogenesis].
Length = 97
Score = 61.5 bits (149), Expect = 8e-14
Identities = 37/70 (52%), Positives = 53/70 (75%)
Query: 37 RPSRLKGIQTKNTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRLGTHIRAK 96
RPSR KG +K T+F R +VRE+ G +PYE+R +EL++ S+DKRA K K+RLG+ RAK
Sbjct: 25 RPSRKKGQLSKRTEFVRSIVREIAGLSPYERRVIELIRNSQDKRARKLAKKRLGSLKRAK 84
Query: 97 RKREELSNIL 106
K EEL++++
Sbjct: 85 AKVEELTSVI 94
>gnl|CDD|163636 cd07393, MPP_DR1119, Deinococcus radiodurans DR1119 and related
proteins, metallophosphatase domain. DR1119 is an
uncharacterized Deinococcus radiodurans protein with a
metallophosphatase domain. The domain present in
members of this family belongs to the metallophosphatase
(MPP) superfamily. MPPs are functionally diverse, but
all share a conserved domain with an active site
consisting of two metal ions (usually manganese, iron,
or zinc) coordinated with octahedral geometry by a cage
of histidine, aspartate, and asparagine residues. The
MPP superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 232
Score = 31.2 bits (71), Expect = 0.080
Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 12/85 (14%)
Query: 30 TSKIVKMRPSRLKGIQTKNTKFTRDLVREVCG--------HAPYEKRAMELLKVSKDKRA 81
SK+ K + N D+ +CG + E LKV +D++
Sbjct: 88 ASKLRKALEESRLALLFNNAYIDDDVA--ICGTRGWDNPGNPWPPIN--ETLKVEEDEKI 143
Query: 82 LKFLKRRLGTHIRAKRKREELSNIL 106
+ RL ++A +KRE+ +
Sbjct: 144 FERELERLELSLKAAKKREKEKIKI 168
>gnl|CDD|215965 pfam00516, GP120, Envelope glycoprotein GP120. The entry of HIV
requires interaction of viral GP120 with CD4 and a
chemokine receptor on the cell surface.
Length = 493
Score = 28.1 bits (63), Expect = 0.90
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 11 LKKGHRNTKIKWANSLAQKTSKIVKMRPSRLKGIQTKNTKFTR 53
+++ N W +L + K+ K+ R KG TK FTR
Sbjct: 309 IRQAWCNFSGNWNEALKEVAKKLRKL--PRYKGQTTKTITFTR 349
>gnl|CDD|220150 pfam09239, Topo-VIb_trans, Topoisomerase VI B subunit, transducer.
Members of this family adopt a structure consisting of a
four-stranded beta-sheet backed by three alpha-helices,
the last of which is over 50 amino acids long and
extends from the body of the protein by several turns.
This domain has been proposed to mediate intersubunit
communication by structurally transducing signals from
the ATP binding and hydrolysis domains to the DNA
binding and cleavage domains of the gyrase holoenzyme.
Length = 160
Score = 27.6 bits (62), Expect = 1.0
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 79 KRALKFLKRRLGTHIRAKRKREEL 102
+ AL+ R+L ++ KRK +E
Sbjct: 134 RLALQEAARKLKRYLSRKRKAKER 157
>gnl|CDD|212677 cd10235, HscC_like_NBD, Nucleotide-binding domain of Escherichia
coli HscC and similar proteins. This subfamily
includes Escherichia coli HscC (also called heat shock
cognate protein C, Hsc62, or YbeW) and the the putative
DnaK-like protein Escherichia coli ECs0689. It belongs
to the heat shock protein 70 (Hsp70) family of
chaperones that assist in protein folding and assembly
and can direct incompetent "client" proteins towards
degradation. Typically, Hsp70s have a nucleotide-binding
domain (NBD) and a substrate-binding domain (SBD). The
nucleotide sits in a deep cleft formed between the two
lobes of the NBD. The two subdomains of each lobe change
conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. Hsp70 chaperone activity is
regulated by various co-chaperones: J-domain proteins
and nucleotide exchange factors (NEFs). Two genes in the
vicinity of the HscC gene code for potential
cochaperones: J-domain containing proteins, DjlB/YbeS
and DjlC/YbeV. HscC and its co-chaperone partners may
play a role in the SOS DNA damage response. HscC does
not appear to require a NEF.
Length = 339
Score = 27.9 bits (63), Expect = 1.1
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 51 FTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRLG 90
FTR L + ++ ++++ RA + KR L
Sbjct: 200 FTRALAEAFLKKHGLDFEKLDPSELARLLRAAERAKRALS 239
>gnl|CDD|233207 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
Family protein. [Transport and binding proteins,
Other].
Length = 617
Score = 28.1 bits (63), Expect = 1.1
Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 10/94 (10%)
Query: 24 NSLAQKTSKIVKMRPSRLKGIQTKNTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALK 83
N+LA ++ K VK S L +R + + + + L V + L
Sbjct: 69 NALAFRSPKGVKGSGSVL----LNGMPIDAKEMRAISAYVQQDDLFIPTLTV---REHLM 121
Query: 84 FLKR-RLGTHIRAKRKREELSNILTQM--RKAAH 114
F R+ + K KRE + +L + RK A+
Sbjct: 122 FQAHLRMPRRVTKKEKRERVDEVLQALGLRKCAN 155
>gnl|CDD|215574 PLN03099, PIR, Protein PIR; Provisional.
Length = 1232
Score = 28.0 bits (62), Expect = 1.4
Identities = 14/31 (45%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 84 FLKRRLGTHIRAK-RKREELSNILTQMRKAA 113
F++ +L T +R RK++ELS IL+ MR A
Sbjct: 444 FVQNKLATMLRTTFRKKKELSRILSDMRTIA 474
>gnl|CDD|222968 PHA03065, PHA03065, Hypothetical protein; Provisional.
Length = 438
Score = 27.3 bits (61), Expect = 1.7
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 79 KRALKFLKRRLGTHIRAKRKREELSNI 105
K++L+ KRR + KRKREE+ +
Sbjct: 81 KQSLRE-KRRKASKNTIKRKREEIEKL 106
>gnl|CDD|235246 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 27.2 bits (61), Expect = 2.4
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 79 KRALKFLKRRLGTHIRAKRKREEL 102
+ AL+ + R+L ++ KRK EE
Sbjct: 445 RLALQEVARKLKKYLSRKRKEEEA 468
>gnl|CDD|216051 pfam00667, FAD_binding_1, FAD binding domain. This domain is found
in sulfite reductase, NADPH cytochrome P450 reductase,
Nitric oxide synthase and methionine synthase reductase.
Length = 217
Score = 25.4 bits (56), Expect = 8.6
Identities = 9/39 (23%), Positives = 19/39 (48%)
Query: 52 TRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRLG 90
T+ L+ + +A E+ L K+S D ++ + +L
Sbjct: 108 TKQLLEALAQYASDEEEKQRLEKLSSDAGKQEYKEWKLN 146
>gnl|CDD|171585 PRK12566, PRK12566, glycine dehydrogenase; Provisional.
Length = 954
Score = 25.7 bits (56), Expect = 8.7
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 67 KRAM--ELLKVSKDKRALKFLKRRLGTHIRAKRKREELSNILT 107
KRAM ++ VS+D R L+ L T + R+ + SNI T
Sbjct: 291 KRAMPGRIIGVSRDARGNTALRMALQTREQHIRREKANSNICT 333
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
0.319 0.130 0.366
Gapped
Lambda K H
0.267 0.0905 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,522,061
Number of extensions: 453776
Number of successful extensions: 521
Number of sequences better than 10.0: 1
Number of HSP's gapped: 518
Number of HSP's successfully gapped: 33
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
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: 53 (23.9 bits)