RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6375
(86 letters)
>gnl|CDD|185507 PTZ00191, PTZ00191, 60S ribosomal protein L23a; Provisional.
Length = 145
Score = 131 bits (332), Expect = 3e-41
Identities = 64/86 (74%), Positives = 73/86 (84%)
Query: 1 MDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP 60
+D ++IIKYPLTTE AMKKIEDNNTLVFIV +ANK IK AV+K+YD+ V KVNTLI P
Sbjct: 60 LDKYSIIKYPLTTEKAMKKIEDNNTLVFIVDQRANKTQIKKAVEKLYDVKVVKVNTLITP 119
Query: 61 DGKKKAYVRLARDYDALDVANKIGII 86
DG KKAY+RL+ D DALDVANKIGII
Sbjct: 120 DGLKKAYIRLSPDVDALDVANKIGII 145
>gnl|CDD|237750 PRK14548, PRK14548, 50S ribosomal protein L23P; Provisional.
Length = 84
Score = 106 bits (268), Expect = 3e-32
Identities = 45/84 (53%), Positives = 62/84 (73%)
Query: 3 AFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDG 62
++IIKYPL TE AM IE N L FIV +A K IK AV++++D+ V KVNTLI P G
Sbjct: 1 PYSIIKYPLVTEKAMNLIEKENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKG 60
Query: 63 KKKAYVRLARDYDALDVANKIGII 86
+KKAYV+LA +YDA ++A+++G+
Sbjct: 61 EKKAYVKLAEEYDAEEIASRLGVF 84
>gnl|CDD|132675 TIGR03636, L23_arch, archaeal ribosomal protein L23. This model
describes the archaeal ribosomal protein L23P and
rigorously excludes the bacterial counterpart L23. In
order to capture every known instance of archaeal L23P,
the trusted cutoff is set lower than a few of the
highest scoring eukaryotic cytosolic ribosomal
counterparts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 77
Score = 98.8 bits (247), Expect = 4e-29
Identities = 41/77 (53%), Positives = 55/77 (71%)
Query: 10 PLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVR 69
PL TE AM IE N L FIV +A K IK AV+K++D+ V KVNTLI P G+KKAYV+
Sbjct: 1 PLVTEKAMNLIEKENKLTFIVDRKATKGDIKRAVEKLFDVKVEKVNTLITPRGEKKAYVK 60
Query: 70 LARDYDALDVANKIGII 86
LA +Y A ++A+++G+
Sbjct: 61 LAEEYAAEEIASRLGVF 77
>gnl|CDD|223167 COG0089, RplW, Ribosomal protein L23 [Translation, ribosomal
structure and biogenesis].
Length = 94
Score = 83.8 bits (208), Expect = 4e-23
Identities = 35/86 (40%), Positives = 48/86 (55%), Gaps = 3/86 (3%)
Query: 3 AFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDG 62
+++IK P+ TE AM +E N VFIV A K IKAAV++++ + V KVNTL
Sbjct: 1 LYDVIKSPVVTEKAMLLMEKENKYVFIVDPDATKPEIKAAVEELFGVKVEKVNTLNTKGK 60
Query: 63 KKKAYVR---LARDYDALDVANKIGI 85
K+A V+ L +DY V K G
Sbjct: 61 TKRAGVKRIGLRKDYKKAYVTLKEGQ 86
>gnl|CDD|235586 PRK05738, rplW, 50S ribosomal protein L23; Reviewed.
Length = 92
Score = 69.0 bits (170), Expect = 3e-17
Identities = 31/82 (37%), Positives = 41/82 (50%), Gaps = 15/82 (18%)
Query: 4 FNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGK 63
+++IK P+ TE + +E N VF V A K IKAAV+K++ + V VNTL GK
Sbjct: 1 YDVIKRPVITEKSTLLMEKQNKYVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVK-GK 59
Query: 64 --------------KKAYVRLA 71
KKA V LA
Sbjct: 60 TKRFGRRIGKRSDWKKAIVTLA 81
>gnl|CDD|144021 pfam00276, Ribosomal_L23, Ribosomal protein L23.
Length = 90
Score = 62.0 bits (151), Expect = 2e-14
Identities = 37/91 (40%), Positives = 48/91 (52%), Gaps = 14/91 (15%)
Query: 5 NIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGK- 63
++IKYP+ TE AM +E N VFIV +ANK IK AV+ ++ + V KVNTLI P
Sbjct: 1 DVIKYPIITEKAMNLLEKPNQYVFIVDKKANKTEIKDAVEHIFGVKVEKVNTLILPGKVK 60
Query: 64 ------------KKAYVRLARDYDALDVANK 82
KKA V L D L A++
Sbjct: 61 RNGQYLGRKKSYKKAIVTLEEG-DILPFASR 90
>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
Length = 158
Score = 47.8 bits (114), Expect = 2e-08
Identities = 28/88 (31%), Positives = 39/88 (44%), Gaps = 14/88 (15%)
Query: 1 MDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP 60
M+ +IK P+ TE + + N F V +ANK IK AV+ ++ + V KVN
Sbjct: 1 MNINEVIKKPILTEKSYSLMSKN-VYTFKVDRRANKIEIKKAVEFIFKVKVLKVNIFNVD 59
Query: 61 -------------DGKKKAYVRLARDYD 75
+ KKAYV LA Y
Sbjct: 60 KKPKRLGRFPGFTNSYKKAYVTLAEGYS 87
>gnl|CDD|176971 CHL00030, rpl23, ribosomal protein L23.
Length = 93
Score = 44.9 bits (107), Expect = 8e-08
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 4 FNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGK 63
+ IKYP+ T+ +++ +E N F V + K IK ++ + + V VN+ R K
Sbjct: 1 MDGIKYPVFTDKSIRLLE-KNQYTFDVDSGSTKTEIKHWIELFFGVKVIAVNSH-RLPRK 58
Query: 64 KK 65
K+
Sbjct: 59 KR 60
>gnl|CDD|237100 PRK12429, PRK12429, 3-hydroxybutyrate dehydrogenase; Provisional.
Length = 258
Score = 27.5 bits (62), Expect = 0.60
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 7/45 (15%)
Query: 30 VHLQANKHHIKAAVKKMYD------INVAKVNTLIRPDGKKKAYV 68
+ L KAA+ M IN+A V+ L+ G K AYV
Sbjct: 111 IMLDGAFLTTKAALPIMKAQGGGRIINMASVHGLVGSAG-KAAYV 154
>gnl|CDD|234457 TIGR04075, bacter_Pnkp, polynucleotide kinase-phosphatase. Members
of this protein family are the bacterial polynucleotide
kinase-phosphatase (Pnkp) whose genes occur paired with
genes for the 3' terminal RNA ribose
2'-O-methyltransferase Hen1. All members of the seed
alignment belong to a cassette with the Hen1. The pair
acts in bacterial RNA repair. This enzyme performs
end-healing reactions on broken RNA, preparing from the
RNA ligase to close the break. The working hypothesis is
that the combination of Pnkp (RNA repair) and Hen1 (RNA
modification) serves to first repair RNA damage from
ribotoxins and then perform a modification that prevents
the damage from recurring [Transcription, RNA
processing].
Length = 851
Score = 27.7 bits (62), Expect = 0.73
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 56 TLIRPDGKKKAYVRLARDYDALDVA 80
T ++P+ +K V LAR+Y L VA
Sbjct: 80 TNVQPEDRKG-LVALAREYHVLPVA 103
>gnl|CDD|138873 PRK12320, PRK12320, hypothetical protein; Provisional.
Length = 699
Score = 27.3 bits (60), Expect = 1.0
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 15 SAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARD 73
S K + +L + HL+++ HH AA + + ++ +L PD + +RL RD
Sbjct: 416 SVAKVVVTARSLALLRHLRSDTHHYVAAADAEH-LAAGQLASL--PDAGLEVRIRLLRD 471
>gnl|CDD|238426 cd00830, KAS_III, Ketoacyl-acyl carrier protein synthase III
(KASIII) initiates the elongation in type II fatty acid
synthase systems. It is found in bacteria and plants.
Elongation of fatty acids in the type II systems occurs
by Claisen condensation of malonyl-acyl carrier protein
(ACP) with acyl-ACP. KASIII initiates this process by
specifically using acetyl-CoA over acyl-CoA.
Length = 320
Score = 26.7 bits (60), Expect = 1.4
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 11 LTTESAMKKIEDNNTLV-----FIVHLQANKHHIKAAVKKMYDINVAKVNTLI 58
L ES + +E F+ H QAN I+A K++ + KV +
Sbjct: 224 LMPESIEEALEKAGLTPDDIDWFVPH-QANLRIIEAVAKRL-GLPEEKVVVNL 274
>gnl|CDD|183740 PRK12779, PRK12779, putative bifunctional glutamate synthase
subunit beta/2-polyprenylphenol hydroxylase;
Provisional.
Length = 944
Score = 26.7 bits (59), Expect = 1.7
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 2 DAFNIIKYPLTTESAMKKIEDNNTLVF 28
DAF+ I PL S + + E N T+VF
Sbjct: 729 DAFSGIAGPLGRASELHRYEGNQTVVF 755
>gnl|CDD|182175 PRK09971, PRK09971, xanthine dehydrogenase subunit XdhB;
Provisional.
Length = 291
Score = 25.0 bits (55), Expect = 6.2
Identities = 11/35 (31%), Positives = 15/35 (42%)
Query: 37 HHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLA 71
+IK A++ DI L R D +RLA
Sbjct: 182 AYIKYAMRDAMDIATIGCAVLCRLDNGNFEDLRLA 216
>gnl|CDD|237661 PRK14291, PRK14291, chaperone protein DnaJ; Provisional.
Length = 382
Score = 24.7 bits (54), Expect = 7.3
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 64 KKAYVRLARDY 74
KKAY RLAR Y
Sbjct: 21 KKAYRRLARKY 31
>gnl|CDD|234169 TIGR03334, IOR_beta, indolepyruvate ferredoxin oxidoreductase,
beta subunit. This model represents the beta subunit
of indolepyruvate ferredoxin oxidoreductase, an
alpha(2)/beta(2) tetramer, as found in Pyrococcus
furiosus and Methanobacterium thermoautotrophicum.
Cofactors for the tetramer include TPP, 4Fe4S, and
3Fe-4S. It shows considerable sequence similarity to
subunits of several other ketoacid oxidoreductases.
Length = 189
Score = 24.4 bits (53), Expect = 7.9
Identities = 7/38 (18%), Positives = 19/38 (50%)
Query: 40 KAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDAL 77
+AA+K + A+ + + + G ++R+ Y ++
Sbjct: 22 EAALKAGLPVRAAETHGMAQRGGSVINHIRIGEVYGSM 59
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
0.321 0.135 0.375
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,310,397
Number of extensions: 342818
Number of successful extensions: 391
Number of sequences better than 10.0: 1
Number of HSP's gapped: 386
Number of HSP's successfully gapped: 26
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
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: 53 (24.0 bits)