RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2756
(112 letters)
>gnl|CDD|240252 PTZ00065, PTZ00065, 60S ribosomal protein L14; Provisional.
Length = 130
Score = 89.8 bits (223), Expect = 2e-24
Identities = 44/104 (42%), Positives = 59/104 (56%), Gaps = 1/104 (0%)
Query: 9 NGAFKRFVQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGPE-TGVPRSALRLNQLHLT 67
FKRFV+ GR+ I GP GKL IVD++ T VLVDG TGV R ++ L +L LT
Sbjct: 1 MPLFKRFVEPGRLCLIQYGPDAGKLCFIVDIVTPTRVLVDGAFITGVKRQSIPLKRLKLT 60
Query: 68 KLKINFPFNARTKVVRKAWKDGQVEEKWSKSLWAQKVANVEKRK 111
KI ART ++KA K E+++K+ +K+ EKR
Sbjct: 61 DEKIKINRGARTGTLKKALKKDNALEEFNKTSLGKKLIIKEKRA 104
>gnl|CDD|190164 pfam01929, Ribosomal_L14e, Ribosomal protein L14. This family
includes the eukaryotic ribosomal protein L14.
Length = 73
Score = 71.8 bits (177), Expect = 4e-18
Identities = 27/57 (47%), Positives = 37/57 (64%)
Query: 56 RSALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQVEEKWSKSLWAQKVANVEKRKK 112
R + L +LHLTK K+ P ART V+KAW+ V EKW++S WA+K+A +KR
Sbjct: 1 RQVINLKRLHLTKFKVKIPRGARTGTVKKAWEKADVLEKWAESSWAKKLAAKKKRAN 57
>gnl|CDD|240512 cd06088, KOW_RPL14, KOW motif of Ribosomal Protein L14. RPL14 is
a component of the large ribosomal subunit in both
archaea and eukaryotes with KOW motif at its N
terminal. KOW domain is known as an RNA-binding motif
that is shared so far among some families of ribosomal
proteins, the essential bacterial transcriptional
elongation factor NusG, the eukaryotic chromatin
elongation factor Spt5, the higher eukaryotic KIN17
proteins and Mtr4. Auto-antibodies to RPL14 in humans
have been associated with systemic lupus erythematosus
. Although RPL14 is well conserved, it is not found in
all archaea, and therefore it is presumably not
essential.
Length = 76
Score = 71.0 bits (175), Expect = 9e-18
Identities = 35/74 (47%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 16 VQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGP-ETGVPRSALRLNQLHLTKLKINFP 74
V+ GRVV G +GKL IVD+I++ VLVDGP TGV L L LT I+ P
Sbjct: 1 VEIGRVVLSKAGRDKGKLYVIVDIIDENVVLVDGPLRTGVKPKKKNLKHLQLTDFVIDIP 60
Query: 75 FNARTKVVRKAWKD 88
ARTK V+KA +
Sbjct: 61 RGARTKGVKKANEK 74
>gnl|CDD|225074 COG2163, RPL14A, Ribosomal protein L14E/L6E/L27E [Translation,
ribosomal structure and biogenesis].
Length = 125
Score = 51.3 bits (123), Expect = 1e-09
Identities = 29/89 (32%), Positives = 45/89 (50%), Gaps = 2/89 (2%)
Query: 12 FKRFVQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGPE--TGVPRSALRLNQLHLTKL 69
+ ++ GRVV ++ G + GK IV +I+ VL+ GP+ GVPR + + L T
Sbjct: 1 MRASLEVGRVVVVTAGRFAGKKVVIVKIIDDNFVLITGPKKVKGVPRRRINIKHLEPTDK 60
Query: 70 KINFPFNARTKVVRKAWKDGQVEEKWSKS 98
I+ A + V+KA + V K KS
Sbjct: 61 VIDLVRGASDEKVKKANEAAGVLAKLDKS 89
>gnl|CDD|235283 PRK04333, PRK04333, 50S ribosomal protein L14e; Validated.
Length = 84
Score = 38.5 bits (90), Expect = 5e-05
Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 16 VQTGRVVRISDGPYRGKLSSIVDVINQTTVLVDGP-ETGVPRSALRLNQLHLTKLKINFP 74
++ GRV + G G+ IVD+I++ VLV GP TGV R + L T K++
Sbjct: 4 IEVGRVCVKTAGREAGRKCVIVDIIDKNFVLVTGPSLTGVKRRRCNIKHLEPTDKKVDIE 63
Query: 75 FNARTKVVRKA 85
A + V+KA
Sbjct: 64 KGASDEEVKKA 74
>gnl|CDD|225179 COG2270, COG2270, Permeases of the major facilitator superfamily
[General function prediction only].
Length = 438
Score = 30.0 bits (68), Expect = 0.24
Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 1/71 (1%)
Query: 8 YNGAFKRFVQTGRVVRISDGPYR-GKLSSIVDVINQTTVLVDGPETGVPRSALRLNQLHL 66
Y+ R + RIS + G L S++ +I G +TG+ L L
Sbjct: 136 YDSMLPRLTTKDNMGRISGLGWALGYLGSVILLIFVVLGFALGQQTGITIILLGLPPADG 195
Query: 67 TKLKINFPFNA 77
++I A
Sbjct: 196 EDVRITGLLAA 206
>gnl|CDD|240504 cd00380, KOW, KOW: an acronym for the authors' surnames
(Kyrpides, Ouzounis and Woese). KOW domain is known as
an RNA-binding motif that is shared so far among some
families of ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. The KOW motif contains an
invariants glycine residue and comprises alternating
blocks of hydrophilic and hydrophobic residues.
Length = 49
Score = 27.6 bits (62), Expect = 0.32
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 19 GRVVRISDGPYRGKLSSIVDVINQT-TVLVDGPETGVPRSALRLNQLHL 66
G VVR+ GPY+G+ +VD+ + V V G TG + L++ +
Sbjct: 1 GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKGA-TGSKGAELKVRFDDV 48
>gnl|CDD|144165 pfam00467, KOW, KOW motif. This family has been extended to
coincide with ref. The KOW (Kyprides, Ouzounis, Woese)
motif is found in a variety of ribosomal proteins and
NusG.
Length = 32
Score = 25.9 bits (58), Expect = 1.1
Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 19 GRVVRISDGPYRGKLSSIVDVI-NQTTVLVD 48
G VVR+ GP++GK +V+V ++ V V+
Sbjct: 2 GDVVRVISGPFKGKKGKVVEVDDSKARVHVE 32
>gnl|CDD|233451 TIGR01531, glyc_debranch, glycogen debranching enzymye. glycogen
debranching enzyme possesses two different catalytic
activities; oligo-1,4-->1,4-glucantransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site
directed mutagenesis studies in S. cerevisiae indicate
that the transferase and glucosidase activities are
independent and located in different regions of the
polypeptide chain. Proteins in this model belong to the
larger alpha-amylase family. The model covers eukaryotic
proteins with a seed composed of human, nematode and
yeast sequences. Yeast seed sequence is well
characterized. The model is quite rigorous; either query
sequence yields large bit score or it fails to hit the
model altogether. There doesn't appear to be any middle
ground [Energy metabolism, Biosynthesis and degradation
of polysaccharides].
Length = 1464
Score = 27.9 bits (62), Expect = 1.3
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 51 ETGVPR--SALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQVEEKWSKSLWAQKVA-NV 107
PR +A+ + L + L+ F + K V K + G +KWS W QK+ N
Sbjct: 1213 IPATPRDGAAVEIVGLLKSALR--FLIELKEKGVFK--RSGVETQKWSYIEWNQKIQDNF 1268
Query: 108 EKR 110
EKR
Sbjct: 1269 EKR 1271
>gnl|CDD|226382 COG3864, COG3864, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 396
Score = 27.2 bits (60), Expect = 1.7
Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 39 VINQTTVLVDGPETGVPRSALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQVEE 93
INQ + +P ++L + H+T+LK + KV+++ + ++
Sbjct: 105 SINQ--YINSLAPWSLPIENVKL-EYHITELKYDKVLEYYVKVIQENINKKEKDK 156
>gnl|CDD|240509 cd06085, KOW_Spt5_5, KOW domain of Spt5, repeat 5. Spt5, an
eukaryotic ortholog of NusG, contains multiple KOW
motifs at its C-terminus. Spt5 is involved in
transcription elongation and termination. KOW domain is
known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the
essential bacterial transcriptional elongation factor
NusG, the eukaryotic chromatin elongation factor Spt5,
the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5
domains play critical roles in recruitment of multiple
other eukaryotic transcription elongation and RNA
biogenesis factors and additionally are involved in the
binding of the eukaryotic Spt5 proteins to RNA
polymerases.
Length = 52
Score = 25.5 bits (57), Expect = 2.0
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 19 GRVVRISDGPYRGKLSSIVDVINQTTVLV 47
G+ VRI GPY+G + + D TT V
Sbjct: 7 GKTVRIRKGPYKGYIGIVKDA-TGTTARV 34
>gnl|CDD|215324 PLN02604, PLN02604, oxidoreductase.
Length = 566
Score = 27.1 bits (60), Expect = 2.1
Identities = 17/66 (25%), Positives = 24/66 (36%), Gaps = 17/66 (25%)
Query: 4 VKHNYNGAFKRF---------------VQTGRVVRISDGPYRGKLSSIVDVI--NQTTVL 46
+K N GAF + SD YR + +S VD+I N T+
Sbjct: 401 LKENLTGAFDQTPPPEGYDFANYDIYAKPNNSNATSSDSIYRLQFNSTVDIILQNANTMN 460
Query: 47 VDGPET 52
+ ET
Sbjct: 461 ANNSET 466
>gnl|CDD|177934 PLN02297, PLN02297, ribose-phosphate pyrophosphokinase.
Length = 326
Score = 27.0 bits (60), Expect = 2.4
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 16/50 (32%)
Query: 10 GAFKRF--------------VQTG--RVVRISDGPYRGKLSSIVDVINQT 43
GA+KRF V+ G R+VRI +G G+ IVD + Q+
Sbjct: 193 GAWKRFHKQFEHFPMVVCTKVREGDKRIVRIKEGNPAGRHVVIVDDLVQS 242
>gnl|CDD|234193 TIGR03388, ascorbase, L-ascorbate oxidase, plant type. Members of
this protein family are the copper-containing enzyme
L-ascorbate oxidase (EC 1.10.3.3), also called
ascorbase. This family is found in flowering plants, and
shows greater sequence similarity to a family of
laccases (EC 1.10.3.2) from plants than to other known
ascorbate oxidases.
Length = 541
Score = 26.6 bits (59), Expect = 2.8
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 23 RISDGPYRGKLSSIVDVINQ 42
+G YR K ++ VDVI Q
Sbjct: 412 TTGNGIYRLKFNTTVDVILQ 431
>gnl|CDD|128978 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) motif. Motif in
ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Length = 28
Score = 24.6 bits (55), Expect = 3.0
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 19 GRVVRISDGPYRGKLSSIVDVI 40
G VR+ GP++GK+ +++V
Sbjct: 5 GDTVRVIAGPFKGKVGKVLEVD 26
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 26.1 bits (57), Expect = 4.8
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 84 KAWKDGQVEEKWSK 97
+AWK GQ EKW K
Sbjct: 439 RAWKGGQSREKWLK 452
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 26.0 bits (57), Expect = 5.0
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 84 KAWKDGQVEEKWSK 97
KAWK GQ E W K
Sbjct: 460 KAWKGGQSRETWLK 473
>gnl|CDD|225460 COG2908, COG2908, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 237
Score = 25.3 bits (56), Expect = 7.6
Identities = 8/41 (19%), Positives = 15/41 (36%)
Query: 58 ALRLNQLHLTKLKINFPFNARTKVVRKAWKDGQVEEKWSKS 98
+++ L L +N P R ++ K +K K
Sbjct: 127 RYKVHWAWLQLLFLNLPLRVRRRIAYKIRSLSSWAKKKVKK 167
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
0.318 0.133 0.392
Gapped
Lambda K H
0.267 0.0941 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,564,046
Number of extensions: 455869
Number of successful extensions: 370
Number of sequences better than 10.0: 1
Number of HSP's gapped: 366
Number of HSP's successfully gapped: 31
Length of query: 112
Length of database: 10,937,602
Length adjustment: 76
Effective length of query: 36
Effective length of database: 7,566,698
Effective search space: 272401128
Effective search space used: 272401128
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 (21.7 bits)
S2: 53 (23.8 bits)