RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780713|ref|YP_003065126.1| 16S rRNA-processing protein
[Candidatus Liberibacter asiaticus str. psy62]
(190 letters)
>gnl|CDD|31149 COG0806, RimM, RimM protein, required for 16S rRNA processing
[Translation, ribosomal structure and biogenesis].
Length = 174
Score = 125 bits (316), Expect = 6e-30
Identities = 57/176 (32%), Positives = 88/176 (50%), Gaps = 8/176 (4%)
Query: 1 MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDLNRY--VLYSNDNRELRILKM---YR 55
M K + L+L+ I +THG+ GEV + S+ + P L Y L E + L + +
Sbjct: 1 MTKPENLLLVGKIVSTHGIRGEVRVKSFTDFPESLFDYGPWLLLKPGGEWQELTVESVRK 60
Query: 56 KNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKY 115
I F GID+ ++A L+ +++ R + ELEEDEF+ DL +E G+
Sbjct: 61 HKNLLILKFKGIDDRNAAEALKGYEIFVDRSEL--PELEEDEFYYHDLIGLEVVTEDGEL 118
Query: 116 WGQVCGVYNFGAGSILEIKN-TMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGLN 170
G+V + GA +L +K +K LIPF V EV+L+ KI +DP L+
Sbjct: 119 LGKVTEILETGANDVLVVKAKGGKKERLIPFVDAVVKEVDLEAKKIEVDPDEGLLD 174
>gnl|CDD|145113 pfam01782, RimM, RimM N-terminal domain. The RimM protein is
essential for efficient processing of 16S rRNA. The
RimM protein was shown to have affinity for free
ribosomal 30S subunits but not for 30S subunits in the
70S ribosomes. This N-terminal domain is found
associated with a PRC-barrel domain.
Length = 84
Score = 61.0 bits (149), Expect = 2e-10
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 5/84 (5%)
Query: 9 LMATIGTTHGLNGEVYIDSYANNPIDL----NRYVLYSNDN-RELRILKMYRKNKRFIAT 63
L+ I THGL GEV + S+ + P + ++L + L + + K I
Sbjct: 1 LVGKIVGTHGLKGEVKVKSFTDFPEAIFDYGPWFLLKKKGEWKPLTVESVRLHKKGLIVK 60
Query: 64 FSGIDNIHSASELRDLKLYAKRQD 87
F G+D+ +A L+ +LY R D
Sbjct: 61 FEGVDDRDAAEALKGAELYVPRSD 84
>gnl|CDD|147440 pfam05239, PRC, PRC-barrel domain. The PRC-barrel is an all beta
barrel domain found in photosystem reaction centre
subunit H of the purple bacteria and RNA metabolism
proteins of the RimM group. PRC-barrels are
approximately 80 residues long, and found widely
represented in bacteria, archaea and plants. This domain
is also present at the carboxyl terminus of the
pan-bacterial protein RimM, which is involved in
ribosomal maturation and processing of 16S rRNA. A
family of small proteins conserved in all known
euryarchaea are composed entirely of a single
stand-alone copy of the domain.
Length = 77
Score = 45.7 bits (109), Expect = 7e-06
Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 9/79 (11%)
Query: 95 EDEFFNTDLEEMETFDRQGKYWGQVCGVY-NFGAGSILEIK-----NTMEKTFLIPFTKF 148
EDEF+ +DL +E + G+ G+V V + G G +L + +K LIPFTK
Sbjct: 1 EDEFYASDLIGLEVYTEDGEKLGKVKDVVIDEGEGDVLYLVVSVGGFLGDKEVLIPFTK- 59
Query: 149 AVLEVNLQENKILIDPIAA 167
LEV+L +++I++D
Sbjct: 60 --LEVDLGKDRIIVDAPKE 76
>gnl|CDD|147584 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 809
Score = 30.0 bits (68), Expect = 0.40
Identities = 20/95 (21%), Positives = 37/95 (38%), Gaps = 14/95 (14%)
Query: 27 SYANNPIDLNRYVLYSNDNRELRI-------LKMYRKNKRFIATFSGIDNIHSASELRDL 79
+ P +LN L + EL+I + +N + T ++N + +EL D+
Sbjct: 506 QVLDTPGNLNPGYLNLSGTLELKINLTISEVYRDCEQN-EPLYTVLQLNNSYDLNELLDI 564
Query: 80 KLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGK 114
K Y D+ELE +L + + +
Sbjct: 565 KQYTPEI---DQELES---LKVNLSTITLLTPEAR 593
>gnl|CDD|37205 KOG1994, KOG1994, KOG1994, Predicted RNA binding protein, contains
G-patch and Zn-finger domains [RNA processing and
modification].
Length = 268
Score = 28.1 bits (62), Expect = 1.6
Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 3/93 (3%)
Query: 43 NDNRELRILKMYRKNKRFIATFSGIDNIHSASELRDL-KLYAKRQDFKDEELEE--DEFF 99
ND + ++ M R++ G S L+ + + KD EL E +E
Sbjct: 165 NDEDKKNMIPMVRESLEASPALKGEKGFGRPSTLKKCETSIIESRITKDTELAELEEEII 224
Query: 100 NTDLEEMETFDRQGKYWGQVCGVYNFGAGSILE 132
L ++ F R Y+ CG+ + E
Sbjct: 225 EERLTKINIFLRSEHYYCFFCGIKYKDEEDLYE 257
>gnl|CDD|36928 KOG1716, KOG1716, KOG1716, Dual specificity phosphatase [Defense
mechanisms].
Length = 285
Score = 26.7 bits (58), Expect = 3.8
Identities = 8/39 (20%), Positives = 17/39 (43%)
Query: 65 SGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDL 103
GI ++ + S + K Q K + ++ +TD+
Sbjct: 99 LGITHVLNVSSSCPNPRFLKEQGIKYLRIPVEDNPSTDI 137
>gnl|CDD|143429 cd07111, ALDH_F16, Aldehyde dehydrogenase family 16A1-like.
Uncharacterized aldehyde dehydrogenase family 16 member
A1 (ALDH16A1) and other related sequences are present in
this CD. The active site cysteine and glutamate residues
are not conserved in the human ALDH16A1 protein
sequence.
Length = 480
Score = 26.6 bits (59), Expect = 4.8
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 9/54 (16%)
Query: 49 RILKMYRKNKRFIATFSGIDNIHSASELRDLKL---------YAKRQDFKDEEL 93
RI + +K++R A +DN E RD + +A D EL
Sbjct: 89 RIARHIQKHQRLFAVLESLDNGKPIRESRDCDIPLVARHFYHHAGWAQLLDTEL 142
>gnl|CDD|38012 KOG2801, KOG2801, KOG2801, Probable Rab-GAPs [Intracellular
trafficking, secretion, and vesicular transport].
Length = 559
Score = 25.8 bits (56), Expect = 7.7
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 85 RQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQ 118
+ D ++L E T+L+E++ RQG YW Q
Sbjct: 14 KMDAAIQDLGPKELSCTELQELKQLARQG-YWAQ 46
>gnl|CDD|35665 KOG0444, KOG0444, KOG0444, Cytoskeletal regulator Flightless-I
(contains leucine-rich and gelsolin repeats)
[Cytoskeleton].
Length = 1255
Score = 25.8 bits (56), Expect = 8.0
Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 2/24 (8%)
Query: 91 EELEEDEFFNTDLEEMETFDRQGK 114
E+L E+ +N DLE ME+F +GK
Sbjct: 885 EQLMEE--WNYDLELMESFVLEGK 906
>gnl|CDD|37149 KOG1938, KOG1938, KOG1938, Protein with predicted involvement in
meiosis (GSG1) [Cell cycle control, cell division,
chromosome partitioning].
Length = 960
Score = 25.8 bits (56), Expect = 8.5
Identities = 11/44 (25%), Positives = 14/44 (31%)
Query: 32 PIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASE 75
D +LYS D+ E + K F D HS
Sbjct: 161 APDNTLGILYSFDSGEFQTRKGADLLFMFGHPNLAFDAYHSTKR 204
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.318 0.137 0.392
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,295,805
Number of extensions: 119136
Number of successful extensions: 310
Number of sequences better than 10.0: 1
Number of HSP's gapped: 305
Number of HSP's successfully gapped: 21
Length of query: 190
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 102
Effective length of database: 4,362,145
Effective search space: 444938790
Effective search space used: 444938790
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: 54 (24.6 bits)